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Francisco LFV, da Silva RN, Oliveira MA, Dos Santos Neto MF, Gonçalves IZ, Marques MMC, Silveira HCS. Occupational Exposures and Risks of Non-Hodgkin Lymphoma: A Meta-Analysis. Cancers (Basel) 2023; 15:cancers15092600. [PMID: 37174074 PMCID: PMC10177442 DOI: 10.3390/cancers15092600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/15/2023] Open
Abstract
Non-Hodgkin lymphoma (NHL) is a heterogeneous group with different types of diseases. It remains unclear as to what has led to an increase in incidences of NHL, however, chemical substance exposure is known to be one of the risk factors for the disease. Therefore, we performed a systematic review and meta-analysis including case-control, cohort, and cross-sectional observational epidemiological studies to verify the association between occupational exposure to carcinogens and NHL risk. Articles between the years 2000 and 2020 were collected. Two different reviewers performed a blind selection of the studies using the Rayyan QCRI web app. Post-completion, the selected articles were extracted and analyzed via the RedCap platform. Our review resulted in 2719 articles, of which 51 were included in the meta-analysis, resulting in an overall OR of 1.27 (95% CI 1.04-1.55). Furthermore, it was observed that the main occupation associated with the increased risk of NHL was that in which workers are exposed to pesticides. We therefore conclude that the evidence synthesis of the epidemiological literature supports an increased risk for NHL, regardless of subtype, considering occupational exposure to certain chemical compounds, mainly pesticides, benzene, and trichlorethylene, and certain classes of work, primarily in the field of agriculture.
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Affiliation(s)
| | - Rogério Nunes da Silva
- Postgraduate Program in Environment and Health, University of Cuiabá, Cuiabá 78008-000, MT, Brazil
| | - Marco Antônio Oliveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-390, SP, Brazil
| | | | | | - Márcia M C Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-390, SP, Brazil
| | - Henrique C S Silveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-390, SP, Brazil
- Postgraduate Program in Environment and Health, University of Cuiabá, Cuiabá 78008-000, MT, Brazil
- Campus São Paulo, University of Anhanguera, São Paulo 04119-901, SP, Brazil
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2
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Neuber AC, Komoto TT, da Silva ECA, Duval VDS, Scapulatempo-Neto C, Marques MMC. Quality Assessment of Cryopreserved Human Biological Samples from the Biobank of Barretos Cancer Hospital. Biopreserv Biobank 2023; 21:74-80. [PMID: 35613409 DOI: 10.1089/bio.2021.0131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Biobanks process, store, and supply biological materials for research. Preanalytical factors, especially storage time and temperature, must be controlled and standardized at all stages when handling biospecimen samples, especially because the literature reports highly contradictory optimal parameters. As large-sample studies are required to better understand the influence of time and temperature on cryopreserved samples' quality for genomic research, this study evaluated the integrity and quality of cryopreserved samples stored for up to 9 years at the biobank of Barretos Cancer Hospital, one of the largest biobanks in Latin America. Methods: We randomly selected 447 samples with tumor tissue paired with buffy coat or peripheral blood mononuclear cells (PBMCs) that were stored from 2008 to 2016. The genetic material quality was evaluated based on RNA integrity (RIN) and DNA integrity (DIN) ≥7, which indicated undegraded samples, and compared with storage time, which means that for DNA storage time, samples <8.1 and ≥8.1 years and for RNA <4.5 and ≥4.5 were used. Results: A total of 190 tumor tissues were eligible for DNA and RNA extraction. Those stored for 8 years had lower DIN (68%) than those stored for a shorter period (92%). A similar pattern, based on storage time (<8.1 and ≥8.1 years), was observed in the buffy coat (74% and 95%, respectively) and PBMCs (54% and 96%, respectively). For RNA extracted from tumor tissues, we observed lower RIN in samples stored for 4.5 years (17%) than in samples stored for a shorter period (45%). Buffy coat and PBMC samples stored at -30°C exhibited greater degradation (26%) than those stored at -80°C (1%). The DIN (p = 0.15) and RNA (p = 0.18) were unrelated to topography type. Conclusion: The temperature, particularly cryopreservation methodology, and storage time were the main factors that affected nucleic acid integrity, especially RNA, during cryopreservation of biospecimens.
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Affiliation(s)
| | | | | | - Vinicius da Silva Duval
- Barretos Cancer Hospital Biobank, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Márcia M C Marques
- Barretos Cancer Hospital Biobank, Barretos, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Health Sciences, Barretos, Brazil
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Neuber AC, Tostes CH, Ribeiro AG, Marczynski GT, Komoto TT, Rogeri CD, da Silva VD, Mauad EC, Reis RM, Marques MMC. The biobank of barretos cancer hospital: 14 years of experience in cancer research. Cell Tissue Bank 2021; 23:271-284. [PMID: 34216325 DOI: 10.1007/s10561-021-09941-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/20/2021] [Indexed: 01/15/2023]
Abstract
Despite the developments in cancer research over years, cancer is still one of the leading causes of death worldwide. In Brazil, the number of cancer cases for the several next years (2020-2022) is expected to increase up to 625,000. Thus, translational research has been vital to determine the potential risk, prognostic, and predictive biomarkers in cancer. Therefore, Barretos Cancer Hospital implemented a biobank (BB-BCH) in 2006, which is responsible for processing, storage, and provision of biological materials from cancer and non-cancer participants. Hence, this article aimed to describe BB-BCH's history, experiences, and outcomes and explore its impact on Brazilian translational oncology research scenario. BB-BCH has a multidisciplinary team who are responsible for guaranteeing the quality of all processes as recommended by international guidelines for biobanks. Furthermore, BB-BCH has ample equipment to ensure the quality of all material requested by researchers as genetic material (DNA and RNA) and/or entire biospecimens. From 2006 to 2019, BB-BCH contained 252,069 samples from 44,933 participants, the whole collection is represented by 15 different types of biospecimens collected from them. According to our data, the most collected and stored topography in men is head and neck (29%); in women is breast (28%); and in children is torso and limb (27%) samples. Finally, we supported national and international consortia and projects such as The Cancer Genome Atlas. BB-BCH is a vital knowledge source for scientific community, enabling the development of high-quality studies, with a wide variety of tumor categories and high national representativeness of Brazilian population.
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Affiliation(s)
| | | | - Adeylson Guimarães Ribeiro
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil
| | | | | | | | - Vinicius Duval da Silva
- Barretos Cancer Hospital Biobank, São Paulo, Brazil.,Department of Pathology, Barretos Cancer Hospital, São Paulo, Brazil
| | - Edmundo Carvalho Mauad
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil
| | - Rui Manuel Reis
- Barretos Cancer Hospital Biobank, São Paulo, Brazil.,Department of Prevention, 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, Portugal
| | - Márcia M C Marques
- Barretos Cancer Hospital Biobank, São Paulo, Brazil. .,Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil. .,Barretos School of Health Sciences, Barretos, SP, Brazil.
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4
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Dionísio MR, Vieira AF, Carvalho R, Conde I, Oliveira M, Gomes M, Pinto MT, Pereira P, Pimentel J, Souza C, Marques MMC, Duval da Silva V, Barroso A, Preto D, Cameselle-Teijeiro JF, Schmitt F, Ribeiro AS, Paredes J. BR-BCSC Signature: The Cancer Stem Cell Profile Enriched in Brain Metastases that Predicts a Worse Prognosis in Lymph Node-Positive Breast Cancer. Cells 2020; 9:cells9112442. [PMID: 33182375 PMCID: PMC7695320 DOI: 10.3390/cells9112442] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/30/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
Brain metastases remain an unmet clinical need in breast oncology, being frequently found in HER2-overexpressing and triple-negative carcinomas. These tumors were reported to be highly cancer stem-like cell-enriched, suggesting that brain metastases probably arise by the seeding of cancer cells with stem features. Accordingly, we found that brain-tropic breast cancer cells show increased stem cell activity and tumorigenic capacity in the chick embryo choriallantoic membrane when compared to the parental cell line. These observations were supported by a significant increase in their stem cell frequency and by the enrichment for the breast cancer stem cell (BCSC) phenotype CD44+CD24−/low. Based on this data, the expression of BCSC markers (CD44, CD49f, P-cadherin, EpCAM, and ALDH1) was determined and found to be significantly enriched in breast cancer brain metastases when compared to primary tumors. Therefore, a brain (BR)-BCSC signature was defined (3–5 BCSC markers), which showed to be associated with decreased brain metastases-free and overall survival. Interestingly, this signature significantly predicted a worse prognosis in lymph node-positive patients, acting as an independent prognostic factor. Thus, an enrichment of a BCSC signature was found in brain metastases, which can be used as a new prognostic factor in clinically challenging breast cancer patients.
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Affiliation(s)
- Maria Rita Dionísio
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Centro Hospitalar de Lisboa Norte, 1649-035 Lisboa, Portugal; (P.P.); (J.P.)
| | - André F. Vieira
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Rita Carvalho
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Inês Conde
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Mónica Oliveira
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Madalena Gomes
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Marta T. Pinto
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- In vivo CAM assays, i3S - Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal
| | - Pedro Pereira
- Centro Hospitalar de Lisboa Norte, 1649-035 Lisboa, Portugal; (P.P.); (J.P.)
| | - José Pimentel
- Centro Hospitalar de Lisboa Norte, 1649-035 Lisboa, Portugal; (P.P.); (J.P.)
| | - Cristiano Souza
- Department of Breast and Gynecologic Oncology, Barretos Cancer Hospital, Barretos-SP 14784-400, Brazil; (C.S.); (A.B.); (D.P.)
| | - Márcia M. C. Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos-SP 14784-400, Brazil;
- Barretos School of Health Sciences - FACISB, Barretos-SP 14784-400, Brazil
| | | | - Alison Barroso
- Department of Breast and Gynecologic Oncology, Barretos Cancer Hospital, Barretos-SP 14784-400, Brazil; (C.S.); (A.B.); (D.P.)
| | - Daniel Preto
- Department of Breast and Gynecologic Oncology, Barretos Cancer Hospital, Barretos-SP 14784-400, Brazil; (C.S.); (A.B.); (D.P.)
| | | | - Fernando Schmitt
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of Porto University (FMUP), 4200-135 Porto, Portugal
| | - Ana Sofia Ribeiro
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
| | - Joana Paredes
- Epithelial Interactions in Cancer (EPIC) group, i3S, Institute of Investigation and Innovation in Health, University of Porto, 4200-135 Porto, Portugal; (M.R.D.); (A.F.V.); (R.C.); (I.C.); (M.O.); (M.G.); (M.T.P.); (F.S.); (A.S.R.)
- IPATIMUP- Institute of Pathology and Immunology, University of Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine of Porto University (FMUP), 4200-135 Porto, Portugal
- Correspondence: ; Tel.: +35-12-2557-0700
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Souza CP, Cinegaglia NC, Felix TF, Evangelista AF, Oliveira RA, Hasimoto EN, Cataneo DC, Cataneo AJM, Scapulatempo Neto C, Viana CR, de Paula FE, Drigo SA, Carvalho RF, Marques MMC, Reis RM, Reis PP. Deregulated microRNAs Are Associated with Patient Survival and Predicted to Target Genes That Modulate Lung Cancer Signaling Pathways. Cancers (Basel) 2020; 12:E2711. [PMID: 32971741 PMCID: PMC7563870 DOI: 10.3390/cancers12092711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/05/2020] [Accepted: 09/09/2020] [Indexed: 12/24/2022] Open
Abstract
(1) Background: Although the advances in diagnostic and treatment strategies, lung cancer remains the leading cause of cancer-related deaths, worldwide, with survival rates as low as 16% in developed countries. Low survival rates are mainly due to late diagnosis and the lack of effective treatment. Therefore, the identification of novel, clinically useful biomarkers is still needed for patients with advanced disease stage and poor survival. Micro(mi)RNAs are non-coding RNAs and potent regulators of gene expression with a possible role as diagnostic, prognostic and predictive biomarkers in cancer. (2) Methods: We applied global miRNA expression profiling analysis using TaqMan® arrays in paired tumor and normal lung tissues (n = 38) from treatment-naïve patients with lung adenocarcinoma (AD; n = 23) and lung squamous cell carcinoma (SCC; n = 15). miRNA target genes were validated using The Cancer Genome Atlas (TCGA) lung AD (n = 561) and lung SCC (n = 523) RNA-Seq datasets. (3) Results: We identified 33 significantly deregulated miRNAs (fold change, FC ≥ 2.0 and p < 0.05) in tumors relative to normal lung tissues, regardless of tumor histology. Enrichment analysis confirmed that genes targeted by the 33 miRNAs are aberrantly expressed in lung AD and SCC, and modulate known pathways in lung cancer. Additionally, high expression of miR-25-3p was significantly associated (p < 0.05) with poor patient survival, when considering both tumor histologies. (4) Conclusions: miR-25-3p may be a potential prognostic biomarker in non-small cell lung cancer. Genes targeted by miRNAs regulate EGFR and TGFβ signaling, among other known pathways relevant to lung tumorigenesis.
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Affiliation(s)
- Cristiano P. Souza
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Naiara C. Cinegaglia
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
| | - Tainara F. Felix
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
| | - Adriane F. Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Rogério A. Oliveira
- Department of Biostatistics, Plant Biology, Parasitology, and Zoology, Institute of Biosciences, São Paulo State University UNESP, Botucatu 18618-689, SP, Brazil;
| | - Erica N. Hasimoto
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
| | - Daniele C. Cataneo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
| | - Antônio J. M. Cataneo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
| | - Cristovam Scapulatempo Neto
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Cristiano R. Viana
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Flávia E. de Paula
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
| | - Sandra A. Drigo
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
| | - Robson F. Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, UNESP, Botucatu 18618-689, SP, Brazil;
| | - Márcia M. C. Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
- Barretos School of Health Sciences, Barretos 14785-002, SP, Brazil
| | - Rui M. Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos 14784-400, SP, Brazil; (A.F.E.); (C.S.N.); (C.R.V.); (F.E.d.P.); (M.M.C.M.); (R.M.R.)
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s-PT Government Associate Laboratory, 410-057 Braga/Guimarães, Portugal
| | - Patricia P. Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (C.P.S.); (E.N.H.); (D.C.C.); (A.J.M.C.); (S.A.D.)
- Experimental Research Unity (UNIPEX), São Paulo State University, UNESP, Botucatu 18618-687, SP, Brazil; (N.C.C.); (T.F.F.)
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Fornari TA, Donate PB, Macedo C, Marques MMC, Magalhães DA, Passos GAS. Age-related deregulation of Aire and peripheral tissue antigen genes in the thymic stroma of non-obese diabetic (NOD) mice is associated with autoimmune type 1 diabetes mellitus (DM-1). Mol Cell Biochem 2010; 342:21-8. [PMID: 20414703 DOI: 10.1007/s11010-010-0464-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2009] [Accepted: 04/12/2010] [Indexed: 12/16/2022]
Abstract
Gene expression of peripheral tissue antigens (PTAs) in stromal medullary thymic epithelial cells (mTECs) is a key process to the negative selection of autoreactive thymocytes. This phenomenon was termed "promiscuous gene expression" (PGE), which is partially controlled by the Aire gene. Nevertheless, reasons for the correlation of Aire and PTAs with the emergence of autoimmune diseases are largely unknown, though it may be a result of a chronological effect. Although the effect of Aire mutations in pathogenic autoimmunity is well know, it could not be a unique cause for autoimmunity. Independently of mutations, temporal deregulation of Aire expression may imbalance Aire-dependent PTAs and/or wide PGE. This deregulation may be an early warning sign for autoimmune diseases as it guarantees autoantigen representation in the thymus. To assess this hypothesis, we studied the expression levels of Aire, Aire-dependent (Ins2) and Aire-independent (Gad67 and Col2a1) PTAs using real-time-PCR of the thymic stromal cells of NOD mice during the development of autoimmune type 1 diabetes mellitus (DM-1). Wide PGE was studied by microarrays in which the PTA genes were identified through parallel CD80(+) mTEC 3.10 cell line expression profiling. The results show that Aire gene was down-regulated in young pre-autoimmune (pre-diabetic) NOD mice. PGE and specific PTA genes were down-regulated in adult autoimmune diabetic animals. These findings represent evidence indicating that chronological deregulation of genes important to negative selection may be associated with the development of an autoimmune disease (DM-1) in mice.
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Affiliation(s)
- Thaís A Fornari
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine of Ribeirão Preto, University of São Paulo (USP), 3900 Via Bandeirantes, Ribeirão Preto, SP, Brazil
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Dernowsek JA, Fontana V, Evangelista AF, Junta CM, Marques MMC, Macedo C, Simões BP, Prado KFB, Passos GAS. Comparative expression and transcriptional networks of human‐mouse syntenic genes during osteoblastic differentiation of bone marrow mesenchymal stem cells. FASEB J 2009. [DOI: 10.1096/fasebj.23.1_supplement.465.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Rassi DM, Junta CM, Fachin AL, Sandrin-Garcia P, Mello S, Marques MMC, Fernandes APM, Foss-Freitas MC, Foss MC, Sakamoto-Hojo ET, Passos GAS, Donadi EA. Metabolism genes are among the differentially expressed ones observed in lymphomononuclear cells of recently diagnosed type 1 diabetes mellitus patients. Ann N Y Acad Sci 2007; 1079:171-6. [PMID: 17130550 DOI: 10.1196/annals.1375.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The large-scale differential gene expression in lymphomononuclear cells of six patients with recently diagnosed type), and six normal individuals matched to patients for sex and age were studied. Glass slides containing 4608 cDNAs from the IMAGE library were spotted using robotic technology. Statistical analysis was carried out by the SAM program, and gene function assessed by the FATIGO program. Thirty differentially expressed genes (21 induced and 9 repressed) were disclosed when DM-1 patients were compared with controls. Although presenting with distinct biological function, most of the induced or repressed genes were related with protein, phosphate, DNA, RNA, carboxylic acid, and fatty acid metabolism. Although some of these genes have been previously associated with the pathogenesis of T1DM, many other genes were identified for further studies.
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Affiliation(s)
- Diane M Rassi
- Divisão de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, 14049-900 São Paulo, S.P., Brazil
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9
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Sousa Cardoso R, Magalhães DAR, Baião AMT, Junta CM, Macedo C, Marques MMC, Sakamoto-Hojo ET, Donadi EA, Passos GAS. Onset of promiscuous gene expression in murine fetal thymus organ culture. Immunology 2006; 119:369-75. [PMID: 16903901 PMCID: PMC1819582 DOI: 10.1111/j.1365-2567.2006.02441.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
T-cell differentiation and induction of tolerance to self-antigens occurs mainly in the thymus. Thymic stromal cells, specifically medullary thymic epithelial cells, express a diverse set of genes encoding parenchymal organ-specific proteins. This phenomenon has been termed promiscuous gene expression (PGE) and has been implicated in preventing organ-specific autoimmunity by inducing T-cell tolerance to self antigens. Early thymopoiesis and the critical factors involved in T-cell differentiation can be reproduced in vitro by murine fetal thymus organ culture (FTOC), which mimics the natural thymic microenvironment. To evaluate the occurrence of PGE in FTOC, gene expression profiling during in vitro thymic development in BALB/c mice was performed using a set of nylon cDNA microarrays containing 9216 sequences. The statistical analysis of the microarray data (sam program) revealed the temporal repression and induction of 57 parenchymal and seven lymphoid organ-specific genes. Most of the genes analysed are repressed during early thymic development (15-17 days post-coitum). The expression of the autoimmune regulator (AIRE) gene at 16 days post-coitum marks the onset of PGE. This precedes the induction of parenchymal organ genes during the late developmental phase at 20 days post-coitum. The mechanism of T-cell tolerance induction begins during fetal development and continues into adulthood. Our findings are significant because they show a fine demarcation of PGE onset, which plays a central role in induction of T-cell tolerance.
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Affiliation(s)
- Renato Sousa Cardoso
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine, University of Sao Paulo, Sao Paulo, Brazil
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Trevisan GL, Rassi DM, Baião AMT, Sandrin-Garcia P, Mello SS, Tamia-Ferreira MC, Junta CM, Fachin AL, Marques MMC, Sakamoto-Hojo ET, Donadi EA, Passos GAS. Using cDNA microarrays to identify human CD19+ B cell gene products (ESTs) originated from systemic lupus erythematosus susceptibility loci. Autoimmun Rev 2006; 5:319-23. [PMID: 16782556 DOI: 10.1016/j.autrev.2005.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2005] [Accepted: 11/22/2005] [Indexed: 11/21/2022]
Abstract
Systemic lupus erythematosus (SLE) is a prototype of autoimmune disease which arises from interactions between susceptibility genes and environmental factors. Despite the heterogeneous manifestations in this disease, all SLE patients present plasma autoantibodies recognizing nuclear components. Thus, auto reactive B cells represent key effectors to be investigated. Human linkage analysis is providing the localization of susceptibility loci distributed in chromosomes contributing to elucidate the manner in which interactions between these loci mediate SLE pathogenesis. We associate the cDNA microarray technology to investigate the differential gene expression of CD19(+) B cells with genetic linkage data. Bioinformatics programs served to evidentiate the differentially expressed sequences and the design of the microarray allowed hierarchical clustering of patients and controls. Sequencing allowed the identification of 8 new gene products differentially expressed (ESTs) that were co-localized in SLE or other autoimmune diseases susceptibility loci on chromosome 1p21, 2q21, 13q33, 16p12.1 and 16q12.1. These findings strongly suggest that chromosomal regions previously identified as SLE susceptibility loci are in fact transcribed in CD19(+) B cells of patients. In this review, we delineate a new possibility for the use of cDNA microarrays in studies focusing the control of gene expression of disease susceptibility loci identified by genetic linkage.
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Affiliation(s)
- Glauce L Trevisan
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine, University of São Paulo (USP), 14040-900 Ribeirão Preto, SP, Brazil
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Marques MMC, Junta CM, Cardoso RS, Mello SS, Sakamoto-Hojo ET, Donadi EA, Passos GAS. Changes in the gene expression profiling of the thymus in response to fibrosarcoma growth. Mol Cell Biochem 2005; 276:81-8. [PMID: 16132688 DOI: 10.1007/s11010-005-3240-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 03/03/2005] [Indexed: 10/25/2022]
Abstract
The aim of this study was to determine whether subcutaneous injection of tumor cells into Balb-c mice, which induces a fibrosarcoma at the site of injection, produced a differential expression profile in the thymus that could be correlated with tumor growth. A dynamic transcriptional profile of the thymus in response to tumor development was observed using nylon cDNA microarrays. The Cluster-Tree View and the SAM programs were used to reveal induced and repressed genes during tumor growth. This experimental model-system showed that this approach is adequate to detect the presence of tumor cells in vivo.
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Affiliation(s)
- Márcia M C Marques
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine, University of São Paulo (USP), 14040-900, Ribeirão Preto, SP, Brazil
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12
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Cardoso RS, Junta CM, Macedo C, Magalhães DAR, Silveira ELV, Paula MO, Marques MMC, Mello SS, Zárate-Bladés CR, Nguyen C, Houlgatte R, Donadi EA, Sakamoto-Hojo ET, Passos GAS. Hybridization signatures of gamma-irradiated murine fetal thymus organ culture (FTOC) reveal modulation of genes associated with T-cell receptor V(D)J recombination and DNA repair. Mol Immunol 2005; 43:464-72. [PMID: 16337489 DOI: 10.1016/j.molimm.2005.03.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2004] [Accepted: 03/04/2005] [Indexed: 10/25/2022]
Abstract
In this study, we observed the occurrence of TRBV8.1-DB2.1 V(D)J recombination in murine fetal thymus organ culture (FTOC), in which the thymic microenvironment is mimicked. Since ionizing radiation affects T-cell development, we irradiated FTOCs with gamma rays to evaluate the modulation of genes implicated in TRBV8.1-BD2.1 rearrangements. The nylon cDNA microarray method was employed to monitor the expression of 9216 genes, which were organized in coexpression clusters. Clustering analysis showed similar expression profiling of genes implicated in the V(D)J recombination and DNA double strand break (DSB) repair processes such as XRCC4, RAG-2, Artemis and DNA-PK-cs, thus suggesting overlap between the two processes. The RUNX3 gene, whose coded protein binds to the enhancers of TR genes, was also modulated and the DNA cross-linking LR1 gene, which plays a role in the opening of hairpin DNA structures and whose expression pattern is similar to Artemis, may play a role in the control of V(D)J recombination. Furthermore, our data demonstrate that the FTOC model system and cDNA microarray method are useful tools to evidentiate genes that may play a role in both processes V(D)J recombination and DNA repair.
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Affiliation(s)
- Renato S Cardoso
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine, University of São Paulo (USP), 14040-900 Ribeirão Preto, SP, Brazil
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Magalhães DAR, Macedo C, Junta CM, Mello SS, Marques MMC, Cardoso RS, Sakamoto-Hojo ET, Donadi EA, Passos GAS. Hybridization signatures during thymus ontogeny reveals modulation of genes coding for T-cell signaling proteins. Mol Immunol 2004; 42:1043-8. [PMID: 15829294 DOI: 10.1016/j.molimm.2004.09.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Accepted: 09/29/2004] [Indexed: 11/22/2022]
Abstract
Non-manipulated inbred mouse strains constitutes an interesting model-system for in vivo studies on thymus ontogeny due to the possibility to observe the molecular events of the thymocyte maturation. In previous studies, using RT-PCR method, we have found that several immune system genes such as interleukins and MHC are differentially expressed during ontogeny of the thymus whose genes act as modulators of T-cell differentiation. To determine which other genes are modulated on a large-scale basis, we measured the levels of mRNA expression in mouse fetal thymus (14-17 days of gestation) by hybridization with cDNA microarrays containing 1,576 cDNA sequences derived from the IMAGE MTB library. T-cell maturation was monitored by detection of the T-cell receptor beta TRBV8.1-BD2.1 rearranged DNA segment. Each developmental phase of thymus, displayed a characteristic expression profile, as evaluated by the Cluster and Tree-View softwares. Genes differentially and significantly expressed were selected on the basis of significance analysis of the microarray data (SAM program). With the reclustering of only significantly expressed genes, it was possible to characterize the phases of thymus ontogeny, based on the differential profile of expression. Our method provided the detection of genes implicated in the cell signaling, such as the hematopoietic cell signal transducer gene, genes implicated in T-cell calcium influx (tyrosine phosphatase) and calcium signaling proteins (vesicle transport binding protein 3, proline rich Gla, casein kinase alpha 1 and Down syndrome homolog protein 1) and a gene important for the protein transport, including T-cell receptors chains, towards the cell membrane (Golgi SNAP receptor complex member 2). The results demonstrate that the cDNA microarray used to explore the gene expression was useful for understanding the modulation of several cell-signaling genes, including the calcium cascade pathway, which is important for individual stages of T-cell maturation and control of anergy during thymus ontogeny.
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Affiliation(s)
- Danielle A R Magalhães
- Molecular Immunogenetics Group, Department of Genetics, Faculty of Medicine, University of São Paulo (USP), 14040-900 Ribeirão Preto, SP, Brazil
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