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Gomes ÁNDM, Oliveira KK, Marchi FA, Bettim BB, Germano JN, Gonçalves Filho J, Pinto CAL, Lourenço SV, Coutinho-Camillo CM. TGFβ signaling pathway in salivary gland tumors. Arch Oral Biol 2024; 162:105943. [PMID: 38479278 DOI: 10.1016/j.archoralbio.2024.105943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/05/2024] [Accepted: 03/03/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVE Pleomorphic adenoma (PA), mucoepidermoid carcinoma (MEC), and adenoid cystic carcinoma (ACC) are the most prevalent salivary gland tumors. Their pathogenesis has been recently associated with complex molecular cascades, including the TGFβ signaling pathway. The aim of this study was to evaluate the expression of genes associated with the TGFβ signaling pathway (TGFB1, ITGB6, SMAD2, SMAD4, FBN1, LTBP1, and c-MYC) to map possible downstream alterations in the TGFβ cascade. DESIGN Thirteen PA, 17 MEC, 13 ACC, and 10 non-neoplastic salivary gland samples were analyzed by real-time RT-PCR. RESULTS Cases of PA presented increased TGFB1, LTPB1, c-MYC, and FBN1 expressions, whereas SMAD2 expression was decreased when compared to non-neoplastic tissue. MEC patients displayed increased expressions of TGFB1, ITGB6, FBN1, and c-MYC and decreased expressions of SMAD2 and SMAD4. ACC cases exhibited elevated expressions of the investigated genes except TGFB1. The present results suggest that decreased expression of SMAD2 and SMAD4 does not impede the transcriptional regulation of c-MYC, especially in PA and MEC. Increased expressions of ITGB6, TGFB1, LTBP1, and FBN1 appear to be related to the regulation of the TGFβ signaling pathway in these tumors. Additionally, we observed a higher expression of SMAD4 in ACC and a raised expression of ITGB6 and lowered expression of SMAD2 in MEC. CONCLUSIONS Our study demonstrated the differential expression of TGFβ cascade members in salivary gland tumors such as SMAD2/SMAD4 and c-MYC as well as the participation of ITGB6, TGFB1, LTBP1, and FBN1, contributing to the understanding of the mechanisms involved in tumor progression.
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Affiliation(s)
- Ágatha Nagli de Mello Gomes
- International Research Center, A.C.Camargo Cancer Center, São Paulo, Brazil; National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil
| | | | - Fabio Albuquerque Marchi
- Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo, Brazil; Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo, Brazil
| | | | | | - João Gonçalves Filho
- Department of Head and Neck Surgery and Otorhinolaringology, A.C.Camargo Cancer Center, São Paulo, Brazil
| | | | | | - Cláudia Malheiros Coutinho-Camillo
- International Research Center, A.C.Camargo Cancer Center, São Paulo, Brazil; National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, São Paulo, Brazil.
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2
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Sousa ACDS, Fernandes BLNC, da Silva JPA, Stevanato Filho PR, Coimbra LBDCT, de Oliveira Beserra A, Alvarenga AL, Maida G, Guimaraes CT, Nakamuta IM, Marchi FA, Alves C, Lichtenfels M, de Farias CB, Kupper BEC, Costa FD, de Mello CAL, Carraro DM, Torrezan GT, Lopes A, dos Santos TG. A Case Study of a Rare Undifferentiated Spindle Cell Sarcoma of the Penis: Establishment and Characterization of Patient-Derived Models. Genes (Basel) 2024; 15:424. [PMID: 38674359 PMCID: PMC11049969 DOI: 10.3390/genes15040424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/28/2024] Open
Abstract
Rare sarcomas present significant treatment challenges compared to more prevalent soft tissue sarcomas due to limited treatment options and a poor understanding of their biology. This study investigates a unique case of penile sarcoma, providing a comprehensive morphological and molecular analysis. Through the creation of experimental patient-derived models-including patient-derived xenograft (PDX), 3D, and monolayer primary cultures-we successfully replicated crucial molecular traits observed in the patient's tumor, such as smooth muscle actin and CD99 expression, along with specific mutations in genes like TSC2 and FGFR4. These models are helpful in assessing the potential for an in-depth exploration of this tumor's biology. This comprehensive approach holds promise in identifying potential therapeutic avenues for managing this exceedingly rare soft tissue sarcoma.
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Affiliation(s)
- Ariane Cavalcante dos Santos Sousa
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
- Graduate Program of A.C.Camargo Cancer Center, Sao Paulo 01508-020, Brazil;
| | | | | | - Paulo Roberto Stevanato Filho
- Reference Center in Sarcoma, A.C. Camargo Cancer Center, Sao Paulo 01509-900, Brazil; (P.R.S.F.); (B.E.C.K.); (F.D.C.); (A.L.)
| | - Luiza Bitencourt de Carvalho Terci Coimbra
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
| | - Adriano de Oliveira Beserra
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
- Graduate Program of A.C.Camargo Cancer Center, Sao Paulo 01508-020, Brazil;
| | - Ana Luiza Alvarenga
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
| | - Giovanna Maida
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
| | - Camila Tokumoto Guimaraes
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
| | - Ingrid Martinez Nakamuta
- Graduate Program of A.C.Camargo Cancer Center, Sao Paulo 01508-020, Brazil;
- Heart Institute of School of Medicine, University of Sao Paulo, Sao Paulo 05403-900, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of Sao Paulo (ICESP), Clinical Hospital of the University of Sao Paulo Medical School (HCFMUSP), Sao Paulo 01246-000, Brazil;
| | - Camila Alves
- Ziel Biosciences, Department of Translational Research, Porto Alegre 90050-170, Brazil; (C.A.); (M.L.); (C.B.d.F.)
| | - Martina Lichtenfels
- Ziel Biosciences, Department of Translational Research, Porto Alegre 90050-170, Brazil; (C.A.); (M.L.); (C.B.d.F.)
| | - Caroline Brunetto de Farias
- Ziel Biosciences, Department of Translational Research, Porto Alegre 90050-170, Brazil; (C.A.); (M.L.); (C.B.d.F.)
| | - Bruna Elisa Catin Kupper
- Reference Center in Sarcoma, A.C. Camargo Cancer Center, Sao Paulo 01509-900, Brazil; (P.R.S.F.); (B.E.C.K.); (F.D.C.); (A.L.)
| | - Felipe D’Almeida Costa
- Reference Center in Sarcoma, A.C. Camargo Cancer Center, Sao Paulo 01509-900, Brazil; (P.R.S.F.); (B.E.C.K.); (F.D.C.); (A.L.)
- Anatomic Pathology Department, A.C. Camargo Cancer Center, Sao Paulo 01509-900, Brazil
| | - Celso Abdon Lopes de Mello
- Reference Center in Sarcoma, A.C. Camargo Cancer Center, Sao Paulo 01509-900, Brazil; (P.R.S.F.); (B.E.C.K.); (F.D.C.); (A.L.)
| | - Dirce Maria Carraro
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
| | - Giovana Tardin Torrezan
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
| | - Ademar Lopes
- Reference Center in Sarcoma, A.C. Camargo Cancer Center, Sao Paulo 01509-900, Brazil; (P.R.S.F.); (B.E.C.K.); (F.D.C.); (A.L.)
| | - Tiago Goss dos Santos
- Clinical and Functional Genomics Group, A.C. Camargo Cancer Center, Sao Paulo 01508-010, Brazil; (A.C.d.S.S.); (L.B.d.C.T.C.); (A.d.O.B.); (A.L.A.); (G.M.); (C.T.G.); (D.M.C.); (G.T.T.)
- National Institute of Science and Technology in Oncogenomics and Therapeutic Innovation, Sao Paulo 01508-010, Brazil
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Sorroche BP, Miranda KC, Beltrami CM, Arantes LMRB, Kowalski LP, Marchi FA, Rogatto SR, Almeida JD. HOXA1 3'UTR Methylation Is a Potential Prognostic Biomarker in Oral Squamous cell Carcinoma. Cancers (Basel) 2024; 16:874. [PMID: 38473236 DOI: 10.3390/cancers16050874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/15/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND HOXA1 is a prognostic marker and a potential predictive biomarker for radioresistance in head and neck tumors. Its overexpression has been associated with promoter methylation and a worse prognosis in oral squamous cell carcinoma (OSCC) patients. However, opposite outcomes are also described. The effect of the methylation of this gene on different gene regions, other than the promoter, remains uncertain. We investigated the methylation profile at different genomic regions of HOXA1 in OSCC and correlated differentially methylated CpG sites with clinicopathological data. METHODS The HOXA1 DNA methylation status was evaluated by analyzing data from The Cancer Genome Atlas and three Gene Expression Omnibus datasets. Significant differentially methylated CpG sites were considered with a |∆β| ≥ 0.10 and a Bonferroni-corrected p-value < 0.01. Differentially methylated CpGs were validated by pyrosequencing using two independent cohorts of 15 and 47 OSCC patients, respectively. RESULTS Compared to normal tissues, we found significantly higher DNA methylation levels in the 3'UTR region of HOXA1 in OSCC. Higher methylation levels in tumor samples were positively correlated with smoking habits and patients' overall survival. CONCLUSIONS Our findings suggest that HOXA1 gene body methylation is a promising prognostic biomarker for OSCC with potential clinical applications in patient monitoring.
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Affiliation(s)
- Bruna Pereira Sorroche
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil
| | - Keila Cristina Miranda
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
| | | | | | - Luiz Paulo Kowalski
- Head and Neck Surgery and Otorhinolaryngology Department, AC Camargo Cancer Center, Latin American Cooperative Oncology Group, São Paulo 01509-010, Brazil
- Head and Neck Surgery Department and LIM 28, University of São Paulo Medical School, São Paulo 01246-903, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, Brazil
- Clinical Hospital of the University of Sao Paulo Medical School (HCFMUSP), São Paulo 05403-010, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, 5230 Odense, Denmark
| | - Janete Dias Almeida
- Department of Biosciences and Oral Diagnosis, Institute of Science and Technology, São Paulo State University (UNESP), São José dos Campos 12224-300, Brazil
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4
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Calanca N, Francisco ALN, Bizinelli D, Kuasne H, Barros Filho MC, Flores BCT, Pinto CAL, Rainho CA, Soares MBP, Marchi FA, Kowalski LP, Rogatto SR. DNA methylation-based depiction of the immune microenvironment and immune-associated long non-coding RNAs in oral cavity squamous cell carcinomas. Biomed Pharmacother 2023; 167:115559. [PMID: 37742611 DOI: 10.1016/j.biopha.2023.115559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2023] Open
Abstract
Oral cavity squamous cell carcinoma (OSCC) is a complex and dynamic disease characterized by clinicopathological and molecular heterogeneity. Spatial and temporal heterogeneity of cell subpopulations has been associated with cancer progression and implicated in the prognosis and therapy response. Emerging evidence indicates that aberrant epigenetic profiles in OSCC may foster an immunosuppressive tumor microenvironment by modulating the expression of immune-related long non-coding RNAs (lncRNAs). DNA methylation analysis was performed in 46 matched OSCC and normal adjacent tissue samples using a genome-wide platform (Infinium HumanMethylation450 BeadChip). Reference-based computational deconvolution (MethylCIBERSORT) was applied to infer the immune cell composition of the bulk samples. The expression levels of genes encoding immune markers and differentially methylated lncRNAs were investigated using The Cancer Genome Atlas dataset. OSCC specimens presented distinct immune cell composition, including the enrichment of monocyte lineage cells, natural killer cells, cytotoxic T-lymphocytes, regulatory T-lymphocytes, and neutrophils. In contrast, B-lymphocytes, effector T-lymphocytes, and fibroblasts were diminished in tumor samples. The hypomethylation of three immune-associated lncRNAs (MEG3, MIR155HG, and WFDC21P) at individual CpG sites was confirmed by bisulfite-pyrosequencing. Also, the upregulation of a set of immune markers (FOXP3, GZMB, IL10, IL2RA, TGFB, IFNG, TDO2, IDO1, and HIF1A) was detected. The immune cell composition, immune markers alteration, and dysregulation of immune-associated lncRNAs reinforce the impact of the immune microenvironment in OSCC. These concurrent factors contribute to tumor heterogeneity, suggesting that epi-immunotherapy could be an efficient alternative to treat OSCC.
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Affiliation(s)
- Naiade Calanca
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark; Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil
| | - Ana Lucia Noronha Francisco
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Daniela Bizinelli
- International Research Center (CIPE), A.C.Camargo Cancer Center, São Paulo 01508-010, SP, Brazil
| | - Hellen Kuasne
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal H3A1A3, QC, Canada
| | | | - Bianca Campos Troncarelli Flores
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark
| | | | - Claudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, SP, Brazil
| | - Milena Botelho Pereira Soares
- Health Technology Institute, SENAI CIMATEC, Salvador 41650-010, BA, Brazil; Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
| | - Fabio Albuquerque Marchi
- Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo 05402-000, SP, Brazil
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil; Department of Head and Neck Surgery, University of São Paulo Medical School, São Paulo 05402-000, SP, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark-Vejle, Institute of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark.
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Miranda-Galvis M, Carneiro Soares C, Moretto Carnielli C, Ramalho Buttura J, Sales de Sá R, Kaminagakura E, Marchi FA, Paes Leme AF, Lópes Pinto CA, Santos-Silva AR, Moraes Castilho R, Kowalski LP, Squarize CH. New Insights into the Impact of Human Papillomavirus on Oral Cancer in Young Patients: Proteomic Approach Reveals a Novel Role for S100A8. Cells 2023; 12:cells12091323. [PMID: 37174723 PMCID: PMC10177374 DOI: 10.3390/cells12091323] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/29/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Human papillomavirus (HPV) infection has recently been linked to a subset of cancers affecting the oral cavity. However, the molecular mechanisms underlying HPV-driven oral squamous cell carcinoma (OSCC) onset and progression are poorly understood. METHODS We performed MS-based proteomics profiling based on HPV status in OSCC in young patients, following biological characterization and cell assays to explore the proteome functional landscape. RESULTS Thirty-nine proteins are differentially abundant between HPV (+) and HPV (-) OSCC. Among them, COPS3, DYHC1, and S100A8 are unfavorable for tumor recurrence and survival, in contrast to A2M and Serpine1, low levels of which show an association with better DFS. Remarkably, S100A8 is considered an independent prognostic factor for lower survival rates, and at high levels, it alters tumor-associated immune profiling, showing a lower proportion of M1 macrophages and dendritic cells. HPV (+) OSCC also displayed the pathogen-associated patterns receptor that, when activated, triggered the S100A8 and NFκB inflammatory responses. CONCLUSION HPV (+) OSCC has a peculiar microenvironment pattern distinctive from HPV (-), involving the expression of pathogen-associated pattern receptors, S100A8 overexpression, and NFκB activation and responses, which has important consequences in prognosis and may guide therapeutic decisions.
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Affiliation(s)
- Marisol Miranda-Galvis
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Carolina Carneiro Soares
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
- Department of Microbiology, Immune Biology, and Genetics, Center for Molecular Biology, University of Vienna, 1030 Vienna, Austria
| | - Carolina Moretto Carnielli
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Jaqueline Ramalho Buttura
- Laboratory of Bioinformatics and Computational Biology, A.C.Camargo Cancer Center (CIPE), São Paulo 01508-010, SP, Brazil
| | - Raisa Sales de Sá
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Estela Kaminagakura
- Department of Bioscience and Oral Diagnosis, Science and Technology Institute, University of São Paulo State (UNESP), São José dos Campos 01049-010, SP, Brazil
| | - Fabio Albuquerque Marchi
- Center for Translational Research in Oncology, Cancer Institute of the State of São Paulo (ICESP), São Paulo 01246-000, SP, Brazil
- Comprehensive Center for Precision Oncology, University of São Paulo, São Paulo 05508-900, SP, Brazil
| | - Adriana Franco Paes Leme
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, SP, Brazil
| | - Clóvis A Lópes Pinto
- Department of Anatomic Pathology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Alan Roger Santos-Silva
- Oral Diagnosis Department, Piracicaba Dental School, University of Campinas (UNICAMP), Piracicaba 13414-903, SP, Brazil
| | - Rogerio Moraes Castilho
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Luiz Paulo Kowalski
- Head and Neck Surgery Department, Medical School, University of São Paulo, São Paulo 05508-900, SP, Brazil
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo 01509-001, SP, Brazil
| | - Cristiane Helena Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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Cury SS, Kuasne H, Souza JDS, Muñoz JJM, da Silva JP, Lopes A, Scapulatempo-Neto C, Faria EF, Delaissé JM, Marchi FA, Rogatto SR. Interplay Between Immune and Cancer-Associated Fibroblasts: A Path to Target Metalloproteinases in Penile Cancer. Front Oncol 2022; 12:935093. [PMID: 35928876 PMCID: PMC9343588 DOI: 10.3389/fonc.2022.935093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Extracellular matrix (ECM) remodeling and inflammation have been reported in penile carcinomas (PeCa). However, the cell types and cellular crosstalk involved in PeCa are unexplored. We aimed to characterize the complexity of cells and pathways involved in the tumor microenvironment (TME) in PeCa and propose target molecules associated with the TME. We first investigated the prognostic impact of cell types with a secretory profile to identify drug targets that modulate TME-enriched cells. The secretome analysis using the PeCa transcriptome revealed the enrichment of inflammation and extracellular matrix pathways. Twenty-three secreted factors were upregulated, mainly collagens and matrix metalloproteinases (MMPs). The deregulation of collagens and MMPs was confirmed by Quantitative reverse transcription - polymerase chain reaction (RT-qPCR). Further, the deconvolution method (digital cytometry) of the bulk samples revealed a high proportion of macrophages and dendritic cells (DCs) and B cells. Increased DCs and B cells were associated with better survival. A high proportion of cancer-associated fibroblasts (CAFs) was observed in low-survival patients. Patients with increased CAFs had decreased immune cell proportions. The treatment with the MMP inhibitor GM6001 in CAF cells derived from PeCa resulted in altered cell viability. We reported a crosstalk between immune cells and CAFs, and the proportion of these cell populations was associated with prognosis. We demonstrate that a drug targeting MMPs modulates CAFs, expanding the therapeutic options of PeCa.
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Affiliation(s)
- Sarah Santiloni Cury
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu, Brazil
| | - Hellen Kuasne
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Denmark
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- International Research Center (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Jeferson dos Santos Souza
- Department of Structural and Functional Biology, São Paulo State University (UNESP), Botucatu, Brazil
| | - Juan Jose Moyano Muñoz
- International Research Center (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil
- Universidad Señor de Sipán, Chiclayo, Peru
| | | | - Ademar Lopes
- Pelvic Surgery Department, A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Department of Pathology, Diagnósticos da América - DASA, Barueri, Brazil
| | - Eliney Ferreira Faria
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Uro-oncology and Robotic Surgery, Hospital Felicio Rocho, Belo Horizonte, Brazil
| | - Jean-Marie Delaissé
- Clinical Cell Biology, Lillebaelt Hospital, University Hospital of Southern Denmark, Vejle, Denmark
- Department of Clinical Research, Clinical Cell Biology, University of Southern Denmark, Odense, Denmark
| | | | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, Denmark
- Institute of Regional Health Research, University of Southern Denmark, Odense, Denmark
- *Correspondence: Silvia Regina Rogatto,
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7
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Appolinário CM, Daly JM, Emes RD, Marchi FA, Ribeiro BLD, Megid J. Gene Expression Profile Induced by Two Different Variants of Street Rabies Virus in Mice. Viruses 2022; 14:v14040692. [PMID: 35458422 PMCID: PMC9031335 DOI: 10.3390/v14040692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/20/2022] [Accepted: 03/24/2022] [Indexed: 12/10/2022] Open
Abstract
Pathogenicity and pathology of rabies virus (RABV) varies according to the variant, but the mechanisms are not completely known. In this study, gene expression profile in brains of mice experimentally infected with RABV isolated from a human case of dog rabies (V2) or vampire bat-acquired rabies (V3) were analyzed. In total, 138 array probes associated with 120 genes were expressed differentially between mice inoculated with V2 and sham-inoculated control mice at day 10 post-inoculation. A single probe corresponding to an unannotated gene was identified in V3 versus control mice. Gene ontology (GO) analysis revealed that all of the genes upregulated in mice inoculated with V2 RABV were involved in the biological process of immune defense against pathogens. Although both variants are considered pathogenic, inoculation by the same conditions generated different gene expression results, which is likely due to differences in pathogenesis between the dog and bat RABV variants. This study demonstrated the global gene expression in experimental infection due to V3 wild-type RABV, from the vampire bat Desmodus rotundus, an important source of infection for humans, domestic animals and wildlife in Latin America.
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Affiliation(s)
- Camila M. Appolinário
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubião Júnior, s/n, CEP, Botucatu 18618-970, SP, Brazil;
- Correspondence: (C.M.A.); (J.M.)
| | - Janet M. Daly
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (J.M.D.); (R.D.E.)
| | - Richard D. Emes
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK; (J.M.D.); (R.D.E.)
| | | | - Bruna Leticia Devidé Ribeiro
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubião Júnior, s/n, CEP, Botucatu 18618-970, SP, Brazil;
| | - Jane Megid
- Faculdade de Medicina Veterinária e Zootecnia, Universidade Estadual Paulista, Julio de Mesquita Filho, Distrito de Rubião Júnior, s/n, CEP, Botucatu 18618-970, SP, Brazil;
- Correspondence: (C.M.A.); (J.M.)
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8
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Kerche LE, de Sousa EA, Squarize CH, Oliveira KK, Marchi FA, Bettim BB, Kowalski LP, Soares FA, Lourenço SV, Coutinho-Camillo CM. EMT in salivary gland tumors: the expression of microRNAs miR-155 and miR-200c is associated with clinical-pathological parameters. Mol Biol Rep 2022; 49:2157-2167. [PMID: 34981333 DOI: 10.1007/s11033-021-07033-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/26/2021] [Indexed: 12/27/2022]
Abstract
BACKGROUND Epithelial to mesenchymal transition promotes cell adhesion loss, enabling invasion and metastasis. MicroRNAs are a class of small non-codifying RNAs that regulate gene expression. OBJECTIVES The aim of this study was to evaluate the expression of microRNAs that could regulate the expression of EMT factors in salivary gland tumors (SGTs). METHODS AND RESULTS The expression of microRNAs miR-9, miR-34a, miR-101, miR-138, miR-155, and miR-200c-described in the literature to target EMT factors-was evaluated by Real-time RT-PCR (qPCR) in pleomorphic adenoma (PA), mucoepidermoid carcinoma (MEC) and adenoid cystic carcinoma (ACC) samples. Bioinformatics tools were applied to identify miR targets and immunohistochemistry was used to examine the expression of the proteins E-cadherin, Twist, ZEB-1, β-Catenin, and c-Kit. Comparing miR expression among SGT types, we observed increased expression of miR-9, and miR-138 in PAs, and increased miR-155 expression in MECs. Low-grade MECs exhibited increased miR-155 expression (p = 0.032). MECs that generated lymph node metastases had increased miR-200c levels (p = 0.018). MECs tended to have decreased expression of EMT-related proteins when compared to the other SGT types (c-Kit p < 0.001, Twist p = 0.014, and ZEB p = 0.012). Notably, increased c-Kit expression was associated with the presence of perineural infiltration in ACC (p = 0.050). CONCLUSIONS This study provides evidence of alterations in the expression of EMT-factors regulating miRs, especially of miR-9, miR-138, miR-155, and miR-200c. No significant relationships were found between the expression of these miRs and proteins associated with EMT in SGTs.
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Affiliation(s)
- Leandra Ernst Kerche
- International Research Center, A.C.Camargo Cancer Center, Centro Internacional de Pesquisa, Rua Taguá, 440-Primeiro andar, São Paulo, SP, Brazil
| | - Elen Alves de Sousa
- International Research Center, A.C.Camargo Cancer Center, Centro Internacional de Pesquisa, Rua Taguá, 440-Primeiro andar, São Paulo, SP, Brazil
| | - Cristiane Helena Squarize
- Laboratory of Epithelial Biology, Department of Periodontics and Oral Medicine, University of Michigan School of Dentistry, Ann Arbor, MI, USA.,The Michigan Medicine Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Katia Klug Oliveira
- International Research Center, A.C.Camargo Cancer Center, Centro Internacional de Pesquisa, Rua Taguá, 440-Primeiro andar, São Paulo, SP, Brazil
| | - Fabio Albuquerque Marchi
- International Research Center, A.C.Camargo Cancer Center, Centro Internacional de Pesquisa, Rua Taguá, 440-Primeiro andar, São Paulo, SP, Brazil
| | - Bárbara Beltrame Bettim
- International Research Center, A.C.Camargo Cancer Center, Centro Internacional de Pesquisa, Rua Taguá, 440-Primeiro andar, São Paulo, SP, Brazil
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | | | - Silvia Vanessa Lourenço
- Department of General Pathology, Dental School, University of São Paulo, São Paulo, SP, Brazil
| | - Cláudia Malheiros Coutinho-Camillo
- International Research Center, A.C.Camargo Cancer Center, Centro Internacional de Pesquisa, Rua Taguá, 440-Primeiro andar, São Paulo, SP, Brazil.
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9
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Tarazona JGR, Abdallah EA, Flores BDCT, Braun AC, Camillo CMC, Marchi FA, Ruano APC, Chinen LTD. MIR-203A-3P AND MMP-2 PROTEINS ARE HIGHLY EXPRESSED IN CIRCULATING TUMOR CELLS FROM PATIENTS WITH PANCREATIC CARCINOMA. Arq Bras Cir Dig 2022; 34:e1628. [PMID: 35107490 PMCID: PMC8846380 DOI: 10.1590/0102-672020210002e1628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/07/2020] [Indexed: 12/05/2022]
Abstract
OBJECTIVES Ductal adenocarcinoma of the pancreas is the fourth most common cancer-associated cause of death in the Western world. The presence of circulating tumor cells (CTCs) can be considered a potential prognostic factor, as these cells represent tumor progression, allowing monitoring of therapeutic efficacy. The objectives of this study were to explore the morphological, molecular, and phenotypic characteristics of CTCs from the blood of patients with pancreatic carcinoma and to correlate the findings with response to treatment, progression-free survival, overall survival (OS), and deep vein thrombosis (DVT). METHODS Peripheral blood (10 mL) was analyzed before the beginning of treatment after 60 and 120 days. CTCs were detected by using ISET® and characterized by immunocytochemistry. For microRNAs (miRNAs) analysis, peripheral leukocytes from the same patients and healthy individuals (controls) were collected in parallel at baseline. The expression of miRNAs was evaluated (in pool) using TaqMan® Array Human MicroRNA Cards v2.0. RESULTS Only nine patients were included. The proteins, namely, matrix metalloproteinase-2 (MMP2) and TGFβ-RI, were highly expressed (77.7%) in CTCs at baseline; at the first follow-up, MMP2 was predominant (80%) and, at the second follow-up, MMP2 and vimentin were predominant (50%). Circulating tumor microemboli (CTMs) were found in two patients and both presented DVT. The miR-203a-3p was highly expressed in CTCs. The miR-203a-3p is involved in the stimulation of epithelial-to-mesenchymal transition (EMT) and is related to worse OS in pancreatic cancer (TCGA data). CONCLUSION Due to the low number of patients and short follow-up, we did not observe a correlation between CTCs and response to treatment. However, there was a correlation between CTM and DVT and also miR-203a-3p was highly expressed in CTCs, corroborating the findings of EMT proteins. This study opens the perspectives concerning the dynamic change in the pattern of proteins expressed along with treatment and the use of miRNAs as new targets in pancreatic carcinoma.
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Affiliation(s)
| | - Emne Ali Abdallah
- Hospital A.C. Camargo Cancer Center, Centro de Pesquisa Internacional - São Paulo - SP - Brasil
| | | | - Alexcia Camila Braun
- Hospital A.C. Camargo Cancer Center, Centro de Pesquisa Internacional - São Paulo - SP - Brasil
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10
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Gomig THB, Gontarski AM, Cavalli IJ, Souza RLRD, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, Urban CDA, Marchi RD, Cavalli LR, Ribeiro EMDSF. Integrated analysis of label-free quantitative proteomics and bioinformatics reveal insights into signaling pathways in male breast cancer. Genet Mol Biol 2021; 44:e20190410. [PMID: 33656060 PMCID: PMC7926483 DOI: 10.1590/1678-4685-gmb-2019-0410] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 01/18/2021] [Indexed: 01/04/2023] Open
Abstract
Male breast cancer (MBC) is a rare malignancy that accounts for about 1.8% of all breast cancer cases. In contrast to the high number of the “omics” studies in breast cancer in women, only recently molecular approaches have been performed in MBC research. High-throughput proteomics based methodologies are promisor strategies to characterize the MBC proteomic signatures and their association with clinico-pathological parameters. In this study, the label-free quantification-mass spectrometry and bioinformatics approaches were applied to analyze the proteomic profiling of a MBC case using the primary breast tumor and the corresponding axillary metastatic lymph nodes and adjacent non-tumor breast tissues. The differentially expressed proteins were identified in the signaling pathways of granzyme B, sirtuins, eIF2, actin cytoskeleton, eNOS, acute phase response and calcium and were connected to the upstream regulators MYC, PI3K SMARCA4 and cancer-related chemical drugs. An additional proteomic comparative analysis was performed with a primary breast tumor of a female patient and revealed an interesting set of proteins, which were mainly involved in cancer biology. Together, our data provide a relevant data source for the MBC research that can help the therapeutic strategies for its management.
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Affiliation(s)
| | - Amanda Moletta Gontarski
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós-graduação em Genética, Curitiba, PR, Brazil
| | - Iglenir João Cavalli
- Universidade Federal do Paraná, Departamento de Genética, Programa de Pós-graduação em Genética, Curitiba, PR, Brazil
| | | | | | - Michel Batista
- Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brazil.,Fundação Oswaldo Cruz (Fiocruz), Plataforma de Espectrometria de Massas, Curitiba, PR, Brazil
| | | | - Fabricio Klerynton Marchini
- Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brazil.,Fundação Oswaldo Cruz (Fiocruz), Plataforma de Espectrometria de Massas, Curitiba, PR, Brazil
| | | | - Rubens Silveira Lima
- Hospital Nossa Senhora das Graças, Centro de Doenças da Mama, Curitiba, PR, Brazil
| | | | | | - Luciane Regina Cavalli
- Instituto de Pesquisa Pelé Pequeno Príncipe, Curitiba, PR, Brazil.,Georgetown University, Lombardi Comprehensive Cancer Center, Washington, USA
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11
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Ferreira WAS, Amorim CKN, Burbano RR, Villacis RAR, Marchi FA, Medina TS, Lima MMCD, Oliveira EHCD. Genomic and transcriptomic characterization of the human glioblastoma cell line AHOL1. ACTA ACUST UNITED AC 2021; 54:e9571. [PMID: 33470396 PMCID: PMC7812907 DOI: 10.1590/1414-431x20209571] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.
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Affiliation(s)
- W A S Ferreira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brasil
| | - C K N Amorim
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brasil
| | - R R Burbano
- Laboratório de Citogenética Humana, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, Brasil.,Núcleo de Pesquisas em Oncologia, Hospital Universitário João de Barros Barreto, Belém, PA, Brasil.,Laboratório de Biologia Molecular, Hospital Ophir Loyola, Belém, PA, Brasil
| | - R A R Villacis
- Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, DF, Brasil
| | - F A Marchi
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - T S Medina
- Centro Internacional de Pesquisa, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - M M C de Lima
- Instituto de Ciências Biológicas, Faculdade de Biomedicina, Universidade Federal do Pará, Belém, PA, Brasil
| | - E H C de Oliveira
- Laboratório de Cultura de Tecidos e Citogenética, SAMAM, Instituto Evandro Chagas, Ananindeua, PA, Brasil.,Instituto de Ciências Exatas e Naturais, Faculdade de Ciências Naturais, Universidade Federal do Pará, Belém, PA, Brasil
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12
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Assao A, Domingues MAC, Minicucci EM, Marchi FA, Coutinho-Camillo CM, Oliveira DT. The relevance of miRNAs as promising biomarkers in lip cancer. Clin Oral Investig 2021; 25:4591-4598. [PMID: 33439343 DOI: 10.1007/s00784-020-03773-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/30/2020] [Indexed: 02/07/2023]
Abstract
OBJECTIVES This study aimed to analyze the expression of miR-181b, miR-21, miR-31, and miR-345 in actinic cheilitis with and without epithelial dysplasia and lower lip squamous cell carcinomas, and to verify if the deregulated expression of these miRNAs would be indicative of malignant transformation. MATERIALS AND METHODS The sample was selected from formalin-fixed paraffin-embedded tissues of 19 actinic cheilitis without epithelial dysplasia, 32 actinic cheilitis with epithelial dysplasia, 42 lower lip squamous cell carcinomas, and 10 nonaltered oral mucosa of the lip. The microRNA (miR, miRNA) expression was quantified by real-time RT-PCR and the expression of the selected miRNAs among the groups of actinic cheilitis and lower lip cancer was compared by chi-square. RESULTS A higher expression of miR-181b, miR-31, and miR-345 was found in actinic cheilitis without epithelial dysplasia in comparison to that in actinic cheilitis with epithelial dysplasia and with lower lip cancer. There were no differences in miR-21 expression between actinic cheilitis and lower lip cancer. Hierarchical clustering analysis showed a tendency for a downregulation of miR-181b, miR-21, miR-31, and miR-345 in most patients with lower lip cancers. CONCLUSIONS The upregulation of miR-181b, miR-31, and miR-345 expression in actinic cheilitis without epithelial dysplasia and the decrease in the expression of these miRNAs in actinic cheilitis with epithelial dysplasia and in lower lip cancer are potential biomarkers of malignant progression. CLINICAL RELEVANCE This miRNA signature can help to identify actinic cheilitis with potential to progress to lip cancer.
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Affiliation(s)
- Agnes Assao
- Department of Surgery, Stomatology, Pathology and Radiology, Area of Pathology, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, 9-75, Bauru, São Paulo, 17012-901, Brazil
| | | | - Eliana Maria Minicucci
- Department of Histopathology, Botucatu Medical School, Paulista State University, São Paulo, Brazil
| | | | | | - Denise Tostes Oliveira
- Department of Surgery, Stomatology, Pathology and Radiology, Area of Pathology, Bauru School of Dentistry, University of São Paulo, Alameda Octávio Pinheiro Brisolla, 9-75, Bauru, São Paulo, 17012-901, Brazil.
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13
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da Silva SD, Marchi FA, Su J, Yang L, Valverde L, Hier J, Bijian K, Hier M, Mlynarek A, Kowalski LP, Alaoui-Jamali MA. Co-Overexpression of TWIST1-CSF1 Is a Common Event in Metastatic Oral Cancer and Drives Biologically Aggressive Phenotype. Cancers (Basel) 2021; 13:cancers13010153. [PMID: 33466385 PMCID: PMC7795342 DOI: 10.3390/cancers13010153] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/18/2020] [Indexed: 12/24/2022] Open
Abstract
Invasive oral squamous cell carcinoma (OSCC) is often ulcerated and heavily infiltrated by pro-inflammatory cells. We conducted a genome-wide profiling of tissues from OSCC patients (early versus advanced stages) with 10 years follow-up. Co-amplification and co-overexpression of TWIST1, a transcriptional activator of epithelial-mesenchymal-transition (EMT), and colony-stimulating factor-1 (CSF1), a major chemotactic agent for tumor-associated macrophages (TAMs), were observed in metastatic OSCC cases. The overexpression of these markers strongly predicted poor patient survival (log-rank test, p = 0.0035 and p = 0.0219). Protein analysis confirmed the enhanced expression of TWIST1 and CSF1 in metastatic tissues. In preclinical models using OSCC cell lines, macrophages, and an in vivo matrigel plug assay, we demonstrated that TWIST1 gene overexpression induces the activation of CSF1 while TWIST1 gene silencing down-regulates CSF1 preventing OSCC invasion. Furthermore, excessive macrophage activation and polarization was observed in co-culture system involving OSCC cells overexpressing TWIST1. In summary, this study provides insight into the cooperation between TWIST1 transcription factor and CSF1 to promote OSCC invasiveness and opens up the potential therapeutic utility of currently developed antibodies and small molecules targeting cancer-associated macrophages.
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Affiliation(s)
- Sabrina Daniela da Silva
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (L.V.); (J.H.); (M.H.); (A.M.)
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.); (K.B.)
- Correspondence: or (S.D.d.S.); (M.A.A.-J.); Tel.: +1-514-340-8222 (S.D.d.S.)
| | - Fabio Albuquerque Marchi
- Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), São Paulo 01509-010, Brazil; (F.A.M.); (L.P.K.)
| | - Jie Su
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.); (K.B.)
| | - Long Yang
- School of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China;
| | - Ludmila Valverde
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (L.V.); (J.H.); (M.H.); (A.M.)
| | - Jessica Hier
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (L.V.); (J.H.); (M.H.); (A.M.)
| | - Krikor Bijian
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.); (K.B.)
| | - Michael Hier
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (L.V.); (J.H.); (M.H.); (A.M.)
| | - Alex Mlynarek
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, QC H3T 1E2, Canada; (L.V.); (J.H.); (M.H.); (A.M.)
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), São Paulo 01509-010, Brazil; (F.A.M.); (L.P.K.)
| | - Moulay A. Alaoui-Jamali
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, QC H3T 1E2, Canada; (J.S.); (K.B.)
- Correspondence: or (S.D.d.S.); (M.A.A.-J.); Tel.: +1-514-340-8222 (S.D.d.S.)
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14
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do Canto LM, Barros-Filho MC, Rainho CA, Marinho D, Kupper BEC, Begnami MDFDS, Scapulatempo-Neto C, Havelund BM, Lindebjerg J, Marchi FA, Baumbach J, Aguiar S, Rogatto SR. Comprehensive Analysis of DNA Methylation and Prediction of Response to NeoadjuvantTherapy in Locally Advanced Rectal Cancer. Cancers (Basel) 2020; 12:cancers12113079. [PMID: 33105711 PMCID: PMC7690383 DOI: 10.3390/cancers12113079] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 12/19/2022] Open
Abstract
The treatment for locally advanced rectal carcinomas (LARC) is based on neoadjuvant chemoradiotherapy (nCRT) and surgery, which results in pathological complete response (pCR) in up to 30% of patients. Since epigenetic changes may influence response to therapy, we aimed to identify DNA methylation markers predictive of pCR in LARC patients treated with nCRT. We used high-throughput DNA methylation analysis of 32 treatment-naïve LARC biopsies and five normal rectal tissues to explore the predictive value of differentially methylated (DM) CpGs. External validation was carried out with The Cancer Genome Atlas-Rectal Adenocarcinoma (TCGA-READ 99 cases). A classifier based on three-CpGs DM (linked to OBSL1, GPR1, and INSIG1 genes) was able to discriminate pCR from incomplete responders with high sensitivity and specificity. The methylation levels of the selected CpGs confirmed the predictive value of our classifier in 77 LARCs evaluated by bisulfite pyrosequencing. Evaluation of external datasets (TCGA-READ, GSE81006, GSE75546, and GSE39958) reproduced our results. As the three CpGs were mapped near to regulatory elements, we performed an integrative analysis in regions associated with predicted cis-regulatory elements. A positive and inverse correlation between DNA methylation and gene expression was found in two CpGs. We propose a novel predictive tool based on three CpGs potentially useful for pretreatment screening of LARC patients and guide the selection of treatment modality.
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Affiliation(s)
- Luisa Matos do Canto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- International Research Center–CIPE, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (M.C.B.-F.); (F.A.M.)
| | - Mateus Camargo Barros-Filho
- International Research Center–CIPE, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (M.C.B.-F.); (F.A.M.)
- Department of Head and Neck Surgery, Hospital das Clinicas HCFMUSP, Sao Paulo 01246-903, Brazil
| | - Cláudia Aparecida Rainho
- Department of Chemical and Biological Sciences, Institute of Biosciences, Sao Paulo State University (Unesp), Botucatu 18618-689, Brazil;
| | - Diogo Marinho
- Institute of Biological Psychiatry, Psykiatrisk Center Sct. Hans, 4000 Roskilde, Denmark;
| | - Bruna Elisa Catin Kupper
- Colorectal Cancer Service, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (B.E.C.K.); (S.A.J.)
| | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos – 14784-400, and Diagnósticos da América (DASA), Barueri 06455010, Brazil;
| | - Birgitte Mayland Havelund
- Department of Oncology, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark;
| | - Jan Lindebjerg
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark;
- Department of Pathology, University Hospital of Southern Denmark, 7100 Vejle, Denmark
| | - Fabio Albuquerque Marchi
- International Research Center–CIPE, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (M.C.B.-F.); (F.A.M.)
| | - Jan Baumbach
- TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany;
| | - Samuel Aguiar
- Colorectal Cancer Service, A.C. Camargo Cancer Center, Sao Paulo 04002-010, Brazil; (B.E.C.K.); (S.A.J.)
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
- Danish Colorectal Cancer Center South, 7100 Vejle, Denmark;
- Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, 5000 Odense, Denmark
- Correspondence: ; Tel.: +45-7940-6669
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15
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Pinheiro M, Lupinacci FCS, Santiago KM, Drigo SA, Marchi FA, Fonseca-Alves CE, Andrade SCDS, Aagaard MM, Basso TR, dos Reis MB, Villacis RAR, Roffé M, Hajj GNM, Jurisica I, Kowalski LP, Achatz MI, Rogatto SR. Germline Mutation in MUS81 Resulting in Impaired Protein Stability is Associated with Familial Breast and Thyroid Cancer. Cancers (Basel) 2020; 12:cancers12051289. [PMID: 32443704 PMCID: PMC7281423 DOI: 10.3390/cancers12051289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 01/10/2023] Open
Abstract
Multiple primary thyroid cancer (TC) and breast cancer (BC) are commonly diagnosed, and the lifetime risk for these cancers is increased in patients with a positive family history of both TC and BC. Although this phenotype is partially explained by TP53 or PTEN mutations, a significant number of patients are negative for these alterations. We judiciously recruited patients diagnosed with BC and/or TC having a family history of these tumors and assessed their whole-exome sequencing. After variant prioritization, we selected MUS81 c.1292G>A (p.R431H) for further investigation. This variant was genotyped in a healthy population and sporadic BC/TC tissues and investigated at the protein level and cellular models. MUS81 c.1292G>A was the most frequent variant (25%) and the strongest candidate due to its function of double-strand break repair. This variant was confirmed in four relatives from two families. MUS81 p.R431H protein exhibited lower expression levels in tumors from patients positive for the germline variant, compared with wild-type BC, and normal breast and thyroid tissues. Using cell line models, we showed that c.1292G>A induced protein instability and affected DNA damage response. We suggest that MUS81 is a novel candidate involved in familial BC/TC based on its low frequency in healthy individuals and proven effect in protein stability.
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Affiliation(s)
- Maisa Pinheiro
- Faculty of Medicine, Sao Paulo State University, UNESP, Botucatu SP 18618-687, Brazil;
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Fernanda Cristina Sulla Lupinacci
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Karina Miranda Santiago
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Sandra Aparecida Drigo
- Department of Surgery and Orthopedics, Experimental Research Unity, Faculty of Medicine, São Paulo State University, UNESP, Botucatu SP 18618-687, Brazil;
| | - Fabio Albuquerque Marchi
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Carlos Eduardo Fonseca-Alves
- Department of Veterinary Surgery and Anesthesiology, São Paulo State University, UNESP, Botucatu SP 18618-681, Brazil;
| | | | - Mads Malik Aagaard
- Department of Clinical Genetics, Vejle University Hospital, 7100 Vejle, Denmark;
| | - Tatiane Ramos Basso
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Mariana Bisarro dos Reis
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Rolando André Rios Villacis
- Department of Genetics and Morphology, Institute of Biological Sciences, University of Brasília, UnB, Brasília DF 70910-900, Brazil;
| | - Martin Roffé
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Glaucia Noeli Maroso Hajj
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Igor Jurisica
- Krembil Research Institute, UHN, University of Toronto, Toronto, ON M5G 2C4, Canada;
- Institute of Neuroimmunology, Slovak Academy of Sciences, 845 10 Bratislava, Slovakia
| | - Luiz Paulo Kowalski
- International Research Center, A.C. Camargo Cancer Center, São Paulo SP 01508-010, Brazil; (F.C.S.L.); (K.M.S.); (F.A.M.); (T.R.B.); (M.B.d.R.); (M.R.); (G.N.M.H.); (L.P.K.)
| | - Maria Isabel Achatz
- Cancer Genetics Unit, Centro de Oncologia, Hospital Sirio Libanês, São Paulo SP 01308-050, Brazil;
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, Vejle University Hospital, Institute of Regional Health Research, University of Southern Denmark, 5000 Odense, Denmark
- Correspondence:
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16
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De Souza MF, Kuasne H, Barros-Filho MDC, Cilião HL, Marchi FA, Fuganti PE, Rogatto SR, Cólus IMDS. Circulating mRNA signature as a marker for high-risk prostate cancer. Carcinogenesis 2019; 41:139-145. [DOI: 10.1093/carcin/bgz129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 06/06/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
Abstract
Prostate cancer (PCa) is the second most common cancer in men. The indolent course of the disease makes the treatment choice a challenge for physicians and patients. In this study, a minimally invasive method was used to evaluate the potential of molecular markers in identifying patients with aggressive disease. Cell-free plasma samples from 60 PCa patients collected before radical prostatectomy were used to evaluate the levels of expression of eight genes (AMACR, BCL2, NKX3-1, GOLM1, OR51E2, PCA3, SIM2 and TRPM8) by quantitative real-time PCR. Overexpression of AMACR, GOLM1, TRPM8 and NKX3-1 genes was significantly associated with aggressive disease characteristics, including extracapsular extension, tumor stage and vesicular seminal invasion. A trio of genes (GOLM1, NKX3-1 and TRPM8) was able to identify high-risk PCa cases (85% of sensitivity and 58% of specificity), yielding a better overall performance compared with the biopsy Gleason score and prostate-specific antigen, routinely used in the clinical practice. Although more studies are required, these circulating markers have the potential to be used as an additional test to improve the diagnosis and treatment decision of high-risk PCa patients.
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Affiliation(s)
| | - Hellen Kuasne
- International Research Center—CIPE—A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | | | | | | | | | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
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17
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Canto LMD, Cury SS, Barros-Filho MC, Kupper BEC, Begnami MDFDS, Scapulatempo-Neto C, Carvalho RF, Marchi FA, Olsen DA, Madsen JS, Havelund BM, Aguiar S, Rogatto SR. Locally advanced rectal cancer transcriptomic-based secretome analysis reveals novel biomarkers useful to identify patients according to neoadjuvant chemoradiotherapy response. Sci Rep 2019; 9:8702. [PMID: 31213644 PMCID: PMC6582145 DOI: 10.1038/s41598-019-45151-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 05/31/2019] [Indexed: 12/24/2022] Open
Abstract
Most patients with locally advanced rectal cancer (LARC) present incomplete pathological response (pIR) to neoadjuvant chemoradiotherapy (nCRT). Despite the efforts to predict treatment response using tumor-molecular features, as differentially expressed genes, no molecule has proved to be a strong biomarker. The tumor secretome analysis is a promising strategy for biomarkers identification, which can be assessed using transcriptomic data. We performed transcriptomic-based secretome analysis to select potentially secreted proteins using an in silico approach. The tumor expression profile of 28 LARC biopsies collected before nCRT was compared with normal rectal tissues (NT). The expression profile showed no significant differences between complete (pCR) and incomplete responders to nCRT. Genes with increased expression (pCR = 106 and pIR = 357) were used for secretome analysis based on public databases (Vesiclepedia, Human Cancer Secretome, and Plasma Proteome). Seventeen potentially secreted candidates (pCR = 1, pIR = 13 and 3 in both groups) were further investigated in two independent datasets (TCGA and GSE68204) confirming their over-expression in LARC and association with nCRT response (GSE68204). The expression of circulating amphiregulin and cMET proteins was confirmed in serum from 14 LARC patients. Future studies in liquid biopsies could confirm the utility of these proteins for personalized treatment in LARC patients.
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Affiliation(s)
- Luisa Matos do Canto
- International Research Center - CIPE, A.C.Camargo Cancer Center, Sao Paulo, 04002-010, Brazil.,Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Sarah Santiloni Cury
- Department of Morphology - Institute of Bioscience, São Paulo State University (UNESP), Botucatu, 18618689, Brazil
| | | | | | | | | | - Robson Francisco Carvalho
- Department of Morphology - Institute of Bioscience, São Paulo State University (UNESP), Botucatu, 18618689, Brazil
| | | | - Dorte Aalund Olsen
- Department of Biochemistry and Immunology, University Hospital of Southern Denmark, Vejle, 7100, Denmark
| | - Jonna Skov Madsen
- Department of Biochemistry and Immunology, University Hospital of Southern Denmark, Vejle, 7100, Denmark.,Danish Colorectal Cancer Center South, Vejle, 7100, Denmark.,Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Vejle, 7100, Denmark
| | - Birgitte Mayland Havelund
- Danish Colorectal Cancer Center South, Vejle, 7100, Denmark.,Department of Oncology, University Hospital of Southern Denmark, 7100, Vejle, Denmark
| | - Samuel Aguiar
- Department of Pelvic Surgery, A.C.Camargo Cancer Center, Sao Paulo, 04002-010, Brazil
| | - Silvia Regina Rogatto
- Department of Clinical Genetics, University Hospital of Southern Denmark, Vejle, 7100, Denmark. .,Danish Colorectal Cancer Center South, Vejle, 7100, Denmark. .,Institute of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Vejle, 7100, Denmark.
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18
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Gomig THB, Cavalli IJ, Souza RLRD, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, Urban CDA, Cavalli LR, Ribeiro EMDSF. High-throughput mass spectrometry and bioinformatics analysis of breast cancer proteomic data. Data Brief 2019; 25:104125. [PMID: 31294064 PMCID: PMC6595893 DOI: 10.1016/j.dib.2019.104125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 05/28/2019] [Accepted: 05/31/2019] [Indexed: 12/23/2022] Open
Abstract
Data present here describe a comparative proteomic analysis among the malignant [primary breast tumor (PT) and axillary metastatic lymph nodes (LN)], and the non-tumor [contralateral (NCT) and adjacent (ANT)] breast tissues. Protein identification and quantification were performed through label-free mass spectrometry using a nano-liquid chromatography coupled to an electrospray ionization-mass spectrometry (nLC-ESI-MS/MS). The mass spectrometry proteomic data have been deposited to the ProteomeXchange Consortium via PRIDE partner repository with the dataset identifier PXD012431. A total of 462 differentially expressed proteins was identified among these tissues and was analyzed in six groups' comparisons (named NCTxANT, PTxNCT, PTxANT, LNxNCT, LNxANT and PTxLN). Proteins at 1.5 log2 fold change were submitted to the Ingenuity® Pathway Analysis (IPA) software version 2.3 (QIAGEN Inc.) to identify biological pathways, disease and function annotation, and interaction networks related to cancer biology. The detailed data present here provides information about the proteome alterations and their role on breast tumorigenesis. This information can lead to novel biological insights on cancer research. For further interpretation of these data, please see our research article 'Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer' [2].
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Affiliation(s)
| | | | | | | | - Michel Batista
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil.,Mass Spectrometry Facility - RPT02H, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | | | - Fabricio Klerynton Marchini
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil.,Mass Spectrometry Facility - RPT02H, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | | | | | | | - Luciane Regina Cavalli
- Research Institute Pele Pequeno Principe, Curitiba, Brazil.,Lombardi Comprehensive Cancer Center, Georgetown University, USA
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19
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Lapa RML, Barros-Filho MC, Marchi FA, Domingues MAC, de Carvalho GB, Drigo SA, Kowalski LP, Rogatto SR. Integrated miRNA and mRNA expression analysis uncovers drug targets in laryngeal squamous cell carcinoma patients. Oral Oncol 2019; 93:76-84. [PMID: 31109699 DOI: 10.1016/j.oraloncology.2019.04.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/20/2019] [Accepted: 04/24/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVES The current treatment of laryngeal squamous cell carcinoma (LSCC) is based on radical surgery and radiotherapy resulting in high morbidity. Chemoradiotherapy has been used as alternative to organ sparing; however, several advanced cases presented resistance to treatment, which contributes to a high risk of recurrence and mortality. Coding RNAs and miRNAs have potential to be used as biomarkers or targets for cancer therapy. MATERIALS AND METHODS In this study, 36 LSCC and 5 non-neoplastic control samples were investigated using miRNA and mRNA large-scale expression analysis and a cross-validation was performed using the TCGA database (116 LSCC and 12 surrounding normal tissues). RESULTS The large-scale profiling revealed the involvement of 28 miRNAs and 817 genes differentially expressed in LSCC. An integrative analysis comprising predicted and experimentally validated miRNA/mRNA interactions (negatively correlated), resulted in 28 miRNAs and 543 mRNAs. Decreased expression of miR-199b was significantly associated with shorter disease-free survival in LSCC (internal and TCGA datasets). The expression levels of selected miRNAs (miR-199b-5p, miR-29c-3p, miR-204-5p, miR-125b-5p and miR-92a-3p) and genes (COL3A1, COL10A1, ERBB4, HMGA2, HLF, TOP2A, MMP3, MMP13, MMP10 and PPP1R3) were confirmed as altered in LSCC by RT-qPCR. Additionally, a drug target prediction analysis revealed drug combinations based on miRNA and mRNA expression, pointing out novel alternatives to optimize the LSCC treatment. CONCLUSION Collectively, these findings provide new insights in the LSCC transcriptional deregulation and potential drug targets.
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Affiliation(s)
- Rainer Marco Lopez Lapa
- International Research Center, CIPE - A.C.Camargo Cancer Center, São Paulo, Brazil; Department of Genetics, Institute of Bioscience, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | | | | | | | | | - Sandra Aparecida Drigo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University - UNESP, Botucatu, SP, Brazil
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A.C.Camargo Cancer Center, São Paulo Brazil
| | - Silvia Regina Rogatto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University - UNESP, Botucatu, SP, Brazil; Department of Clinical Genetics, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Denmark.
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20
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Baptistella AR, Landemberger MC, Dias MVS, Giudice FS, Rodrigues BR, da Silva PPCE, Cassinela EK, Lacerda TC, Marchi FA, Leme AFP, Begnami MD, Aguiar S, Martins VR. Rab5C enhances resistance to ionizing radiation in rectal cancer. J Mol Med (Berl) 2019; 97:855-869. [DOI: 10.1007/s00109-019-01760-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/08/2019] [Accepted: 02/18/2019] [Indexed: 11/30/2022]
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21
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Gomig THB, Cavalli IJ, Souza RLRD, Vieira E, Lucena ACR, Batista M, Machado KC, Marchini FK, Marchi FA, Lima RS, de Andrade Urban C, Cavalli LR, Ribeiro EMDSF. Quantitative label-free mass spectrometry using contralateral and adjacent breast tissues reveal differentially expressed proteins and their predicted impacts on pathways and cellular functions in breast cancer. J Proteomics 2019; 199:1-14. [PMID: 30772490 DOI: 10.1016/j.jprot.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 01/27/2019] [Accepted: 02/11/2019] [Indexed: 02/08/2023]
Abstract
Proteins play an essential role in the biological processes associated with cancer. Their altered expression levels can deregulate critical cellular pathways and interactive networks. In this study, the mass spectrometry-based label-free quantification followed by functional annotation was performed to investigate the most significant deregulated proteins among tissues of primary breast tumor (PT) and axillary metastatic lymph node (LN) and corresponding non-tumor tissues contralateral (NCT) and adjacent (ANT) from patients diagnosed with invasive ductal carcinoma. A total of 462 proteins was observed as differentially expressed (DEPs) among the groups analyzed. A high level of similarity was observed in the proteome profile of both non-tumor breast tissues and DEPs (n = 12) were mainly predicted in the RNA metabolism. The DEPs among the malignant and non-tumor breast tissues [n = 396 (PTxNCT) and n = 410 (LNxNCT)] were related to pathways of the LXR/RXR, NO, eNOS, eIF2 and sirtuins, tumor-related functions, fatty acid metabolism and oxidative stress. Remarkable similarity was observed between both malignant tissues, which the DEPs were related to metastatic capabilities. Altogether, our findings revealed differential proteomic profiles that affected cancer associated and interconnected signaling processes. Validation studies are recommended to demonstrate the potential of individual proteins and/or pathways as biological markers in breast cancer. SIGNIFICANCE: The proteomic analysis of this study revealed high similarity in the proteomic profile of the contralateral and adjacent non-tumor breast tissues. Significant differences were identified among the proteome of the malignant and non-tumor tissue groups of the same patients, providing relevant insights into the hallmarks, signaling pathways, biological functions, and interactive protein networks that act during tumorigenesis and breast cancer progression. These proteins are suggested as targets of relevant interest to be explored as potential biological markers related to tumor development and metastatic progression in the breast cancer disease.
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Affiliation(s)
| | | | | | - Evelyn Vieira
- Genetics Department, Federal University of Parana, Curitiba, Brazil
| | | | - Michel Batista
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility - RPT02H, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | | | - Fabricio Klerynton Marchini
- Functional Genomics Laboratory, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil; Mass Spectrometry Facility - RPT02H, Carlos Chagas Institute, Fiocruz, Curitiba, Parana, Brazil
| | | | | | | | - Luciane Regina Cavalli
- Research Institute Pele Pequeno Principe, Curitiba, Brazil; Lombardi Comprehensive Cancer Center, Georgetown University, USA
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22
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Alves MR, Do Amaral NS, Marchi FA, Silva FIDB, Da Costa AABA, Carvalho KC, Baiocchi G, Soares FA, De Brot L, Rocha RM. Prostaglandin D2 expression is prognostic in high‑grade serous ovarian cancer. Oncol Rep 2019; 41:2254-2264. [PMID: 30720106 DOI: 10.3892/or.2019.6984] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/02/2018] [Indexed: 11/05/2022] Open
Abstract
To identify biomarkers that could predict response or lack of response to conventional chemotherapy at the time of diagnosis of high‑grade serous ovarian carcinoma (HGSOC), the present study compared large‑scale gene expression from patients with short or long disease‑free survival times, according to the last cycle of chemotherapy, and validated these findings using reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) and conventional immunohistochemical (IHC) analysis. Samples were selected for microarray evaluation, at the time of diagnosis, using the following criteria: Identical debulking primary surgery, International Federation of Gynaecology and Obstetrics staging, histological subtype and grade. These were divided into 2 groups, regarding the outcome after 2 years of follow-up. Prostaglandin D2 synthase 21 kDa (brain) (PTGDS) was found to be expressed at a significantly higher level in the tumours of patients with a short disease‑free survival time, and this was validated by RT‑qPCR in all samples. Furthermore, the study evaluated PGD2, the protein product of the PTGDS gene, in a large cohort of 114 HGSOC patients using the Ventana Benchmark automated platform, and IHC positivity was correlated with clinicopathological data and outcome. The global gene expression analysis identified 1,149 genes that were differentially expressed in microarray data, according to the patient outcome. Further analysis RT‑qPCR validated PTGDS gene expression in the same samples (r=0.945; P<0.001). IHC analysis showed an inverse profile, with positivity for PGD2 strongly associated with an increase in disease‑free survival (P=0.009), the absence of relapse (P=0.039) and sensitivity to platinum‑based therapy (P=0.016). Multiple Cox regression showed that IHC evaluation of PGD2 was also a prognostic marker associated with relapse (hazard ratio, 0.37; P=0.002). Overall, the results showed that IHC evaluation of PGD2 is an independent marker of good prognosis in HGSOC. This finding contributes to our understanding of the mechanism of tumour regulation and to investigations into biomarkers that predict response to chemotherapy.
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Affiliation(s)
- Mariana Rezende Alves
- Department of Anatomical Pathology, A.C. Camargo Cancer Center, São Paulo 01509‑010, Brazil
| | - Nayra Soares Do Amaral
- Department of Anatomical Pathology, A.C. Camargo Cancer Center, São Paulo 01509‑010, Brazil
| | | | | | | | - Kátia Cândido Carvalho
- Department of Obstetrics and Gynaecology, Faculty of Medicine, University of São Paulo, São Paulo 01246‑903, Brazil
| | - Glauco Baiocchi
- Department of Gynaecological Oncology, A.C. Camargo Cancer Center, São Paulo 01509‑010, Brazil
| | | | - Louise De Brot
- Department of Anatomical Pathology, A.C. Camargo Cancer Center, São Paulo 01509‑010, Brazil
| | - Rafael Malagoli Rocha
- Molecular Gynaecology Laboratory, Department of Gynaecology, Federal University of São Paulo, São Paulo 04021‑001, Brazil
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23
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da Silva SD, Xu B, Maschietto M, Marchi FA, Alkailani MI, Bijian K, Xiao D, Alaoui-Jamali MA. TRAF2 Cooperates with Focal Adhesion Signaling to Regulate Cancer Cell Susceptibility to Anoikis. Mol Cancer Ther 2018; 18:139-146. [PMID: 30373932 DOI: 10.1158/1535-7163.mct-17-1261] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 05/14/2018] [Accepted: 10/23/2018] [Indexed: 11/16/2022]
Abstract
TRAF2, a RING finger adaptor protein, plays an important function in tumor necrosis factor (TNF)- and TNF-like weak inducer of apoptosis (TWEAK)-dependent signaling, in particular during inflammatory and immune responses. We identified a functional interaction of TRAF2 with focal adhesion (FA) signaling involving the focal adhesion kinase (FAK) in the regulation of cell susceptibility to anoikis. Comparison of TRAF2-proficient (TRAF2+/+) versus TRAF2-deficient (TRAF2-/-), and FAK-proficient (FAK+/+) versus FAK-deficient (FAK-/-) mouse embryonic fibroblasts and their matched reconstituted cells demonstrated that TRAF2 interacts physically with the N-terminal portion of FAK and colocalizes to cell membrane protrusions. This interaction was found to be critical for promoting resistance to cell anoikis. Similar results were confirmed in the human breast cancer cell line MDA-MB-231, where TRAF2 and FAK downregulation promoted cell susceptibility to anoikis. In human breast cancer tissues, genomic analysis of The Cancer Genome Atlas database revealed coamplification of TRAF2 and FAK in breast cancer tissues with a predictive value for shorter survival, further supporting a potential role of TRAF2-FAK cooperative signaling in cancer progression.
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Affiliation(s)
- Sabrina Daniela da Silva
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.,Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Bin Xu
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | | | - Fabio Albuquerque Marchi
- AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), São Paulo, Brazil
| | - Maisa I Alkailani
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Krikor Bijian
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Dingzhang Xiao
- Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong, China
| | - Moulay A Alaoui-Jamali
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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Ortiz IMD, Barros-Filho MDC, Reis MBD, Beltrami CM, Marchi FA, Kuasne H, Pinto C, Kowalski L, Rogatto S. Abstract 4416: MiRNAs genes are regulated by methylation in papillary thyroid carcinomas. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-4416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Papillary thyroid cancer (PTC) is the most common thyroid malignancy. DNA methylation associated with microRNAs (miRNA) regulation is an effective epigenetic mechanism for controlling gene expression. This mechanism is poorly explored in PTC. Patients and Methods: To investigate miRNAs genes regulated by methylation, global DNA methylation (Infinium® Human Methylation450 BeadChip, Illumina) analysis was performed in 50 matched PTC and normal tissues (NT) and compared with those deposited in The Cancer Genome Atlas (TCGA) (515 PTC and 56 NT). An integrative analysis was performed in 510 cases evaluated by whole methylation and miRNA expression analysis (TCGA). Using these findings, three miRNAs were investigated by RT-qPCR and pyrosequencing in PTC (N=103), normal thyroid tissues (NT, N=40) and benign thyroid lesions (BTL, N=32). In addition, seven target genes of these miRNAs were evaluated by RT-qPCR (44PTC, 30BTL and 28NT). Functional assays using three PTC cell lines (TPC1, K1 and BCPAP) were used to investigate the role of methylation in the miRNAs expression. Results: We found 50 differentially methylated probes of which 42 (27 microRNA genes) were confirmed in the TCGA database. The miRNA expression data from TCGA presented 67 differentially expressed miRNAs in PTC. The integrative analysis revealed three miRNAs (hsa-miR-146b-5p, hsa-miR-146b-3p and hsa-miR-21-5p) as candidates to be regulated by methylation. A significant hypomethylation pattern in PTC compared to NT and BTL (thyroid benign lesions) was found for these three miRNAs. Increased expression levels of hsa-miR-21-5p and hsa-miR-146b-5p were detected in PTC compared to NT and BTL. Combining these two miRNAs expression values, 45/47 PTC were distinguished from 66/67 non-malignant tissues (96% sensitivity and 99% specificity). Similarly, the association of methylation and expression data distinguished 41/45 PTC from 55/60 non-malignant tissues (91% sensitivity and 92% specificity) for MIR21 gene and 45/47 PTC from 61/61 NT/BTL (96% sensitivity and 100% specificity) for MIR146B gene. Seven target genes (MPPED2, STXBP5L, MRO, FHL1, FLRT1, DOK6 and MOB3B) of these miRNAs were significantly down regulated in PTC compared to NT and BTL. The BRAFV600E mutation was significantly associated to hypomethylation and overexpression of hsa-miR-21-5p and hsa-miR-146b-5p. Methylation and expression data in these three cell lines revealed that MIR146B is putatively regulated by methylation. Conclusion: We provide evidences that MIR21 and MIR146B genes are regulated by methylation having control in the expression of target genes associated with PTC. These miRNAs have a strong potential to be used as diagnostic markers in the clinical practice.
Citation Format: Isabella Maria D. Ortiz, Mateus de Camargo Barros-Filho, Mariana B. dos Reis, Caroline Moraes Beltrami, Fabio Albuquerque Marchi, Hellen Kuasne, Clovis Pinto, Luiz Kowalski, Silvia Rogatto. MiRNAs genes are regulated by methylation in papillary thyroid carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4416.
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Affiliation(s)
| | | | - Mariana B. dos Reis
- 2Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Dinamarca, Denmark
| | | | | | | | | | | | - Silvia Rogatto
- 3Institute of Regional Health Research - University of Southern Denmark, Vejle, Denmark
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de Souza MF, Kuasne H, Barros-Filho MDC, Cilião HL, Marchi FA, Fuganti PE, Paschoal AR, Rogatto SR, Cólus IMDS. Circulating mRNAs and miRNAs as candidate markers for the diagnosis and prognosis of prostate cancer. PLoS One 2017; 12:e0184094. [PMID: 28910345 PMCID: PMC5598937 DOI: 10.1371/journal.pone.0184094] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 08/17/2017] [Indexed: 02/07/2023] Open
Abstract
Circulating nucleic acids are found in free form in body fluids and may serve as minimally invasive tools for cancer diagnosis and prognosis. Only a few studies have investigated the potential application of circulating mRNAs and microRNAs (miRNAs) in prostate cancer (PCa). The Cancer Genome Atlas (TCGA) database was used for an in silico analysis to identify circulating mRNA and miRNA as potential markers of PCa. A total of 2,267 genes and 49 miRNAs were differentially expressed between normal and tumor samples. The prediction analyses of target genes and integrative analysis of mRNA and miRNA expression revealed eleven genes and eight miRNAs which were validated by RT-qPCR in plasma samples from 102 untreated PCa patients and 50 cancer-free individuals. Two genes, OR51E2 and SIM2, and two miRNAs, miR-200c and miR-200b, showed significant association with PCa. Expression levels of these transcripts distinguished PCa patients from controls (67% sensitivity and 75% specificity). PCa patients and controls with prostate-specific antigen (PSA) ≤ 4.0 ng/mL were discriminated based on OR51E2 and SIM2 expression levels. The miR-200c expression showed association with Gleason score and miR-200b, with bone metastasis, bilateral tumor, and PSA > 10.0 ng/mL. The combination of circulating mRNA and miRNA was useful for the diagnosis and prognosis of PCa.
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Affiliation(s)
| | - Hellen Kuasne
- CIPE, AC Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | | | | | | | | | - Alexandre Rossi Paschoal
- Department of Computing, Federal University of Technology—Paraná, UTFPR, Cornélio Procópio, Paraná, Brazil
| | - Silvia Regina Rogatto
- CIPE, AC Camargo Cancer Center, São Paulo, São Paulo, Brazil
- Department of Clinical Genetics, Vejle Hospital and Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
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Marchi FA, Martins DC, Barros-Filho MC, Kuasne H, Busso Lopes AF, Brentani H, Trindade Filho JCS, Guimarães GC, Faria EF, Scapulatempo-Neto C, Lopes A, Rogatto SR. Multidimensional integrative analysis uncovers driver candidates and biomarkers in penile carcinoma. Sci Rep 2017; 7:6707. [PMID: 28751665 PMCID: PMC5532302 DOI: 10.1038/s41598-017-06659-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 06/19/2017] [Indexed: 01/24/2023] Open
Abstract
Molecular data generation and their combination in penile carcinomas (PeCa), a significant public health problem in poor and underdeveloped countries, remain virtually unexplored. An integrativemethodology combin ing genome-wide copy number alteration, DNA methylation, miRNA and mRNA expression analysis was performed in a set of 20 usual PeCa. The well-ranked 16 driver candidates harboring genomic alterations and regulated by a set of miRNAs, including hsa-miR-31, hsa-miR-34a and hsa-miR-130b, were significantly associated with over-represented pathways in cancer, such as immune-inflammatory system, apoptosis and cell cycle. Modules of co-expressed genes generated from expression matrix were associated with driver candidates and classified according to the over-representation of passengers, thus suggesting an alteration of the pathway dynamics during the carcinogenesis. This association resulted in 10 top driver candidates (AR, BIRC5, DNMT3B, ERBB4, FGFR1, PML, PPARG, RB1, TNFSF10 and STAT1) selected and confirmed as altered in an independent set of 33 PeCa samples. In addition to the potential driver genes herein described, shorter overall survival was associated with BIRC5 and DNMT3B overexpression (log-rank test, P = 0.026 and P = 0.002, respectively) highlighting its potential as novel prognostic marker for penile cancer.
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Affiliation(s)
| | - David Correa Martins
- Center of Mathematics, Computing and Cognition, Federal University of ABC - UFABC, Santo André, SP, Brazil
| | | | | | | | - Helena Brentani
- Department of Psychiatry, Medical School, University of Sao Paulo - USP, São Paulo, SP, Brazil
| | | | | | - Eliney F Faria
- Department of Urology, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | | | - Ademar Lopes
- A.C.Camargo Cancer Center, São Paulo, SP, Brazil
| | - Silvia Regina Rogatto
- Department of Urology, Faculty of Medicine, Sao Paulo State University - UNESP, Botucatu, SP, Brazil.
- Department of Clinical Genetics, Vejle Hospital and Institute of Regional Health, University of Southern Denmark, Odense, Denmark.
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Reis MBD, Beltrami CM, Barros-Filho MC, Marchi FA, Kuasne H, Ambatipudi S, Herceg Z, Kowalski LP, Rogatto SR. Abstract 3358: Epigenetic signatures associated with patient outcome in thyroid carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
BACKGROUND: Thyroid cancer (TC) is the most frequent endocrine neoplasia composed essentially by well-differentiated tumors (90%). These tumors generally are indolent and the patients show a favorable outcome. However, a set of TC patients presents aggressive outcome. Global deregulation of DNA methylation has been described as involved in thyroid cancer (TC) development. In this study, DNA methylation profile was performed aiming to identify a prognostic signature in TC.
PATIENTS AND METHODS: The methylation profile of 50 non-neoplastic thyroid tissues (NT), 17 benign thyroid lesions and 74 TC (60 papillary, 8 follicular, 2 Hürthle cell, 1 poorly differentiated and 3 anaplastic thyroid carcinomas) were investigated using the Methylation 450 Human Infinium®BeadChip platform (Illumina). The data were normalized and analyzed using SVA, wateRmelon and LIMMA packages. The threshold delta beta of 0.2 and adjusted p-value <0.05 were used to identify differentially methylated probes among the histological subtypes. The delta beta of 0.1 and adjusted p-value <0.05 were used in the prognostic features analysis in WDTC (well differentiated thyroid cancer) cases. An epigenetic classifier according to WDTC was identified using diagonal linear discriminant analysis. The results were compared with The Cancer Genome Atlas (TCGA) database.
RESULTS: Methylation analyses revealed a specific epigenetic profile according to the histological subtypes. A global hypermethylation was observed in benign lesions and follicular carcinomas, while papillary and undifferentiated carcinomas were widely hypomethylated compared with NT. An epigenetic signature comprising 21 probes differentially methylated (delta beta 0.1) was able to predict poor outcome in WDTC patients. This classifier reveled 63% of sensitivity and 92% of specificity, which was confirmed by TCGA database (64% of sensitivity and 88% of specificity). Using the established signature, we were able to confirm the involvement of poor prognosis markers with high-risk scores (multivariable analysis; P<0.001).
CONCLUSION: Thyroid tumors showed different methylation profile according to the histological subtypes. Genes regulated by methylation in TC and associated with the tumor development were identified and confirmed by TCGA. In addition, a meaningful algorithm was designed and confirmed as capable to predict recurrence in WDTC.
FINANCIAL SUPPORT: FAPESP (2015/20548-5) and National Institute of Science and Technology in Oncogenomics (FAPESP 2008/57887-9 and CNPq 573589/08-9), CNPq (302606/2011-4).
Note: This abstract was not presented at the meeting.
Citation Format: Mariana Bisarro dos Reis, Caroline Moraes Beltrami, Mateus Camargo Barros-Filho, Fabio Albuquerque Marchi, Hellen Kuasne, Skirant Ambatipudi, Zdenko Herceg, Luiz Paulo Kowalski, Silvia Regina Rogatto. Epigenetic signatures associated with patient outcome in thyroid carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3358. doi:10.1158/1538-7445.AM2017-3358
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Affiliation(s)
| | | | | | | | | | | | - Zdenko Herceg
- 3International Agency for Research on Cancer, France
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28
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Pinheiro M, Drigo SA, Tonhosolo R, Andrade SC, Marchi FA, Jurisica I, Kowalski LP, Achatz MI, Rogatto SR. HABP2 p.G534E variant in patients with family history of thyroid and breast cancer. Oncotarget 2017; 8:40896-40905. [PMID: 28402931 PMCID: PMC5522276 DOI: 10.18632/oncotarget.16639] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/13/2017] [Indexed: 01/07/2023] Open
Abstract
Familial Papillary Thyroid Carcinoma (PTC) has been described as a hereditary predisposition cancer syndrome associated with mutations in candidate genes including HABP2. Two of 20 probands from families with history of PTC and breast carcinoma (BC) were evaluated by whole exome sequencing (WES) revealing HABP2 p.G534E. Sanger sequencing was used to confirm the involvement of this variant in three families (F1: 7 relatives; F2: 3 and F3: 3). The proband and his sister (with no malignant tumor so far) from F1 were homozygous for the variant whereas one relative with PTC from F2 was negative for the variant. Although the proband of the F3 with PTC was HABP2 wild type, three relatives presented the variant. Five of 170 healthy Brazilian individuals with no family history of BC or PTC and three of 50 sporadic PTC presented the p.G534E. These findings suggested no association of this variant with our familial PTC cases. Genes potentially associated with deregulation of the extracellular matrix organization pathway (CTSB, TNXB, COL4A3, COL16A1, COL24A1, COL5A2, NID1, LOXL2, MMP11, TRIM24 and MUSK) and DNA repair function (NBN and MSH2) were detected by WES, suggesting that other cancer-associated genes have pathogenic effects in the risk of familial PTC development.
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Affiliation(s)
- Maisa Pinheiro
- CIPE - International Research Center, A. C. Camargo Cancer Center, Sao Paulo, SP, Brazil
- Department of Urology, Faculty of Medicine, São Paulo State University, UNESP, Botucatu, SP, Brazil
| | - Sandra Aparecida Drigo
- Department of Urology, Faculty of Medicine, São Paulo State University, UNESP, Botucatu, SP, Brazil
| | - Renata Tonhosolo
- CIPE - International Research Center, A. C. Camargo Cancer Center, Sao Paulo, SP, Brazil
| | - Sonia C.S. Andrade
- Department of Genetics and Evolutionary Biology, University of Sao Paulo, USP, Sao Paulo, SP, Brazil
| | | | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network and The University of Toronto, Toronto, ON, Canada
- Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, A. C. Camargo Cancer Center, Sao Paulo, SP, Brazil
| | - Maria Isabel Achatz
- CIPE - International Research Center, A. C. Camargo Cancer Center, Sao Paulo, SP, Brazil
- Division of Cancer Epidemiology and Genetics, National Cancer Institute/National Institutes of Health, Bethesda, MD, USA
| | - Silvia Regina Rogatto
- CIPE - International Research Center, A. C. Camargo Cancer Center, Sao Paulo, SP, Brazil
- Department of Urology, Faculty of Medicine, São Paulo State University, UNESP, Botucatu, SP, Brazil
- Department of Clinical Genetics, Vejle Hospital, Institute of Regional Health Research, University of Southern Denmark, Vejle, Denmark
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Beltrami CM, dos Reis MB, Barros-Filho MC, Marchi FA, Kuasne H, Pinto CAL, Ambatipudi S, Herceg Z, Kowalski LP, Rogatto SR. Integrated data analysis reveals potential drivers and pathways disrupted by DNA methylation in papillary thyroid carcinomas. Clin Epigenetics 2017; 9:45. [PMID: 28469731 PMCID: PMC5414166 DOI: 10.1186/s13148-017-0346-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 04/14/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Papillary thyroid carcinoma (PTC) is a common endocrine neoplasm with a recent increase in incidence in many countries. Although PTC has been explored by gene expression and DNA methylation studies, the regulatory mechanisms of the methylation on the gene expression was poorly clarified. In this study, DNA methylation profile (Illumina HumanMethylation 450K) of 41 PTC paired with non-neoplastic adjacent tissues (NT) was carried out to identify and contribute to the elucidation of the role of novel genic and intergenic regions beyond those described in the promoter and CpG islands (CGI). An integrative and cross-validation analysis were performed aiming to identify molecular drivers and pathways that are PTC-related. RESULTS The comparisons between PTC and NT revealed 4995 methylated probes (88% hypomethylated in PTC) and 1446 differentially expressed transcripts cross-validated by the The Cancer Genome Atlas data. The majority of these probes was found in non-promoters regions, distant from CGI and enriched by enhancers. The integrative analysis between gene expression and DNA methylation revealed 185 and 38 genes (mainly in the promoter and body regions, respectively) with negative and positive correlation, respectively. Genes showing negative correlation underlined FGF and retinoic acid signaling as critical canonical pathways disrupted by DNA methylation in PTC. BRAF mutation was detected in 68% (28 of 41) of the tumors, which presented a higher level of demethylation (95% hypomethylated probes) compared with BRAF wild-type tumors. A similar integrative analysis uncovered 40 of 254 differentially expressed genes, which are potentially regulated by DNA methylation in BRAFV600E-positive tumors. The methylation and expression pattern of six selected genes (ERBB3, FGF1, FGFR2, GABRB2, HMGA2, and RDH5) were confirmed as altered by pyrosequencing and RT-qPCR. CONCLUSIONS DNA methylation loss in non-promoter, poor CGI and enhancer-enriched regions was a significant event in PTC, especially in tumors harboring BRAFV600E. In addition to the promoter region, gene body and 3'UTR methylation have also the potential to influence the gene expression levels (both, repressing and inducing). The integrative analysis revealed genes potentially regulated by DNA methylation pointing out potential drivers and biomarkers related to PTC development.
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Affiliation(s)
- Caroline Moraes Beltrami
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
| | - Mariana Bisarro dos Reis
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
- Department of Urology, Faculty of Medicine, UNESP, Sao Paulo State University, Botucatu, São Paulo Brazil
| | - Mateus Camargo Barros-Filho
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
| | - Fabio Albuquerque Marchi
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
| | - Hellen Kuasne
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
- Department of Urology, Faculty of Medicine, UNESP, Sao Paulo State University, Botucatu, São Paulo Brazil
| | | | - Srikant Ambatipudi
- Epigenetics Group; International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- Epigenetics Group; International Agency for Research on Cancer (IARC), Lyon, France
| | - Luiz Paulo Kowalski
- International Research Center-CIPE–A.C. Camargo Cancer Center and National Institute of Science and Technology in Oncogenomics (INCiTO), São Paulo, Brazil
- Department of Head and Neck Surgery and Otorhinolaryngology, A. C. Camargo Cancer Center, São Paulo, SP Brazil
| | - Silvia Regina Rogatto
- Department of Urology, Faculty of Medicine, UNESP, Sao Paulo State University, Botucatu, São Paulo Brazil
- Department of Clinical Genetics, Vejle Hospital and Institute of Regional Health Research, University of Southern Denmark, Kabbeltoft 25, Vejle, 7100 Denmark
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da Silva SD, Marchi FA, Xu B, Bijian K, Alobaid F, Mlynarek A, Rogatto SR, Hier M, Kowalski LP, Alaoui-Jamali MA. Predominant Rab-GTPase amplicons contributing to oral squamous cell carcinoma progression to metastasis. Oncotarget 2016; 6:21950-63. [PMID: 26110570 PMCID: PMC4673138 DOI: 10.18632/oncotarget.4277] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 06/03/2015] [Indexed: 11/25/2022] Open
Abstract
Metastatic oral squamous cell carcinoma (OSCC) is frequently associated with recurrent gene abnormalities at specific chromosomal loci. Here, we utilized array comparative genomic hybridization and genome-wide screening of metastatic and non-metastatic tongue tumors to investigate genes potentially contributing to OSCC progression to metastasis. We identified predominant amplifications of chromosomal regions that encompass the RAB5, RAB7 and RAB11 genes (3p24-p22, 3q21.3 and 8p11-12, respectively) in metastatic OSCC. The expression of these Rab GTPases was confirmed by immunohistochemistry in OSCC tissues from a cohort of patients with a follow-up of 10 years. A significant overexpression of Rab5, Rab7 and Rab11 was observed in advanced OSCC cases and co-overexpression of these Rabs was predictive of poor survival (log-rank test, P = 0.006). We generated a Rab interaction network and identified central Rab interactions of relevance to metastasis signaling, including focal adhesion proteins. In preclinical models, mRNA and protein expression levels of these Rab members were elevated in a panel of invasive OSCC cell lines, and their down-regulation prevented cell invasion at least in part via inhibition of focal adhesion disassembly. In summary, our results provide insights into the cooperative role of Rab gene amplifications in OSCC progression and support their potential utility as prognostic markers and therapeutic approach for advanced OSCC.
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Affiliation(s)
- Sabrina Daniela da Silva
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada.,Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada.,Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), Brazil
| | - Fabio Albuquerque Marchi
- NeoGene Laboratory, Department of Urology, Faculty of Medicine, UNESP, and International Research Center (CIPE), AC Camargo Cancer Center, Brazil.,Inter-Institutional Grad Program on Bioinformatics, University of São Paulo, Brazil
| | - Bin Xu
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada
| | - Krikor Bijian
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada
| | - Faisal Alobaid
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada
| | - Alex Mlynarek
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada
| | - Silvia Regina Rogatto
- NeoGene Laboratory, Department of Urology, Faculty of Medicine, UNESP, and International Research Center (CIPE), AC Camargo Cancer Center, Brazil
| | - Michael Hier
- Department of Otolaryngology Head and Neck Surgery, Sir Mortimer B. Davis-Jewish General Hospital, Canada
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), Brazil
| | - Moulay A Alaoui-Jamali
- Segal Cancer Centre and Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Departments of Medicine, Oncology, and Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Canada
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Beltrami CM, dos Reis MB, Barros-Filho MC, Marchi FA, Kuasne H, Ambatipudi S, Herceg Z, Kowalski LP, Rogatto SR. Abstract 3829: DNA methylation profile in papillary thyroid cancer according to BRAF (V600E) mutation. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-3829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Thyroid cancer is an important health burden and the endocrine neoplasia with highest incidence in worldwide. Papillary thyroid cancer (PTC), the most common thyroid malignancy, is frequently associated with BRAF V600E mutation. This mutation occurs in around 45% of PTC cases and it has been associated with aberrant gene methylation. This finding suggests an association between genetic and epigenetic alterations in tumor development. The goal of this study was to evaluate the methylation profile in PTC samples according to BRAF mutation.
Patients and Method: Forty-two PTC were included in this study (28 positive for BRAF V600E mutation). Normal and tumoral samples were obtained from patients submitted to total thyroidectomy and radioiodine therapy. The pyrosequencing method was used to detect and quantify the BRAF V600E mutation in tumor samples. The methylation analysis was performed by microarray platform Methylation 450 Human Infinium®BeadChip (Illumina), according to the manufacturer's recommendations. The data were normalized and analyzed using SVA, wateRmelon and LIMMA package. It was considered only probes with Delta-Beta (β) = 0.1 and p value ≤ 0.001. Integrative analyses were performed using expression data generated from previous analysis. The findings were compared with 56 samples from The Cancer Genome Atlas (TCGA). Genes enrichment to biological pathways were performed using Ingenuity Pathway Analysis software.
Results: It was identified 404 differentially methylated probes (291 hypomethylated and 113 hypermethylated) of which 195 were validated by TCGA. After the integrative analysis with expression data, nine TOP genes (INF2, TACSTD2, RAB15, TM7SF4, GJB3, CDSN, BHLHE41, GTF2IRD1, CXXC5) were selected with hypomethylation and overexpression. Three of them, BHLHE41, CDSN and INF2, were enriched to cancer and endocrine system disorders pathways (P = 4,47×10−2), highlighting the relevance of these genes in PTC
Conclusion: This study point out putative drivers in PTC according to BRAF mutation revealing epigenetic mechanisms that contributes with cell proliferation and aggressiveness in thyroid carcinoma.
Citation Format: Caroline Moraes Beltrami, Mariana Bisarro dos Reis, Mateus Camargo Barros-Filho, Fabio Albuquerque Marchi, Hellen Kuasne, Srikant Ambatipudi, Zdenko Herceg, Luiz Paulo Kowalski, Silvia Regina Rogatto. DNA methylation profile in papillary thyroid cancer according to BRAF (V600E) mutation. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3829. doi:10.1158/1538-7445.AM2015-3829
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Affiliation(s)
| | | | | | | | | | | | - Zdenko Herceg
- 3International Agency for Research on Cancer, Lyon, France
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Voorwald FA, Marchi FA, Villacis RAR, Alves CEF, Toniollo GH, Amorim RL, Drigo SA, Rogatto SR. Molecular Expression Profile Reveals Potential Biomarkers and Therapeutic Targets in Canine Endometrial Lesions. PLoS One 2015. [PMID: 26222498 PMCID: PMC4519320 DOI: 10.1371/journal.pone.0133894] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Cystic endometrial hyperplasia (CEH), mucometra, and pyometra are common uterine diseases in intact dogs, with pyometra being a life threatening disease. This study aimed to determine the gene expression profile of these lesions and potential biomarkers for closed-cervix pyometra, the most severe condition. Total RNA was extracted from 69 fresh endometrium samples collected from 21 healthy female dogs during diestrus, 16 CEH, 15 mucometra and 17 pyometra (eight open and nine closed-cervixes). Global gene expression was detected using the Affymetrix Canine Gene 1.0 ST Array. Unsupervised analysis revealed two clusters, one mainly composed of diestrus and CEH samples and the other by 12/15 mucometra and all pyometra samples. When comparing pyometra with other groups, 189 differentially expressed genes were detected. SLPI, PTGS2/COX2, MMP1, S100A8, S100A9 and IL8 were among the top up-regulated genes detected in pyometra, further confirmed by external expression data. Notably, a particular molecular profile in pyometra from animals previously treated with exogenous progesterone compounds was observed in comparison with pyometra from untreated dogs as well as with other groups irrespective of exogenous hormone treatment status. In addition to S100A8 and S100A9 genes, overexpression of the inflammatory cytokines IL1B, TNF and IL6 as well as LTF were detected in the pyometra from treated animals. Interestingly, closed pyometra was more frequently detected in treated dogs (64% versus 33%), with IL1B, TNF, LBP and CXCL10 among the most relevant overexpressed genes. This molecular signature associated with potential biomarkers and therapeutic targets, such as CXCL10 and COX2, should guide future clinical studies. Based on the gene expression profile we suggested that pyometra from progesterone treated dogs is a distinct molecular entity.
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Affiliation(s)
- Fabiana Azevedo Voorwald
- Veterinary Clinic and Department of Surgery, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | | | | | | | - Gilson Hélio Toniollo
- Veterinary Clinic and Department of Surgery, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Renee Laufer Amorim
- Veterinary Clinic Department, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Sandra Aparecida Drigo
- Department of Urology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Silvia Regina Rogatto
- International Research Center (CIPE), A. C. Camargo Cancer Center, São Paulo, Brazil
- Department of Urology, Faculty of Medicine, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- * E-mail:
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Barros-Filho MC, Marchi FA, Pinto CA, Rogatto SR, Kowalski LP. High Diagnostic Accuracy Based on CLDN10, HMGA2, and LAMB3 Transcripts in Papillary Thyroid Carcinoma. J Clin Endocrinol Metab 2015; 100:E890-9. [PMID: 25867809 DOI: 10.1210/jc.2014-4053] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Thyroid nodules are common in adult population and papillary thyroid carcinoma (PTC) is the most frequent malignant finding. The natural history of PTC remains poorly understood and current diagnostic methods limitations are responsible for a significant number of potentially avoidable surgeries. OBJECTIVE This study aimed to identify molecular markers to improve the diagnosis of thyroid lesions. DESIGN Gene expression profiling was performed using microarray in 61 PTC and 13 surrounding normal tissues (NT). A reliable gene list was established using cross-study validation (138 matched PTC/NT from external databases). Results were collectively interpreted by in silico analysis. A panel of 28 transcripts was evaluated by RT-qPCR, including benign thyroid lesions (BTL) and other follicular cell-derived thyroid carcinomas (OFDTC). A diagnostic algorithm was developed (training set: 23 NT, 8 BTL, and 86 PTC), validated (independent set: 10 NT, 140 BTL, 120 PTC, and 12 OFDTC) and associated with clinical features. RESULTS GABRB2 was ranked as the most frequently up-regulated gene in PTC (cross-study validation). Altered genes in PTC suggested a loss of T4 responsiveness and dysregulation of retinoic acid metabolism, highlighting the putative activation of EZH2 and histone deacetylases (predicted in silico). An algorithm combining CLDN10, HMGA2, and LAMB3 transcripts was able to discriminate tumors from BTL samples (94% sensitivity and 96% specificity in validation set). High algorithm scores were associated with regional lymph node metastases. CONCLUSIONS A promising tool with high performance for PTC diagnosis based on three transcripts was designed with the potential to predict lymph node metastasis risk.
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Affiliation(s)
- Mateus Camargo Barros-Filho
- International Research Center/AC Camargo Cancer Center (M.C.B.F., F.A.M., C.A.P., S.R.R., S.R.R.), Sao Paulo 01509-010, SP, Brazil; and Faculty of Medicine (S.R.R.), Sao Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Fabio Albuquerque Marchi
- International Research Center/AC Camargo Cancer Center (M.C.B.F., F.A.M., C.A.P., S.R.R., S.R.R.), Sao Paulo 01509-010, SP, Brazil; and Faculty of Medicine (S.R.R.), Sao Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Clóvis Antônio Pinto
- International Research Center/AC Camargo Cancer Center (M.C.B.F., F.A.M., C.A.P., S.R.R., S.R.R.), Sao Paulo 01509-010, SP, Brazil; and Faculty of Medicine (S.R.R.), Sao Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Silvia Regina Rogatto
- International Research Center/AC Camargo Cancer Center (M.C.B.F., F.A.M., C.A.P., S.R.R., S.R.R.), Sao Paulo 01509-010, SP, Brazil; and Faculty of Medicine (S.R.R.), Sao Paulo State University, Botucatu 18618-970, SP, Brazil
| | - Luiz Paulo Kowalski
- International Research Center/AC Camargo Cancer Center (M.C.B.F., F.A.M., C.A.P., S.R.R., S.R.R.), Sao Paulo 01509-010, SP, Brazil; and Faculty of Medicine (S.R.R.), Sao Paulo State University, Botucatu 18618-970, SP, Brazil
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Fortes FP, Kuasne H, Marchi FA, Miranda PM, Rogatto SR, Achatz MI. DNA methylation patterns of candidate genes regulated by thymine DNA glycosylase in patients with TP53 germline mutations. ACTA ACUST UNITED AC 2015; 48:610-5. [PMID: 25945745 PMCID: PMC4512099 DOI: 10.1590/1414-431x20154026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 02/05/2015] [Indexed: 01/07/2023]
Abstract
Li-Fraumeni syndrome (LFS) is a rare, autosomal dominant, hereditary cancer predisposition disorder. In Brazil, the p.R337H TP53 founder mutation causes the variant form of LFS, Li-Fraumeni-like syndrome. The occurrence of cancer and age of disease onset are known to vary, even in patients carrying the same mutation, and several mechanisms such as genetic and epigenetic alterations may be involved in this variability. However, the extent of involvement of such events has not been clarified. It is well established that p53 regulates several pathways, including the thymine DNA glycosylase (TDG) pathway, which regulates the DNA methylation of several genes. This study aimed to identify the DNA methylation pattern of genes potentially related to the TDG pathway (CDKN2A, FOXA1, HOXD8, OCT4, SOX2, and SOX17) in 30 patients with germline TP53 mutations, 10 patients with wild-type TP53, and 10 healthy individuals. We also evaluated TDG expression in patients with adrenocortical tumors (ADR) with and without the p.R337H TP53 mutation. Gene methylation patterns of peripheral blood DNA samples assessed by pyrosequencing revealed no significant differences between the three groups. However, increased TDG expression was observed by quantitative reverse transcription PCR in p.R337H carriers with ADR. Considering the rarity of this phenotype and the relevance of these findings, further studies using a larger sample set are necessary to confirm our results.
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Affiliation(s)
- F P Fortes
- CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - H Kuasne
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - F A Marchi
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - P M Miranda
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - S R Rogatto
- CIPE, Laboratrio NeoGene, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
| | - M I Achatz
- CIPE, Laboratrio de Oncogentica Molecular, A.C. Camargo Cancer Center, São Paulo, SP, Brasil
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Kuasne H, Cólus IMDS, Busso AF, Hernandez-Vargas H, Barros-Filho MC, Marchi FA, Scapulatempo-Neto C, Faria EF, Lopes A, Guimarães GC, Herceg Z, Rogatto SR. Genome-wide methylation and transcriptome analysis in penile carcinoma: uncovering new molecular markers. Clin Epigenetics 2015; 7:46. [PMID: 25908946 PMCID: PMC4407795 DOI: 10.1186/s13148-015-0082-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/06/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Despite penile carcinoma (PeCa) being a relatively rare neoplasm, it remains an important public health issue for poor and developing countries. Contrary to most tumors, limited data are available for markers that are capable of assisting in diagnosis, prognosis, and treatment of PeCa. We aimed to identify molecular markers for PeCa by evaluating their epigenomic and transcriptome profiles and comparing them with surrounding non-malignant tissue (SNT) and normal glans (NG). RESULTS Genome-wide methylation analysis revealed 171 hypermethylated probes in PeCa. Transcriptome profiling presented 2,883 underexpressed and 1,378 overexpressed genes. Integrative analysis revealed a panel of 54 genes with an inverse correlation between methylation and gene expression levels. Distinct methylome and transcriptome patterns were found for human papillomavirus (HPV)-positive (38.6%) and negative tumors. Interestingly, grade 3 tumors showed a distinct methylation profile when compared to grade 1. In addition, univariate analysis revealed that low BDNF methylation was associated with lymph node metastasis and shorter disease-free survival. CpG hypermethylation and gene underexpression were confirmed for a panel of genes, including TWIST1, RSOP2, SOX3, SOX17, PROM1, OTX2, HOXA3, and MEIS1. CONCLUSIONS A unique methylome signature was found for PeCa compared to SNT, with aberrant DNA methylation appearing to modulate the expression of specific genes. This study describes new pathways with the potential to regulate penile carcinogenesis, including stem cell regulatory pathways and markers associated to a worse prognosis. These findings may be instrumental in the discovery and application of new genetic and epigenetic biomarkers in PeCa.
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Affiliation(s)
- Hellen Kuasne
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
- />Department of Biology, Londrina State University, Londrina, PR Brazil
| | | | - Ariane Fidelis Busso
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
| | | | - Mateus Camargo Barros-Filho
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
| | - Fabio Albuquerque Marchi
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
- />Inter-institutional Grad Program on Bioinformatics, Institute of Mathematics and Statistics, USP, São Paulo, SP Brazil
| | - Cristovam Scapulatempo-Neto
- />Department of Pathology, CPOM - Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP Brazil
| | | | - Ademar Lopes
- />Department of Pelvic Surgery, AC Camargo Cancer Center, São Paulo, Brazil
| | | | - Zdenko Herceg
- />Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Silvia Regina Rogatto
- />CIPE - International Research Center, AC Camargo Cancer Center, Rua Taguá, 440, CEP: 01508-010, Liberdade, São Paulo, SP Brazil
- />Department of Urology, Faculty of Medicine, UNESP, Botucatu, SP Brazil
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Silveira SM, da Cunha IW, Marchi FA, Busso AF, Lopes A, Rogatto SR. Genomic screening of testicular germ cell tumors from monozygotic twins. Orphanet J Rare Dis 2014; 9:181. [PMID: 25424124 PMCID: PMC4254261 DOI: 10.1186/s13023-014-0181-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 11/04/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Testicular germ cell tumors (TGCTs) account for 1-2% of all tumors in young and middle aged men. A 75-fold increase in TCGT development has been reported for monozygotic (MZ) twins. Therefore, the occurrence of simultaneous tumors in MZ twins emphasizes the importance of genetic factors that influence the risk of developing these tumors. Genomic screening was performed for one family containing MZ twins with testicular germ cell tumors, in order to define alterations associated with risk of tumor development. METHODS Copy number alterations were evaluated using array-CGH (4x44K, Agilent Technologies) in one seminoma and one embryonal carcinoma (EC) from MZ twins. In addition, genomic alterations from the tumors and peripheral blood cells of the twins were compared to the parental genomes via their peripheral blood cells. RESULTS Embryonal carcinoma (Twin-1 t) presented a lower frequency of genomic alterations compared to the seminoma (Twin-2 t). One minimal common region of loss was observed in 9p13.1-p12 in the comparison between DNA from blood samples for Twin-1 and Twin-2. In this region is mapped the CNTNAP3 gene which was confirmed as involved in losses by qPCR. Comparative analysis of novel CNVs between the Twin-1 t and Twin-2 t showed five minimal common regions involving gain at chromosomes 12 (12p12.3-p11.1 and 12p13.33-p12.3), while losses were observed at 10p15.3-p15.2, 13q21.1-q21.2 and 15q11.1-q11.2. In addition, one exclusive rare copy number alteration was detected in Twin-1 t and Twin-2 t, and 19 novel alterations were identified in the Twin-2 t. CONCLUSION Distinct genomic profiles for MZ twins with phenotypically different TGCT were described. Of particular interest, 12p gains were detected exclusively in tumor samples. In peripheral blood samples, loss of 9p13.1-p12 was the unique novel CNV shared by the twins, confirming the involvement of CNTNAP3 gene in TGCTs development. Although similar CNV profiles were shared by both the peripheral blood and tumor samples of the twins, tumor-specific CNV loci were identified for seminoma and non-seminomatous tumors. These findings suggest the presence of de novo germline structural alterations and TGCT predisposition.
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Affiliation(s)
| | | | - Fabio Albuquerque Marchi
- Institute of Mathematics and Statistics, Inter-Institutional Program on Bioinformatics, USP, São Paulo, Brazil.
| | | | - Ademar Lopes
- Nucleus of Sarcoma, Department of Pelvic Surgery, A.C. Camargo Cancer Center, São Paulo, Brazil.
| | - Silvia Regina Rogatto
- Neogene Laboratory, CIPE, A. C. Camargo Cancer Center, São Paulo, Brazil. .,Department of Urology, Faculty of Medicine, UNESP, Botucatu, São Paulo, Brazil.
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Silveira SM, Villacis RAR, Marchi FA, Barros Filho MDC, Drigo SA, Neto CS, Lopes A, da Cunha IW, Rogatto SR. Genomic signatures predict poor outcome in undifferentiated pleomorphic sarcomas and leiomyosarcomas. PLoS One 2013; 8:e67643. [PMID: 23825676 PMCID: PMC3692486 DOI: 10.1371/journal.pone.0067643] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 05/22/2013] [Indexed: 12/16/2022] Open
Abstract
Undifferentiated high-grade pleomorphic sarcomas (UPSs) display aggressive clinical behavior and frequently develop local recurrence and distant metastasis. Because these sarcomas often share similar morphological patterns with other tumors, particularly leiomyosarcomas (LMSs), classification by exclusion is frequently used. In this study, array-based comparative genomic hybridization (array CGH) was used to analyze 20 UPS and 17 LMS samples from untreated patients. The LMS samples presented a lower frequency of genomic alterations compared with the UPS samples. The most frequently altered UPS regions involved gains at 20q13.33 and 7q22.1 and losses at 3p26.3. Gains at 8q24.3 and 19q13.12 and losses at 9p21.3 were frequently detected in the LMS samples. Of these regions, gains at 1q21.3, 11q12.2-q12.3, 16p11.2, and 19q13.12 were significantly associated with reduced overall survival times in LMS patients. A multivariate analysis revealed that gains at 1q21.3 were an independent prognostic marker of shorter survival times in LMS patients (HR = 13.76; P = 0.019). Although the copy number profiles of the UPS and LMS samples could not be distinguished using unsupervised hierarchical clustering analysis, one of the three clusters presented cases associated with poor prognostic outcome (P = 0.022). A relative copy number analysis for the ARNT, SLC27A3, and PBXIP1 genes was performed using quantitative real-time PCR in 11 LMS and 16 UPS samples. Gains at 1q21-q22 were observed in both tumor types, particularly in the UPS samples. These findings provide strong evidence for the existence of a genomic signature to predict poor outcome in a subset of UPS and LMS patients.
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Affiliation(s)
| | | | - Fabio Albuquerque Marchi
- Institute of Mathematics and Statistics, Inter-Institutional Program on Bioinformatics, USP, São Paulo, São Paulo, Brazil
| | | | | | | | - Ademar Lopes
- Department of Pelvic Surgery, A. C. Camargo Cancer Center, São Paulo, São Paulo, Brazil
| | | | - Silvia Regina Rogatto
- Neogene Laboratory, A. C. Camargo Cancer Center, São Paulo, São Paulo, Brazil
- Department of Urology, Faculty of Medicine, UNESP, Botucatu, São Paulo, Brazil
- * E-mail:
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Kuasne H, Marchi FA, Rogatto SR, de Syllos Cólus IM. Epigenetic mechanisms in penile carcinoma. Int J Mol Sci 2013; 14:10791-808. [PMID: 23702847 PMCID: PMC3709702 DOI: 10.3390/ijms140610791] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/02/2013] [Accepted: 05/09/2013] [Indexed: 11/16/2022] Open
Abstract
Penile carcinoma (PeCa) represents an important public health problem in poor and developing countries. Despite its unpredictable behavior and aggressive treatment, there have only been a few reports regarding its molecular data, especially epigenetic mechanisms. The functional diversity in different cell types is acquired by chromatin modifications, which are established by epigenetic regulatory mechanisms involving DNA methylation, histone acetylation, and miRNAs. Recent evidence indicates that the dysregulation in these processes can result in the development of several diseases, including cancer. Epigenetic alterations, such as the methylation of CpGs islands, may reveal candidates for the development of specific markers for cancer detection, diagnosis and prognosis. There are a few reports on the epigenetic alterations in PeCa, and most of these studies have only focused on alterations in specific genes in a limited number of cases. This review aims to provide an overview of the current knowledge of the epigenetic alterations in PeCa and the promising results in this field. The identification of epigenetically altered genes in PeCa is an important step in understanding the mechanisms involved in this unexplored disease.
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Affiliation(s)
- Hellen Kuasne
- Department of General Biology, Londrina State University, Londrina, PR 86055-900, Brazil; E-Mails: (H.K.); (I.M.S.C.)
- International Research and Teaching Center, CIPE, AC Camargo Cancer Center, São Paulo, SP 01508-010, Brazil
| | - Fabio Albuquerque Marchi
- Inter-institutional Grad Program on Bioinformatics, Institute of Mathematics and Statistics, USP—São Paulo University, São Paulo, SP 05508-090, Brazil; E-Mail:
| | - Silvia Regina Rogatto
- International Research and Teaching Center, CIPE, AC Camargo Cancer Center, São Paulo, SP 01508-010, Brazil
- Department of Urology, Faculty of Medicine, UNESP, Botucatu, SP 18618-970, Brazil
- Author to whom correspondence should be addressed; E-Mail: or ; Tel.: +55-11-3811-6436; Fax: +55-11-3811-6271
| | - Ilce Mara de Syllos Cólus
- Department of General Biology, Londrina State University, Londrina, PR 86055-900, Brazil; E-Mails: (H.K.); (I.M.S.C.)
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Sato-Kuwabara Y, Marchi FA, Klock C, Scapulatempo C, Coimbra F, Rogatto SR, Soares FA. Abstract 3155: Integrated analysis of genomic and transcriptomic data in esophageal squamous cell carcinoma. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-3155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Esophageal squamous cell carcinoma (ESCC) is the 8th most common cancer worldwide and the 6th tumor in frequency in Brazil. Most of cases are diagnosed at an advanced stage and despite the improvement of various treatment modalities the overall survival rates still remain low. In order to identify new possible molecular markers, genomic and transcriptomic data were evaluated using integrative analysis in ESCC samples. Thirty frozen samples of ESCC were carried out in genome-wide expression (GWE) profiling using the Agilent Whole Human Genome Microarray 44K and in Array-CGH (aCGH) using the Agilent Human Genome CGH Microarray 44K following the manufacturer's protocol. Data were extracted and flagged with Feature Extraction and processed using NEXUS 6.0 and TMEV 4.8 Software. A subset of genes identified by the integrated analysis was analyzed for signaling networks using Ingenuity Pathway Analysis (IPA) software. The aCGH analysis revealed 14 significant genomic alterations including 7 gains and 7 losses. Gains were detected at 3q27.3-q28, 3q28-q29, 3q29, 7q21.3-q22.1, 8p11.23-p11.2, 11q13.2-q13.4 and 12p13.31; losses were found at 1p21.1-p13.3, 3p11.1-q11.1, 3p12.1-p11.2, 6q16.3, 9q21.13, 9p21.3 and 13q21.31. A total of 375 genes were mapped to these regions of which 343 genes were involved in genomic gains and 32 in losses. GWE profile identified 1770 differentially expressed genes in comparison with normal tissue including 573 up regulated and 1197 down-regulated. The integrated analysis showed that genomic and transcriptomic results were concordant in 39 genes, in which 36 were up regulated and involved in gain of DNA copy number and 3 genes were down-regulated and associated to genomic losses. According to IPA analysis three significant networks could be defined comprising these genes. The first network comprised 14 of the concordant genes and was associated to functions as cellular assembly and organization, cardiovascular system development and function and cell morphology. The second network (11 genes) was related to cancer, immunological disease and cell cycle. The third network (9 genes) was associated to cancer, RNA post-transcriptional modification and organismal development. A total of 11 genes were involved in genomic gains by aCGH but were considered down-regulated by GWE profiling, while two genes were involved in losses but their transcripts were up-regulated. The IPA analysis showed that these genes are associated to function as drug metabolism, small molecule biochemistry and nucleic acid metabolism. In this study, it was detected significant genomic alterations and genes differentially expressed involved in important signaling networks that could have an impact on tumor development or progression in ESCC. These genes might be useful as a first step to identify molecular markers for improved diagnostic and therapeutic modalities in this tumor.
Citation Format: Yukie Sato-Kuwabara, Fabio Albuquerque Marchi, Clóvis Klock, Cristovam Scapulatempo, Felipe Coimbra, Silvia Regina Rogatto, Fernando Augusto Soares. Integrated analysis of genomic and transcriptomic data in esophageal squamous cell carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3155. doi:10.1158/1538-7445.AM2013-3155
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Silveira SM, Andre Rios Villacis RR, Marchi FA, de Camargo Barros Filho M, Linde SD, Neto CS, da Cunha IW, Lopes A, Rogatto SR. Copy number alteration signature defines undifferentiated pleomorphic sarcomas and leiomyosarcomas with poor prognosis. BMC Proc 2013. [PMCID: PMC3624497 DOI: 10.1186/1753-6561-7-s2-p64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Sato-Kuwabara Y, Marchi FA, Klock C, Coimbra F, Rogatto SR, Soares FA. Abstract 4201: Analysis of gene expression profile and signaling networks potentially involved in lymph node metastasis in esophageal squamous cell carcinoma. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Esophageal squamous cell carcinoma (ESCC) is the 8th most common cancer worldwide and the 6th tumor in frequency in Brazil. Most of cases are diagnosed at an advanced stage and despite the improvement of various treatment modalities the overall survival rates still remain low. The aim of this study was to analyze the gene expression profile to identify the genes related to lymph node metastasis in ESCC samples. Genome-wide expression profiling was carried out in total RNA extracted from 17 frozen tissue samples using the Agilent Whole Human Genome Microarray 44K following the manufacturer's protocol. Data were extracted and flagged with Feature Extraction and processed using TMEV Software. A supervised hierarchical clustering was performed using the Pearson distance metric. Paired t-test analysis with 1000 permutations was performed to generate a list of differentially expressed genes from the comparison between the different groups. Only genes showing a false discovery rate (Q value) <5% were accepted as differentially expressed. The Ingenuity Pathway Analysis (IPA) Software was used to assess the involvement of significantly differentially expressed genes in known pathways and networks. Hierarchical clustering showed two distinct groups according to lymph node metastasis: Group 1 comprised 6 node-negative cases and Group 2 with 11 node-positive cases. The gene expression profiling revealed 338 genes differentially expressed between the two groups, of which 321 showed lower expression and 17 showed a higher expression in cases of Group 2 when compared to those of Group 1. According to IPA analysis five significant networks could be defined comprising the genes differentially expressed between the two groups. The first network with a score of 43 comprised 21 of the differentially expressed genes and was associated to functions as cell-to-cell signaling and interaction, lipid metabolism and molecular transport. The second network (score 22, 13 genes) was related to nucleic acid metabolism, small molecules biochemistry and energy production. The third network (score 21, 14 genes) was associated to cellular signaling, molecular transport and small molecular biochemistry. The network 4 (score of 21, 12 genes) was associated to cancer, DNA replication, recombination and repair and gene expression. The fifth network (score 21, 12 genes) was related to cellular movement, cardiovascular system development and function and neurological disease. In this study, it was detected genes differentially expressed between cases with and without lymph node metastasis involved in important signaling networks that could have an impact on tumor development or progression in ESCC. The identified genes might be useful as a first step to identify molecular markers to predict lymph node metastasis for improved diagnostic and therapeutic modalities in this tumor.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4201. doi:1538-7445.AM2012-4201
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Affiliation(s)
| | - Fabio Albuquerque Marchi
- 2Inter-institutional Grad Program on Bioinformatics of University of São Paulo, São Paulo, Brazil
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