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Bu R, Siraj AK, Parvathareddy SK, Iqbal K, Azam S, Qadri Z, Al-Rasheed M, Haqawi W, Diaz M, Alobaisi K, Annaiyappanaidu P, Siraj N, AlHusaini H, Alomar O, Al-Badawi IA, Al-Dayel F, Al-Kuraya KS. Lynch Syndrome Identification in Saudi Cohort of Endometrial Cancer Patients Screened by Universal Approach. Int J Mol Sci 2022; 23:ijms232012299. [PMID: 36293153 PMCID: PMC9603045 DOI: 10.3390/ijms232012299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/08/2022] [Accepted: 10/12/2022] [Indexed: 12/09/2022] Open
Abstract
Lynch syndrome (LS) is the most common cause of inherited endometrial cancer (EC). The prevalence and molecular characteristic of LS in Middle Eastern women with EC have been underexplored. To evaluate the frequency of LS in a cohort of EC patients from Saudi Arabia, a total of 436 EC cases were screened utilizing immunohistochemistry (IHC), MLH1 promoter methylation analysis and next-generation sequencing technology. A total of 53 of 436 (12.2%) ECs were classified as DNA mismatch repair-deficient (dMMR). MLH1 promoter hypermethylation was detected in 30 ECs (6.9%). Three ECs (0.7%) were found to be LS harboring germline pathogenic variants (PVs)/likely pathogenic variants (LPVs): two in the MSH2 gene and one in the MSH6 gene. Three ECs (0.7%) were Lynch-like syndrome (LLS) carrying double somatic MSH2 PVs/LPVs. Seven cases were found to have variants of uncertain significance in cancer-related genes other than MMR genes. Our results indicate that LS prevalence is low among Saudi EC patients and LLS is as common as LS in this ethnicity. Our findings could help in better understanding of the prevalence and mutational spectrum of this syndrome in Saudi Arabia, which may help in defining best strategies for LS identification, prevention and genetic counseling for EC patients.
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Affiliation(s)
- Rong Bu
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Abdul K. Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sandeep Kumar Parvathareddy
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Kaleem Iqbal
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Zeeshan Qadri
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maha Al-Rasheed
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Wael Haqawi
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Mark Diaz
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Khadija Alobaisi
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Padmanaban Annaiyappanaidu
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Nabil Siraj
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Hamed AlHusaini
- Department of Medical Oncology, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Osama Alomar
- Department of Obstetrics-Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ismail A. Al-Badawi
- Department of Obstetrics-Gynecology, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, Riyadh 11211, Saudi Arabia
| | - Khawla S. Al-Kuraya
- Human Cancer Genomic Research, Research Center, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Correspondence: ; Tel.: +966-1-205-5167
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Ogawa M, Tanaka A, Namba K, Shia J, Wang JY, Roehrl MH. Early-Stage Loss of GALNT6 Predicts Poor Clinical Outcome in Colorectal Cancer. Front Oncol 2022; 12:802548. [PMID: 35692787 PMCID: PMC9185839 DOI: 10.3389/fonc.2022.802548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/27/2022] [Indexed: 12/22/2022] Open
Abstract
Colorectal adenocarcinomas arise from luminal lining epithelium of the colorectal tract which is covered with highly glycosylated mucins. Mucin O-glycosylation is initiated by a family of polypeptide N-acteylgalactosaminyltransferases (GALNTs). This study examined GALNT6 protein expression in 679 colorectal tumors, including 574 early-stage and 105 late-stage cancers. GALNT6 expression in cancer tissue varied widely between patients ranging from high levels to complete loss. Loss of GALNT6 occurred in 9.9% of early-stage and 15.2% of late-stage cancers and was more prevalent in grade 3 or MSI subtype tumors. Survival analyses revealed that loss of GALNT6 expression is prognostic of reduced overall survival, and univariate and multivariate analyses demonstrated that loss of GALNT6 is an independent risk variable. We also analyzed 508-case TCGA and 63-case CPTAC colorectal cancer cohorts for all members of the GALNT enzyme family, the mucin family, as well as KRAS and BRAF mutations. GLANT6 mRNA expression showed no strong correlation with other GALNTs or mucins but was significantly higher in KRAS mutated or BRAF wild-type early-stage cancers. Using large cohorts of patients and different approaches, this study shows that loss of GALNT6 enzyme in early-stage colorectal cancer predicts poor clinical outcomes.
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Affiliation(s)
- Makiko Ogawa
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Atsushi Tanaka
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Kei Namba
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Department of Thoracic Surgery and Breast and Endocrine Surgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Jinru Shia
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | | | - Michael H Roehrl
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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Rosa RCA, Santis JO, Teixeira LA, Molfetta GA, Dos Santos JTT, Ribeiro VDS, Chahud F, Ribeiro-Silva A, Brunaldi MO, Silva WA, Ferraz VEDF. Lynch syndrome identification in a Brazilian cohort of endometrial cancer screened by a universal approach. Gynecol Oncol 2020; 159:229-238. [PMID: 32694065 DOI: 10.1016/j.ygyno.2020.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/07/2020] [Indexed: 12/27/2022]
Abstract
OBJECTIVE To report the frequency of Lynch syndrome (LS) in a cohort of patients from Southeast Brazil bearing endometrial cancer (EC), using a tumor screening universal approach. METHODS A total of 242 endometrial carcinomas were screened by immunohistochemistry (IHC) and microsatellite instability (MSI) for detection of DNA mismatch repair deficiency (dMMR). MLH1 methylation was assessed to identify sporadic cases. Patients with dMMR tumors were recruited for germline variant analysis by next-generation sequencing of the MLH1, MSH2, MSH6, PMS2, and EPCAM genes. RESULTS Ninety-three out of 242 tumors (38.5%) were classified as dMMR based on MSI and IHC results. Of these, 54 cases were selected for germline analysis, and 37/54 (68.5%) were available for sequencing. Ten patients (10/37, 27%) harbored germline pathogenic or likely pathogenic variants, most of them in the MSH6 gene (4/10, 40%). Seven variants of uncertain significance were found. Eight novel germline variants were identified. The LS prevalence in our cohort was of at least 4.1%. LS patients presented lower mean age at cancer diagnosis compared with patients diagnosed with sporadic EC. Individuals with dMMR tumors, without germline pathogenic variants detected in LS-genes ("Lynch-like" syndrome), had an intermediate mean age at cancer diagnosis between LS and sporadic cases. CONCLUSION This is the first report of the LS prevalence in EC screened by a universal approach in Brazil. Our findings contribute to a better understanding of the mutational landscape of this syndrome in Brazil, which is relevant for improved identification, genetic counseling, prevention and control of cancer in LS.
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Affiliation(s)
- Reginaldo Cruz Alves Rosa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Regional Blood Center at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Jessica Oliveira Santis
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Regional Blood Center at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Lorena Alves Teixeira
- Department of Gynecology and Obstetrics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Greice Andreotti Molfetta
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Regional Blood Center at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | | | - Vanessa Dos Santos Ribeiro
- Inter-institutional Doctoral Program in Nursing, Ribeirão Preto College of Nursing, University of São Paulo, Ribeirão Preto, Brazil.
| | - Fernando Chahud
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Alfredo Ribeiro-Silva
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Mariângela Ottoboni Brunaldi
- Department of Pathology and Legal Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Wilson Araújo Silva
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Regional Blood Center at University Hospital of the Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil.
| | - Victor Evangelista de Faria Ferraz
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil; Center for Medical Genomics at Clinical Hospital of the Ribeirão Preto Medical School, University of São Paulo, Brazil.
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Larsson C, Cordeddu L, Siggens L, Pandzic T, Kundu S, He L, Ali MA, Pristovšek N, Hartman K, Ekwall K, Sjöblom T. Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression. Clin Epigenetics 2020; 12:74. [PMID: 32471474 PMCID: PMC7257146 DOI: 10.1186/s13148-020-00863-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 05/14/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The histone 3 lysine 4 (H3K4) monomethylase KMT2C is mutated across several cancer types; however, the effects of mutations on epigenome organization, gene expression, and cell growth are not clear. A frequently recurring mutation in colorectal cancer (CRC) with microsatellite instability is a single nucleotide deletion within the exon 38 poly-A(9) repeat (c.8390delA) which results in frameshift preceding the functional carboxy-terminal SET domain. To study effects of KMT2C expression in CRC cells, we restored one allele to wild type KMT2C in the two CRC cell lines RKO and HCT116, which both are homozygous c.8390delA mutant. RESULTS Gene editing resulted in increased KMT2C expression, increased H3K4me1 levels, altered gene expression profiles, and subtle negative effects on cell growth, where higher dependence and stronger effects of KMT2C expression were observed in RKO compared to HCT116 cells. Surprisingly, we found that the two RKO and HCT116 CRC cell lines have distinct baseline H3K4me1 epigenomic profiles. In RKO cells, a flatter genome-wide H3K4me1 profile was associated with more increased H3K4me1 deposition at enhancers, reduced cell growth, and more differential gene expression relative to HCT116 cells when KMT2C was restored. Profiling of H3K4me1 did not indicate a highly specific regulation of gene expression as KMT2C-induced H3K4me1 deposition was found globally and not at a specific enhancer sub-set in the engineered cells. Although we observed variation in differentially regulated gene sets between cell lines and individual clones, differentially expressed genes in both cell lines included genes linked to known cancer signaling pathways, estrogen response, hypoxia response, and aspects of immune system regulation. CONCLUSIONS Here, KMT2C restoration reduced CRC cell growth and reinforced genome-wide H3K4me1 deposition at enhancers; however, the effects varied depending upon the H3K4me1 status of KMT2C deficient cells. Results indicate that KMT2C inactivation may promote colorectal cancer development through transcriptional dysregulation in several pathways with known cancer relevance.
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Affiliation(s)
- Chatarina Larsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Lina Cordeddu
- Department of Biosciences and Nutrition, NEO, Karolinska Institute, SE-141 83, Huddinge, Sweden
| | - Lee Siggens
- Department of Biosciences and Nutrition, NEO, Karolinska Institute, SE-141 83, Huddinge, Sweden
| | - Tatjana Pandzic
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Snehangshu Kundu
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Liqun He
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Muhammad Akhtar Ali
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.,Present address: School of Biological Sciences, University of the Punjab, Lahore, Pakistan
| | - Nuša Pristovšek
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.,Present address: The Novo Nordisk Foundation for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Karin Hartman
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden
| | - Karl Ekwall
- Department of Biosciences and Nutrition, NEO, Karolinska Institute, SE-141 83, Huddinge, Sweden
| | - Tobias Sjöblom
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85, Uppsala, Sweden.
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5
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Leung KK, Wilson GM, Kirkemo LL, Riley NM, Coon JJ, Wells JA. Broad and thematic remodeling of the surfaceome and glycoproteome on isogenic cells transformed with driving proliferative oncogenes. Proc Natl Acad Sci U S A 2020; 117:7764-7775. [PMID: 32205440 PMCID: PMC7148585 DOI: 10.1073/pnas.1917947117] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The cell surface proteome, the surfaceome, is the interface for engaging the extracellular space in normal and cancer cells. Here we apply quantitative proteomics of N-linked glycoproteins to reveal how a collection of some 700 surface proteins is dramatically remodeled in an isogenic breast epithelial cell line stably expressing any of six of the most prominent proliferative oncogenes, including the receptor tyrosine kinases, EGFR and HER2, and downstream signaling partners such as KRAS, BRAF, MEK, and AKT. We find that each oncogene has somewhat different surfaceomes, but the functions of these proteins are harmonized by common biological themes including up-regulation of nutrient transporters, down-regulation of adhesion molecules and tumor suppressing phosphatases, and alteration in immune modulators. Addition of a potent MEK inhibitor that blocks MAPK signaling brings each oncogene-induced surfaceome back to a common state reflecting the strong dependence of the oncogene on the MAPK pathway to propagate signaling. Cell surface protein capture is mediated by covalent tagging of surface glycans, yet current methods do not afford sequencing of intact glycopeptides. Thus, we complement the surfaceome data with whole cell glycoproteomics enabled by a recently developed technique called activated ion electron transfer dissociation (AI-ETD). We found massive oncogene-induced changes to the glycoproteome and differential increases in complex hybrid glycans, especially for KRAS and HER2 oncogenes. Overall, these studies provide a broad systems-level view of how specific driver oncogenes remodel the surfaceome and the glycoproteome in a cell autologous fashion, and suggest possible surface targets, and combinations thereof, for drug and biomarker discovery.
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Affiliation(s)
- Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Gary M Wilson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Lisa L Kirkemo
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143
| | - Nicholas M Riley
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Joshua J Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, CA 94143;
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6
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do Canto LM, Larsen SJ, Catin Kupper BE, Begnami MDFDS, Scapulatempo-Neto C, Petersen AH, Aagaard MM, Baumbach J, Aguiar S, Rogatto SR. Increased Levels of Genomic Instability and Mutations in Homologous Recombination Genes in Locally Advanced Rectal Carcinomas. Front Oncol 2019; 9:395. [PMID: 31192117 PMCID: PMC6527873 DOI: 10.3389/fonc.2019.00395] [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: 12/21/2018] [Accepted: 04/26/2019] [Indexed: 12/11/2022] Open
Abstract
Pre-operative 5-fluoracil-based chemoradiotherapy (nCRT) is the standard treatment for patients with locally advanced rectal cancer (LARC). Patients with pathological complete response (pCR–0% of tumor cells in the surgical specimen after nCRT) have better overall survival and lower risk of recurrence in comparison with incomplete responders (pIR). Predictive biomarkers to be used for new therapeutic strategies and capable of stratifying patients to avoid overtreatment are needed. We evaluated the genomic profiles of 33 pre-treatment LARC biopsies using SNP array and targeted-next generation sequencing (tNGS). Based on the large number of identified genomic alterations, we calculated the genomic instability index (GII) and three homologous recombination deficiency (HRD) scores, which have been reported as impaired DNA repair markers. We observed high GII in our LARC cases, which was confirmed in 165 rectal cancer cases from TCGA. Patients with pCR presented higher GII compared with pIR. Moreover, a negative correlation between GII and the fraction of tumor cells remaining after surgery was observed (ρ = –0.382, P = 0.02). High HRD scores were detected in 61% of LARC, of which 70% were incomplete responders. Using tNGS (105 cancer-related genes, 13 involved in HR and 5 in mismatch repair pathways), we identified 23% of cases with mutations in HR genes, mostly in pIR cases (86% of mutated cases). In agreement, the analysis of the TCGA dataset (N = 145) revealed 21% of tumors with mutations in HR genes. The HRD scores were shown to be predictive of better response to PARP-inhibitors and platinum-based chemotherapy in breast and ovarian cancer. Our results suggest that the same strategy could be applied in a set of LARC patients with HRD. In conclusion, we identified high genomic instability in LARC, which was related to alterations in the HR pathway, especially in pIR. These findings suggest that patients with impaired HRD would clinically benefit from PARP-inhibitors and platinum-based therapy.
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Affiliation(s)
- Luisa Matos do Canto
- International Research Center-Center for International Private Enterprise (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil.,Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Simon J Larsen
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | | | | | | | | | - Mads M Aagaard
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark
| | - Jan Baumbach
- TUM School of Life Sciences Weihenstephan, Technical University of Munich (TUM), Freising, Germany
| | - Samuel Aguiar
- Department of Pelvic Surgery, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Silvia R Rogatto
- Department of Clinical Genetics, Vejle Hospital, Vejle, Denmark.,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark.,Danish Colorectal Cancer Center South, Vejle, Denmark
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Class-3 Semaphorins and Their Receptors: Potent Multifunctional Modulators of Tumor Progression. Int J Mol Sci 2019; 20:ijms20030556. [PMID: 30696103 PMCID: PMC6387194 DOI: 10.3390/ijms20030556] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/21/2019] [Accepted: 01/22/2019] [Indexed: 12/28/2022] Open
Abstract
Semaphorins are the products of a large gene family containing 28 genes of which 21 are found in vertebrates. Class-3 semaphorins constitute a subfamily of seven vertebrate semaphorins which differ from the other vertebrate semaphorins in that they are the only secreted semaphorins and are distinguished from other semaphorins by the presence of a basic domain at their C termini. Class-3 semaphorins were initially characterized as axon guidance factors, but have subsequently been found to regulate immune responses, angiogenesis, lymphangiogenesis, and a variety of additional physiological and developmental functions. Most class-3 semaphorins transduce their signals by binding to receptors belonging to the neuropilin family which subsequently associate with receptors of the plexin family to form functional class-3 semaphorin receptors. Recent evidence suggests that class-3 semaphorins also fulfill important regulatory roles in multiple forms of cancer. Several class-3 semaphorins function as endogenous inhibitors of tumor angiogenesis. Others were found to inhibit tumor metastasis by inhibition of tumor lymphangiogenesis, by direct effects on the behavior of tumor cells, or by modulation of immune responses. Notably, some semaphorins such as sema3C and sema3E have also been found to potentiate tumor progression using various mechanisms. This review focuses on the roles of the different class-3 semaphorins in tumor progression.
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Dominguez-Valentin M, Nakken S, Tubeuf H, Vodak D, Ekstrøm PO, Nissen AM, Morak M, Holinski-Feder E, Martins A, Møller P, Hovig E. Potentially pathogenic germline CHEK2 c.319+2T>A among multiple early-onset cancer families. Fam Cancer 2019; 17:141-153. [PMID: 28608266 DOI: 10.1007/s10689-017-0011-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
To study the potential contribution of genes other than BRCA1/2, PTEN, and TP53 to the biological and clinical characteristics of multiple early-onset cancers in Norwegian families, including early-onset breast cancer, Cowden-like and Li-Fraumeni-like syndromes (BC, CSL and LFL, respectively). The Hereditary Cancer Biobank from the Norwegian Radium Hospital was used to identify early-onset BC, CSL or LFL for whom no pathogenic variants in BRCA1/2, PTEN, or TP53 had been found in routine diagnostic DNA sequencing. Forty-four cancer susceptibility genes were selected and analyzed by our in-house designed TruSeq amplicon-based assay for targeted sequencing. Protein- and RNA splicing-dedicated in silico analyses were performed for all variants of unknown significance (VUS). Variants predicted as the more likely to affect splicing were experimentally analyzed by minigene assay. We identified a CSL individual carrying a variant in CHEK2 (c.319+2T>A, IVS2), here considered as likely pathogenic. Out of the five VUS (BRCA2, CDH1, CHEK2, MAP3K1, NOTCH3) tested in the minigene splicing assay, only NOTCH3 c.14090C>T (p.Ser497Leu) showed a significant effect on RNA splicing, notably by inducing partial skipping of exon 9. Among 13 early-onset BC, CSL and LFL patients, gene panel sequencing identified a potentially pathogenic variant in CHEK2 that affects a canonical RNA splicing signal. Our study provides new information on genetic loci that may affect the risk of developing cancer in these patients and their families, demonstrating that genes presently not routinely tested in molecular diagnostic settings may be important for capturing cancer predisposition in these families.
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Affiliation(s)
- Mev Dominguez-Valentin
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
| | - Sigve Nakken
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hélène Tubeuf
- Normandy Centre for Genomic and Personalized Medicine, Inserm-U1245, UNIROUEN, Normandie Univ, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Daniel Vodak
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Per Olaf Ekstrøm
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anke M Nissen
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Monika Morak
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Elke Holinski-Feder
- Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Alexandra Martins
- Normandy Centre for Genomic and Personalized Medicine, Inserm-U1245, UNIROUEN, Normandie Univ, Rouen, France
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Human Medicine, Universität Witten/Herdecke, Witten, Germany.,Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway.,Instituteof Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
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9
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Zhu X, Wang Z, Qiu X, Wang W, Bei C, Tan C, Qin L, Ren Y, Tan S. Rs2303428 of MSH2 Is Associated with Hepatocellular Carcinoma Prognosis in a Chinese Population. DNA Cell Biol 2018; 37:634-641. [PMID: 29874113 DOI: 10.1089/dna.2018.4224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The defects of DNA repair genes may lead to genomic instability and cancer. As an important DNA mismatch repair gene that maintains genomic stability from DNA replication errors, genetic variants of mutS homolog 2 (MSH2) are associated with some cancers. In this study, 1021 hepatocellular carcinoma (HCC) cases and 1021 non-HCC controls from Guangxi were included to explore the association between MSH2 single-nucleotide polymorphisms (SNPs) and HCC. Among the eight MSH2 SNPs, only genotype distribution of rs2303428 was significantly different from HCC and non-HCC patients (p < 0.05). Moreover, CT, TT, and CT/TT genotype of rs2303428 could increase HCC risk [OR (95% CI) = 1.758 (1.195-2.657), 1.846 (1.213-2.896), and 1.823 (1.219-2.763), respectively] and decrease the survival time of HCC patients [codominant, HR (95% CI) = 1.267 (1.046-1.535); dominant, HR (95% CI) = 1.675 (1.162-2.414)]. In addition, rs2303428 was found to interact with HBV infection and family history to increase HCC risk by gene-environment analysis (p < 0.05). Finally, multivariate COX regression analysis showed that rs2303428, tumor number, tumor staging, and metastasis had a significant influence on HCC prognosis. Our results provide MSH2 SNP, rs2303428, as a new prognostic biomarker for HCC patients.
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Affiliation(s)
- Xiaonian Zhu
- 1 Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University , Guilin, China
| | - Zhigang Wang
- 1 Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University , Guilin, China
| | - Xiaoqiang Qiu
- 2 Department of Epidemiology and Statistics, School of Public Health, Guangxi Medical University , Nanning, China
| | - Weiwei Wang
- 3 Department of Liver Transplantation, People's Hospital of Zhengzhou University , Zhengzhou, China
| | - Chunhua Bei
- 1 Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University , Guilin, China
| | - Chao Tan
- 1 Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University , Guilin, China
| | - Linyuan Qin
- 1 Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University , Guilin, China
| | - Yuan Ren
- 1 Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University , Guilin, China
| | - Shengkui Tan
- 1 Department of Epidemiology and Statistics, School of Public Health, Guilin Medical University , Guilin, China
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10
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Okawa R, Banno K, Iida M, Yanokura M, Takeda T, Iijima M, Kunitomi-Irie H, Nakamura K, Adachi M, Umene K, Nogami Y, Masuda K, Kobayashi Y, Tominaga E, Aoki D. Aberrant chromatin remodeling in gynecological cancer. Oncol Lett 2017; 14:5107-5113. [PMID: 29113150 DOI: 10.3892/ol.2017.6891] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/11/2017] [Indexed: 12/16/2022] Open
Abstract
Epigenetic regulatory mechanisms are a current focus in studies investigating cancer. Chromatin remodeling alters chromatin structure and regulates gene expression, and aberrant chromatin remodeling is involved in carcinogenesis. AT-rich interactive domain-containing protein 1A (ARID1A) and SWItch/sucrose non-fermentable-related, matrix-associated, actin-dependent regulator of chromatin, subfamily a, member 4 are remodeling factors that are mutated in numerous types of cancer. In gynecological cancer, ARID1A mutations have been identified in 46-57% of clear cell carcinoma and 30% of endometrioid carcinoma. Mutations of chromodomain helicase, DNA-binding protein 4 have been detected in 17-21% of endometrial serous cancer, and mutations of ARID1A and mixed-lineage leukemia 3 occur in 36 and 27% of uterine carcinosarcoma, respectively. These data suggest that aberrant chromatin remodeling is a potential cause of cancer, and have led to the development of novel proteins targeting these processes. Additional accumulation of information on the mechanisms of chromatin remodeling and markers for these events may promote personalized anticancer therapies.
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Affiliation(s)
- Ryuichiro Okawa
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kouji Banno
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Miho Iida
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Megumi Yanokura
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Takashi Takeda
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Moito Iijima
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Haruko Kunitomi-Irie
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kanako Nakamura
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masataka Adachi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kiyoko Umene
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yuya Nogami
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Kenta Masuda
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yusuke Kobayashi
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Eiichiro Tominaga
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-8582, Japan
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11
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Nejadtaghi M, Jafari H, Farrokhi E, Samani KG. Familial Colorectal Cancer Type X (FCCTX) and the correlation with various genes-A systematic review. Curr Probl Cancer 2017; 41:388-397. [PMID: 29096939 DOI: 10.1016/j.currproblcancer.2017.10.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 05/10/2017] [Accepted: 10/12/2017] [Indexed: 02/09/2023]
Abstract
Familial Colorectal Cancer Type X (FCCTX) is a type of hereditary nonpolyposis colorectal cancer in accordance to Amsterdam criteria-1 for Lynch syndrome, with no related mutation in mismatch repair gene. FCCTX is microsatellite stable and is accounted for 40% of families with Amsterdam criteria-1 with a high age of onset. Thus, the carcinogenesis of FCCTX is different compared to Lynch syndrome. In addition to the microsatellite stability and the presence of less predominant tumors in proximal colon, various clinical features have also been associated with FCCTX in comparison with Lynch syndrome such as no increased risk of extra-colonic cancers, older age of diagnosis and higher adenoma/carcinoma rate. Genetic etiology of this type of cancer which is autosomal dominant is unknown. In this review, we focus on the genes and their variants identified in this type of CRC. In order to find out the correlation between FCCTX and various genes database such as PubMed and PMC, search engine such as Google scholar and portals such as Springer and Elsevier have been searched. Based on our literature search, several studies suggest that FCCTX is a heterogeneous type of disease with different genetic variants. Recent studies describe the correlation between FCCTX and genes such as BRCA2, SEMA4, NTS, RASSF9, GALNT12, KRAS, BRAF, APC, BMPR1A, and RPS20. Considering the fact that BRCA2 has the highest mutation rate (60%) and is one of the most crucial DNA repair genes, it will be considered as a big role player in this type of cancer in comparison with other genes.
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Affiliation(s)
- Mahdieh Nejadtaghi
- Cellular and Molecular Research Center, Shahrekord University of Medical Science, Shahrekord, Iran
| | - Hamideh Jafari
- Cellular and Molecular Research Center, Shahrekord University of Medical Science, Shahrekord, Iran
| | - Effat Farrokhi
- Cellular and Molecular Research Center, Shahrekord University of Medical Science, Shahrekord, Iran.
| | - Keihan Ghatreh Samani
- Clinical Biochemistry Research Center, Shahrekord University of Medical Science, Shahrekord, Iran
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12
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Villacis RAR, Basso TR, Canto LM, Pinheiro M, Santiago KM, Giacomazzi J, de Paula CAA, Carraro DM, Ashton-Prolla P, Achatz MI, Rogatto SR. Rare germline alterations in cancer-related genes associated with the risk of multiple primary tumor development. J Mol Med (Berl) 2017; 95:523-533. [PMID: 28093616 DOI: 10.1007/s00109-017-1507-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 12/07/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022]
Abstract
Multiple primary tumors (MPT) have been described in carriers of inherited cancer predisposition genes. However, the genetic etiology of a large proportion of MPT cases remains unclear. We reviewed 267 patients with hereditary cancer predisposition syndromes (HCPS) that underwent genetic counseling and selected 22 patients with MPT to perform genomic analysis (CytoScan HD Array, Affymetrix) aiming to identify new alterations related to a high risk of developing MPT. Twenty patients had a positive family history of cancer and 11 met phenotypic criteria for HCPS. Genetic testing for each of the genes associated with these syndromes revealed negative results for pathogenic mutations. Seventeen rare germline copy number variations (CNVs) covering 40 genes were identified in 11 patients, including an EPCAM/MSH2 deletion in one Lynch syndrome patient. An enrichment analysis revealed a significant number of genes (where the CNVs are mapped) associated with carcinogenesis and/or related to functions implicated with tumor development, such as proliferation and cell survival. An interaction network analysis highlighted the importance of TP53 pathway in cancer emergence. A high number of germline copy-neutral loss of heterozygosity (cnLOH) was identified in nine cases, particularly in two patients. Eighteen genes were covered by both rare CNVs and cnLOH, including 14 related to tumorigenesis and seven genes (ABCC1, KDM4C, KIAA0430, MYH11, NDE1, PIWIL2, and ULK2) specifically associated with cellular growth and proliferation. Overall, we identified 14 cases with rare CNVs and/or cnLOH that may contribute to the risk of MPT development. KEY MESSAGE CNVs may explain the risk of hereditary cancer syndromes in MPT patients. CNVs affecting genes related to cancer are candidates to be involved in MPT risk. EPCAM/MSH2 deletions should be investigated in patients suspected to have LS. Gene enrichment related to the TP53 network is associated with MPT development. cnLOH and CNVs contribute to the risk of MPT development.
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Affiliation(s)
- Rolando A R Villacis
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Tatiane R Basso
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Luisa M Canto
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Maísa Pinheiro
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Karina M Santiago
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Juliana Giacomazzi
- Department of Genetics, Federal University of Rio Grande do Sul (UFRGS) and Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Cláudia A A de Paula
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Dirce M Carraro
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Patrícia Ashton-Prolla
- Department of Genetics, Federal University of Rio Grande do Sul (UFRGS) and Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Maria I Achatz
- Department of Oncogenetics, A.C. Camargo Cancer Center, São Paulo, SP, Brazil.,Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI)/National Institutes of Health (NIH), Bethesda, MD, USA
| | - Silvia R Rogatto
- International Center for Research (CIPE), A.C. Camargo Cancer Center, São Paulo, SP, Brazil. .,Department of Clinical Genetics, Vejle Sygehus, Kabbeltoft 25, 7100, Vejle, Denmark. .,Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark.
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13
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Diniz MG, Duarte AP, Villacis RA, Guimarães BVA, Duarte LCP, Rogatto SR, Gomez RS, Gomes CC. Rare copy number alterations and copy-neutral loss of heterozygosity revealed in ameloblastomas by high-density whole-genome microarray analysis. J Oral Pathol Med 2016; 46:371-376. [PMID: 27682262 DOI: 10.1111/jop.12505] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/19/2016] [Indexed: 02/07/2023]
Abstract
BACKGROUND Ameloblastoma (unicystic, UA, or multicystic, MA) is a rare tumor associated with bone destruction and facial deformity. Its malignant counterpart is the ameloblastic carcinoma (AC). The BRAFV600E mutation is highly prevalent in all these tumors subtypes and cannot account for their different clinical behaviors. METHODS We assessed copy number alterations (CNAs) and copy-neutral loss of heterozygosity (cnLOH) in UA (n = 2), MA (n = 3), and AC (n = 1) using the CytoScan HD Array (Affymetrix) and the BRAFV600E status. RT-qPCR was applied in four selected genes (B4GALT1, BAG1, PKD1L2, and PPP2R5A) covered by rare alterations, also including three MA and four normal oral tissues. RESULTS Fifty-seven CNAs and cnLOH were observed in the ameloblastomas and six CNAs in the AC. Seven of the CNAs were rare (six in UA and one in MA), four of them encompassing genes (gains of 7q11.21, 1q32.3, and 9p21.1 and loss of 16q23.2). We found positive correlation between rare CNA gene dosage and the expression of B4GALT1, BAG1, PKD1L2, and PPP2R5A. The AC and 1 UA were BRAF wild-type; however, this UA showed rare genomic alterations encompassing genes associated with RAF/MAPK activation. CONCLUSION Ameloblastomas show rare CNAs and cnLOH, presenting a specific genomic profile with no overlapping of the rare alterations among UA, MA, and AC. These genomic changes might play a role in tumor evolution and in BRAFV600E-negative tumors.
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Affiliation(s)
- Marina Gonçalves Diniz
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, MG, Brazil
| | - Alessandra Pires Duarte
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, MG, Brazil
| | - Rolando A Villacis
- International Center for Research - CIPE, A. C. Camargo Cancer Center, São Paulo, SP, Brazil.,Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasilia - UnB, Brasilia, DF, Brazil
| | - Bruna V A Guimarães
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, MG, Brazil
| | - Luiz Cláudio Pires Duarte
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, MG, Brazil
| | - Sílvia R Rogatto
- Clinical Genetics Department and Institute of Regional Health, University of Southern Denmark, Odense, Denmark.,Urology Department, Faculty of Medicine, UNESP, Botucatu, SP, Brazil
| | - Ricardo Santiago Gomez
- Department of Oral Surgery and Pathology, School of Dentistry, Universidade Federal de Minas Gerais-UFMG, Belo Horizonte, MG, Brazil
| | - Carolina Cavaliéri Gomes
- Department of Pathology, Biological Sciences Institute, Universidade Federal de Minas Geras-UFMG, Belo Horizonte, MG, Brazil
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