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Xu Q, Wang J, Wang J, Zhang O, Gao Y, Cui X, Zhao C, Liu F, Chen X. Integrative Analysis of the Role of MRPL21 in Human Pan-Cancer and Its Relationship with the Progression of Lung Adenocarcinoma. Mol Biotechnol 2025:10.1007/s12033-024-01348-7. [PMID: 39775548 DOI: 10.1007/s12033-024-01348-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2024] [Accepted: 12/04/2024] [Indexed: 01/11/2025]
Abstract
Mitochondrial ribosomal protein L21 (MRPL21) is essential for normal cell function and may play a significant role in cancer development. In this study, we performed a comprehensive pan-cancer analysis to explore MRPL21's function across different cancers, utilizing multiple online data platforms such as TCGA. Our analysis covered its clinical significance and biological functions, including expression levels, survival and diagnostic analysis, gene mutations, multidimensional immune-correlation analysis, tumor heterogeneity, and cancer-associated signaling pathways. Additionally, we constructed a prognostic nomogram for lung adenocarcinoma (LUAD) patients based on MRPL21 and validated its biological function through in vitro experiments. Our findings revealed that MRPL21 is commonly overexpressed in various cancers and is associated with poor prognosis. It significantly impacts cancer-related pathways, particularly those related to cell cycle activation. Moreover, MRPL21 is critical in the tumor microenvironment and is closely linked to immune infiltration across several cancer types. Its expression correlates with essential factors such as tumor mutational burden, microsatellite instability, immune checkpoint, and methylation patterns. In LUAD, MRPL21 was identified as an independent risk factor and demonstrated that MRPL21 promotes LUAD progression. Overall, MRPL21 holds potential as both a diagnostic and prognostic marker in cancer and could serve as a promising therapeutic target, particularly for LUAD.
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Affiliation(s)
- Qi Xu
- Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Nanyang Medical College, Nanyang, China
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jiale Wang
- Department of Internal Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
- Department of Medical Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jing Wang
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Ou Zhang
- The First Affiliated Hospital of Nanyang Medical College, Nanyang, China
| | - Yuwan Gao
- The First Affiliated Hospital of Nanyang Medical College, Nanyang, China
| | - Xiaoqiao Cui
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Chengyi Zhao
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Feng Liu
- Department of Breast Surgery, Harbin Medical University Cancer Hospital, Harbin, China.
| | - Xiaohui Chen
- Department of Breast and Thyroid Surgery, The Second Affiliated Hospital of Guilin Medical University, Guilin, China.
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2
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Nishimura Y, Bittel AJ, Stead CA, Chen YW, Burniston JG. Facioscapulohumeral Muscular Dystrophy is Associated With Altered Myoblast Proteome Dynamics. Mol Cell Proteomics 2023; 22:100605. [PMID: 37353005 PMCID: PMC10392138 DOI: 10.1016/j.mcpro.2023.100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 05/31/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023] Open
Abstract
Proteomic studies in facioscapulohumeral muscular dystrophy (FSHD) could offer new insight into disease mechanisms underpinned by post-transcriptional processes. We used stable isotope (deuterium oxide; D2O) labeling and peptide mass spectrometry to investigate the abundance and turnover rates of proteins in cultured muscle cells from two individuals affected by FSHD and their unaffected siblings (UASb). We measured the abundance of 4420 proteins and the turnover rate of 2324 proteins in each (n = 4) myoblast sample. FSHD myoblasts exhibited a greater abundance but slower turnover rate of subunits of mitochondrial respiratory complexes and mitochondrial ribosomal proteins, which may indicate an accumulation of "older" less viable mitochondrial proteins in myoblasts from individuals affected by FSHD. Treatment with a 2'-O-methoxyethyl modified antisense oligonucleotide targeting exon 3 of the double homeobox 4 (DUX4) transcript tended to reverse mitochondrial protein dysregulation in FSHD myoblasts, indicating the effect on mitochondrial proteins may be a DUX4-dependent mechanism. Our results highlight the importance of post-transcriptional processes and protein turnover in FSHD pathology and provide a resource for the FSHD research community to explore this burgeoning aspect of FSHD.
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Affiliation(s)
- Yusuke Nishimura
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Adam J Bittel
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA
| | - Connor A Stead
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | - Yi-Wen Chen
- Center for Genetic Medicine Research, Children's National Medical Center, Washington, District of Columbia, USA.
| | - Jatin G Burniston
- Research Institute for Sport & Exercise Sciences, Liverpool John Moores University, Liverpool, United Kingdom.
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3
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Yuan L, Li JX, Yang Y, Chen Y, Ma TT, Liang S, Bu Y, Yu L, Nan Y. Depletion of MRPL35 inhibits gastric carcinoma cell proliferation by regulating downstream signaling proteins. World J Gastroenterol 2021; 27:1785-1804. [PMID: 33967557 PMCID: PMC8072187 DOI: 10.3748/wjg.v27.i16.1785] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/04/2021] [Accepted: 03/11/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Gastric carcinoma (GC) is a digestive system disease with high morbidity and mortality. However, early clinical detection is difficult, and the therapeutic effect for advanced disease is not satisfactory. Thus, finding new tumor markers and therapeutic targets conducive to the treatment of GC is imperative. MRPL35 is a member of the large subunit family of mitochondrial ribosomal protein. MRPL35 shows the characteristic of oncogene in colorectal cancer and esophageal cancer, which promotes the exploration of the correlation between MRPL35 and GC. We proposed that the expression of MRPL35 might be critical in GC.
AIM To study the effect of MRPL35 knockdown on GC cell proliferation.
METHODS The expression of MRPL35 in GC was evaluated based on data from the public tumor database UALCAN (http://www.ualcan.path.uab.edu). The effect of the expression of MRPL35 on the prognosis was evaluated with KMplot (http://www.kmplot.com). The expression of MRPL35 was assessed on the tissue microarray by immunohistochemistry and the level of MRPL35 mRNA in 25 pairs of clinical GC tissues and matched adjacent tissues was detected by quantitative reverse transcription-polymerase chain reaction. Celigo cell count assay, colony formation assay, and flow cytometry were used to assess the role of MRPL35 in GC cell proliferation and apoptosis in vitro. Additionally, tumor formation experiment in BALB/c nude mice was utilized to determine the effect of MRPL35 on GC cell proliferation. After knockdown of MRPL35, related proteins were identified by isobaric tags for relative and absolute quantification analysis, and the expression of related proteins was detected by Western blot.
RESULTS The expression of MRPL35 was up-regulated in GC (P = 1.77 × 10-4). The Kaplan-Meier plots of the overall survival indicated that high expression of MRPL35 was associated with a poor survival in GC. Compared with adjacent tissues, the expression of MRPL35 in GC tissues was increased, which was related to age (P = 0.03), lymph node metastasis (P = 0.007), and pathological tumor-node-metastasis stage (P = 0.024). Knockdown of MRPL35 inhibited GC cell proliferation and colony formation and induced apoptosis. Animal experiment results showed that knockdown of MRPL35 inhibited tumor formation in BALB/c nude mice. Western blotting analysis showed that after knockdown of MRPL35, the expression of PICK1 and BCL-XL proteins decreased, and that of AGR2 protein increased.
CONCLUSION Collectively, our findings demonstrate that knockdown of MRPL35 inhibits GC cell proliferation through related proteins including PICK1, BCL-XL, and AGR2.
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Affiliation(s)
- Ling Yuan
- Pharmacy College of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
- Key Laboratory of Hui Ethnic Medicine Modernization of Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Jia-Xin Li
- Pharmacy College of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yi Yang
- Pharmacy College of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yan Chen
- Traditional Chinese Medicine College, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Ting-Ting Ma
- Pharmacy College of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Shuang Liang
- Department of Oncology and Endocrinology, Yinchuan Hospital of Traditional Chinese Medicine Affiliated to Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Yang Bu
- Department of Hepatobiliary Surgery, General Hospital of Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
| | - Lei Yu
- Department of Infectious Diseases, The Fourth Hospital of Harbin Medical University, Harbin 150001, Heilongjiang Province, China
| | - Yi Nan
- Key Laboratory of Hui Ethnic Medicine Modernization of Ministry of Education, Ningxia Medical University, Yinchuan 750004, Ningxia Hui Autonomous Region, China
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4
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Gonçalves AM, Pereira-Santos AR, Esteves AR, Cardoso SM, Empadinhas N. The Mitochondrial Ribosome: A World of Opportunities for Mitochondrial Dysfunction Toward Parkinson's Disease. Antioxid Redox Signal 2021; 34:694-711. [PMID: 32098485 DOI: 10.1089/ars.2019.7997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Significance: Mitochondrial ribosomes (mitoribosomes) are organelles that translate mitochondrial messenger RNA in the matrix and, in mammals, have evolved to translate 13 polypeptides of the pathway that performs oxidative phosphorylation (OXPHOS). Although a number of devastating diseases result from defects in this mitochondrial translation apparatus, most are associated with genetic mutations and little is known about allelopathic defects caused by antibiotics, toxins, or nonproteinogenic amino acids. Recent Advances: The levels of mitochondrial ribosomal subunits 12S and 16S ribosomal RNA (rRNA) in cells/tissues from patients carrying mutations in these genes have been associated with alterations in mitochondrial translation efficiency and with impaired OXPHOS activities, as well as with the severity of clinical phenotypes. In recent decades, important studies revealed a prominent role of mitochondrial dysfunction in Parkinson's disease (PD); however, the involvement of mitoribosomes remains largely unknown. Critical Issues: Considering that mitoribosomal structure and function can determine the efficiency of OXPHOS and that an impaired mitochondrial respiratory chain is a common finding in PD, we argue that the mitoribosome may be key to disease onset and progression. With this review, we comprehensively integrate the available knowledge on the composition, assembly, and role of the mitoribosome in mitochondrial efficiency, reflecting on its possible involvement in the etiopathogenesis of this epidemic disease as an appealing research avenue. Future Directions: If a direct correlation between mitoribosome failure and PD pathology is demonstrated, these mitochondrial organelles will provide valuable early clinical markers and potentially attractive targets for the development of innovative PD-directed therapeutic agents.
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Affiliation(s)
- Ana Mafalda Gonçalves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Pereira-Santos
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Ana Raquel Esteves
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal
| | - Sandra M Cardoso
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Nuno Empadinhas
- CNC-Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal.,CIBB-Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra, Portugal.,IIIUC-Institute for Interdisciplinary Research, University of Coimbra, Coimbra, Portugal
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5
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Tao Z, Suo H, Zhang L, Jin Z, Wang Z, Wang D, Wu M, Peng N, Zhao Y, Chen B. MRPL13 is a Prognostic Cancer Biomarker and Correlates with Immune Infiltrates in Breast Cancer. Onco Targets Ther 2020; 13:12255-12268. [PMID: 33273831 PMCID: PMC7708783 DOI: 10.2147/ott.s263998] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/13/2020] [Indexed: 01/19/2023] Open
Abstract
Objective To study the expression of MRPL13 in breast cancer tissues using TCGA database, analyze the correlation between the expression and clinicopathological characteristics of patients, and explore the role of MRPL13 in the development of breast cancer (BC). Methods The BC mRNA data and clinical information were downloaded from TCGA database. The correlation between MRPL13 expression and clinicopathological parameters was analyzed. Cox regression multivariate analysis was used to explore the factors affecting the prognosis of BC patients. The UALCAN database was used to analyze the expression level of MRPL13 in BC and its relationship with clinical pathological factors. The GSEA method was used to predict the possible regulatory pathways of MRPL13. Immune responses of MRPL13 expression were analyzed using TISIDB and CIBERSORT. Additionally, GEPIA, K-M survival analysis and data from the HPA were used to validate the outcomes. Results The expression of MRPL13 in BC tissues was significantly higher than normal counterparts, patients with low MRPL13 expression had a better survival prognosis, also indicated an independent prognostic factor. GSEA analysis showed that the regulation of cell migration, positive regulation of endothelial cell migration, and Notch signaling pathway were enriched in tissues with low expression of MRPL13. Additionally, depleting MRPL13 expression inhibited invasion in MCF-10A and MCF-7 cells. Furthermore, PCR showed that MRPL13 affected VEGFA and MMP gene expression. CIBERSORT analysis revealed that the amount of NK cells decreased when MRPL13 expression was high. Conclusion The expression of MRPL13 mRNA is upregulated in BC tissues, and the expression level of MRPL13 is significantly related to the clinicopathological factors of patients. High MRPL13 expression is a poor prognostic factor for BC, and it can be used as a molecular marker for prognosis judgment and as a potential therapeutic target.
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Affiliation(s)
- Zuo Tao
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Huandan Suo
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Lei Zhang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Zining Jin
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Zhen Wang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Danyu Wang
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Ming Wu
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Nanxi Peng
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Yujie Zhao
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
| | - Bo Chen
- Department of Breast Surgery, The First Hospital of China Medical University, Shenyang, Liaoning Province 110001, People's Republic of China
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6
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Abnormal Expression of Mitochondrial Ribosomal Proteins and Their Encoding Genes with Cell Apoptosis and Diseases. Int J Mol Sci 2020; 21:ijms21228879. [PMID: 33238645 PMCID: PMC7700125 DOI: 10.3390/ijms21228879] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/15/2020] [Accepted: 11/17/2020] [Indexed: 12/11/2022] Open
Abstract
Mammalian mitochondrial ribosomes translate 13 proteins encoded by mitochondrial genes, all of which play roles in the mitochondrial respiratory chain. After a long period of reconstruction, mitochondrial ribosomes are the most protein-rich ribosomes. Mitochondrial ribosomal proteins (MRPs) are encoded by nuclear genes, synthesized in the cytoplasm and then, transported to the mitochondria to be assembled into mitochondrial ribosomes. MRPs not only play a role in mitochondrial oxidative phosphorylation (OXPHOS). Moreover, they participate in the regulation of cell state as apoptosis inducing factors. Abnormal expressions of MRPs will lead to mitochondrial metabolism disorder, cell dysfunction, etc. Many researches have demonstrated the abnormal expression of MRPs in various tumors. This paper reviews the basic structure of mitochondrial ribosome, focuses on the structure and function of MRPs, and their relationships with cell apoptosis and diseases. It provides a reference for the study of the function of MRPs and the disease diagnosis and treatment.
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7
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Fang X, Yin H, Zhang H, Wu F, Liu Y, Fu Y, Yu D, Zong L. p53 mediates hydroxyurea resistance in aneuploid cells of colon cancer. Exp Cell Res 2019; 376:39-48. [PMID: 30684461 DOI: 10.1016/j.yexcr.2019.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/11/2019] [Accepted: 01/22/2019] [Indexed: 01/08/2023]
Abstract
Aneuploidy refers to aberrancies in cellular chromosome count, which is prevalent in most human cancers. Chemotherapy is an effective cancer treatment; however, the development of drug resistance is a major concern of conventional chemotherapy. The chemotherapy agent hydroxyurea (HU) targets proliferating cells and has long been applied to treat various human cancers. It remains elusive whether aneuploidy affects the drug sensitivity of hydroxyurea. By generating an inducible aneuploidy model, we found that aneuploid colon cancer cells were resistant to HU treatment compared to euploid controls. Surprisingly, further analyses showed that the HU resistance was dependent on the expression of wild type p53. Activation of the p53 pathway in aneuploidy cells reduced cell proliferation but generated resistance of tumor cells to HU treatment. HU resistance was abrogated in aneuploid cells if p53 was absent but re-gained when inducing proliferation repression in cells by serum deprivation. Our results demonstrate that the HU resistance developed in aneuploid colon cancer cells is mediated by wild type p53 and indicates the prognostic value of combining karyotypic and p53 status in clinical cancer treatment.
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Affiliation(s)
- Xiao Fang
- Peking University Health Science Center, Beijing 100191, China; Clinical Medical College, Yangzhou University, Yangzhou 225001, Jiangsu, China; Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou 225001, China; Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Hua Yin
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou 225001, China; Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Hanqing Zhang
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou 225001, China; Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Fan Wu
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou 225001, China; Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Yin Liu
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou 225001, China; Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China
| | - Yi Fu
- School of Biology and Basic Medical Science, Soochow University, Suzhou 215123, China
| | - Duonan Yu
- Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yangzhou University, Yangzhou 225001, China; Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou 225001, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Disease and Zoonosis, Yangzhou, China.
| | - Liang Zong
- Clinical Medical College, Yangzhou University, Yangzhou 225001, Jiangsu, China.
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8
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Abstract
Mammalian mitochondrial ribosomal proteins are functionally involved in protein synthesis in mitochondrion. Recently numerous studies have illuminated the role of mitochondrion in cancer development. However, the precise function of mitochondrial ribosomal protein L42 (MRPL42) remains unclear. Here in the present study, we identified MRPL42 as a novel oncogene in glioma. By analyzing the Cancer Genome Atlas (TCGA) database, we first found that MRPL42 was significantly up-regulated in glioma tissues compared with normal tissues. Functionally, we silenced MRPL42 in glioma cells and revealed that MRPL42 knockdown largely blunted the proliferation of U251 and A172 cells. Mechanistically, our results suggested that MRPL42 silencing resulted in increased distribution of cell cycle in G1 and G2/M phases, while the S-phase decreased. In addition, the apoptosis and caspase3/7 activity were both activated after MRPL42 knockdown. Taken together, MRPL42 is a novel oncogene in glioma and might help us develop promising targetted therapies for glioma patients.
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9
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Zeng L, Zhong J, He G, Li F, Li J, Zhou W, Liu W, Zhang Y, Huang S, Liu Z, Deng X. Identification of Nucleobindin-2 as a Potential Biomarker for Breast Cancer Metastasis Using iTRAQ-based Quantitative Proteomic Analysis. J Cancer 2017; 8:3062-3069. [PMID: 28928897 PMCID: PMC5604457 DOI: 10.7150/jca.19619] [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: 02/12/2017] [Accepted: 03/17/2017] [Indexed: 12/19/2022] Open
Abstract
Metastasis is a lethal step in the progression of breast cancer. None of the metastasis-associated biomarkers identified up to now has a definite prognostic value in breast cancer patients. This study was designed to identify biomarkers for breast cancer metastasis and predictors of the prognosis of breast cancer patients. The differentially expressed proteins between 23 paired primary breast tumor and metastatic lymph nodes were identified by quantitative iTRAQ proteomic analysis. Immunohistochemistry was applied to locate and assess the expression of NUCB2 in paired primary breast tumor and metastatic lymph node tissues (n = 106). The relationship between NUCB2 expression and the clinicopathological characteristics of breast cancer patients (n = 189) were analyzed by χ2 test. Kaplan-Meier analysis and Cox hazard regression analysis were utilized to investigate the relationship between its expression and prognosis of breast cancer patients. The iTRAQ proteomic results showed that 4,837 confidential proteins were identified, 643 of which were differentially expressed in the primary breast cancer tissues and the paired metastatic lymph nodes. NUCB2 protein was found decreased in paired metastatic lymph nodes (P = 0.000), with the positive expression rate being 82% in primary breast cancer tissues and 47% in paired metastatic lymph nodes, respectively. According to Kaplan-Meier analysis, the overall survival time of patients with positive expression of NUCB2 protein were shorter than those with negative NUCB2 expression (P = 0.004). Cox regression model suggested that NUCB2 was a risk factor of breast cancer patients (P = 0.045, RR = 1.854). We conclude that NUCB2 can be used as a potential biomarker for breast cancer metastasis and a prognostic predictor of breast cancer patients.
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Affiliation(s)
- Liang Zeng
- Department of Pathology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong 510623, China.,Department of Pathology, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Jingmin Zhong
- Department of Pathology, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Guangchun He
- Department of Pathology, Hunan Normal University Medical College, Changsha, Hunan 410013, China
| | - Fangjun Li
- Department of Social Medicine, Hunan Provincial People's Hospital & The Affiliated Hospital of Hunan Normal University, Changsha, Hunan 410007, China
| | - Jing Li
- Department of Breast Internal Medicine, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Wen Zhou
- Key Laboratory of Cancer of the Ministry of Health, Cancer Research Institute, Xiangya School of Medicine, Central South University, Changsha, Hunan 4100078, China
| | - Wenbin Liu
- Department of Pathology, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Yun Zhang
- Department of Pathology, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Sanqian Huang
- Department of Pathology, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Zhihong Liu
- Department of Pathology, Hunan Cancer Hospital & The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, China
| | - Xiyun Deng
- Department of Pathology, Hunan Normal University Medical College, Changsha, Hunan 410013, China
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10
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Gao Y, Li F, Zhou H, Yang Y, Wu R, Chen Y, Li W, Li Y, Xu X, Ke C, Pei Z. Down-regulation of MRPS23 inhibits rat breast cancer proliferation and metastasis. Oncotarget 2017; 8:71772-71781. [PMID: 29069745 PMCID: PMC5641088 DOI: 10.18632/oncotarget.17888] [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: 10/31/2016] [Accepted: 04/28/2017] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial ribosomal protein S23 (MRPS23) has been shown to be involved in breast cancer cell proliferation and metastatic phenotypes of cervical cancer. Here we investigated its biological features in breast cancer for the first time. It demonstrated that knockdown of MRPS23 reduced breast cancer cell proliferation and induced apoptosis in vitro. Besides, shRNA targeting MRPS23 (shMRPS23) inhibited tumour proliferation and metastasis by blocking tumor angiogenesis in breast cancer xenograft rat model. Small animal positron emission tomography/computed tomography (PET/CT) with 2′-deoxy-2′-[18F] fluoro-D-glucose (FDG) was performed at four weeks after tumour cell injection. We found that FDG maximum standardized uptake value (SUVmax) significantly decreased by 31 ± 3% in the shMRPS23-treated group. But this change was not independent of metabolic tumour size. In addition, we also found that shMRPS23 could significantly suppress breast cancer metastasis through inhibiting epithelial mesenchymal transition (EMT) phenotype. The epithelial marker E-cadherin was increased, whereas the metastasis associated gene vimentin was decreased. Mechanistically, shMRPS23-treated tumours failed to progress through p53 and p21WAF1/CIP1 activation, but not cytochrome c-mediated pathway. These findings suggest that MRPS23 is a potential therapeutic target for interference of breast cancer proliferation, angiogenesis and metastasis.
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Affiliation(s)
- Yan Gao
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Fuyan Li
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Hong Zhou
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Yi Yang
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Ruimin Wu
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Yijia Chen
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Wei Li
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Yang Li
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Xueqin Xu
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Changbin Ke
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
| | - Zhijun Pei
- Department of PET Center and Institute of Anesthesiology and Pain, Taihe Hospital, Hubei University of medicine, Hubei, China
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Abstract
Mitochondria play fundamental roles in the regulation of life and death of eukaryotic cells. They mediate aerobic energy conversion through the oxidative phosphorylation (OXPHOS) system, and harbor and control the intrinsic pathway of apoptosis. As a descendant of a bacterial endosymbiont, mitochondria retain a vestige of their original genome (mtDNA), and its corresponding full gene expression machinery. Proteins encoded in the mtDNA, all components of the multimeric OXPHOS enzymes, are synthesized in specialized mitochondrial ribosomes (mitoribosomes). Mitoribosomes are therefore essential in the regulation of cellular respiration. Additionally, an increasing body of literature has been reporting an alternative role for several mitochondrial ribosomal proteins as apoptosis-inducing factors. No surprisingly, the expression of genes encoding for mitoribosomal proteins, mitoribosome assembly factors and mitochondrial translation factors is modified in numerous cancers, a trait that has been linked to tumorigenesis and metastasis. In this article, we will review the current knowledge regarding the dual function of mitoribosome components in protein synthesis and apoptosis and their association with cancer susceptibility and development. We will also highlight recent developments in targeting mitochondrial ribosomes for the treatment of cancer.
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12
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Gong C, Sun S, Liu B, Wang J, Chen X. Identification of potential therapeutic target genes, key miRNAs and mechanisms in oral lichen planus by bioinformatics analysis. Arch Oral Biol 2017; 78:122-128. [PMID: 28237528 DOI: 10.1016/j.archoralbio.2017.02.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/16/2022]
Abstract
The study aimed to identify the potential target genes and key miRNAs as well as to explore the underlying mechanisms in the pathogenesis of oral lichen planus (OLP) by bioinformatics analysis. The microarray data of GSE38617 were downloaded from Gene Expression Omnibus (GEO) database. A total of 7 OLP and 7 normal samples were used to identify the differentially expressed genes (DEGs) and miRNAs. The DEGs were then performed functional enrichment analyses. Furthermore, DEG-miRNA network and miRNA-function network were constructed by Cytoscape software. Total 1758 DEGs (598 up- and 1160 down-regulated genes) and 40 miRNAs (17 up- and 23 down-regulated miRNAs) were selected. The up-regulated genes were related to nuclear factor-Kappa B (NF-κB) signaling pathway, while down-regulated genes were mainly enriched in the function of ribosome. Tumor necrosis factor (TNF), caspase recruitment domain family, member 11 (CARD11) and mitochondrial ribosomal protein (MRP) genes were identified in these functions. In addition, miR-302 was a hub node in DEG-miRNA network and regulated cyclin D1 (CCND1). MiR-548a-2 was the key miRNA in miRNA-function network by regulating multiple functions including ribosomal function. The NF-κB signaling pathway and ribosome function may be the pathogenic mechanisms of OLP. The genes such as TNF, CARD11, MRP genes and CCND1 may be potential therapeutic target genes in OLP. MiR-548a-2 and miR-302 may play important roles in OLP development.
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Affiliation(s)
- Cuihua Gong
- Department of General Emergency, Dalian Hospital of Stomatology, Dalian, Liaoning, 116021, China
| | - Shangtong Sun
- Department of Periodontal Mucosa, Dalian Hospital of Stomatology, Dalian, Liaoning, 116021, China
| | - Bing Liu
- Department of Orthopedic Trauma, the First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, China
| | - Jing Wang
- Department of Cosmetic Surgery, The First Affiliated Hospital of Dalian Medical University, Dalian, Liaoning, 116011, China.
| | - Xiaodong Chen
- Department of Reconstruction Surgery, Dalian Hospital of Stomatology, No. 935 Changjiang Rd, Shahekou District, Dalian, Liaoning, 116021, China.
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13
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Zhang W, Tong D, Liu F, Li D, Li J, Cheng X, Wang Z. RPS7 inhibits colorectal cancer growth via decreasing HIF-1α-mediated glycolysis. Oncotarget 2016; 7:5800-14. [PMID: 26735579 PMCID: PMC4868722 DOI: 10.18632/oncotarget.6807] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 12/09/2015] [Indexed: 12/30/2022] Open
Abstract
Ribosomal protein S7 (RPS7) acts as a tumor suppressor in primary tumorigenesis but its role in cancer metabolism remains unclear. In this study, we demonstrate that RPS7 inhibits the colorectal cancer (CRC) cell glycolysis by suppressing the expression of hypoxia-inducible transcription factor-1α (HIF-1α) and the metabolic promoting proteins glucose transporter 4 (GLUT4) and lactate dehydrogenase B (LDHB). Further study found that the enhanced expression of HIF-1α abrogates the overexpression effects of RPS7 on CRC. In vivo assays also demonstrate that RPS7 suppresses colorectal cancer tumorigenesis and glycolysis. Clinically, the tissue microarray (TMA) analysis discloses the negative regulatory association between RPS7 and HIF-1α in colorectal cancer. Meanwhile, overexpression of RPS7 in colorectal cancer tissues predicts good overall survival and progression-free survival, but high expression level of HIF-1α indicates poor overall survival and progression-free survival. Overall, we reveal that RPS7 inhibits colorectal cancer glycolysis through HIF-1α-associated signaling and may be a promising biomarker for prognosis prediction and a potential target for therapeutic treatment.
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Affiliation(s)
- Wen Zhang
- Cancer Institute and Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Duo Tong
- Cancer Institute and Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fei Liu
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Dawei Li
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
| | - Jiajia Li
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Cheng
- Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Ziliang Wang
- Cancer Institute and Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Gynecological Oncology, Fudan University Shanghai Cancer Center, Shanghai 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
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14
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Grassi ML, Palma CDS, Thomé CH, Lanfredi GP, Poersch A, Faça VM. Proteomic analysis of ovarian cancer cells during epithelial-mesenchymal transition (EMT) induced by epidermal growth factor (EGF) reveals mechanisms of cell cycle control. J Proteomics 2016; 151:2-11. [PMID: 27394697 DOI: 10.1016/j.jprot.2016.06.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 05/20/2016] [Accepted: 06/07/2016] [Indexed: 12/11/2022]
Abstract
Epithelial to mesenchymal transition (EMT) is a well-orchestrated process that culminates with loss of epithelial phenotype and gain of a mesenchymal and migratory phenotype. EMT enhances cancer cell invasiveness and drug resistance, favoring metastasis. Dysregulation of transcription factors, signaling pathways, miRNAs and growth factors including EGF, TGF-beta and HGF can trigger EMT. In ovarian cancer, overexpression of the EGFR family is associated with more aggressive clinical behavior. Here, the ovarian adenocarcinoma cell line Caov-3 was induced to EMT with EGF in order to identify specific mechanisms controlled by this process. Caov-3 cells induced to EMT were thoroughly validated and a combination of subcellular proteome enrichment, GEL-LC-MS/MS and SILAC strategy allowed consistent proteome identification and quantitation. Protein network analysis of differentially expressed proteins highlighted regulation of metabolism and cell cycle. Activation of relevant signaling pathways, such as PI3K/Akt/mTOR and Ras/Erk MAPK, in response to EGF-induced EMT was validated. Also, EMT did not affected the proliferation rate of Caov-3 cells, but led to cell cycle arrest in G1 phase regulated by increased levels of p21Waf1/Cip1, independently of p53. Furthermore, a decrease in G1 and G2 checkpoint proteins was observed, supporting the involvement of EGF-induced EMT in cell cycle control. BIOLOGICAL SIGNIFICANCE Cancer is a complex multistep process characterized by accumulation of several hallmarks including epithelial to mesenchymal transition (EMT), which promotes cellular and microenvironmental changes resulting in invasion and migration to distant sites, favoring metastasis. EMT can be triggered by different extracellular stimuli, including growth factors such as EGF. In ovarian cancer, the most lethal gynecological cancer, overexpression of the EGFR family is associated with more aggressive clinical behavior, increasing mortality rate caused by metastasis. Our proteomic data, together with specific validation of specific cellular mechanisms demonstrated that EGF-induced EMT in Caov-3 cells leads to important alterations in metabolic process (protein synthesis) and cell cycle control, supporting the implication of EGF/EMT in cancer metastasis, cancer stem cell generation and, therefore, poor prognosis for the disease.
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Affiliation(s)
- Mariana Lopes Grassi
- Dept. Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil; Cell-Based Therapy Center, Ribeirão Preto Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Camila de Souza Palma
- Dept. Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil; Cell-Based Therapy Center, Ribeirão Preto Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Carolina Hassibe Thomé
- Dept. Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil; Cell-Based Therapy Center, Ribeirão Preto Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Guilherme Pauperio Lanfredi
- Dept. Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil; Cell-Based Therapy Center, Ribeirão Preto Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Aline Poersch
- Dept. Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
| | - Vitor Marcel Faça
- Dept. Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil; Cell-Based Therapy Center, Ribeirão Preto Blood Center, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
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15
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de Las Heras-Rubio A, Perucho L, Paciucci R, Vilardell J, LLeonart ME. Ribosomal proteins as novel players in tumorigenesis. Cancer Metastasis Rev 2015; 33:115-41. [PMID: 24375388 DOI: 10.1007/s10555-013-9460-6] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ribosome biogenesis is the most demanding energetic and metabolic expenditure of the cell. The nucleolus, a nuclear compartment, coordinates rRNA transcription, maturation, and assembly into ribosome subunits. The transcription process is highly coordinated with ribosome biogenesis. In this context, ribosomal proteins (RPs) play a crucial role. In the last decade, an increasing number of studies have associated RPs with extraribosomal functions related to proliferation. Importantly, the expression of RPs appears to be deregulated in several human disorders due, at least in part, to genetic mutations. Although the deregulation of RPs in human malignancies is commonly observed, a more complex mechanism is believed to be involved, favoring the tumorigenic process, its progression and metastasis. This review explores the roles of the most frequently mutated oncogenes and tumor suppressor genes in human cancer that modulate ribosome biogenesis, including their interaction with RPs. In this regard, we propose a new focus for novel therapies.
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Affiliation(s)
- A de Las Heras-Rubio
- Oncology and Pathology Group, Institut de Recerca Hospital Vall d'Hebron, Passeig Vall d'Hebron 119-129, 08035, Barcelona, Spain
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16
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Heck MV, Azizov M, Stehning T, Walter M, Kedersha N, Auburger G. Dysregulated expression of lipid storage and membrane dynamics factors in Tia1 knockout mouse nervous tissue. Neurogenetics 2015; 15:135-44. [PMID: 24659297 PMCID: PMC3994287 DOI: 10.1007/s10048-014-0397-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 03/03/2014] [Indexed: 12/13/2022]
Abstract
During cell stress, the transcription and translation of immediate early genes are prioritized, while most other messenger RNAs (mRNAs) are stored away in stress granules or degraded in processing bodies (P-bodies). TIA-1 is an mRNA-binding protein that needs to translocate from the nucleus to seed the formation of stress granules in the cytoplasm. Because other stress granule components such as TDP-43, FUS, ATXN2, SMN, MAPT, HNRNPA2B1, and HNRNPA1 are crucial for the motor neuron diseases amyotrophic lateral sclerosis (ALS)/spinal muscular atrophy (SMA) and for the frontotemporal dementia (FTD), here we studied mouse nervous tissue to identify mRNAs with selective dependence on Tia1 deletion. Transcriptome profiling with oligonucleotide microarrays in comparison of spinal cord and cerebellum, together with independent validation in quantitative reverse transcriptase PCR and immunoblots demonstrated several strong and consistent dysregulations. In agreement with previously reported TIA1 knock down effects, cell cycle and apoptosis regulators were affected markedly with expression changes up to +2-fold, exhibiting increased levels for Cdkn1a, Ccnf, and Tprkb vs. decreased levels for Bid and Inca1 transcripts. Novel and surprisingly strong expression alterations were detected for fat storage and membrane trafficking factors, with prominent +3-fold upregulations of Plin4, Wdfy1, Tbc1d24, and Pnpla2 vs. a −2.4-fold downregulation of Cntn4 transcript, encoding an axonal membrane adhesion factor with established haploinsufficiency. In comparison, subtle effects on the RNA processing machinery included up to 1.2-fold upregulations of Dcp1b and Tial1. The effect on lipid dynamics factors is noteworthy, since also the gene deletion of Tardbp (encoding TDP-43) and Atxn2 led to fat metabolism phenotypes in mouse. In conclusion, genetic ablation of the stress granule nucleator TIA-1 has a novel major effect on mRNAs encoding lipid homeostasis factors in the brain, similar to the fasting effect.
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Affiliation(s)
- Melanie Vanessa Heck
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Mekhman Azizov
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Tanja Stehning
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
| | - Michael Walter
- Institute for Medical Genetics, Eberhard-Karls-University of Tuebingen, 72076 Tübingen, Germany
| | - Nancy Kedersha
- Division of Rheumatology, Immunology and Allergy, Brigham and Women’s Hospital, Smith 652, One Jimmy Fund Way, Boston, MA 02115 USA
| | - Georg Auburger
- Experimental Neurology, Department of Neurology, Goethe University Medical School, Building 89, 3rd floor, Theodor Stern Kai 7, 60590 Frankfurt am Main, Germany
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17
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Wang W, Nag S, Zhang X, Wang MH, Wang H, Zhou J, Zhang R. Ribosomal proteins and human diseases: pathogenesis, molecular mechanisms, and therapeutic implications. Med Res Rev 2014; 35:225-85. [PMID: 25164622 DOI: 10.1002/med.21327] [Citation(s) in RCA: 156] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ribosomes are essential components of the protein synthesis machinery. The process of ribosome biogenesis is well organized and tightly regulated. Recent studies have shown that ribosomal proteins (RPs) have extraribosomal functions that are involved in cell proliferation, differentiation, apoptosis, DNA repair, and other cellular processes. The dysfunction of RPs has been linked to the development and progression of hematological, metabolic, and cardiovascular diseases and cancer. Perturbation of ribosome biogenesis results in ribosomal stress, which triggers activation of the p53 signaling pathway through RPs-MDM2 interactions, resulting in p53-dependent cell cycle arrest and apoptosis. RPs also regulate cellular functions through p53-independent mechanisms. We herein review the recent advances in several forefronts of RP research, including the understanding of their biological features and roles in regulating cellular functions, maintaining cell homeostasis, and their involvement in the pathogenesis of human diseases. We also highlight the translational potential of this research for the identification of molecular biomarkers, and in the discovery and development of novel treatments for human diseases.
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Affiliation(s)
- Wei Wang
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106; Cancer Biology Center, School of Pharmacy, Texas Tech University Health Sciences Center, Amarillo, Texas, 79106
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18
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Moody R, Zhu Y, Huang Y, Cui X, Jones T, Bedolla R, Lei X, Bai Z, Gao SJ. KSHV microRNAs mediate cellular transformation and tumorigenesis by redundantly targeting cell growth and survival pathways. PLoS Pathog 2013; 9:e1003857. [PMID: 24385912 PMCID: PMC3873467 DOI: 10.1371/journal.ppat.1003857] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Accepted: 11/14/2013] [Indexed: 12/31/2022] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is causally linked to several human cancers, including Kaposi's sarcoma, primary effusion lymphoma and multicentric Castleman's disease, malignancies commonly found in HIV-infected patients. While KSHV encodes diverse functional products, its mechanism of oncogenesis remains unknown. In this study, we determined the roles KSHV microRNAs (miRs) in cellular transformation and tumorigenesis using a recently developed KSHV-induced cellular transformation system of primary rat mesenchymal precursor cells. A mutant with a cluster of 10 precursor miRs (pre-miRs) deleted failed to transform primary cells, and instead, caused cell cycle arrest and apoptosis. Remarkably, the oncogenicity of the mutant virus was fully restored by genetic complementation with the miR cluster or several individual pre-miRs, which rescued cell cycle progression and inhibited apoptosis in part by redundantly targeting IκBα and the NF-κB pathway. Genomic analysis identified common targets of KSHV miRs in diverse pathways with several cancer-related pathways preferentially targeted. These works define for the first time an essential viral determinant for KSHV-induced oncogenesis and identify NF-κB as a critical pathway targeted by the viral miRs. Our results illustrate a common theme of shared functions with hierarchical order among the KSHV miRs. Kaposi's sarcoma-associated herpesvirus (KSHV) is the causal agent of several human cancers. KSHV encodes over two dozen genes that regulate diverse cellular pathways. However, the molecular mechanism of KSHV-induced oncogenesis remains unknown. In this study, we determined the roles of KSHV microRNAs (miRs) in KSHV-induced oncogenesis using a recently developed KSHV cellular transformation system of primary rat mesenchymal precursor cells. A KSHV mutant with a cluster of 10 precursor miRs (pre-miRs) deleted failed to transform primary cells, and instead, caused cell cycle arrest and apoptosis. Expression of the miR cluster or several pre-miRs was sufficient to restore the oncogenicity of the mutant virus. KSHV miRs regulated cell cycle progression and inhibited apoptosis in part by redundantly targeting IκBα and the NF-κB pathway. By integrating gene expression profiling and target prediction, we identified common targets of KSHV miRs in diverse pathways. Importantly, several cancer-related pathways were preferentially targeted by KSHV miRs. These works have demonstrated for the first time the important roles of KSHV miRs in oncogenesis and identified NF-κB as a critical pathway targeted by the miRs. Our results reveal that shared function is a common theme of KSHV miRs, which manifest functional hierarchical order.
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Affiliation(s)
- Rosalie Moody
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Ying Zhu
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Yufei Huang
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America
- * E-mail: (YH); (SJG)
| | - Xiaodong Cui
- Department of Electrical and Computer Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America
| | - Tiffany Jones
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Roble Bedolla
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Xiufen Lei
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Zhiqiang Bai
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
| | - Shou-Jiang Gao
- Department of Pediatrics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Microbiology and Immunology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, United States of America
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- * E-mail: (YH); (SJG)
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19
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Jiang J, Liu L, Li X, Tao D, Hu J, Qin J. Defining the restriction point in normal asynchronous human peripheral blood lymphocytes. Cytometry A 2013; 83:944-51. [PMID: 23926097 DOI: 10.1002/cyto.a.22341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 11/10/2022]
Abstract
Although the restriction point (R-point) was proposed in animal cells several decades ago, its existence in normal cells is still controversial, because, in most studies, long-term cultured cell lines rather than primary normal cells were used. Furthermore, cell synchronization was generally applied, resulting in growth imbalance between DNA synthesis and protein expression in cells. Finally, R-point was originally proposed as a unique arrest point that may be in G0 phase; however, generally believed R-point locates within G1 phase. Thus, up to now, there is no solid experimental evidence that supports the existence of R-point in asynchronous primary normal cells. In this study, we used freshly purified peripheral human blood lymphocytes, as asynchronous primary normal cells, to confirm the existence of restriction point in G1 not G0 phase. Our findings may help uncover the mystery of the deregulation of cell cycle progression in malignant tumors. © 2013 International Society for Advancement of Cytometry.
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Affiliation(s)
- Jianwu Jiang
- Department of Surgery and Molecular Medical Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, People's Republic of China
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20
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Conde JA, Claunch CJ, Romo HE, Benito-Martín A, Ballestero RP, González-García M. Identification of a motif in BMRP required for interaction with Bcl-2 by site-directed mutagenesis studies. J Cell Biochem 2013; 113:3498-508. [PMID: 22711503 DOI: 10.1002/jcb.24226] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Bcl-2 is an anti-apoptotic protein that inhibits apoptosis elicited by multiple stimuli in a large variety of cell types. BMRP (also known as MRPL41) was identified as a Bcl-2 binding protein and shown to promote apoptosis. Previous studies indicated that the amino-terminal two-thirds of BMRP contain the domain(s) required for its interaction with Bcl-2, and that this region of the protein is responsible for the majority of the apoptosis-inducing activity of BMRP. We have performed site-directed mutagenesis analyses to further characterize the BMRP/Bcl-2 interaction and the pro-apoptotic activity of BMRP. The results obtained indicate that the 13-17 amino acid region of BMRP is necessary for its binding to Bcl-2. Further mutagenesis of this motif shows that amino acid residue aspartic acid (D) 16 of BMRP is essential for the BMRP/Bcl-2 interaction. Functional analyses conducted in mammalian cells with BMRP site-directed mutants BMRP(13Ala17) and BMRP(D16A) indicate that these mutants induce apoptosis through a caspase-mediated pathway, and that they kill cells slightly more potently than wild-type BMRP. Bcl-2 is still able to counteract BMRP(D16A)-induced cell death significantly, but not as completely as when tested against wild-type BMRP. These results suggest that the apoptosis-inducing ability of wild-type BMRP is blocked by Bcl-2 through several mechanisms.
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Affiliation(s)
- Juan A Conde
- Department of Chemistry, Texas A&M University-Kingsville, Kingsville, Texas 78363, USA
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21
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Guo X, Shi Y, Gou Y, Li J, Han S, Zhang Y, Huo J, Ning X, Sun L, Chen Y, Sun S, Fan D. Human ribosomal protein S13 promotes gastric cancer growth through down-regulating p27(Kip1). J Cell Mol Med 2012; 15:296-306. [PMID: 19912438 PMCID: PMC3822796 DOI: 10.1111/j.1582-4934.2009.00969.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Our previous works revealed that human ribosomal protein S13 (RPS13) was up-regulated in multidrug-resistant gastric cancer cells and overexpression of RPS13 could protect gastric cancer cells from drug-induced apoptosis. The present study was designed to explore the role of RPS13 in tumorigenesis and development of gastric cancer. The expression of RPS13 in gastric cancer tissues and normal gastric mucosa was evaluated by immunohistochemical staining and Western blot analysis. It was found RPS13 was expressed at a higher level in gastric cancer tissues than that in normal gastric mucosa. RPS13 was then genetically overexpressed in gastric cancer cells or knocked down by RNA interference. It was demonstrated that up-regulation of RPS13 accelerated the growth, enhanced in vitro colony forming and soft agar cologenic ability and promoted in vivo tumour formation potential of gastric cancer cells. Meanwhile, down-regulation of RPS13 in gastric cancer cells resulted in complete opposite effects. Moreover, overexpression of RPS13 could promote G1 to S phase transition whereas knocking down of RPS13 led to G1 arrest of gastric cancer cells. It was further demonstrated that RPS13 down-regulated p27kip1 expression and CDK2 kinase activity but did not change the expression of cyclin D, cyclin E, CDK2, CDK4 and p16INK4A. Taken together, these data indicate that RPS13 could promote the growth and cell cycle progression of gastric cancer cells at least through inhibiting p27kip1 expression.
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Affiliation(s)
- Xueyan Guo
- State Key Laboratory of Cancer Biology and Institute of Digestive Diseases, Xijing Hospital, The Fourth Military Medical University, Xi'an, Shaanxi, China
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22
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Malladi S, Parsa KVL, Bhupathi D, Rodríguez-González MA, Conde JA, Anumula P, Romo HE, Claunch CJ, Ballestero RP, González-García M. Deletion mutational analysis of BMRP, a pro-apoptotic protein that binds to Bcl-2. Mol Cell Biochem 2011; 351:217-32. [PMID: 21253851 DOI: 10.1007/s11010-011-0729-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 01/10/2011] [Indexed: 12/21/2022]
Abstract
Bcl-2 is an anti-apoptotic member of the Bcl-2 family of proteins that protects cells from apoptosis induced by a large variety of stimuli. The protein BMRP (MRPL41) was identified as a Bcl-2 binding partner and shown to have pro-apoptotic activity. We have performed deletion mutational analyses to identify the domain(s) of Bcl-2 and BMRP that are involved in the Bcl-2/BMRP interaction, and the region(s) of BMRP that mediate its pro-apoptotic activity. The results of these studies indicate that both the BH4 domain of Bcl-2 and its central region encompassing its BH1, BH2, and BH3 domains are required for its interaction with BMRP. The loop region and the transmembrane domain of Bcl-2 were found to be dispensable for this interaction. The Bcl-2 deletion mutants that do not interact with BMRP were previously shown to be functionally inactive. Deletion analyses of the BMRP protein delimited the region of BMRP needed for its interaction with Bcl-2 to the amino-terminal two-thirds of the protein (amino acid residues 1-92). Further deletions at either end of the BMRP(1-92) truncated protein resulted in lack of binding to Bcl-2. Functional studies performed with BMRP deletion mutants suggest that the cell death-inducing domains of the protein reside mainly within its amino-terminal two-thirds. The region of BMRP required for the interaction with Bcl-2 is very relevant for the cell death-inducing activity of the protein, suggesting that one possible mechanism by which BMRP induces cell death is by binding to and blocking the anti-apoptotic activity of Bcl-2.
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Affiliation(s)
- Srinivas Malladi
- Department of Chemistry, Texas A&M University-Kingsville, 700 University Blvd., Kingsville, TX 78363-8202, USA
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23
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Shutt TE, Shadel GS. A compendium of human mitochondrial gene expression machinery with links to disease. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:360-79. [PMID: 20544879 PMCID: PMC2886302 DOI: 10.1002/em.20571] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Mammalian mitochondrial DNA encodes 37 essential genes required for ATP production via oxidative phosphorylation, instability or misregulation of which is associated with human diseases and aging. Other than the mtDNA-encoded RNA species (13 mRNAs, 12S and 16S rRNAs, and 22 tRNAs), the remaining factors needed for mitochondrial gene expression (i.e., transcription, RNA processing/modification, and translation), including a dedicated set of mitochondrial ribosomal proteins, are products of nuclear genes that are imported into the mitochondrial matrix. Herein, we inventory the human mitochondrial gene expression machinery, and, while doing so, we highlight specific associations of these regulatory factors with human disease. Major new breakthroughs have been made recently in this burgeoning area that set the stage for exciting future studies on the key outstanding issue of how mitochondrial gene expression is regulated differentially in vivo. This should promote a greater understanding of why mtDNA mutations and dysfunction cause the complex and tissue-specific pathology characteristic of mitochondrial disease states and how mitochondrial dysfunction contributes to more common human pathology and aging.
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Affiliation(s)
- Timothy E. Shutt
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, P.O. Box 208023, New haven, CT 06520-8023
| | - Gerald S. Shadel
- Department of Pathology, Yale University School of Medicine, 310 Cedar Street, P.O. Box 208023, New haven, CT 06520-8023
- Department of Genetics, Yale University School of Medicine, 333 Cedar Street, P.O. Box 208005, New haven, CT 06520-8005
- corresponding author: Department of Pathology, Yale University School of Medicine, P.O. Box 208023, New Haven, CT 06520-8023 phone: (203) 785-2475 FAX: (203) 785-2628
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24
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Kim JC, Kim SY, Roh SA, Cho DH, Kim DD, Kim JH, Kim YS. Gene expression profiling: Canonical molecular changes and clinicopathological features in sporadic colorectal cancers. World J Gastroenterol 2008; 14:6662-72. [PMID: 19034969 PMCID: PMC2773308 DOI: 10.3748/wjg.14.6662] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate alternative or subordinate pathways involved in colorectal tumorigenesis and tumor growth, possibly determining at-risk populations and predicting responses to treatment.
METHODS: Using microarray gene-expression analysis, we analyzed patterns of gene expression relative to canonical molecular changes and clinicopathological features in 84 sporadic colorectal cancer patients, standardized by tumor location. Subsets of differentially expressed genes were confirmed by real-time reverse-transcript polymerase chain reaction (RT-PCR).
RESULTS: The largest number of genes identified as being differentially expressed was by tumor location, and the next largest number by lymphovascular or neural invasion of tumor cells and by mismatch repair (MMR) defects. Amongst biological processes, the immune response was significantly implicated in entire molecular changes observed during colorectal tumorigenesis (P < 0.001). Amongst 47 differentially expressed genes, seven (PISD, NIBP, BAI2, STOML1, MRPL21, MRPL16, and MKKS) were newly found to correlate with tumorigenesis and tumor growth. Most location-associated molecular changes had distinct effects on gene expression, but the effects of the latter were sometimes contradictory.
CONCLUSION: We show that several differentially expressed genes were associated with canonical molecular changes in sporadic colorectal cancers, possibly constituting alternative or subordinate pathways of tumorigenesis. As tumor location was the dominant factor influencing differential gene expression, location-specific analysis may identify location-associated pathways and enhance the accuracy of class prediction.
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25
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Haque ME, Grasso D, Miller C, Spremulli LL, Saada A. The effect of mutated mitochondrial ribosomal proteins S16 and S22 on the assembly of the small and large ribosomal subunits in human mitochondria. Mitochondrion 2008; 8:254-61. [PMID: 18539099 PMCID: PMC2517634 DOI: 10.1016/j.mito.2008.04.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 04/17/2008] [Accepted: 04/23/2008] [Indexed: 10/22/2022]
Abstract
Mutations in mitochondrial small subunit ribosomal proteins MRPS16 or MRPS22 cause severe, fatal respiratory chain dysfunction due to impaired translation of mitochondrial mRNAs. The loss of either MRPS16 or MRPS22 was accompanied by the loss of most of another small subunit protein MRPS11. However, MRPS2 was reduced only about 2-fold in patient fibroblasts. This observation suggests that the small ribosomal subunit is only partially able to assemble in these patients. Two large subunit ribosomal proteins, MRPL13 and MRPL15, were present in substantial amounts suggesting that the large ribosomal subunit is still present despite a non-functional small subunit.
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Affiliation(s)
- Md. Emdadul Haque
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC-27599-3290
| | - Domenick Grasso
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC-27599-3290
| | - Chaya Miller
- Metabolic Disease Unit, Hadassah Medical Center, P.O.B. 12000, 91120 Jerusalem, Israel
| | - Linda L Spremulli
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC-27599-3290
| | - Ann Saada
- Metabolic Disease Unit, Hadassah Medical Center, P.O.B. 12000, 91120 Jerusalem, Israel
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26
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Huang CJ, Chien CC, Yang SH, Chang CC, Sun HL, Cheng YC, Liu CC, Lin SC, Lin CM. Faecal ribosomal protein L19 is a genetic prognostic factor for survival in colorectal cancer. J Cell Mol Med 2008; 12:1936-43. [PMID: 18266979 PMCID: PMC4506161 DOI: 10.1111/j.1582-4934.2008.00253.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Ribosomal proteins are encoded by a gene family, members of which are overexpressed in human cancers. Many of them have been found, using oligonucleotide microarray hybridization, to be differentially expressed in the faeces of patients with various stages of col-orectal cancer (CRC). The gene encoding ribosomal protein L19 (RPL19), a prognostic marker for human prostate cancer, is differentially expressed in CRC patients. Measurement of faecal RPL19 mRNA might improve prognostic prediction for CRC patients. Using quantitative real-time reverse transcription PCR, levels of RPL19 mRNA were detected in samples of colonic tissues from 44 CRC patients, in the faeces of 54 CRC patients and 15 controls, and in 11 colonic cell lines. Seven of 24 patients with late-stage CRC (Dukes' stages C and D) expressed over 2-fold more RPL19 in colonic tumour tissues than in corresponding normal tissues (P= 0.038). The mean faecal RPL19 mRNA levels of late-staged patients were higher than those of controls (P= 0.003) and early-staged patients (P= 0.008). Patients with both high serum levels of carcinoembryonic antigen (CEA; >5 ng/mL) and high-faecal RPL19 mRNA (≥0.0069) had higher risk (odds ratio, 8.0; P= 0.015) and lower overall 48-month survival (33.8 ± 13.7%, P= 0.013). Oligonucleotide microarray hybridization analysis of faecal molecules identified gene transcripts differentially present in faeces. In conclusion, faecal RPL19 expression is associated with advanced tumour stages and addictive to serum CEA in predicting prognosis of CRC patients.
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Affiliation(s)
- C-J Huang
- Molecular Genetics and Biochemistry Laboratory, Cathay Medical Research Institute, Cathay General Hospital, Taipei, Taiwan
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27
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Bot1p is required for mitochondrial translation, respiratory function, and normal cell morphology in the fission yeast Schizosaccharomyces pombe. EUKARYOTIC CELL 2008; 7:619-29. [PMID: 18245278 DOI: 10.1128/ec.00048-07] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Maintenance of cell morphology is essential for normal cell function. For eukaryotic cells, a growing body of recent evidence highlights a close interdependence between mitochondrial function, the cytoskeleton, and cell cycle control mechanisms; however, the molecular details of this interconnection are still not completely understood. We have identified a novel protein, Bot1p, in the fission yeast Schizosaccharomyces pombe. The bot1 gene is essential for cell viability. bot1Delta mutant cells expressing lower levels of Bot1p display altered cell size and cell morphology and a disrupted actin cytoskeleton. Bot1p localizes to the mitochondria in live cells and cofractionates with purified mitochondrial ribosomes. Reduced levels of Bot1p lead to mitochondrial fragmentation, decreased mitochondrial protein translation, and a corresponding decrease in cell respiration. Overexpression of Bot1p results in cell cycle delay, with increased cell size and cell length and enhanced cell respiration rate. Our results show that Bot1p has a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery. Our observations also indicate that in fission yeast, alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms.
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28
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 PMCID: PMC2266750 DOI: 10.1186/1471-2229-8-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - H Esteban Hopp
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
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29
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 DOI: 10.1186/147-2229.8-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina.
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30
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Identification of genes differentially expressed during larval molting and metamorphosis of Helicoverpa armigera. BMC DEVELOPMENTAL BIOLOGY 2007; 7:73. [PMID: 17588272 PMCID: PMC1925068 DOI: 10.1186/1471-213x-7-73] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 06/25/2007] [Indexed: 12/25/2022]
Abstract
BACKGROUND Larval molting and metamorphosis are important physiological processes in the life cycle of the holometabolous insect. We used suppression subtractive hybridization (SSH) to identify genes differentially expressed during larval molting and metamorphosis. RESULTS We performed SSH between tissues from a variety of developmental stages, including molting 5th and feeding 6th instar larvae, metamorphically committed and feeding 5th instar larvae, and feeding 5th instar and metamorphically committed larvae. One hundred expressed sequence tags (ESTs) were identified and included 73 putative genes with similarity to known genes, and 27 unknown ESTs. SSH results were further characterized by dot blot, Northern blot, and RT-PCR. The expression levels of eleven genes were found to change during larval molting or metamorphosis, suggesting a functional role during these processes. CONCLUSION These results provide a new set of genes expressed specifically during larval molt or metamorphosis that are candidates for further studies into the regulatory mechanisms of those stage-specific genes during larval molt and metamorphosis.
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31
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Chen YC, Chang MY, Shiau AL, Yo YT, Wu CL. Mitochondrial ribosomal protein S36 delays cell cycle progression in association with p53 modification and p21WAF1/CIP1 expression. J Cell Biochem 2007; 100:981-90. [PMID: 17131359 DOI: 10.1002/jcb.21079] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Ribosomal biogenesis is correlated with cell cycle, cell proliferation, cell growth and tumorigenesis. Some oncogenes and tumor suppressors are involved in regulating the formation of mature ribosome and affecting the ribosomal biogenesis. In previous studies, the mitochondrial ribosomal protein L41 was reported to be involved in cell proliferation regulating through p21(WAF1/CIP1) and p53 pathway. In this report, we have identified a mitochondrial ribosomal protein S36 (mMRPS36), which is localized in the mitochondria, and demonstrated that overexpression of mMRPS36 in cells retards the cell proliferation and delays cell cycle progression. In addition, the mMRPS36 overexpression induces p21(WAF1/CIP1) expression, and regulates the expression and phosphorylation of p53. Our result also indicate that overexpression of mMRPS36 affects the mitochondrial function. These results suggest that mMRPS36 plays an important role in mitochondrial ribosomal biogenesis, which may cause nucleolar stress, thereby leading to cell cycle delay.
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Affiliation(s)
- Yeong-Chang Chen
- Institute of Basic Medical Sciences, National Cheng Kung University Medical College, Tainan, Taiwan
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32
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Wang J, Jing W, Yuan S, Sheng Y, Jiang S, Jang S. The ribosomal protein L32-2 (RPL32-2) of S. pombe exhibits a novel extraribosomal function by acting as a potential transcriptional regulator. FEBS Lett 2006; 580:1827-32. [PMID: 16516201 DOI: 10.1016/j.febslet.2006.02.040] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2006] [Revised: 02/04/2006] [Accepted: 02/14/2006] [Indexed: 11/17/2022]
Abstract
Ribosomal proteins play important roles in stabilizing the rRNA structure to facilitate protein synthesis in ribosome. In the present study, we analyzed the potential extraribosomal function of the ribosomal protein L32-2 (RPL32-2), which was expressed by a gene clone isolated from a cDNA library of Schizosaccharomyces pombe (S. pombe). RPL32-2 fused with the GAL4 DNA-bind domain or the GAL4 transcriptional activating domain could, respectively, activate transcriptions of reporter genes in yeast strain AH109. The RPL32-2 mutants with truncation of either the N- or the C-terminal domain resulted in abolishment of this regulatory effect. The DNA binding site for RPL32-2 of S. pombe was identified by using a random oligonucleotide selection strategy and gel motility shift assay and Western blotting confirmed its binding specificity. Moreover, we found RPL32-2 was also able to interact with a to-be-identified AT sequence binding protein. These data suggest that RPL32-2 of S. pombe, besides its ribosomal function, may also act as a potential transcriptional regulator in nucleus.
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Affiliation(s)
- Jing Wang
- Jiangsu Key Lab for Biodiversity and Biotechnology, NNU Key Lab of Microbial Technology, College of Life Science, Nanjing Normal University, 122 Ninghai Lu, Nanjing 210097, PR China
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