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Peng L, Liu Z, Liu P, Guo W, Liu T, Lei Z, Chang Q, Zhang M, Lin X, Wang F, Wu S. Genome-wide association analysis to search for new loci associated with stroke risk in Northwestern Chinese population. Gene 2024; 928:148807. [PMID: 39094715 DOI: 10.1016/j.gene.2024.148807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND AND PURPOSE Genetic factors play an important role in the pathogenesis of stroke(S). This study aimed to screen the loci associated with S risk in northwestern Chinese population by genome-wide association analysis (GWAS). METHODS A total of 1394 subjects, including 682 S patients and 692 controls, were enrolled in this study. SPSS 25.0 software was used for statistical analysis, and the independent sample t-test as well as Chi-square test were used to analyze the differences in age and gender between the case and control groups. The Precision Medicine Diversity Array (PMDA) genotyping chip was used in this study. The genotyping platform was the Gene Titan multi-channel instrument, and the Axiom Analysis Suite 6.0 software was used for the data analyzing. Besides, the LASSO analysis, SNP-SNP and GO/KEGG analysis were conducted to analyze the association between significant loci and S risk. RESULTS A total of 30 SNPs were found to be associated with the S risk based on additive model (p < 5 × 10-8). After the LASSO screening, 22 SNPs showed the diagnostic value in S. The SNPs interaction analysis further screened the SNP-SNP interaction groups associated with the S risk(p < 0.05). Finally, the GO/KEGG analysis discovered the suggestive significance loci could be involved in the S development mainly by immune-related functions and pathways. CONCLUSION This study discovered 30 S related SNPs and analyzed the potential pathways associated with genes located on the 30 SNPs, which were beneficial for enriching the genetic mechanism analysis of S in northwestern Chinese population.
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Affiliation(s)
- Linna Peng
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Zhongzhong Liu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China; Department of Epidemiology and Biostatistics, School of Public Health of Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Pei Liu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Weiyan Guo
- Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Tong Liu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Zhen Lei
- College of Life Science, Northwest University, Xi'an 710069, China
| | - Qiaoqiao Chang
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Mi Zhang
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Xuemei Lin
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Fang Wang
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China
| | - Songdi Wu
- Department of Neurology, Xi'an No.1 Hospital, The First Affiliated Hospital of Northwest University, Xi'an 710002, China; Xi'an Key Laboratory for Innovation and Translation of Neuroimmunological Diseases, Xi'an 710002, China; College of Life Science, Northwest University, Xi'an 710069, China.
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Wang H, Zhang S, Yuan X, Xiao S, Zeng X, Yang X, Wei Y, Wu Z. mRNA expression profile and prognostic values of the CDHR family genes in lung adenocarcinoma. Int J Biol Macromol 2024; 281:136642. [PMID: 39419138 DOI: 10.1016/j.ijbiomac.2024.136642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2024] [Revised: 10/08/2024] [Accepted: 10/14/2024] [Indexed: 10/19/2024]
Abstract
Lung adenocarcinoma (LUAD), the predominant subtype of lung cancer, has a high incidence and annual mortality worldwide. Members of the cadherin-related (CDHR) family are associated with many malignant tumor types. However, their role and clinical significance in LUAD have not been clarified. We analyzed the association of CDHRs mRNA expression profiles with prognostic significance, immune infiltration, and potential biological functional signatures in several public databases. We constructed a co-expressed mRNA network, and performed an intrinsic molecular structure and function enrichment analysis. Our results showed that CDHR2 mRNA expression was upregulated in LUAD, whereas CDHR1, CDHR3, CDHR4, and CDHR5 mRNAs were downregulated. Upregulation of CDHR2 mRNA is associated with a poor prognosis in patients with LUAD. Next, the correlation between CDHR family members and immune infiltration was observed. A receiver operating characteristic curve showed that the CDHR family is valuable for diagnosing LUAD. In this study, we found that CDHR2 mRNA expression was upregulated in LUAD. Upregulation of CDHR2 mRNA was associated with a poor prognosis in patients with LUAD.
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Affiliation(s)
- Hong Wang
- School of Clinical Medicine, Chengdu Medical College, Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Shuai Zhang
- School of Clinical Medicine, Chengdu Medical College, Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Xi Yuan
- School of Clinical Medicine, Chengdu Medical College, Department of Anesthesia, First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China
| | - Sanling Xiao
- Department of Respiratory Medicine, Pengzhou People's Hospital, Chengdu 611930, Sichuan Province, China
| | - Xiaofei Zeng
- School of Clinical Medicine, Chengdu Medical College, Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China.
| | - Xin Yang
- School of Clinical Medicine, Chengdu Medical College, Department of Pediatrics, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China.
| | - Yong Wei
- School of Clinical Medicine, Chengdu Medical College,Emergency Department, First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500,Sichuan Province,China.
| | - Zhiqiang Wu
- School of Clinical Medicine, Chengdu Medical College, Department of Cardiothoracic Surgery, The First Affiliated Hospital of Chengdu Medical College, Chengdu 610500, Sichuan Province, China.
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Cencer CS, Robinson KL, Tyska MJ. Loss of intermicrovillar adhesion factor CDHR2 impairs basolateral junctional complexes in transporting epithelia. Mol Biol Cell 2024; 35:br21. [PMID: 39292922 PMCID: PMC11617098 DOI: 10.1091/mbc.e24-03-0113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/28/2024] [Accepted: 09/11/2024] [Indexed: 09/20/2024] Open
Abstract
Transporting epithelial cells in the gut and kidney rely on protocadherin-based apical adhesion complexes to organize microvilli that extend into luminal space. In these systems, CDHR2 and CDHR5 localize to the distal ends of microvilli, where they form an intermicrovillar adhesion complex (IMAC) that links the tips of these structures, promotes the formation of a well-ordered array of protrusions, and thus maximizes apical membrane surface area. Recently, we discovered that IMACs can also form between microvilli that extend from neighboring cells, across cell-cell junctions. As an additional point of physical contact between cells, transjunctional IMACs are well positioned to impact the integrity of canonical tight and adherens junctions that form more basolaterally. To begin to test this idea, we examined cell culture and mouse models that lacked CDHR2 expression and were unable to form IMACs. CDHR2 knockout perturbed cell and junction morphology, reduced key components from tight and adherens junctions, impaired barrier function, and increased the motility of single cells within established monolayers. These results support the hypothesis that, in addition to organizing apical microvilli, IMACs provide a layer of cell-cell contact that functions in parallel with canonical tight and adherens junctions to promote epithelial functions.
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Affiliation(s)
- Caroline S. Cencer
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Kianna L. Robinson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Matthew J. Tyska
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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Tah I, Haertter D, Crawford JM, Kiehart DP, Schmidt CF, Liu AJ. Minimal vertex model explains how the amnioserosa avoids fluidization during Drosophila dorsal closure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.20.572544. [PMID: 38187730 PMCID: PMC10769242 DOI: 10.1101/2023.12.20.572544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Dorsal closure is a process that occurs during embryogenesis of Drosophila melanogaster . During dorsal closure, the amnioserosa (AS), a one-cell thick epithelial tissue that fills the dorsal opening, shrinks as the lateral epidermis sheets converge and eventually merge. During this process, both shape index and aspect ratio of amnioserosa cells increase markedly. The standard 2-dimensional vertex model, which successfully describes tissue sheet mechanics in multiple contexts, would in this case predict that the tissue should fluidize via cell neighbor changes. Surprisingly, however, the amnioserosa remains an elastic solid with no such events. We here present a minimal extension to the vertex model that explains how the amnioserosa can achieve this unexpected behavior. We show that continuous shrinkage of the preferred cell perimeter and cell perimeter polydispersity lead to the retention of the solid state of the amnioserosa. Our model accurately captures measured cell shape and orientation changes and predicts non-monotonic junction tension that we confirm with laser ablation experiments. Significance Statement During embryogenesis, cells in tissues can undergo significant shape changes. Many epithelial tissues fluidize, i.e. cells exchange neighbors, when the average cell shape index increases above a threshold value, consistent with the standard vertex model. During dorsal closure in Drosophila melanogaster , however, the amnioserosa tissue remains solid even as the average cell shape index increases well above threshold. We introduce perimeter polydispersity and allow the preferred cell perimeters, usually held fixed in vertex models, to decrease linearly with time as seen experimentally. With these extensions to the standard vertex model, we capture experimental observations quantitatively. Our results demonstrate that vertex models can describe the behavior of the amnioserosa in dorsal closure by allowing normally fixed parameters to vary with time.
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Stubler R, Dooley SA, Edens R, Nicholson MR, Engevik AC. Intestinal Tuft Cells Are Enriched With Protocadherins. J Histochem Cytochem 2024; 72:611-622. [PMID: 39360911 PMCID: PMC11471013 DOI: 10.1369/00221554241287267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 08/23/2024] [Indexed: 10/13/2024] Open
Abstract
Intestinal tuft cells are rare cells that regulate diverse functions. They harbor chemosensory receptors and signal to the mucosal immune system in response to external stimuli, though their full function and structure remain unclear. Named for their apical "tuft" of long actin-rich microvilli, tuft cells facilitate chemoreception and other physiological responses. In enterocytes, microvilli are stabilized by intermicrovillar adhesion complexes (IMACs) composed of several proteins, including cadherin-related family member-2 (CDHR2) and cadherin-related family member-5 (CDHR5), Myosin 7b, and Usher syndrome type 1 C (USH1C). We hypothesized that IMACs would be enriched in tuft cells to regulate microvillar organization. Immunostaining of murine intestinal tissue revealed that CDHR2 and CDHR5 colocalize with the tuft cell markers, DCLK1, phospho-EGFR, advillin, and cytokeratin 18. CDHR2 was dispersed throughout murine tuft cells, while CDHR5 was concentrated on the apical surface. USH1C and Myosin 7b were present in tuft cells, but at lower levels. Human single-cell RNA sequencing revealed robust CDHR2 and CDHR5 expression in tuft cells in the small intestine and colon. Immunostaining of human intestinal tissue confirmed CDHR2 and CDHR5 localization to the apical surface of tuft cells. Our findings demonstrate that protocadherins are key components of murine and human intestinal tuft cells.
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Affiliation(s)
- Rachel Stubler
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC
| | - Sarah A. Dooley
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC
| | - Rachel Edens
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC
| | - Maribeth R. Nicholson
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Monroe Carell Jr. Children’s Hospital at Vanderbilt, Nashville, TN
| | - Amy C. Engevik
- Department of Regenerative Medicine & Cell Biology, Medical University of South Carolina, Charleston, SC
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Cencer CS, Robinson KL, Tyska MJ. Loss of intermicrovillar adhesion impairs basolateral junctional complexes in transporting epithelia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585733. [PMID: 38562895 PMCID: PMC10983982 DOI: 10.1101/2024.03.19.585733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Transporting epithelial cells in the gut and kidney rely on protocadherin-based apical adhesion complexes to organize microvilli that extend into the luminal space. In these systems, CDHR2 and CDHR5 localize to the distal ends of microvilli, where they form an intermicrovillar adhesion complex (IMAC) that links the tips of these structures, promotes the formation of a well-ordered array of protrusions, and in turn maximizes apical membrane surface area. Recently, we discovered that IMACs can also form between microvilli that extend from neighboring cells, across cell-cell junctions. As an additional point of physical contact between cells, transjunctional IMACs are well positioned to impact the integrity of canonical tight and adherens junctions that form more basolaterally. Here, we sought to test this idea using cell culture and mouse models that lacked CDHR2 expression and were unable to form IMACs. CDHR2 knockout perturbed cell and junction morphology, led to loss of key components from tight and adherens junctions, and impaired barrier function and wound healing. These results indicate that, in addition to organizing apical microvilli, IMACs provide a layer of cell-cell contact that functions in parallel with canonical tight and adherens junctions to support the physiological functions of transporting epithelia.
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Yang R, Yang N, Yin P, Xue Z, Sun F, Fan R, Liang J, Lv X, Wu S, Sun L. PCDH8 is a novel prognostic biomarker in thyroid cancer and promotes cell proliferation and viability. Funct Integr Genomics 2024; 24:35. [PMID: 38368303 PMCID: PMC10874333 DOI: 10.1007/s10142-024-01312-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/19/2024]
Abstract
Protocadherin 8 (PCDH8), a calcium-dependent transmembrane protein in the protocadherin family, regulates cell adhesion and signal transduction. While some studies have provided indirect evidence that PCDH8 has cancer-promoting properties, this association is controversial. In particular, its involvement in thyroid cancer (THCA) remains unclear. We aimed to elucidate the role of PCDH8 in THCA using bioinformatic analysis. Subsequently, the results were experimentally validated. The analysis conducted using the R programming language and online web tools explored PCDH8 expression levels, prognostic, and clinical implications, and its relationship with the tumor immune microenvironment in THCA. Furthermore, we examined the association between PCDH8 and co-expressed genes, highlighting their involvement in several biological processes relevant to THCA. The potential of PCDH8 as a therapeutic target for this pathology was also explored. Immunohistochemical (IHC) staining was performed on samples from 98 patients with THCA, and experimental validation was carried out. PCDH8 was significantly elevated in cancer tissues and associated with poor prognosis, several clinical factors, and immune cell and checkpoint abundance. Cox regression and survival analyses, together with Receiver Operating Curves (ROC) indicated that PCDH8 was an independent prognostic factor for THCA. Furthermore, PCDH8 impacts cell viability and proliferation, promoting tumorigenesis. Also, it influences tumor cell sensitivity to various drugs. Thus, PCDH8 might be a potential therapeutic target for THCA. IHC, cell culture, MTT, and colony formation experiments further confirmed our findings. This analysis provided insights into the potential carcinogenic role of PCDH8 in THCA, as it impacts cell viability and proliferation. Thus, PCDH8 might play an important role in its prognosis, immune infiltration, and diagnosis.
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Affiliation(s)
- Ruida Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Nan Yang
- Department of Oncology, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Pan Yin
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Zihan Xue
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Feidi Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Ruihan Fan
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - JiaFu Liang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Xinru Lv
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China
| | - Shaobo Wu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China.
| | - Liankang Sun
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, People's Republic of China.
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Zhang S, Jiang C, Jiang L, Chen H, Huang J, Gao X, Xia Z, Tran LJ, Zhang J, Chi H, Yang G, Tian G. Construction of a diagnostic model for hepatitis B-related hepatocellular carcinoma using machine learning and artificial neural networks and revealing the correlation by immunoassay. Tumour Virus Res 2023; 16:200271. [PMID: 37774952 PMCID: PMC10638043 DOI: 10.1016/j.tvr.2023.200271] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/21/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023] Open
Abstract
HBV infection profoundly escalates hepatocellular carcinoma (HCC) susceptibility, responsible for a majority of HCC cases. HBV-driven immune-mediated hepatocyte impairment significantly fuels HCC progression. Regrettably, inconspicuous early HCC symptoms often culminate in belated diagnoses. Nevertheless, surgically treated early-stage HCC patients relish augmented five-year survival rates. In contrast, advanced HCC exhibits feeble responses to conventional interventions like radiotherapy, chemotherapy, and surgery, leading to diminished survival rates. This investigation endeavors to unearth diagnostic hallmark genes for HBV-HCC leveraging a bioinformatics framework, thus refining early HBV-HCC detection. Candidate genes were sieved via differential analysis and Weighted Gene Co-Expression Network Analysis (WGCNA). Employing three distinct machine learning algorithms unearthed three feature genes (HHIP, CXCL14, and CDHR2). Melding these genes yielded an innovative Artificial Neural Network (ANN) diagnostic blueprint, portending to alleviate patient encumbrance and elevate life quality. Immunoassay scrutiny unveiled accentuated immune damage in HBV-HCC patients relative to solitary HCC. Through consensus clustering, HBV-HCC was stratified into two subtypes (C1 and C2), the latter potentially indicating milder immune impairment. The diagnostic model grounded in these feature genes showcased robust and transferrable prognostic potentialities, introducing a novel outlook for early HBV-HCC diagnosis. This exhaustive immunological odyssey stands poised to expedite immunotherapeutic curatives' emergence for HBV-HCC.
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Affiliation(s)
- Shengke Zhang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Chenglu Jiang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Lai Jiang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Haiqing Chen
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Jinbang Huang
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Xinrui Gao
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China
| | - Zhijia Xia
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany
| | - Lisa Jia Tran
- Department of General, Visceral, and Transplant Surgery, Ludwig-Maximilians-University Munich, Munich, 81377, Germany
| | - Jing Zhang
- Division of Basic Biomedical Sciences, The University of South Dakota Sanford School of Medicine, Vermillion, 57069, USA
| | - Hao Chi
- Clinical Medical College, Southwest Medical University, Luzhou, 646000, China.
| | - Guanhu Yang
- Department of Specialty Medicine, Ohio University, Athens, 45701, USA.
| | - Gang Tian
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China.
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Rumpf M, Pautz S, Drebes B, Herberg FW, Müller HAJ. Microtubule-Associated Serine/Threonine (MAST) Kinases in Development and Disease. Int J Mol Sci 2023; 24:11913. [PMID: 37569286 PMCID: PMC10419289 DOI: 10.3390/ijms241511913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/17/2023] [Accepted: 07/19/2023] [Indexed: 08/13/2023] Open
Abstract
Microtubule-Associated Serine/Threonine (MAST) kinases represent an evolutionary conserved branch of the AGC protein kinase superfamily in the kinome. Since the discovery of the founding member, MAST2, in 1993, three additional family members have been identified in mammals and found to be broadly expressed across various tissues, including the brain, heart, lung, liver, intestine and kidney. The study of MAST kinases is highly relevant for unraveling the molecular basis of a wide range of different human diseases, including breast and liver cancer, myeloma, inflammatory bowel disease, cystic fibrosis and various neuronal disorders. Despite several reports on potential substrates and binding partners of MAST kinases, the molecular mechanisms that would explain their involvement in human diseases remain rather obscure. This review will summarize data on the structure, biochemistry and cell and molecular biology of MAST kinases in the context of biomedical research as well as organismal model systems in order to provide a current profile of this field.
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Affiliation(s)
- Marie Rumpf
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Sabine Pautz
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Benedikt Drebes
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
| | - Friedrich W. Herberg
- Department of Biochemistry, Institute of Biology, University of Kassel, 34321 Kassel, Germany
| | - Hans-Arno J. Müller
- Department of Developmental Genetics, Institute of Biology, University of Kassel, 34321 Kassel, Germany; (M.R.)
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Vega-Benedetti AF, Loi E, Moi L, Zavattari P. DNA methylation alterations at RE1-silencing transcription factor binding sites and their flanking regions in cancer. Clin Epigenetics 2023; 15:98. [PMID: 37301955 PMCID: PMC10257853 DOI: 10.1186/s13148-023-01514-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND DNA methylation changes, frequent early events in cancer, can modulate the binding of transcription factors. RE1-silencing transcription factor (REST) plays a fundamental role in regulating the expression of neuronal genes, and in particular their silencing in non-neuronal tissues, by inducing chromatin modifications, including DNA methylation changes, not only in the proximity of its binding sites but also in the flanking regions. REST has been found aberrantly expressed in brain cancer and other cancer types. In this work, we investigated DNA methylation alterations at REST binding sites and their flanking regions in a brain cancer (pilocytic astrocytoma), two gastrointestinal tumours (colorectal cancer and biliary tract cancer) and a blood cancer (chronic lymphocytic leukemia). RESULTS Differential methylation analyses focused on REST binding sites and their flanking regions were conducted between tumour and normal samples from our experimental datasets analysed by Illumina microarrays and the identified alterations were validated using publicly available datasets. We discovered distinct DNA methylation patterns between pilocytic astrocytoma and the other cancer types in agreement with the opposite oncogenic and tumour suppressive role of REST in glioma and non-brain tumours. CONCLUSIONS Our results suggest that these DNA methylation alterations in cancer may be associated with REST dysfunction opening the enthusiastic possibility to develop novel therapeutic interventions based on the modulation of this master regulator in order to restore the aberrant methylation of its target regions into a normal status.
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Affiliation(s)
| | - Eleonora Loi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Loredana Moi
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy
| | - Patrizia Zavattari
- Department of Biomedical Sciences, Unit of Biology and Genetics, University of Cagliari, 09042, Cagliari, Italy.
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11
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Lindholm C, Batakis P, Altimiras J, Lees J. Intermittent fasting induces chronic changes in the hepatic gene expression of Red Jungle Fowl (Gallus gallus). BMC Genomics 2022; 23:304. [PMID: 35421924 PMCID: PMC9009039 DOI: 10.1186/s12864-022-08533-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/06/2022] [Indexed: 11/23/2022] Open
Abstract
Background Intermittent fasting (IF), the implementation of fasting periods of at least 12 consecutive hours on a daily to weekly basis, has received a lot of attention in recent years for imparting the life-prolonging and health-promoting effects of caloric restriction with no or only moderate actual restriction of caloric intake. IF is also widely practiced in the rearing of broiler breeders, the parent stock of meat-type chickens, who require strict feed restriction regimens to prevent the serious health problems associated with their intense appetites. Although intermittent fasting has been extensively used in this context to reduce feed competition and its resulting stress, the potential of IF in chickens as an alternative and complementary model to rodents has received less investigation. In both mammals and birds, the liver is a key component of the metabolic response to IF, responding to variations in energy balance. Here we use a microarray analysis to examine the liver transcriptomics of wild-type Red Jungle Fowl chickens fed either ad libitum, chronically restricted to around 70% of ad libitum daily or intermittently fasted (IF) on a 2:1 (2 days fed, 1 day fasted) schedule without actual caloric restriction. As red junglefowl are ancestral to domestic chicken breeds, these data serve as a baseline to which existing and future transcriptomic results from farmed birds such as broiler breeders can be compared. Results We find large effects of feeding regimen on liver transcriptomics, with most of the affected genes relating to energy metabolism. A cluster analysis shows that IF is associated with large and reciprocal changes in genes related to lipid and carbohydrate metabolism, but also chronic changes in genes related to amino acid metabolism (generally down-regulated) and cell cycle progression (generally up-regulated). The overall transcription pattern appears to be one of promoting high proliferative plasticity in response to fluctuations in available energy substrates. A small number of inflammation-related genes also show chronically changed expression profiles, as does one circadian rhythm gene. Conclusions The increase in proliferative potential suggested by the gene expression changes reported here indicates that birds and mammals respond similarly to intermittent fasting practices. Our findings therefore suggest that the health benefits of periodic caloric restriction are ubiquitous and not restricted to mammals alone. Whether a common fundamental mechanism, for example involving leptin, underpins these benefits remains to be elucidated. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08533-5.
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12
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Buenafe AC, Dorrell C, Reddy AP, Klimek J, Marks DL. Proteomic analysis distinguishes extracellular vesicles produced by cancerous versus healthy pancreatic organoids. Sci Rep 2022; 12:3556. [PMID: 35241737 PMCID: PMC8894448 DOI: 10.1038/s41598-022-07451-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/14/2022] [Indexed: 02/07/2023] Open
Abstract
Extracellular vesicles (EVs) are produced and released by both healthy and malignant cells and bear markers indicative of ongoing biological processes. In the present study we utilized high resolution flow cytometry to detect EVs in the plasma of patients with pancreatic ductal adenocarcinoma (PDAC) and in the supernatants of PDAC and healthy control (HC) pancreatic organoid cultures. Using ultrafiltration and size exclusion chromatography, PDAC and HC pancreatic organoid EVs were isolated for mass spectrometry analysis. Proteomic and functional protein network analysis showed a striking distinction in that EV proteins profiled in pancreatic cancer organoids were involved in vesicular transport and tumorigenesis while EV proteins in healthy organoids were involved in cellular homeostasis. Thus, the most abundant proteins identified in either case represented non-overlapping cellular programs. Tumor-promoting candidates LAMA5, SDCBP and TENA were consistently upregulated in PDAC EVs. Validation of specific markers for PDAC EVs versus healthy pancreatic EVs will provide the biomarkers and enhanced sensitivity necessary to monitor early disease or disease progression, with or without treatment. Moreover, disease-associated changes in EV protein profiles provide an opportunity to investigate alterations in cellular programming with disease progression.
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Affiliation(s)
- Abigail C Buenafe
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA.
| | - Craig Dorrell
- Oregon Stem Cell Center, Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
| | - Ashok P Reddy
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, USA
| | - John Klimek
- Proteomics Shared Resource, Oregon Health and Science University, Portland, OR, USA
| | - Daniel L Marks
- Papé Family Pediatric Research Institute, Oregon Health and Science University, Portland, OR, USA
- Knight Cancer Institute, Oregon Health and Science University, Portland, OR, USA
- Brenden-Colson Center for Pancreatic Care, Oregon Health and Science University, Portland, OR, USA
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13
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Tanca A, Abbondio M, Fiorito G, Pira G, Sau R, Manca A, Muroni MR, Porcu A, Scanu AM, Cossu-Rocca P, De Miglio MR, Uzzau S. Metaproteomic Profile of the Colonic Luminal Microbiota From Patients With Colon Cancer. Front Microbiol 2022; 13:869523. [PMID: 35495697 PMCID: PMC9048685 DOI: 10.3389/fmicb.2022.869523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
Recent studies have provided evidence of interactions among the gut microbiota (GM), local host immune cells, and intestinal tissues in colon carcinogenesis. However, little is known regarding the functions exerted by the GM in colon cancer (CC), particularly with respect to tumor clinical classification and lymphocyte infiltration. In addition, stool, usually employed as a proxy of the GM, cannot fully represent the original complexity of CC microenvironment. Here, we present a pilot study aimed at characterizing the metaproteome of CC-associated colonic luminal contents and identifying its possible associations with CC clinicopathological features. Colonic luminal contents were collected from 24 CC tissue specimens immediately after surgery. Samples were analyzed by shotgun metaproteomics. Almost 30,000 microbial peptides were quantified in the samples, enabling the achievement of the taxonomic and functional profile of the tumor-associated colonic luminal metaproteome. Upon sample aggregation based on tumor stage, grade, or tumor-infiltrating lymphocytes (TILs), peptide sets enabling discrimination of sample groups were identified through discriminant analysis (DA). As a result, Bifidobacterium and Bacteroides fragilis were significantly enriched in high-stage and high-grade CC, respectively. Among metabolic functions, formate-tetrahydrofolate ligase was significantly associated with high-stage CC. Finally, based on the results of this pilot study, we assessed the optimal sample size for differential metaproteomic studies analyzing colonic luminal contents. In conclusion, we provide a detailed picture of the microbial and host components of the colonic luminal proteome and propose promising associations between GM taxonomic/functional features and CC clinicopathological features. Future studies will be needed to verify the prognostic value of these data and to fully exploit the potential of metaproteomics in enhancing our knowledge concerning CC progression.
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Affiliation(s)
- Alessandro Tanca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Marcello Abbondio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanni Fiorito
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy.,Medical Research Council (MRC), Centre for Environment and Health, Imperial College London, London, United Kingdom
| | - Giovanna Pira
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Rosangela Sau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Alessandra Manca
- Department of Pathology, Azienda Ospedaliero-Universitaria di Sassari, Sassari, Italy
| | - Maria Rosaria Muroni
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Alberto Porcu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Antonio Mario Scanu
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Paolo Cossu-Rocca
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy.,Surgical Pathology Unit, Department of Diagnostic Services, "Giovanni Paolo II" Hospital, Area Socio-Sanitaria Locale (ASSL) Olbia-Azienda per la Tutela della Salute (ATS) Sardegna, Olbia, Italy
| | - Maria Rosaria De Miglio
- Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
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14
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Bersuder E, Terciolo C, Lechevrel M, Martin E, Quesnelle C, Freund JN, Reimund JM, Gross I. Mesalazine initiates an anti-oncogenic β-catenin / MUCDHL negative feed-back loop in colon cancer cells by cell-specific mechanisms. Biomed Pharmacother 2021; 146:112543. [PMID: 34929577 DOI: 10.1016/j.biopha.2021.112543] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 01/18/2023] Open
Abstract
Chronic inflammation associated with intestinal architecture and barrier disruption puts patients with inflammatory bowel disease (IBD) at increased risk of developing colorectal cancer (CRC). Widely used to reduce flares of intestinal inflammation, 5-aminosalicylic acid derivatives (5-ASAs) such as mesalazine appear to also exert more direct mucosal healing and chemopreventive activities against CRC. The mechanisms underlying these activities are poorly understood and may involve the up-regulation of the cadherin-related gene MUCDHL (CDHR5). This atypical cadherin is emerging as a new actor of intestinal homeostasis and opposes colon tumorigenesis. Here, we showed that mesalazine increase mRNA levels of MUCDHL and of other genes involved in the intestinal barrier function in most intestinal cell lines. In addition, using gain / loss of function experiments (agonists, plasmid or siRNAs transfections), luciferase reporter genes and chromatin immunoprecipitation, we thoroughly investigated the molecular mechanisms triggered by mesalazine that lead to the up-regulation of MUCDHL expression. We found that basal transcription of MUCDHL in different CRC cell lines is regulated positively by CDX2 and negatively by β-catenin through a negative feed-back loop. However, mesalazine-stimulation of MUCDHL transcription is controlled by cell-specific mechanisms, involving either enhanced activation of CDX2 and PPAR-γ or repression of the β-catenin inhibitory effect. This work highlights the importance of the cellular and molecular context in the activity of mesalazine and suggests that its efficacy against CRC depends on the genetic alterations of transformed cells.
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Affiliation(s)
- Emilie Bersuder
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Chloe Terciolo
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Mathilde Lechevrel
- Université de Caen / Basse-Normandie, UFR de Médecine, EA 4652, F-14032 Caen, France
| | - Elisabeth Martin
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Celine Quesnelle
- Université de Caen / Basse-Normandie, UFR de Médecine, EA 4652, F-14032 Caen, France
| | - Jean-Noel Freund
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France
| | - Jean-Marie Reimund
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France; Université de Caen / Basse-Normandie, UFR de Médecine, EA 4652, F-14032 Caen, France; Service Hépato-Gastroentérologie, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France; Institut Hospitalo-Universitaire de Strasbourg, Hôpitaux Universitaires de Strasbourg, F-67000 Strasbourg, France.
| | - Isabelle Gross
- Université de Strasbourg, Inserm, IRFAC / UMR-S1113, FHU ARRIMAGE, FMTS, Strasbourg, France.
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15
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Gray ME, Johnson ZR, Modak D, Tamilselvan E, Tyska MJ, Sotomayor M. Heterophilic and homophilic cadherin interactions in intestinal intermicrovillar links are species dependent. PLoS Biol 2021; 19:e3001463. [PMID: 34871294 PMCID: PMC8691648 DOI: 10.1371/journal.pbio.3001463] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 12/21/2021] [Accepted: 10/30/2021] [Indexed: 11/19/2022] Open
Abstract
Enterocytes are specialized epithelial cells lining the luminal surface of the small intestine that build densely packed arrays of microvilli known as brush borders. These microvilli drive nutrient absorption and are arranged in a hexagonal pattern maintained by intermicrovillar links formed by 2 nonclassical members of the cadherin superfamily of calcium-dependent cell adhesion proteins: protocadherin-24 (PCDH24, also known as CDHR2) and the mucin-like protocadherin (CDHR5). The extracellular domains of these proteins are involved in heterophilic and homophilic interactions important for intermicrovillar function, yet the structural determinants of these interactions remain unresolved. Here, we present X-ray crystal structures of the PCDH24 and CDHR5 extracellular tips and analyze their species-specific features relevant for adhesive interactions. In parallel, we use binding assays to identify the PCDH24 and CDHR5 domains involved in both heterophilic and homophilic adhesion for human and mouse proteins. Our results suggest that homophilic and heterophilic interactions involving PCDH24 and CDHR5 are species dependent with unique and distinct minimal adhesive units.
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Affiliation(s)
- Michelle E. Gray
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Zachary R. Johnson
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Debadrita Modak
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
| | - Elakkiya Tamilselvan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Program, The Ohio State University, Columbus, Ohio, United States of America
| | - Matthew J. Tyska
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Marcos Sotomayor
- Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, United States of America
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio, United States of America
- Biophysics Program, The Ohio State University, Columbus, Ohio, United States of America
- * E-mail:
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16
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Nastase A, Mandal A, Lu SK, Anbunathan H, Morris-Rosendahl D, Zhang YZ, Sun XM, Gennatas S, Rintoul RC, Edwards M, Bowman A, Chernova T, Benepal T, Lim E, Taylor AN, Nicholson AG, Popat S, Willis AE, MacFarlane M, Lathrop M, Bowcock AM, Moffatt MF, Cookson WOCM. Integrated genomics point to immune vulnerabilities in pleural mesothelioma. Sci Rep 2021; 11:19138. [PMID: 34580349 PMCID: PMC8476593 DOI: 10.1038/s41598-021-98414-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 09/02/2021] [Indexed: 12/21/2022] Open
Abstract
Pleural mesothelioma is an aggressive malignancy with limited effective therapies. In order to identify therapeutic targets, we integrated SNP genotyping, sequencing and transcriptomics from tumours and low-passage patient-derived cells. Previously unrecognised deletions of SUFU locus (10q24.32), observed in 21% of 118 tumours, resulted in disordered expression of transcripts from Hedgehog pathways and the T-cell synapse including VISTA. Co-deletion of Interferon Type I genes and CDKN2A was present in half of tumours and was a predictor of poor survival. We also found previously unrecognised deletions in RB1 in 26% of cases and show sub-micromolar responses to downstream PLK1, CHEK1 and Aurora Kinase inhibitors in primary mesothelioma cells. Defects in Hippo pathways that included RASSF7 amplification and NF2 or LATS1/2 mutations were present in 50% of tumours and were accompanied by micromolar responses to the YAP1 inhibitor Verteporfin. Our results suggest new therapeutic avenues in mesothelioma and indicate targets and biomarkers for immunotherapy.
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Affiliation(s)
- Anca Nastase
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
| | - Amit Mandal
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
| | - Shir Kiong Lu
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
| | - Hima Anbunathan
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
| | - Deborah Morris-Rosendahl
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Yu Zhi Zhang
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Xiao-Ming Sun
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Spyridon Gennatas
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
| | - Robert C Rintoul
- Department of Thoracic Oncology, Papworth Hospital, Cambridge, UK
- Department of Oncology, University of Cambridge, Cambridge, UK
| | - Matthew Edwards
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Alex Bowman
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Tatyana Chernova
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Tim Benepal
- Department of Oncology, St George's Healthcare NHS Foundation Trust, London, UK
| | - Eric Lim
- Department of Thoracic Surgery, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Anthony Newman Taylor
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
| | - Andrew G Nicholson
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
- Department of Histopathology, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Sanjay Popat
- Department of Medicine, Royal Marsden Hospital, London, UK
- The Institute of Cancer Research, London, UK
| | - Anne E Willis
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Marion MacFarlane
- Medical Research Council Toxicology Unit, University of Cambridge, Cambridge, UK
| | - Mark Lathrop
- Department of Human Genetics, McGill Genome Centre, Montreal, QC, Canada
| | - Anne M Bowcock
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK.
| | - William O C M Cookson
- National Heart and Lung Institute, Imperial College London, Dovehouse Street, London, SW36LY, UK.
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17
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Li X, Huang C, Zhang X, Yang T, Zuo S, Fu C, Zhang Y, Yang C, Chen L. Discovery of bladder cancer biomarkers in paired pre- and postoperative urine samples. Transl Androl Urol 2021; 10:3402-3414. [PMID: 34532265 PMCID: PMC8421825 DOI: 10.21037/tau-21-562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/29/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Bladder cancer (BC), a common cancer of the urinary system, has a low mortality but an extremely high recurrence rate. Patients who have undergone initial surgical treatment often undergo frequent prognostic examinations with a substantial burden of discomfort and costs. Urine samples can reflect early disease processes in the urinary system and may be an excellent source of biomarkers. METHODS In the present study, we used the liquid chromatography with tandem mass spectrometry (LC-MS/MS) to perform proteomic analysis of pre- and postoperative urine samples from patients with stage III BC to identify biomarkers of cancer prognosis. Candidate biomarkers from proteomic analysis were simultaneously validated using western blotting in an independent cohort and immunohistochemical (IHC) staining, combined with gene expression data of BC samples in The Cancer Genome Atlas (TCGA). RESULTS The comparison of pre- and postoperative urine samples from the same patients led to the discovery of several significantly differentially expressed proteins, whose functions could be closely related to the occurrence and development of BC. We confirmed a representative group of candidate biomarker molecules, such as cadherin-related family member 2 (CDHR2), heat shock protein beta-1 (HSP27), and heterogeneous nuclear ribonucleoproteins A2/B1 (HNRNPA2B1). CONCLUSIONS The candidate biomarker molecules can distinguish between pre- and postoperative urine samples, and alterations in their expression levels are significantly associated with recurrence rates in patients with BC. Therefore, these molecules may become useful biomarkers for the monitoring and prognosis of BC.
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Affiliation(s)
- Xuechao Li
- Medical School of Chinese PLA, Beijing, China
- Department of Urology, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Chuanxi Huang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Xueli Zhang
- Department of pathology, the Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Tao Yang
- Department of Urology, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Shidong Zuo
- Department of Urology, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Chengwei Fu
- Department of Urology, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Yongjie Zhang
- Department of Urology, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
| | - Chunyuan Yang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Lijun Chen
- Department of Urology, The Fifth Medical Centre of Chinese PLA General Hospital, Beijing, China
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18
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Li X, Kumar S, Harmanci A, Li S, Kitchen RR, Zhang Y, Wali VB, Reddy SM, Woodward WA, Reuben JM, Rozowsky J, Hatzis C, Ueno NT, Krishnamurthy S, Pusztai L, Gerstein M. Whole-genome sequencing of phenotypically distinct inflammatory breast cancers reveals similar genomic alterations to non-inflammatory breast cancers. Genome Med 2021; 13:70. [PMID: 33902690 PMCID: PMC8077918 DOI: 10.1186/s13073-021-00879-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 03/25/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Inflammatory breast cancer (IBC) has a highly invasive and metastatic phenotype. However, little is known about its genetic drivers. To address this, we report the largest cohort of whole-genome sequencing (WGS) of IBC cases. METHODS We performed WGS of 20 IBC samples and paired normal blood DNA to identify genomic alterations. For comparison, we used 23 matched non-IBC samples from the Cancer Genome Atlas Program (TCGA). We also validated our findings using WGS data from the International Cancer Genome Consortium (ICGC) and the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We examined a wide selection of genomic features to search for differences between IBC and conventional breast cancer. These include (i) somatic and germline single-nucleotide variants (SNVs), in both coding and non-coding regions; (ii) the mutational signature and the clonal architecture derived from these SNVs; (iii) copy number and structural variants (CNVs and SVs); and (iv) non-human sequence in the tumors (i.e., exogenous sequences of bacterial origin). RESULTS Overall, IBC has similar genomic characteristics to non-IBC, including specific alterations, overall mutational load and signature, and tumor heterogeneity. In particular, we observed similar mutation frequencies between IBC and non-IBC, for each gene and most cancer-related pathways. Moreover, we found no exogenous sequences of infectious agents specific to IBC samples. Even though we could not find any strongly statistically distinguishing genomic features between the two groups, we did find some suggestive differences in IBC: (i) The MAST2 gene was more frequently mutated (20% IBC vs. 0% non-IBC). (ii) The TGF β pathway was more frequently disrupted by germline SNVs (50% vs. 13%). (iii) Different copy number profiles were observed in several genomic regions harboring cancer genes. (iv) Complex SVs were more frequent. (v) The clonal architecture was simpler, suggesting more homogenous tumor-evolutionary lineages. CONCLUSIONS Whole-genome sequencing of IBC manifests a similar genomic architecture to non-IBC. We found no unique genomic alterations shared in just IBCs; however, subtle genomic differences were observed including germline alterations in TGFβ pathway genes and somatic mutations in the MAST2 kinase that could represent potential therapeutic targets.
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Affiliation(s)
- Xiaotong Li
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Sushant Kumar
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center Houston, Houston, TX USA
| | - Shantao Li
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Robert R. Kitchen
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Yan Zhang
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Biomedical Informatics, College of Medicine, The Ohio State University, Columbus, OH USA
- The Ohio State University Comprehensive Cancer Center (OSUCCC – James), Columbus, OH USA
| | - Vikram B. Wali
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Sangeetha M. Reddy
- Division of Hematology/Oncology, Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX USA
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Wendy A. Woodward
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - James M. Reuben
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
| | - Christos Hatzis
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Naoto T. Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX USA
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Savitri Krishnamurthy
- Morgan Welch Inflammatory Breast Cancer Research Program and Clinic, The University of Texas MD Anderson Cancer Center, Houston, TX USA
| | - Lajos Pusztai
- Yale Cancer Center, Breast Medical Oncology, Yale School of Medicine, 300 George Street, Suite 120, Rm133, New Haven, CT 06511 USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Molecular Biophysics and Biochemistry, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Computer Science, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
- Department of Statistics and Data Science, Yale University, 266 Whitney Ave., Bass 432A, New Haven, CT 06520 USA
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19
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Gabbert L, Dilling C, Meybohm P, Burek M. Deletion of Protocadherin Gamma C3 Induces Phenotypic and Functional Changes in Brain Microvascular Endothelial Cells In Vitro. Front Pharmacol 2020; 11:590144. [PMID: 33390965 PMCID: PMC7774295 DOI: 10.3389/fphar.2020.590144] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/09/2020] [Indexed: 01/25/2023] Open
Abstract
Inflammation of the central nervous system (CNS) is associated with diseases such as multiple sclerosis, stroke and neurodegenerative diseases. Compromised integrity of the blood-brain barrier (BBB) and increased migration of immune cells into the CNS are the main characteristics of brain inflammation. Clustered protocadherins (Pcdhs) belong to a large family of cadherin-related molecules. Pcdhs are highly expressed in the CNS in neurons, astrocytes, pericytes and epithelial cells of the choroid plexus and, as we have recently demonstrated, in brain microvascular endothelial cells (BMECs). Knockout of a member of the Pcdh subfamily, PcdhgC3, resulted in significant changes in the barrier integrity of BMECs. Here we characterized the endothelial PcdhgC3 knockout (KO) cells using paracellular permeability measurements, proliferation assay, wound healing assay, inhibition of signaling pathways, oxygen/glucose deprivation (OGD) and a pro-inflammatory cytokine tumor necrosis factor alpha (TNFα) treatment. PcdhgC3 KO showed an increased paracellular permeability, a faster proliferation rate, an altered expression of efflux pumps, transporters, cellular receptors, signaling and inflammatory molecules. Serum starvation led to significantly higher phosphorylation of extracellular signal-regulated kinases (Erk) in KO cells, while no changes in phosphorylated Akt kinase levels were found. PcdhgC3 KO cells migrated faster in the wound healing assay and this migration was significantly inhibited by respective inhibitors of the MAPK-, β-catenin/Wnt-, mTOR- signaling pathways (SL327, XAV939, or Torin 2). PcdhgC3 KO cells responded stronger to OGD and TNFα by significantly higher induction of interleukin 6 mRNA than wild type cells. These results suggest that PcdhgC3 is involved in the regulation of major signaling pathways and the inflammatory response of BMECs.
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Affiliation(s)
- Lydia Gabbert
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
| | - Christina Dilling
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
| | - Patrick Meybohm
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
| | - Malgorzata Burek
- Department of Anaesthesia and Critical Care, University of Würzburg, Würzburg, Germany
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20
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Losi L, Zanocco-Marani T, Grande A. Cadherins down-regulation: towards a better understanding of their relevance in colorectal cancer. Histol Histopathol 2020; 35:1391-1402. [PMID: 32567668 DOI: 10.14670/hh-18-236] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The down-regulation of cadherin expression in colorectal cancer (CRC) has been widely studied. However, existing data on cadherin expression are highly variable and its relevance to CRC development has not been completely established. This review examines published studies on cadherins whose down-regulation has been already demonstrated in CRC, trying to establish a relationship with promoter methylation, the capacity to influence the Wnt / CTNNB1 (catenin beta 1, beta-catenin) signalling pathway and the clinical implications for disease outcome. Moreover, it also analyses factors that may explain data variability and highlights the importance of considering the altered subcellular localization of the examined cadherins. The results of this survey reveal that thirty of one hundred existing cadherins appear to be down-regulated in CRC. Among these, ten are cadherins, sixteen are protocadherins, equally divided between clustered and non clustered, and four are cadherin - related. These findings suggest that, to better define the role played by cadherin down-regulation in CRC pathogenesis, the expression of multiple rather than individual cadherins should be taken into account and further functional studies are necessary to clarify the relative ability of individual cadherins to inhibit CTNNB1 therefore acting as tumor suppressors.
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Affiliation(s)
- Lorena Losi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
| | | | - Alexis Grande
- Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
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21
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Neubert L, Borchert P, Stark H, Hoefer A, Vogel-Claussen J, Warnecke G, Eubel H, Kuenzler P, Kreipe HH, Hoeper MM, Kuehnel M, Jonigk D. Molecular Profiling of Vascular Remodeling in Chronic Pulmonary Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:1382-1396. [PMID: 32275906 DOI: 10.1016/j.ajpath.2020.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 03/10/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023]
Abstract
Pulmonary hypertension and pulmonary vascular remodeling (PVR) are common in many lung diseases leading to right ventricular dysfunction and death. Differences in PVR result in significant prognostic divergences in both the pulmonary arterial and venous compartments, as in pulmonary arterial hypertension (PAH) and pulmonary veno-occlusive disease (PVOD), respectively. Our goal was to identify compartment-specific molecular hallmarks of PVR, considering the risk of life-threatening pulmonary edema in PVOD, if treated by conventional pulmonary hypertension therapy. Formalin-fixed and paraffin-embedded tissues from fresh explanted human lungs of patients with PVOD (n = 19), PAH (n = 20), idiopathic pulmonary fibrosis (n = 13), and chronic obstructive pulmonary disease (n = 15), were analyzed for inflammation and kinome-related gene regulation. The generated neuronal network differentiated PVOD from PAH samples with a sensitivity of 100% and a specificity of 92% in a randomly chosen validation set, a level far superior to established diagnostic algorithms. Further, various alterations were identified regarding the gene expression of explanted lungs with PVR, compared with controls. Specifically, the dysregulation of microtubule-associated serine/threonine kinase 2 and protein-o-mannose kinase SGK196 in all disease groups suggests a key role in pulmonary vasculopathy for the first time. Our findings promise to help develop novel target-specific interventions and innovative approaches to facilitate clinical diagnostics in an elusive group of diseases.
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Affiliation(s)
- Lavinia Neubert
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany.
| | - Paul Borchert
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Helge Stark
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Anne Hoefer
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Jens Vogel-Claussen
- German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Institute for Radiology, Hannover Medical School, Hannover, Germany
| | - Gregor Warnecke
- German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School
| | - Holger Eubel
- Institute of Plant Genetics, Leibniz University Hanover, Hannover, Germany
| | - Patrick Kuenzler
- Institute of Plant Genetics, Leibniz University Hanover, Hannover, Germany
| | | | - Marius M Hoeper
- German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany; Clinic for Pneumology, Hannover Medical School, Hannover, Germany
| | - Mark Kuehnel
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
| | - Danny Jonigk
- Institute of Pathology, Hannover Medical School, Hannover, Germany; German Center for Lung Research (DZL), Biomedical Research in End-stage and Obstructive Lung Disease Hannover (BREATH), Hannover, Germany
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22
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Ben-Mahmoud A, Al-Shamsi AM, Ali BR, Al-Gazali L. Evaluating the Role of MAST1 as an Intellectual Disability Disease Gene: Identification of a Novel De Novo Variant in a Patient with Developmental Disabilities. J Mol Neurosci 2020; 70:320-327. [PMID: 31721002 DOI: 10.1007/s12031-019-01415-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Intellectual disability (ID) is one of the most common developmental disorders characterized by a congenital limitation in intellectual functioning and adaptive behavior. More than 800 genes have been implicated so far in the pathogenesis of syndromic and non-syndromic ID conditions with the actual number is expected to be over two thousand. The advent of next-generation sequencing resulted in the identification of many novel ID genes with new genes are being reported on weekly basis. The level of evidence on ID genes varies with some of them being preliminary. MAST1 have been hinted at as being causative of ID but the evidence has been very sketchy. Extensive search of the literature identified three heterozygous de novo missense variants in MAST1 as possible causes of syndromic ID in three individuals where intellectual disability has been a major feature. Using exome sequencing, we identified a novel missense variant c.3539T>G, p.(Leu1180Arg) in MAST1 in an Emirati patient with intellectual disability, microcephaly, and dysmorphic features. In silico pathogenicity prediction analyses predict that all the four missense variants reported in this study are likely to be damaging. Immunostaining of cells expressing human MAST1 showed that majority large proportion of the expressed protein is colocalized the microtubule filaments in the cytoplasm. However, the identified variant c.3539T>G, p.(Leu1180Arg) as well as the other three variants seem to localize in a similar pattern to wild-type indicating a disease mechanism not involving mis-targeting. We, therefore, suggest that mutations in MAST1 should be considered as strong candidates for intellectual disability in humans.
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Affiliation(s)
- Afif Ben-Mahmoud
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Aisha M Al-Shamsi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, United Arab Emirates
| | - Bassam R Ali
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Lihadh Al-Gazali
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, P.O. Box 17666, Al Ain, United Arab Emirates.
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23
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Duangkumpha K, Stoll T, Phetcharaburanin J, Yongvanit P, Thanan R, Techasen A, Namwat N, Khuntikeo N, Chamadol N, Roytrakul S, Mulvenna J, Mohamed A, Shah AK, Hill MM, Loilome W. Urine proteomics study reveals potential biomarkers for the differential diagnosis of cholangiocarcinoma and periductal fibrosis. PLoS One 2019; 14:e0221024. [PMID: 31425520 PMCID: PMC6699711 DOI: 10.1371/journal.pone.0221024] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Cholangiocarcinoma (CCA) is a primary malignant tumor of the epithelial lining of biliary track associated with endemic Opisthorchis viverrini (Ov) infection in northeastern Thailand. Ov-associated periductal fibrosis (PDF) is the precancerous lesion for CCA, and can be detected by ultrasonography (US) to facilitate early detection. However, US cannot be used to distinguish PDF from cancer. Therefore, the objective of this study was to discover and qualify potential urine biomarkers for CCA detection in at-risk population. Biomarker discovery was conducted on pooled urine samples, 42 patients per group, with PDF or normal bile duct confirmed by ultrasound. After depletion of high abundance proteins, 338 urinary proteins were identified from the 3 samples (normal-US, PDF-US, CCA). Based on fold change and literature review, 70 candidate proteins were selected for qualification by multiple reaction monitoring mass spectrometry (MRM-MS) in 90 individual urine samples, 30 per group. An orthogonal signal correction projection to latent structures discriminant analysis (O-PLS-DA) multivariate model constructed from the 70 candidate biomarkers significantly discriminated CCA from normal and PDF groups (P = 0.003). As an independent validation, the expression of 3 candidate proteins was confirmed by immunohistochemistry in CCA tissues: Lysosome associated membrane glycoprotein 1 (LAMP1), lysosome associated membrane glycoprotein 2 (LAMP2) and cadherin-related family member 2 (CDHR2). Further evaluation of these candidate biomarkers in a larger cohort is needed to support their applicability in a clinical setting for screening and monitoring early CCA and for CCA surveillance.
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Affiliation(s)
- Kassaporn Duangkumpha
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Thomas Stoll
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jutarop Phetcharaburanin
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Puangrat Yongvanit
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Anchalee Techasen
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen, Thailand
| | - Nisana Namwat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Nittaya Chamadol
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Alok K Shah
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Michelle M Hill
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Watcharin Loilome
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
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24
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A Method for Comprehensive Proteomic Analysis of Human Faecal Samples to Investigate Gut Dysbiosis in Patients with Cystic Fibrosis. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1073:137-160. [PMID: 31236842 DOI: 10.1007/978-3-030-12298-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
BACKGROUND This chapter reports the evaluation of two shotgun metaproteomic workflows. The methods were developed to investigate gut dysbiosis via analysis of the faecal microbiota from patients with cystic fibrosis (CF). We aimed to set up an unbiased and effective method to extract the entire proteome, i.e. to extract sufficient bacterial proteins from the faecal samples in combination with a maximum of host proteins giving information on the disease state. METHODS Two protocols were compared; the first method involves an enrichment of the bacterial proteins while the second method is a more direct method to generate a whole faecal proteome extract. The different extracts were analysed using denaturing polyacrylamide gel electrophoresis followed by liquid chromatography-tandem mass spectrometry aiming a maximal coverage of the bacterial protein content in faecal samples. RESULTS AND CONCLUSIONS In all extracts, microbial proteins are detected, and in addition, nonbacterial proteins are detected in all samples providing information about the host status. Our study demonstrates the huge influence of the used protein extraction method on the obtained result and shows the need for a standardised and appropriate sample preparation for metaproteomic analysis. To address questions on the health status of the patients, a whole protein extract is preferred over a method to enrich the bacterial fraction. In addition, the method of the whole protein fraction is faster, which gives the possibility to analyse more biological replicates.
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25
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Duangkumpha K, Stoll T, Phetcharaburanin J, Yongvanit P, Thanan R, Techasen A, Namwat N, Khuntikeo N, Chamadol N, Roytrakul S, Mulvenna J, Mohamed A, Shah AK, Hill MM, Loilome W. Discovery and Qualification of Serum Protein Biomarker Candidates for Cholangiocarcinoma Diagnosis. J Proteome Res 2019; 18:3305-3316. [DOI: 10.1021/acs.jproteome.9b00242] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kassaporn Duangkumpha
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Thomas Stoll
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Jutarop Phetcharaburanin
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Puangrat Yongvanit
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Anchalee Techasen
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
- Faculty of Associated Medical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nisana Namwat
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Narong Khuntikeo
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Surgery, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nittaya Chamadol
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Radiology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sittiruk Roytrakul
- Proteomics Research Laboratory, Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Jason Mulvenna
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Alok K. Shah
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Michelle M. Hill
- QIMR Berghofer Medical Research Institute, Herston, Queensland 4006, Australia
| | - Watcharin Loilome
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
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26
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Xia Z, Huang M, Zhu Q, Li Y, Ma Q, Wang Y, Chen X, Li J, Qiu L, Zhang J, Zheng J, Lu B. Cadherin Related Family Member 2 Acts As A Tumor Suppressor By Inactivating AKT In Human Hepatocellular Carcinoma. J Cancer 2019; 10:864-873. [PMID: 30854092 PMCID: PMC6400803 DOI: 10.7150/jca.27663] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 01/02/2019] [Indexed: 02/06/2023] Open
Abstract
Cadherin related family member 2 (CDHR2) belongs to the protocadherin family and is abundant in normal liver, kidney, and colon tissues, but weakly expressed in cancers arising from these tissues. In this study, we demonstrated that CDHR2 was highly expressed in para-cancer tissues of human hepatocellular carcinoma (HCC), but significantly downregulated or silenced in 85.7% (6/7) of HCC cell lines by both semi-quantitative PCR and western blot, and 79.1% (19/24) and 80.2% (89/111) of tumor tissues from patients with HCC by semi-quantitative PCR, and immunohistochemistry, respectively. Interestingly, CpG islands in the promoter of CDHR2 gene were hypermethylated in HCC cell lines and tissues compared with the para-cancer tissues by methylation-specific PCR analysis, leading to transcriptional repression and silencing of CDHR2 in HCC. In addition, CDHR2 overexpression by lentiviral vectors had suppressive effects on HCC cell growth and proliferation, as evidenced by prolonged cell doubling time and reduced colony-forming ability in vitro, as well as by decreased tumorigenicity in vivo. Mechanistically, CDHR2 overexpression resulted in AKT dephosphorylation along with downregulation of cyclooxygenase-2 (COX2), a downstream target of AKT. This effect was reversed by myristoylated AKT, a constitutively active form of AKT, suggesting an involvement of CDHR2-AKT-COX2 axis in the suppression of HCC growth. Taken together, our study identified CDHR2 as a novel tumor suppressor in HCC and provided a new therapeutic target for HCC.
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Affiliation(s)
- Ziyuan Xia
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Meijin Huang
- Department of Oncology, 920th Hospital of PLA Joint Logistics support Force, Yunnan, China
| | - Qiangqiang Zhu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Yinghua Li
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Qian Ma
- Department of Pathology, Changhai Hospital, Second Military Medical University, Shanghai, China
| | - Yang Wang
- Department of Pathology, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xia Chen
- Yangpu Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jianzhong Li
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Lei Qiu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Junping Zhang
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Jiaoyang Zheng
- Department of Endocrinology, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Bin Lu
- Department of Biochemical Pharmacy, School of Pharmacy, Second Military Medical University, Shanghai, China
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27
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Assadsangabi A, Evans CA, Corfe BM, Lobo A. Application of Proteomics to Inflammatory Bowel Disease Research: Current Status and Future Perspectives. Gastroenterol Res Pract 2019; 2019:1426954. [PMID: 30774653 PMCID: PMC6350533 DOI: 10.1155/2019/1426954] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing/remitting inflammatory illness of the gastrointestinal tract of unknown aetiology. Despite recent advances in decoding the pathophysiology of IBD, many questions regarding disease pathogenesis remain. Genome-wide association studies (GWAS) and knockout mouse models have significantly advanced our understanding of genetic susceptibility loci and inflammatory pathways involved in IBD pathogenesis. Despite their important contribution to a better delineation of the disease process in IBD, these genetic findings have had little clinical impact to date. This is because the presence of a given gene mutation does not automatically correspond to changes in its expression or final metabolic or structural effect(s). Furthermore, the existence of these gene susceptibility loci in the normal population suggests other driving prerequisites for the disease manifestation. Proteins can be considered the main functional units as almost all intracellular physiological functions as well as intercellular interactions are dependent on them. Proteomics provides methods for the large-scale study of the proteins encoded by the genome of an organism or a cell, to directly investigate the proteins and pathways involved. Understanding the proteome composition and alterations yields insights into IBD pathogenesis as well as identifying potential biomarkers of disease activity, mucosal healing, and cancer progression. This review describes the state of the art in the field with respect to the study of IBD and the potential for translation from biomarker discovery to clinical application.
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Affiliation(s)
- Arash Assadsangabi
- Gastroenterology Unit, Salford Royal Hospital, Salford, UK
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology and Insigneo Institute, University of Sheffield, Sheffield, UK
| | - Caroline A. Evans
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield, UK
| | - Bernard M. Corfe
- Molecular Gastroenterology Research Group, Academic Unit of Surgical Oncology, Department of Oncology and Insigneo Institute, University of Sheffield, Sheffield, UK
| | - Alan Lobo
- Gastroenterology Unit, Salford Royal Hospital, Salford, UK
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28
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Pinette JA, Mao S, Millis BA, Krystofiak ES, Faust JJ, Tyska MJ. Brush border protocadherin CDHR2 promotes the elongation and maximized packing of microvilli in vivo. Mol Biol Cell 2018; 30:108-118. [PMID: 30403560 PMCID: PMC6337912 DOI: 10.1091/mbc.e18-09-0558] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Transporting epithelial cells optimize their morphology for solute uptake by building an apical specialization: a dense array of microvilli that serves to increase membrane surface area. In the intestinal tract, individual cells build thousands of microvilli, which pack tightly to form the brush border. Recent studies implicate adhesion molecule CDHR2 in the regulation of microvillar packing via the formation of adhesion complexes between the tips of adjacent protrusions. To gain insight on how CDHR2 contributes to brush border morphogenesis and enterocyte function under native in vivo conditions, we generated mice lacking CDHR2 expression in the intestinal tract. Although CDHR2 knockout (KO) mice are viable, body weight trends lower and careful examination of tissue, cell, and brush border morphology revealed several perturbations that likely contribute to reduced functional capacity of KO intestine. In the absence of CDHR2, microvilli are significantly shorter, and exhibit disordered packing and a 30% decrease in packing density. These structural perturbations are linked to decreased levels of key solute processing and transporting factors in the brush border. Thus, CDHR2 functions to elongate microvilli and maximize their numbers on the apical surface, which together serve to increase the functional capacity of enterocyte.
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Affiliation(s)
- Julia A Pinette
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Suli Mao
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Bryan A Millis
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Evan S Krystofiak
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - James J Faust
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Matthew J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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29
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Loss of expression of μ-protocadherin and protocadherin-24 in sporadic and hereditary nonpolyposis colorectal cancers. Hum Pathol 2018; 84:299-308. [PMID: 30296522 DOI: 10.1016/j.humpath.2018.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/13/2018] [Accepted: 09/23/2018] [Indexed: 12/25/2022]
Abstract
Colorectal cancer (CRC) is a neoplastic disease in which normal mucosa undergoes a process of malignant transformation due to the progressive accumulation of molecular alterations affecting proto-oncogenes and oncosuppressor genes. Some of these modifications exert their carcinogenic potential by promoting a constitutive activation of the β-catenin signaling proliferation pathway, and when present, loss of cadherin expression also significantly contributes to the same effect. Using a combined approach of molecular and immunohistochemical analysis, we have previously demonstrated that most sporadic CRCs exhibit a down-regulated expression of a cadherin, named μ-protocadherin, that is generally observed in association with a higher proliferation rate and a worse prognosis. The aim of this report was to perform a comparative immunohistochemical assessment of μ-protocadherin and a similar cadherin, named protocadherin-24, in sporadic CRC and hereditary nonpolyposis colorectal cancer. The data obtained put in evidence that double-negative CRCs, lacking both the analyzed protocadherins, are more represented among sporadic tumors, whereas double-positive CRCs, maintaining their expression, exhibit an opposite trend. As expected, loss of protocadherin expression was accompanied by nuclear localization of β-catenin and increased positivity of the Ki-67 proliferation marker. This finding is consistent with the different clinical evolution of the 2 considered CRC sets according to which patients with hereditary nonpolyposis colorectal cancer experience a better prognosis as compared with those affected by a sporadic CRC.
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Zhang T, Guan G, Chen T, Jin J, Zhang L, Yao M, Qi X, Zou J, Chen J, Lu F, Chen X. Methylation of PCDH19 predicts poor prognosis of hepatocellular carcinoma. Asia Pac J Clin Oncol 2018; 14:e352-e358. [PMID: 29749051 DOI: 10.1111/ajco.12982] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 04/05/2018] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Several members of protocadherins (PCDHs) have been identified as tumor suppressor genes in human carcinogenesis, but little is known about PCDH19. The aim of the present study was to assess the expression and methylation of PCDH19 in hepatocellular carcinoma (HCC). METHODS The RNA-seq data from The Cancer Genome Atlas Database were downloaded and used for analyzing PCDH19 expression in HCC patients and normal liver tissues. We collected 63 paired tumor and nontumor liver tissues from hepatitis B virus-related HCC patients. The expression of PCDH19 was detected by real-time quantitative RT-PCR assay. The methylation of PCDH19 gene was analyzed by DNA methylation-sensitive endonuclease digestion and the sequential quantitative PCR. The prognostic value of PCDH19 gene methylation was evaluated by Kaplan-Meier analyses. RESULTS PCDH19 expression was downregulated in HCC tissues and seven HCC cell lines compared to nontumor tissues. PCHD19 promoter was frequently hypermethylated in three (SMMC7721, Hep3B and SNU387) of seven HCC cell lines and 5-aza-dC treatment could significantly increased the PCDH19 expression in these methylated cells. In addition, HCC tumor tissues exhibited significantly increased PCDH19 hypermethylation both in frequency (30.15% vs 9.52%, P = 0.003) and in intensity (P = 0.002) compared to that in nontumor tissues. Kaplan-Meier survival analysis revealed that PCDH19 hypermethylation was correlated with the poor overall survival of HCC patients. CONCLUSION PCDH19 expression was downregulated in HCC, which was mediated at least in part by promoter hypermethylation. PCDH19 hypermethylation might present a potential prognostic marker in HCC patients.
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Affiliation(s)
- Ting Zhang
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Guiwen Guan
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Tingting Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jingling Jin
- Departments of Pediatrics-Oncology and Surgery, Baylor College of Medicine, Texas Children's Hospital, Houston, Texas, USA
| | - Lichun Zhang
- Department of Liver Disease, Taiyuan Third People's Hospital, Taiyuan, China
| | - Mingjie Yao
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xuewei Qi
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jun Zou
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Jiacheng Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Fengmin Lu
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Xiangmei Chen
- Department of Microbiology and Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
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Ye W, Ling S, Liu RY, Pan ZZ, Wang G, Gao S, Wu J, Cao L, Dong L, Li Y, Zhou Y, Du W, Meng X, Chen J, Guan X, He Y, Pan C, Zheng XS, Lu X, Chen S, Huang W. Exome sequencing reveals the genetic landscape and frequent inactivation of PCDHB3 in Chinese rectal cancers. J Pathol 2018. [PMID: 29537081 DOI: 10.1002/path.5073] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Colorectal cancer (CRC) is the third most common cancer worldwide, with more than 1.3 million new cases and 690 000 deaths each year. In China, the incidence of CRC has increased dramatically due to dietary and lifestyle changes, to become the fifth leading cause of cancer-related death. Here, we performed whole-exome sequencing in 50 rectal cancer cases among the Chinese population as part of the International Cancer Genome Consortium research project. Frequently mutated genes and enriched pathways were identified. Moreover, a previously unreported gene, PCDHB3, was found frequently mutated in 5.19% cases. Additionally, PCDHB3 expression was found decreased in 81.6% of CRC tissues and all eight CRC cell lines tested. Low expression and cytoplasmic localization of PCDHB3 predict poor prognosis in advanced CRC. Copy number decrease and/or CpG island hypermethylation contributes to the pervasive decreased expression of PCDHB3. PCDHB3 inhibits CRC cell proliferation, migration, and epithelial-mesenchymal transition. The tumor-suppressive effects of PCDHB3 are partially due to inhibition of NF-κB transcriptional activity through K63 deubiquitination of p50 at lysine 244/252, which increases the binding affinity of inactive p50 homodimer to κB DNA, resulting in competitive inhibition of the transcription of NF-κB target genes by p65 dimers. Our study identified PCDHB3 as a novel tumor suppressor in CRC via inhibition of the NF-κB pathway, and its expression and localization may serve as prognostic markers for advanced CRC. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Wen Ye
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Shaoping Ling
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
| | - Ran-Yi Liu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Zhi-Zhong Pan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Gaoyuan Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Shijuan Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
| | - Jiangxue Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Lihua Cao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
| | - Lili Dong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
| | - Yingchang Li
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Yi Zhou
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Wuying Du
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Xiangqi Meng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Jinna Chen
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Xinyuan Guan
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China.,Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, PR China
| | - Yulong He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
| | - Changchuan Pan
- Medical Oncology, Sichuan Cancer Hospital and Institute, Second People's Hospital of Sichuan Province, Chengdu, PR China
| | - Xf Steven Zheng
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China.,Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Xuemei Lu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China
| | - Shuai Chen
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China
| | - Wenlin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, PR China.,CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China
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Dilling C, Roewer N, Förster CY, Burek M. Multiple protocadherins are expressed in brain microvascular endothelial cells and might play a role in tight junction protein regulation. J Cereb Blood Flow Metab 2017; 37:3391-3400. [PMID: 28094605 PMCID: PMC5624389 DOI: 10.1177/0271678x16688706] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Protocadherins (Pcdhs) are a large family of cadherin-related molecules. They play a role in cell adhesion, cellular interactions, and development of the central nervous system. However, their expression and role in endothelial cells has not yet been characterized. Here, we examined the expression of selected clustered Pcdhs in endothelial cells from several vascular beds. We analyzed human and mouse brain microvascular endothelial cell (BMEC) lines and primary cells, mouse myocardial microvascular endothelial cell line, and human umbilical vein endothelial cells. We examined the mRNA and protein expression of selected Pcdhs using RT-PCR, Western blot, and immunostaining. A strong mRNA expression of Pcdhs was observed in all endothelial cells tested. At the protein level, Pcdhs-gamma were detected using an antibody against the conserved C-terminal domain of Pcdhs-gamma or an antibody against PcdhgC3. Deletion of highly expressed PcdhgC3 led to differences in the tight junction protein expression and mRNA expression of Wnt/mTOR (mechanistic target of rapamycin) pathway genes as well as lower transendothelial electrical resistance. Staining of PcdhgC3 showed diffused cytoplasmic localization in mouse BMEC. Our results suggest that Pcdhs may play a critical role in the barrier-stabilizing pathways at the blood-brain barrier.
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Affiliation(s)
- Christina Dilling
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
| | - Norbert Roewer
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
| | - Carola Y Förster
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
| | - Malgorzata Burek
- University of Würzburg, Department of Anaesthesia and Critical Care, Würzburg, Germany
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Zong Z, Pang H, Yu R, Jiao Y. PCDH8 inhibits glioma cell proliferation by negatively regulating the AKT/GSK3β/β-catenin signaling pathway. Oncol Lett 2017; 14:3357-3362. [PMID: 28927088 PMCID: PMC5588001 DOI: 10.3892/ol.2017.6629] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 02/27/2017] [Indexed: 12/14/2022] Open
Abstract
Protocadherin-8 (PCDH8), a member of the protocadherin superfamily of proteins, is frequently lost in numerous types of cancer. However, the role that PCDH8 serves in human glioma, and the molecular mechanisms underlying this, remain unclear. Data from the present study demonstrated that the expression levels of PCDH8 mRNA and protein were significantly decreased in human glioma tissue compared with normal brain tissue. This suggested that PCDH8 is associated with the development of glioma. Thus, the role of PCDH8 in glioma cell proliferation was investigated by silencing and overexpressing PCDH8 in U251 glioma cells. Overexpression of PCDH8 significantly inhibited glioma cell proliferation, while silencing of PCDH8 using small interfering RNA promoted glioma cell proliferation. Restoration of PCDH8 decreased phosphorylated (p)-Rac-α serine/threonine-protein kinase (AKT) [Threonine (T)308/Serine (S)473] and p-glycogen synthase kinase-3β (p-GSK3β) (S9) protein expression, thereby reducing the level of β-catenin when compared with the control. By contrast, silencing of PCDH8 increased levels of p-AKT (T308/S473) and p-GSK3β (S9), thereby increasing the level of β-catenin. In conclusion, the results of the present study suggested that PCDH8 suppressed glioma cell proliferation, and that the loss of PCDH8 may stimulate the proto-oncogene Wnt/β-catenin signaling pathway and therefore promote glioma cell proliferation.
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Affiliation(s)
- Zhenkun Zong
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Hui Pang
- Department of Cardiovascular Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Affiliated Xuzhou Hospital of Medical College of Southeast University, Xuzhou, Jiangsu 221009, P.R. China
| | - Rutong Yu
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
| | - Yunqi Jiao
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu 221002, P.R. China
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Montorsi L, Parenti S, Losi L, Ferrarini F, Gemelli C, Rossi A, Manco G, Ferrari S, Calabretta B, Tagliafico E, Zanocco-Marani T, Grande A. Expression of μ-protocadherin is negatively regulated by the activation of the β-catenin signaling pathway in normal and cancer colorectal enterocytes. Cell Death Dis 2016; 7:e2263. [PMID: 27310872 PMCID: PMC5143391 DOI: 10.1038/cddis.2016.163] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 01/11/2023]
Abstract
Mu-protocadherin (MUCDHL) is an adhesion molecule predominantly expressed by colorectal epithelial cells which is markedly downregulated upon malignant transformation. Notably, treatment of colorectal cancer (CRC) cells with mesalazine lead to increased expression of MUCDHL, and is associated with sequestration of β-catenin on the plasma membrane and inhibition of its transcriptional activity. To better characterize the causal relationship between β-catenin and MUCDHL expression, we performed various experiments in which CRC cell lines and normal colonic organoids were subjected to culture conditions inhibiting (FH535 treatment, transcription factor 7-like 2 siRNA inactivation, Wnt withdrawal) or stimulating (LiCl treatment) β-catenin activity. We show here that expression of MUCDHL is negatively regulated by functional activation of the β-catenin signaling pathway. This finding was observed in cell culture systems representing conditions of physiological stimulation and upon constitutive activation of β-catenin in CRC. The ability of MUCDHL to sequester and inhibit β-catenin appears to provide a positive feedback enforcing the effect of β-catenin inhibitors rather than serving as the primary mechanism responsible for β-catenin inhibition. Moreover, MUCDHL might have a role as biomarker in the development of CRC chemoprevention drugs endowed with β-catenin inhibitory activity.
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Affiliation(s)
- L Montorsi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - S Parenti
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - L Losi
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | | | - C Gemelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - A Rossi
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - G Manco
- Department of Surgical, Medical, Dental and Morphological Sciences with Interest in Transplant, Oncological and Regenerative Medicine, University of Modena and Reggio Emilia, Modena, Italy
| | - S Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - B Calabretta
- Department of Clinical and Diagnostic Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy.,Department of Cancer Biology and SKKC, Thomas Jefferson University, Philadelphia, PA, USA
| | - E Tagliafico
- Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy.,Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - T Zanocco-Marani
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - A Grande
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
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35
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Ma H, Chen G, Guo M. Mass spectrometry based translational proteomics for biomarker discovery and application in colorectal cancer. Proteomics Clin Appl 2016; 10:503-15. [PMID: 26616366 DOI: 10.1002/prca.201500082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 11/17/2015] [Accepted: 11/25/2015] [Indexed: 12/29/2022]
Abstract
Colorectal cancer (CRC) is a leading cause of cancer-related death in the world. Clinically, early detection of the disease is the most effective approach to tackle this tough challenge. Discovery and development of reliable and effective diagnostic tools for the assessment of prognosis and prediction of response to drug therapy are urgently needed for personalized therapies and better treatment outcomes. Among many ongoing efforts in search for potential CRC biomarkers, MS-based translational proteomics provides a unique opportunity for the discovery and application of protein biomarkers toward better CRC early detection and treatment. This review updates most recent studies that use preclinical models and clinical materials for the identification of CRC-related protein markers. Some new advances in the development of CRC protein markers such as CRC stem cell related protein markers, SRM/MRM-MS and MS cytometry approaches are also discussed in order to address future directions and challenges from bench translational research to bedside clinical application of CRC biomarkers.
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Affiliation(s)
- Hong Ma
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,Haematology and Oncology Division, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Guilin Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China.,University of Chinese Academy of Sciences, Beijing, P. R. China
| | - Mingquan Guo
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Sino-Africa Joint Research Center, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P. R. China
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36
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Loss of PCDH9 is associated with the differentiation of tumor cells and metastasis and predicts poor survival in gastric cancer. Clin Exp Metastasis 2015; 32:417-28. [DOI: 10.1007/s10585-015-9712-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 03/05/2015] [Indexed: 12/23/2022]
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Abstract
Epithelial cells from diverse tissues, including the enterocytes that line the intestinal tract, remodel their apical surface during differentiation to form a brush border: an array of actin-supported membrane protrusions known as microvilli that increases the functional capacity of the tissue. Although our understanding of how epithelial cells assemble, stabilize, and organize apical microvilli is still developing, investigations of the biochemical and physical underpinnings of these processes suggest that cells coordinate cytoskeletal remodeling, membrane-cytoskeleton cross-linking, and extracellular adhesion to shape the apical brush border domain.
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Affiliation(s)
- Scott W Crawley
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
| | - Mark S Mooseker
- Department of Molecular, Cellular and Developmental Biology, Department of Cell Biology, and Department of Pathology, Yale University, New Haven, CT 06520 Department of Molecular, Cellular and Developmental Biology, Department of Cell Biology, and Department of Pathology, Yale University, New Haven, CT 06520 Department of Molecular, Cellular and Developmental Biology, Department of Cell Biology, and Department of Pathology, Yale University, New Haven, CT 06520
| | - Matthew J Tyska
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232
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Lv J, Zhu P, Yang Z, Li M, Zhang X, Cheng J, Chen X, Lu F. PCDH20 functions as a tumour-suppressor gene through antagonizing the Wnt/β-catenin signalling pathway in hepatocellular carcinoma. J Viral Hepat 2015; 22:201-11. [PMID: 24910204 PMCID: PMC4344823 DOI: 10.1111/jvh.12265] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Accepted: 04/22/2014] [Indexed: 12/13/2022]
Abstract
Several members of protocadherins have been found involved in human carcinogenesis, but little is known about PCDH20 in HCC. Here in this study, using quantitative real-time RT-PCR assay, we demonstrated the downregulation of PCDH20 expression in 6 of 7 HCC cell lines tested. Similarly, PCDH20 expression in primary HCC tissues was also significantly downregulated in comparison with that in either disease-free normal liver tissues or the adjacent nontumour liver tissues (P < 0.001, respectively). Among HCC tumour tissues studied, about 48% (51/107) of them showed reduced PCDH20 mRNA level. Further statistic analysis revealed that the reduced PCDH20 mRNA level in tumour tissues was much more common in younger patients group (aged <50 years) than that in older group (≥50 years) (60% vs 33%, P = 0.0303). Loss of heterozygosity (LOH) and promoter hypermethylation analysis revealed that deletion and/or aberrant epigenetic modulation of PCDH20 gene account for its downregulation, at least in a fraction of tumour specimens. Moreover, ectopic expression of PCDH20 in HCC cells significantly suppressed cell proliferation, clonogenicity, migration and tumour formation. Notably, we proved for the first time that, via activating GSK-3β, PCDH20 could inhibit Wnt/β-catenin signalling pathway. Furthermore, our data suggest that PCDH20 may conduct its Wnt/β-catenin signalling antagonizing function through suppressing Akt and Erk activities and promoting GSK-3β signalling activities. However, the detailed mechanism remained undiscovered. In conclusion, our data here strongly suggested that PCDH20 may act as a candidate tumour suppressor in HCC.
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Affiliation(s)
- J Lv
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, China
| | - P Zhu
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China
| | - Z Yang
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China
| | - M Li
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China
| | - X Zhang
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China
| | - J Cheng
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China
| | - X Chen
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China
| | - F Lu
- Department of Microbiology & infectious Disease Center, Peking University Health Science CenterBeijing, China,Department of Infectious Diseases and Hepatology Unit, Nanfang Hospital, Southern Medical UniversityGuangzhou, Guangdong, China
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The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling. J Gastroenterol 2015; 50:46-57. [PMID: 24789573 DOI: 10.1007/s00535-014-0958-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/07/2014] [Indexed: 02/04/2023]
Abstract
BACKGROUND The gastrointestinal tract (GIT) is subdivided into different anatomical organs with many shared functions and characteristics, but also distinct differences. We have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to describe the gene and protein expression patterns that define the human GIT. METHODS RNA sequencing data derived from stomach, duodenum, jejunum/ileum and colon specimens were compared to gene expression levels in 23 other normal human tissues analysed with the same method. Protein profiling based on immunohistochemistry and tissue microarrays was used to sub-localize the corresponding proteins with GIT-specific expression into sub-cellular compartments and cell types. RESULTS Approximately 75% of all human protein-coding genes were expressed in at least one of the GIT tissues. Only 51 genes showed enriched expression in either one of the GIT tissues and an additional 83 genes were enriched in two or more GIT tissues. The list of GIT-enriched genes with validated protein expression patterns included various well-known but also previously uncharacterised or poorly studied genes. For instance, the colon-enriched expression of NXPE family member 1 (NXPE1) was established, while NLR family, pyrin domain-containing 6 (NLRP6) expression was primarily found in the human small intestine. CONCLUSIONS We have applied a genome-wide analysis based on transcriptomics and antibody-based protein profiling to identify genes that are expressed in a specific manner within the human GIT. These genes and proteins constitute important starting points for an improved understanding of the normal function and the different states of disease associated with the GIT.
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Hain D, Langlands A, Sonnenberg HC, Bailey C, Bullock SL, Müller HAJ. The Drosophila MAST kinase Drop out is required to initiate membrane compartmentalisation during cellularisation and regulates dynein-based transport. Development 2014; 141:2119-30. [PMID: 24803657 PMCID: PMC4011086 DOI: 10.1242/dev.104711] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Cellularisation of the Drosophila syncytial blastoderm embryo into the polarised blastoderm epithelium provides an excellent model with which to determine how cortical plasma membrane asymmetry is generated during development. Many components of the molecular machinery driving cellularisation have been identified, but cell signalling events acting at the onset of membrane asymmetry are poorly understood. Here we show that mutations in drop out (dop) disturb the segregation of membrane cortical compartments and the clustering of E-cadherin into basal adherens junctions in early cellularisation. dop is required for normal furrow formation and controls the tight localisation of furrow canal proteins and the formation of F-actin foci at the incipient furrows. We show that dop encodes the single Drosophila homologue of microtubule-associated Ser/Thr (MAST) kinases. dop interacts genetically with components of the dynein/dynactin complex and promotes dynein-dependent transport in the embryo. Loss of dop function reduces phosphorylation of Dynein intermediate chain, suggesting that dop is involved in regulating cytoplasmic dynein activity through direct or indirect mechanisms. These data suggest that Dop impinges upon the initiation of furrow formation through developmental regulation of cytoplasmic dynein.
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Affiliation(s)
- Daniel Hain
- Division of Cell and Developmental Biology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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A nucleotide variant in promoter of the human CDH13 gene which affects its transcription activity is associated with colorectal cancer. Genes Genomics 2014. [DOI: 10.1007/s13258-013-0164-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Characterizing the role of PCDH9 in the regulation of glioma cell apoptosis and invasion. J Mol Neurosci 2013; 52:250-60. [PMID: 24214103 DOI: 10.1007/s12031-013-0133-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Accepted: 09/30/2013] [Indexed: 01/09/2023]
Abstract
PCDH9, a member of the protocadherin superfamily, is frequently lost in many different cancer types. This study aimed to detect PCDH9 expression in glioma tissues. This study also assessed the effects of PCDH9 expression in two different glioma cell lines. This was accomplished by manipulating PCDH9 expression in these glioma cell lines. The data showed that the expression of PCDH9 mRNA and protein was significantly decreased in gliomas compared to normal brain tissues. Lentivirus carrying PCDH9 cDNA restored PCDH9 expression in the U87 and U251 glioma cell lines. PCDH9 restoration in these cell lines reduced tumor cell viability, induced apoptosis, and caused G0/G1 cell cycle arrest. PCDH9 expression also suppressed the colony formation ability and invasion capacity of U87 and U251 cells. Molecularly, the restoration of PCDH9 expression upregulated Bax protein expression, but downregulated Bcl-2 and cyclin D1 expression. These data from the current study suggest that the loss of PCDH9 expression could contribute to glioma development and/or progression. Further studies will evaluate PCDH9 expression as a biomarker for the early detection of gliomas and as a prognostic indicator for this cancer type.
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Ren A, Zhang W, Yarlagadda S, Sinha C, Arora K, Moon CS, Naren AP. MAST205 competes with cystic fibrosis transmembrane conductance regulator (CFTR)-associated ligand for binding to CFTR to regulate CFTR-mediated fluid transport. J Biol Chem 2013; 288:12325-34. [PMID: 23504457 DOI: 10.1074/jbc.m112.432724] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The PDZ (postsynaptic density-95/discs large/zona occludens-1) domain-based interactions play important roles in regulating the expression and function of the cystic fibrosis transmembrane conductance regulator (CFTR). Several PDZ domain-containing proteins (PDZ proteins for short) have been identified as directly or indirectly interacting with the C terminus of CFTR. To better understand the regulation of CFTR processing, we conducted a genetic screen and identified MAST205 (a microtubule-associated serine/threonine kinase with a molecular mass of 205 kDa) as a new CFTR regulator. We found that overexpression of MAST205 increased the expression of CFTR and augmented CFTR-mediated fluid transport in a dose-dependent manner. Conversely, knockdown of MAST205 inhibited CFTR function. The PDZ motif of CFTR is required for the regulatory role of MAST205 in CFTR expression and function. We further demonstrated that MAST205 and the CFTR-associated ligand competed for binding to CFTR, which facilitated the processing of CFTR and consequently up-regulated the expression and function of CFTR at the plasma membrane. More importantly, we found that MAST205 could facilitate the processing of F508del-CFTR mutant and augment its quantity and channel function at the plasma membrane. Taken together, our data suggest that MAST205 plays an important role in regulating CFTR expression and function. Our findings have important clinical implications for treating CFTR-associated diseases such as cystic fibrosis and secretory diarrheas.
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Affiliation(s)
- Aixia Ren
- Department of Physiology, University of Tennessee Health Science Center, Memphis, Tennessee 38163, USA
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Hu X, Sui X, Li L, Huang X, Rong R, Su X, Shi Q, Mo L, Shu X, Kuang Y, Tao Q, He C. Protocadherin 17 acts as a tumour suppressor inducing tumour cell apoptosis and autophagy, and is frequently methylated in gastric and colorectal cancers. J Pathol 2013; 229:62-73. [PMID: 22926751 DOI: 10.1002/path.4093] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Revised: 08/08/2012] [Accepted: 08/15/2012] [Indexed: 01/13/2023]
Abstract
Gastric and colorectal cancers are among the most common cancers worldwide and cause serious cancer mortality. Both epigenetic and genetic disruptions of tumour suppressor genes (TSGs) are frequently involved in their pathogenesis. Here, we studied the epigenetic and genetic alterations of a novel TSG-PCDH17 and its functions in the pathogenesis of these tumours. We found that PCDH17 was frequently silenced and methylated in almost all gastric and colorectal tumour cell lines as well as in ∼95% of primary tumours, but not in normal gastric and colonic mucosa. Moreover, its deletion was detected in only 18% of gastric and 12% of colorectal cancer tissues, suggesting that epigenetic and genetic inactivation of PCDH17 are both involved in gastric and colorectal tumourigenesis. PCDH17 protein expression was significantly correlated with low tumour stage and less lymph node metastasis of gastric and colorectal cancer patients, indicating its potential as a tumour marker. Restoring PCDH17 expression inhibited tumour cell growth in vitro and in vivo through promoting apoptosis, as evidenced by increased TUNEL staining and caspase-3 activation. Furthermore, PCDH17-induced autophagy, along with increased numbers of autophagic vacuoles and up-regulated autophagic proteins Atg-5, Atg-12 and LC3B II. Thus, PCDH17 acts as a tumour suppressor, exerting its anti-proliferative activity through inducing apoptosis and autophagy, and is frequently silenced in gastric and colorectal cancers. PCDH17 methylation is a tumour-specific event that could serve as an epigenetic biomarker for these tumours.
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Affiliation(s)
- Xiaotong Hu
- Biomedical Research Centre and Key Laboratory of Biotherapy of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China
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McIver LJ, McCormick JF, Martin A, Fondon JW, Garner HR. Population-scale analysis of human microsatellites reveals novel sources of exonic variation. Gene 2012; 516:328-34. [PMID: 23274653 DOI: 10.1016/j.gene.2012.12.068] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 12/15/2012] [Indexed: 11/29/2022]
Abstract
Using our microsatellite specific genotyping method, we analyzed tandem repeats, which are known to be highly variable with some recognized as biomarkers causative of disease, in over 500 individuals who were exon sequenced in a 1000 Genomes Project pilot study. We were able to genotype over 97% of the microsatellite loci in the targeted regions. A total of 25,115 variations were observed, including repeat length and single nucleotide polymorphisms, corresponding to an average of 45.6 variations per individual and a density of 1.1 variations per kilobase. Standard variant detection did not report 94.2% of the exonic repeat length variations in part because the alignment techniques are not ideal for repetitive regions. Additionally some standard variation detection tools rely on a database of known variations, making them less likely to call repeat length variations as only a small percent of these loci (~6000) have been accurately characterized. A subset of the hundreds of non-synonymous variations we identified was experimentally validated, indicating an accuracy of 96.5% for our microsatellite-based genotyping method, with some novel variants identified in genes associated with cancer. We propose that microsatellite-based genotyping be used as a part of large scale sequencing studies to identify novel variants.
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Affiliation(s)
- L J McIver
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
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46
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Erickson AR, Cantarel BL, Lamendella R, Darzi Y, Mongodin EF, Pan C, Shah M, Halfvarson J, Tysk C, Henrissat B, Raes J, Verberkmoes NC, Fraser CM, Hettich RL, Jansson JK. Integrated metagenomics/metaproteomics reveals human host-microbiota signatures of Crohn's disease. PLoS One 2012; 7:e49138. [PMID: 23209564 PMCID: PMC3509130 DOI: 10.1371/journal.pone.0049138] [Citation(s) in RCA: 304] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2012] [Accepted: 10/03/2012] [Indexed: 12/11/2022] Open
Abstract
Crohn's disease (CD) is an inflammatory bowel disease of complex etiology, although dysbiosis of the gut microbiota has been implicated in chronic immune-mediated inflammation associated with CD. Here we combined shotgun metagenomic and metaproteomic approaches to identify potential functional signatures of CD in stool samples from six twin pairs that were either healthy, or that had CD in the ileum (ICD) or colon (CCD). Integration of these omics approaches revealed several genes, proteins, and pathways that primarily differentiated ICD from healthy subjects, including depletion of many proteins in ICD. In addition, the ICD phenotype was associated with alterations in bacterial carbohydrate metabolism, bacterial-host interactions, as well as human host-secreted enzymes. This eco-systems biology approach underscores the link between the gut microbiota and functional alterations in the pathophysiology of Crohn's disease and aids in identification of novel diagnostic targets and disease specific biomarkers.
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Affiliation(s)
- Alison R. Erickson
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Brandi L. Cantarel
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Regina Lamendella
- Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Youssef Darzi
- Bioinformatics and Eco-Systems Biology lab, Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Research Group of Microbiology (MICR), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Emmanuel F. Mongodin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Chongle Pan
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Manesh Shah
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jonas Halfvarson
- Department of Internal Medicine, Division of Gastroenterology, Örebro University Hospital and School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Curt Tysk
- Department of Internal Medicine, Division of Gastroenterology, Örebro University Hospital and School of Health and Medical Sciences, Örebro University, Örebro, Sweden
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, Centre national de la recherche scientifique, Universités Aix-Marseille I & II, Marseille, France
| | - Jeroen Raes
- Bioinformatics and Eco-Systems Biology lab, Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium
- Research Group of Microbiology (MICR), Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Nathan C. Verberkmoes
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Claire M. Fraser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Robert L. Hettich
- Chemical Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Janet K. Jansson
- Department of Ecology, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
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Ose R, Oharaa O, Nagase T. Galectin-1 and Galectin-3 Mediate Protocadherin-24-Dependent Membrane Localization of β-catenin in Colon Cancer Cell Line HCT116. CURRENT CHEMICAL GENOMICS 2012; 6:18-26. [PMID: 23115611 PMCID: PMC3480823 DOI: 10.2174/1875397301206010018] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 12/21/2022]
Abstract
Protocadherin-24 (PCDH24) is linked to the suppression of tumor growth and the inhibition of cell proliferation in the colon cancer cell line HCT116. We previously observed that β-catenin is localized to the plasma membrane when PCDH24 is expressed in these cells, but the molecular mechanisms by which PCDH24 induces the membrane localization of β-catenin remain largely unknown. To clarify these mechanisms, we identified molecules that interact with ectopically expressed PCDH24 in HCT116 cells using a HaloTag® pull-down assay. We found that galectin-1 and galectin-3 physically interact with PCDH24 and are retained at the plasma membrane in association with PCDH24 expression. A luciferase-based pull-down assay using HaloTag-fused galectins revealed that an intracellular region of PCDH24 (amino acids 1186–1280) is essential for this interaction. Furthermore, the over-expression of galectin-1 or -3, or the depletion of endogenous galectins by small interfering RNA modulates β-catenin translocation. We also revealed that the retention of galectin-1 and -3 at the plasma membrane results in the inactivation of PI3K activity. From these findings, we propose a model in which the galectin-anchoring activity of PCDH24 leads to the suppression of β-catenin signaling by the localization of β-catenin at the plasma membrane in PCDH24-expressing HCT116 colon cancer cells.
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Affiliation(s)
- Rui Ose
- Department of Human Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan ; Graduate School of Pharmaceutical Sciences & Faculty of Pharmaceutical Sciences, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
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48
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Apostolopoulou M, Ligon L. Cadherin-23 mediates heterotypic cell-cell adhesion between breast cancer epithelial cells and fibroblasts. PLoS One 2012; 7:e33289. [PMID: 22413011 PMCID: PMC3296689 DOI: 10.1371/journal.pone.0033289] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 02/13/2012] [Indexed: 12/31/2022] Open
Abstract
In the early stages of breast cancer metastasis, epithelial cells penetrate the basement membrane and invade the surrounding stroma, where they encounter fibroblasts. Paracrine signaling between fibroblasts and epithelial tumor cells contributes to the metastatic cascade, but little is known about the role of adhesive contacts between these two cell types in metastasis. Here we show that MCF-7 breast cancer epithelial cells and normal breast fibroblasts form heterotypic adhesions when grown together in co-culture, as evidenced by adhesion assays. PCR and immunoblotting show that both cell types express multiple members of the cadherin superfamily, including the atypical cadherin, cadherin-23, when grown in isolation and in co-culture. Immunocytochemistry experiments show that cadherin-23 localizes to homotypic adhesions between MCF-7 cells and also to heterotypic adhesions between the epithelial cells and fibroblasts, and antibody inhibition and RNAi experiments show that cadherin-23 plays a role in mediating these adhesive interactions. Finally, we show that cadherin-23 is upregulated in breast cancer tissue samples, and we hypothesize that heterotypic adhesions mediated by this atypical cadherin may play a role in the early stages of metastasis.
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Affiliation(s)
- Maria Apostolopoulou
- Department of Biology and Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, United States of America
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Kolquist KA, Schultz RA, Slovak ML, McDaniel LD, Brown TC, Tubbs RR, Cook JR, Theil KS, Cawich V, Valentin C, Minier S, Neill NJ, Byerly S, Morton SA, Sahoo T, Ballif BC, Shaffer LG. Evaluation of chronic lymphocytic leukemia by oligonucleotide-based microarray analysis uncovers novel aberrations not detected by FISH or cytogenetic analysis. Mol Cytogenet 2011; 4:25. [PMID: 22087757 PMCID: PMC3253687 DOI: 10.1186/1755-8166-4-25] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Accepted: 11/16/2011] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Cytogenetic evaluation is a key component of the diagnosis and prognosis of chronic lymphocytic leukemia (CLL). We performed oligonucleotide-based comparative genomic hybridization microarray analysis on 34 samples with CLL and known abnormal karyotypes previously determined by cytogenetics and/or fluorescence in situ hybridization (FISH). RESULTS Using a custom designed microarray that targets >1800 genes involved in hematologic disease and other malignancies, we identified additional cryptic aberrations and novel findings in 59% of cases. These included gains and losses of genes associated with cell cycle regulation, apoptosis and susceptibility loci on 3p21.31, 5q35.2q35.3, 10q23.31q23.33, 11q22.3, and 22q11.23. CONCLUSIONS Our results show that microarray analysis will detect known aberrations, including microscopic and cryptic alterations. In addition, novel genomic changes will be uncovered that may become important prognostic predictors or treatment targets for CLL in the future.
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Affiliation(s)
- Kathryn A Kolquist
- Sacred Heart Medical Center, 101 West 8th Avenue, Spokane, WA, 99204, USA
| | - Roger A Schultz
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Marilyn L Slovak
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
- Quest Diagnostics Nichols Institute, 14225 Newbrook Drive, Chantilly, VA, 20151, USA
| | - Lisa D McDaniel
- Sacred Heart Medical Center, 101 West 8th Avenue, Spokane, WA, 99204, USA
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Theresa C Brown
- CSI Laboratories, 11525 Park Woods Circle, Alpharetta, GA, 30005, USA
| | - Raymond R Tubbs
- Cleveland Clinic, Pathology & Laboratory Medicine Institute, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - James R Cook
- Cleveland Clinic, Pathology & Laboratory Medicine Institute, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Karl S Theil
- Cleveland Clinic, Pathology & Laboratory Medicine Institute, 9500 Euclid Avenue, Cleveland, OH, 44195, USA
| | - Victoria Cawich
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Caitlin Valentin
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Sara Minier
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Nicholas J Neill
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Steve Byerly
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - S Annie Morton
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Trilochan Sahoo
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
- Quest Diagnostics Nichols Institute, 33608 Ortega Highway, San Juan Capistrano, CA, 92675, USA
| | - Blake C Ballif
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
| | - Lisa G Shaffer
- Signature Genomic Laboratories, PerkinElmer Inc., 2820 North Astor Street, Spokane, WA, 99207, USA
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50
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Sui X, Wang D, Geng S, Zhou G, He C, Hu X. Methylated promoters of genes encoding protocadherins as a new cancer biomarker family. Mol Biol Rep 2011; 39:1105-11. [PMID: 21598112 DOI: 10.1007/s11033-011-0837-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2010] [Accepted: 05/05/2011] [Indexed: 12/15/2022]
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