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Ferrão Maciel-Fiuza M, Rengel BD, Wachholz GE, do Amaral Gomes J, de Oliveira MR, Kowalski TW, Roehe PM, Luiz Vianna FS, Schüler-Faccini L, Mayer FQ, Varela APM, Fraga LR. New candidate genes potentially involved in Zika virus teratogenesis. Comput Biol Med 2024; 173:108259. [PMID: 38522248 DOI: 10.1016/j.compbiomed.2024.108259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 02/15/2024] [Accepted: 03/06/2024] [Indexed: 03/26/2024]
Abstract
Despite efforts to elucidate Zika virus (ZIKV) teratogenesis, still several issues remain unresolved, particularly on the molecular mechanisms behind the pathogenesis of Congenital Zika Syndrome (CZS). To answer this question, we used bioinformatics tools, animal experiments and human gene expression analysis to investigate genes related to brain development potentially involved in CZS. Searches in databases for genes related to brain development and CZS were performed, and a protein interaction network was created. The expression of these genes was analyzed in a CZS animal model and secondary gene expression analysis (DGE) was performed in human cells exposed to ZIKV. A total of 2610 genes were identified in the databases, of which 1013 were connected. By applying centrality statistics of the global network, 36 candidate genes were identified, which, after selection resulted in nine genes. Gene expression analysis revealed distinctive expression patterns for PRKDC, PCNA, ATM, SMC3 as well as for FGF8 and SHH in the CZS model. Furthermore, DGE analysis altered expression of ATM, PRKDC, PCNA. In conclusion, systems biology are helpful tools to identify candidate genes to be validated in vitro and in vivo. PRKDC, PCNA, ATM, SMC3, FGF8 and SHH have altered expression in ZIKV-induced brain malformations.
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Affiliation(s)
- Miriãn Ferrão Maciel-Fiuza
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Bruna Duarte Rengel
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Gabriela Elis Wachholz
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Julia do Amaral Gomes
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Maikel Rosa de Oliveira
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - Paulo Michel Roehe
- Department of Microbiology, Immunology and Parasitology, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lavínia Schüler-Faccini
- Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Fabiana Quoos Mayer
- Graduate Program in Molecular and Cellular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Ana Paula Muterle Varela
- Graduate Program in Biosciences, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, Brazil.
| | - Lucas Rosa Fraga
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
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2
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Cadore NA, Lord VO, Recamonde-Mendoza M, Kowalski TW, Vianna FSL. Meta-analysis of Transcriptomic Data from Lung Autopsy and Cellular Models of SARS-CoV-2 Infection. Biochem Genet 2024; 62:892-914. [PMID: 37486510 DOI: 10.1007/s10528-023-10453-2] [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: 02/09/2023] [Accepted: 07/12/2023] [Indexed: 07/25/2023]
Abstract
Severe COVID-19 is a systemic disorder involving excessive inflammatory response, metabolic dysfunction, multi-organ damage, and several clinical features. Here, we performed a transcriptome meta-analysis investigating genes and molecular mechanisms related to COVID-19 severity and outcomes. First, transcriptomic data of cellular models of SARS-CoV-2 infection were compiled to understand the first response to the infection. Then, transcriptomic data from lung autopsies of patients deceased due to COVID-19 were compiled to analyze altered genes of damaged lung tissue. These analyses were followed by functional enrichment analyses and gene-phenotype association. A biological network was constructed using the disturbed genes in the lung autopsy meta-analysis. Central genes were defined considering closeness and betweenness centrality degrees. A sub-network phenotype-gene interaction analysis was performed. The meta-analysis of cellular models found genes mainly associated with cytokine signaling and other pathogen response pathways. The meta-analysis of lung autopsy tissue found genes associated with coagulopathy, lung fibrosis, multi-organ damage, and long COVID-19. Only genes DNAH9 and FAM216B were found perturbed in both meta-analyses. BLNK, FABP4, GRIA1, ATF3, TREM2, TPPP, TPPP3, FOS, ALB, JUNB, LMNA, ADRB2, PPARG, TNNC1, and EGR1 were identified as central elements among perturbed genes in lung autopsy and were found associated with several clinical features of severe COVID-19. Central elements were suggested as interesting targets to investigate the relation with features of COVID-19 severity, such as coagulopathy, lung fibrosis, and organ damage.
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Affiliation(s)
- Nathan Araujo Cadore
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Post-Graduation Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Vinicius Oliveira Lord
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Post-Graduation Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.
- Laboratory of Immunobiology and Immunogenetics, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
- Post-Graduation Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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de Albuquerque ALA, Chadanowicz JK, Giudicelli GC, Staub ALP, Weber AC, Silva JMDS, Becker MM, Kowalski TW, Siebert M, Saute JAM. Serum myostatin as a candidate disease severity and progression biomarker of spinal muscular atrophy. Brain Commun 2024; 6:fcae062. [PMID: 38487549 PMCID: PMC10939446 DOI: 10.1093/braincomms/fcae062] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 01/18/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
The identification of biomarkers for spinal muscular atrophy is crucial for predicting disease progression, severity, and response to new disease-modifying therapies. This study aimed to investigate the role of serum levels of myostatin and follistatin as biomarkers for spinal muscular atrophy, considering muscle atrophy secondary to denervation as the main clinical manifestation of the disease. The study evaluated the differential gene expression of myostatin and follistatin in a lesional model of gastrocnemius denervation in mice, as well as in a meta-analysis of three datasets in transgenic mice models of spinal muscular atrophy, and in two studies involving humans with spinal muscular atrophy. Subsequently, a case-control study involving 27 spinal muscular atrophy patients and 27 controls was conducted, followed by a 12-month cohort study with 25 spinal muscular atrophy cases. Serum levels of myostatin and follistatin were analysed using enzyme-linked immunosorbent assay at a single centre in southern Brazil. Skeletal muscle gene expression of myostatin decreased and of follistatin increased following lesional muscle denervation in mice, consistent with findings in the spinal muscular atrophy transgenic mice meta-analysis and in the iliopsoas muscle of five patients with spinal muscular atrophy type 1. Median serum myostatin levels were significantly lower in spinal muscular atrophy patients (98 pg/mL; 5-157) compared to controls (412 pg/mL; 299-730) (P < 0.001). Lower myostatin levels were associated with greater disease severity based on clinician-rated outcomes (Rho = 0.493-0.812; P < 0.05). After 12 months, there was a further reduction in myostatin levels among spinal muscular atrophy cases (P = 0.021). Follistatin levels did not differ between cases and controls, and no significant changes were observed over time. The follistatin:myostatin ratio was significantly increased in spinal muscular atrophy subjects and inversely correlated with motor severity. Serum myostatin levels show promise as a novel biomarker for evaluating the severity and progression of spinal muscular atrophy. The decrease in myostatin levels and the subsequent favourable environment for muscle growth may be attributed to denervation caused by motor neuron dysfunction.
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Affiliation(s)
- Ana Letícia Amorim de Albuquerque
- Graduate Program in Medicine, Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Clinical Neurogenetics research group, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
| | - Júlia Kersting Chadanowicz
- Clinical Neurogenetics research group, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
| | - Giovanna Câmara Giudicelli
- Bioinformatics core, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
- Graduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
| | - Ana Lucia Portella Staub
- Clinical Neurogenetics research group, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
| | - Arthur Carpeggiani Weber
- Clinical Neurogenetics research group, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
| | | | | | - Thayne Woycinck Kowalski
- Bioinformatics core, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
- Graduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul, Porto Alegre 91501-970, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
| | - Marina Siebert
- Unit of Laboratorial Research, Experimental Research Center, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-007, Brazil
- Graduate Program in Gastroenterology and Hepatology, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
| | - Jonas Alex Morales Saute
- Graduate Program in Medicine, Medical Sciences, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
- Clinical Neurogenetics research group, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Brazil
- Department of Internal Medicine, Federal University of Rio Grande do Sul, Porto Alegre 90035-003, Brazil
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4
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Kowalski TW, Giudicelli GC, Pinho MCDF, Rockenbach MK, Maciel-Fiuza MF, Recamonde-Mendoza M, Vianna FSL. Brazilian women in Bioinformatics: Challenges and opportunities. Genet Mol Biol 2024; 46:e20230134. [PMID: 38259034 PMCID: PMC10829893 DOI: 10.1590/1678-4685-gmb-2023-0134] [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: 05/02/2023] [Accepted: 12/06/2023] [Indexed: 01/24/2024] Open
Abstract
Bioinformatics is a growing research field that received great notoriety in the years of the COVID-19 pandemic. It is a very integrative area, comprising professionals from science, technology, engineering, and mathematics (STEM). In agreement with the other STEM areas, several women have greatly contributed to bioinformatics ascension; however, they had to surpass prejudice and stereotypes to achieve recognition and leadership positions, a path that studies have demonstrated to be more comfortable to their male colleagues. In this review, we discuss the several difficulties that women in STEM, including bioinformatics, surpass during their careers. First, we present a historical context on bioinformatics and the main applications for this area. Then, we discuss gender disparity in STEM and present the challenges that still contribute to women's inequality in STEM compared to their male colleagues. We also present the opportunities and the transformation that we can start, acting in academia, inside the family and school environments, and as a society, hence contributing to gender equality in STEM. Finally, we discuss specific challenges in the bioinformatics field and how we can act to overcome them, especially in low and middle-income countries, such as Brazil.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Unidade de Genética Laboratorial, Porto Alegre, RS, Brazil
- Centro Universitário CESUCA, Cachoeirinha, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Laboratório de Imunogenética, Porto Alegre, RS, Brazil
| | - Giovanna Câmara Giudicelli
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Unidade de Genética Laboratorial, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Laboratório de Imunogenética, Porto Alegre, RS, Brazil
| | - Maria Clara de Freitas Pinho
- Centro Universitário CESUCA, Cachoeirinha, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Marília Körbes Rockenbach
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
| | - Miriãn Ferrão Maciel-Fiuza
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Laboratório de Imunogenética, Porto Alegre, RS, Brazil
| | - Mariana Recamonde-Mendoza
- Hospital de Clínicas de Porto Alegre, Núcleo de Bioinformática, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Instituto de Informática, Porto Alegre, RS, Brazil
| | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Unidade de Genética Laboratorial, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Laboratório de Imunogenética, Porto Alegre, RS, Brazil
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5
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Vieira IA, Viola GD, Pezzi EH, Kowalski TW, Fernandes BV, Andreis TF, Bom N, Sonnenstrahl G, Rocha YMDA, Corrêa BDS, Donatti LM, Sant’Anna GDS, Corleta HVE, Brum IS, Rosset C, Vianna FSL, Macedo GS, Palmero EI, Ashton-Prolla P. Exploring the frequency of a TP53 polyadenylation signal variant in tumor DNA from patients diagnosed with lung adenocarcinomas, sarcomas and uterine leiomyomas. Genet Mol Biol 2024; 46:e20230133. [PMID: 38252059 PMCID: PMC10802224 DOI: 10.1590/1678-4685-gmb-2023-0133] [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: 05/19/2023] [Accepted: 11/16/2023] [Indexed: 01/23/2024] Open
Abstract
The TP53 3'UTR variant rs78378222 A>C has been detected in different tumor types as a somatic alteration that reduces p53 expression through modification of polyadenylation and miRNA regulation. Its prevalence is not yet known in all tumors. Herein, we examine tumor tissue prevalence of rs7837822 in Brazilian cohorts of patients from south and southeast regions diagnosed with lung adenocarcinoma (LUAD, n=586), sarcoma (SARC, n=188) and uterine leiomyoma (ULM, n=41). The minor allele (C) was identified in heterozygosity in 6/586 LUAD tumors (prevalence = 1.02 %) and none of the SARC and ULM samples. Additionally, next generation sequencing analysis revealed that all variant-positive tumors (n=4) with sample availability had additional pathogenic or likely pathogenic somatic variants in the TP53 coding regions. Among them, 3/4 (75 %) had the same pathogenic or likely pathogenic sequence variant (allele frequency <0.05 in tumor DNA) namely c.751A>C (p.Ile251Leu). Our results indicate a low somatic prevalence of rs78378222 in LUAD, ULM and SARC tumors from Brazilian patients, which suggests that no further analysis of this variant in the specific studied regions of Brazil is warranted. However, these findings should not exclude tumor molecular testing of this TP53 3'UTR functional variant for different populations.
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Affiliation(s)
- Igor Araujo Vieira
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade do Vale do Rio dos Sinos (UNISINOS), Escola de Saúde, São Leopoldo, RS, Brazil
| | - Guilherme Danielski Viola
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Eduarda Heidrich Pezzi
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de Genética Médica e Populacional, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Genética Médica, Sistema Nacional de Informações sobre Agentes Teratogênicos (SIAT), Porto Alegre, RS, Brazil
- Complexo de Ensino Superior de Cachoeirinha (CESUCA), Cachoeirinha, RS, Brazil
| | - Bruna Vieira Fernandes
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Tiago Finger Andreis
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Natascha Bom
- Universidade do Vale do Rio dos Sinos (UNISINOS), Curso de Graduação em Biomedicina, São Leopoldo, RS, Brazil
| | - Giulianna Sonnenstrahl
- Universidade do Vale do Rio dos Sinos (UNISINOS), Curso de Graduação em Biomedicina, São Leopoldo, RS, Brazil
| | - Yasminne Marinho de Araújo Rocha
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Bruno da Silveira Corrêa
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
| | - Luiza Mezzomo Donatti
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Porto Alegre, RS, Brazil
| | - Gabriela dos Santos Sant’Anna
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
| | - Helena von Eye Corleta
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Ginecologia e Obstetrícia, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Faculdade de Medicina, Departamento de Ginecologia e Obstetrícia, Porto Alegre, RS, Brazil
| | - Ilma Simoni Brum
- Universidade Federal do Rio Grande do Sul, Instituto de Ciências Básicas da Saúde, Departamento de Fisiologia, Laboratório de Biologia Molecular Endócrino e Tumoral, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Ciências Biológicas: Fisiologia, Porto Alegre, RS, Brazil
| | - Clévia Rosset
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Unidade de Pesquisa Laboratorial (UPL), Porto Alegre, RS, Brazil
| | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Laboratório de Genética Médica e Populacional, Porto Alegre, RS, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Serviço de Genética Médica, Sistema Nacional de Informações sobre Agentes Teratogênicos (SIAT), Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul, Departamento de Genética, Laboratório de Imunobiologia e Imunogenética, Porto Alegre, RS, Brazil
| | - Gabriel S. Macedo
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Programa de Medicina Personalizada, Porto Alegre, RS, Brazil
| | - Edenir Inez Palmero
- Instituto Nacional de Câncer (INCA), Departamento de Genética, Rio de Janeiro, RJ, Brazil
- Hospital de Câncer de Barretos, Centro de Pesquisa em Oncologia Molecular, Barretos, SP, Brazil
| | - Patricia Ashton-Prolla
- Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Genética e Biologia Molecular, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Centro de Pesquisa Experimental, Laboratório de Medicina Genômica, Porto Alegre, RS, Brazil
- Universidade Federal do Rio Grande do Sul (UFRGS), Programa de Pós-Graduação em Ciências Médicas: Medicina (PPGCM), Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre (HCPA), Programa de Medicina Personalizada, Porto Alegre, RS, Brazil
- Hospital de Clínicas de Porto Alegre, Serviço de Genética Médica, Porto Alegre, RS, Brazil
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6
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Kowalski TW, Giudicelli GC, Gomes JDA, Recamonde-Mendoza M, Vianna FSL. Bioinformatics Methods for Transcriptome Analysis on Teratogenesis Testing. Methods Mol Biol 2024; 2753:365-376. [PMID: 38285351 DOI: 10.1007/978-1-0716-3625-1_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
Teratogenesis testing can be challenging due to the limitations of both in vitro and in vivo models. Test-systems, based especially on human embryonic cells, have been helping to overcome the difficulties when allied to omics strategies, such as transcriptomics. In these test-systems, cells exposed to different compounds are then analyzed in microarray or RNA-seq platforms regarding the impacts of the potential teratogens in the gene expression. Nevertheless, microarray and RNA-seq dataset processing requires computational resources and bioinformatics knowledge. Here, a pipeline for microarray and RNA-seq processing is presented, aiming to help researchers from any field to interpret the main transcriptome results, such as differential gene expression, enrichment analysis, and statistical interpretation. This chapter also discusses the main difficulties that can be encountered in a transcriptome analysis and the better alternatives to overcome these issues, describing both programming codes and user-friendly tools. Finally, specific issues in the teratogenesis field, such as time-course analysis, are also described, demonstrating how the pipeline can be applied in these studies.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory Genetics Unit, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Teratogens Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Post-Graduation Program in Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Giovanna Câmara Giudicelli
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Julia do Amaral Gomes
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Post-Graduation Program in Informatics, Informatics Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
- Teratogens Information System, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
- Post-Graduation Program in Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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7
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Rosset C, Schuch JB, Recamonde-Mendoza M, Kowalski TW. Editorial: Bioinformatics applied to neuroscience. Front Neurosci 2023; 17:1276346. [PMID: 37811331 PMCID: PMC10552636 DOI: 10.3389/fnins.2023.1276346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 09/08/2023] [Indexed: 10/10/2023] Open
Affiliation(s)
- Clevia Rosset
- Graduate Program in Medical Sciences (PPGCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratory of Genomic Medicine, Experimental Research Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Laboratory Research Unit, Experimental Research Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Jaqueline Bohrer Schuch
- Graduate Program in Psychiatry and Behavioral Sciences, Department of Psychiatry, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Mariana Recamonde-Mendoza
- Graduate Program in Computer Science (PPGC), Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Laboratory of Genomic Medicine, Experimental Research Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Graduate Program in Genetics and Molecular Biology (PPGBM), Department of Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratory Genetics Unit, Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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8
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Kowalski TW, Feira MF, Lord VO, Gomes JDA, Giudicelli GC, Fraga LR, Sanseverino MTV, Recamonde-Mendoza M, Schuler-Faccini L, Vianna FSL. A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors. Int J Mol Sci 2023; 24:11515. [PMID: 37511270 PMCID: PMC10380514 DOI: 10.3390/ijms241411515] [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: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Several molecular mechanisms of thalidomide embryopathy (TE) have been investigated, from anti-angiogenesis to oxidative stress to cereblon binding. Recently, it was discovered that thalidomide and its analogs, named immunomodulatory drugs (IMiDs), induced the degradation of C2H2 transcription factors (TFs). This mechanism might impact the strict transcriptional regulation of the developing embryo. Hence, this study aims to evaluate the TFs altered by IMiDs, prioritizing the ones associated with embryogenesis through transcriptome and systems biology-allied analyses. This study comprises only the experimental data accessed through bioinformatics databases. First, proteins and genes reported in the literature as altered/affected by the IMiDs were annotated. A protein systems biology network was evaluated. TFs beta-catenin (CTNNB1) and SP1 play more central roles: beta-catenin is an essential protein in the network, while SP1 is a putative C2H2 candidate for IMiD-induced degradation. Separately, the differential expressions of the annotated genes were analyzed through 23 publicly available transcriptomes, presenting 8624 differentially expressed genes (2947 in two or more datasets). Seventeen C2H2 TFs were identified as related to embryonic development but not studied for IMiD exposure; these TFs are potential IMiDs degradation neosubstrates. This is the first study to suggest an integration of IMiD molecular mechanisms through C2H2 TF degradation.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Mariléa Furtado Feira
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Vinícius Oliveira Lord
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Julia do Amaral Gomes
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Giovanna Câmara Giudicelli
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Lucas Rosa Fraga
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90010-150, Brazil
| | - Maria Teresa Vieira Sanseverino
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Computer Science, Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
| | - Lavinia Schuler-Faccini
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Fernanda Sales Luiz Vianna
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
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Rockenbach MK, Fraga LR, Kowalski TW, Sanseverino MTV. Expression profiles of meiotic genes in male vs. female gonads and gametes: Insights into fertility issues. Front Genet 2023; 14:1125097. [PMID: 36999055 PMCID: PMC10045993 DOI: 10.3389/fgene.2023.1125097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/02/2023] [Indexed: 03/16/2023] Open
Abstract
Gametes are specialized cells that, at fertilization, give rise to a totipotent zygote capable of generating an entire organism. Female and male germ cells undergo meiosis to produce mature gametes; however, sex-specific events of oogenesis and spermatogenesis contribute to specific roles of gametes in reproductive issues. We investigate the differential gene expression (DGE) of meiosis-related genes in human female and male gonads and gametes in normal and pathological conditions. The transcriptome data for the DGE analysis was obtained through the Gene Expression Omnibus repository, comprising human ovary and testicle samples of the prenatal period and adulthood, additionally to male (non-obstructive azoospermia (NOA) and teratozoospermia), and female (polycystic ovary syndrome (PCOS) and advanced maternal age) reproductive conditions. Gene ontology terms related to meiosis were associated with 678 genes, of which 17 genes in common were differentially expressed between the testicle and ovary during the prenatal period and adulthood. Except for SERPINA5 and SOX9, the 17 meiosis-related genes were downregulated in the testicle during the prenatal period and upregulated in adulthood compared to the ovary. No differences were observed in the oocytes of PCOS patients; however, meiosis-related genes were differentially expressed according to the patient’s age and maturity of the oocyte. In NOA and teratozoospermia, 145 meiosis-related genes were differentially expressed in comparison to the control, including OOEP; despite no recognized role in male reproduction, OOEP was co-expressed with genes related to male fertility. Taking together, these results shed light on potential genes that might be relevant to comprehend human fertility disorders.
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Affiliation(s)
- Marília Körbes Rockenbach
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Postgraduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Centro Universitário CESUCA, Cachoeirinha, Brazil
- *Correspondence: Thayne Woycinck Kowalski, ,
| | - Maria Teresa Vieira Sanseverino
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- School of Medicine, Pontifícia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil
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10
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Colombelli F, Kowalski TW, Recamonde-Mendoza M. A hybrid ensemble feature selection design for candidate biomarkers discovery from transcriptome profiles. Knowl Based Syst 2022. [DOI: 10.1016/j.knosys.2022.109655] [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: 10/15/2022]
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11
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Rengel BD, Kowalski TW, Bremm JM, do Amaral Gomes J, Schüler-Faccini L, Vianna FSL, Fraga LR. Genetic evaluation of HAND2 gene and its effects on thalidomide embryopathy. Birth Defects Res 2022; 114:1354-1363. [PMID: 36177858 DOI: 10.1002/bdr2.2092] [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: 04/25/2022] [Revised: 07/28/2022] [Accepted: 09/04/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND HAND2 is a transcription factor important for embryonic development, required for limbs and cardiovascular development. Thalidomide is a drug responsible to a spectrum of congenital anomalies known as Thalidomide Embryopathy (TE), which includes mainly limb and heart defects. It is known that HAND2 interaction with TBX5, an important protein for limbs and heart development, is inhibited by Thalidomide. The aim of this study was to evaluate and characterize HAND2 in the context of TE, and to evaluate its variability in TE individuals. METHODS DNA from 35 TE subjects was extracted from saliva samples and PCR was performed for amplification and Sanger sequencing of HAND2 coding sequence. RESULTS The analysis showed only one variant; a synonymous variant p.P51 (rs59621536) in exon 1 found in three individuals. Further in silico evaluation confirmed highly HAND2 conservation, being the 3'UTR the most polymorphic region of the gene. Additional computational analyses classified the variant as neutral, without alteration in splicing and miRNA sites. In silico predictions pointed to alteration of two CpG islands adjacent to the variant; however, we did not observe any alterations on the methylation pattern of HAND2 gene in our sample. Moreover, alteration of the binding site of MeCP2, a nuclear protein involved in DNA methylation, was predicted along with alteration in HAND2 mRNA structure. CONCLUSIONS Considering HAND2 being a well conserved gene, further studies with a larger sample should be performed to evaluate the role this gene on genetic susceptibility to TE.
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Affiliation(s)
- Bruna Duarte Rengel
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - João Matheus Bremm
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Julia do Amaral Gomes
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil
| | - Lavínia Schüler-Faccini
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Postgraduate Program in Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Laboratory of Medical Genetics and Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Brazilian Teratogen Information Service (SIAT), Medical Genetics Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Postgraduate Program in Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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12
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Kowalski TW, Lord VO, Sgarioni E, Gomes JDA, Mariath LM, Recamonde-Mendoza M, Vianna FSL. Transcriptome meta-analysis of valproic acid exposure in human embryonic stem cells. Eur Neuropsychopharmacol 2022; 60:76-88. [PMID: 35635998 DOI: 10.1016/j.euroneuro.2022.04.008] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 11/04/2022]
Abstract
Valproic acid (VPA) is a widely used antiepileptic drug not recommended in pregnancy because it is teratogenic. Many assays have assessed the impact of the VPA exposure on the transcriptome of human embryonic stem-cells (hESC), but the molecular perturbations that VPA exerts in neurodevelopment are not completely understood. This study aimed to perform a transcriptome meta-analysis of VPA-exposed hESC to elucidate the main biological mechanisms altered by VPA effects on the gene expression. Publicly available microarray and RNA-seq transcriptomes were selected in the Gene Expression Omnibus (GEO) repository. Samples were processed according to the standard pipelines for each technology in the Galaxy server and R. Meta-analysis was performed using the Fisher-P method. Overrepresented genes were obtained by evaluating ontologies, pathways, and phenotypes' databases. The meta-analysis performed in seven datasets resulted in 61 perturbed genes, 54 upregulated. Ontology and pathway enrichments suggested neurodevelopment and neuroinflammatory effects; phenotype overrepresentation included epilepsy-related genes, such as SCN1A and GABRB2. The NDNF gene upregulation was also identified; this gene is involved in neuron migration and survival during development. Sub-network analysis proposed TGFβ and BMP pathways activation. These results suggest VPA exerts effects in epilepsy-related genes even in embryonic cells. Neurodevelopmental genes, such as NDNF were upregulated and VPA might also disturb several development pathways. These mechanisms might help to explain the spectrum of VPA-induced congenital anomalies and the molecular effects on neurodevelopment.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; National Institute of Medical Population Genetics (INAGEMP), Porto Alegre, Brazil; Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; Centro Universitário CESUCA, Cachoeirinha, Brazil.
| | - Vinícius Oliveira Lord
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - Eduarda Sgarioni
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Julia do Amaral Gomes
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; National Institute of Medical Population Genetics (INAGEMP), Porto Alegre, Brazil
| | - Luiza Monteavaro Mariath
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-Graduation Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil; National Institute of Medical Population Genetics (INAGEMP), Porto Alegre, Brazil.
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13
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Schuler-Faccini L, Del Campo M, García-Alix A, Ventura LO, Boquett JA, van der Linden V, Pessoa A, van der Linden Júnior H, Ventura CV, Leal MC, Kowalski TW, Rodrigues Gerzson L, Skilhan de Almeida C, Santi L, Beys-da-Silva WO, Quincozes-Santos A, Guimarães JA, Garcez PP, Gomes JDA, Vianna FSL, Anjos da Silva A, Fraga LR, Vieira Sanseverino MT, Muotri AR, Lopes da Rosa R, Abeche AM, Marcolongo-Pereira C, Souza DO. Neurodevelopment in Children Exposed to Zika in utero: Clinical and Molecular Aspects. Front Genet 2022; 13:758715. [PMID: 35350244 PMCID: PMC8957982 DOI: 10.3389/fgene.2022.758715] [Citation(s) in RCA: 4] [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] [Received: 08/14/2021] [Accepted: 01/27/2022] [Indexed: 12/15/2022] Open
Abstract
Five years after the identification of Zika virus as a human teratogen, we reviewed the early clinical manifestations, collectively called congenital Zika syndrome (CZS). Children with CZS have a very poor prognosis with extremely low performance in motor, cognitive, and language development domains, and practically all feature severe forms of cerebral palsy. However, these manifestations are the tip of the iceberg, with some children presenting milder forms of deficits. Additionally, neurodevelopment can be in the normal range in the majority of the non-microcephalic children born without brain or eye abnormalities. Vertical transmission and the resulting disruption in development of the brain are much less frequent when maternal infection occurs in the second half of the pregnancy. Experimental studies have alerted to the possibility of other behavioral outcomes both in prenatally infected children and in postnatal and adult infections. Cofactors play a vital role in the development of CZS and involve genetic, environmental, nutritional, and social determinants leading to the asymmetric distribution of cases. Some of these social variables also limit access to multidisciplinary professional treatment.
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Affiliation(s)
- Lavínia Schuler-Faccini
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Miguel Del Campo
- Department of Pediatrics, School of Medicine, University of California San Diego, and Rady Children's Hospital San Diego, San Diego, CA, United States
| | | | - Liana O Ventura
- Department of Ophthalmology, Fundação Altino Ventura, FAV, Recife, Brazil
| | | | | | - André Pessoa
- Hospital Infantil Albert Sabin, Fortaleza, Brazil.,Universidade Estadual do Ceará, Fortaleza, Brazil
| | | | - Camila V Ventura
- Department of Ophthalmology, Fundação Altino Ventura, FAV, Recife, Brazil
| | | | - Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,CESUCA-Centro Universitário, Cachoeirinha, Brazil
| | | | | | - Lucélia Santi
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Walter O Beys-da-Silva
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | | | - Jorge A Guimarães
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | | | | | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - André Anjos da Silva
- School of Medicine, Graduate Program in Medical Sciences-Universidade do Vale do Taquari-UNIVATES, Lajeado, Brazil.,School of Medicine, Universidade do Vale do Rio dos Sinos-UNISINOS, São Leopoldo, Brazil
| | - Lucas Rosa Fraga
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Maria Teresa Vieira Sanseverino
- Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Pontifícia Universidade Católica do Rio Grande do Sul, PUCRS, Porto Alegre, Brazil
| | - Alysson R Muotri
- Department of Pediatrics, School of Medicine, University of California San Diego, and Rady Children's Hospital San Diego, San Diego, CA, United States
| | | | - Alberto Mantovani Abeche
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clinicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | | | - Diogo O Souza
- Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
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14
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Maciel-Fiuza MF, Costa PDSS, Kowalski TW, Schuler-Faccini L, Bonamigo RR, Vetoratto R, Eidt LM, de Moraes PC, Silveira MIDS, Camargo LMA, Callegari-Jacques SM, Castro SMDJ, Vianna FSL. Evaluation of Polymorphisms in Toll-Like Receptor Genes as Biomarkers of the Response to Treatment of Erythema Nodosum Leprosum. Front Med (Lausanne) 2022; 8:713143. [PMID: 35141236 PMCID: PMC8819000 DOI: 10.3389/fmed.2021.713143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 12/09/2021] [Indexed: 01/18/2023] Open
Abstract
Erythema nodosum leprosum (ENL) is an inflammatory complication caused by a dysregulated immune response to Mycobacterium leprae. Some Toll-like receptors (TLRs) have been identified as capable of recognizing antigens from M. leprae, triggering a wide antimicrobial and inflammatory response. Genetic polymorphisms in these receptors could influence in the appearance of ENL as well as in its treatment. Thus, the objective of this work was to evaluate the association of genetic variants of TLRs genes with the response to treatment of ENL with thalidomide and prednisone. A total of 162 ENL patients were recruited from different regions of Brazil and clinical information was collected from their medical records. Genomic DNA was isolated from blood and saliva samples and genetic variants in TLR1 (rs4833095), TLR2 (rs3804099), TLR4 (rs1927914), and TLR6 (rs5743810) genes were genotyped by TaqMan real-time PCR system. In order to evaluate the variants' association with the dose of the medications used during the treatment, we applied the Generalized Estimating Equations (GEE) analysis. In the present sample, 123 (75.9%) patients were men and 86 (53.1%) were in treatment for leprosy during the ENL episode. We found an association between polymorphisms in TLR1/rs4833095, TLR2/rs3804099, TLR4/rs1927914, and TLR6/rs5783810 with the dose variation of thalidomide in a time-dependent manner, i.e., the association with the genetic variant and the dose of the drug was different depending on the moment of the treatment evaluated. In addition, we identified that the association of polymorphisms in TLR1/rs4833095, TLR2/rs3804099, and TLR6/rs5783810 with the dose variation of prednisone also were time-dependent. Despite these associations, in all the interactions found, the influence of genetic variants on dose variation was not clinically relevant for therapeutic changes. The results obtained in this study show that TLRs polymorphism might play a role in the response to ENL treatment, however, in this context, they could not be considered as useful biomarkers in the clinical setting due small differences in medication doses. A larger sample size with patients with a more genetic profile is fundamental in order to estimate the association of genetic variants with the treatment of ENL and their clinical significance.
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Affiliation(s)
- Miriãn Ferrão Maciel-Fiuza
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | | | - Thayne Woycinck Kowalski
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
- Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Renan Rangel Bonamigo
- Post-graduate Program in Pathology, Universidade Federal De Ciências Da Saúde de Porto Alegre, Porto Alegre, Brazil
- Dermatology Service of Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Rodrigo Vetoratto
- Dermatology Service of Santa Casa Hospital of Porto Alegre, Porto Alegre, Brazil
| | - Letícia Maria Eidt
- Sanitary Dermatology Clinic, Secretaria De Saúde Do Estado Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Paulo Cezar de Moraes
- Postgraduate Program in Medicine, Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Sanitary Dermatology Clinic, Secretaria De Saúde Do Estado Do Rio Grande Do Sul, Porto Alegre, Brazil
| | | | - Luis Marcelo Aranha Camargo
- National Reference Center for Health Dermatology Dona Libania, Fortaleza, Brazil
- Center for Research in Tropical Medicine, Porto Velho, Rondonia, Brazil
- National Institute of Science and Technology-EpiAmo, Rondonia, Brazil
- Department of Medicine, Centro Universitario São Lucas, Porto Velho, Rondônia, Brazil
- National Institute of Science and Technology/CNPq-EpiAmo, Rondonia, Brazil
| | - Sidia Maria Callegari-Jacques
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Department of Statistics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Stela Maris de Jezus Castro
- Department of Statistics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Epidemiology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil
- Genomics Medicine Laboratory, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
- Laboratory of Immunobiology and Immunogenetics, Postgraduate Program in Genetics and Molecular Biology, Department of Genetics, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
- Postgraduate Program in Medicine, Medical Sciences, Universidade Federal Do Rio Grande Do Sul, Porto Alegre, Brazil
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15
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Costa PDSS, Maciel-Fiuza MF, Kowalski TW, Fraga LR, Feira MF, Camargo LMA, Caldoncelli DIDO, Silveira MIDS, Schuler-Faccini L, Vianna FSL. Evaluation of the influence of genetic variants in Cereblon gene on the response to the treatment of erythema nodosum leprosum with thalidomide. Mem Inst Oswaldo Cruz 2022; 117:e220039. [DOI: 10.1590/0074-02760220039] [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] [Received: 02/10/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Perpétua do Socorro Silva Costa
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Universidade Federal do Maranhão, Brazil
| | - Miriãn Ferrão Maciel-Fiuza
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil
| | - Thayne Woycinck Kowalski
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Hospital de Clínicas de Porto Alegre, Brasil
| | - Lucas Rosa Fraga
- Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Universidade Federal do Rio Grande do Sul, Brazil
| | - Mariléa Furtado Feira
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil
| | - Luís Marcelo Aranha Camargo
- Universidade de São Paulo, Brazil; Centro de Pesquisa em Medicina Tropical, Brasil; Instituto Nacional de Ciência e Tecnologia de Epidemiologia da Amazônia Ocidental, Brasil; Centro Universitário São Lucas, Brazil
| | | | | | - Lavínia Schuler-Faccini
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil
| | - Fernanda Sales Luiz Vianna
- Universidade Federal do Rio Grande do Sul, Brazil; Instituto Nacional de Genética Médica Populacional, Brasil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil; Hospital de Clínicas de Porto Alegre, Brasil; Universidade Federal do Rio Grande do Sul, Brazil
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16
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Bremm JM, Boquett JA, Silva Michels M, Kowalski TW, Gomes FG, Vianna FSL, Vieira Sanseverino MT, Fraga LR. Investigating the role of EGF-CFC gene family in recurrent pregnancy loss through bioinformatics and molecular approaches. Syst Biol Reprod Med 2021; 67:450-462. [PMID: 34498535 DOI: 10.1080/19396368.2021.1965673] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Recurrent pregnancy loss (RPL) is the most common reproductive failure, reaching 1-5% of women throughout their lives, and having unknown etiology in 50% of the cases. In humans, EGF-CFC1 (Epidermal Growth Factors & Cripto/FRL-1/Cryptic) gene family is composed by TDGF1 and CFC1, two developmental genes. The aim of this study was to investigate the role of EGF-CFC on RPL. To this, multiple approaches were performed; we conducted an expression analysis of TDGF1 and CFC1 using publicly available data from Gene Omnibus Expression (GEO), systems biology analyses and functional prediction; and a molecular analysis carried out in a case-control study. Our GEO analysis showed a decrease in TDGF1 expression in the endometrium (p=0.049) and CFC1 expression in placenta (p=0.015) of women with RPL. Network analysis, gene ontology and literature pointed to a strong connection between EGF-CFC1 gene family to pathways that play key roles during pregnancy, including TGF-β, c-Src/MAPK/AKT, Notch, TNFα, IFNγ and IL-6. A pathogenicity score developed for this gene family showed that the c.-14+1429T>C (rs3806702) variant in the TDGF1 and the p.Arg47Gln (rs201431919) variant in CFC1 gene would be the ones with the highest deleterious effect for RPL. In the case-control study, which involved 149 women with RPL and 159 controls, no statistical difference was observed in the allele and genotype distributions of the variants studied in the two groups. In this study, we performed extensive bioinformatics analysis for biomarker prioritization followed by experimental validation of proposed selected markers. Although there is no statistical difference in the frequencies of these variants between RPL and controls, the expression analysis results suggest that TDGF1 and CFC1 genes might play a role in RPL. In addition, systems biology analyzes raise the hypothesis that genes in other signaling pathways that may be related to RPL as good candidates for future studies.Abbreviations RPL: recurrent pregnancy loss; EGF-CFC1: Epidermal Growth Factors - Cripto/FRL-1; GEO: Gene Omnibus Expression; KEGG: Kyoto Encyclopedia of Genes and Genomes.
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Affiliation(s)
- João Matheus Bremm
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Juliano André Boquett
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-graduate Program in Child and Adolescent Health, Faculty of Medicine, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Marcus Silva Michels
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Flávia Gobetti Gomes
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Post-Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Maria Teresa Vieira Sanseverino
- Post-graduate Program in Genetics and Molecular Biology, Department of Genetics, Biosciences Institute, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Post-Graduate Program in Medicine: Medical Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Experimental Research Center, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Department of Morphological Science, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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17
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Kowalski TW, Caldas-Garcia GB, Gomes JDA, Fraga LR, Schuler-Faccini L, Recamonde-Mendoza M, Paixão-Côrtes VR, Vianna FSL. Comparative Genomics Identifies Putative Interspecies Mechanisms Underlying Crbn-Sall4-Linked Thalidomide Embryopathy. Front Genet 2021; 12:680217. [PMID: 34249098 PMCID: PMC8262662 DOI: 10.3389/fgene.2021.680217] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/18/2021] [Indexed: 11/21/2022] Open
Abstract
The identification of thalidomide–Cereblon-induced SALL4 degradation has brought new understanding for thalidomide embryopathy (TE) differences across species. Some questions, however, regarding species variability, still remain. The aim of this study was to detect sequence divergences between species, affected or not by TE, and to evaluate the regulated gene co-expression in a murine model. Here, we performed a comparative analysis of proteins experimentally established as affected by thalidomide exposure, evaluating 14 species. The comparative analysis, regarding synteny, neighborhood, and protein conservation, was performed in 42 selected genes. Differential co-expression analysis was performed, using a publicly available assay, GSE61306, which evaluated mouse embryonic stem cells (mESC) exposed to thalidomide. The comparative analyses evidenced 20 genes in the upstream neighborhood of NOS3, which are different between the species who develop, or not, the classic TE phenotype. Considering protein sequence alignments, RECQL4, SALL4, CDH5, KDR, and NOS2 proteins had the biggest number of variants reported in unaffected species. In co-expression analysis, Crbn was a gene identified as a driver of the co-expression of other genes implicated in genetic, non-teratogenic, limb reduction defects (LRD), such as Tbx5, Esco2, Recql4, and Sall4; Crbn and Sall4 were shown to have a moderate co-expression correlation, which is affected after thalidomide exposure. Hence, even though the classic TE phenotype is not identified in mice, a deregulatory Crbn-induced mechanism is suggested in this animal. Functional studies are necessary, especially evaluating the genes responsible for LRD syndromes and their interaction with thalidomide–Cereblon.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - Gabriela Barreto Caldas-Garcia
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Post-Graduation Program in Biodiversity and Evolution, PPGBioEvo Institute of Biology, Universidade Federal da Bahia, UFBA, Salvador, Brazil
| | - Julia do Amaral Gomes
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Post-Graduation Program in Medical Science, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Teratogen Information System, SIAT, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Teratogen Information System, SIAT, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Institute of Informatics, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
| | - Vanessa Rodrigues Paixão-Côrtes
- Post-Graduation Program in Biodiversity and Evolution, PPGBioEvo Institute of Biology, Universidade Federal da Bahia, UFBA, Salvador, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Post-Graduation Program in Medical Science, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Teratogen Information System, SIAT, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil
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18
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Gomes JDA, Olstad EW, Kowalski TW, Gervin K, Vianna FSL, Schüler-Faccini L, Nordeng HME. Genetic Susceptibility to Drug Teratogenicity: A Systematic Literature Review. Front Genet 2021; 12:645555. [PMID: 33981330 PMCID: PMC8107476 DOI: 10.3389/fgene.2021.645555] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/19/2021] [Indexed: 12/19/2022] Open
Abstract
Since the 1960s, drugs have been known to cause teratogenic effects in humans. Such teratogenicity has been postulated to be influenced by genetics. The aim of this review was to provide an overview of the current knowledge on genetic susceptibility to drug teratogenicity in humans and reflect on future directions within the field of genetic teratology. We focused on 12 drugs and drug classes with evidence of teratogenic action, as well as 29 drugs and drug classes with conflicting evidence of fetal safety in humans. An extensive literature search was performed in the PubMed and EMBASE databases using terms related to the drugs of interest, congenital anomalies and fetal development abnormalities, and genetic variation and susceptibility. A total of 29 studies were included in the final data extraction. The eligible studies were published between 1999 and 2020 in 10 different countries, and comprised 28 candidate gene and 1 whole-exome sequencing studies. The sample sizes ranged from 20 to 9,774 individuals. Several drugs were investigated, including antidepressants (nine studies), thalidomide (seven studies), antiepileptic drugs (five studies), glucocorticoids (four studies), acetaminophen (two studies), and sex hormones (estrogens, one study; 17-alpha hydroxyprogesterone caproate, one study). The main neonatal phenotypic outcomes included perinatal complications, cardiovascular congenital anomalies, and neurodevelopmental outcomes. The review demonstrated that studies on genetic teratology are generally small, heterogeneous, and exhibit inconsistent results. The most convincing findings were genetic variants in SLC6A4, MTHFR, and NR3C1, which were associated with drug teratogenicity by antidepressants, antiepileptics, and glucocorticoids, respectively. Notably, this review demonstrated the large knowledge gap regarding genetic susceptibility to drug teratogenicity, emphasizing the need for further efforts in the field. Future studies may be improved by increasing the sample size and applying genome-wide approaches to promote the interpretation of results. Such studies could support the clinical implementation of genetic screening to provide safer drug use in pregnant women in need of drugs.
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Affiliation(s)
- Julia do Amaral Gomes
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Sistema Nacional de Informação sobre Agentes Teratogênicos (SIAT), Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Emilie Willoch Olstad
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Thayne Woycinck Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Complexo de Ensino Superior de Cachoeirinha (CESUCA), Cachoeirinha, Brazil
| | - Kristina Gervin
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Division of Clinical Neuroscience, Department of Research and Innovation, Oslo University Hospital, Oslo, Norway
| | - Fernanda Sales Luiz Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Sistema Nacional de Informação sobre Agentes Teratogênicos (SIAT), Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Lavínia Schüler-Faccini
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Sistema Nacional de Informação sobre Agentes Teratogênicos (SIAT), Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
- Instituto Nacional de Genética Médica Populacional (INAGEMP), Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Hedvig Marie Egeland Nordeng
- Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
- Department of Child Health and Development, Norwegian Institute of Public Health, Oslo, Norway
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19
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Kowalski TW, Gomes JDA, Feira MF, Dupont ÁDV, Recamonde-Mendoza M, Vianna FSL. Anticonvulsants and Chromatin-Genes Expression: A Systems Biology Investigation. Front Neurosci 2020; 14:591196. [PMID: 33328862 PMCID: PMC7732676 DOI: 10.3389/fnins.2020.591196] [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: 08/04/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Embryofetal development is a critical process that needs a strict epigenetic control, however, perturbations in this balance might lead to the occurrence of congenital anomalies. It is known that anticonvulsants potentially affect epigenetics-related genes, however, it is not comprehended whether this unbalance could explain the anticonvulsants-induced fetal syndromes. In the present study, we aimed to evaluate the expression of epigenetics-related genes in valproic acid, carbamazepine, or phenytoin exposure. We selected these three anticonvulsants exposure assays, which used murine or human embryonic stem-cells and were publicly available in genomic databases. We performed a differential gene expression (DGE) and weighted gene co-expression network analysis (WGCNA), focusing on epigenetics-related genes. Few epigenetics genes were differentially expressed in the anticonvulsants' exposure, however, the WGCNA strategy demonstrated a high enrichment of chromatin remodeling genes for the three drugs. We also identified an association of 46 genes related to Fetal Valproate Syndrome, containing SMARCA2 and SMARCA4, and nine genes to Fetal Hydantoin Syndrome, including PAX6, NEUROD1, and TSHZ1. The evaluation of stem-cells under drug exposure can bring many insights to understand the drug-induced damage to the embryofetal development. The candidate genes here presented are potential biomarkers that could help in future strategies for the prevention of congenital anomalies.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Postgraduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratory of Immunobiology and Immunogenetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Centro Universitário CESUCA, Cachoeirinha, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Julia do Amaral Gomes
- Postgraduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratory of Immunobiology and Immunogenetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Mariléa Furtado Feira
- Postgraduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratory of Immunobiology and Immunogenetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Ágata de Vargas Dupont
- Laboratory of Immunobiology and Immunogenetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Postgraduation Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratory of Immunobiology and Immunogenetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Genomic Medicine Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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20
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Woycinck Kowalski T, Brussa Reis L, Finger Andreis T, Ashton-Prolla P, Rosset C. Systems Biology Approaches Reveal Potential Phenotype-Modifier Genes in Neurofibromatosis Type 1. Cancers (Basel) 2020; 12:cancers12092416. [PMID: 32858845 PMCID: PMC7565824 DOI: 10.3390/cancers12092416] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 12/18/2022] Open
Abstract
Neurofibromatosis type (NF1) is a syndrome characterized by varied symptoms, ranging from mild to more aggressive phenotypes. The variation is not explained only by genetic and epigenetic changes in the NF1 gene and the concept of phenotype-modifier genes in extensively discussed in an attempt to explain this variability. Many datasets and tools are already available to explore the relationship between genetic variation and disease, including systems biology and expression data. To suggest potential NF1 modifier genes, we selected proteins related to NF1 phenotype and NF1 gene ontologies. Protein–protein interaction (PPI) networks were assembled, and network statistics were obtained by using forward and reverse genetics strategies. We also evaluated the heterogeneous networks comprising the phenotype ontologies selected, gene expression data, and the PPI network. Finally, the hypothesized phenotype-modifier genes were verified by a random-walk mathematical model. The network statistics analyses combined with the forward and reverse genetics strategies, and the assembly of heterogeneous networks, resulted in ten potential phenotype-modifier genes: AKT1, BRAF, EGFR, LIMK1, PAK1, PTEN, RAF1, SDC2, SMARCA4, and VCP. Mathematical models using the random-walk approach suggested SDC2 and VCP as the main candidate genes for phenotype-modifiers.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
- CESUCA - Faculdade Inedi, Cachoeirinha 94935-630, Rio Grande do Sul, Brazil
| | - Larissa Brussa Reis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Tiago Finger Andreis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Programa de Pós-Graduação em Genética e Biologia Molecular, PPGBM, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre 91501-970, Rio Grande do Sul, Brazil
- Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil; (T.W.K.); (L.B.R.); (T.F.A.); (P.A.-P.)
- Unidade de Pesquisa Laboratorial, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre 90035-007, Rio Grande do Sul, Brazil
- Correspondence: ; Tel.: +55-51-3359-7661
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21
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Arruda AP, Cardoso-Dos-Santos AC, Mariath LM, Feira MF, Kowalski TW, Bezerra KRF, da Silva LACT, Ribeiro EM, Schuler-Faccini L. A large family with CYLD cutaneous syndrome: medical genetics at the community level. J Community Genet 2020; 11:279-284. [PMID: 31792733 PMCID: PMC7295879 DOI: 10.1007/s12687-019-00447-2] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/12/2019] [Indexed: 01/12/2023] Open
Abstract
Germline mutations in the cylindromatosis gene (CYLD) are associated with a rare autosomal dominant disease known as CYLD cutaneous syndrome (CCS). Patients present multiple neoplasms originating from skin appendages. Here, we investigated the main clinical and molecular features of a large family with CCS having lived in a small Brazilian town for 6 generations, making its prevalence significantly high. We observed a predominance of the disease among males and a wide phenotypic variation. A high frequency of basal cell carcinomas among affected people was found. The mutation c.2806C>T, p.Arg936* in the CYLD gene was detected in all patients. In this work, a geographical cluster of CCS was found, which raised some community genetics issues related not only to the high prevalence of a rare disease in a limited area but also to the strong social stigma associated with the disease.
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Affiliation(s)
- Anderson Pontes Arruda
- Post-graduate Program in Genetics and Molecular Biology, Department of Biosciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Augusto César Cardoso-Dos-Santos
- Post-graduate Program in Genetics and Molecular Biology, Department of Biosciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Luiza Monteavaro Mariath
- Post-graduate Program in Genetics and Molecular Biology, Department of Biosciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Mariléa Furtado Feira
- Post-graduate Program in Genetics and Molecular Biology, Department of Biosciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | - Thayne Woycinck Kowalski
- Post-graduate Program in Genetics and Molecular Biology, Department of Biosciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil
| | | | | | | | - Lavinia Schuler-Faccini
- Post-graduate Program in Genetics and Molecular Biology, Department of Biosciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, 91501-970, Brazil.
- Department of Genetics, INAGEMP-Instituto Nacional de Genética Médica, Universidade Federal do Rio Grande do Sul, 91501, Porto Alegre, RS, -970, Brazil.
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22
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Cardoso-Dos-Santos AC, Oliveira Silva T, Silveira Faccini A, Woycinck Kowalski T, Bertoli-Avella A, Morales Saute JA, Schuler-Faccini L, de Oliveira Poswar F. Novel AHDC1 Gene Mutation in a Brazilian Individual: Implications of Xia-Gibbs Syndrome. Mol Syndromol 2020; 11:24-29. [PMID: 32256298 DOI: 10.1159/000505843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2019] [Indexed: 12/18/2022] Open
Abstract
Xia-Gibbs syndrome (XGS) is a rare neurological disorder characterized by global developmental delay, hypotonia, intellectual disability, seizures, and sleep apnea. XGS is defined by monoallelic pathogenic variants in AHDC1. In this study, we identified a Brazilian patient carrying a likely de novo AHDC1 nonsense mutation (c.451C>T; p.Arg151*) which was absent in both parents. All disease-causative variants already associated with XGS have been reviewed and the mutation described here corresponds to the closest one to the N-terminal region. Our findings were discussed based on the suggested genotype-phenotype correlation of the disease.
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Affiliation(s)
| | - Thiago Oliveira Silva
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | | | | | | | - Jonas A Morales Saute
- Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.,Internal Medicine Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavinia Schuler-Faccini
- Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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23
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Kowalski TW, Gomes JDA, Garcia GBC, Fraga LR, Paixao-Cortes VR, Recamonde-Mendoza M, Sanseverino MTV, Schuler-Faccini L, Vianna FSL. CRL4-Cereblon complex in Thalidomide Embryopathy: a translational investigation. Sci Rep 2020; 10:851. [PMID: 31964914 PMCID: PMC6972723 DOI: 10.1038/s41598-020-57512-x] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 12/28/2019] [Indexed: 01/13/2023] Open
Abstract
The Cereblon-CRL4 complex has been studied predominantly with regards to thalidomide treatment of multiple myeloma. Nevertheless, the role of Cereblon-CRL4 in Thalidomide Embryopathy (TE) is still not understood. Not all embryos exposed to thalidomide develop TE, hence here we evaluate the role of the CRL4-Cereblon complex in TE variability and susceptibility. We sequenced CRBN, DDB1, CUL4A, IKZF1, and IKZF3 in individuals with TE. To better interpret the variants, we suggested a score and a heatmap comprising their regulatory effect. Differential gene expression after thalidomide exposure and conservation of the CRL4-Cereblon protein complex were accessed from public repositories. Results suggest a summation effect of Cereblon variants on pre-axial longitudinal limb anomalies, and heatmap scores identify the CUL4A variant rs138961957 as potentially having an effect on TE susceptibility. CRL4-Cereblon gene expression after thalidomide exposure and CLR4-Cereblon protein conservation does not explain the difference in Thalidomide sensitivity between species. In conclusion, we suggest that CRL4-Cereblon variants act through several regulatory mechanisms, which may influence CRL4-Cereblon complex assembly and its ability to bind thalidomide. Human genetic variability must be addressed not only to further understand the susceptibility to TE, but as a crucial element in therapeutics, including in the development of pharmacogenomics strategies.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,Laboratory of Medical and Population Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil. .,Genomic Medicine Laboratory, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil. .,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil. .,Complexo de Ensino Superior de Cachoeirinha (CESUCA), Cachoeirinha, Brazil.
| | - Julia do Amaral Gomes
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratory of Medical and Population Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Genomic Medicine Laboratory, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Gabriela Barreto Caldas Garcia
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Laboratory of Medical and Population Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Genomic Medicine Laboratory, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | | | - Mariana Recamonde-Mendoza
- Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Bioinformatics Core, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Maria Teresa Vieira Sanseverino
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratory of Medical and Population Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,School of Medicine - Pontificia Universidade Catolica do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavinia Schuler-Faccini
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Laboratory of Medical and Population Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Postgraduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,Laboratory of Medical and Population Genetics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil. .,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil. .,Genomic Medicine Laboratory, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil. .,National System of Information on Teratogenic Agents (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil. .,Immunobiology and Immunogenetics Laboratory, Departamento de Genética, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.
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24
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Kowalski TW, Dupont ÁDV, Rengel BD, Sgarioni E, Gomes JDA, Fraga LR, Schuler-Faccini L, Vianna FSL. Assembling systems biology, embryo development and teratogenesis: What do we know so far and where to go next? Reprod Toxicol 2019; 88:67-75. [PMID: 31362043 DOI: 10.1016/j.reprotox.2019.07.015] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 06/28/2019] [Accepted: 07/19/2019] [Indexed: 01/19/2023]
Abstract
The recognition of molecular mechanisms of a teratogen can provide insights to understand its embryopathy, and later to plan strategies for the prevention of new exposures. In this context, experimental research is the most invested approach. Despite its relevance, these assays require financial and time investment. Hence, the evaluation of such mechanisms through systems biology rise as an alternative for this conventional methodology. Systems biology is an integrative field that connects experimental and computational analyses, assembling interaction networks between genes, proteins, and even teratogens. It is a valid strategy to generate new hypotheses, that can later be confirmed in experimental assays. Here, we present a literature review of the application of systems biology in embryo development and teratogenesis studies. We provide a glance at the data available in public databases, and evaluate common mechanisms between different teratogens. Finally, we discuss the advantages of using this strategy in future teratogenesis researches.
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Affiliation(s)
- Thayne Woycinck Kowalski
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil; Sistema Nacional de Informação sobre Agentes Teratogênicos, SIAT, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
| | - Ágata de Vargas Dupont
- Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Bruna Duarte Rengel
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Sistema Nacional de Informação sobre Agentes Teratogênicos, SIAT, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Eduarda Sgarioni
- Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Julia do Amaral Gomes
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil; Sistema Nacional de Informação sobre Agentes Teratogênicos, SIAT, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Sistema Nacional de Informação sobre Agentes Teratogênicos, SIAT, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil; Sistema Nacional de Informação sobre Agentes Teratogênicos, SIAT, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil; Sistema Nacional de Informação sobre Agentes Teratogênicos, SIAT, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Group of Post-Graduation Research, GPPG, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil.
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25
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do Socorro Silva Costa P, Woycinck Kowalski T, Rosa Fraga L, Furtado Feira M, Nazário AP, MarceloAranha Camargo L, Iop de Oliveira Caldoncelli D, Irismar da Silva Silveira M, Hutz MH, Schüler-Faccini L, Sales Luiz Vianna F. NR3C1, ABCB1, TNF and CYP2C19 polymorphisms association with the response to the treatment of erythema nodosum leprosum. Pharmacogenomics 2019; 20:503-516. [PMID: 31124417 DOI: 10.2217/pgs-2018-0192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 02/06/2023] Open
Abstract
Aim: To evaluate the effects of gene polymorphisms in the treatment of erythema nodosum leprosum with prednisone/thalidomide. Patients & methods: A total of 152 patients from different regions of Brazil were included. Generalized estimating equation was used to evaluate the influence of polymorphisms and haplotypes on the drug dose variation throughout the treatment. Results: An association between the genotype tuberculoid of polymorphism ABCB1 3435C>T (rs1045642; p = 0.02) and prednisone dose was found in the recessive model. An association between the haplotypes 1031T/-863C/-857C/-308A/-238G (p = 0.006) and 1031T/-863C/-857T/-308A/-238G (p = 0.040) of the TNF gene and the CYP2C19*2 polymorphism were also identified, in relation to thalidomide dosage variation over the course of treatment. Conclusion: This work presents the first pharmacogenetic report of association between gene polymorphisms and erythema nodosum leprosum treatment with prednisone/thalidomide.
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Affiliation(s)
- Perpétua do Socorro Silva Costa
- Postgraduate Program in Genetics & Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, RS, Brazil.,Center of Social Sciences, Health & Technology, Universidade Federal do Maranhão, Imperatriz, MA, Brazil
| | - Thayne Woycinck Kowalski
- Postgraduate Program in Genetics & Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, RS, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Lucas Rosa Fraga
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, RS, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Mariléa Furtado Feira
- INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, RS, Brazil.,Center of Experimental Research, Genomics Medicine Laboratory & Laboratory of Research in Bioethics & Ethics in Research (LAPEBEC), Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Ana Paula Nazário
- Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brazil
| | - Luis MarceloAranha Camargo
- Institute of Biomedical Sciences-5, Universidade de São Paulo, Monte Negro, Rondônia, Brazil.,Center for Research in Tropical Medicine, Porto Velho, Rondônia, Brazil.,National Institute of Science and Technology-EpiAmo, Rondônia, Brazil.,Department of Medicine, Centro Universitário São Lucas, Porto Velho, Rondônia, Brazil
| | | | | | - Mara Helena Hutz
- Postgraduate Program in Genetics & Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lavínia Schüler-Faccini
- Postgraduate Program in Genetics & Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, RS, Brazil.,Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Fernanda Sales Luiz Vianna
- Postgraduate Program in Genetics & Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.,INAGEMP, Instituto Nacional de Genética Médica Populacional, Porto Alegre, RS, Brazil.,Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil.,Center of Experimental Research, Genomics Medicine Laboratory & Laboratory of Research in Bioethics & Ethics in Research (LAPEBEC), Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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26
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Magalhães ODA, Kowalski TW, Wachholz GE, Schuler-Faccini L. Whole-exome sequencing in familial keratoconus: the challenges of a genetically
complex disorder. Arq Bras Oftalmol 2019; 82:453-459. [DOI: 10.5935/0004-2749.20190087] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Accepted: 01/01/2019] [Indexed: 11/20/2022] Open
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27
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Fortis MF, Fraga LR, Boquett JA, Kowalski TW, Dutra CG, Gonçalves RO, Vianna FSL, Schüler-Faccini L, Sanseverino MTV. Angiogenesis and oxidative stress-related gene variants in recurrent pregnancy loss. Reprod Fertil Dev 2018; 30:498-506. [PMID: 28825972 DOI: 10.1071/rd17117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 07/23/2017] [Indexed: 01/18/2023] Open
Abstract
Recurrent pregnancy loss (RPL) affects ~3-5% of couples attempting to conceive and in around 50% of cases the aetiology remains unknown. Adequate vascularisation and placental circulation are indispensable for the development of a normal pregnancy. Prostaglandin-endoperoxide synthase 2 (PTGS2), vascular endothelial growth factor (VEGF) and the nitric oxide (NO) systems play important roles in reproductive physiology, participating in several steps including implantation and apoptosis of trophoblast cells. In this study we evaluated genetic polymorphisms in the inducible nitric oxide synthase (NOS2), PTGS2 and VEGFA genes as susceptibility factors for RPL. A case-control study was conducted in 149 women having two or more miscarriages and 208 controls. Allele and genotype distributions of the polymorphisms studied in the two groups were not statistically different. However, the dominant model showed that the presence of variant T (TT/GT) of rs2779249 (-1290G>T) of NOS2 was significantly associated with RPL (OR=1.58, CI 95%=1.03-2.44; P=0.037). The increased risk remained significant when adjusted for number of pregnancies, alcohol consumption and ethnicity (OR=1.92, CI95%=1.18-3.11; P=0.008). These results suggest that the variant genotypes of the functional polymorphism rs2779249 in the NOS2 promoter are a potential risk for RPL, possibly due to oxidative stress mechanisms.
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Affiliation(s)
- Marcela Felix Fortis
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
| | - Lucas Rosa Fraga
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
| | - Juliano André Boquett
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
| | - Thayne Woycinck Kowalski
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
| | - Caroline Gross Dutra
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
| | - Rozana Oliveira Gonçalves
- Obstetrics, Gynaecology and Human Reproduction Department, Federal University of Bahia, Salvador, 40110-100, Brazil
| | - Fernanda Sales Luiz Vianna
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
| | - Lavinia Schüler-Faccini
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
| | - Maria Teresa Vieira Sanseverino
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, 91501-970, Brazil
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28
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Costa PDSS, Fraga LR, Kowalski TW, Daxbacher ELR, Schuler-Faccini L, Vianna FSL. Erythema Nodosum Leprosum: Update and challenges on the treatment of a neglected condition. Acta Trop 2018; 183:134-141. [PMID: 29474830 DOI: 10.1016/j.actatropica.2018.02.026] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/09/2018] [Accepted: 02/11/2018] [Indexed: 01/25/2023]
Abstract
Erythema Nodosum Leprosum (ENL) occurs due to the immunological complication of multibacillary leprosy and is characterized by painful nodules and systemic compromising. It is usually recurrent and/or chronic and has both physical and economic impact on the patient, being a very important cause of disability. In addition, ENL is a major health problem in countries where leprosy is endemic. Therefore, adequate control of this condition is important. The management of ENL aims to control acute inflammation and neuritis and prevent the onset of new episodes. However, all currently available treatment modalities have one or two drawbacks and are not effective for all patients. Corticosteroid is the anti-inflammatory of choice in ENL but may cause dependence, especially for chronic patients. Thalidomide has a rapid action but its use is limited due the teratogenicity and neurotoxicity. Clofazimine and pentoxifylline have slow action and have important adverse effects. Finally, there is no pattern or guidelines for treating these patients, becoming more difficult to evaluate and to control this condition. This review aims to show the main drugs used in the treatment of ENL and the challenges in the management of the reaction.
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29
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Gomes JDA, Kowalski TW, Fraga LR, Tovo-Rodrigues L, Sanseverino MTV, Schuler-Faccini L, Vianna FSL. Genetic susceptibility to thalidomide embryopathy in humans: Study of candidate development genes. Birth Defects Res 2017; 110:456-461. [PMID: 29193903 DOI: 10.1002/bdr2.1163] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/03/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022]
Abstract
Thalidomide is a drug used worldwide for several indications, but the molecular mechanisms of its teratogenic property are not fully understood. Studies in animal models suggest the oxidative stress, the inhibition of angiogenesis, and the binding to E3-ubiquitin ligase complex as mechanisms by which thalidomide can change the expression of genes important to embryonic development. In this study, seven polymorphisms in genes related to development (FGF8, FGF10, BMP4, SHH, TP53, TP63, and TP73) were analyzed in people with thalidomide embryopathy (TE) and compared to people without malformations. The sample consisted of 36 people with TE and 135 unrelated and nonsyndromic people who had their DNA genotyped by PCR real-time. Although no allelic or genotypic differences were observed between the groups, we hypothesized that other regions in these genes and related genes may play an important role in thalidomide teratogenesis, which is known to have a genetic contribution. Identifying such molecular mechanisms is essential for the development of a molecule that will be analogue to thalidomide but safe enough to avoid the emergence of new cases of TE.
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Affiliation(s)
- Julia do Amaral Gomes
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil
| | - Thayne Woycinck Kowalski
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Medical Genetics Service at the Porto Alegre Clinics Hospital, Brazilian Teratogen Information Service (SIAT), Porto Alegre, Brazil
| | - Luciana Tovo-Rodrigues
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Maria Teresa Vieira Sanseverino
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Medical Genetics Service at the Porto Alegre Clinics Hospital, Brazilian Teratogen Information Service (SIAT), Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Medical Genetics Service at the Porto Alegre Clinics Hospital, Brazilian Teratogen Information Service (SIAT), Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- Postgraduate Program in Genetics and Molecular Biology, Federal University of Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,National Institute of Population Medical Genetics (INAGEMP), Porto Alegre, Brazil.,Medical Genetics Service at the Porto Alegre Clinics Hospital, Brazilian Teratogen Information Service (SIAT), Porto Alegre, Brazil.,Genomic Medicine Laboratory at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.,Laboratory of Research in Bioethics and Ethics in Research (LAPEBEC), at Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil
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30
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Mariath LM, Silva AMD, Kowalski TW, Gattino GS, Araujo GAD, Figueiredo FG, Tagliani-Ribeiro A, Roman T, Vianna FSL, Schuler-Faccini L, Schuch JB. Music genetics research: Association with musicality of a polymorphism in the AVPR1A gene. Genet Mol Biol 2017; 40:421-429. [PMID: 28534928 PMCID: PMC5488451 DOI: 10.1590/1678-4685-gmb-2016-0021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [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: 02/08/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023] Open
Abstract
Musicality is defined as a natural tendency, sensibility, knowledge, or talent to
create, perceive, and play music. Musical abilities involve a great range of social
and cognitive behaviors, which are influenced by both environmental and genetic
factors. Although a number of studies have yielded insights into music genetics
research, genes and biological pathways related to these traits are not fully
understood. Our hypothesis in the current study is that genes associated with
different behaviors could also influence the musical phenotype. Our aim was to
investigate whether polymorphisms in six genes (AVPR1A, SLC6A4, ITGB3, COMT, DRD2 and
DRD4) related to social and cognitive traits are associated with musicality in a
sample of children. Musicality was assessed through an individualized music therapy
assessment profile (IMTAP) which has been validated in Brazil to measure musical
ability. We show here that the RS1 microsatellite of the AVPR1A gene is nominally
associated with musicality, corroborating previous results linking AVPR1A with
musical activity. This study is one of the first to investigate musicality in a
comprehensive way, and it contributes to better understand the genetic basis
underlying musical ability.
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Affiliation(s)
- Luiza Monteavaro Mariath
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alexandre Mauat da Silva
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Thayne Woycinck Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gustavo Schulz Gattino
- Programa de Pos-Graduação em Saúde da Criança e Adolescente, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Gustavo Andrade de Araujo
- Programa de Pos-Graduação em Saúde da Criança e Adolescente, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Felipe Grahl Figueiredo
- Programa de Pos-Graduação em Saúde da Criança e Adolescente, Faculdade de Medicina, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Alice Tagliani-Ribeiro
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Tatiana Roman
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Fernanda Sales Luiz Vianna
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Lavínia Schuler-Faccini
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Jaqueline Bohrer Schuch
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
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31
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Kowalski TW, Fraga LR, Tovo-Rodrigues L, Sanseverino MTV, Hutz MH, Schuler-Faccini L, Vianna FSL. Angiogenesis-related genes and thalidomide teratogenesis in humans: an approach on genetic variation and review of past in vitro studies. Reprod Toxicol 2017; 70:133-140. [PMID: 28161597 DOI: 10.1016/j.reprotox.2017.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 12/16/2016] [Revised: 01/19/2017] [Accepted: 01/30/2017] [Indexed: 12/13/2022]
Abstract
Thalidomide embryopathy (TE) has affected more than 10,000 babies worldwide. The hypothesis of antiangiogenesis as the teratogenic mechanism of thalidomide has been investigated in several experimental models; but, in humans, it has only been accessed by in vitro studies. Here, we hypothesized the effect of thalidomide upon angiogenesis-related molecules or proteins, previously identified in human embryonic cells, through the in silico STRING-tool. We also investigated ten polymorphisms in angiogenesis-related genes in 38 Brazilian TE individuals and 136 non-affected Brazilians. NOS2, PTGS2, and VEGFA polymorphisms were chosen for genotyping. The STRING-tool suggested nitric oxide and β-catenin as the central angiogenesis-related molecules affected by thalidomide's antiangiogenic property. We did not identify a significant difference of allelic, genotypic or haplotypic frequencies between the groups. We could not predict a risk allele or a protective one for TE in NOS2, PTGS2, or VEGFA, although other genes should be analyzed in larger samples. The role of nitric oxide and β-catenin must be further evaluated, regarding thalidomide teratogenesis complex etiology.
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Affiliation(s)
- Thayne Woycinck Kowalski
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Luciana Tovo-Rodrigues
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Post-Graduate Program of Epidemiology, Universidade Federal de Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Maria Teresa Vieira Sanseverino
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil
| | - Mara Helena Hutz
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- INAGEMP-Instituto Nacional de Genética Médica Populacional, Porto Alegre, Brazil; Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil; Service of Experimental Research, Genomics Medicine Laboratory, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Brazil.
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32
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de Souza LT, Kowalski TW, Ferrari J, Monlléo IL, Ribeiro EM, de Souza J, Fett-Conte AC, de Araujo TK, Gil-da-Silva-Lopes VL, Ribeiro-dos-Santos ÂKC, dos Santos SEB, Félix TM. Study ofIRF6and 8q24 region in non-syndromic oral clefts in the Brazilian population. Oral Dis 2016; 22:241-5. [DOI: 10.1111/odi.12432] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/24/2015] [Accepted: 12/17/2015] [Indexed: 02/03/2023]
Affiliation(s)
- LT de Souza
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - TW Kowalski
- Programa de Pós-Graduação em Genética e Biologia Molecular; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
| | - J Ferrari
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
| | - IL Monlléo
- Serviço de Genética Clínica; Faculdade de Medicina; Hospital Universitário Professor Alberto Antunes; Universidade Federal de Alagoas; Maceió Brazil
| | - EM Ribeiro
- Hospital Infantil Albert Sabin; Fortaleza Brazil
| | - J de Souza
- Centro de Atendimento Integral ao Fissurado Lábio-palatal; Curitiba Brazil
| | - AC Fett-Conte
- Serviço de Genética; Faculdade de Medicina de São José do Rio Preto; São José do Rio Preto Brazil
| | - TK de Araujo
- Departamento de Genética Médica; Faculdade de Ciências Médicas; Universidade de Campinas; Campinas Brazil
| | - VL Gil-da-Silva-Lopes
- Departamento de Genética Médica; Faculdade de Ciências Médicas; Universidade de Campinas; Campinas Brazil
| | - ÂKC Ribeiro-dos-Santos
- Laboratório de Genética Humana e Médica; Instituto de Ciências Biológicas; Universidade Federal do Pará; Belém Brazil
| | - SEB dos Santos
- Laboratório de Genética Humana e Médica; Instituto de Ciências Biológicas; Universidade Federal do Pará; Belém Brazil
| | - TM Félix
- Laboratório de Medicina Genômica - Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
- Programa de Pós-Graduação em Saúde da Criança e do Adolescente; Universidade Federal do Rio Grande do Sul; Porto Alegre Brazil
- Serviço de Genética Médica; Hospital de Clínicas de Porto Alegre; Porto Alegre Brazil
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33
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Kowalski TW, Sanseverino MTV, Schuler-Faccini L, Vianna FSL. Thalidomide embryopathy: Follow-up of cases born between 1959 and 2010. ACTA ACUST UNITED AC 2015; 103:794-803. [PMID: 26043318 DOI: 10.1002/bdra.23376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [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: 09/11/2014] [Revised: 11/07/2014] [Accepted: 11/26/2014] [Indexed: 12/12/2022]
Abstract
BACKGROUND Thalidomide is a known teratogen and it is estimated that more than ten thousand babies were affected by thalidomide embryopathy (TE), which is characterized mainly by limb defects, but can involve many organs and systems. Most people with TE were only evaluated at birth and it is not well established if thalidomide exposure during embryonic development leads to later effects. We analyzed the clinical history of adults with TE to better understand this gap in the clinical findings of TE. METHODS Brazilian individuals with TE were invited to answer a clinical questionnaire which considered family history, social information, medical history, and current clinical and psychological health status. A clinical examination was also performed, including on the infant subjects to evaluate congenital anomalies. The characterization of the features was analyzed using descriptive statistics and Chi-square or Fisher's exact test. RESULTS The congenital anomalies caused by thalidomide were reviewed in 28 Brazilian individuals, and the questionnaire was applied to the 23 adult subjects with TE (aged 19 to 55). Progressive deafness and dental loss were reported. From the comparison of TE individuals with the general Brazilian population, the early onset of cardiovascular diseases (p = 0.009) and a higher frequency of psychological disorders (p = 0.011) were observed. CONCLUSION Although there is no sufficient evidence that thalidomide exposure caused or worsened the described events, this approach helps to better understand the TE phenotype, improves the clinical diagnosis, and can lead to adequate health support for these individuals.
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Affiliation(s)
- Thayne Woycinck Kowalski
- PPGBM (Programa de Pós Graduação em Genética e Biologia Molecular), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Population Medical Genetics, INAGEMP, Porto Alegre, Brazil
| | - Maria Teresa Vieira Sanseverino
- PPGBM (Programa de Pós Graduação em Genética e Biologia Molecular), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil
| | - Lavinia Schuler-Faccini
- PPGBM (Programa de Pós Graduação em Genética e Biologia Molecular), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil
| | - Fernanda Sales Luiz Vianna
- PPGBM (Programa de Pós Graduação em Genética e Biologia Molecular), Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.,National Institute of Population Medical Genetics, INAGEMP, Porto Alegre, Brazil.,Teratogen Information Service, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, Brazil.,Programa de Pós Graduação em Epidemiologia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
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Souza LT, Kowalski TW, Collares MVM, Félix TM. MSX1 gene and nonsyndromic oral clefts in a Southern Brazilian population. Braz J Med Biol Res 2013; 46:555-8. [PMID: 23903689 PMCID: PMC3859340 DOI: 10.1590/1414-431x20133054] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 02/21/2013] [Accepted: 05/02/2013] [Indexed: 11/22/2022] Open
Abstract
Nonsyndromic oral clefts (NSOC) are the most common craniofacial birth defects in
humans. The etiology of NSOC is complex, involving both genetic and
environmental factors. Several genes that play a role in cellular proliferation,
differentiation, and apoptosis have been associated with clefting. For example,
variations in the homeobox gene family member MSX1, including a
CA repeat located within its single intron, may play a role in clefting. The aim
of this study was to investigate the association between MSX1
CA repeat polymorphism and NSOC in a Southern Brazilian population using a
case-parent triad design. We studied 182 nuclear families with NSOC recruited
from the Hospital de Clínicas de Porto Alegre in Southern Brazil. The
polymorphic region was amplified by the polymerase chain reaction and analyzed
by using an automated sequencer. Among the 182 families studied, four different
alleles were observed, at frequencies of 0.057 (175 bp), 0.169 (173 bp), 0.096
(171 bp) and 0.67 (169 bp). A transmission disequilibrium test with a
family-based association test (FBAT) software program was used for analysis.
FBAT analysis showed overtransmission of the 169 bp allele in NSOC (P=0.0005).
These results suggest that the CA repeat polymorphism of the
MSX1 gene may play a role in risk of NSOC in populations
from Southern Brazil.
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Affiliation(s)
- L T Souza
- Laborato´ rio de Medicina Genoˆ mica, Centro de Pesquisa Experimental, Hospital de Clinicas de Porto Alegre, Porto Alegre, RS, Brasil
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Souza LTD, Kowalski TW, Vanz AP, Giugliani R, Félix TM. TGFA/Taq I polymorphism and environmental factors in non-syndromic oral clefts in Southern Brazil. Braz Oral Res 2012; 26:431-5. [DOI: 10.1590/s1806-83242012005000016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 07/06/2012] [Indexed: 11/22/2022] Open
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