Navegando por Autor "Ribeiro-dos-Santos, André M."

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Bioinformatics analysis of the human surfaceome reveals new targets for a variety of tumor types
(Hindawi, 2016-10-18) Fonseca, André L.; Silva, Vandeclécio Lira da; Fonseca, Marbella M.; Meira, Isabella Tanus Job e; Silva, Thayná Emília Oliveira; Kroll, José Eduardo; Ribeiro-dos-Santos, André M.; Freitas, Cléber R.; Furtado, Raimundo; Souza, Jorge Estefano Santana de; Ferreira, Beatriz Stransky; Souza, Sandro José de
It is estimated that 10 to 20% of all genes in the human genome encode cell surface proteins and due to their subcellular localization these proteins represent excellent targets for cancer diagnosis and therapeutics. Therefore, a precise characterization of the surfaceome set in different types of tumor is needed. Using TCGA data from 15 different tumor types and a new method to identify cancer genes, the -score, we identified several potential therapeutic targets within the surfaceome set. This allowed us to expand a previous analysis from us and provided a clear characterization of the human surfaceome in the tumor landscape. Moreover, we present evidence that a three-gene set—WNT5A, CNGA2, and IGSF9B—can be used as a signature associated with shorter survival in breast cancer patients. The data made available here will help the community to develop more efficient diagnostic and therapeutic tools for a variety of tumor types
Bioinformatics Analysis of the Human Surfaceome Reveals New Targets for a Variety of Tumor Types
(2016-10-18) Fonseca, André L.; Silva, Vandeclécio L. da; Fonseca, Marbella M.; Meira, Isabella T. J.; Silva, Thayná E. da; Kroll, José Eduardo; Ribeiro-dos-Santos, André M.; Freitas, Cléber R.; Furtado, Raimundo; Souza, Sandro José de; Ferreira, Beatriz Stransky; Souza, Sandro José de
It is estimated that 10 to 20% of all genes in the human genome encode cell surface proteins and due to their subcellular localization these proteins represent excellent targets for cancer diagnosis and therapeutics. Therefore, a precise characterization of the surfaceome set in different types of tumor is needed. Using TCGA data from 15 different tumor types and a new method to identify cancer genes, the -score, we identified several potential therapeutic targets within the surfaceome set. This allowed us to expand a previous analysis from us and provided a clear characterization of the human surfaceome in the tumor landscape. Moreover, we present evidence that a three-gene set—WNT5A, CNGA2, and IGSF9B—can be used as a signature associated with shorter survival in breast cancer patients. The data made available here will help the community to develop more efficient diagnostic and therapeutic tools for a variety of tumor types.
Exome sequencing of native populations from the Amazon reveals patterns on the peopling of South America
(Frontiers Media SA, 2020-10-29) Ribeiro-dos-Santos, André M.; Vidal, Amanda Ferreira; Vinasco-Sandoval, Tatiana; Guerreiro, João; Santos, Sidney; Ribeiro-dos-Santos, Ândrea; Souza, Sandro José de
Studies on the peopling of South America have been limited by the paucity of sequence data from Native Americans, especially from the east part of the Amazon region. Here, we investigate the whole exome variation from 58 Native American individuals (eight different populations) from the Amazon region and draw insights into the peopling of South America. By using the sequence data generated here together with data from the public domain, we confirmed a strong genetic distinction between Andean and Amazonian populations. By testing distinct demographic models, our analysis supports a scenario of South America occupation that involves migrations along the Pacific and Atlantic coasts. Occupation of the southeast part of South America would involve migrations from the north, rather than from the west of the continent
High-Throughput Sequencing of a South American Amerindian
(2013-12-30) Ribeiro-dos-Santos, André M.; Souza, Jorge Estefano Santana de; Almeida, Renan; Alencar, Dayse O.; Barbosa, Maria Silvanira; Gusmão, Leonor; Silva Jr., Wilson A.; Souza, Sandro José de; Silva, Artur; Ribeiro-dos-Santos, Ândrea; Darnet, Sylvain; Santos, Sidney
The emergence of next-generation sequencing technologies allowed access to the vast amounts of information that are contained in the human genome. This information has contributed to the understanding of individual and population-based variability and improved the understanding of the evolutionary history of different human groups. However, the genome of a representative of the Amerindian populations had not been previously sequenced. Thus, the genome of an individual from a South American tribe was completely sequenced to further the understanding of the genetic variability of Amerindians. A total of 36.8 giga base pairs (Gbp) were sequenced and aligned with the human genome. These Gbp corresponded to 95.92% of the human genome with an estimated miscall rate of 0.0035 per sequenced bp. The data obtained from the alignment were used for SNP (single-nucleotide) and INDEL (insertion-deletion) calling, which resulted in the identification of 502,017 polymorphisms, of which 32,275 were potentially new high-confidence SNPs and 33,795 new INDELs, specific of South Native American populations. The authenticity of the sample as a member of the South Native American populations was confirmed through the analysis of the uniparental (maternal and paternal) lineages. The autosomal comparison distinguished the investigated sample from others continental populations and revealed a close relation to the Eastern Asian populations and Aboriginal Australian. Although, the findings did not discard the classical model of America settlement; it brought new insides to the understanding of the human population history. The present study indicates a remarkable genetic variability in human populations that must still be identified and contributes to the understanding of the genetic variability of South Native American populations and of the human populations history.
Populational landscape of INDELs affecting transcription factor-binding sites in humans
(2015) Ribeiro-dos-Santos, André M.; Silva, Vandeclécio L. da; Souza, Jorge E.S. de; Souza, Sandro José de
Background Differences in gene expression have a significant role in the diversity of phenotypes in humans. Here we integrated human public data from ENCODE, 1000 Genomes and Geuvadis to explore the populational landscape of INDELs affecting transcription factor-binding sites (TFBS). A significant fraction of TFBS close to the transcription start site of known genes is affected by INDELs with a consequent effect at the expression of the associated gene. Results Hundreds of TFBS-affecting INDELs (TFBS-ID) show a differential frequency between human populations, suggesting a role of natural selection in the spread of such variant INDELs. A comparison with a dataset of known human genomic regions under natural selection allowed us to identify several cases of TFBS-ID likely involved in populational adaptations. Ontology analyses on the differential TFBS-ID further indicated several biological processes under natural selection in different populations. Conclusion Together, our results strongly suggest that INDELs have an important role in modulating gene expression patterns in humans. The dataset we make available, together with other data reporting variability at both regulatory and coding regions of genes, represent a powerful tool for studies aiming to better understand the evolution of gene regulatory networks in humans.
Whole genome sequencing of the Pirarucu (Arapaima gigas) supports independent emergence of major teleost clades
(2018-07-05) Vialle, Ricardo Assunção; Souza, Jorge Estefano Santana de; Lopes, Katia de Paiva; Teixeira, Diego Gomes; Alves Sobrinho, Pitágoras de Azevedo; Ribeiro-dos-Santos, André M.; Furtado, Carolina; Sakamoto, Tetsu; Silva, Fábio Augusto Oliveira; Oliveira, Edivaldo Herculano Corrêa de; Hamoy, Igor Guerreiro; Assumpção, Paulo Pimentel; Ribeiro-dos-Santos, Ândrea; Lima, João Paulo Matos Santos; Seuánez, Héctor N.; Souza, Sandro José de; Santos, Sidney
The Pirarucu (Arapaima gigas) is one of the world's largest freshwater fishes and member of the superorder Osteoglossomorpha (bonytongues), one of the oldest lineages of ray-finned fishes. This species is an obligate air-breather found in the basin of the Amazon River with an attractive potential for aquaculture. Its phylogenetic position among bony fishes makes the Pirarucu a relevant subject for evolutionary studies of early teleost diversification. Here, we present, for the first time, a draft genome version of the A. gigas genome, providing useful information for further functional and evolutionary studies. The A. gigas genome was assembled with 103 Gb raw reads sequenced in an Illumina platform. The final draft genome assembly was approximately 661 Mb, with a contig N50 equal to 51.23 kb and scaffold N50 of 668 kb. Repeat sequences accounted for 21.69% of the whole genome, and a total of 24,655 protein-coding genes were predicted from the genome assembly, with an average of 9 exons per gene. Phylogenomic analysis based on 24 fish species supported the postulation that Osteoglossomorpha and Elopomorpha (eels, tarpons and bonefishes) are sister groups, both forming a sister lineage with respect to Clupeocephala (remaining teleosts). Divergence time estimations suggested that Osteoglossomorpha and Elopomorpha lineages emerged independently in a period of approximately 30 million years in the Jurassic. The draft genome of A. gigas provides a valuable genetic resource for further investigations of evolutionary studies and may also offer a valuable data for economic applications.

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Navegando por Autor "Ribeiro-dos-Santos, André M."