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Nishimura FG, Sampaio BB, Komoto TT, da Silva WJ, da Costa MMG, Haddad GI, Peronni KC, Evangelista AF, Hossain M, Dimmock JR, Bandy B, Beleboni RO, Marins M, Fachin AL. Exploring CDKN1A Upregulation Mechanisms: Insights into Cell Cycle Arrest Induced by NC2603 Curcumin Analog in MCF-7 Breast Cancer Cells. Int J Mol Sci 2024; 25:4989. [PMID: 38732206 PMCID: PMC11084481 DOI: 10.3390/ijms25094989] [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: 04/04/2024] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
Breast cancer stands out as one of the most prevalent malignancies worldwide, necessitating a nuanced understanding of its molecular underpinnings for effective treatment. Hormone receptors in breast cancer cells substantially influence treatment strategies, dictating therapeutic approaches in clinical settings, serving as a guide for drug development, and aiming to enhance treatment specificity and efficacy. Natural compounds, such as curcumin, offer a diverse array of chemical structures with promising therapeutic potential. Despite curcumin's benefits, challenges like poor solubility and rapid metabolism have spurred the exploration of analogs. Here, we evaluated the efficacy of the curcumin analog NC2603 to induce cell cycle arrest in MCF-7 breast cancer cells and explored its molecular mechanisms. Our findings reveal potent inhibition of cell viability (IC50 = 5.6 μM) and greater specificity than doxorubicin toward MCF-7 vs. non-cancer HaCaT cells. Transcriptome analysis identified 12,055 modulated genes, most notably upregulation of GADD45A and downregulation of ESR1, implicating CDKN1A-mediated regulation of proliferation and cell cycle genes. We hypothesize that the curcumin analog by inducing GADD45A expression and repressing ESR1, triggers the expression of CDKN1A, which in turn downregulates the expression of many important genes of proliferation and the cell cycle. These insights advance our understanding of curcumin analogs' therapeutic potential, highlighting not just their role in treatment, but also the molecular pathways involved in their activity toward breast cancer cells.
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Affiliation(s)
- Felipe Garcia Nishimura
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | - Beatriz Borsani Sampaio
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | - Tatiana Takahasi Komoto
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | - Wanessa Julia da Silva
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | - Mariana Mezencio Gregório da Costa
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | - Gabriela Inforçatti Haddad
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | | | - Adriane Feijó Evangelista
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro 21040-900, Brazil;
| | - Mohammad Hossain
- School of Sciences, Indiana University Kokomo, Kokomo, IN 46904, USA;
| | - Jonathan R. Dimmock
- College of Pharmacy and Nutrition, University of Saskatchewan (USask), Saskatoon, SK S7N 5A2, Canada; (J.R.D.); (B.B.)
| | - Brian Bandy
- College of Pharmacy and Nutrition, University of Saskatchewan (USask), Saskatoon, SK S7N 5A2, Canada; (J.R.D.); (B.B.)
| | - Rene Oliveira Beleboni
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | - Mozart Marins
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
| | - Ana Lucia Fachin
- Unidade de Biotecnologia, Universidade de Ribeirão Preto (UNAERP), Ribeirao Preto 14096-900, Brazil; (F.G.N.); (B.B.S.); (T.T.K.); (W.J.d.S.); (M.M.G.d.C.); (G.I.H.); (R.O.B.); (M.M.)
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Campanella NC, Gomes INF, Alves ALV, Leal LF, Evangelista AF, Rosa MN, Melendez ME, Silva VAO, Dias RLK, Abrahão-Machado LF, Santana I, Martinho O, Guimarães DP, Faça VM, Reis RM. Biological and therapeutic implications of RKIP in Gastrointestinal Stromal Tumor (GIST): an integrated transcriptomic and proteomic analysis. Cancer Cell Int 2023; 23:256. [PMID: 37907993 PMCID: PMC10619323 DOI: 10.1186/s12935-023-03102-6] [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: 12/22/2022] [Accepted: 10/16/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND Gastrointestinal stromal tumors (GIST) represent a significant clinical challenge due to their metastatic potential and limited treatment options. Raf kinase inhibitor protein (RKIP), a suppressor of the MAPK signaling pathway, is downregulated in various cancers and acts as a metastasis suppressor. Our previous studies demonstrated low RKIP expression in GIST and its association with poor outcomes. This study aimed to expand on the previous findings and investigate the biological and therapeutic implications of RKIP loss on GIST. METHODS To validate the RKIP prognostic significance, its expression was evaluated by immunohistochemistry in 142 bona fide GIST cases. The functional role of RKIP was evaluated in vitro, using the GIST-T1 cell line, which was knocked out for RKIP. The biological and therapeutic implications of RKIP were evaluated by invasion, migration, apoptosis, and 2D / 3D viability assays. Additionally, the transcriptome and proteome of RKIP knockout cells were determined by NanoString and mass spectrometry, respectively. RESULTS Immunohistochemical analysis revealed the absence of RKIP in 25.3% of GIST cases, correlating with a tendency toward poor prognosis. Functional assays demonstrated that RKIP knockout increased GIST cells' invasion and migration potential by nearly 60%. Moreover, we found that RKIP knockout cells exhibited reduced responsiveness to Imatinib treatment and higher cellular viability in 2D and 3D in vitro models, as assessed by apoptosis-related protein expression. Through comprehensive genetic and proteomic profiling of RKIP knockout cells, we identified several putative RKIP-regulated proteins in GIST, such as COL3A1. CONCLUSIONS Using a multidimensional integrative analysis, we identified, for the first time in GIST, molecules and pathways modulated by RKIP that may potentially drive metastasis and, consequently, poor prognosis in this disease.
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Affiliation(s)
- Nathália Cristina Campanella
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
| | - Izabela Natalia Faria Gomes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
| | - Ana Laura Vieira Alves
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
| | - Leticia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
- School of Health Sciences Dr. Paulo Prata (FACISB), Barretos, 14785-002, Brazil
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
| | - Marcela Nunes Rosa
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
| | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
- Molecular Carcinogenesis Program, National Cancer Institute, Rio de Janeiro, 20231-050, Brazil
| | - Viviane Aline Oliveira Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
- Department of Pathology, School of Medicine, Federal University of Bahia, Salvador, 40110-909, Brazil
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, 40296-710, Brazil
| | - Richard Lucas Konichi Dias
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
- School of Health Sciences Dr. Paulo Prata (FACISB), Barretos, 14785-002, Brazil
| | | | - Iara Santana
- Department of Pathology, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Olga Martinho
- ICVS/3B's - PT Government Associate Laboratory, Braga, 4806-909, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, 4710-057, Portugal
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Vitor Marcel Faça
- Department of Biochemistry and Immunology, Faculdade de Medicina de Ribeirão Preto da Universidade de São Paulo, Ribeirão Preto, 14049-900, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Villela, 1331, CEP 14784 400, Barretos, S. Paulo, 14784-400, Brazil.
- ICVS/3B's - PT Government Associate Laboratory, Braga, 4806-909, Portugal.
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, 4710-057, Portugal.
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Komoto TT, Nishimura FG, Evangelista AF, de Freitas AJA, da Silva G, Silva WA, Peronni K, Marques MMC, Marins M, Fachin AL. Exploring the Therapeutic Potential of trans-Chalcone: Modulation of MicroRNAs Linked to Breast Cancer Progression in MCF-7 Cells. Int J Mol Sci 2023; 24:10785. [PMID: 37445965 DOI: 10.3390/ijms241310785] [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: 05/05/2023] [Revised: 06/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Breast cancer is responsible for 25% of all cancers that affect women. Due to its high heterogeneity pattern in clinical diagnosis and its molecular profile differences, researchers have been seeking new targets and therapies, with more specificity and fewer side effects. Thus, one compound that has garnered our attention is trans-chalcone, which is naturally occurring in various plants and possesses promising biological properties, including antitumor effects. MiRNA is an extensive class of non-coding small, endogenous, and single-stranded RNAs, and it is involved in post-translational gene regulation. Therefore, the objective of this study was to investigate the effects of TChal on miRNAs expression and its relationship with anticancer activity against MCF-7. Initially, the trans-chalcone IC50 value was established by MTT assay for MCF-7and HaCat (non-cancer cell), in which we found out that it was 53.73 and 44.18 μM, respectively. Subsequently, we treated MCF-7 cells with trans-chalcone at its IC50 concentration and performed Mi-seq analysis, which unveiled 23 differentially expressed miRNAs. From this set, we selected five miRNAs (miR-25-5p, miR-27a-3p, miR-891a, miR-449a, and miR-4485) for further validation using qRT-PCR, guided by in silico analysis and their known association with tumorigenesis. In conclusion, our research provides valuable insights into the potential use of TChal to reveal MicroRNAs molecular targets that can be applied in breast cancer therapy.
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Affiliation(s)
- Tatiana Takahasi Komoto
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, Brazil
| | - Felipe Garcia Nishimura
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
| | - Adriane Feijó Evangelista
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro 21040-361, Brazil
| | - Ana Julia Aguiar de Freitas
- Molecular Oncology Research Center, Barretos Cancer Hospital, Teaching and Research Institute, Barretos 14784-400, Brazil
| | - Gabriel da Silva
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
| | - Wilson Araujo Silva
- Center for Medical Genomics at the Clinics Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | - Kamila Peronni
- Center for Medical Genomics at the Clinics Hospital of Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
| | | | - Mozart Marins
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
| | - Ana Lucia Fachin
- Biotechnology Unit, University of Ribeirão Preto, SP, Av. Costábile Romano, 2201, Ribeirão Preto 14096-900, Brazil
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Zanon MF, Scapulatempo-Neto C, Gama RR, Marques MMC, Reis RM, Evangelista AF. Identification of MicroRNA Expression Profiles Related to the Aggressiveness of Salivary Gland Adenoid Cystic Carcinomas. Genes (Basel) 2023; 14:1220. [PMID: 37372400 DOI: 10.3390/genes14061220] [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: 03/21/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Adenoid cystic carcinoma (ACC) has been reported as the second most common carcinoma of the salivary glands. Few studies have associated miRNA expression with ACC aggressiveness. In this study, we evaluated the miRNA profile of formalin-fixed, paraffin-embedded (FFPE) samples of salivary gland ACC patients using the NanoString platform. We studied the miRNA expression levels associated with the solid growth pattern, the more aggressive histologic feature of ACCs, compared with the tubular and cribriform growth patterns. Moreover, the perineural invasion status, a common clinicopathological feature of the disease that is frequently associated with the clinical progression of ACC, was investigated. The miRNAs showing significant differences between the study groups were selected for target prediction and functional enrichment, which included associations with the disease according to dedicated databases. We observed decreased expression of miR-181d, miR-23b, miR-455, miR-154-5p, and miR-409 in the solid growth pattern compared with tubular and cribriform growth patterns. In contrast, miR-29c, miR-140, miR-195, miR-24, miR-143, and miR-21 were overexpressed in patients with perineural invasion. Several target genes of the miRNAs identified have been associated with molecular processes involved in cell proliferation, apoptosis, and tumor progression. Together, these findings allowed the characterization of miRNAs potentially associated with aggressiveness in salivary gland adenoid cystic carcinoma. Our results highlight important new miRNA expression profiles involved in ACC carcinogenesis that could be associated with the aggressive behavior of this tumor type.
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Affiliation(s)
- Maicon Fernando Zanon
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil
| | | | - Ricardo Ribeiro Gama
- Department of Head and Neck Surgery, Barretos Cancer Hospital, Barretos 14784-400, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, 4710-057 Braga, Portugal
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Manguinhos, Rio de Janeiro 21040-361, Brazil
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Causin RL, Sussuchi da Silva L, Leal LF, Possati-Resende JC, Evangelista AF, Matsushita GM, Scapulatempo-Neto C, Tavares Guerreiro Fregnani JH, Antônio de Oliveira M, Musselwhite LW, Chiquitelli Marques MM, Reis RM. The digital expression profile of BMP7, CDKN2C, HIST1H3G, and PKMYT1 genes improves high-grade cervical lesion detection in liquid-based cytology. Cancer Cytopathol 2023. [PMID: 37069588 DOI: 10.1002/cncy.22704] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/03/2023] [Accepted: 03/07/2023] [Indexed: 04/19/2023]
Abstract
BACKGROUND Some studies reported that differential gene expression could be used as a biomarker for high-grade cervical lesion identification. The aim was to evaluate the gene expression profile of cervical intraepithelial neoplasia (CIN) to identify a gene expression signature of CIN2+ in liquid-based cytology (LBC) samples. METHODS LBC samples (n = 85) obtained from women who underwent colposcopy were included with benign (n = 13), CIN1 (n = 26), CIN2 (n = 16), and CIN3 (n = 30) diagnoses. After RNA isolation, gene expression profiling was performed using the nCounter PanCancer Pathways, which consists of 730 cancer-related genes. The genes identified were in silico expression evaluated using the UALCAN database. An accurate prediction model to discriminate CIN2+ from <CIN2 lesions was determined. Immunohistochemistry was performed to assess the expression of p16 and Ki67 proteins. RESULTS This study identified a gene expression profile that significantly differentiates CIN2+ cases from <CIN2. The gene signature comprised 18 genes, two genes downregulated and 16 upregulated. In silico analysis corroborated the differential expression of 11 of those genes. Further observed was that high expression of BMP7 (odds ratio [OR], 4.202), CDKN2C (OR, 5.326), HIST1H3G (OR, 3.522), PKMYT1 (OR, 4.247), and menarche age (OR, 1.608) were age-adjusted and associated with CIN2+. This model demonstrates a probability of 43% leading to an area under the curve (of .979; sensitivity of 94.9%, and specificity of 91.2% for CIN2+ prediction. It was observed that p16 expression was significantly associated with CDKN2A mRNA overexpression (p = .0015). CONCLUSION A gene expression profile that may be helpful in the identification of patients with CIN2+ was identified. This approach could be used together with currently used LBC in a clinical setting, allowing the identification of patients with high risk of CIN2+.
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Affiliation(s)
| | | | - Leticia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Barretos School of Health Sciences, Dr. Paulo Prata-FACISB, Barretos, São Paulo, Brazil
| | | | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Sergio Arouca National School of Public Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
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de Oliveira Silva M, Bisarro dos Reis M, Pinto IA, Pontes NZ, Chiarantano RS, De Marchi P, Ferreira da Silva FA, Evangelista AF, Reis RM, Leal LF. PP.20 Concordance of Actionable Mutations in Liquid Biopsies and Matched Tumor Tissue of Brazilian Non-small Cell Lung Cancer (NSCLC). J Thorac Oncol 2023. [DOI: 10.1016/j.jtho.2023.01.048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
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Garcia FADO, Evangelista AF, Mançano BM, Moreno DA, Berardinelli GN, de Paula FE, Antoniazzi AP, Júnior CA, Lombardi I, Santana I, Teixeira GR, Costa CE, Reis RM. Genomic profile of two Brazilian choroid plexus tumors by whole-exome sequencing. Cold Spring Harb Mol Case Stud 2023; 9:mcs.a006245. [PMID: 36963804 PMCID: PMC10111795 DOI: 10.1101/mcs.a006245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 02/24/2023] [Indexed: 03/26/2023] Open
Abstract
Choroid plexus tumors (CPTs) are rare intracranial neoplasms, representing <1% of all brain tumors, yet they represent 20% of first-year pediatric brain tumors. Although these tumors have been linked to TP53 germline mutations in the context of Li-Fraumeni syndrome, their somatic driver alterations remain poorly understood. In this study, we report two cases of lateral ventricle tumors: 3-yr-old male diagnosed with an atypical choroid plexus papilloma (aCPP), and a 6-mo-old female diagnosed with a choroid plexus carcinoma (CPC). We performed whole-exome sequencing of paired blood and tumor tissue in both patients, categorized somatic variants, and determined copy-number alterations. Our analysis revealed a tier II variant (Association for Molecular Pathology [AMP] criteria) in BRD1, a H3 and TP53 acetylation agent, in the aCPP. In addition, we detected copy-number gains on Chromosomes 12, 18, and 20 and copy-number losses on Chromosomes 13q and 22q (BRD1 locus) in this tumor. The CPC tumor had only a pathogenic germline TP53 variant, based on American College of Medical Genetics (ACMG) criteria, with a clinical and familiar history of Li-Fraumeni syndrome. The CPC patient presented loss of heterozygosity (LoH) of TP53 loci and hyperdiploid genome. Both tumors were microsatellite-stable. This is the first study performing whole-exome sequencing in Brazilian choroid plexus tumors, and in line with the literature, we corroborate the absence of recurrent somatic mutations in these tumors. Further studies with larger sample sizes are necessary to confirm our findings and better understand the underlying biology of these tumors.
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Affiliation(s)
| | | | - Bruna Minniti Mançano
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Daniel Antunes Moreno
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | | | | | | | | | - Ismael Lombardi
- Neurosurgery Department, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Iara Santana
- Pathology Department, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Gustavo Ramos Teixeira
- Pathology Department, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
- Barretos School of Health Sciences Dr. Paulo Prata-FACISB 14785-002
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400, Brazil;
- Laboratory of Molecular Diagnostics, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, 4710-057, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, 4710-057, Portugal
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Vicente ALSA, Novoloaca A, Cahais V, Awada Z, Cuenin C, Spitz N, Carvalho AL, Evangelista AF, Crovador CS, Reis RM, Herceg Z, de Lima Vazquez V, Ghantous A. Cutaneous and acral melanoma cross-OMICs reveals prognostic cancer drivers associated with pathobiology and ultraviolet exposure. Nat Commun 2022; 13:4115. [PMID: 35840550 PMCID: PMC9287446 DOI: 10.1038/s41467-022-31488-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 10/16/2021] [Accepted: 06/16/2022] [Indexed: 11/08/2022] Open
Abstract
Ultraviolet radiation (UV) is causally linked to cutaneous melanoma, yet the underlying epigenetic mechanisms, known as molecular sensors of exposure, have not been characterized in clinical biospecimens. Here, we integrate clinical, epigenome (DNA methylome), genome and transcriptome profiling of 112 cutaneous melanoma from two multi-ethnic cohorts. We identify UV-related alterations in regulatory regions and immunological pathways, with multi-OMICs cancer driver potential affecting patient survival. TAPBP, the top gene, is critically involved in immune function and encompasses several UV-altered methylation sites that were validated by targeted sequencing, providing cost-effective opportunities for clinical application. The DNA methylome also reveals non UV-related aberrations underlying pathological differences between the cutaneous and 17 acral melanomas. Unsupervised epigenomic mapping demonstrated that non UV-mutant cutaneous melanoma more closely resembles acral rather than UV-exposed cutaneous melanoma, with the latter showing better patient prognosis than the other two forms. These gene-environment interactions reveal translationally impactful mechanisms in melanomagenesis.
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Affiliation(s)
- Anna Luiza Silva Almeida Vicente
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France.
| | - Alexei Novoloaca
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Vincent Cahais
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Zainab Awada
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Cyrille Cuenin
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Natália Spitz
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - André Lopes Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Early Detection Prevention and Infections Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | | | - Camila Souza Crovador
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal
- ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Zdenko Herceg
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France
| | - Vinicius de Lima Vazquez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
- Department of Surgery-Melanoma and Sarcoma, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Akram Ghantous
- Epigenomics and Mechanisms Branch, International Agency for Research on Cancer (IARC), Lyon, France.
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9
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Garcia FADO, de Andrade ES, de Campos Reis Galvão H, da Silva Sábato C, Campacci N, de Paula AE, Evangelista AF, Santana IVV, Melendez ME, Reis RM, Palmero EI. New insights on familial colorectal cancer type X syndrome. Sci Rep 2022; 12:2846. [PMID: 35181726 PMCID: PMC8857274 DOI: 10.1038/s41598-022-06782-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 06/29/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Familial colorectal cancer type X (FCCTX) is a heterogeneous colorectal cancer predisposition syndrome that, although displays a cancer pattern similar to Lynch syndrome, is mismatch repair proficient and does not exhibit microsatellite instability. Besides, its genetic etiology remains to be elucidated. In this study we performed germline exome sequencing of 39 cancer-affected patients from 34 families at risk for FCCTX. Variant classification followed the American College of Medical Genetics and Genomics (ACMG) guidelines. Pathogenic/likely pathogenic variants were identified in 17.65% of the families. Rare and potentially pathogenic alterations were identified in known hereditary cancer genes (CHEK2), in putative FCCTX candidate genes (OGG1 and FAN1) and in other cancer-related genes such as ATR, ASXL1, PARK2, SLX4 and TREX1. This study provides novel important clues that can contribute to the understanding of FCCTX genetic basis.
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Affiliation(s)
- Felipe Antonio de Oliveira Garcia
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | - Edilene Santos de Andrade
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | | | - Natália Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil
| | | | - Matias Eliseo Melendez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Department of Molecular Carcinogenesis, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela Street, 1331, Barretos, São Paulo, CEP 14784-400, Brazil. .,Department of Genetics, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
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10
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Munari FF, Dos Santos W, Evangelista AF, Carvalho AC, Pastrez PA, Bugatti D, Wohnrath DR, Scapulatempo-Neto C, Guimarães DP, Longatto-Filho A, Reis RM. Profile of esophageal squamous cell carcinoma mutations in Brazilian patients. Sci Rep 2021; 11:20596. [PMID: 34663841 PMCID: PMC8523676 DOI: 10.1038/s41598-021-00208-7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 10/08/2021] [Indexed: 12/24/2022] Open
Abstract
Esophageal cancer is an aggressive tumor that has a high rate of incidence and mortality worldwide. It is the 10th most frequent type in Brazil, being squamous cell carcinoma (ESCC) the predominant subtype. There is currently an incessant search to identify the frequently altered genes associated with esophageal squamous cell carcinoma biology that could be druggable. This study aimed to analyze the somatic mutation profile of a large panel of cancer-related genes in Brazilian ESCC. In a series of 46 ESCC diagnoses at Barretos Cancer Hospital, DNA isolated from paired fresh-frozen and blood tissue, a panel of 150 cancer-related genes was analyzed by next-generation sequencing. The genes with the highest frequency of mutations were TP53 (39/46, 84.8%), followed by NOTCH1 (7/46, 15.2%), NFE2L2 (5/46, 10.8%), RB1 (3/46, 6.5%), PTEN (3/46, 6.5%), CDKN2A (3/46, 6.5%), PTCH1 (2/46, 4.3%) and PIK3CA (2/46, 4.3%). There was no significant association between molecular and patients' clinicopathological features. Applying an evolutionary action score of p53 (EAp53), we observed that 14 (35.9%) TP53 mutations were classified as high-risk, yet no association with overall survival was observed. Concluding, this the largest mutation profile of Brazilian ESCC patients, which helps in the elucidation of the major cancer-related genes in this population.
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Affiliation(s)
- Fernanda Franco Munari
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil
| | - Wellington Dos Santos
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil
| | - Ana Carolina Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil
| | - Paula Aguiar Pastrez
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil
| | - Diego Bugatti
- Department of Upper Digestive, Barretos Cancer Hospital, Barretos, Brazil
| | - Durval R Wohnrath
- Department of Upper Digestive, Barretos Cancer Hospital, Barretos, Brazil
| | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, Brazil
| | - Adhemar Longatto-Filho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil.,Medical Laboratory of Medical Investigation (LIM) 14, Department of Pathology, Medical School, University of São Paulo, São Paulo, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Antenor Duarte Villela, 1331, Barretos, São Paulo, 14784 400, Brazil. .,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal. .,ICVS/3B's-PT Government Associate Laboratory, Braga, Guimarães, Portugal.
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11
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de Andrade DAP, da Silva LS, Laus AC, de Lima MA, Berardinelli GN, da Silva VD, Matsushita GDM, Bonatelli M, da Silva ALV, Evangelista AF, Carvalho JP, Reis RM, Dos Reis R. A 4-Gene Signature Associated With Recurrence in Low- and Intermediate-Risk Endometrial Cancer. Front Oncol 2021; 11:729219. [PMID: 34485158 PMCID: PMC8416164 DOI: 10.3389/fonc.2021.729219] [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: 06/22/2021] [Accepted: 07/30/2021] [Indexed: 12/28/2022] Open
Abstract
Background The molecular profile of endometrial cancer has become an important tool in determining patient prognosis and their optimal adjuvant treatment. In addition to The Cancer Genome Atlas (TCGA), simpler tools have been developed, such as the Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE). We attempted to determine a genetic signature to build a recurrence risk score in patients diagnosed with low- and intermediate-risk endometrial cancer. Methods A case-control study was conducted. The eligible patients were women diagnosed with recurrence low- and intermediate-risk endometrial cancer between January 2009 and December 2014 at a single institution; the recurrence patients were matched to two nonrecurrence patients with the same diagnosis by age and surgical staging. Following RNA isolation of 51 cases, 17 recurrence and 34 nonrecurrence patients, the expression profile was determined using the nCounter® PanCancer Pathways Panel, which contains 770 genes. Results The expression profile was successfully characterized in 49/51 (96.1%) cases. We identified 12 genes differentially expressed between the recurrence and nonrecurrence groups. The ROC curve for each gene was generated, and all had AUCs higher than 0.7. After backward stepwise logistic regression, four genes were highlighted: FN1, DUSP4, LEF1, and SMAD9. The recurrence risk score was calculated, leading to a ROC curve of the 4-gene model with an AUC of 0.93, sensitivity of 100%, and specificity of 72.7%. Conclusion We identified a four-gene signature that may be associated with recurrence in patients with low- and intermediate-risk endometrial cancer. This finding suggests a new prognostic factor in this poorly explored group of patients with endometrial cancer.
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Affiliation(s)
- Diocésio Alves Pinto de Andrade
- InORP ONCOCLÍNICAS Group, Oncology Institute of Ribeirão Preto, Ribeirão Preto, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Marcos Alves de Lima
- Epidemiology and Biostatistics Nucleus, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | - Murilo Bonatelli
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Jesus Paula Carvalho
- Discipline of Gynecology, Instituto do Cancer do Estado de São Paulo (ICESP), Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Ricardo Dos Reis
- Department of Gynecologic Oncology, Barretos Cancer Hospital, Barretos, Brazil
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12
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Silva GSA, Evangelista AF, Santos GC, Santana TA, Stimamiglio MA, Soares MBP, Villarreal CF. ANTINOCICEPTIVE PROPERTIES OF EXTRACELLULAR VESICLES DERIVED FROM MESENQUIMAL CELLS IN DIABETIC SENSORY NEUROPATHY IN MICE. Cytotherapy 2021. [DOI: 10.1016/j.jcyt.2021.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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13
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Fernandes FG, Silveira HCS, Júnior JNA, da Silveira RA, Zucca LE, Cárcano FM, Sanches AON, Neder L, Scapulatempo-Neto C, Serrano SV, Jonasch E, Reis RM, Evangelista AF. Somatic Copy Number Alterations and Associated Genes in Clear-Cell Renal-Cell Carcinoma in Brazilian Patients. Int J Mol Sci 2021; 22:2265. [PMID: 33668731 PMCID: PMC7956176 DOI: 10.3390/ijms22052265] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 10/23/2020] [Revised: 01/13/2021] [Accepted: 01/22/2021] [Indexed: 12/24/2022] Open
Abstract
Somatic copy number aberrations (CNAs) have been associated with clear-cell renal carcinoma (ccRCC) pathogenesis and are a potential source of new diagnostic, prognostic and therapeutic biomarkers. Recurrent CNAs include loss of chromosome arms 3p, 14q, 9p, and gains of 5q and 8q. Some of these regional CNAs are suspected of altering gene expression and could influence clinical outcomes. Despite many studies of CNAs in RCC, there are currently no descriptions of genomic copy number alterations in a Brazilian ccRCC cohort. This study was designed to evaluate the chromosomal profile of CNAs in Brazilian ccRCC tumors and explore clinical associations. A total of 92 ccRCC Brazilian patients that underwent nephrectomy at Barretos Cancer Hospital were analyzed for CNAs by array comparative genomic hybridization. Most patients in the cohort had early-stage localized disease. The most significant alterations were loss of 3p (87.3%), 14q (35.8%), 6q (29.3%), 9p (28.6%) and 10q (25.0%), and gains of 5q (59.7%), 7p (29.3%) and 16q (20.6%). Bioinformatics analysis revealed 19 genes mapping to CNA significant regions, including SETD2, BAP1, FLT4, PTEN, FGFR4 and NSD1. Moreover, gain of 5q34-q35.3 (FLT4 and NSD1) and loss of 6q23.2-q23.3 (MYB) and 9p21.3 (MLLT3) had gene expression levels that correlated with TCGA data and was also associated with advanced disease features, such as larger tumors, Fuhrman 3, metastasis at diagnosis and death. The loss of region 14q22.1 which encompasses the NIN gene was associated with poor overall survival. Overall, this study provides the first CNA landscape of Brazilian patients and pinpoints genomic regions and specific genes worthy of more detailed investigations. Our results highlight important genes that are associated with copy number changes involving large chromosomal regions that are potentially related to ccRCC tumorigenesis and disease biology for future clinical investigations.
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Affiliation(s)
- Flávia Gonçalves Fernandes
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
| | | | - João Neif Antonio Júnior
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Rosana Antunes da Silveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
| | - Luis Eduardo Zucca
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Flavio Mavignier Cárcano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
- Barretos School of Health Sciences Dr Paulo Prata-FACISB, Barretos 14785-002, Brazil
| | - André Octavio Nicolau Sanches
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
| | - Luciano Neder
- Department of Pathology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (L.N.); (C.S.-N.)
| | | | - Sergio Vicente Serrano
- Department of Medical Oncology, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (J.N.A.J.); (L.E.Z.); (F.M.C.); (A.O.N.S.); (S.V.S.)
- Barretos School of Health Sciences Dr Paulo Prata-FACISB, Barretos 14785-002, Brazil
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
- Life and Health Sci Research Institute (ICVS), Medical School, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, Brazil; (F.G.F.); (H.C.S.S.); (R.A.d.S.)
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14
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Novaes LAC, Sussuchi da Silva L, De Marchi P, Cavagna RDO, de Paula FE, Zanon MF, Evangelista AF, Albino da Silva EC, Duval da Silva V, Leal LF, Reis RM. Simultaneous analysis of ALK, RET, and ROS1 gene fusions by NanoString in Brazilian lung adenocarcinoma patients. Transl Lung Cancer Res 2021; 10:292-303. [PMID: 33569313 PMCID: PMC7867767 DOI: 10.21037/tlcr-20-740] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Gene fusions have been successfully employed as therapeutic targets for lung adenocarcinoma. However, tissue availability for molecular testing of multiples alterations is frequently unfeasible. We aimed to detect the presence of ALK, RET, and ROS1 rearrangements by a RNA-based single assay in Brazilian lung adenocarcinomas and to associate with clinicopathological features and genetic ancestry. Methods From a FFPE series of 444 molecularly characterized lung adenocarcinomas, 253 EGFR/KRAS wild-type cases were eligible for gene rearrangement analysis. Following RNA isolation, ALK, RET, and ROS1 rearrangements were simultaneously analyzed employing the ElementsXT Custom panel (NanoString Technologies). Rearrangements were further associated with clinicopathological features and genetic ancestry of the patients. Results The NanoString platform was performed in subset of 142 cases. Gene fusion results were conclusive for 94.4% (n=134) cases (failure rate =5.6%). ALK rearrangements were observed in 21 out of 134 cases, and associated with younger, never smokers, metastatic disease, and metastases in the central nervous system. RET and ROS1 fusions were detected in two and one out of 134 cases, respectively. Genetic ancestry was not associated with gene fusions. Overall, considering all cases for which a molecular analysis was conclusive (EGFR/KRAS/ALK/RET/ROS1), ALK fusions frequency was observed in 6.5% (21/325), RET in 0.6% (2/325), and ROS1 in 0.3% (1/325). Conclusions This study successfully used a RNA-based single assay for the simultaneous analysis of ALK, RET, and ROS1 fusions employing routine biopsies from Brazilian patients lung adenocarcinoma allowing an extensive molecular testing for actionable rearrangements contributing to guide clinical strategies.
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Affiliation(s)
| | | | - Pedro De Marchi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Medical Oncology, Barretos Cancer Hospital, Barretos, Brazil.,Oncoclinicas Group, Rio de Janeiro, Brazil
| | - Rodrigo de Oliveira Cavagna
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Maicon Fernando Zanon
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | - Vinícius Duval da Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Medicine Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Letícia Ferro Leal
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Medicine Dr. Paulo Prata - FACISB, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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15
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Evangelista AF, de Menezes WP, Berardinelli GN, Dos Santos W, Scapulatempo-Neto C, Guimarães DP, Calin GA, Reis RM. Pyknon-Containing Transcripts Are Downregulated in Colorectal Cancer Tumors, and Loss of PYK44 Is Associated With Worse Patient Outcome. Front Genet 2020; 11:581454. [PMID: 33304384 PMCID: PMC7693444 DOI: 10.3389/fgene.2020.581454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 09/14/2020] [Indexed: 01/19/2023] Open
Abstract
Pyknons are specific human/primate-specific DNA motifs at least 16 nucleotides long that are repeated in blocks in intergenic and intronic regions of the genome and can be located in a new class of non-coding RNAs of variable length. Recent studies reported that pyknon deregulation could be involved in the carcinogenesis process, including colorectal cancer. We evaluated the expression profile of a set of 12 pyknons in a set of molecularly characterized colorectal cancer (CRC) patients. The pyknons (PYK10, PYK14, PYK17, PYK26, PYK27, PYK40, PYK41, PYK42, PYK43, PYK44, PYK83, and PYK90) expression was determined by qRT-PCR. A pilot analysis of 20 cases was performed, and consistent results were obtained for PYK10, PYK17, PYK42, PYK44, and PYK83. Further, the expression of the selected pyknons was evaluated in 73 CRC cases. Moreover, in 52 patients, we compared the expression profile in both tumor and normal tissues. All five pyknons analyzed showed significantly lower expression levels in the tumor compared to normal tissue. It was observed an association between expression of PYK10 with TP53 mutations (p = 0.029), PYK17 to histologic grade (p = 0.035), and PYK44 to clinical staging (p = 0.016). Moreover, levels of PYK44 were significantly associated with the patient's poor overall survival (p = 0.04). We reported the significant downregulation of pyknons motifs in tumor tissue compared with the normal counterpart, and the association of lower PYK44 expression with worse patient outcome. Further studies are needed to extend and validate these findings and determine the clinical-pathological impact.
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Affiliation(s)
| | | | | | | | - Cristovam Scapulatempo-Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Department of Endoscopy, Barretos Cancer Hospital, Barretos, Brazil
| | - George A Calin
- Translational Molecular Pathology Department, University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Guimarães, Portugal
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16
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Grasel RS, Felicio PS, de Paula AE, Campacci N, Garcia FADO, de Andrade ES, Evangelista AF, Fernandes GC, Sabato CDS, De Marchi P, Souza CDP, de Paula CAA, Torrezan GT, Galvão HDCR, Carraro DM, Palmero EI. Using Co-segregation and Loss of Heterozygosity Analysis to Define the Pathogenicity of Unclassified Variants in Hereditary Breast Cancer Patients. Front Oncol 2020; 10:571330. [PMID: 33134171 PMCID: PMC7566163 DOI: 10.3389/fonc.2020.571330] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 06/10/2020] [Accepted: 08/28/2020] [Indexed: 12/18/2022] Open
Abstract
The use of gene panels introduces a new dilemma in the genetics field due to the high frequency of variants of uncertain significance (VUS). The objective of this study was to provide evidence that may help in the classification of these germline variants in terms of their clinical impact and association with the disease in question. A total of 52 unrelated women at-risk for HBOC and negative for BRCA1/BRCA2 pathogenic variants were evaluated through a gene panel comprising 14 breast and/or ovarian cancer susceptibility genes. Of the 453 germline variants identified, 15 variants (classes 3, 4, and 5) in the ATM, BRIP1, CHEK2, MRE11A, MUTHY, PALB2, RAD50, and RAD51C genes were evaluated via databases, co-segregation studies and loss of heterozygosity in the tumor. The co-segregation analysis allowed the establishment of an association with the presence of variants and the risk of cancer for variant c.316C>T in the BRIP1 gene. Four variants of uncertain significance showed loss of heterozygosity in the tumor (ATM c.4709T>C; CHEK2 c.1036C>T; PALB2 c.1001A>G, and RAD50 c.281T>C), which is an indication of pathogenicity. Thus, the present study provides novel evidence that favors the association of variants in moderate-risk genes with the development of hereditary breast cancer.
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Affiliation(s)
| | - Paula Silva Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
| | | | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil
| | | | | | | | | | | | - Pedro De Marchi
- Department of Medical Oncology, Barretos Cancer Hospital, São Paulo, Brazil.,Oncoclinicas, Rio de Janeiro, Brazil
| | - Cristiano de Pádua Souza
- Department of Medical Oncology, Barretos Cancer Hospital, São Paulo, Brazil.,Department of Oncogenetics, Barretos Cancer Hospital, São Paulo, Brazil
| | | | | | | | - Dirce Maria Carraro
- Genomic Diagnostic Center, AC Camargo Cancer Center, São Paulo, Brazil.,Genomics and Molecular Biology Group, CIPE - A. C. Camargo Cancer Center, São Paulo, Brazil
| | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, São Paulo, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, São Paulo, Brazil.,Pele Little Prince Research Institute, Curitiba, Brazil.,Faculdades Pequeno Príncipe, Curitiba, Brazil
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17
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Romualdo GR, Prata GB, da Silva TC, Evangelista AF, Reis RM, Vinken M, Moreno FS, Cogliati B, Barbisan LF. The combination of coffee compounds attenuates early fibrosis-associated hepatocarcinogenesis in mice: involvement of miRNA profile modulation. J Nutr Biochem 2020; 85:108479. [PMID: 32795656 DOI: 10.1016/j.jnutbio.2020.108479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 12/16/2019] [Revised: 06/19/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Abstract
Aberrant microRNA expression implicates on hepatocellular carcinoma (HCC) development. Conversely, coffee consumption reduces by ~40% the risk for fibrosis/cirrhosis and HCC, while decaffeinated coffee does not. It is currently unknown whether these protective effects are related to caffeine (CAF), or to its combination with other common and/or highly bioavailable coffee compounds, such as trigonelline (TRI) and chlorogenic acid (CGA). We evaluated whether CAF individually or combined with TRI and/or CGA alleviates fibrosis-associated hepatocarcinogenesis, examining the involvement of miRNA profile modulation. Then, male C3H/HeJ mice were submitted to a diethylnitrosamine/carbon tetrachloride-induced model. Animals received CAF (50 mg/kg), CAF+TRI (50 and 25 mg/kg), CAF+CGA (50 and 25 mg/kg) or CAF+TRI+CGA (50, 25 and 25 mg/kg), intragastrically, 5×/week, for 10 weeks. Only CAF+TRI+CGA combination reduced the incidence, number and proliferation (Ki-67) of hepatocellular preneoplastic foci while enhanced apoptosis (cleaved caspase-3) in adjacent parenchyma. CAF+TRI+CGA treatment also decreased hepatic oxidative stress and enhanced the antioxidant Nrf2 axis. CAF+TRI+CGA had the most pronounced effects on decreasing hepatic pro-inflammatory IL-17 and NFκB, contributing to reduce CD68-positive macrophage number, stellate cell activation, and collagen deposition. In agreement, CAF+TRI+CGA upregulated tumor suppressors miR-144-3p, miR-376a-3p and antifibrotic miR-15b-5p, frequently deregulated in human HCC. CAF+TRI+CGA reduced the hepatic protein levels of pro-proliferative EGFR (miR-144-3p target), antiapoptotic Bcl-2 family members (miR-15b-5p targets), and the number of PCNA (miR-376a-3p target) positive hepatocytes in preneoplastic foci. Our results suggest that the combination of most common and highly bioavailable coffee compounds, rather than CAF individually, attenuates fibrosis-associated hepatocarcinogenesis by modulating miRNA expression profile.
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Affiliation(s)
- Guilherme Ribeiro Romualdo
- Department of Pathology, Botucatu Medical School, São Paulo State University (UNESP), Botucatu, - SP, Brazil
| | - Gabriel Bacil Prata
- Department of Structural and Functional Biology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, - SP, Brazil
| | - Tereza Cristina da Silva
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, - SP, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, - SP, Brazil; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal; 3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Fernando Salvador Moreno
- Department of Food and Experimental Nutrition, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, - SP, Brazil
| | - Bruno Cogliati
- Department of Pathology, School of Veterinary Medicine and Animal Science, University of São Paulo (USP), São Paulo, - SP, Brazil
| | - Luís Fernando Barbisan
- Department of Structural and Functional Biology, Biosciences Institute, São Paulo State University (UNESP), Botucatu, - SP, Brazil.
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18
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Pessôa-Pereira D, Evangelista AF, Causin RL, da Costa Vieira RA, Abrahão-Machado LF, Santana IVV, da Silva VD, de Souza KCB, de Oliveira-Silva RJ, Fernandes GC, Reis RM, Palmero EI, Marques MMC. miRNA expression profiling of hereditary breast tumors from BRCA1- and BRCA2-germline mutation carriers in Brazil. BMC Cancer 2020; 20:143. [PMID: 32087690 PMCID: PMC7036228 DOI: 10.1186/s12885-020-6640-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 10/07/2019] [Accepted: 02/17/2020] [Indexed: 12/15/2022] Open
Abstract
Background MicroRNAs (miRNAs) are small non-coding RNAs involved in post-transcriptional gene expression regulation and have been described as key regulators of carcinogenesis. Aberrant miRNA expression has been frequently reported in sporadic breast cancers, but few studies have focused on profiling hereditary breast cancers. In this study, we aimed to identify specific miRNA signatures in hereditary breast tumors and to compare with sporadic breast cancer and normal breast tissues. Methods Global miRNA expression profiling using NanoString technology was performed on 43 hereditary breast tumors (15 BRCA1, 14 BRCA2, and 14 BRCAX), 23 sporadic breast tumors and 8 normal breast tissues. These normal breast tissues derived from BRCA1- and BRCA2- mutation carriers (n = 5) and non-mutation carriers (n = 3). Subsequently, we performed receiver operating characteristic (ROC) curve analyses to evaluate the diagnostic performance of differentially expressed miRNAs. Putative target genes of each miRNAs considered as potential biomarkers were identified using miRDIP platform and used for pathway enrichment analysis. Results miRNA expression analyses identified several profiles that were specific to hereditary breast cancers. A total of 25 miRNAs were found to be differentially expressed (fold change: > 2.0 and p < 0.05) and considered as potential biomarkers (area under the curve > 0.75) in hereditary breast tumors compared to normal breast tissues, with an expressive upregulation among BRCAX cases. Furthermore, bioinformatic analysis revealed that these miRNAs shared target genes involved in ErbB, FoxO, and PI3K-Akt signaling pathways. Conclusions Our results showed that miRNA expression profiling can differentiate hereditary from sporadic breast tumors and normal breast tissues. These miRNAs were remarkably deregulated in BRCAX hereditary breast cancers. Therefore, miRNA signatures can be used as potential novel diagnostic biomarkers for the prediction of BRCA1/2- germline mutations and may be useful for future clinical management.
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Affiliation(s)
| | | | - Rhafaela Lima Causin
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Center of Molecular Diagnosis, Barretos Cancer Hospital, Barretos, SP, Brazil.,Department of Oncogenetics, Barretos Cancer Hospital, Barretos, SP, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, SP, Brazil
| | - Márcia Maria Chiquitelli Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil. .,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, SP, Brazil. .,Tumor Biobank, Barretos Cancer Hospital, Barretos, SP, Brazil.
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19
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Leandro GS, Evangelista AF, Lobo RR, Xavier DJ, Moriguti JC, Sakamoto-Hojo ET. Changes in Expression Profiles Revealed by Transcriptomic Analysis in Peripheral Blood Mononuclear Cells of Alzheimer's Disease Patients. J Alzheimers Dis 2019; 66:1483-1495. [PMID: 30400085 DOI: 10.3233/jad-170205] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Alzheimer's disease (AD) is an age-related neurodegenerative pathology associated with accumulation of DNA damage. Inflammation and cell cycle alterations seem to be implicated in the pathogenesis of AD, although the molecular mechanisms have not been thoroughly elucidated to date. The aim of the present study was to evaluate whether peripheral blood mononuclear cells (PBMCs) of AD patients display alterations in gene expression profiles, focusing on finding markers that might improve the diagnosis of AD. Blood samples were collected from 22 AD patients and 13 healthy individuals to perform genome-wide mRNA expression. We found 593 differentially expressed genes in AD compared to controls, from which 428 were upregulated, and 165 were downregulated. By performing a gene set enrichment analysis, we observed pathways involved in inflammation, DNA damage response, cell cycle, and neuronal processes. Moreover, functional annotation analyses indicated that differentially expressed genes are strongly related to pathways associated with the cell cycle and the immune system. The results were compared with those of an independent study on hippocampus samples, and a number of genes in common between both studies were identified as potential peripheral biomarkers for AD, including DUSP1, FOS, SLC7A2, RGS1, GFAP, CCL2, ANGPTL4, and SSPN. Taken together, our results demonstrate that PBMCs of AD patients do present alterations in gene expression profiles, and these results are comparable to those previously reported in the literature for AD neurons, supporting the hypothesis that blood peripheral mononuclear cells express molecular changes that occur in the neurons of AD patients.
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Affiliation(s)
- Giovana Silva Leandro
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
| | | | - Romulo Rebouças Lobo
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
| | - Danilo Jordão Xavier
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
| | - Julio César Moriguti
- Department of Internal Medicine, Ribeirão Preto Medical School, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
| | - Elza Tiemi Sakamoto-Hojo
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo - USP, Ribeirão Preto, SP, Brazil.,Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo - USP, Ribeirão Preto, SP, Brazil
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20
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Silva VAO, Rosa MN, Tansini A, Martinho O, Tanuri A, Evangelista AF, Cruvinel Carloni A, Lima JP, Pianowski LF, Reis RM. Semi-Synthetic Ingenol Derivative from Euphorbia tirucalli Inhibits Protein Kinase C Isotypes and Promotes Autophagy and S-phase Arrest on Glioma Cell Lines. Molecules 2019; 24:molecules24234265. [PMID: 31771098 PMCID: PMC6930609 DOI: 10.3390/molecules24234265] [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] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 11/06/2019] [Indexed: 12/18/2022] Open
Abstract
The identification of signaling pathways that are involved in gliomagenesis is crucial for targeted therapy design. In this study we assessed the biological and therapeutic effect of ingenol-3-dodecanoate (IngC) on glioma. IngC exhibited dose-time-dependent cytotoxic effects on large panel of glioma cell lines (adult, pediatric cancer cells, and primary cultures), as well as, effectively reduced colonies formation. Nevertheless, it was not been able to attenuate cell migration, invasion, and promote apoptotic effects when administered alone. IngC exposure promoted S-phase arrest associated with p21CIP/WAF1 overexpression and regulated a broad range of signaling effectors related to survival and cell cycle regulation. Moreover, IngC led glioma cells to autophagy by LC3B-II accumulation and exhibited increased cytotoxic sensitivity when combined to a specific autophagic inhibitor, bafilomycin A1. In comparison with temozolomide, IngC showed a mean increase of 106-fold in efficacy, with no synergistic effect when they were both combined. When compared with a known compound of the same class, namely ingenol-3-angelate (I3A, Picato®), IngC showed a mean 9.46-fold higher efficacy. Furthermore, IngC acted as a potent inhibitor of protein kinase C (PKC) activity, an emerging therapeutic target in glioma cells, showing differential actions against various PKC isotypes. These findings identify IngC as a promising lead compound for the development of new cancer therapy and they may guide the search for additional PKC inhibitors.
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Affiliation(s)
- Viviane Aline Oliveira Silva
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil; (V.A.O.S.); (M.N.R.); (A.T.); (O.M.); (A.F.E.); (A.C.C.)
| | - Marcela Nunes Rosa
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil; (V.A.O.S.); (M.N.R.); (A.T.); (O.M.); (A.F.E.); (A.C.C.)
| | - Aline Tansini
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil; (V.A.O.S.); (M.N.R.); (A.T.); (O.M.); (A.F.E.); (A.C.C.)
| | - Olga Martinho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil; (V.A.O.S.); (M.N.R.); (A.T.); (O.M.); (A.F.E.); (A.C.C.)
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
| | - Amilcar Tanuri
- Laboratory of Molecular Virology, Departaments of genetics, IB, Federal University of Rio de Janeiro, Rio de Janeiro 21941-902, Brazil;
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil; (V.A.O.S.); (M.N.R.); (A.T.); (O.M.); (A.F.E.); (A.C.C.)
| | - Adriana Cruvinel Carloni
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil; (V.A.O.S.); (M.N.R.); (A.T.); (O.M.); (A.F.E.); (A.C.C.)
| | - João Paulo Lima
- Medical Oncology, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil;
- Medical Oncology Department, A C Camargo Cancer Center, São Paulo 01509-010, SP, Brazil
| | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil; (V.A.O.S.); (M.N.R.); (A.T.); (O.M.); (A.F.E.); (A.C.C.)
- Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, 4806-909 Braga/Guimarães, Portugal
- Correspondence: ; Tel.: +55-1733216600 (ext. 7090)
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21
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Dos Santos W, Sobanski T, de Carvalho AC, Evangelista AF, Matsushita M, Berardinelli GN, de Oliveira MA, Reis RM, Guimarães DP. Mutation profiling of cancer drivers in Brazilian colorectal cancer. Sci Rep 2019; 9:13687. [PMID: 31548566 PMCID: PMC6757044 DOI: 10.1038/s41598-019-49611-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [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: 05/10/2019] [Accepted: 08/28/2019] [Indexed: 12/24/2022] Open
Abstract
The molecular basis of colorectal cancer (CRC) can guide patient prognosis and therapy. In Brazil, knowledge on the CRC mutation landscape is limited. Here, we investigated the mutation profile of 150 cancer-related genes by next-generation sequencing and associated with microsatellite instability (MSI) and genetic ancestry in a series of 91 Brazilian CRC patients. Driver mutations were found in the APC (71.4%), TP53 (56.0%), KRAS (52.7%), PIK3CA (15.4%) and FBXW7 (10.9%) genes. Overall, genes in the MAPK/ERK, PIK3/AKT, NOTCH and receptor tyrosine kinase signaling pathways were mutated in 68.0%, 23.1%, 16.5%, and 15.3% of patients, respectively. MSI was found in 13.3% of tumors, most of which were proximal (52.4%, P< 0.001) and had a high mutation burden. European genetic ancestry was predominant (median of 83.1%), followed by Native American (4.1%), Asian (3.4%) and African (3.2%). NF1 and BRAF mutations were associated with African ancestry, while TP53 and PIK3CA mutations were inversely correlated with Native American ancestry. Our study suggests that Brazilian CRC patients exhibit a mutation profile similar to other populations and identify the most frequently mutated genes, which could be useful in future target therapies and molecular cancer screening strategies.
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Affiliation(s)
| | - Thais Sobanski
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | | | | | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
- Life and Health Sciences Research Institute (ICVS), Medical School, University of Minho, Braga, 4710-057, Portugal.
- 3ICVS/3B's-PT Government Associate Laboratory, Braga, 4710-057, Portugal.
| | - Denise Peixoto Guimarães
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
- Department of Endoscopy, Barretos Cancer Hospital, Barretos, Brazil.
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22
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Causin RL, Pessôa-Pereira D, Souza KCB, Evangelista AF, Reis RMV, Fregnani JHTG, Marques MMC. Identification and performance evaluation of housekeeping genes for microRNA expression normalization by reverse transcription-quantitative PCR using liquid-based cervical cytology samples. Oncol Lett 2019; 18:4753-4761. [PMID: 31611985 PMCID: PMC6781752 DOI: 10.3892/ol.2019.10824] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [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: 04/01/2019] [Accepted: 07/02/2019] [Indexed: 12/14/2022] Open
Abstract
Screening for cervical cancer by cytology has been effective in reducing the worldwide incidence and mortality rates of this disease. However, a number of studies have demonstrated that the sensitivity of conventional cervical cytology may be too low for detection of cervical intraepithelial neoplasias (CIN). Therefore, it is important to incorporate more sensitive molecular diagnostic tests that could substantially improve the detection rates and accuracy for identifying CIN lesions. MicroRNAs (miRNAs) are a class of small non-coding RNAs with the potential to provide robust non-invasive cancer biomarkers for detecting CIN lesions in liquid-based cervical cytology (LBC) samples. At present, there is no consensus on which are the best housekeeping genes for miRNA normalization in LBC. The present study aimed to identify housekeeping genes with consistent and reproducible performance for normalization of reverse transcription-quantitative PCR (RT-qPCR) expression analysis of miRNA using LBC samples. The present study firstly selected six potential candidate housekeeping genes based on a systematic literature evaluation. Subsequently, the expression levels of microRNAs U6, RNU-44, RNU-47, RNU-48, RNU-49 and hsa-miR-16 were measured in 40 LBC samples using RT-qPCR. The stability of each potential housekeeping gene was assessed using the NormFinder algorithm. The results revealed that U6 and RNU-49 were the most stable genes among all candidates requiring fewer amplification cycles and smaller variation across the sample set. However, RNU-44, RNU-47, RNU-48 and hsa-miR-16 stability exceeded the recommended housekeeping value suitable for normalization. The findings revealed that U6 may be a reliable housekeeping gene for normalization of miRNA RT-qPCR expression analysis using LBC samples.
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Affiliation(s)
- Rhafaela Lima Causin
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | - Danielle Pessôa-Pereira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | | | | | - Rui Manuel Vieira Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil
| | | | - Márcia Maria Chiquitelli Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo 14784-400, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, São Paulo 14785-002, Brazil
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23
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Felicio PS, Bidinotto LT, Melendez ME, Grasel RS, Campacci N, Galvão HCR, Scapulatempo-Neto C, Dufloth RM, Evangelista AF, Palmero EI. Genetic alterations detected by comparative genomic hybridization in BRCAX breast and ovarian cancers of Brazilian population. Oncotarget 2018; 9:27525-27534. [PMID: 29938003 PMCID: PMC6007956 DOI: 10.18632/oncotarget.25537] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [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: 08/09/2017] [Accepted: 05/14/2018] [Indexed: 12/19/2022] Open
Abstract
Background About 5–10% of breast/ovarian cancers are hereditary. However, for a large proportion of cases (around 50%), the genetic cause remains unknown. These cases are grouped in a separated BRCAX category. The aim of this study was to identify genomic alterations in BRCA1/BRCA2 wild-type tumor samples from women with family history strongly suggestive of hereditary breast/ovarian cancer. Results A cohort of 31 Brazilian women was included in the study. Using the GISTIC algorithm, we identified 20 regions with genomic gains and 31 with losses. The most frequent altered regions were 1q21.2, 6p22.1 and 8p23.3 in breast tumors and Xq26 and Xp22.32-22.31 among the ovarian cancer cases. An interesting association identified was the loss of 22q13.31-13.32 and the presence of ovarian cancer cases. Among the genes present in the frequently altered regions, we found FGFR1, NSMCE2, CTTN, CRLF2, ERBB2, STARD3, MIR3201 and several genes of RAET and ULBP family. Conclusions In conclusion, our results suggest that alterations on chromosomes 1, 6, 8 and X are common on BRCAX tumors and that the loss on 22q can be associated with the presence of ovarian cancer. Methods DNA copy number alterations were analyzed by 60K array comparative genomic hybridization in breast and ovarian FFPE tumors.
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Affiliation(s)
- Paula Silva Felicio
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | - Lucas Tadeu Bidinotto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, SP, Brazil
| | | | | | - Natalia Campacci
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil
| | | | | | | | | | - Edenir Inêz Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, SP, Brazil.,Barretos School of Health Sciences-FACISB, Barretos, SP, Brazil
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24
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Barros-Silva D, Costa-Pinheiro P, Duarte H, Sousa EJ, Evangelista AF, Graça I, Carneiro I, Martins AT, Oliveira J, Carvalho AL, Marques MM, Henrique R, Jerónimo C. MicroRNA-27a-5p regulation by promoter methylation and MYC signaling in prostate carcinogenesis. Cell Death Dis 2018; 9:167. [PMID: 29415999 PMCID: PMC5833437 DOI: 10.1038/s41419-017-0241-y] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [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: 07/04/2017] [Revised: 12/10/2017] [Accepted: 12/18/2017] [Indexed: 12/14/2022]
Abstract
Upregulation of MYC and miRNAs deregulation are common in prostate cancer (PCa). Overactive MYC may cause miRNAs’ expression deregulation through transcriptional and post-transcriptional mechanisms and epigenetic alterations are also involved in miRNAs dysregulation. Herein, we aimed to elucidate the role of regulatory network between MYC and miRNAs in prostate carcinogenesis. MYC expression was found upregulated in PCa cases and matched precursor lesions. MicroRNA’s microarray analysis of PCa samples with opposed MYC levels identified miRNAs significantly overexpressed in high-MYC PCa. However, validation of miR-27a-5p in primary prostate tissues disclosed downregulation in PCa, instead, correlating with aberrant promoter methylation. In a series of castration-resistant PCa (CRPC) cases, miR-27a-5p was upregulated, along with promoter hypomethylation. MYC and miR-27a-5p expression levels in LNCaP and PC3 cells mirrored those observed in hormone-naíve PCa and CRPC, respectively. ChIP analysis showed that miR-27a-5p expression is only regulated by c-Myc in the absence of aberrant promoter methylation. MiR-27a-5p knockdown in PC3 cells promoted cell growth, whereas miRNA forced expression in LNCaP and stable MYC-knockdown PC3 cells attenuated the malignant phenotype, suggesting a tumor suppressive role for miR-27a-5p. Furthermore, miR-27a-5p upregulation decreased EGFR/Akt1/mTOR signaling. We concluded that miR-27a-5p is positively regulated by MYC, and its silencing due to aberrant promoter methylation occurs early in prostate carcinogenesis, concomitantly with loss of MYC regulatory activity. Our results further suggest that along PCa progression, miR-27a-5p promoter becomes hypomethylated, allowing for MYC to resume its regulatory activity. However, the altered cellular context averts miR-27a-5p from successfully accomplishing its tumor suppressive function at this stage of disease.
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Affiliation(s)
- Daniela Barros-Silva
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Pedro Costa-Pinheiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Henrique Duarte
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Elsa Joana Sousa
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | | | - Inês Graça
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Isa Carneiro
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Ana Teresa Martins
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Master in Oncology, Institute of Biomedical Sciences Abel Salazar-University of Porto (ICBAS-UP), Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072, Porto, Portugal
| | - André L Carvalho
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - Márcia M Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil.,Barretos School of Health Sciences, Barretos, São Paulo, Brazil
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal.,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal. .,Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar (ICBAS)-University of Porto, Porto, Portugal.
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25
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Santos W, Evangelista AF, Durães R, Matsushita M, Reis RM, Guimarães DP. Abstract A35: Somatic mutation profile of a panel of oncogenes and tumor suppressor genes in colorectal cancer in a Brazilian population. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-a35] [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
Colorectal cancer (CRC) is the third most frequent cancer worldwide and the fourth leading cause of death due to cancer. The development of this disease usually occurs due to the progression of precursor lesions in the normal intestinal mucosa to tumor. Environment, age, lifestyle, and genetic background are considered risk factors for the development and progression of CRC. The molecular abnormalities involved in the progression of CRC have been well characterized, including mutations, microsatellite instability, and epigenetic changes. Although the molecular profile of colorectal cancer is well known in developed countries, in the Brazilian population information is still very limited. Therefore, in the present study we intended to characterize the mutation profile of a Brazilian population and associate this with their clinicopathologic features. A total of 61 colorectal cancer cases of different stages were included. DNA was extracted from frozen fresh tumors and sequenced using a panel of 298 genes by next-generation sequencing (NGS). The mean age of patients was 63 years old; 57.4% were male. Three patients had CRC in stage 0, 16 in stage I, 29 in stage II, 10 in stage III, and three in stage IV. Considering only nonsynonymous alterations, we found on average 7.24 mutations per patient. The majority were missense (61.8%), followed by nonsense (15.2%) and frameshift mutations (10.9%). The genes most frequently mutated were APC (78.7%), TP53 (72.1%), KRAS (60.7%), PIK3CA (14.8%), and FBXW7 (14.8%). Alterations in tumor suppressor genes such as APC and TP53 were found throughout the entire gene. On the other hand, oncogenes such as KRAS had alterations in hotspots of the gene. In conclusion, the frequency of alterations in genes sequenced in our population was similar to that found in the international literature for other populations.
Citation Format: Wellington Santos, Adriane Feijó Evangelista, Ronilson Durães, Marcus Matsushita, Rui Manuel Reis, Denise Peixoto Guimarães. Somatic mutation profile of a panel of oncogenes and tumor suppressor genes in colorectal cancer in a Brazilian population [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A35.
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Batista M. R. B. LR, Kuhlmann PA, Melendez ME, Laus AC, Carvalho ACD, Marchi PRMD, Evangelista AF, Luciano VDS, André CL. Abstract A34: SNPs as predictors in the tailoring of treatment for HNSCC patients undergoing organ preservation protocols. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-a34] [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: The treatment of early-stage head and neck squamous cell carcinoma (HNSCC) tumors is conducted through a multimodality approach including surgery, radiation, and chemotherapy, with curative rates of approximately 80-90%. However, only 30-50% of patients with locally advanced disease survive more than five years, despite the advances in surgical techniques and the recognized benefits of chemoradiation. In this scenario, improvement in patients' survival requires both early detection as well as the possibility of predicting, at the moment of diagnosis, which patients will benefit from a specific treatment. Tailoring the treatment is of great importance and may help in the management of treatment planning and follow-up, improving survival rates.
Objectives: The aim of the present study was to evaluate SNPs in genes involved in induction chemotherapy with cisplatin and paclitaxel, which are able to predict the response to an organ-preservation protocol based on chemoradiation.
Materials and Methods: For this purpose, we assessed the profile of 3.223 SNPs of 59 HNSCC patients with locally advanced and unresectable tumors undergoing treatment using the IonTorrent plataform.
Results: From 3,223 SPNs, only 323 were present in the study population and 21 SNPs showed a significant association with response to induction chemotherapy and/or concomitance. Regarding induction chemotherapy response, thirteen polymorphisms were statistically associated. The presence of SNPs rs776746 (CYP3A5 gene) (p=0.03), rs1883322 (PPARD gene) (p=0.03), rs10932374 (ERBB4 gene) (p=0.03), and rs2230806 (ABCA1 gene) (p=0.04) was associated with a favorable treatment response, whereas the remaining polymorphisms with statistical significance were associated with a lack of therapeutic response. It is interesting to note that the presence of three polymorphisms (rs10509681 (p=0.001), rs1058930 (p=0.03), and rs11572080 (p≤0.001)) in the CYP2C8 gene was associated with treatment resistance, showing the importance of these polymorphisms in the process of chemotherapy resistance. Similarly, polymorphisms rs12415607 (p=0.01), rs4353229 (p=0.02), and rs2227310 (p=0.02) in the CASP7 gene were associated with resistance to chemotherapy.
Conclusion: The results of this study suggest that the evaluation of SNPs could be an important tool for treatment planning and a prognosis predictor for HNSCC patients undergoing organ preservation protocols.
Citation Format: Lidia Rebolho Batista M. R. B., Pamela Angelique Kuhlmann, Matias Eliseo Melendez, Ana Carolina Laus, Ana Carolina de Carvalho, Pedro Rafael Martins De Marchi, Adriane Feijó Evangelista, Viana de Souza Luciano, Carvalho Lopes André. SNPs as predictors in the tailoring of treatment for HNSCC patients undergoing organ preservation protocols [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A34.
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Cruvinel-Carloni A, Silva-Oliveira RJD, Oliveira-Silva VA, Rosa MN, Bidinotto LT, Berdinarelli GN, Torrieri R, Evangelista AF, Martinho OC, Gonçalves VM, Clara C, Almeida GCD, Reis RM. Abstract A29: Omics profile of two immortalized Brazilian glioblastoma cell cultures. Clin Cancer Res 2018. [DOI: 10.1158/1557-3265.tcm17-a29] [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: Glioblastomas are the most frequent and deadly brain tumors. Genomic alterations, as well as its high heterogeneity, are important features of these tumors. Despite the advances in the biology of these tumors, it is essential to develop models, such as primary tumor cell lines, that better mimic their genomic diversity and therapeutic behavior. We aimed to characterize the molecular profile of two (HCB2 and HCB151) established immortalized glioblastoma cell lines.
Methods: Immortalized glioblastoma cell lines, HCB2 and HCB151, were established from Barretos Cancer Hospital patients diagnosed with glioblastoma. The cells were cultured with DMEM+10%BFS+1%PS and molecularly characterized, using arrayCGH, next-generation sequencing (Ion Torrent) and validated by Sanger sequencing, miRNA expression and CNV using the NanoString platform, and BD Lyoplate™ Human Cell Surface Marker Screening Panel using Accuri™ C6 flow cytometer. The tumorigenic capacity was further determined in vivo by the chicken chorioallantoic membrane (CAM) assay, and its response to temozolomide-based chemotherapy was done by MTS.
Results: The aCGH analysis showed that the most frequent events was the gain of chromosome 7 and loss of chromosomes 10, 13, and 17p. HCB2 exhibited mutations in the TERT gene, while HCB151 showed mutations in the TP53, PTEN, LZTR1, and TERT genes. The immortalized cultures present an unique miRNA profile. The CAM assay showed that HCB2 and HCB151 were able to form vascularized tumors, with HCB151 more aggressive than HCB2. In addition, both HCB2 (IC50>1000 µM) and HCB151 (IC50=783 µM) showed resistance to TMZ when compared to commercial glioblastomas cell lines (23-441 µM).
Conclusion: The present findings showed that the immortalized glioblastoma cell lines showed classic genomic features of glioblastomas and exhibited a similar biologic behavior, suggesting that these cell lines are a good model for glioblastoma preclinical studies.
Citation Format: Adriana Cruvinel-Carloni, Renato José da Silva-Oliveira, Viviane Aline Oliveira-Silva, Marcela Nunes Rosa, Lucas Tadeu Bidinotto, Gustavo Noriz Berdinarelli, Raul Torrieri, Adriane Feijó Evangelista, Olga Catarina Martinho, Vera Mónica Gonçalves, Carlos Clara, Gisele Caravina de Almeida, Rui Manuel Reis. Omics profile of two immortalized Brazilian glioblastoma cell cultures [abstract]. In: Proceedings of the AACR International Conference held in cooperation with the Latin American Cooperative Oncology Group (LACOG) on Translational Cancer Medicine; May 4-6, 2017; São Paulo, Brazil. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(1_Suppl):Abstract nr A29.
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Affiliation(s)
| | | | | | | | | | | | - Raul Torrieri
- 1Barretos Cancer Hospital, Barretos, São Paulo, SP, Brazil,
| | | | | | | | - Carlos Clara
- 1Barretos Cancer Hospital, Barretos, São Paulo, SP, Brazil,
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Martinho O, Silva-Oliveira R, Cury FP, Barbosa AM, Granja S, Evangelista AF, Marques F, Miranda-Gonçalves V, Cardoso-Carneiro D, de Paula FE, Zanon M, Scapulatempo-Neto C, Moreira MA, Baltazar F, Longatto-Filho A, Reis RM. HER Family Receptors are Important Theranostic Biomarkers for Cervical Cancer: Blocking Glucose Metabolism Enhances the Therapeutic Effect of HER Inhibitors. Theranostics 2017; 7:717-732. [PMID: 28255362 PMCID: PMC5327645 DOI: 10.7150/thno.17154] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 11/21/2016] [Indexed: 12/17/2022] Open
Abstract
Persistent HPV infection alone is not sufficient for cervical cancer development, which requires additional molecular alterations for tumor progression and metastasis ultimately leading to a lethal disease. In this study, we performed a comprehensive analysis of HER family receptor alterations in cervical adenocarcinoma. We detected overexpression of HER protein, mainly HER2, which was an independent prognostic marker for these patients. By using in vitro and in vivo approaches, we provided evidence that HER inhibitors, allitinib and lapatinib, were effective in reducing cervical cancer aggressiveness. Furthermore, combination of these drugs with glucose uptake blockers could overcome the putative HIF1-α-mediated resistance to HER-targeted therapies. Thus, we propose that the use of HER inhibitors in association with glycolysis blockers can be a potentially effective treatment option for HER-positive cervical cancer patients.
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Bordinhão ALR, Evangelista AF, Oliveira RJS, Macedo T, Silveira HC, Reis RM, Marques MM. MicroRNA profiling in human breast cancer cell lines exposed to the anti-neoplastic drug cediranib. Oncol Rep 2016; 36:3197-3206. [PMID: 27748845 DOI: 10.3892/or.2016.5153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/15/2016] [Indexed: 11/06/2022] Open
Abstract
Cediranib, a pan-tyrosine kinase inhibitor is showing promising results for the treatment of several solid tumours. In breast cancer, its effects remain unclear, and there are no predictive biomarkers. Several studies have examined the expression profiles of microRNAs (miRNAs) in response to different chemotherapy treatments and found that the expression patterns may be associated with the treatment response. Therefore, our aim was to evaluate the cellular behaviour and differential expression profiles of miRNAs in breast cancer cell lines exposed to cediranib. The biological effect of this drug was measured by viability, migration, invasion and cell death in in vitro assays. Signaling pathways were assessed using a human phospho-receptor tyrosine kinase array. Furthermore, using a miRNA array and quantitative real-time PCR (qRT‑PCR), we assessed the relative expression of miRNAs following cediranib treatment. The breast cancer cell lines exhibited a distinct cytotoxic response to cediranib treatment. Cediranib exposure resulted in a decrease in the cell migration and invasion of all the breast cancer cell lines. Treatment with cediranib appeared to be able to modulate the activation of several RTKs that are targets of cediranib such as EGFR and a new potential target ROR2. Furthermore, this drug was able to modulate the expression profile of different microRNAs such as miR-494, miR-923, miR-449a, miR-449b and miR-886-3 in breast cancer cell lines. These miRNAs are reported to regulate genes involved in important molecular processes, according to bioinformatics prediction tools.
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Affiliation(s)
- A L R Bordinhão
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - A F Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - R J S Oliveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - T Macedo
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - H C Silveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - R M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - M M Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
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Fernando RC, de Carvalho F, Mazzotti DR, Evangelista AF, Braga WMT, de Lourdes Chauffaille M, Leme AFP, Colleoni GWB. Multiple myeloma cell lines and primary tumors proteoma: protein biosynthesis and immune system as potential therapeutic targets. Genes Cancer 2016; 6:462-471. [PMID: 26807199 PMCID: PMC4701225 DOI: 10.18632/genesandcancer.88] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [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] [Indexed: 01/08/2023] Open
Abstract
Despite great advance in multiple myeloma (MM) treatment since 2000s, it is still an incurable disease and novel therapies are welcome. Therefore, the purpose of this study was to explore MM plasma cells' (MM-PC) proteome, in comparison with their normal counterparts (derived from palatine tonsils of normal donors, ND-PC), in order to find potential therapeutic targets expressed on the surface of these cells. We also aimed to evaluate the proteome of MM cell lines with different genetic alterations, to confirm findings obtained with primary tumor cells. Bone marrow (BM) samples from eight new cases of MM and palatine tonsils from seven unmatched controls were submitted to PC separation and, in addition to two MM cell lines (U266, RPMI-8226), were submitted to protein extraction for mass spectrometry analyses. A total of 81 proteins were differentially expressed between MM-PC and ND-PC - 72 upregulated and nine downregulated; U266 vs. RPMI 8226 cell lines presented 61 differentially expressed proteins - 51 upregulated and 10 downregulated. On primary tumors, bioinformatics analyses highlighted upregulation of protein biosynthesis machinery, as well as downregulation of immune response components, such as MHC class I and II, and complement receptors. We also provided comprehensive information about U266 and RPMI-8226 cell lines' proteome and could confirm some patients' findings.
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Affiliation(s)
- Rodrigo Carlini Fernando
- Departamento de Oncologia Clínica e Experimental, Disciplina de Hematologia e Hemoterapia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Fabricio de Carvalho
- Departamento de Oncologia Clínica e Experimental, Disciplina de Hematologia e Hemoterapia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Diego Robles Mazzotti
- Departamento de Psicobiologia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | | | - Walter Moisés Tobias Braga
- Departamento de Oncologia Clínica e Experimental, Disciplina de Hematologia e Hemoterapia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Maria de Lourdes Chauffaille
- Departamento de Oncologia Clínica e Experimental, Disciplina de Hematologia e Hemoterapia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
| | - Adriana Franco Paes Leme
- Laboratório de Espectrometria de Massas, Laboratório Nacional de Biociências, LNBio, Conselho Nacional de Pesquisa em Energia e Materiais, CNPEM, Campinas, Brazil
| | - Gisele Wally Braga Colleoni
- Departamento de Oncologia Clínica e Experimental, Disciplina de Hematologia e Hemoterapia, Universidade Federal de São Paulo, UNIFESP, São Paulo, Brazil
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de Carvalho AC, Scapulatempo-Neto C, Maia DCC, Evangelista AF, Morini MA, Carvalho AL, Vettore AL. Erratum: Accuracy of microRNAs as markers for the detection of neck lymph node metastases in patients with head and neck squamous cell carcinoma. BMC Med 2015; 13:155. [PMID: 26129943 PMCID: PMC4487505 DOI: 10.1186/s12916-015-0406-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 06/18/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ana Carolina de Carvalho
- Laboratory of Cancer Molecular Biology, Department of Biological Sciences, Federal University of São Paulo, Diadema, Brazil. .,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.
| | | | - Danielle Calheiros Campelo Maia
- Laboratory of Cancer Molecular Biology, Department of Biological Sciences, Federal University of São Paulo, Diadema, Brazil.
| | | | | | - André Lopes Carvalho
- Department of Head and Neck Surgery, Barretos Cancer Hospital, Barretos, Brazil. .,Departamento de Cirurgia de Cabeça e Pescoço, Hospital de Câncer de Barretos, Rua Antenor Duarte Villela, 1331, Barretos, SP, 14784-400, Brazil.
| | - André Luiz Vettore
- Laboratory of Cancer Molecular Biology, Department of Biological Sciences, Federal University of São Paulo, Diadema, Brazil. .,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore. .,Laboratório de Biologia Molecular do Câncer, UNIFESP, Rua Pedro de Toledo, 669 - 11° andar, L11B, São Paulo, SP, 04039-032, Brazil.
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de Carvalho AC, Scapulatempo-Neto C, Maia DCC, Evangelista AF, Morini MA, Carvalho AL, Vettore AL. Accuracy of microRNAs as markers for the detection of neck lymph node metastases in patients with head and neck squamous cell carcinoma. BMC Med 2015; 13:108. [PMID: 25956054 PMCID: PMC4493814 DOI: 10.1186/s12916-015-0350-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/20/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The presence of metastatic disease in cervical lymph nodes of head and neck squamous cell carcinoma (HNSCC) patients is a very important determinant in therapy choice and prognosis, with great impact in overall survival. Frequently, routine lymph node staging cannot detect occult metastases and the post-surgical histologic evaluation of resected lymph nodes is not sensitive in detecting small metastatic deposits. Molecular markers based on tissue-specific microRNA expression are alternative accurate diagnostic markers. Herein, we evaluated the feasibility of using the expression of microRNAs to detect metastatic cells in formalin-fixed paraffin-embedded (FFPE) lymph nodes and in fine-needle aspiration (FNA) biopsies of HNSCC patients. METHODS An initial screening compared the expression of 667 microRNAs in a discovery set comprised by metastatic and non-metastatic lymph nodes from HNSCC patients. The most differentially expressed microRNAs were validated by qRT-PCR in two independent cohorts: i) 48 FFPE lymph node samples, and ii) 113 FNA lymph node biopsies. The accuracy of the markers in identifying metastatic samples was assessed through the analysis of sensitivity, specificity, accuracy, negative predictive value, positive predictive value, and area under the curve values. RESULTS Seven microRNAs highly expressed in metastatic lymph nodes from the discovery set were validated in FFPE lymph node samples. MiR-203 and miR-205 identified all metastatic samples, regardless of the size of the metastatic deposit. Additionally, these markers also showed high accuracy when FNA samples were examined. CONCLUSIONS The high accuracy of miR-203 and miR-205 warrant these microRNAs as diagnostic markers of neck metastases in HNSCC. These can be evaluated in entire lymph nodes and in FNA biopsies collected at different time-points such as pre-treatment samples, intraoperative sentinel node biopsy, and during patient follow-up. These markers can be useful in a clinical setting in the management of HNSCC patients from initial disease staging and therapy planning to patient surveillance.
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Affiliation(s)
- Ana Carolina de Carvalho
- Laboratory of Cancer Molecular Biology, Department of Biological Sciences, Diadema Campus, Federal University of São Paulo, Rua Pedro de Toledo, 669, São Paulo, SP, 04039-032, Brazil. .,Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil.
| | - Cristovam Scapulatempo-Neto
- Department of Pathology, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil.
| | - Danielle Calheiros Campelo Maia
- Laboratory of Cancer Molecular Biology, Department of Biological Sciences, Diadema Campus, Federal University of São Paulo, Rua Pedro de Toledo, 669, São Paulo, SP, 04039-032, Brazil.
| | - Adriane Feijó Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil.
| | - Mariana Andozia Morini
- Department of Pathology, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil.
| | - André Lopes Carvalho
- Department of Head and Neck Surgery, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, Barretos, SP, 14784-400, Brazil.
| | - André Luiz Vettore
- Laboratory of Cancer Molecular Biology, Department of Biological Sciences, Diadema Campus, Federal University of São Paulo, Rua Pedro de Toledo, 669, São Paulo, SP, 04039-032, Brazil. .,Cancer Stem Cell Biology Program, Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore.
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Soares DA, Oliveira MB, Evangelista AF, Venancio EJ, Andrade RV, Felipe MSS, Petrofeza S. Phospholipase gene expression during Paracoccidioides brasiliensis morphological transition and infection. Mem Inst Oswaldo Cruz 2014; 108:808-11. [PMID: 24037207 PMCID: PMC3970691 DOI: 10.1590/0074-0276108062013021] [Citation(s) in RCA: 7] [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: 08/17/2012] [Accepted: 06/07/2013] [Indexed: 11/24/2022] Open
Abstract
Phospholipase is an important virulence factor for pathogenic fungi. In this
study, we demonstrate the following: (i) the Paracoccidioides
brasiliensis pld gene is preferentially expressed in mycelium
cells, (ii) the plb1 gene is mostly up-regulated by infection
after 6 h of co-infection of MH-S cells or during BALB/c mice
lung infection, (iii) during lung infection, plb1,
plc and pld gene expression are
significantly increased 6-48 h post-infection compared to 56 days after
infection, strongly suggesting that phospholipases play a role in the early
events of infection, but not during the chronic stages of pulmonary infection by
P. brasiliensis.
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Affiliation(s)
- Deyze Alencar Soares
- Instituto de Ciências Biológicas, Universidade Federal de Goiás, GoiâniaGO, Brasil
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Pela FP, Evangelista AF, Rassi D, Foss MC, Foss M, Nunes GT, Mendes CT, Lucena N, Donadi EA. P055. Hum Immunol 2014. [DOI: 10.1016/j.humimm.2014.08.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Melo-Lima BL, Evangelista AF, de Magalhães DAR, Passos GA, Moreau P, Donadi EA. Differential transcript profiles of MHC class Ib(Qa-1, Qa-2, and Qa-10) and Aire genes during the ontogeny of thymus and other tissues. J Immunol Res 2014; 2014:159247. [PMID: 24829926 PMCID: PMC4009201 DOI: 10.1155/2014/159247] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 01/08/2014] [Accepted: 03/07/2014] [Indexed: 11/17/2022] Open
Abstract
Qa-2 and Qa-1 are murine nonclassical MHC class I molecules involved in the modulation of immune responses by interacting with T CD8(+) and NK cell inhibitory receptors. During thymic education, the Aire gene imposes the expression of thousands of tissue-related antigens in the thymic medulla, permitting the negative selection events. Aiming to characterize the transcriptional profiles of nonclassical MHC class I genes in spatial-temporal association with the Aire expression, we evaluated the gene expression of H2-Q7(Qa-2), H2-T23(Qa-1), H2-Q10(Qa-10), and Aire during fetal and postnatal development of thymus and other tissues. In the thymus, H2-Q7(Qa-2) transcripts were detected at high levels throughout development and were positively correlated with Aire expression during fetal ages. H2-Q7(Qa-2) and H2-T23(Qa-1) showed distinct expression patterns with gradual increasing levels according to age in most tissues analyzed. H2-Q10(Qa-10) was preferentially expressed by the liver. The Aire transcriptional profile showed increased levels during the fetal period and was detectable in postnatal ages in the thymus. Overall, nonclassical MHC class I genes started to be expressed early during the ontogeny. Their levels varied according to age, tissue, and mouse strain analyzed. This differential expression may contribute to the distinct patterns of mouse susceptibility/resistance to infectious and noninfectious disorders.
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Affiliation(s)
- Breno Luiz Melo-Lima
- Basic and Applied Immunology Program, Division of Clinical Immunology, Department of Medicine, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Avenida Bandeirantes 3900, 14049-900 Ribeirão Preto, SP, Brazil
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Therapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, Bâtiment Lailler, 75475 Paris Cedex 10, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75475 Paris Cedex 10, France
| | - Adriane Feijó Evangelista
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Avenida Bandeirantes 3900, 14049-900 Ribeirão Preto, SP, Brazil
| | - Danielle Aparecida Rosa de Magalhães
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Avenida Bandeirantes 3900, 14049-900 Ribeirão Preto, SP, Brazil
| | - Geraldo Aleixo Passos
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Avenida Bandeirantes 3900, 14049-900 Ribeirão Preto, SP, Brazil
| | - Philippe Moreau
- Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut des Maladies Emergentes et des Therapies Innovantes, Service de Recherches en Hémato-Immunologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, Bâtiment Lailler, 75475 Paris Cedex 10, France
- Université Paris-Diderot, Sorbonne Paris-Cité, UMR E5, Institut Universitaire d'Hématologie, Hôpital Saint-Louis, 1 avenue Claude Vellefaux, 75475 Paris Cedex 10, France
| | - Eduardo Antonio Donadi
- Basic and Applied Immunology Program, Division of Clinical Immunology, Department of Medicine, Faculty of Medicine of Ribeirão Preto, University of São Paulo, Avenida Bandeirantes 3900, 14049-900 Ribeirão Preto, SP, Brazil
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Rassi DM, Junta CM, Fachin AL, Sandrin-Garcia P, Mello S, Silva GL, Evangelista AF, Magalhães DA, Wastowski IJ, Crispim JO, Martelli-Palomino G, Fernandes APM, Deghaide NNHS, Foss-Freitas MC, Foss MC, Soares CP, Sakamoto-Hojo ET, Passos GAS, Donadi EA. Gene expression profiles stratified according to type 1 diabetes mellitus susceptibility regions. Ann N Y Acad Sci 2009; 1150:282-9. [PMID: 19120314 DOI: 10.1196/annals.1447.064] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The MHC region (6p21) aggregates the major genes that contribute to susceptibility to type 1 diabetes (T1D). Three additional relevant susceptibility regions mapped on chromosomes 1p13 (PTPN22), 2q33 (CTLA-4), and 11p15 (insulin) have also been described by linkage studies. To evaluate the contribution of these susceptibility regions and the chromosomes that house these regions, we performed a large-scale differential gene expression on lymphomononuclear cells of recently diagnosed T1D patients, pinpointing relevant modulated genes clustered in these regions and their respective chromosomes. A total of 4608 cDNAs from the IMAGE library were spotted onto glass slides using robotic technology. Statistical analysis was carried out using the SAM program, and data regarding gene location and biological function were obtained at the SOURCE, NCBI, and FATIGO programs. Three induced genes were observed spanning around the MHC region (6p21-6p23), and seven modulated genes (5 repressed and 2 repressed) were seen spanning around the 6q21-24 region. Additional modulated genes were observed in and around the 1p13, 2q33, and 11p15 regions. Overall, modulated genes in these regions were primarily associated with cellular metabolism, transcription factors and signaling transduction. The differential gene expression characterization may identify new genes potentially involved with diabetes pathogenesis.
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Affiliation(s)
- Diane Meyre Rassi
- Molecular Immunogenetics Group, Faculty of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil.
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