Navegando por Autor "Santos, André Mauricio Ribeiro dos"

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Gain of transcription factor binding sites is associated to changes in the expression signature of human brain and testis and is correlated to genes with higher expression breadth
(2019-03-22) Silva, Vandeclécio Lira da; Santos, André Mauricio Ribeiro dos; Blanco, Wilfredo; Souza, Sandro José de
The gain of transcription factor binding sites (TFBS) is believed to represent one of the major causes of biological innovation. Here we used strategies based on comparative genomics to identify 21,822 TFBS specific to the human lineage (TFBS-HS), when compared to chimpanzee and gorilla genomes. More than 40% (9,206) of these TFBS-HS are in the vicinity of 1,283 genes. A comparison of the expression pattern of these genes and the corresponding orthologs in chimpanzee and gorilla identified genes differentially expressed in human tissues. These genes show a more divergent expression pattern in the human testis and brain, suggesting a role for positive selection in the fixation of TFBS gains. Genes associated with TFBS-HS were enriched in gene ontology categories related to transcriptional regulation, signaling, differentiation/development and nervous system. Furthermore, genes associated with TFBS-HS present a higher expression breadth when compared to genes in general. This biased distribution is due to a preferential gain of TFBS in genes with higher expression breadth rather than a shift in the expression pattern after the gain of TFBS.
Incidence of hereditary gastric cancer may be much higher than reported
(MDPI AG, 2022-12) Assumpção, Paula Baraúna de; Assumpção, Paulo Pimentel de; Moreira, Fabiano Cordeiro; Santos, Andrea Kely Campos Ribeiro dos; Vidal, Amanda Ferreira; Magalhães, Leandro; Khayat, André Salim; Santos, André Mauricio Ribeiro dos; Cavalcante, Giovanna Chaves; Pereira, Adenilson Leão; Medeiros, Inácio Gomes; Souza, Sandro José de; Burbano, Rommel Mario Rodríguez; Souza, Jorge Estefano Santana de; Santos, Sidney Emanuel Batista dos
Hereditary gastric cancers (HGCs) are supposed to be rare and difficult to identify. Nonetheless, many cases of young patients with gastric cancer (GC) fulfill the clinical criteria for considering this diagnosis but do not present the defined pathogenic mutations necessary to meet a formal diagnosis of HGC. Moreover, GC in young people is a challenging medical situation due to the usual aggressiveness of such cases and the potential risk for their relatives when related to a germline variant. Aiming to identify additional germline alterations that might contribute to the early onset of GC, a complete exome sequence of blood samples from 95 GC patients under 50 and 94 blood samples from non-cancer patients was performed and compared in this study. The number of identified germline mutations in GC patients was found to be much higher than that from individuals without a cancer diagnosis. Specifically, the number of high functional impact mutations, including those affecting genes involved in medical diseases, cancer hallmark genes, and DNA replication and repair processes, was much higher, strengthening the hypothesis of the potential causal role of such mutations in hereditary cancers. Conversely, classically related HGC mutations were not found and the number of mutations in genes in the CDH1 pathway was not found to be relevant among the young GC patients, reinforcing the hypothesis that existing alternative germline contributions favor the early onset of GC. The LILRB1 gene variants, absent in the world's cancer datasets but present in high frequencies among the studied GC patients, may represent essential cancer variants specific to the Amerindian ancestry's contributions. Identifying non-reported GC variants, potentially originating from under-studied populations, may pave the way for additional discoveries and translations to clinical interventions for GC management. The newly proposed approaches may reduce the discrepancy between clinically suspected and molecularly proven hereditary GC and shed light on similar inconsistencies among other cancer types. Additionally, the results of this study may support the development of new blood tests for evaluating cancer risk that can be used in clinical practice, helping physicians make decisions about strategies for surveillance and risk-reduction interventions
Metagenoma do músculo caudal de um exemplar do camarão Penaeus vannamei infectado pelo vírus da síndrome da mancha branca
(2019-03-11) Soares, Paulo Eduardo Toscano; Lanza, Daniel Carlos Ferreira; ; ; Souza, Jorge Estefano Santana de; ; Santos, André Mauricio Ribeiro dos;
O camarão de patas brancas (Penaeus vannamei) é a espécie mais cultivada na aquicultura mundial. O cultivo comercial geralmente ocorre em densidades altas, o que pode resultar na seleção de patógenos virulentos e surtos de doenças. Assim, estratégias de monitoramento da microbiota nos cultivos tornam-se necessárias e, neste contexto, o uso de metagenômica tem sido sugerido na aquicultura. A metagenômica shotgun é capaz de recuperar a informação genômica do hospedeiro e microbiota associada, incluindo vírus, permitindo descobrir sua composição taxonômica e funcional. Neste estudo foram analisados dados de sequenciamento shotgun do músculo caudal de um espécime de P. vannamei infectado pelo vírus da síndrome da mancha branca (WSSV), com o intuito de prospectar sequências e informações do metagenoma. Classificações taxonômicas e funcionais foram realizadas para se obter os respectivos perfis dos dados. P. vannamei e WSSV foram os organismos mais abundantes na classificação taxonômica. A classificação funcional foi realizada através do software MEGAN, mostrando várias funções relacionadas com as vias metabólicas de carboidratos, lipídios e proteínas, além de funções relacionadas com virulência (liberação da latência viral, integrase, CRISPR associated helicase, cas3 e resistência a acriflavina). Uma classificação taxonômica a partir do BLASTx realizada via MEGAN apresentou resultados similares aos da classificação usando BLASTn, reforçando-os. Os resultados do BLASTn guiaram a montagem do genoma mitocondrial completo do P. vannamei, no qual foi feito um estudo preliminar de caracterização da região d-loop e avaliação do seu potencial de barcoding. Também neste estudo foram anotados 287 contigs para P. vannamei, ainda sem um genoma de referência disponível. Por fim, este estudo revelou baixa diversidade taxonômica e funcional no músculo do camarão, além da caracterização do d-loop mitocondrial da espécie P. vannamei.
Molecular profile of variants in CDH1, TP53, PSCA, PRKAA1, and TTN genes related to gastric cancer susceptibility in Amazonian indigenous populations
(MDPI AG, 2023-09) Aguiar, Kaio Evandro Cardoso; Oliveira, Izabela De Sousa; Paes, Amanda de Nazaré Cohen; Coelho, Rita de Cássia Calderaro; Vinagre, Lui Wallacy Morikawa Souza; Rodrigues, Juliana Carla Gomes; Santos, André Mauricio Ribeiro dos; Souza, Sandro José de; Santos, Andrea Kely Campos Ribeiro dos; Guerreiro, João Farias; Assumpção, Paulo Pimentel de; Santos, Sidney Emanuel Batista dos; Santos, Ney Pereira Carneiro dos; Fernandes, Marianne Rodrigues
Gastric Cancer is a disease associated with environmental and genetic changes, becoming one of the most prevalent cancers around the world and with a high incidence in Brazil. However, despite being a highly studied neoplastic type, few efforts are aimed at populations with a unique background and genetic profile, such as the indigenous peoples of the Brazilian Amazon. Our study characterized the molecular profile of five genes associated with the risk of developing gastric cancer by sequencing the complete exome of 64 indigenous individuals belonging to 12 different indigenous populations in the Amazon. The analysis of the five genes found a total of 207 variants, of which 15 are new in our indigenous population, and among these are two with predicted high impact, present in the TTN and CDH1 genes. In addition, at least 20 variants showed a significant difference in the indigenous population in comparison with other world populations, and three are already associatively related to some type of cancer. Our study reaffirms the unique genetic profile of the indigenous population of the Brazilian Amazon and allows us to contribute to the conception of early diagnosis of complex diseases such as cancer, improving the quality of life of individuals potentially suffering from the disease
Molecular profile of variants potentially associated with severe forms of COVID-19 in Amazonian indigenous populations
(MDPI AG, 2024-02) Coelho, Rita de Cássia Calderaro; Martins, Carlliane Lima e Lins Pinto; Pastana, Lucas Favacho; Rodrigues, Juliana Carla Gomes; Aguiar, Kaio Evandro Cardoso; Paes, Amanda de Nazaré Cohen; Gellen, Laura Patrícia Albarello; Moraes, Francisco Cezar Aquino de; Calderaro, Maria Clara Leite; Assunção, Letícia Almeida de; Silva, Natasha Monte da; Pereira, Esdras Edgar Batista; Santos, André Mauricio Ribeiro dos; Santos, Andrea Kely Campos Ribeiro dos; Burbano, Rommel Mario Rodriguez; Souza, Sandro José de; Guerreiro, João Farias; Assumpção, Paulo Pimentel de; Santos, Sidney Emanuel Batista dos; Fernandes, Marianne Rodrigues; Santos, Ney Pereira Carneiro dos
Coronavirus disease 2019 (COVID-19) is an infection caused by SARS-CoV-2. Genome-wide association studies (GWASs) have suggested a strong association of genetic factors with the severity of the disease. However, many of these studies have been completed in European populations, and little is known about the genetic variability of indigenous peoples’ underlying infection by SARS-CoV-2. The objective of the study is to investigate genetic variants present in the genes AQP3, ARHGAP27, ELF5L, IFNAR2, LIMD1, OAS1 and UPK1A, selected due to their association with the severity of COVID-19, in a sample of indigenous people from the Brazilian Amazon in order to describe potential new and already studied variants. We performed the complete sequencing of the exome of 64 healthy indigenous people from the Brazilian Amazon. The allele frequency data of the population were compared with data from other continental populations. A total of 66 variants present in the seven genes studied were identified, including a variant with a high impact on the ARHGAP27 gene (rs201721078) and three new variants located in the Amazon Indigenous populations (INDG) present in the AQP3, IFNAR2 and LIMD1 genes, with low, moderate and modifier impact, respectively
Severe toxicities in amazonian populations and the role of precision medicine in acute lymphoblastic leukemia treatment
(Springer Science and Business Media LLC, 2024-11) Leitão, Luciana Pereira Colares; Monte, Natasha; Rodrigues, Juliana Carla Gomes; Freitas, Lilian Marques de; Santos, André Mauricio Ribeiro dos; Santos, Andrea Kely Campos Ribeiro dos; Santos, Sidney; Souza, Sandro José de; Fernandes, Marianne Rodrigues; Santos, Ney Pereira Carneiro dos
Corticosteroids, such as prednisone or dexamethasone, constitute integral components of antineoplastic regimens for Acute Lymphoblastic Leukemia (ALL) therapy, albeit accompanied by significant adverse effects. The multifactorial nature of interindividual variability in drug response, encompassing genetic polymorphisms, underscores the complexity of pharmacotherapy outcomes. However, pharmacogenetic investigations hitherto have predominantly focused on cohorts of European and North American descent, thus limiting the generalizability of findings to populations with minimal representation. Indigenous populations in Brazil, particularly those inhabiting the Amazon region, exhibit a distinctive genetic heritage, predominantly characterized by Native American ancestry. These populations frequently manifest suboptimal therapeutic responses and elevated mortality rates following ALL treatment. Therefore, delineating the molecular signatures of genes implicated in the corticosteroid pathway within these indigenous cohorts assumes paramount importance. This study identified novel variants within genes associated with the glucocorticoid pathway in indigenous Amazonian populations and conducted comparative analyses of variant frequencies across diverse global populations. The findings underscore the genetic uniqueness of indigenous groups and highlight the potential impact of genetic factors on adverse responses to ALL treatment. Precision medicine approaches tailored to the genetic peculiarities of indigenous populations emerge as imperative strategies for optimizing therapeutic efficacy and mitigating treatment-related toxicities in these communities

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Navegando por Autor "Santos, André Mauricio Ribeiro dos"