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Banho CA, Mérel V, Oliveira TYK, Carareto CMA, Vieira C. Comparative transcriptomics between Drosophila mojavensis and D. arizonae reveals transgressive gene expression and underexpression of spermatogenesis-related genes in hybrid testes. Sci Rep 2021; 11:9844. [PMID: 33972659 PMCID: PMC8110761 DOI: 10.1038/s41598-021-89366-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 04/19/2021] [Indexed: 01/02/2023] Open
Abstract
Interspecific hybridization is a stressful condition that can lead to sterility and/or inviability through improper gene regulation in Drosophila species with a high divergence time. However, the extent of these abnormalities in hybrids of recently diverging species is not well known. Some studies have shown that in Drosophila, the mechanisms of postzygotic isolation may evolve more rapidly in males than in females and that the degree of viability and sterility is associated with the genetic distance between species. Here, we used transcriptomic comparisons between two Drosophila mojavensis subspecies and D. arizonae (repleta group, Drosophila) and identified greater differential gene expression in testes than in ovaries. We tested the hypothesis that the severity of the interspecies hybrid phenotype is associated with the degree of gene misregulation. We showed limited gene misregulation in fertile females and an increase in the amount of misregulation in males with more severe sterile phenotypes (motile vs. amotile sperm). In addition, for these hybrids, we identified candidate genes that were mostly associated with spermatogenesis dysfunction.
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Affiliation(s)
- Cecilia A Banho
- Department of Biology, UNESP - São Paulo State University, São José do Rio Preto, São Paulo State (SP), Brazil.,Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Claude Bernard Lyon 1, University of Lyon, 69622, Villeurbanne, France
| | - Vincent Mérel
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Claude Bernard Lyon 1, University of Lyon, 69622, Villeurbanne, France
| | - Thiago Y K Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Claudia M A Carareto
- Department of Biology, UNESP - São Paulo State University, São José do Rio Preto, São Paulo State (SP), Brazil
| | - Cristina Vieira
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Claude Bernard Lyon 1, University of Lyon, 69622, Villeurbanne, France.
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Mouquet H, Klein F, Scheid JF, Warncke M, Pietzsch J, Oliveira TYK, Velinzon K, Seaman MS, Nussenzweig MC. Memory B cell antibodies to HIV-1 gp140 cloned from individuals infected with clade A and B viruses. PLoS One 2011; 6:e24078. [PMID: 21931643 PMCID: PMC3169578 DOI: 10.1371/journal.pone.0024078] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 07/29/2011] [Indexed: 11/20/2022] Open
Abstract
Understanding the antibody response to HIV-1 in humans that show broad neutralizing serologic activity is a crucial step in trying to reproduce such responses by vaccination. Investigating antibodies with cross clade reactivity is particularly important as these antibodies may target conserved epitopes on the HIV envelope gp160 protein. To this end we have used a clade B YU-2 gp140 trimeric antigen and single-cell antibody cloning methods to obtain 189 new anti-gp140 antibodies representing 51 independent B cell clones from the IgG memory B cells of 3 patients infected with HIV-1 clade A or B viruses and exhibiting broad neutralizing serologic activity. Our results support previous findings showing a diverse antibody response to HIV gp140 envelope protein, characterized by differentially expanded B-cell clones producing highly hypermutated antibodies with heterogenous gp140-specificity and neutralizing activity. In addition to their high-affinity binding to the HIV spike, the vast majority of the new anti-gp140 antibodies are also polyreactive. Although none of the new antibodies are as broad or potent as VRC01 or PG9, two clonally-related antibodies isolated from a clade A HIV-1 infected donor, directed against the gp120 variable loop 3, rank in the top 5% of the neutralizers identified in our large collection of 185 unique gp140-specific antibodies in terms of breadth and potency.
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Affiliation(s)
- Hugo Mouquet
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Florian Klein
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Johannes F. Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
- Charite Universitaetsmedizin, Berlin, Germany
| | - Malte Warncke
- Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - John Pietzsch
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Thiago Y. K. Oliveira
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
- Medical School of Ribeirao Preto/USP, Department of Genetics, National Institute of Science and Technology for Stem Cells and Cell Therapy and Center for Cell-Based Therapy, Ribeirao Preto, Brazil
| | - Klara Velinzon
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
| | - Michael S. Seaman
- Beth Israel Deaconess Medical Center, Boston, Maryland, United States of America
| | - Michel C. Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, New York, United States of America
- Howard Hughes Medical Institute, The Rockefeller University, New York City, New York, United States of America
- * E-mail:
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Scheid JF, Mouquet H, Ueberheide B, Diskin R, Klein F, Oliveira TYK, Pietzsch J, Fenyo D, Abadir A, Velinzon K, Hurley A, Myung S, Boulad F, Poignard P, Burton DR, Pereyra F, Ho DD, Walker BD, Seaman MS, Bjorkman PJ, Chait BT, Nussenzweig MC. Sequence and structural convergence of broad and potent HIV antibodies that mimic CD4 binding. Science 2011; 333:1633-7. [PMID: 21764753 DOI: 10.1126/science.1207227] [Citation(s) in RCA: 928] [Impact Index Per Article: 71.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Passive transfer of broadly neutralizing HIV antibodies can prevent infection, which suggests that vaccines that elicit such antibodies would be protective. Thus far, however, few broadly neutralizing HIV antibodies that occur naturally have been characterized. To determine whether these antibodies are part of a larger group of related molecules, we cloned 576 new HIV antibodies from four unrelated individuals. All four individuals produced expanded clones of potent broadly neutralizing CD4-binding-site antibodies that mimic binding to CD4. Despite extensive hypermutation, the new antibodies shared a consensus sequence of 68 immunoglobulin H (IgH) chain amino acids and arise independently from two related IgH genes. Comparison of the crystal structure of one of the antibodies to the broadly neutralizing antibody VRC01 revealed conservation of the contacts to the HIV spike.
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Affiliation(s)
- Johannes F Scheid
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
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Galante PAF, Parmigiani RB, Zhao Q, Caballero OL, de Souza JE, Navarro FCP, Gerber AL, Nicolás MF, Salim ACM, Silva APM, Edsall L, Devalle S, Almeida LG, Ye Z, Kuan S, Pinheiro DG, Tojal I, Pedigoni RG, de Sousa RGMA, Oliveira TYK, de Paula MG, Ohno-Machado L, Kirkness EF, Levy S, da Silva WA, Vasconcelos ATR, Ren B, Zago MA, Strausberg RL, Simpson AJG, de Souza SJ, Camargo AA. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res 2011; 39:6056-68. [PMID: 21493686 PMCID: PMC3152357 DOI: 10.1093/nar/gkr221] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [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] [Indexed: 11/12/2022] Open
Abstract
Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein-protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation.
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Affiliation(s)
- Pedro A F Galante
- Ludwig Institute for Cancer Research, São Paulo Branch at Hospital Alemão Oswaldo Cruz, São Paulo 01323-903, Brazil
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Silva IT, Vêncio RZN, Oliveira TYK, Molfetta GA, Silva WA. ProbFAST: Probabilistic functional analysis system tool. BMC Bioinformatics 2010; 11:161. [PMID: 20353576 PMCID: PMC2868004 DOI: 10.1186/1471-2105-11-161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 03/30/2010] [Indexed: 01/01/2023] Open
Abstract
Background The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regulation under distinct biological conditions and can be performed by analyzing the Multiple Differential Expression (MDE) of genes associated with normal and abnormal biological processes. Currently MDE analyses are limited to usual methods of differential expression initially designed for paired analysis. Results We proposed a web platform named ProbFAST for MDE analysis which uses Bayesian inference to identify key genes that are intuitively prioritized by means of probabilities. A simulated study revealed that our method gives a better performance when compared to other approaches and when applied to public expression data, we demonstrated its flexibility to obtain relevant genes biologically associated with normal and abnormal biological processes. Conclusions ProbFAST is a free accessible web-based application that enables MDE analysis on a global scale. It offers an efficient methodological approach for MDE analysis of a set of genes that are turned on and off related to functional information during the evolution of a tumor or tissue differentiation. ProbFAST server can be accessed at http://gdm.fmrp.usp.br/probfast.
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Affiliation(s)
- Israel T Silva
- Department of Genetics, Faculty of Medicine, University of São Paulo, Ribeirão Preto, Brazil.
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Domingos ALB, Granzotto LA, Belini Junior E, Oliveira TYK, Domingos ACB, Bonini-Domingos CR. Perfil de beta talassemia heterozigota obtido a partir de análise data mining em banco de dados. Rev Bras Hematol Hemoter 2010. [DOI: 10.1590/s1516-84842010000100018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Chiromatzo AO, Oliveira TYK, Pereira G, Costa AY, Montesco CAE, Gras DE, Yosetake F, Vilar JB, Cervato M, Prado PRR, Cardenas RGCCL, Cerri R, Borges RL, Lemos RN, Alvarenga SM, Perallis VRC, Pinheiro DG, Silva IT, Brandão RM, Cunha MAV, Giuliatti S, Silva WA. miRNApath: a database of miRNAs, target genes and metabolic pathways. Genet Mol Res 2007; 6:859-865. [PMID: 18058708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs that regulate target gene expression and hence play important roles in metabolic pathways. Recent studies have evidenced the interrelation of miRNAs with cell proliferation, differentiation, development, and diseases. Since they are involved in gene regulation, they are intrinsically related to metabolic pathways. This leads to questions that are particularly interesting for investigating medical and laboratorial applications. We developed an miRNApath online database that uses miRNA target genes to link miRNAs to metabolic pathways. Currently, databases about miRNA target genes (DIANA miRGen), genomic maps (miRNAMap) and sequences (miRBase) do not provide such correlations. Additionally, miRNApath offers five search services and a download area. For each search, there is a specific type of input, which can be a list of target genes, miRNAs, or metabolic pathways, which results in different views, depending upon the input data, concerning relationships between the target genes, miRNAs and metabolic pathways. There are also internal links that lead to a deeper analysis and cross-links to other databases with more detailed information. miRNApath is being continually updated and is available at http://lgmb.fmrp.usp.br/mirnapath.
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Affiliation(s)
- A O Chiromatzo
- Departamento de Genética, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brasil.
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