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Andrade DAP, Bonatelli M, de Paula FE, Berardinelli GN, Teixeira GR, dos Reis MT, Barbin FF, Andrade CEMDC, Aguiar VP, Hermoza AD, Hirai WY, Schmidt RL, Reis RM, dos Reis R. Implementation of the ProMisE classifier and validation of its prognostic impact in Brazilian endometrial carcinomas. Front Oncol 2024; 14:1503901. [PMID: 39735598 PMCID: PMC11671357 DOI: 10.3389/fonc.2024.1503901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2024] [Accepted: 11/25/2024] [Indexed: 12/31/2024] Open
Abstract
Purpose Molecular classification of endometrial cancer (EC) has emerged as a key approach to individualize therapy and define prognostic outcomes. This study aimed to implement the traditional ProMisE classification in a Brazilian population, compared with a molecular setting of ProMisE biomarkers, and evaluate its impact on patients' prognosis. Patient and methods A prospective cohort of 114 patients with primary EC treated at Barretos Cancer Hospital (BCH) between October 2020 and December 2022 was conducted. Pathology diagnosis, staging, treatment, and follow-up data were collected. The traditional ProMisE methodology was carried out by POLE hotspot sequencing and immunohistochemistry (IHC) for p53 and mismatch repair (MMR) proteins. We further evaluate the MMR and TP53 status by molecular approach, namely microsatellite instability (MSI) by PCR-based and TP53 mutation analysis by next-generation sequencing (NGS). The results of the 4 molecular groups in both methodologies were compared regarding agreement accuracy and survival outcomes. Results Among the 114 cases, the traditional ProMisE groups were: POLEmut 15.8%, MMRd 28.1%, p53abn 27.2%, and no specific molecular profile (NSMP) 28.9%. Considering the molecular classification approach, we observed a POLEmut group of 15.8%, MSI group of 23.7%, TP53 mutation of 27.2%, and NSMP of 33.3%. The concordance rate of both approaches was 86.8% (99/114 cases) with an overall accuracy of 0.87. Importantly, both traditional and molecular ProMisE approaches were associated with significant distinct overall survival (OS) and progression-free survival (PFS) outcomes, with POLEmut patients exhibiting a better prognosis (93.8% OS, at 24 months), whereas the p53abn having a worse survival time (68.9% of OS, at 24 months). Conclusion We reported for the first time the Brazilian profile of the ProMisE classification of endometrial cancer and demonstrated the prognostic impact of the traditional and molecular ProMisE classification on patient outcomes.
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Affiliation(s)
| | - Murilo Bonatelli
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, São Paulo, Brazil
| | | | | | - Gustavo Ramos Teixeira
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, São Paulo, Brazil
- Pathology Laboratory, Barretos Cancer Hospital, São Paulo, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata, FACISB, São Paulo, Brazil
| | | | | | - Carlos Eduardo Mattos da Cunha Andrade
- Barretos School of Health Sciences Dr. Paulo Prata, FACISB, São Paulo, Brazil
- Gynecologic Oncology Department, Barretos Cancer Hospital, São Paulo, Brazil
| | | | | | - Welinton Yoshio Hirai
- Department of Epidemiology and Biostatistics, Barretos Cancer Hospital, São Paulo, Brazil
| | - Ronaldo Luís Schmidt
- Department of Surgical Oncology, Lagarto Unit, Barretos Cancer Hospital, Sergipe, Brazil
| | - Rui Manuel Reis
- Molecular Diagnostic Laboratory, Barretos Cancer Hospital, São Paulo, Brazil
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal
| | - Ricardos dos Reis
- Gynecologic Oncology Department, Barretos Cancer Hospital, São Paulo, Brazil
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Vieira RADC, Sant'Anna D, Laus AC, Reis RM. Ancestry and self-reported race in Brazilian breast cancer women. REVISTA DA ASSOCIACAO MEDICA BRASILEIRA (1992) 2023; 69:e20230767. [PMID: 37909531 PMCID: PMC10615220 DOI: 10.1590/1806-9282.20230767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 08/15/2023] [Indexed: 11/03/2023]
Abstract
OBJECTIVE This study aimed to evaluate the association between self-reported race/color and ancestry in Brazilian patients with breast cancer. METHODS This was an observational, transversal, epidemiological study, evaluating race and ancestry in 1,127 patients with breast cancer. For genetic ancestry, a 46-AIM-INDEL panel was used. The ancestral profile was evaluated with the Structure v.2.3.3 software. Descriptive statistics were performed. To assess differences between race and ancestry, an analysis of variance with Bonferoni adjustment was used. RESULTS The race distribution was 77.7% white, 17.6% brown, 4.1% black, 0.4% yellow, and 0.3% cafuse. The African ancestry proportion was significantly (p<0.001) more evident in black [0.63±0.21 (0.17-0.96)], followed by brown [0.25±0.16 (0.02-0.70)], and less frequent in white skin color. The European ancestry proportion was significantly (p<0.001) higher in white [0.72±0.17 (0.02-0.97)], followed by brown [0.57±0.19 (0.12-0.92)], yellow [0.27±0.31 (0.12-0.620], and black [0.24±0.19 (0.02-0.72)]. The Asiatic ancestry proportion is significantly (p<0.001) higher in yellow [0.48±0.51 (0.04-0.93)]. The Amerindian ancestry proportion frequency was the least frequent in all groups, and cafuse patients did not express differences between all race groups. The brown race group presented differences in African and European ancestry. CONCLUSION Although we found many similarities between white European ancestry, black African ancestry, and yellow Asian ancestry, there is great miscegenation between patients. Although they can be labeled as having one race, they do present many ancestral genes that would allow their inclusion in another race group.
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Affiliation(s)
- René Aloisio da Costa Vieira
- Hospital de Câncer de Barretos, Molecular Oncology Research Center – Barretos (SP), Brazil
- Hospital de Câncer de Barretos, Postgraduate Program in Oncology – Barretos (SP), Brazil
- Faculdade de Medicina de Botucatu, Postgraduate Program in Tocogynecology – Botucatu (SP), Brazil
| | - Débora Sant'Anna
- Hospital de Câncer de Barretos, Molecular Oncology Research Center – Barretos (SP), Brazil
| | - Ana Carolina Laus
- Hospital de Câncer de Barretos, Molecular Oncology Research Center – Barretos (SP), Brazil
| | - Rui Manuel Reis
- Hospital de Câncer de Barretos, Molecular Oncology Research Center – Barretos (SP), Brazil
- Hospital de Câncer de Barretos, Postgraduate Program in Oncology – Barretos (SP), Brazil
- University of Minho, School of Medicine, Life and Health Sciences Research Institute – Braga, Portugal
- Life and Health Sciences Research Institute/3B's Research Group (Biomaterials, Biodegradables and Biomimetics)-PT Government Associate Laboratory – Braga/Guimarães, Portugal
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Bartels S, Grote I, Wagner M, Boog J, Schipper E, Reineke‐Plaass T, Kreipe H, Lehmann U. Concordance in detection of microsatellite instability by PCR and NGS in routinely processed tumor specimens of several cancer types. Cancer Med 2023; 12:16707-16715. [PMID: 37376830 PMCID: PMC10501280 DOI: 10.1002/cam4.6293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 06/14/2023] [Accepted: 06/15/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Microsatellite instability (MSI) occurs in several cancer types and is commonly used for prognosis and as a predictive biomarker for immune checkpoint therapy. METHODS We analyzed n = 263 formalin-fixed paraffin-embedded (FFPE) tumor specimens (127 colorectal cancer (CRC), 55 endometrial cancer (EC), 33 stomach adenocarcinoma (STAD), and 48 solid tumor specimens of other tumor types) with a capillary electrophoresis based multiplex monomorphic marker MSI-PCR panel and an amplicon-based NGS assay for microsatellite instability (MSI+). In total, n = 103 (39.2%) cases with a known defect of the DNA mismatch repair system (dMMR), determined by a loss in protein expression of MSH2/MSH6 (n = 48, 46.6%) or MLH1/PMS2 (n = 55, 53.4%), were selected. Cases with an isolated loss of MSH6 or PMS2 were excluded. RESULTS The overall sensitivity and specificity of the NGS assay in comparison with the MSI-PCR were 92.2% and 98.8%. With CRC cases a nearly optimal concordance was reached (sensitivity 98.1% and specificity 100.0%). Whereas EC cases only show a sensitivity of 88.6% and a specificity of 95.2%, caused by several cases with instability in less than five monomorphic markers, which could be difficult to analyze by NGS (subtle MSI+ phenotype). CONCLUSIONS MSI analysis of FFPE DNA by NGS is feasible and the results show a high concordance in comparison with the monomorphic marker MSI-PCR. However, cases with a subtle MSI+ phenotype, most frequently manifest in EC, have a risk of a false-negative result by NGS and should be preferentially analyzed by capillary electrophoresis.
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Affiliation(s)
- Stephan Bartels
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | - Isabel Grote
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | | | - Jannik Boog
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | - Elisa Schipper
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | | | - Hans Kreipe
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical SchoolHannoverGermany
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Yakushina V, Kavun A, Veselovsky E, Grigoreva T, Belova E, Lebedeva A, Mileyko V, Ivanov M. Microsatellite Instability Detection: The Current Standards, Limitations, and Misinterpretations. JCO Precis Oncol 2023; 7:e2300010. [PMID: 37315263 DOI: 10.1200/po.23.00010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 04/06/2023] [Accepted: 04/26/2023] [Indexed: 06/16/2023] Open
Affiliation(s)
- Valentina Yakushina
- OncoAtlas LLC, Moscow, Russian Federation
- Laboratory of Epigenetics, Research Centre for Medical Genetics, Moscow, Russian Federation
| | | | - Egor Veselovsky
- OncoAtlas LLC, Moscow, Russian Federation
- Department of Evolutionary Genetics of Development, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Tatiana Grigoreva
- OncoAtlas LLC, Moscow, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Ekaterina Belova
- OncoAtlas LLC, Moscow, Russian Federation
- Lomonosov Moscow State University, Moscow, Russian Federation
| | | | | | - Maxim Ivanov
- OncoAtlas LLC, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Moscow, Russian Federation
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da Costa Vieira RA, Sant'Anna D, Laus AC, Bacchi CE, Silva RJC, de Oliveira-Junior I, da Silva VD, Pereira R, Reis RM. Genetic Ancestry of 1127 Brazilian Breast Cancer Patients and Its Correlation With Molecular Subtype and Geographic Region. Clin Breast Cancer 2023:S1526-8209(23)00086-1. [PMID: 37183096 DOI: 10.1016/j.clbc.2023.04.001] [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: 01/03/2022] [Revised: 03/25/2023] [Accepted: 04/09/2023] [Indexed: 05/16/2023]
Abstract
PURPOSE Breast cancer molecular subtypes show significant differences in different ethnic groups in the United States, but no study has evaluated genetic ancestry in breast cancer in Brazilian women. METHODS Breast cancer patients from distinct parts of Brazil were evaluated. Molecular subtypes were determined by immunohistochemistry. Genetic ancestry was evaluated using a panel of 46 AIMs (ancestry informative markers), which classified genetic ancestry as European, African, Asian, and Amerindian. PCR products were subjected to capillary electrophoresis and analyzed using GeneMapper 4.0 software. Ancestry was evaluated with Structure v.2.3.3 software. Ancestry was tested for correlations with geographic region and molecular subtype. The chi-square test and ANOVA with Bonferroni adjustment were applied. RESULTS Genetic ancestry and clinical data were evaluated in 1127 patients. Higher rates of self-reported white ethnicity, European ancestry, and HER-2- luminal tumors were identified in the South region, which may influence age at diagnosis and result in a higher rate of early tumors. Conversely, higher rates of African ancestry in the North and Northeast regions, self-reported nonwhite ethnicity, HER-2+ tumors, and triple-negative tumors were noted. Triple-negative and HER-2+ tumors were associated with higher advanced and metastatic disease rates at diagnosis, with triple-negative tumors being more frequent in young women. CONCLUSION Differences in genetic ancestry, self-reported ethnicity, and molecular subtype were found between Brazilian demographic regions. Knowledge of these features may contribute to a better understanding of age at diagnosis and the molecular distribution of breast cancer in Brazil.
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Affiliation(s)
- René Aloisio da Costa Vieira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Tocogynecology, Botucatu School of Medicine, Botucatu, SP, Brazil.
| | - Débora Sant'Anna
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | - Idam de Oliveira-Junior
- Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Tocogynecology, Botucatu School of Medicine, Botucatu, SP, Brazil
| | - Vinicius Duval da Silva
- Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Bacchi Laboratory, Botucatu, SP, Brazil; Department of Pathology, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil; Postgraduate Program in Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil; Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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Garcia FADO, Evangelista AF, Mançano BM, Moreno DA, Berardinelli GN, de Paula FE, Antoniazzi AP, Júnior CA, Lombardi I, Santana I, Teixeira GR, Costa CE, Reis RM. Genomic profile of two Brazilian choroid plexus tumors by whole-exome sequencing. Cold Spring Harb Mol Case Stud 2023; 9:mcs.a006245. [PMID: 36963804 PMCID: PMC10111795 DOI: 10.1101/mcs.a006245] [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: 09/23/2022] [Accepted: 02/24/2023] [Indexed: 03/26/2023] Open
Abstract
Choroid plexus tumors (CPTs) are rare intracranial neoplasms, representing <1% of all brain tumors, yet they represent 20% of first-year pediatric brain tumors. Although these tumors have been linked to TP53 germline mutations in the context of Li-Fraumeni syndrome, their somatic driver alterations remain poorly understood. In this study, we report two cases of lateral ventricle tumors: 3-yr-old male diagnosed with an atypical choroid plexus papilloma (aCPP), and a 6-mo-old female diagnosed with a choroid plexus carcinoma (CPC). We performed whole-exome sequencing of paired blood and tumor tissue in both patients, categorized somatic variants, and determined copy-number alterations. Our analysis revealed a tier II variant (Association for Molecular Pathology [AMP] criteria) in BRD1, a H3 and TP53 acetylation agent, in the aCPP. In addition, we detected copy-number gains on Chromosomes 12, 18, and 20 and copy-number losses on Chromosomes 13q and 22q (BRD1 locus) in this tumor. The CPC tumor had only a pathogenic germline TP53 variant, based on American College of Medical Genetics (ACMG) criteria, with a clinical and familiar history of Li-Fraumeni syndrome. The CPC patient presented loss of heterozygosity (LoH) of TP53 loci and hyperdiploid genome. Both tumors were microsatellite-stable. This is the first study performing whole-exome sequencing in Brazilian choroid plexus tumors, and in line with the literature, we corroborate the absence of recurrent somatic mutations in these tumors. Further studies with larger sample sizes are necessary to confirm our findings and better understand the underlying biology of these tumors.
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Affiliation(s)
| | | | - Bruna Minniti Mançano
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Daniel Antunes Moreno
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | | | | | | | | | - Ismael Lombardi
- Neurosurgery Department, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Iara Santana
- Pathology Department, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Gustavo Ramos Teixeira
- Pathology Department, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB 14785-002
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400, Brazil;
- Laboratory of Molecular Diagnostics, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, 4710-057, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, 4710-057, Portugal
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Marques RF, Moreno DA, da Silva L, Leal LF, de Paula FE, Santana I, Teixeira G, Saggioro F, Neder L, Junior CA, Mançano B, Reis RM. Digital expression profile of immune checkpoint genes in medulloblastomas identifies CD24 and CD276 as putative immunotherapy targets. Front Immunol 2023; 14:1062856. [PMID: 36825029 PMCID: PMC9941636 DOI: 10.3389/fimmu.2023.1062856] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 01/24/2023] [Indexed: 02/10/2023] Open
Abstract
Introduction Medulloblastoma is the most common and lethal pediatric malignant brain tumor. It comprises four main molecular subgroups: WNT-activated, SHH-activated, Group 3, and Group 4. Medulloblastoma treatment is surgical resection, craniospinal radiation, and chemotherapy. However, many patients do not respond to therapy, and most suffer severe side effects. Cancer immunotherapy targeting immune checkpoints (IC) (PD-1, PD-L1, and CTLA4) has been getting disappointing outcomes in brain tumors. Nevertheless, other less explored immune checkpoints may be promising candidates for medulloblastoma therapy. Objectives In the present study, we aimed to characterize the expression profile of 19 immune checkpoints in medulloblastoma. Methods We analyzed 88 formalin-fixed paraffin-embedded medulloblastomas previously classified for each molecular subgroup and three non-tumoral brain tissue. mRNA levels of 19 immune checkpoint-related genes were quantified using the nCounter (PanCancer Immune Profiling Panel) assay. Further in silico analysis was performed in two larger public microarray datasets, one of which enabled comparisons between tumoral and non-tumoral tissues. Immunohistochemistry of PD-L1 was performed in a subset of cases. Microsatellite instability was also molecularly analyzed. Results We observed an absence of expression of the canonic ICs, namely PDCD1 (PD-1), CD274 (PD-L1), and CTLA4, as well as CD80, CD86, BTLA, IDO1, CD48, TNFSF14, CD160, CEACAM1, and CD244. PD-L1 protein expression was also practically absent. We found higher mRNA levels of CD24, CD47, CD276 (B7-H3), and PVR, and lower mRNA levels of HAVCR2, LAG3, and TIGIT genes, with significant differences across the four molecular subgroups. Compared to the non-tumor tissues, the expression levels of CD276 in all subgroups and CD24 in SHH, Group 3, and Group 4 subgroups are significantly higher. The in silico analysis confirmed the expression profile found in the Brazilian cohort, including the lower/absent expression of the canonic ICs. Moreover, it confirmed the overexpression of CD24 and CD276 in medulloblastomas compared with the non-tumor tissue. Additionally, CD276 and CD24 high levels were associated with worse survival. Conclusion These results highlight the low or absence of mRNA levels of the canonic targetable ICs in medulloblastomas. Importantly, the analysis revealed overexpression of CD24 and CD276, which can constitute prognostic biomarkers and attractive immunotherapy targets for medulloblastomas.
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Affiliation(s)
- Rui Ferreira Marques
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's -PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | | | - Luciane da Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Leticia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Faculty of Health Sciences of Barretos Dr. Paulo Prata (FACISB), School of Medicine, Barretos, Brazil
| | | | - Iara Santana
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Gustavo Teixeira
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Fabiano Saggioro
- Department of Pathology and Forensic Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luciano Neder
- Department of Pathology and Forensic Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Bruna Mançano
- Barretos Children's Cancer Hospital, Barretos, Brazil
| | - Rui Manuel Reis
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's -PT Government Associate Laboratory, Braga, Guimarães, Portugal.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Laboratory of Molecular Diagnostic, Barretos Cancer Hospital, Barretos, Brazil
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Moreno DA, da Silva LS, Gomes I, Leal LF, Berardinelli GN, Gonçalves GM, Pereira CA, Santana IVV, Matsushita MDM, Bhat K, Lawler S, Reis RM. Cancer immune profiling unveils biomarkers, immunological pathways, and cell type score associated with glioblastoma patients' survival. Ther Adv Med Oncol 2022; 14:17588359221127678. [PMID: 36579028 PMCID: PMC9791289 DOI: 10.1177/17588359221127678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/02/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction Glioblastoma (GBM), isocitrate dehydrogenase (IDH) wild-type (IDH wt), and grade 4 astrocytomas, IDH mutant (IDH mut), are the most common and aggressive primary malignant brain tumors in adults. A better understanding of the tumor immune microenvironment may provide new biomarkers and therapeutic opportunities. Objectives We aimed to evaluate the expression profile of 730 immuno-oncology-related genes in patients with IDH wt GBM and IDH mut tumors and identify prognostic biomarkers and a gene signature associated with patient survival. Methods RNA was isolated from formalin-fixed, paraffin-embedded sections of 99 tumor specimens from patients treated with standard therapy. Gene expression profile was assessed using the Pan-Cancer Immune Profiling Panel (Nanostring Technologies, Inc., Seattle, WA, USA). Data analysis was performed using nSolverSoftware and validated in The Cancer Genome Atlas. In addition, we developed a prognostic signature using the cox regression algorithm (Least Absolute Shrinkage and Selection Operator). Results We found 88 upregulated genes, high immunological functions, and a high macrophage score in IDH wt GBM compared to IDH mut tumors. Regarding IDH wt GBM, we found 24 upregulated genes in short-term survivors (STS) and overexpression of CD274 (programmed death-ligand 1, PD-L1). Immune pathways, CD45, cytotoxic, and macrophage scores were upregulated in STS. Two different prognostic groups were found based on the 12-gene signature (CXCL14, PSEN2, TNFRSF13C, IL13RA1, MAP2K1, TNFSF14, THY1, CTSL, ITGAE, CHUK, CD207, and IFITM1). Conclusion The elevated expression of immune-oncology-related genes was associated with worse outcome in IDH wt GBM patients. Increased immune functions, CD45, cytotoxic cells, and macrophage scores were associated with a more aggressive phenotype and may provide promising possibilities for therapy. Moreover, a 12 gene-based signature could predict patients' prognosis.
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Affiliation(s)
| | | | - Isabella Gomes
- Molecular Oncology Research Center, Barretos, São Paulo, Brazil
| | | | | | | | | | | | | | - Krishna Bhat
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sean Lawler
- Harvard Medical School, Boston, MA, USA Brown University, Pathology and Laboratory Medicine, Providence, Rhode Island, USA
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Marques AC, Ferraro-Peyret C, Michaud F, Song L, Smith E, Fabre G, Willig A, Wong MML, Xing X, Chong C, Brayer M, Fenouil T, Hervieu V, Bancel B, Devouassoux M, Balme B, Meyronet D, Menu P, Lopez J, Xu Z. Improved NGS-based detection of microsatellite instability using tumor-only data. Front Oncol 2022; 12:969238. [PMID: 36465367 PMCID: PMC9714634 DOI: 10.3389/fonc.2022.969238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/18/2022] [Indexed: 01/09/2024] Open
Abstract
Microsatellite instability (MSI) is a molecular signature of mismatch repair deficiency (dMMR), a predictive marker of immune checkpoint inhibitor therapy response. Despite its recognized pan-cancer value, most methods only support detection of this signature in colorectal cancer. In addition to the tissue-specific differences that impact the sensitivity of MSI detection in other tissues, the performance of most methods is also affected by patient ethnicity, tumor content, and other sample-specific properties. These limitations are particularly important when only tumor samples are available and restrict the performance and adoption of MSI testing. Here we introduce MSIdetect, a novel solution for NGS-based MSI detection. MSIdetect models the impact of indel burden and tumor content on read coverage at a set of homopolymer regions that we found are minimally impacted by sample-specific factors. We validated MSIdetect in 139 Formalin-Fixed Paraffin-Embedded (FFPE) clinical samples from colorectal and endometrial cancer as well as other more challenging tumor types, such as glioma or sebaceous adenoma or carcinoma. Based on analysis of these samples, MSIdetect displays 100% specificity and 96.3% sensitivity. Limit of detection analysis supports that MSIdetect is sensitive even in samples with relatively low tumor content and limited microsatellite instability. Finally, the results obtained using MSIdetect in tumor-only data correlate well (R=0.988) with what is obtained using tumor-normal matched pairs, demonstrating that the solution addresses the challenges posed by MSI detection from tumor-only data. The accuracy of MSI detection by MSIdetect in different cancer types coupled with the flexibility afforded by NGS-based testing will support the adoption of MSI testing in the clinical setting and increase the number of patients identified that are likely to benefit from immune checkpoint inhibitor therapy.
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Affiliation(s)
| | - Carole Ferraro-Peyret
- Cancer Research Centre of Lyon, INSERM 1052, Centre National de la Recherche Scientifique (CNRS) 5286, University of Lyon, Lyon, France
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | | | - Lin Song
- SOPHiA GENETICS, Saint-Sulpice, Switzerland
| | - Ewan Smith
- SOPHiA GENETICS, Saint-Sulpice, Switzerland
| | | | | | | | | | | | | | - Tanguy Fenouil
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | - Valérie Hervieu
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | - Brigitte Bancel
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | - Mojgan Devouassoux
- Hospices Civils de Lyon, Department of Anatomopathology, Lyon-Sud Hospital, Lyon, France
| | - Brigitte Balme
- Hospices Civils de Lyon, Department of Anatomopathology, Lyon-Sud Hospital, Lyon, France
| | - David Meyronet
- Hospices Civils de Lyon, Biopathology of Tumours, GH Est (GHE) Hospital, Bron, France
| | | | - Jonathan Lopez
- Cancer Research Centre of Lyon, INSERM 1052, Centre National de la Recherche Scientifique (CNRS) 5286, University of Lyon, Lyon, France
- Hospices Civils de Lyon, Biochemistry and Molecular Biology Department, Lyon-Sud Hospital, Lyon, France
| | - Zhenyu Xu
- SOPHiA GENETICS, Saint-Sulpice, Switzerland
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10
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Cavalcante LN, Porto J, Mazo D, Longatto-Filho A, Stefano JT, Lyra AC, Carrilho FJ, Reis RM, Alves VAF, Sanyal AJ, Oliveira CP. African genetic ancestry is associated with lower frequency of PNPLA3 G allele in non-alcoholic fatty liver in an admixed population. Ann Hepatol 2022; 27:100728. [PMID: 35710086 DOI: 10.1016/j.aohep.2022.100728] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/06/2022] [Accepted: 05/19/2022] [Indexed: 02/04/2023]
Abstract
INTRODUCTION AND OBJECTIVES PNPLA3 (rs738409) and TM6SF2 (rs58542926) variants, interindividual and ethnic differences may be risk factors for non-alcoholic fatty liver disease (NAFLD). The PNPLA3 G allele is associated with worse NAFLD evolution in Hispanics and Caucasians. TM6SF2 is associated with hypertriglyceridemia, NAFLD, and cardiovascular disease. We aimed to evaluate the association between genetic ancestry by Ancestry Informative Markers (AIM), PNPLA3 and TM6SF2 polymorphisms in patients with biopsy-proven NAFLD in an admixed population. METHODS We included adults with biopsy-proven NAFLD and excluded patients with the presence of other chronic liver disease, alcohol intake >100g/week, HIV, drug-induced fatty liver disease, or liver transplantation. We classified NAFLD using the Non-Alcoholic Steatohepatitis Clinical Research Network (NASH-CRN) histological scoring system. The PNPLA3 (rs738409 c.444C>G) and TM6SF2 (rs58542926 c.449C>T) genotyping were performed by RT-PCR. Genetic ancestry was determined using 46 insertion-deletion AIM; α<0.05 was considered significant. RESULTS A total of 248 patients with NAFLD were enrolled [34 with simple steatosis (NAFL); 214 with NASH]. Overall, we detected a greater European ancestry contribution (0.645), followed by African (0.173), Amerindian (0.095), and East Asian (0.087) ancestry contribution, without differences between NAFL and NASH patients. However, we found a higher African genetic ancestry contribution among patients with NAFL who had the PNPLA3 C/C genotype than those with the G allele (0.216 ± 0.205 versus 0.105 ± 0.101, respectively; p=0.047). Ancestry contributions did not differ among TM6SF2 genotypes. CONCLUSION Among NAFL patients, greater African genetic ancestry was associated to a lower frequency of the PNPLA3 G allele, demonstrating a possible NASH ancestry-related protective factor.
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Affiliation(s)
| | - Jun Porto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos-SP, Brazil
| | - Daniel Mazo
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Adhemar Longatto-Filho
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Department of Pathology (LIM-14), Faculty of Medicine, University of São Paulo, Brazil; Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - José Tadeu Stefano
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Andre Castro Lyra
- Federal University of Bahia, School of Medicine, Gastroenterology and Hepatology Services & Salvador-BA, Brazil
| | - Flair Jose Carrilho
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil; Department of Pathology (LIM-14), Faculty of Medicine, University of São Paulo, Brazil; Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
| | - Venâncio A F Alves
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Department of Pathology (LIM-14), Faculty of Medicine, University of São Paulo, Brazil
| | - Arun J Sanyal
- Institute of Liver Disease and Metabolic Health; Interim Chair, Div. of Gastroenterology; Virginia Commonwealth University, USA
| | - Claudia P Oliveira
- University of Sao Paulo, School of Medicine, Sao Paulo-SP, Brazil; Laboratory of Clinical and Experimental Gastroenterology (LIM-07), Division of Clinical Gastroenterology and Hepatology, Department of Gastroenterology, Faculty of Medicine, University of São Paulo, São Paulo, SP, Brazil
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11
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Fanaei K, Salahshourifar I, Ameli F, Esfandbod M, Irani S. High Frequency of Microsatellite Instability among Non-Metastatic Gastric Cancer. Int J Hematol Oncol Stem Cell Res 2022; 16:239-249. [PMID: 36883110 PMCID: PMC9985814 DOI: 10.18502/ijhoscr.v16i4.10882] [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: 06/05/2021] [Accepted: 09/12/2021] [Indexed: 11/05/2022] Open
Abstract
Background: Microsatellite instability (MSI) is considered a key factor in carcinogenesis and a genetic alteration pattern in many types of cancers such as gastric cancer (GC). Although the role of MSI in colorectal cancer (CRC) is well known, its prognostic impact on GC has not been clearly defined. The assessment of MSI in GC has not been documented in the Iranian population yet. Therefore, this study analyzed the association of MSI status with GC in Iranian patients. Materials and Methods: We compared the frequency of MSI at 5 loci from formalin-fixed paraffin-embedded (FFPE) gastrectomy specimens, between metastatic and non-metastatic cases of GC (N = 60). A panel of five quasi-monomorphic markers and a single dinucleotide marker with linker-based fluorescent primers was used. Results: MSI was observed in 46.6% of cases, including MSI-high (H) (33.3%) and MSI-Low (L) (13.3%). Moreover, the most unstable and stable markers in our study were NR-21 and BAT-26 accordingly. MSI-H and MSI were seen more frequently in non-metastatic tumors (p= 0.028 and p= 0.019, respectively). Conclusion: The current study showed MSI status more frequently in non-metastatic GC which may reflect a good prognostic factor in GC like CRC. Although, larger and more comprehensive studies are needed to confirm this statement. A panel consisting of NR-21, BAT-25, and NR-27 mononucleotide markers appears to be reliable and useful markers for detecting MSI in GC in Iranian patients.
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Affiliation(s)
- Khadijeh Fanaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Iman Salahshourifar
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fereshteh Ameli
- Department of Pathology, Cancer Institute, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohsen Esfandbod
- Department of Hematology and Oncology, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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12
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Microsatellite Instability: From the Implementation of the Detection to a Prognostic and Predictive Role in Cancers. Int J Mol Sci 2022; 23:ijms23158726. [PMID: 35955855 PMCID: PMC9369169 DOI: 10.3390/ijms23158726] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/26/2022] [Accepted: 08/03/2022] [Indexed: 02/07/2023] Open
Abstract
Microsatellite instability (MSI) has been identified in several tumors arising from either germline or somatic aberration. The presence of MSI in cancer predicts the sensitivity to immune checkpoint inhibitors (ICIs), particularly PD1/PD-L1 inhibitors. To date, the predictive role of MSI is currently used in the selection of colorectal cancer patients for immunotherapy; moreover, the expansion of clinical trials into other cancer types may elucidate the predictive value of MSI for non-colorectal tumors. In clinical practice, several assays are used for MSI testing, including immunohistochemistry (IHC), polymerase chain reaction (PCR) and next-generation sequencing (NGS). In this review, we provide an overview of MSI in various cancer types, highlighting its potential predictive/prognostic role and the clinical trials performed. Finally, we focus on the comparison data between the different assays used to detect MSI in clinical practice.
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13
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Association of microsatellite instability (MSI) status with the 5-year outcome and genetic ancestry in a large Brazilian cohort of colorectal cancer. Eur J Hum Genet 2022; 30:824-832. [PMID: 35474354 PMCID: PMC9259739 DOI: 10.1038/s41431-022-01104-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/04/2022] [Accepted: 04/12/2022] [Indexed: 12/22/2022] Open
Abstract
Colorectal cancer (CRC) has a high incidence and mortality worldwide. Microsatellite instability (MSI) is crucial in CRC, with distinct molecular and clinicopathological features in patients. Nowadays, it is a predictive marker for immunotherapy. We proposed to evaluate the 5-year outcome of MSI status in 1002 Brazilian CRC, and associate it with genetic ancestry, molecular and clinicopathological features. MSI evaluation was performed using molecular markers. MSI+ tumors were analyzed for alterations in 23 MSI-targeted genes. Genetic ancestry was evaluated using an Ancestry-Informative markers panel. MSI status was analyzed in relation to CRC specific survival and other clinical and genetic variables. MSI+ status was observed in 10.5% of cases. MSI+ status was significantly associated with the anatomic site right colon, mucinous histological type, clinical stage II, histological grade III/undifferentiated, no recurrence of disease, and live cases without cancer. No association of MSI status with genetic ancestry components was observed. MSI-targeted genes analyses showed the most frequently altered genes: ATM, EGFR, MRE11, ROCK1, and TGFBRII. There was a statistically significant difference in cancer-specific survival between cases according to MSI status. This study constitutes the most comprehensive analyses of the MSI impact on the Brazilian CRC. MSI+ frequency in Brazilian CRC agreed with the literature and was associated with several clinicopathological features related with less aggressive tumors, independently of their genetic ancestry.
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14
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Koizumi Y, Ahmad S, Ikeda M, Yashima-Abo A, Espina G, Sugimoto R, Sugai T, Iwaya T, Tamura G, Koeda K, Liotta LA, Takahashi F, Nishizuka SS. Helicobacter pylori modulated host immunity in gastric cancer patients with S-1 adjuvant chemotherapy. J Natl Cancer Inst 2022; 114:1149-1158. [PMID: 35437596 PMCID: PMC9360472 DOI: 10.1093/jnci/djac085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/13/2021] [Accepted: 04/11/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Paradoxically, Helicobacter pylori-positive (HP+) advanced gastric cancer patients have a better prognosis than those who are HP-negative (HP-). Immunologic and statistical analyses can be used to verify whether systemic mechanisms modulated by HP are involved in this more favorable outcome. METHODS A total of 658 advanced gastric cancer patients who underwent gastrectomy were enrolled. HP infection, mismatch repair, programmed death-ligand 1 (PD-L1), and CD4/CD8 proteins, and microsatellite instability were analyzed. Overall survival (OS) and relapse free survival (RFS) rates were analyzed after stratifying clinicopathological factors. Cox proportional hazards regression analysis was performed to identify independent prognostic factors. RESULTS Among 491 cases that were analyzed, 175 (36%) and 316 (64%) cases were HP+ and HP⁻, respectively. Analysis of RFS indicated an interaction of HP status among the subgroups for S-1 dose (Pinteraction=0.0487) and PD-L1 (P = .016). HP+ patients in the PD-L1⁻ group had significantly higher five-year OS and RFS than HP- patients (81% vs. 68%; P = .0011; HR 0.477; 95% CI, 0.303-0.751 and 76% vs. 63% P = .0011; HR 0.508; 95% CI, 0.335-0.771, respectively). The five-year OS and RFS was also significantly higher for HP+ compared to HP- patients in the PD-L1-/S-1-reduced group (86% vs. 46%; P = .0014; HR 0.205; 95% CI, 0.07-0.602 and 83% vs. 34%; P = .001; HR 0.190; 95% CI, 0.072-0.498, respectively). Thus, HP status was identified as one of the most potentially important independent factors to predict prolonged survival. CONCLUSION This retrospective study suggests that an HP-modulated host immune system may contribute to prolonged survival in the absence of immune escape mechanisms of gastric cancer.
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Affiliation(s)
- Yuka Koizumi
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Sheny Ahmad
- Aspirating Scientists Summer Internship Program, George Mason University, Manassas, VA USA.,Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Miyuki Ikeda
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Akiko Yashima-Abo
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
| | - Ginny Espina
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Ryo Sugimoto
- Department of Molecular Diagnostic Pathology, Iwate Medical University School of Medicine,Yahaba, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, Iwate Medical University School of Medicine,Yahaba, Japan
| | - Takeshi Iwaya
- Molecular Therapeutics Laboratory, Department of Surgery, Iwate Medical University School of Medicine
| | - Gen Tamura
- Department of Laboratory Medicine, Yamagata Prefectural Central Hospital, Yamagata, Japan
| | - Keisuke Koeda
- Department of Medical Safety Science, Iwate Medical University School of Medicine,Yahaba, Japan
| | - Lance A Liotta
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA USA
| | - Fumiaki Takahashi
- Division of Medical Engineering, Department of Information Science, Iwate Medical University, Yahaba, Japan
| | - Satoshi S Nishizuka
- Division of Biomedical Research and Development, Iwate Medical University Institute for Biomedical Sciences, Yahaba, Japan
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15
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Fanale D, Corsini LR, Scalia R, Brando C, Cucinella A, Madonia G, Dimino A, Filorizzo C, Barraco N, Bono M, Fiorino A, Magrin L, Sciacchitano R, Perez A, Russo TDB, Pantuso G, Russo A, Bazan V. Can the tumor-agnostic evaluation of MSI/MMR status be the common denominator for the immunotherapy treatment of patients with several solid tumors? Crit Rev Oncol Hematol 2022; 170:103597. [PMID: 35033663 DOI: 10.1016/j.critrevonc.2022.103597] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/24/2022] Open
Abstract
Alterations in short-repetitive DNA sequences, known as microsatellite instability (MSI), can reflect deficiencies in Mismatch Repair (MMR) system which represents a major player in DNA integrity maintenance. The incidence of MSI-H/dMMR has been shown to be variable depending on the tumor type. Several studies confirmed that dMMR/MSI status, although less frequent than PD-L1 expression, may better predict response to immune-checkpoint inhibitors (ICIs) in patients with solid tumors. In October 2016, the FDA granted pembrolizumab as breakthrough therapy for the treatment of non-CRC, MSI-H/dMMR tumors, providing, for the first time, a tumor-agnostic indication. In the next future, the tissue-agnostic evaluation of MSI-H/dMMR could become the common denominator for the immunotherapy treatment of patients with different advanced solid tumors, in order to select patient subgroups which may benefit from this therapy. In this Review we provided an overview of the main clinical studies describing the association between MSI-H/dMMR tumors and immunotherapy response.
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Affiliation(s)
- Daniele Fanale
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Lidia Rita Corsini
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Raimondo Scalia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Chiara Brando
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Alessandra Cucinella
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Giorgio Madonia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Alessandra Dimino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Clarissa Filorizzo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Marco Bono
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Alessia Fiorino
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Luigi Magrin
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Roberta Sciacchitano
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Alessandro Perez
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Tancredi Didier Bazan Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Gianni Pantuso
- Unit of Oncological Surgery, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127, Palermo, Italy.
| | - Viviana Bazan
- Department of Biomedicine, Neuroscience and Advanced Diagnostics, University of Palermo, 90127, Palermo, Italy
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16
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De Marchi P, Berardinelli GN, Cavagna RDO, Pinto IA, da Silva FAF, Duval da Silva V, Santana IVV, da Silva ECA, Ferro Leal L, Reis RM. Microsatellite Instability Is Rare in the Admixed Brazilian Population of Non-Small Cell Lung Cancer: A Cohort of 526 Cases. Pathobiology 2021; 89:101-106. [PMID: 34781284 DOI: 10.1159/000520023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/30/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Microsatellite instability (MSI) in non-small cell lung cancer (NSCLC) is uncommon; however, most studies refer to European and Asian populations. There are currently no data on MSI frequency in highly admixed populations, such as the one represented by Brazilian NSCLC patients. AIM This study aimed to evaluate the frequency of MSI in Brazilian NSCLC patients. METHODS We evaluated 526 patients diagnosed with NSCLC at the Barretos Cancer Hospital (Brazil). The molecular MSI evaluation was performed using a hexa-plex marker panel by polymerase chain reaction followed by fragment analysis. The mutation profile of MSI-positive cases was performed using next-generation sequencing. RESULTS Only 1 patient was MSI positive (0.19%). This patient was a female, white, and active smoker, and she was diagnosed with clinical stage IV lung adenocarcinoma at 75 years old. The molecular profile exhibited 4 Tumor Protein p53 (TP53) mutations and the absence of actionable mutations in the Epidermal Growth Factor Receptor (EGFR), Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS), or V-Raf Murine Sarcoma Viral Oncogene Homolog B1 (BRAF) genes. CONCLUSIONS The frequency of MSI in Brazilian NSCLC patients is equally rare, a finding that is consistent with the current literature based on other populations such as Europeans, North Americans, and Asians.
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Affiliation(s)
- Pedro De Marchi
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil.,Oncoclinicas, Rio de Janeiro, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Icaro Alves Pinto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Vinicius Duval da Silva
- Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Leticia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Laboratory of Molecular Diagnoses, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
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17
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Kang SY, Kim KM. Highly sensitive duplex MSI test and BAT40 germline polymorphism. APMIS 2021; 129:607-615. [PMID: 34342050 DOI: 10.1111/apm.13170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/16/2021] [Indexed: 12/01/2022]
Abstract
Tumors exhibiting DNA mismatch repair (MMR) deficiency and microsatellite instability (MSI) are responsive to immune checkpoint blockade. MSI is frequently diagnosed using five quasimonomorphic mononucleotide (pentaplex) markers; however, the assays have several technical limitations, including the lack of sensitivity of some of the markers. Although markers with increased sensitivity, such as CAT25 and BAT40, have been introduced, the majority of multiplex MSI tests have only been studied in Western populations and require further evaluation in an Asian cohort. This study tested the efficacy of BAT26, CAT25, and BAT40 mononucleotide MSI markers via triplex PCR on 300 samples from patients with advanced cancers from a Korean clinical population. The results were directly compared with those of a pentaplex MSI test and tumor mutation burden (TMB) status, and an additional 60 MSI-H cancers were used for further validation. Four (1.3%) out of 300 advanced tumors were MSI-high (MSI-H). In the pentaplex PCR assay, two colorectal cancers (0.7%) exhibited instability only with the BAT25 mononucleotide marker and were interpreted as MSI-low (MSI-L). In the triplex PCR assay, BAT40 was unstable in 64 cases (21%) and the results did not overlap with those of MSI-L from pentaplex. Given the high frequency of isolated BAT40 instability, we performed the same triplex PCR with DNA obtained from normal controls and found BAT40 polymorphisms in 37 cases (90%). Interestingly, the median TMB of the cases with BAT40 polymorphism was significantly higher (7.0 mt/Mb) than that of BAT40 wild-type cases (5.5 mt/Mb) (p = 0.003). The triplex PCR results from 60 additional MSI-H cancers correlated perfectly (100%) with those of pentaplex PCR, and the results were consistent for two (BAT26 and CAT25) markers. BAT40 germline polymorphism is common in the Korean population and is associated with higher TMB values. The simple duplex (BAT26 and CAT25) MSI test provided the same sensitivity and specificity as pentaplex PCR tests.
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Affiliation(s)
- So Young Kang
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine
| | - Kyoung-Mee Kim
- Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine.,Center of Companion Diagnostics, Samsung Medical Center, Seoul, Korea
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18
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Sychevskaya KA, Risinskaya NV, Kravchenko SK, Nikulina EE, Misyurina AE, Magomedova AU, Sudarikov AB. Pitfalls in mononucleotide microsatellite repeats instability assessing (MSI) in the patients with B-cell lymphomas. Klin Lab Diagn 2021; 66:181-186. [PMID: 33793119 DOI: 10.51620/0869-2084-2021-66-3-181-186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Analysis of microsatellite instability (MSI) is a routine study in the diagnostics of solid malignancies. The standard for determining MSI is a pentaplex PCR panel of mononucleotide repeats: NR-21, NR-24, NR-27, BAT-25, BAT-26. The presence of MSI is established based on differences in the length of markers in the tumor tissue and in the control, but due to the quasimonomorphic nature of standard mononucleotide loci the use of a control sample is not necessary in the diagnosis of MSI-positive solid tumors. The significance of the MSI phenomenon in oncohematology has not been established. This paper presents the results of a study of MSI in B-cell lymphomas: follicular lymphoma (FL), diffuse large B-cell lymphoma (DLBCL), high-grade B-cell lymphoma (HGBL). We have shown that aberrations of mononucleotide markers occur in these diseases, but the nature of the changes does not correspond to the classical MSI in solid neoplasms. This fact requires further study of the pathogenesis of such genetic disorders. Due to the possibility of ambiguous interpretation of the results of the MSI study for previously uncharacterized diseases, strict compliance with the methodology of parallel analysis of the tumor tissue and the control sample is mandatory.
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19
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de Paula AE, Galvão HDCR, Bonatelli M, Sabato C, Fernandes GC, Berardinelli GN, Andrade CEM, Neto MC, Romagnolo LGC, Campacci N, Scapulatempo-Neto C, Reis RM, Palmero EI. Clinicopathological and molecular characterization of Brazilian families at risk for Lynch syndrome. Cancer Genet 2021; 254-255:82-91. [PMID: 33647816 DOI: 10.1016/j.cancergen.2021.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/14/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022]
Abstract
Lynch syndrome (LS), is the most common hereditary colorectal cancer syndrome. However, it is poorly characterized in Brazil. Therefore, we aimed to determine the spectrum of pathogenic variants in Mismatch Repair (MMR) genes and investigate the MLH1 promotor methylation role as a second hit in LS tumors. Tumor screening through microsatellite instability and immunohistochemistry for MMR proteins was performed in 323 cases who met clinical criteria. BRAF-V600E and MLH1 promoter methylation were analyzed for all MLH1-deficient tumors. Patients with MMR deficient tumor proceeded to germline genetic testing. MMR deficient tumors were detected in 41% of patients recruited. About half of patients carried a pathogenic germline variant. Two recurrent variants in MLH1 and three novel pathogenic variants were identified. Furthermore, pathogenic germline variants with concomitant somatic MLH1 hypermethylation were found in 6% of cases. Predictive genetic testing was offered to 387 relatives. Overall, 127 tumors were diagnosed in 100 LS patients, from 62 unrelated families. Our molecular data provide new information about the spectrum of MMR mutations, which contributes to a better characterization of LS in Brazil. Furthermore, we call attention to the possibility of failure in the diagnosis of germline MLH1 mutation carriers when somatic MLH1 hypermethylation is used to rule out LS.
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Affiliation(s)
| | | | - Murilo Bonatelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristina Sabato
- Molecular Diagnosis Laboratory, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | | | | | | | | | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Rui Manuel Reis
- Molecular Diagnosis Laboratory, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inêz Palmero
- Molecular Diagnosis Laboratory, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil; Pele Pequeno Principe Research Institute, Curitiba, Brazil; Faculdades Pequeno Principe, Curitiba, Brazil.
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20
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Yang G, Zheng RY, Tan Q, Dong CJ, Jin ZS. Clinical characteristics and responses to chemotherapy and immune checkpoint inhibitor treatment for microsatellite instability gastric cancer. Am J Cancer Res 2020; 10:4123-4133. [PMID: 33414990 PMCID: PMC7783766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/22/2020] [Indexed: 06/12/2023] Open
Abstract
During the process of DNA replication, insertions or deletions of repeat sequences easily occur in microsatellites due to DNA polymerase slippage in instances of defective mismatch repair; this phenomenon is known as microsatellite instability. Based on genetic profiling, microsatellite instability gastric cancer is regarded as a separate subtype of gastric cancer that is associated with old age, the female sex, a distal gastric location, and a lower number of lymph node metastases. According to numerous retrospective studies, microsatellite instability is a favourable predictive marker for prognosis. However, during the perioperative period, gastric cancer patients with microsatellite instability after chemotherapy often exhibit a poor and unfavourable prognosis. This result still remains controversial. The efficacy of adjuvant chemotherapy in microsatellite instability-high tumours ranges from detrimental to beneficial effects. Due to the widespread expression of immune checkpoint molecules (such as programmed death-1 and programmed death-ligand 1) in tumours with microsatellite instability, immune checkpoint inhibitors have been utilized to treat microsatellite instability gastric cancer and tremendously improve the efficacy of treatment and survival of microsatellite instability patients. In this review, we attempt to outline the definitions of microsatellites and microsatellite instability, the methods used to screen for microsatellite instability, the clinical characteristics of microsatellite instability gastric cancer, and its responses to chemotherapy and immune checkpoint inhibitor treatment. Overall, determining the status of microsatellites is essential before developing a tailored treatment strategy for patients with microsatellite instability gastric cancer.
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Affiliation(s)
- Guang Yang
- Department of Pathology, Mudanjiang Medical UniversityMudanjiang, Heilongjiang, China
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical SciencesOkayama, Japan
| | - Ru-Yi Zheng
- Medical Imaging Center, The Mine Hospital of Xu ZhouXuzhou, Jiangsu, China
| | - Qiang Tan
- Department of Oncology, Affiliated Hospital of Xiangnan UniversityChenzhou, Hunan, China
| | - Cheng-Ji Dong
- Department of Hepatobiliary and Pancreas Surgery, The First Hospital of Jilin UniversityChangchun, China
| | - Zai-Shun Jin
- Department of Pathology, Mudanjiang Medical UniversityMudanjiang, Heilongjiang, China
- Department of Pathology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical SciencesOkayama, Japan
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21
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de Carvalho AC, Perdomo S, Dos Santos W, Fernandes GC, de Jesus LM, Carvalho RS, Scapulatempo-Neto C, de Almeida GC, Sorroche BP, Arantes LMRB, Melendez ME, De Marchi P, Hayes N, Reis RM, Carvalho AL. Impact of genetic variants in clinical outcome of a cohort of patients with oropharyngeal squamous cell carcinoma. Sci Rep 2020; 10:9970. [PMID: 32561788 PMCID: PMC7305218 DOI: 10.1038/s41598-020-66741-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Tobacco- or human papillomavirus- driven oropharyngeal squamous cell carcinomas (OpSCC) represent distinct clinical, biological and epidemiological entities. The aim of this study was to identify genetic variants based on somatic alterations in OpSCC samples from an admixed population, and to test for association with clinical features. The entire coding region of 15 OpSCC driver genes was sequenced by next-generation sequencing in 51 OpSCC FFPE samples. Thirty-five percent of the patients (18/51) were HPV-positive and current or past tobacco consumption was reported in 86.3% (44/51). The mutation profile identified an average of 2.67 variants per sample. Sixty-three percent of patients (32/51; 62.7%) were mutated for at least one of the genes tested and TP53 was the most frequently mutated gene. The presence of mutation in NOTCH1 and PTEN, significantly decreased patient's recurrence-free survival, but only NOTCH1 mutation remained significant after stepwise selection, with a risk of recurrence of 4.5 (HR 95% CI = 1.11-14.57; Cox Regression p = 0.034). These results show that Brazilian OpSCC patients exhibit a similar clinical and genetic profile in comparison to other populations. Molecular characterization is a promising tool for the definition of clinical subgroups, aiding in a more precise tailoring of treatment and prognostication.
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Affiliation(s)
| | - Sandra Perdomo
- Institute of Nutrition, Genetics and Metabolism Research, Faculty of Medicine, Universidad El Bosque, Bogotá, Colombia
- International Agency of Research on Cancer, Lyon, France
| | | | | | | | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
- Pathology and Molecular Diagnostics Service, Diagnósticos da América-DASA, São Paulo, SP, Brazil
| | | | | | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
- Pelé Little Prince Research Institute, Curitiba, PR, Brazil
- Little Prince College, Curitiba, PR, Brazil
| | - Pedro De Marchi
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, SP, Brazil
- Oncoclinicas, Rio de Janeiro, RJ, Brazil
| | - Neil Hayes
- Department of Medicine, Division of Oncology, UTHSC Center for Cancer Research, University of Tennessee Health Science Center, Memphis, USA
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.
- International Agency of Research on Cancer, Lyon, France.
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22
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Vicente ALSA, Crovador CS, Macedo G, Scapulatempo-Neto C, Reis RM, Vazquez VL. Mutational Profile of Driver Genes in Brazilian Melanomas. J Glob Oncol 2020; 5:1-14. [PMID: 31756131 PMCID: PMC6882511 DOI: 10.1200/jgo.19.00169] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
PURPOSE Mutation testing of the key genes involved in melanoma oncogenesis is now mandatory for the application of targeted therapeutics. However, knowledge of the mutational profile of melanoma remains largely unknown in Brazil. PATIENTS AND METHODS In this study, we assessed the mutation status of melanoma driver genes BRAF, NRAS, TERT, KIT, and PDGFRA in a cohort of 459 patients attended at Barretos Cancer Hospital between 2001 and 2012. We used polymerase chain reaction followed by Sanger sequencing to analyze the hot spot mutations of BRAF exon 15 (V600E), NRAS (codons 12/13 and 61), TERT (promoter region), KIT (exons 9, 11, 13, and 17), and PDGFRA (exons 12, 14, and 18) in tumors. The mutational profile was investigated for associations with demographic, histopathologic, and clinical features of the disease. RESULTS The nodular subtype was most frequent (38.9%) followed by the superficial spreading subtype (34.4%). The most frequent tumor location was in the limbs (50.0%). The mutation rates were 34.3% for TERT and 34.1% for BRAF followed by NRAS (7.9%), KIT (6.2%), and PDGFRA (2.9%). The BRAF (P = .014) and TERT (P = .006) mutations were associated with younger patients and with different anatomic locations, particularly in the trunk, for the superficial spreading and nodular subtypes, respectively (P = .0001 for both). PDGFRA mutations were associated with black skin color (P = .023) and TERT promoter mutations with an absence of ulceration (P = .037) and lower levels of lactate dehydrogenase. There was no association between patient survival rates and mutational status. CONCLUSION The similar mutational profile we observe in melanomas in Brazil compared with other populations will help to guide precision medicine in this country.
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Affiliation(s)
| | | | | | | | - Rui M Reis
- Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga and Guimarães, Portugal
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23
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Bai H, Wang R, Cheng W, Shen Y, Li H, Xia W, Ding Z, Zhang Y. Evaluation of Concordance Between Deficient Mismatch Repair and Microsatellite Instability Testing and Their Association with Clinicopathological Features in Colorectal Cancer. Cancer Manag Res 2020; 12:2863-2873. [PMID: 32425600 PMCID: PMC7187941 DOI: 10.2147/cmar.s248069] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Accepted: 04/08/2020] [Indexed: 12/20/2022] Open
Abstract
Background Microsatellite instability (MSI) is one of the most important molecular characteristics of colorectal cancer (CRC), which mainly results from defective DNA mismatch repair (MMR). This study was performed to investigate the concordance between deficient MMR and MSI testing, and to evaluate the association of these two results with clinicopathological characteristics in Chinese CRC patients. Methods A total of 738 CRC patients were included. Tumor tissues and paired peripheral blood specimens were obtained. Screening for MMR was investigated using immunohistochemical (IHC) technique, and multiple polymerase chain reaction-capillary electrophoresis (PCR-CE) method was performed to detect the MSI status. All clinicopathological data, immunohistochemistry and microsatellite instability analyses were then statistically analyzed. Results Of the 738 (17.75%) CRC patients, 131 expressed as deficient mismatch repair (dMMR) status, and postmeiotic segregation increased 2 (PMS2) deficiency was the most frequent deficiency among these four MMR proteins. MSI-high (MSI-H) status occurred in 74 of the 738 (10.03%) CRC patients, 55 of whom showed instability at all six mononucleotides repeat markers. dMMR was significantly associated with MSI-H and moderate concordance was observed between IHC and PCR-CE in evaluating deficient MMR/MSI through Kappa test. Statistically, dMMR was significantly associated with younger age, right-sided colon and poor differentiation. MSI-H was associated with younger age, right-sided colon, poor differentiation, mucinous type and tumor, node, metastasis (TNM) stage II. Conclusion A moderate concordance between deficient MMR and MSI testing indicates that both IHC and PCR-CE methods should be routinely tested to provide reliable data for clinical treatment decisions.
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Affiliation(s)
- Huili Bai
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Rong Wang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China.,Department of Laboratory Medicine, Guangyuan Central Hospital, Guangyuan, Sichuan, People's Republic of China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Yifan Shen
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Haijun Li
- Department of Laboratory Medicine, Guangyuan Central Hospital, Guangyuan, Sichuan, People's Republic of China
| | - Wei Xia
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
| | - Zhenglin Ding
- Department of Laboratory Medicine, The People's Hospital of Nanchuan, Chongqing, People's Republic of China
| | - Yuhong Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing, People's Republic of China
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24
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Durães RO, Berardinelli GN, da Costa AM, Scapulatempo-Neto C, Pereira R, Oliveira MA, Guimarães DP, Reis RM. Role of Genetic Ancestry in 1,002 Brazilian Colorectal Cancer Patients From Barretos Cancer Hospital. Front Oncol 2020; 10:145. [PMID: 32195168 PMCID: PMC7065467 DOI: 10.3389/fonc.2020.00145] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/27/2020] [Indexed: 12/24/2022] Open
Abstract
Background: Colorectal cancer (CRC) is the third most frequent and the second deadliest cancer worldwide. The ethnic structure of the population has been gaining prominence as a cancer player. The purpose of this study was to determine the genetic ancestry of Brazilian CRC patients. Moreover, we intended to interrogate its impact on patients' clinicopathological features. Methods: Retrospective observational cohort study with 1,002 patients with CRC admitted from 2000 to 2014 at Barretos Cancer Hospital. Following tumor DNA isolation, genetic ancestry was assessed using a specific panel of 46 ancestry informative markers. Survival rates were obtained by the Kaplan–Meier method, and the log-rank test was used to compare the survival curves. Multivariable Cox proportional regression models were used to estimate hazard ratios (HRs). Results: We observed considerable admixture in the genetic composition, with the following average proportions: European 74.2%, African 12.7%, Asian 6.5%, and Amerindian 6.6%. The multivariate analysis for cancer-specific survival showed that clinical stage, lymphovascular invasion, and the presence of recurrence were associated with an increased relative risk of death from cancer (p < 0.05). High African proportion was associated with younger age at diagnosis, while high Amerindian proportion was associated with the mucinous histological subtype. Conclusions: This represents the larger assessment of genetic ancestry in a population of Brazilian patients with CRC. Brazilian CRC patients exhibited similar clinicopathological features as described in Western countries. Impact: Genetic ancestry components corroborated the significant admixture, and importantly, patients with high African proportion develop cancer at a younger age.
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Affiliation(s)
- Ronilson Oliveira Durães
- Molecular Oncology Research Centre, Barretos Cancer Hospital, Barretos, Brazil.,Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Centre, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Rui Pereira
- IPATIMUP (Institute of Molecular Pathology and Immunology of the University of Porto), Porto, Portugal.,i3S (Instituto de Investigação e Inovação em Saúde, Universidade Do Porto), Porto, Portugal
| | | | - Denise Peixoto Guimarães
- Molecular Oncology Research Centre, Barretos Cancer Hospital, Barretos, Brazil.,Endoscopy Department, Barretos Cancer Hospital, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Centre, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Guimarães, Portugal
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25
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Abstract
Sarcomas represent less than 1% of all solid neoplasms in adults and over 20% in children. Their etiology is unclear, but genetic susceptibility plays an important role in this scenario. Sarcoma is central in Li-Fraumeni Syndrome (LFS), a familial predisposition cancer syndrome. In Brazil, the high prevalence of p.Arg337His mutations in the TP53 gene brings about a unique condition: a cluster of LFS. In the present work, we studied 502 sarcoma patients not selected by age or family history in an attempt to assess the impact of the so-called "Brazilian germline TP53 mutation" (p.Arg337His) on this tumor type. We found that 8% of patients are carriers, with leiomyosarcoma being the main histologic type of sarcoma, corresponding to 52.5% of the patients with the mutated TP53 gene. These findings emphasize the importance of genetic counseling and can better guide the management of sarcoma patients.
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26
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Kwak Y, Seo AN, Lee HE, Lee HS. Tumor immune response and immunotherapy in gastric cancer. J Pathol Transl Med 2019; 54:20-33. [PMID: 31674166 PMCID: PMC6986974 DOI: 10.4132/jptm.2019.10.08] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/08/2019] [Indexed: 02/07/2023] Open
Abstract
Remarkable developments in immuno-oncology have changed the landscape of gastric cancer (GC) treatment. Because immunotherapy intervenes with tumor immune response rather than directly targeting tumor cells, it is important to develop a greater understanding of tumor immunity. This review paper summarizes the tumor immune reaction and immune escape mechanisms while focusing on the role of T cells and their co-inhibitory signals, such as the immune checkpoint molecules programmed death-1 and programmed deathligand 1 (PD-L1). This paper also describes past clinical trials of immunotherapy for patients with GC and details their clinical implications. Strong predictive markers are essential to improve response to immunotherapy. Microsatellite instability, Epstein-Barr virus, PD-L1 expression, and tumor mutational burden are now regarded as potent predictive markers for immunotherapy in patients with GC. Novel immunotherapy and combination therapy targeting new immune checkpoint molecules such as lymphocyte-activation gene 3, T cell immunoglobulin, and mucin domain containing-3, and indoleamine 2,3-dioxygenase have been suggested, and trials are ongoing to evaluate their safety and efficacy. Immunotherapy is an important treatment option for patients with GC and has great potential for improving patient outcome, and further research in immuno-oncology should be carried out.
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Affiliation(s)
- Yoonjin Kwak
- Department of Pathology, Seoul National University Hospital, Seoul, Korea.,Department of Pathology, Seoul National University College of Medicine, Seoul, Korea
| | - An Na Seo
- Department of Pathology, School of Medicine, Kyungpook National University, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Hee Eun Lee
- Division of Anatomic Pathology, Mayo Clinic, Rochester, MN, USA
| | - Hye Seung Lee
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.,Department of Pathology, Seoul National University Bundang Hospital, Seongnam, Korea
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27
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Dos Santos W, Sobanski T, de Carvalho AC, Evangelista AF, Matsushita M, Berardinelli GN, de Oliveira MA, Reis RM, Guimarães DP. Mutation profiling of cancer drivers in Brazilian colorectal cancer. Sci Rep 2019; 9:13687. [PMID: 31548566 PMCID: PMC6757044 DOI: 10.1038/s41598-019-49611-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
The molecular basis of colorectal cancer (CRC) can guide patient prognosis and therapy. In Brazil, knowledge on the CRC mutation landscape is limited. Here, we investigated the mutation profile of 150 cancer-related genes by next-generation sequencing and associated with microsatellite instability (MSI) and genetic ancestry in a series of 91 Brazilian CRC patients. Driver mutations were found in the APC (71.4%), TP53 (56.0%), KRAS (52.7%), PIK3CA (15.4%) and FBXW7 (10.9%) genes. Overall, genes in the MAPK/ERK, PIK3/AKT, NOTCH and receptor tyrosine kinase signaling pathways were mutated in 68.0%, 23.1%, 16.5%, and 15.3% of patients, respectively. MSI was found in 13.3% of tumors, most of which were proximal (52.4%, P< 0.001) and had a high mutation burden. European genetic ancestry was predominant (median of 83.1%), followed by Native American (4.1%), Asian (3.4%) and African (3.2%). NF1 and BRAF mutations were associated with African ancestry, while TP53 and PIK3CA mutations were inversely correlated with Native American ancestry. Our study suggests that Brazilian CRC patients exhibit a mutation profile similar to other populations and identify the most frequently mutated genes, which could be useful in future target therapies and molecular cancer screening strategies.
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Affiliation(s)
| | - Thais Sobanski
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, 4710-057, Portugal.
- 3ICVS/3B's-PT Government Associate Laboratory, Braga, 4710-057, Portugal.
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, Brazil.
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28
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Pabla S, Andreas J, Lenzo FL, Burgher B, Hagen J, Giamo V, Nesline MK, Wang Y, Gardner M, Conroy JM, Papanicolau-Sengos A, Morrison C, Glenn ST. Development and analytical validation of a next-generation sequencing based microsatellite instability (MSI) assay. Oncotarget 2019; 10:5181-5193. [PMID: 31497248 PMCID: PMC6718258 DOI: 10.18632/oncotarget.27142] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 07/29/2019] [Indexed: 12/14/2022] Open
Abstract
Background We have developed and analytically validated a next-generation sequencing (NGS) assay to classify microsatellite instability (MSI) in formalin-fixed paraffin-embedded (FFPE) tumor specimens. Methodology The assay relies on DNA-seq evaluation of insertion/deletion (indel) variability at 29 highly informative genomic loci to estimate MSI status without the requirement for matched-normal tissue. The assay has a clinically relevant five-day turnaround time and can be conducted on as little as 20 ng genomic DNA with a batch size of up to forty samples in a single run. Results The MSI detection method was developed on a training set (n = 94) consisting of 22 MSI-H, 24 MSS, and 47 matched normal samples and tested on an independent test set of 24 MSI-H and 24 MSS specimens. Assay performance with respect to accuracy, reproducibility, precision as well as control sample performance was estimated across a wide range of FFPE samples of multiple histologies to address pre-analytical variability (percent tumor nuclei), and analytical variability (batch size, run, day, operator). Analytical precision studies demonstrated that the assay is highly reproducible and accurate as compared to established gold standard PCR methodology and has been validated through NYS CLEP. Significance This assay provides clinicians with robust and reproducible NGS-based MSI testing without the need of matched normal tissue to inform clinical decision making for patients with solid tumors.
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Affiliation(s)
- Sarabjot Pabla
- OmniSeq Inc., Buffalo, NY 14203, USA.,These authors contributed equally to this work
| | - Jonathan Andreas
- OmniSeq Inc., Buffalo, NY 14203, USA.,These authors contributed equally to this work
| | | | | | | | | | | | | | | | - Jeffrey M Conroy
- OmniSeq Inc., Buffalo, NY 14203, USA.,Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | | | - Carl Morrison
- OmniSeq Inc., Buffalo, NY 14203, USA.,Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
| | - Sean T Glenn
- OmniSeq Inc., Buffalo, NY 14203, USA.,Center for Personalized Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA.,Department of Molecular and Cellular Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USA
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29
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González ML, Causada-Calo N, Santino JP, Dominguez-Valentin M, Ferro FA, Sammartino I, Kalfayan PG, Verzura MA, Piñero TA, Cajal AR, Pavicic W, Vaccaro C. Universal determination of microsatellite instability using BAT26 as a single marker in an Argentine colorectal cancer cohort. Fam Cancer 2019; 17:395-402. [PMID: 29128931 DOI: 10.1007/s10689-017-0052-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Microsatellite instability (MSI) is a hallmark tool for Lynch syndrome (LS) screening and a prognostic marker for sporadic colorectal cancer (CRC). In regions with limited resources and scarce CRC molecular characterization as South America, the implementation of universal MSI screening is under debate for both its purposes. We sought to estimate the frequency of BAT26 in colorectal adenocarcinomas and to determine associated clinical and histological features. Consecutive patients from a CRC registry were included. BAT26 determination was performed in all cases; if instability was found, immunohistochemistry (IHC) and BRAF mutation analyses were done, as appropriate. Differences were assessed by chi-squared or Fisher's exact test, or by T test or Mann-Whitney. Multiple logistic regression was used to identify factors independently associated with BAT26-unstable tumors. We included 155 patients; mean age was 65.6 (SD 14.4) and 56.1% were male. The frequency of BAT26-unstable tumors was 22% (95% CI 15.7-29.3). Factors independently associated with BAT26-unstable tumors were right colon localization (OR 3.4, 95% CI 1.3-8.7), histological MSI features (OR 5.1, 95% CI 1.9-13.6) and Amsterdam criteria (OR 23.2, 95% CI 1.9-286.7). IHC was altered in 85.3% BAT26-unstable tumors and 70.6% lacked MLH1 expression; 47.8% of these harbored BRAF V600E mutation. We provide evidence to link the frequency of BAT26 to an increased diagnostic yield (up to 1.4-folds) of suspected LS cases in comparison to the revised Bethesda guidelines alone. In regions with limited resources, clinical and histological features associated with BAT26-unstable status could be useful to direct MSI screening in sporadic CRCs and may help guide clinical care and future research.
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Affiliation(s)
- María Laura González
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina. .,Gastroenterology Department, Hospital Italiano de Buenos Aires, 4190 Juan D. Perón St. (C1199ABD), Buenos Aires, Argentina.
| | - Natalia Causada-Calo
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.,Gastroenterology Department, Hospital Italiano de Buenos Aires, 4190 Juan D. Perón St. (C1199ABD), Buenos Aires, Argentina.,Department of Medicine, Farncombe Family Digestive Research Institute, McMaster University, Hamilton, ON, Canada
| | - Juan Pablo Santino
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.,Pathology Department, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Fabiana Alejandra Ferro
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Inés Sammartino
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Pablo Germán Kalfayan
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Maria Alicia Verzura
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Tamara Alejandra Piñero
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.,Instituto Universitario, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Andrea Romina Cajal
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.,Instituto Universitario, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Walter Pavicic
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
| | - Carlos Vaccaro
- Programa de Cáncer Hereditario (ProCanHe), Hospital Italiano de Buenos Aires, Buenos Aires, Argentina.,Surgery Department, Hospital Italiano de Buenos Aires, Buenos Aires, Argentina
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30
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Mutational profile of Brazilian lung adenocarcinoma unveils association of EGFR mutations with high Asian ancestry and independent prognostic role of KRAS mutations. Sci Rep 2019; 9:3209. [PMID: 30824880 PMCID: PMC6397232 DOI: 10.1038/s41598-019-39965-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/06/2019] [Indexed: 01/05/2023] Open
Abstract
Lung cancer is the deadliest cancer worldwide. The mutational frequency of EGFR and KRAS genes in lung adenocarcinoma varies worldwide per ethnicity and smoking. The impact of EGFR and KRAS mutations in Brazilian lung cancer remains poorly explored. Thus, we investigated the frequency of EGFR and KRAS mutations in a large Brazilian series of lung adenocarcinoma together with patients’ genetic ancestry, clinicopathological and sociodemographic characteristics. The mutational frequency of EGFR was 22.7% and KRAS was 20.4%. The average ancestry proportions were 73.1% for EUR, 13.1% for AFR, 6.5% for AME and 7.3% for ASN. EGFR mutations were independently associated with never-smokers, high-Asian ancestry, and better performance status. KRAS mutations were independently associated with tobacco exposure and non-Asian ancestry. EGFR-exon 20 mutations were associated with worse outcome. The Cox regression model indicated a worse outcome for patients whose were older at diagnosis (>61 y), solid histological subtype, loss of weight (>10%), worse performance status (≥2), and presence of KRAS mutations and EGFR mutational status in TKi non-treated patients. In conclusion, we assessed the clinicopathological and ethnic impact of EGFR and KRAS mutations in the largest series reported of Brazilian lung adenocarcinomas. These findings can support future clinical strategies for Brazilian lung cancer patients.
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Proença MA, Biselli JM, Succi M, Severino FE, Berardinelli GN, Caetano A, Reis RM, Hughes DJ, Silva AE. Relationship between Fusobacterium nucleatum, inflammatory mediators and microRNAs in colorectal carcinogenesis. World J Gastroenterol 2018; 24:5351-5365. [PMID: 30598580 PMCID: PMC6305535 DOI: 10.3748/wjg.v24.i47.5351] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 11/29/2018] [Accepted: 12/13/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To examine the effect of Fusobacterium nucleatum (F. nucleatum) on the microenvironment of colonic neoplasms and the expression of inflammatory mediators and microRNAs (miRNAs).
METHODS Levels of F. nucleatum DNA, cytokine gene mRNA (TLR2, TLR4, NFKB1, TNF, IL1B, IL6 and IL8), and potentially interacting miRNAs (miR-21-3p, miR-22-3p, miR-28-5p, miR-34a-5p, miR-135b-5p) were measured by quantitative polymerase chain reaction (qPCR) TaqMan® assays in DNA and/or RNA extracted from the disease and adjacent normal fresh tissues of 27 colorectal adenoma (CRA) and 43 colorectal cancer (CRC) patients. KRAS mutations were detected by direct sequencing and microsatellite instability (MSI) status by multiplex PCR. Cytoscape v3.1.1 was used to construct the postulated miRNA:mRNA interaction network.
RESULTS Overabundance of F. nucleatum in neoplastic tissue compared to matched normal tissue was detected in CRA (51.8%) and more markedly in CRC (72.1%). We observed significantly greater expression of TLR4, IL1B, IL8, and miR-135b in CRA lesions and TLR2, IL1B, IL6, IL8, miR-34a and miR-135b in CRC tumours compared to their respective normal tissues. Only two transcripts for miR-22 and miR-28 were exclusively downregulated in CRC tumour samples. The mRNA expression of IL1B, IL6, IL8 and miR-22 was positively correlated with F. nucleatum quantification in CRC tumours. The mRNA expression of miR-135b and TNF was inversely correlated. The miRNA:mRNA interaction network suggested that the upregulation of miR-34a in CRC proceeds via a TLR2/TLR4-dependent response to F. nucleatum. Finally, KRAS mutations were more frequently observed in CRC samples infected with F. nucleatum and were associated with greater expression of miR-21 in CRA, while IL8 was upregulated in MSI-high CRC.
CONCLUSION Our findings indicate that F. nucleatum is a risk factor for CRC by increasing the expression of inflammatory mediators through a possible miRNA-mediated activation of TLR2/TLR4.
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Affiliation(s)
- Marcela Alcântara Proença
- Department of Biology, UNESP, Univ. Estadual Paulista, Campus of São José do Rio Preto, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Joice Matos Biselli
- Department of Biology, UNESP, Univ. Estadual Paulista, Campus of São José do Rio Preto, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Maysa Succi
- Department of Biology, UNESP, Univ. Estadual Paulista, Campus of São José do Rio Preto, São José do Rio Preto, São Paulo 15054-000, Brazil
| | - Fábio Eduardo Severino
- Department of Surgery and Orthopedics, Faculty of Medicine, UNESP, Univ. Estadual Paulista, Campus of Botucatu, Botucatu, São Paulo 18618-687, Brazil
| | | | - Alaor Caetano
- Endoscopy Center of Rio Preto, São José do Rio Preto, São Paulo 15015-700, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
- Life and Health Sciences Research Institute, University of Minho, Campus Gualtar, Braga 4710-057, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, Campus Gualtar, Braga 4710-057, Portugal
| | - David J Hughes
- Cancer Biology and Therapeutics Group, UCD Conway Institute, University College Dublin, Dublin D04 V1W8, Ireland
| | - Ana Elizabete Silva
- Department of Biology, UNESP, Univ. Estadual Paulista, Campus of São José do Rio Preto, São José do Rio Preto, São Paulo 15054-000, Brazil
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Berardinelli GN, Scapulatempo-Neto C, Durães R, Antônio de Oliveira M, Guimarães D, Reis RM. Advantage of HSP110 (T17) marker inclusion for microsatellite instability (MSI) detection in colorectal cancer patients. Oncotarget 2018; 9:28691-28701. [PMID: 29983889 PMCID: PMC6033349 DOI: 10.18632/oncotarget.25611] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/04/2018] [Indexed: 12/19/2022] Open
Abstract
Colorectal cancer (CRC) is a leading cause of cancer death worldwide. Microsatellite instability (MSI) is a genetic pathway leading to CRC, associated with particular clinicopathological features, and recently a major biomarker of immunotherapy response. There is little information the frequency MSI among Brazilian CRC patients, and it is still debatable the ideal methodology for MSI screening in countries with limited resources. We proposed to evaluate MSI by molecular and immunohistochemistry (IHC) methods, to compare both methodologies and also to assess the inclusion of a novel microsatellite marker, HSP110 (T17). The molecular MSI evaluation was performed using a PCR-multiplex panel in a total of 1013 CRC patients. Mismatch repair (MMR) proteins (MLH1, MSH2, MSH6 and PMS2) expression were evaluated by IHC. HSP110 (T17) marker was analyzed by fragment analysis. Molecularly, 89.5% of cases were MSI-negative and 10.5% were MSI-positive. The IHC showed that 88.9% of cases exhibited MMR-proficient status, 10.2% were MMR-deficient and 0.9% was inconclusive. Genotyping of the HSP110 (T17) in 106 MSI-positive and 215 MSI-negative cases showed its alteration only among the MSI-positive cases. We observed agreement (0.956, Kappa Test) between both molecular and IHC methodologies, with only eight discordant results, and in this subset of cases the HSP110 (T17) corroborate the molecular findings. This study suggests the use of molecular assays over IHC for MSI analysis and proposes the inclusion HSP110 (T17) marker as a complementary analysis in discordant cases.
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Affiliation(s)
| | | | - Ronílson Durães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Oncology, Barretos Cancer Hospital, Jales, São Paulo, Brazil
| | | | - Denise Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health sciences Research Institute, University of Minho, Gualtar Campus, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Gualtar Campus, Braga, Portugal
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33
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Campanella NC, Lacerda CF, Berardinelli GN, Abrahão-Machado LF, Cruvinel-Carloni A, De Oliveira ATT, Scapulatempo-Neto C, Crema E, Adad SJ, Rodrigues MAM, Henry MACA, Guimarães DP, Reis RM. Presence of microsatellite instability in esophageal squamous cell carcinoma associated with chagasic megaesophagus. Biomark Med 2018; 12:573-582. [PMID: 29873509 DOI: 10.2217/bmm-2017-0329] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
AIM The molecular pathogenesis of esophageal squamous cell carcinoma (ESCC) has been increasingly studied, but there is no report on the role of MSI in ESCC development associated with chagasic megaesophagus (CM).Results/methodology: In four ESCC/CM (4/19) we found microsatellite instability (MSI) alterations (21.1%), being three MSI-L (15.8%) and one MSI-H (5.3%). Four out of 35 ESCC cases showed MSI-L (11.4%) and only one out of 26 CM cases presented MSI-L (3.9%). The MSI-H was observed in an ESCC/CM patient that presents lack of MSH6 immunostaining corroborating deficiency in MMR pathway. Interestingly, the MSI-H ESCC/CM case also presented a deletion the HSP110 poly(T)17 gene. DISCUSSION/CONCLUSION Taking together, we concluded that MSI is a rare event in esophageal squamous cell carcinoma, but can be associated with CM.
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Affiliation(s)
- Nathália C Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Croider Franco Lacerda
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Digestive Surgery, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | | | | | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Pathology & Molecular Diagnostics, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Eduardo Crema
- Department of Digestive Surgery & Pathology, Medical School, UFTM -Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | - Sheila Jorge Adad
- Department of Digestive Surgery & Pathology, Medical School, UFTM -Federal University of Triângulo Mineiro, Uberaba, Minas Gerais, Brazil
| | | | | | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life & Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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34
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Fernandes GC, Michelli RAD, Galvão HCR, Paula AE, Pereira R, Andrade CE, Felicio PS, Souza CP, Mendes DRP, Volc S, Berardinelli GN, Grasel RS, Sabato CS, Viana DV, Mauad EC, Scapulatempo-Neto C, Arun B, Reis RM, Palmero EI. Prevalence of BRCA1/BRCA2 mutations in a Brazilian population sample at-risk for hereditary breast cancer and characterization of its genetic ancestry. Oncotarget 2018; 7:80465-80481. [PMID: 27741520 PMCID: PMC5348334 DOI: 10.18632/oncotarget.12610] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 10/01/2016] [Indexed: 11/25/2022] Open
Abstract
Background There are very few data about the mutational profile of families at-risk for hereditary breast and ovarian cancer (HBOC) from Latin America (LA) and especially from Brazil, the largest and most populated country in LA. Results Of the 349 probands analyzed, 21.5% were BRCA1/BRCA2 mutated, 65.3% at BRCA1 and 34.7% at BRCA2 gene. The mutation c.5266dupC (former 5382insC) was the most frequent alteration, representing 36.7% of the BRCA1 mutations and 24.0% of all mutations identified. Together with the BRCA1 c.3331_3334delCAAG mutation, these mutations constitutes about 35% of the identified mutations and more than 50% of the BRCA1 pathogenic mutations. Interestingly, six new mutations were identified. Additionally, 39 out of the 44 pathogenic mutations identified were not previously reported in the Brazilian population. Besides, 36 different variants of unknown significance (VUS) were identified. Regarding ancestry, average ancestry proportions were 70.6% European, 14.5% African, 8.0% Native American and 6.8% East Asian. Materials and methods This study characterized 349 Brazilian families at-risk for HBOC regarding their germline BRCA1/BRCA2 status and genetic ancestry. Conclusions This is the largest report of BRCA1/BRCA2 assessment in an at-risk HBOC Brazilian population. We identified 21.5% of patients harboring BRCA1/BRCA2 mutations and characterized the genetic ancestry of a sample group at-risk for hereditary breast cancer showing once again how admixed is the Brazilian population. No association was found between genetic ancestry and mutational status. The knowledge of the mutational profile in a population can contribute to the definition of more cost-effective strategies for the identification of HBOC families.
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Affiliation(s)
- Gabriela C Fernandes
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Henrique C R Galvão
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - André E Paula
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Pereira
- Institute of Research and Innovation in Health, University of Porto, Porto, Portugal.,Institute of Molecular Pathology and Immunology at the University of Porto (IPATIMUP), Porto, Portugal
| | - Carlos E Andrade
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Paula S Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristiano P Souza
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Deise R P Mendes
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Sahlua Volc
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Rebeca S Grasel
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristina S Sabato
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Danilo V Viana
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Edmundo C Mauad
- Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Prevention Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Cristovam Scapulatempo-Neto
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Pathology Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Banu Arun
- MD Anderson Cancer Center, Houston, Texas, USA
| | - Rui M Reis
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir I Palmero
- Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Oncogenetics Department, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata-FACISB, São Paulo, Brazil
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35
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Marques D, Ferreira-Costa LR, Ferreira-Costa LL, Correa RDS, Borges AMP, Ito FR, Ramos CCDO, Bortolin RH, Luchessi AD, Ribeiro-dos-Santos Â, Santos S, Silbiger VN. Association of insertion-deletions polymorphisms with colorectal cancer risk and clinical features. World J Gastroenterol 2017; 23:6854-6867. [PMID: 29085228 PMCID: PMC5645618 DOI: 10.3748/wjg.v23.i37.6854] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Revised: 06/24/2017] [Accepted: 08/15/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To investigate the association between 16 insertion-deletions (INDEL) polymorphisms, colorectal cancer (CRC) risk and clinical features in an admixed population.
METHODS One hundred and forty patients with CRC and 140 cancer-free subjects were examined. Genomic DNA was extracted from peripheral blood samples. Polymorphisms and genomic ancestry distribution were assayed by Multiplex-PCR reaction, separated by capillary electrophoresis on the ABI 3130 Genetic Analyzer instrument and analyzed on GeneMapper ID v3.2. Clinicopathological data were obtained by consulting the patients’ clinical charts, intra-operative documentation, and pathology scoring.
RESULTS Logistic regression analysis showed that polymorphism variations in IL4 gene was associated with increased CRC risk, while TYMS and UCP2 genes were associated with decreased risk. Reference to anatomical localization of tumor Del allele of NFKB1 and CASP8 were associated with more colon related incidents than rectosigmoid. In relation to the INDEL association with tumor node metastasis (TNM) stage risk, the Ins alleles of ACE, HLAG and TP53 (6 bp INDEL) were associated with higher TNM stage. Furthermore, regarding INDEL association with relapse risk, the Ins alleles of ACE, HLAG, and UGT1A1 were associated with early relapse risk, as well as the Del allele of TYMS. Regarding INDEL association with death risk before 10 years, the Ins allele of SGSM3 and UGT1A1 were associated with death risk.
CONCLUSION The INDEL variations in ACE, UCP2, TYMS, IL4, NFKB1, CASP8, TP53, HLAG, UGT1A1, and SGSM3 were associated with CRC risk and clinical features in an admixed population. These data suggest that this cancer panel might be useful as a complementary tool for better clinical management, and more studies need to be conducted to confirm these findings.
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Affiliation(s)
- Diego Marques
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
- Programa de Pós-graduação em Ciências Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém 66055-080, Pará, Brazil
| | - Layse Raynara Ferreira-Costa
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
| | - Lorenna Larissa Ferreira-Costa
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
| | - Romualdo da Silva Correa
- Departamento de Cirurgia Oncológica, Liga Norte Riograndense Contra o Câncer, Natal 59040-000, Rio Grande do Norte, Brazil
| | - Aline Maciel Pinheiro Borges
- Departamento de Cirurgia Oncológica, Liga Norte Riograndense Contra o Câncer, Natal 59040-000, Rio Grande do Norte, Brazil
| | - Fernanda Ribeiro Ito
- Departamento de Cirurgia Oncológica, Liga Norte Riograndense Contra o Câncer, Natal 59040-000, Rio Grande do Norte, Brazil
| | - Carlos Cesar de Oliveira Ramos
- Laboratório de Patologia e Citopatologia, Liga Norte Riograndense Contra o Câncer, Natal 59040-000, Rio Grande do Norte, Brazil
| | - Raul Hernandes Bortolin
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
- Programa de Pós-graduação em Ciências Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
| | - André Ducati Luchessi
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
- Programa de Pós-graduação em Ciências Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
| | - Ândrea Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém 66055-080, Pará, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Pará, Brazil
| | - Sidney Santos
- Laboratório de Genética Humana e Médica, Universidade Federal do Pará, Belém 66055-080, Pará, Brazil
- Núcleo de Pesquisas em Oncologia, Universidade Federal do Pará, Belém 66073-005, Pará, Brazil
| | - Vivian Nogueira Silbiger
- Laboratório de Bioanálise e Biotecnologia Molecular, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
- Departamento de Análises Clínicas e Toxicológicas, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
- Programa de Pós-graduação em Ciências Farmacêutica, Universidade Federal do Rio Grande do Norte, Natal 59012-570, Rio Grande do Norte, Brazil
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36
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Campanella NC, Scapulatempo-Neto C, Abrahão-Machado LF, Torres De Oliveira AT, Berardinelli GN, Guimarães DP, Reis RM. Lack of microsatellite instability in gastrointestinal stromal tumors. Oncol Lett 2017; 14:5221-5228. [PMID: 29113157 PMCID: PMC5662911 DOI: 10.3892/ol.2017.6884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/09/2017] [Indexed: 12/18/2022] Open
Abstract
The microsatellite instability (MSI) phenotype may constitute an important biomarker for patient response to immunotherapy, particularly to anti-programmed death-1 inhibitors. MSI is a type of genomic instability caused by a defect in DNA mismatch repair (MMR) proteins, which is present mainly in colorectal cancer and its hereditary form, hereditary nonpolyposis colorectal cancer. Gastrointestinal stromal tumor (GIST) development is associated with activating mutations of KIT proto-oncogene receptor tyrosine kinase (KIT) or platelet-derived growth factor receptor α (PDGFRA), which are oncogenes that predict the response to imatinib mesylate. In addition to KIT/PDGFRA mutations, other molecular alterations are important in GIST development. In GISTs, the characterization of the MSI phenotype is scarce and the results are not consensual. The present study aimed to assess MSI in a series of 79 GISTs. The evaluation of MSI was performed by pentaplex polymerase chain reaction comprising five markers, followed by capillary electrophoresis. The expression of MMR proteins was evaluated by immunohistochemistry. Regarding the KIT/PDGFRA/B-Raf proto-oncogene, serine/threonine kinase molecular profile of the 79 GISTs, 83.6% of the tumors possessed KIT mutations, 10.1% had PDGFRA mutations and 6.3% were triple wild-type. The mutated-PDGFRA cases were associated with gastric location and a lower mitotic index compared with KIT-mutated and wild-types, and these patients were more likely to be alive and without cancer. MSI analysis identified 4 cases with instability in one marker, however, additional evaluation of normal tissue and immunohistochemical staining of MMR proteins confirmed their microsatellite-stable nature. The results of the present study indicated that MSI is not involved in GIST tumorigenesis and, therefore, cannot serve as a biomarker to immunotherapy response in GIST.
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Affiliation(s)
- Nathália C Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | | | | | - Gustavo N Berardinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Rui M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Life and Health Sciences Research Institute, Health Sciences School, University of Minho, Guimarães, Braga 4704-553, Portugal.,Life and Health Sciences Research Institute/3B's-PT Government Associate Laboratory, University of Minho, Guimarães, Braga 4704-553, Portugal
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37
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Palmero EI, Galvão HCR, Fernandes GC, Paula AED, Oliveira JC, Souza CP, Andrade CE, Romagnolo LGC, Volc S, C Neto M, Sabato C, Grasel R, Mauad E, Reis RM, Michelli RAD. Oncogenetics service and the Brazilian public health system: the experience of a reference Cancer Hospital. Genet Mol Biol 2016; 39:168-77. [PMID: 27192127 PMCID: PMC4910553 DOI: 10.1590/1678-4685-gmb-2014-0364] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 07/21/2015] [Indexed: 11/22/2022] Open
Abstract
The identification of families at-risk for hereditary cancer is extremely important
due to the prevention potential in those families. However, the number of Brazilian
genetic services providing oncogenetic care is extremely low for the continental
dimension of the country and its population. Therefore, at-risk patients do not
receive appropriate assistance. This report describes the creation, structure and
management of a cancer genetics service in a reference center for cancer prevention
and treatment, the Barretos Cancer Hospital (BCH). The Oncogenetics Department (OD)
of BCH offers, free of charge, to all patients/relatives with clinical criteria, the
possibility to perform i) genetic counseling, ii) preventive examinations and iii)
genetic testing with the best quality standards. The OD has a multidisciplinary team
and is integrated with all specialties. The genetic counseling process consists
(mostly) of two visits. In 2014, 614 individuals (371 families) were seen by the OD.
To date, over 800 families were referred by the OD for genetic testing. The support
provided by the Oncogenetics team is crucial to identify at-risk individuals and to
develop preventive and personalized behaviors for each situation, not only to the
upper-middle class population, but also to the people whose only possibility is the
public health system.
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Affiliation(s)
- Edenir I Palmero
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil.,Faculdade de Ciências de Saúde de Barretos, Dr. Paulo Prata - FACISB, Barretos, SP, Brazil.,Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Henrique C R Galvão
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Gabriela C Fernandes
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil.,Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - André E de Paula
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil.,Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Junea C Oliveira
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Cristiano P Souza
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Carlos E Andrade
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Luis G C Romagnolo
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Sahlua Volc
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Maximiliano C Neto
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Cristina Sabato
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil.,Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Rebeca Grasel
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Edmundo Mauad
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil.,Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
| | - Rui M Reis
- Centro de Pesquisa em Oncologia Molecular, Hospital de Câncer de Barretos, Barretos, SP, Brazil.,Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Rodrigo A D Michelli
- Departamento de Oncogenética, Hospital de Câncer de Barretos, Barretos, SP, Brazil
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38
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Comparative Polymorphism of BAT-26 between Healthy Individuals and Cancer Patients and Its Cancer Risk Implication for Local Chinese. Int J Biol Markers 2016; 31:e252-7. [PMID: 26659721 DOI: 10.5301/jbm.5000179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2015] [Indexed: 11/20/2022]
Abstract
Purpose BAT-26 is one of the representative markers for microsatellite instability evaluation and presents different polymorphisms in different ethnic populations. The current knowledge of its comparative polymorphism between healthy individuals and cancer patients in the Chinese population is insufficient. This study aims to analyze germline polymorphic variations of BAT-26 between healthy individuals and cancer patients in Chinese from Jiangsu province and the associated cancer risk implications. Methods The various BAT-26 alleles and their percentages in cervical cells from 500 healthy women were assessed by direct sequencing. Twenty of these samples were also analyzed by fragment analysis. BAT-26 of blood DNA from 24 healthy individuals and 247 cancer patients was analyzed by fragment analysis. Results Compared with the sequencing results, 122.6-122.9 bp, 123.4-123.8 bp and 124.1-124.8 bp corresponded to the A25, A26 and A27 alleles, respectively. The 524 healthy individuals showed 4.58%, 92.18% and 3.24% of A25, A26 and A27, respectively. The variant alleles A18, A24, A28, A29 and A32 were only found in cancer patients, accounting for 0.81%, 0.40%, 0.40%, 0.40% and 0.40%, respectively; the A25, A26 and A27 alleles in cancer patients accounted for 6.48%, 77.33% and 13.77%. Conclusions Healthy individuals had a stable BAT-26 profile within the quasimonomorphic variation range (QMVR), but cancer patients harbored variant alleles outside QMVR and showed a trend from quasimonomorph to polymonomorph, suggesting that variant alleles of BAT-26 in germline cells may be regarded as a potential marker of higher cancer risk in the Chinese population from Jiangsu province.
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39
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Abstract
Copy number alterations (CNA) are one of the driving mechanisms of glioma tumorigenesis, and are currently used as important biomarkers in the routine setting. Therefore, we performed CNA profiling of 65 astrocytomas of distinct malignant grades (WHO grade I–IV) of Brazilian origin, using array-CGH and microsatellite instability analysis (MSI), and investigated their correlation with TERT and IDH1 mutational status and clinico-pathological features. Furthermore, in silico analysis using the Oncomine database was performed to validate our findings and extend the findings to gene expression level. We found that the number of genomic alterations increases in accordance with glioma grade. In glioblastomas (GBM), the most common alterations were gene amplifications (PDGFRA, KIT, KDR, EGFR, and MET) and deletions (CDKN2A and PTEN). Log-rank analysis correlated EGFR amplification and/or chr7 gain with better survival of the patients. MSI was observed in 11% of GBMs. A total of 69% of GBMs presented TERT mutation, whereas IDH1 mutation was most frequent in diffuse (85.7%) and anaplastic (100%) astrocytomas. The combination of 1p19q deletion and TERT and IDH1 mutational status separated tumor groups that showed distinct age of diagnosis and outcome. In silico validation pointed to less explored genes that may be worthy of future investigation, such as CDK2, DMRTA1, and MTAP. Herein, using an extensive integrated analysis, we indicated potentially important genes, not extensively studied in gliomas, that could be further explored to assess their biological and clinical impact in astrocytomas.
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40
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Cárcano FM, Lengert AH, Vidal DO, Scapulatempo Neto C, Queiroz L, Marques H, Baltazar F, Berardinelli GN, Martinelli CMS, da Silva ECA, Reis RM, Lopes LF. Absence of microsatellite instability and BRAF (V600E) mutation in testicular germ cell tumors. Andrology 2016; 4:866-72. [PMID: 27153176 DOI: 10.1111/andr.12200] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 03/16/2016] [Accepted: 03/18/2016] [Indexed: 12/27/2022]
Abstract
Testicular germ cell tumors (TGCT) are the most common malignant neoplasm in young men. DNA mismatch repair deficiency can lead to microsatellite instability (MSI), an important mechanism of genetic instability. A mutation of the BRAF gene has been implicated in the pathogenesis of several solid tumors and has recently become an important therapeutic target. The role of MSI and BRAF gene mutation in TGCT, particularly in refractory disease, is poorly understood and reported findings are controversial. In this study, we aimed to determine the frequency and clinical impact of MSI status and BRAF mutations in TGCT. DNA was isolated from formalin-fixed paraffin embedded (FFPE) tissue from 150 TGCT cases. The MSI phenotype was evaluated using multiplex PCR for five quasimonomorphic mononucleotide repeat markers. Exon 15 of the BRAF oncogene (V600E) was analyzed by PCR, followed by direct sequencing. Sixteen percent of cases were considered to have refractory disease. In a small subset of cases (17 for MSI and 18 for BRAF), the quantity and quality of DNA recovery were poor and therefore, were unable to be analyzed. The remaining 133 TGCT cases showed a complete absence of MSI. Of the 132 cases successfully evaluated for BRAF mutations, all were V600E wild-type. In conclusion, despite a distinct response of testicular germ cell tumors to therapy, microsatellite instability, and the BRAF V600E mutation were absent in all testicular germ cell tumors tested in this study.
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Affiliation(s)
- F M Cárcano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - A H Lengert
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos Children's Cancer Hospital, Barretos, Brazil
| | - D O Vidal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos Children's Cancer Hospital, Barretos, Brazil
| | - C Scapulatempo Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - L Queiroz
- Department of Medical Oncology, Hospital de Braga, Braga, Guimarães, Portugal
| | - H Marques
- Department of Medical Oncology, Hospital de Braga, Braga, Guimarães, Portugal
| | - F Baltazar
- Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - G N Berardinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - C M S Martinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - E C A da Silva
- Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - R M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), Health Sciences School, University of Minho, Braga, Guimarães, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - L F Lopes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos Children's Cancer Hospital, Barretos, Brazil
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Paskulin DD, Giacomazzi J, Achatz MI, Costa S, Reis RM, Hainaut P, dos Santos SEB, Ashton-Prolla P. Ancestry of the Brazilian TP53 c.1010G>A (p.Arg337His, R337H) Founder Mutation: Clues from Haplotyping of Short Tandem Repeats on Chromosome 17p. PLoS One 2015; 10:e0143262. [PMID: 26618902 PMCID: PMC4664269 DOI: 10.1371/journal.pone.0143262] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/01/2015] [Indexed: 11/22/2022] Open
Abstract
Rare germline mutations in TP53 (17p13.1) cause a highly penetrant predisposition to a specific spectrum of early cancers, defining the Li-Fraumeni Syndrome (LFS). A germline mutation at codon 337 (p.Arg337His, c1010G>A) is found in about 0.3% of the population of Southern Brazil. This mutation is associated with partially penetrant LFS traits and is found in the germline of patients with early cancers of the LFS spectrum unselected for familial history. To characterize the extended haplotypes carrying the mutation, we have genotyped 9 short tandem repeats on chromosome 17p in 12 trios of Brazilian p.Arg337His carriers. Results confirm that all share a common ancestor haplotype of Caucasian/Portuguese-Iberic origin, distant in about 72–84 generations (2000 years assuming a 25 years intergenerational distance) and thus pre-dating European migration to Brazil. So far, the founder p.Arg337His haplotype has not been detected outside Brazil, with the exception of two residents of Portugal, one of them of Brazilian origin. On the other hand, increased meiotic recombination in p.Arg337His carriers may account for higher than expected haplotype diversity. Further studies comparing haplotypes in populations of Brazil and of other areas of Portuguese migration are needed to understand the historical context of this mutation in Brazil.
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Affiliation(s)
- Diego Davila Paskulin
- Post-Graduate Program, Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
- * E-mail:
| | - Juliana Giacomazzi
- Post-Graduate Program, Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
| | | | - Sandra Costa
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Rui Manoel Reis
- Life and Health Sciences Research Institute, University of Minho, Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Pierre Hainaut
- International Prevention Research Institute, Lyon and Institut Albert Bonniot/INSERM 823, Grenoble, France
| | | | - Patricia Ashton-Prolla
- Post-Graduate Program, Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre, Brazil
- Genomic Medicine Laboratory, Experimental Research Center, Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
- Medical Genetics Service), Hospital de Clinicas de Porto Alegre, Porto Alegre, Brazil
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42
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Campanella NC, Penna V, Ribeiro G, Abrah�o-Machado LF, Scapulatempo-Neto C, Reis RM. Absence of Microsatellite Instability In Soft Tissue Sarcomas. Pathobiology 2015; 82:36-42. [DOI: 10.1159/000369906] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 11/14/2014] [Indexed: 11/19/2022] Open
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43
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Yamane LS, Scapulatempo-Neto C, Alvarenga L, Oliveira CZ, Berardinelli GN, Almodova E, Cunha TR, Fava G, Colaiacovo W, Melani A, Fregnani JH, Reis RM, Guimarães DP. KRAS and BRAF mutations and MSI status in precursor lesions of colorectal cancer detected by colonoscopy. Oncol Rep 2014; 32:1419-26. [PMID: 25050586 DOI: 10.3892/or.2014.3338] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/04/2014] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most frequent cancers worldwide. Adenoma is the main precursor lesion and, recently, the serrated polyps were described as a group of colorectal lesions with malignant potential. The morphologic and biologic characterizations of serrated polyps remain limited. The aim of the present study was to determine the frequency of KRAS and BRAF mutations and microsatellite instability (MSI) in CRC precursor lesions, to evaluate the association between molecular, pathologic and morphologic alterations in precursor lesions and to compare with the alterations detected in CRC. A series of 342 precursor lesions were removed from 155 patients during colonoscopy. After morphologic classification, molecular analysis was performed in 103 precursor lesions, and their genetic profile compared with 47 sporadic CRCs. Adenomas were the main precursor lesions (70.2%). Among the serrated polyps, the main precursor lesion was hyperplastic polyps (HPs) (82.4%), followed by sessile serrated adenomas (12.7%) and traditional serrated adenomas (2.0%). KRAS mutations were detected in 13.6% of the precursor lesions, namely in adenomas and in HPs, but in no serrated adenoma. BRAF mutations were found in 9 (8.7%) precursor lesions, mainly associated with serrated polyps and absent in adenomas (P<0.001). High MSI (MSI-H) was absent in precursor lesions. In the 47 CCR cases, 46.8% exhibited KRAS mutation, 6.5% BRAF mutations and 10.6% MSI-H. This study confirms the role of KRAS and BRAF mutations in CRC carcinogenesis, a crucial step in implementing CRC screening strategies.
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Affiliation(s)
- L S Yamane
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - C Scapulatempo-Neto
- Department of Pathology, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - L Alvarenga
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - C Z Oliveira
- Department of Epidemiology and Biostatistics, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - G N Berardinelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - E Almodova
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - T R Cunha
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - G Fava
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - W Colaiacovo
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - A Melani
- Department of Digestive Surgery, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - J H Fregnani
- Department of Epidemiology and Biostatistics, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - R M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - D P Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
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44
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Lee JS. Expression of Microsatellite Instability (MSI) from Colorectal Carcinoma Patients. KOREAN JOURNAL OF CLINICAL LABORATORY SCIENCE 2014. [DOI: 10.15324/kjcls.2014.46.2.59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jae-Sik Lee
- Department of Clinical Laboratory Science, Hyejeon College, Hongseong 350-702, Korea
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