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da Silva-Júnior RMP, Bueno AC, Martins CS, Coelli-Lacchini F, Okanobo Ozaki JG, de Almeida E Silva DC, Marrero-Gutiérrez J, Dos Santos AC, Garcia-Peral C, Machado HR, Volpon Dos Santos M, Elias PL, Moreira AC, Colli LM, Vêncio RZN, Antonini SR, de Castro M. Integrating methylome and transcriptome signatures expands the molecular classification of the pituitary tumors. J Clin Endocrinol Metab 2022; 108:1452-1463. [PMID: 36504388 DOI: 10.1210/clinem/dgac703] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 10/31/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
PURPOSE To explore pituitary tumors by methylome and transcriptome signatures in a heterogeneous ethnic population. DESIGN Retrospective cross-sectional study. PATIENTS AND METHODS Clinicopathological features, methylome and transcriptome were evaluated in pituitary tumors from 77 patients (61% women, age: 12-72 years) followed due to functioning (FPT: GH-secreting n = 18, ACTH-secreting n = 14) and non-functioning pituitary tumors (NFPT, n = 45) at Ribeirao Preto Medical School, University of Sao Paulo. RESULTS Unsupervised hierarchical clustering analysis (UHCA) of methylome (n = 77) and transcriptome (n = 65 out of 77) revealed three clusters each: one enriched by FPT, other by NFPT, and another by ACTH-secreting and NFPT. Comparison between each omics-derived clusters identified 3,568 and 5,994 differentially methylated and expressed genes, respectively, which were associated with each other, with tumor clinical presentation, and with 2017 and 2022 WHO classifications. UHCA considering 11 transcripts related to pituitary development/differentiation also supported three clusters: POU1F1-driven somatotroph, TBX19-driven corticotroph, and NR5A1-driven gonadotroph adenomas, with rare exceptions (NR5A1 expressed in few GH-secreting and corticotroph-silent adenomas; POU1F1 in few ACTH-secreting adenomas; and TBX19 in few NFPTs). CONCLUSIONS This large heterogenic ethnic Brazilian cohort confirms that integrated methylome and transcriptome signatures classify FPT and NFPT, which are associated with clinical presentation and tumor invasiveness. Moreover, the cluster NFPT/ACTH-secreting adenomas raises interest regarding tumor heterogeneity, supporting the challenge raised by the 2017 and 2022 WHO definition regarding the discrepancy, in rare cases, between clinical presentation and pituitary lineage markers. Finally, making our data publicly available enables further studies to validate genes/pathways involved in pituitary tumor pathogenesis and prognosis.
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Affiliation(s)
| | - Ana Carolina Bueno
- Department of Pediatrics, University of São Paulo, Ribeirao Preto, SP, Brazil
| | | | | | | | - Danillo Cunha de Almeida E Silva
- Department of Computation and Mathematics Biology, Faculty of Philosophy, Sciences and Letters at Ribeirao Preto, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Junier Marrero-Gutiérrez
- Department of Medical Imaging, Hematology, and Oncology, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Antônio Carlos Dos Santos
- Department of Medical Imaging, Hematology, and Oncology, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Carlos Garcia-Peral
- Institute of Neuroscience of Castilla y León, University of Salamanca, Salamanca, Spain
| | - Hélio Rubens Machado
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Marcelo Volpon Dos Santos
- Department of Surgery and Anatomy, Ribeirao Preto Medical School, University of São Paulo, Ribeirao Preto, SP, Brazil
| | | | - Ayrton C Moreira
- Department of Internal Medicine, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Leandro M Colli
- Department of Medical Imaging, Hematology, and Oncology, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Ricardo Z N Vêncio
- Department of Computation and Mathematics Biology, Faculty of Philosophy, Sciences and Letters at Ribeirao Preto, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Sonir R Antonini
- Department of Pediatrics, University of São Paulo, Ribeirao Preto, SP, Brazil
| | - Margaret de Castro
- Department of Internal Medicine, University of São Paulo, Ribeirao Preto, SP, Brazil
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Neri de Souza Reis V, Tahira AC, Daguano Gastaldi V, Mari P, Portolese J, Feio dos Santos AC, Lisboa B, Mari J, Caetano SC, Brunoni D, Bordini D, Silvestre de Paula C, Vêncio RZN, Quackenbush J, Brentani H. Environmental Influences Measured by Epigenetic Clock and Vulnerability Components at Birth Impact Clinical ASD Heterogeneity. Genes (Basel) 2021; 12:genes12091433. [PMID: 34573415 PMCID: PMC8467464 DOI: 10.3390/genes12091433] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 11/16/2022] Open
Abstract
Although Autism Spectrum Disorders (ASD) is recognized as being heavily influenced by genetic factors, the role of epigenetic and environmental factors is still being established. This study aimed to identify ASD vulnerability components based on familial history and intrauterine environmental stress exposure, explore possible vulnerability subgroups, access DNA methylation age acceleration (AA) as a proxy of stress exposure during life, and evaluate the association of ASD vulnerability components and AA to phenotypic severity measures. Principal Component Analysis (PCA) was used to search the vulnerability components from 67 mothers of autistic children. We found that PC1 had a higher correlation with psychosocial stress (maternal stress, maternal education, and social class), and PC2 had a higher correlation with biological factors (psychiatric family history and gestational complications). Comparing the methylome between above and below PC1 average subgroups we found 11,879 statistically significant differentially methylated probes (DMPs, p < 0.05). DMPs CpG sites were enriched in variably methylated regions (VMRs), most showing environmental and genetic influences. Hypermethylated probes presented higher rates in different regulatory regions associated with functional SNPs, indicating that the subgroups may have different affected regulatory regions and their liability to disease explained by common variations. Vulnerability components score moderated by epigenetic clock AA was associated with Vineland Total score (p = 0.0036, adjR2 = 0.31), suggesting risk factors with stress burden can influence ASD phenotype.
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Affiliation(s)
- Viviane Neri de Souza Reis
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Ana Carolina Tahira
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
- Instituto Butantan, São Paulo 05503-900, SP, Brazil
| | - Vinícius Daguano Gastaldi
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Paula Mari
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Joana Portolese
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Ana Cecilia Feio dos Santos
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
- Laboratório de Pesquisas Básicas em Malária—Entomologia, Seção de Parasitologia—Instituto Evandro Chagas/SVS/MS, Ananindeua 66093-020, PA, Brazil
| | - Bianca Lisboa
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
| | - Jair Mari
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
| | - Sheila C. Caetano
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
| | - Décio Brunoni
- Centro de Ciências Biológicas e da Saúde, Universidade Presbiteriana Mackenzie (UPM), São Paulo 01302-907, SP, Brazil;
| | - Daniela Bordini
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
| | - Cristiane Silvestre de Paula
- Departamento de Psiquiatria, Universidade Federal de São Paulo (UNIFESP), São Paulo 04023-062, SP, Brazil; (J.M.); (S.C.C.); (D.B.); (C.S.d.P.)
- Centro de Ciências Biológicas e da Saúde, Universidade Presbiteriana Mackenzie (UPM), São Paulo 01302-907, SP, Brazil;
| | - Ricardo Z. N. Vêncio
- Departamento de Computação e Matemática FFCLRP-USP, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil;
| | - John Quackenbush
- Center for Cancer Computational Biology, Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; or
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Helena Brentani
- Departamento & Instituto de Psiquiatria, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo 05403-903, SP, Brazil; (V.N.d.S.R.); (A.C.T.); (V.D.G.); (P.M.); (J.P.); (A.C.F.d.S.); (B.L.)
- Correspondence: ; Tel.: +55-(11)-99-931-4349
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Ibrahim AGAER, Vêncio RZN, Lorenzetti APR, Koide T. Halobacterium salinarum and Haloferax volcanii Comparative Transcriptomics Reveals Conserved Transcriptional Processing Sites. Genes (Basel) 2021; 12:genes12071018. [PMID: 34209065 PMCID: PMC8303175 DOI: 10.3390/genes12071018] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/25/2021] [Accepted: 05/27/2021] [Indexed: 01/15/2023] Open
Abstract
Post-transcriptional processing of messenger RNA is an important regulatory strategy that allows relatively fast responses to changes in environmental conditions. In halophile systems biology, the protein perspective of this problem (i.e., ribonucleases which implement the cleavages) is generally more studied than the RNA perspective (i.e., processing sites). In the present in silico work, we mapped genome-wide transcriptional processing sites (TPS) in two halophilic model organisms, Halobacterium salinarum NRC-1 and Haloferax volcanii DS2. TPS were established by reanalysis of publicly available differential RNA-seq (dRNA-seq) data, searching for non-primary (monophosphorylated RNAs) enrichment. We found 2093 TPS in 43% of H. salinarum genes and 3515 TPS in 49% of H. volcanii chromosomal genes. Of the 244 conserved TPS sites found, the majority were located around start and stop codons of orthologous genes. Specific genes are highlighted when discussing antisense, ribosome and insertion sequence associated TPS. Examples include the cell division gene ftsZ2, whose differential processing signal along growth was detected and correlated with post-transcriptional regulation, and biogenesis of sense overlapping transcripts associated with IS200/IS605. We hereby present the comparative, transcriptomics-based processing site maps with a companion browsing interface.
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Affiliation(s)
- Amr Galal Abd El-Raheem Ibrahim
- Department of Computation and Mathematics, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil; (A.G.A.E.-R.I.); (R.Z.N.V.)
| | - Ricardo Z. N. Vêncio
- Department of Computation and Mathematics, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil; (A.G.A.E.-R.I.); (R.Z.N.V.)
| | - Alan P. R. Lorenzetti
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil;
| | - Tie Koide
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto 14040-900, Brazil;
- Correspondence: ; Tel.: +55-16-3315-3107
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Bueno AC, Stecchini MF, de Lima Neto DF, Coeli-Lacchini FB, Ramalho LNZ, Moreira AC, Brandalise S, Yunes A, Castro MD, Vêncio RZN, Antonini SRR. SAT-LB36 Distinct Vitamin D Receptor DNA Methylation Profiles Are Associated With the Outcome of Pediatric Patients With Adrenocortical Tumors. J Endocr Soc 2020. [PMCID: PMC7208805 DOI: 10.1210/jendso/bvaa046.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Pediatric adrenocortical tumors (pACT) are rare, display complex genomic background and lack robust prognostic markers. Very recently, distinct genomic methylation profiles of pACT were associated with prognosis. The vitamin D receptor (VDR) was shown to be underexpressed in ACT, especially in carcinomas (ACC). In adult ACC, VDR inactivation by methylation was demonstrated. On the other hand, VDR activation was shown to inhibit ACC proliferation in vitro and in vivo. Aim: To evaluate VDR DNA methylation profile and its clinical and prognostic significance in pediatric ACT. Methods: Genomic DNA methylation from 57 pACTs [40 girls; median age: 2.1 (0.2-16.4) years] was assessed using Infininium Methylation EPIC BeadChip Array. Unsupervised hierarchical clustering analysis (Ward method, R Stats Package) was performed considering the M-values of the 49 probes targeting the whole extension of VDR gene contained in the array. Clinical, histopathological and molecular features, as well as pACT VDR mRNA levels (qPCR) and nuclear immunoreactivity (IHC) were used for association analysis. Results: Hierarchical clustering identified three clusters of pACT. Methylated VDR-targeted probes (M-values different from 0; n=37) composed the VDR methylation profile, which differed significantly between the clusters [M-values: C1=1.77 (1.1-1.9) (low), C2=2.15 (1.7-2.7) (intermediate), and C3=2.65 (2.2-3.1) (high); p<0.0001]. The C1 cluster comprised a set of patients with favorable outcome (n=18), who were younger (p=0.035), did not present metastasis at diagnosis (IPACTR stage IV) or after surgery, nor were diagnosed with carcinomas (Wieneke criteria >=4), were not carriers of somatic Beta-catenin activating mutations, or died. Although cluster C2 patients (n=21) presented intermediary disease features, only 2 patients died and the overall outcome was positive. Instead, the C3 cluster concentrated patients (n=18) with non-localized/metastatic disease (IPACTR stages I/II vs. III/IV; p=0.004), post-surgical metastasis/recurrence (p=0.009), and patients who needed adjuvant chemotherapy (p=0.005). Moreover, C3 patients had lower overall and disease-free survival rates (log-rank: p=0.001 and p=0.014, respectively). VDR methylation was not associated with sex, clinical presentation, P53 mutations, nor with tumor VDR mRNA expression or nuclear immunoreactivity. Conclusions: Three VDR methylation profiles were associated with distinct pACT clinical features and outcome. High VDR methylation was associated with worst outcome. Fully functioning VDR may play a beneficial role against pediatric adrenocortical tumorigenesis. This finding highlights the potential of targeting VDR as an adjuvant therapeutic target.
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Affiliation(s)
- Ana Carolina Bueno
- Ribeirao Preto Medical School - University of Sao Paulo, Ribeirao Preto, Brazil
| | | | | | | | - Leandra N Z Ramalho
- Ribeirao Preto Medical School - University of Sao Paulo, Ribeirao Preto, Brazil
| | | | - Silvia Brandalise
- Boldrini Children’s Center - State University of Campinas, Campinas, Brazil
| | - Andres Yunes
- Boldrini Children’s Center - State University of Campinas, Campinas, Brazil
| | - Margaret De Castro
- Ribeirao Preto Medical School - University of Sao Paulo, Ribeirao Preto, Brazil
| | - Ricardo Z N Vêncio
- Computation and Mathematics, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto - University of Sao Paulo, Ribeirao Preto, Brazil
| | - Sonir R R Antonini
- Ribeirao Preto Medical School - University of Sao Paulo, Ribeirao Preto, Brazil
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Kanan AD, Corey E, Vêncio RZN, Ishwar A, Liu AY. Lineage relationship between prostate adenocarcinoma and small cell carcinoma. BMC Cancer 2019; 19:518. [PMID: 31146720 PMCID: PMC6543672 DOI: 10.1186/s12885-019-5680-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/07/2019] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Prostate cancer displays different morphologies which, in turn, affect patient outcome. This fact prompted questions about the lineage relationship between differentiated, more treatable prostate adenocarcinoma and poorly differentiated, less treatable non-adenocarcinoma including small cell carcinoma, and the molecular mechanism underlying prostate cancer differentiation. METHODS Newly available non-adenocarcinoma/small cell carcinoma PDX LuCaP lines were analyzed for expression of stem cell transcription factors (scTF) LIN28A, NANOG, POU5F1, SOX2, which are responsible for reprogramming or de-differentiation. cDNA of these genes were cloned from small cell carcinoma LuCaP 145.1 into expression vectors to determine if they could function in reprogramming. RESULTS Expression of scTF was detected in small cell carcinoma LuCaP 93, 145.1, 145.2, and non-adenocarcinoma LuCaP 173.1, 173.2A. Transfection of scTF from LuCaP 145.1 altered the gene expression of prostate non-small cell carcinoma cells, as well as fibroblasts. The resultant cells grew in stem-like colonies. Of note was a 10-fold lower expression of B2M in the transfected cells. Low B2M was also characteristic of LuCaP 145.1. Conversely, B2M was increased when stem cells were induced to differentiate. CONCLUSIONS This work suggested a pathway in the emergence of non-adenocarcinoma/small cell carcinoma from adenocarcinoma through activation of scTF genes that produced cancer de-differentiation.
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Affiliation(s)
- Adelle D Kanan
- Department of Urology, University of Washington, Box 358056, 850 Republican Street, Seattle, Washington, 98195-6100, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA.
| | - Eva Corey
- Department of Urology, University of Washington, Box 358056, 850 Republican Street, Seattle, Washington, 98195-6100, USA
| | - Ricardo Z N Vêncio
- Department of Mathematics, University of Sao Paulo, 3900 Ave Bandeirantes, Vila Monte Alegre, Ribeirão Preto, 14040-900, Brazil
| | - Arjun Ishwar
- Thermo Fisher Scientific, 168 3rd Ave, Waltham, Massachutts, 02451, USA
- Sophia Genetics, 1550 E Campbell Ave. #4032, Phoenix, Arizona, 85014, USA
| | - Alvin Y Liu
- Department of Urology, University of Washington, Box 358056, 850 Republican Street, Seattle, Washington, 98195-6100, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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Ten-Caten F, Vêncio RZN, Lorenzetti APR, Zaramela LS, Santana AC, Koide T. Internal RNAs overlapping coding sequences can drive the production of alternative proteins in archaea. RNA Biol 2018; 15:1119-1132. [PMID: 30175688 PMCID: PMC6161675 DOI: 10.1080/15476286.2018.1509661] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Prokaryotic genomes show a high level of information compaction often with different molecules transcribed from the same locus. Although antisense RNAs have been relatively well studied, RNAs in the same strand, internal RNAs (intraRNAs), are still poorly understood. The question of how common is the translation of overlapping reading frames remains open. We address this question in the model archaeon Halobacterium salinarum. In the present work we used differential RNA-seq (dRNA-seq) in H. salinarum NRC-1 to locate intraRNA signals in subsets of internal transcription start sites (iTSS) and establish the open reading frames associated to them (intraORFs). Using C-terminally flagged proteins, we experimentally observed isoforms accurately predicted by intraRNA translation for kef1, acs3 and orc4 genes. We also recovered from the literature and mass spectrometry databases several instances of protein isoforms consistent with intraRNA translation such as the gas vesicle protein gene gvpC1. We found evidence for intraRNAs in horizontally transferred genes such as the chaperone dnaK and the aerobic respiration related cydA in both H. salinarum and Escherichia coli. Also, intraRNA translation evidence in H. salinarum, E. coli and yeast of a universal elongation factor (aEF-2, fusA and eEF-2) suggests that this is an ancient phenomenon present in all domains of life.
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Affiliation(s)
- Felipe Ten-Caten
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ricardo Z N Vêncio
- b Department of Computation and Mathematics, Faculdade de Filosofia , Ciências e Letras de Ribeirão Preto, University of São Paulo , Ribeirão Preto , Brazil
| | - Alan Péricles R Lorenzetti
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Livia Soares Zaramela
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Ana Carolina Santana
- c Department of Cell and Molecular Biology and Pathogenic Bioagents , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
| | - Tie Koide
- a Department of Biochemistry and Immunology , Ribeirão Preto Medical School, University of São Paulo , Ribeirão Preto , Brazil
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Borges GT, Vêncio EF, Quek SI, Chen A, Salvanha DM, Vêncio RZN, Nguyen HM, Vessella RL, Cavanaugh C, Ware CB, Troisch P, Liu AY. Conversion of Prostate Adenocarcinoma to Small Cell Carcinoma-Like by Reprogramming. J Cell Physiol 2016; 231:2040-7. [PMID: 26773436 DOI: 10.1002/jcp.25313] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/14/2022]
Abstract
The lineage relationship between prostate adenocarcinoma and small cell carcinoma was studied by using the LuCaP family of xenografts established from primary neoplasm to metastasis. Expression of four stem cell transcription factor (TF) genes, LIN28A, NANOG, POU5F1, SOX2, were analyzed in the LuCaP lines. These genes, when force expressed in differentiated cells, can reprogram the recipients into stem-like induced pluripotent stem (iPS) cells. Most LuCaP lines expressed POU5F1, while LuCaP 145.1, representative of small cell carcinoma, expressed all four. Through transcriptome database query, many small cell carcinoma genes were also found in stem cells. To test the hypothesis that prostate cancer progression from "differentiated" adenocarcinoma to "undifferentiated" small cell carcinoma could involve re-expression of stem cell genes, the four TF genes were transduced via lentiviral vectors into five adenocarcinoma LuCaP lines-70CR, 73CR, 86.2, 92, 105CR-as done in iPS cell reprogramming. The resultant cells from these five transductions displayed a morphology of small size and dark appearing unlike the parentals. Transcriptome analysis of LuCaP 70CR* ("*" to denote transfected progeny) revealed a unique gene expression close to that of LuCaP 145.1. In a prostate principal components analysis space based on cell-type transcriptomes, the different LuCaP transcriptome datapoints were aligned to suggest a possible ordered sequence of expression changes from the differentiated luminal-like adenocarcinoma cell types to the less differentiated, more stem-like small cell carcinoma types, and LuCaP 70CR*. Prostate cancer progression can thus be molecularly characterized by loss of differentiation with re-expression of stem cell genes. J. Cell. Physiol. 231: 2040-2047, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Gisely T Borges
- Department of Urology, University of Washington, Seattle, Washington.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.,Pharmacy School, Federal University of Goiás, Goiânia, Brazil
| | - Eneida F Vêncio
- Department of Urology, University of Washington, Seattle, Washington.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.,Department of Oral Pathology, Dental School, Federal University of Goiás, Goiânia, Brazil
| | - Sue-Ing Quek
- Department of Urology, University of Washington, Seattle, Washington.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Adeline Chen
- Department of Urology, University of Washington, Seattle, Washington.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Diego M Salvanha
- Department of Computing and Mathematics, FFCLRP, University of São Paulo, São Paulo, Brazil
| | - Ricardo Z N Vêncio
- Department of Computing and Mathematics, FFCLRP, University of São Paulo, São Paulo, Brazil
| | - Holly M Nguyen
- Department of Urology, University of Washington, Seattle, Washington
| | - Robert L Vessella
- Department of Urology, University of Washington, Seattle, Washington.,Puget Sound VA Medical Center, Seattle, Washington
| | - Christopher Cavanaugh
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.,Department of Comparative Medicine, University of Washington, Seattle, Washington
| | - Carol B Ware
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington.,Department of Comparative Medicine, University of Washington, Seattle, Washington
| | | | - Alvin Y Liu
- Department of Urology, University of Washington, Seattle, Washington.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
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Gomes-Filho JV, Zaramela LS, Italiani VCDS, Baliga NS, Vêncio RZN, Koide T. Sense overlapping transcripts in IS1341-type transposase genes are functional non-coding RNAs in archaea. RNA Biol 2016; 12:490-500. [PMID: 25806405 PMCID: PMC4615843 DOI: 10.1080/15476286.2015.1019998] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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] [Indexed: 01/08/2023] Open
Abstract
The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional.
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Affiliation(s)
- José Vicente Gomes-Filho
- a Department of Biochemistry and Immunology ; Ribeirão Preto Medical School ; University of São Paulo ; Ribeirão Preto , Brazil
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Quek SI, Wong OM, Chen A, Borges GT, Ellis WJ, Salvanha DM, Vêncio RZN, Weaver B, Ench YM, Leach RJ, Thompson IM, Liu AY. Processing of voided urine for prostate cancer RNA biomarker analysis. Prostate 2015; 75:1886-95. [PMID: 26306723 DOI: 10.1002/pros.23066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 08/06/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Voided urine samples have been shown to contain cells released from prostate tumors. Could good quality RNA from cells in urine be obtained from every donor for multimarker analysis? In addition, could urine donation be as simple as possible, a practical consideration for a lab test, without involving a prostate massage (as indicated for PCA3 testing), which precludes frequent collection; needing it done at a specific time of day (e.g., first or second urine); and requiring prompt processing of samples in clinics with limited molecular biology capability? METHODS Collected urine samples were pelleted, and the RNA isolated was processed for cDNA synthesis and in vitro transcription to generate amplified sense aRNA. The resultant aRNA was rigorously analyzed for possible introduced changes. DMSO was used as a cell preservative for frozen storage of urine samples. RESULTS Good quality aRNA was obtained for over 100 samples collected at two different institutions. The process of RNA amplification removed co-isolated DNA in some samples, which did not affect RNA amplification. Amplification did not amplify genes that were absent and produce other expression alterations. The sense aRNA could be used to generate urinary transcriptomes specific to individual patients. No chaotropic agents for RNA preservation were added to the urine samples so that the supernatant could be used for analysis of secreted protein biomarkers. The time of donation was not important since patients were seen during the entire day. DMSO was an effective cell preservative for freezing urine. CONCLUSIONS Urinary RNA can be readily isolated and amplified for prostate cancer biomarker analysis. Individual patients had unique set of transcripts derived from their tumor.
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Affiliation(s)
- Sue-Ing Quek
- Department of Urology, University of Washington, Seattle, Washington
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Olivia M Wong
- Department of Urology, University of Washington, Seattle, Washington
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Adeline Chen
- Department of Urology, University of Washington, Seattle, Washington
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - Gisely T Borges
- Department of Urology, University of Washington, Seattle, Washington
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
| | - William J Ellis
- Department of Urology, University of Washington, Seattle, Washington
| | - Diego M Salvanha
- Department of Computation and Mathematics, University of São Paulo at Riberão Preto, Brazil
| | - Ricardo Z N Vêncio
- Department of Computation and Mathematics, University of São Paulo at Riberão Preto, Brazil
| | - Brandi Weaver
- Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Yasmin M Ench
- Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Robin J Leach
- Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Ian M Thompson
- Department of Urology and The Cancer Therapy and Research Center, The University of Texas Health Science Center at San Antonio, San Antonio, Texas
| | - Alvin Y Liu
- Department of Urology, University of Washington, Seattle, Washington
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington
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Abstract
Gene expression studies are generally performed through multi-step analysis processes, which require the integrated use of a number of analysis tools. In order to facilitate tool/data integration, an increasing number of analysis tools have been developed as or adapted to semantic web services. In recent years, some approaches have been defined for the development and semantic annotation of web services created from legacy software tools, but these approaches still present many limitations. In addition, to the best of our knowledge, no suitable approach has been defined for the functional genomics domain. Therefore, this paper aims at defining an integrated methodology for the implementation of RESTful semantic web services created from gene expression analysis tools and the semantic annotation of such services. We have applied our methodology to the development of a number of services to support the analysis of different types of gene expression data, including microarray and RNASeq. All developed services are publicly available in the Gene Expression Analysis Services (GEAS) Repository at http://dcm.ffclrp.usp.br/lssb/geas. Additionally, we have used a number of the developed services to create different integrated analysis scenarios to reproduce parts of two gene expression studies documented in the literature. The first study involves the analysis of one-color microarray data obtained from multiple sclerosis patients and healthy donors. The second study comprises the analysis of RNA-Seq data obtained from melanoma cells to investigate the role of the remodeller BRG1 in the proliferation and morphology of these cells. Our methodology provides concrete guidelines and technical details in order to facilitate the systematic development of semantic web services. Moreover, it encourages the development and reuse of these services for the creation of semantically integrated solutions for gene expression analysis.
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Affiliation(s)
- Gabriela D. A. Guardia
- Department of Computer Science and Mathematics—Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP)—University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Luís Ferreira Pires
- Faculty of Electrical Engineering, Mathematics and Computer Science—University of Twente, Enschede, the Netherlands
| | - Ricardo Z. N. Vêncio
- Department of Computer Science and Mathematics—Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP)—University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Kelen C. R. Malmegrim
- Department of Clinical, Toxicological and Bromatological Analysis—Faculty of Pharmaceutical Sciences of Ribeirão Preto—University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Cléver R. G. de Farias
- Department of Computer Science and Mathematics—Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP)—University of São Paulo (USP), Ribeirão Preto, Brazil
- * E-mail:
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Abstract
Prostate cancer progression is characterized by tumor dedifferentiation. Cancer cells of less differentiated tumors have a gene expression/transcriptome more similar to that of stem cells. In dedifferentiation, cancer cells may follow a specific program of gene expression changes to a stem-like state. In order to treat cancer effectively, the stem-like cancer cells and cancer differentiation pathway need to be identified and studied. Due to the very low abundance of stem-like cancer cells, their isolation from fresh human tumors is technically challenging. Induced pluripotent stem cell technology can reprogram differentiated cells into stem-like, and this may be a tool to generate sufficient stem-like cancer cells.
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Affiliation(s)
- Gisely T Borges
- School of Pharmacology, Federal University of Goiás, Goiânia, Brazil,
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Ernst M, Silva DB, Silva R, Monge M, Semir J, Vêncio RZN, Lopes NP. A metabolomic protocol for plant systematics by matrix-assisted laser-desorption/ionization time-of flight mass spectrometry. Anal Chim Acta 2015; 859:46-58. [PMID: 25622605 DOI: 10.1016/j.aca.2015.01.002] [Citation(s) in RCA: 6] [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: 05/30/2014] [Revised: 12/25/2014] [Accepted: 01/01/2015] [Indexed: 01/05/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of flight mass spectrometry (MALDI-TOF MS) has been widely used for the identification and classification of microorganisms based on their proteomic fingerprints. However, the use of MALDI-TOF MS in plant research has been very limited. In the present study, a first protocol is proposed for metabolic fingerprinting by MALDI-TOF MS using three different MALDI matrices with subsequent multivariate data analysis by in-house algorithms implemented in the R environment for the taxonomic classification of plants from different genera, families and orders. By merging the data acquired with different matrices, different ionization modes and using careful algorithms and parameter selection, we demonstrate that a close taxonomic classification can be achieved based on plant metabolic fingerprints, with 92% similarity to the taxonomic classifications found in literature. The present work therefore highlights the great potential of applying MALDI-TOF MS for the taxonomic classification of plants and, furthermore, provides a preliminary foundation for future research.
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Affiliation(s)
- Madeleine Ernst
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Denise B Silva
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Ricardo Silva
- Department of Computing and Mathematics, FFCLRP, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Marcelo Monge
- Department of Plant Biology, Institute of Biology, UNICAMP, CP 6109, 13083-970 Campinas, SP, Brazil
| | - João Semir
- Department of Plant Biology, Institute of Biology, UNICAMP, CP 6109, 13083-970 Campinas, SP, Brazil
| | - Ricardo Z N Vêncio
- Department of Computing and Mathematics, FFCLRP, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, São Paulo, Brazil
| | - Norberto P Lopes
- Núcleo de Pesquisa em Produtos Naturais e Sintéticos, Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences, University of São Paulo, Av. do Café, s/n, 14040-903 Ribeirão Preto, São Paulo, Brazil.
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Zaramela LS, Vêncio RZN, ten-Caten F, Baliga NS, Koide T. Transcription start site associated RNAs (TSSaRNAs) are ubiquitous in all domains of life. PLoS One 2014; 9:e107680. [PMID: 25238539 PMCID: PMC4169567 DOI: 10.1371/journal.pone.0107680] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 08/18/2014] [Indexed: 01/06/2023] Open
Abstract
A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in both eukaryotes and bacteria. Here, we provide evidence for existence of TSSaRNAs in several archaeal transcriptomes including: Halobacterium salinarum, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus. We validated TSSaRNAs from the model archaeon Halobacterium salinarum NRC-1 by deep sequencing two independent small-RNA enriched (RNA-seq) and a primary-transcript enriched (dRNA-seq) strand-specific libraries. We identified 652 transcripts, of which 179 were shown to be primary transcripts (∼7% of the annotated genome). Distinct growth-associated expression patterns between TSSaRNAs and their cognate genes were observed, indicating a possible role in environmental responses that may result from RNA polymerase with varying pausing rhythms. This work shows that TSSaRNAs are ubiquitous across all domains of life.
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Affiliation(s)
- Livia S. Zaramela
- Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Ricardo Z. N. Vêncio
- Department of Computing and Mathematics, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe ten-Caten
- Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Nitin S. Baliga
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Tie Koide
- Department Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
- * E-mail:
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Silva RR, Jourdan F, Salvanha DM, Letisse F, Jamin EL, Guidetti-Gonzalez S, Labate CA, Vêncio RZN. ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. ACTA ACUST UNITED AC 2014; 30:1336-7. [PMID: 24443383 PMCID: PMC3998140 DOI: 10.1093/bioinformatics/btu019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Summary: We present ProbMetab, an R package that promotes substantial improvement in automatic probabilistic liquid chromatography–mass spectrometry-based metabolome annotation. The inference engine core is based on a Bayesian model implemented to (i) allow diverse source of experimental data and metadata to be systematically incorporated into the model with alternative ways to calculate the likelihood function and (ii) allow sensitive selection of biologically meaningful biochemical reaction databases as Dirichlet-categorical prior distribution. Additionally, to ensure result interpretation by system biologists, we display the annotation in a network where observed mass peaks are connected if their candidate metabolites are substrate/product of known biochemical reactions. This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand-alone versions. Availability and implementation: ProbMetab was implemented in a modular manner to fit together with established upstream (xcms, CAMERA, AStream, mzMatch.R, etc) and downstream R package tools (GeneNet, RCytoscape, DiffCorr, etc). ProbMetab, along with extensive documentation and case studies, is freely available under GNU license at: http://labpib.fmrp.usp.br/methods/probmetab/. Contact:rvencio@usp.br Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ricardo R Silva
- LabPIB, Department of Computing and Mathematics FFCLRP-USP, University of Sao Paulo, Ribeirao Preto, Brazil, INRA UMR1331, Toxalim, Research Centre in Food Toxicology, Universit de Toulouse, INSA, UPS, INP; LISBP, Toulouse, France, Institute for Systems Biology, Seattle, Washington, USA, CNRS, UMR5504, Toulouse, France, Department of Genetics ESALQ-USP, University of Sao Paulo, Piracicaba, Brazil and Laboratorio Nacional de Ciencia e Tecnologia do Bioetanol CTBE, Campinas, Brazil
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15
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Ernst M, Silva DB, Silva RR, Vêncio RZN, Lopes NP. Mass spectrometry in plant metabolomics strategies: from analytical platforms to data acquisition and processing. Nat Prod Rep 2014; 31:784-806. [DOI: 10.1039/c3np70086k] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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16
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Miyazaki FA, Guardia GDA, Vêncio RZN, de Farias CRG. Semantic integration of gene expression analysis tools and data sources using software connectors. BMC Genomics 2013; 14 Suppl 6:S2. [PMID: 24341380 PMCID: PMC3908368 DOI: 10.1186/1471-2164-14-s6-s2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heterogeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. RESULTS We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. CONCLUSIONS The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.
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Abstract
Background Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology.
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Affiliation(s)
- Gabriela D A Guardia
- Department of Computer Science and Mathematics, DCM/FFCLRP, University of Sao Paulo Av Bandeirantes, 3900 Monte Alegre Ribeirao Preto, SP 14040-901, Brazil.
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Vêncio EF, Nelson AM, Cavanaugh C, Ware CB, Milller DG, Garcia JCO, Vêncio RZN, Loprieno MA, Liu AY. Reprogramming of prostate cancer-associated stromal cells to embryonic stem-like. Prostate 2012; 72:1453-63. [PMID: 22314551 DOI: 10.1002/pros.22497] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Accepted: 01/11/2012] [Indexed: 02/06/2023]
Abstract
BACKGROUND CD90(+) prostate cancer-associated (CP) stromal cells represent a diseased cell type found only in tumor tissue. They differ from their normal counterpart in gene expression and inductive signaling. Genetic reprogramming by induced pluripotent stem (iPS) cell technology can effectively change adult cells into stem-like cells through wholesale alteration of the gene expression program. This technology might be used to 'erase' the abnormal gene expression of diseased cells. The resultant iPS cells would no longer express the disease phenotype, and behave like stem cells. METHODS CP stromal cells, isolated from tumor tissue of a surgically resected prostate by anti-CD90-mediated sorting and cultured in vitro, were transfected with in vitro packaged lentiviral expression vectors containing stem cell transcription factor genes POU5F1, LIN28, NANOG, and SOX2. RESULTS Alkaline phosphatase-positive iPS cells were obtained in about 3 weeks post-transfection at a frequency of 10(-4) . Their colony morphology was indistinguishable from that of human embryonic stem (ES) cells. Transcriptome analysis showed a virtually complete match in gene expression between the iPS and ES cells. CONCLUSIONS Genes of CP stromal cells could be fully inactivated by genetic reprogramming. As a consequence, the disease phenotype was 'cured'.
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Affiliation(s)
- Eneida F Vêncio
- Department of Urology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
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Liu AY, Vêncio RZN, Page LS, Ho ME, Loprieno MA, True LD. Bladder expression of CD cell surface antigens and cell-type-specific transcriptomes. Cell Tissue Res 2012; 348:589-600. [PMID: 22427119 DOI: 10.1007/s00441-012-1383-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2011] [Accepted: 02/23/2012] [Indexed: 12/13/2022]
Abstract
Many cell types have no known functional attributes. In the bladder and prostate, basal epithelial and stromal cells appear similar in cytomorphology and share several cell surface markers. Their total gene expression (transcriptome) should provide a clear measure of the extent to which they are alike functionally. Since urologic stromal cells are known to mediate organ-specific tissue formation, these cells in cancers might exhibit aberrant gene expression affecting their function. For transcriptomes, cluster designation (CD) antigens have been identified for cell sorting. The sorted cell populations can be analyzed by DNA microarrays. Various bladder cell types have unique complements of CD molecules. CD9(+) urothelial, CD104(+) basal and CD13(+) stromal cells of the lamina propria were therefore analyzed, as were CD9(+) cancer and CD13(+) cancer-associated stromal cells. The transcriptome datasets were compared by principal components analysis for relatedness between cell types; those with similarity in gene expression indicated similar function. Although bladder and prostate basal cells shared CD markers such as CD104, CD44 and CD49f, they differed in overall gene expression. Basal cells also lacked stem cell gene expression. The bladder luminal and stromal transcriptomes were distinct from their prostate counterparts. In bladder cancer, not only the urothelial but also the stromal cells showed gene expression alteration. The cancer process in both might thus involve defective stromal signaling. These cell-type transcriptomes provide a means to monitor in vitro models in which various CD-isolated cell types can be combined to study bladder differentiation and bladder tumor development based on cell-cell interaction.
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Affiliation(s)
- Alvin Y Liu
- Department of Urology and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195, USA.
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Pascal LE, Ai J, Vêncio RZN, Vêncio EF, Zhou Y, Page LS, True LD, Wang Z, Liu AY. Differential Inductive Signaling of CD90 Prostate Cancer-Associated Fibroblasts Compared to Normal Tissue Stromal Mesenchyme Cells. Cancer Microenviron 2011; 4:51-9. [PMID: 21505567 PMCID: PMC3047627 DOI: 10.1007/s12307-010-0061-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 12/16/2010] [Indexed: 12/16/2022]
Abstract
Prostate carcinomas are surrounded by a layer of stromal fibroblastic cells that are characterized by increased expression of CD90. These CD90+ cancer-associated stromal fibroblastic cells differ in gene expression from their normal counterpart, CD49a+CD90lo stromal smooth muscle cells; and were postulated to represent a less differentiated cell type with altered inductive properties. CD90+ stromal cells were isolated from tumor tissue specimens and co-cultured with the pluripotent embryonal carcinoma cell line NCCIT in order to elucidate the impact of tumor-associated stroma on stem cells, and the ‘cancer stem cell.’ Transcriptome analysis identified a notable decreased induction of smooth muscle and prostate stromal genes such as PENK, BMP2 and ChGn compared to previously determined NCCIT response to normal prostate stromal cell induction. CD90+ stromal cell secreted factors induced an increased expression of CD90 and differential induction of genes involved in extracellular matrix remodeling and the RECK pathway in NCCIT. These results suggest that, compared to normal tissue stromal cells, signaling from cancer-associated stromal cells has a markedly different effect on stem cells as represented by NCCIT. Given that stromal cells are important in directing organ-specific differentiation, stromal cells in tumors appear to be defective in this function, which may contribute to abnormal differentiation found in diseases such as cancer.
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Affiliation(s)
- Laura E. Pascal
- Department of Urology, and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
- Institute for Systems Biology, Seattle, WA 98103 USA
- Department of Urology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232 USA
| | - Junkui Ai
- Department of Urology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232 USA
| | - Ricardo Z. N. Vêncio
- Institute for Systems Biology, Seattle, WA 98103 USA
- Department of Genetics, University of São Paulo’s Medical School, Ribeirão Preto, Brazil
| | - Eneida F. Vêncio
- Department of Urology, and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
- Institute for Systems Biology, Seattle, WA 98103 USA
- Present Address: Department of Pathology, School of Dentistry, Federal University of Goias, Goiania, GO Brazil
| | - Yong Zhou
- Institute for Systems Biology, Seattle, WA 98103 USA
| | - Laura S. Page
- Department of Urology, and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
- Institute for Systems Biology, Seattle, WA 98103 USA
| | - Lawrence D. True
- Department of Pathology, University of Washington, Seattle, WA 98195 USA
| | - Zhou Wang
- Department of Urology, University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15232 USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, University of Pittsburgh Cancer Institute, Pittsburgh, PA 15232 USA
| | - Alvin Y. Liu
- Department of Urology, and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98195 USA
- Institute for Systems Biology, Seattle, WA 98103 USA
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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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Pascal LE, Vêncio RZN, Page LS, Liebeskind ES, Shadle CP, Troisch P, Marzolf B, True LD, Hood LE, Liu AY. Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes. BMC Cancer 2009; 9:452. [PMID: 20021671 PMCID: PMC2809079 DOI: 10.1186/1471-2407-9-452] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [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: 03/12/2009] [Accepted: 12/18/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Prostate cancer cells in primary tumors have been typed CD10-/CD13-/CD24hi/CD26+/CD38lo/CD44-/CD104-. This CD phenotype suggests a lineage relationship between cancer cells and luminal cells. The Gleason grade of tumors is a descriptive of tumor glandular differentiation. Higher Gleason scores are associated with treatment failure. METHODS CD26+ cancer cells were isolated from Gleason 3+3 (G3) and Gleason 4+4 (G4) tumors by cell sorting, and their gene expression or transcriptome was determined by Affymetrix DNA array analysis. Dataset analysis was used to determine gene expression similarities and differences between G3 and G4 as well as to prostate cancer cell lines and histologically normal prostate luminal cells. RESULTS The G3 and G4 transcriptomes were compared to those of prostatic cell types of non-cancer, which included luminal, basal, stromal fibromuscular, and endothelial. A principal components analysis of the various transcriptome datasets indicated a closer relationship between luminal and G3 than luminal and G4. Dataset comparison also showed that the cancer transcriptomes differed substantially from those of prostate cancer cell lines. CONCLUSIONS Genes differentially expressed in cancer are potential biomarkers for cancer detection, and those differentially expressed between G3 and G4 are potential biomarkers for disease stratification given that G4 cancer is associated with poor outcomes. Differentially expressed genes likely contribute to the prostate cancer phenotype and constitute the signatures of these particular cancer cell types.
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Affiliation(s)
- Laura E Pascal
- Department of Urology, University of Washington, Seattle, WA 98195, USA.
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Pascal LE, Vêncio RZN, Goo YA, Page LS, Shadle CP, Liu AY. Temporal expression profiling of the effects of secreted factors from prostate stromal cells on embryonal carcinoma stem cells. Prostate 2009; 69:1353-65. [PMID: 19455603 DOI: 10.1002/pros.20982] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
BACKGROUND There is a growing body of evidence indicating that epigenetic influences originating from stromal cells in the immediate microenvironment may play a role in carcinogenesis. Determining the molecular mechanisms involved in stromal-stem cell interaction could provide critical insight into prostate development and disease progression, particularly with regard to their relationship to and influence on the putative cancer stem cell. METHODS Prostate and bladder stromal cells prepared from tissue specimens were co-cultured with the pluripotent embryonal carcinoma cell line NCCIT. Transcriptome analysis was used to characterize NCCIT cell response to prostate or bladder signaling. RESULTS A systems approach demonstrated that prostate stromal cells were capable of inducing gene expression changes in NCCIT through secreted factors. Induction led to a loss of embryonic stem cell markers, with concurrent up-regulation of many genes characteristic of stromal mesenchyme cells as well as some of epithelial and cancer stem cells. Bladder stromal signaling produced gene expression changes different from those of prostate signaling. CONCLUSIONS This study indicates that paracrine stromal cell signaling can affect cancer stem cell response in an organ-specific manner and may provide insight for future development of treatment strategies such as differentiation therapy.
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Affiliation(s)
- Laura E Pascal
- Department of Urology, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA.
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Papini-Terzi FS, Rocha FR, Vêncio RZN, Felix JM, Branco DS, Waclawovsky AJ, Del Bem LEV, Lembke CG, Costa MDL, Nishiyama MY, Vicentini R, Vincentz MGA, Ulian EC, Menossi M, Souza GM. Sugarcane genes associated with sucrose content. BMC Genomics 2009; 10:120. [PMID: 19302712 PMCID: PMC2666766 DOI: 10.1186/1471-2164-10-120] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [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: 11/14/2008] [Accepted: 03/21/2009] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Sucrose content is a highly desirable trait in sugarcane as the worldwide demand for cost-effective biofuels surges. Sugarcane cultivars differ in their capacity to accumulate sucrose and breeding programs routinely perform crosses to identify genotypes able to produce more sucrose. Sucrose content in the mature internodes reach around 20% of the culms dry weight. Genotypes in the populations reflect their genetic program and may display contrasting growth, development, and physiology, all of which affect carbohydrate metabolism. Few studies have profiled gene expression related to sugarcane's sugar content. The identification of signal transduction components and transcription factors that might regulate sugar accumulation is highly desirable if we are to improve this characteristic of sugarcane plants. RESULTS We have evaluated thirty genotypes that have different Brix (sugar) levels and identified genes differentially expressed in internodes using cDNA microarrays. These genes were compared to existing gene expression data for sugarcane plants subjected to diverse stress and hormone treatments. The comparisons revealed a strong overlap between the drought and sucrose-content datasets and a limited overlap with ABA signaling. Genes associated with sucrose content were extensively validated by qRT-PCR, which highlighted several protein kinases and transcription factors that are likely to be regulators of sucrose accumulation. The data also indicate that aquaporins, as well as lignin biosynthesis and cell wall metabolism genes, are strongly related to sucrose accumulation. Moreover, sucrose-associated genes were shown to be directly responsive to short term sucrose stimuli, confirming their role in sugar-related pathways. CONCLUSION Gene expression analysis of sugarcane populations contrasting for sucrose content indicated a possible overlap with drought and cell wall metabolism processes and suggested signaling and transcriptional regulators to be used as molecular markers in breeding programs. Transgenic research is necessary to further clarify the role of the genes and define targets useful for sugarcane improvement programs based on transgenic plants.
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Affiliation(s)
- Flávia S Papini-Terzi
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, SP, Brazil.
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Fernandez-Becerra C, Yamamoto MM, Vêncio RZN, Lacerda M, Rosanas-Urgell A, del Portillo HA. Plasmodium vivax and the importance of the subtelomeric multigene vir superfamily. Trends Parasitol 2008; 25:44-51. [PMID: 19036639 DOI: 10.1016/j.pt.2008.09.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2007] [Revised: 06/02/2008] [Accepted: 09/30/2008] [Indexed: 11/25/2022]
Abstract
Plasmodium vivax is responsible for more than 100 million clinical cases yearly. Unlike P. falciparum, in which infected red blood cells cytoadhere via variant proteins, avoiding passage through the spleen, P.-vivax-infected reticulocytes seem not to cytoadhere. However, a variant subtelomeric multigene vir family has been identified in P. vivax. Thus, questions remain about how P. vivax circulates through the spleen and the role of Vir proteins. In this review, the importance of the vir multigene superfamily is reviewed in the light of the completion of the entire genome sequence of P. vivax and from data gathered from experimental infections in reticulocyte-prone non-lethal malaria parasites and natural P. vivax infections.
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Affiliation(s)
- Carmen Fernandez-Becerra
- Barcelona Centre for International Health Research, Hospital Clinic/IDIBAPS, Universitat de Barcelona, Rosello 132, 08036 Barcelona, Spain
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Costafreda SG, Brammer MJ, Vêncio RZN, Mourão ML, Portela LAP, de Castro CC, Giampietro VP, Amaro E. Multisite fMRI reproducibility of a motor task using identical MR systems. J Magn Reson Imaging 2008; 26:1122-6. [PMID: 17896376 DOI: 10.1002/jmri.21118] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
PURPOSE To estimate between-scanner functional MRI (fMRI) reproducibility in a multisite study. MATERIALS AND METHODS A total of five identical 1.5T MR systems were used to repeatedly scan five subjects while performing a finger tapping task. A two-way (scanners, subjects) random effects analysis of variance (ANOVA) was used to estimate between-scanner and between-subject variability on two outcome variables: task-related mean blood oxygenation level dependent (BOLD) signal change and volume of activation within a motor region-of-interest (ROI). RESULTS Between-scanner variability of fMRI data accounted for a small proportion of the total variation in the BOLD signal change (8.34%, P = 0.114) and volume of activation (5.46%, P = 0.203). Between-subject variation accounted for more than half of the total variation for both measurements (57.17% and 54.46%, respectively, P < 0.01). CONCLUSION These results support the feasibility of multisite studies using identical scanner systems.
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Affiliation(s)
- Sergi G Costafreda
- Brain Image Analysis Unit, Institute of Psychiatry, King's College London, UK.
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27
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Abstract
Different statistical methods have been used to classify a gene as differentially expressed in microarray experiments. They usually require a number of experimental observations to be adequately applied. However, many microarray experiments are constrained to low replication designs for different reasons, from financial restrictions to scarcely available RNA samples. Although performed in a high-throughput framework, there are few experimental replicas for each gene to allow the use of traditional or state-of-art statistical methods. In this work, we present a web-based bioinformatics tool that deals with real-life problems concerning low replication experiments. It uses an empirically derived criterion to classify a gene as differentially expressed by combining two widely accepted ideas in microarray analysis: self-self experiments to derive intensity-dependent cutoffs and non-parametric estimation techniques. To help laboratories without a bioinformatics infrastructure, we implemented the tool in a user-friendly website (http://blasto.iq.usp.br/~rvencio/HTself).
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Affiliation(s)
- Ricardo Z N Vêncio
- BIOINFO-USP-Núcleo de Pesquisas em Bioinformática, Universidade de São Paulo, São Paulo, Brazil.
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Abstract
Background As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. Results We developed an open-source R-based software to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for the enrichment problem is built using the expectation of a Bernoulli Scheme stochastic process given the categorization probabilities. An on-line interface was created to allow usage by non-programmers and is available at: . Conclusion We present an analysis framework and software tools to address the issue of uncertainty in categorical data analysis. In particular, concerning the enrichment analysis, ProbCD can accommodate: (i) the stochastic nature of the high-throughput experimental techniques and (ii) probabilistic gene annotation.
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Affiliation(s)
- Ricardo Z N Vêncio
- Institute for Systems Biology, 1441 North 34th street, Seattle, WA 98103-8904, USA.
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Severino P, Dussurget O, Vêncio RZN, Dumas E, Garrido P, Padilla G, Piveteau P, Lemaître JP, Kunst F, Glaser P, Buchrieser C. Comparative transcriptome analysis of Listeria monocytogenes strains of the two major lineages reveals differences in virulence, cell wall, and stress response. Appl Environ Microbiol 2007; 73:6078-88. [PMID: 17704270 PMCID: PMC2075013 DOI: 10.1128/aem.02730-06] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Accepted: 08/06/2007] [Indexed: 01/02/2023] Open
Abstract
Listeria monocytogenes is a food-borne, opportunistic, bacterial pathogen causing a wide spectrum of diseases, including meningitis, septicemia, abortion, and gastroenteritis, in humans and animals. Among the 13 L. monocytogenes serovars described, human listeriosis is mostly associated with strains of serovars 4b, 1/2b, and 1/2a. Within the species L. monocytogenes, three phylogenetic lineages are described. Serovar 1/2a belongs to phylogenetic lineage I, while serovars 4b and 1/2b group in phylogenetic lineage II. To explore the role of gene expression in the adaptation of L. monocytogenes strains of these two major lineages to different environments, as well as in virulence, we performed whole-genome expression profiling of six L. monocytogenes isolates of serovars 4b, 1/2b, and 1/2a of distinct origins, using a newly constructed Listeria multigenome DNA array. Comparison of the global gene expression profiles revealed differences among strains. The expression profiles of two strains having distinct 50% lethal doses, as assessed in the mouse model, were further analyzed. Gene ontology term enrichment analysis of the differentially expressed genes identified differences in protein-, nucleic acid-, carbon metabolism-, and virulence-related gene expression. Comparison of the expression profiles of the core genomes of all strains revealed differences between the two lineages with respect to cell wall synthesis, the stress-related sigma B regulon and virulence-related genes. These findings suggest different patterns of interaction with host cells and the environment, key factors for host colonization and survival in the environment.
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Affiliation(s)
- Patricia Severino
- Unité de Génomique des Microorganismes Pathogènes, Institut Pasteur, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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Abstract
Xylella fastidiosa is a phytopathogenic bacterium that is responsible for diseases in many economically important crops. Although different strains have been studied, little is known about X. fastidiosa stress responses. One of the better characterized stress responses in bacteria is the heat shock response, which induces the expression of specific genes to prevent protein misfolding and aggregation and to promote degradation of the irreversibly denatured polypeptides. To investigate X. fastidiosa genes involved in the heat shock response, we performed a whole-genome microarray analysis in a time course experiment. Globally, 261 genes were induced (9.7%) and 222 genes were repressed (8.3%). The expression profiles of the differentially expressed genes were grouped, and their expression patterns were validated by quantitative reverse transcription-PCR experiments. We determined the transcription start sites of six heat shock-inducible genes and analyzed their promoter regions, which allowed us to propose a putative consensus for sigma(32) promoters in Xylella and to suggest additional genes as putative members of this regulon. Besides the induction of classical heat shock protein genes, we observed the up-regulation of virulence-associated genes such as vapD and of genes for hemagglutinins, hemolysin, and xylan-degrading enzymes, which may indicate the importance of heat stress to bacterial pathogenesis. In addition, we observed the repression of genes related to fimbriae, aerobic respiration, and protein biosynthesis and the induction of genes related to the extracytoplasmic stress response and some phage-related genes, revealing the complex network of genes that work together in response to heat shock.
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Affiliation(s)
- Tie Koide
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo, Brazil
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Baptista CS, Vêncio RZN, Abdala S, Carranza JC, Westenberger SJ, Silva MN, Pereira CADB, Galvão LMC, Gontijo ED, Chiari E, Sturm NR, Zingales B. Differential transcription profiles in Trypanosoma cruzi associated with clinical forms of Chagas disease: Maxicircle NADH dehydrogenase subunit 7 gene truncation in asymptomatic patient isolates. Mol Biochem Parasitol 2006; 150:236-48. [PMID: 16996148 DOI: 10.1016/j.molbiopara.2006.08.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 08/18/2006] [Accepted: 08/21/2006] [Indexed: 01/08/2023]
Abstract
The majority of individuals in the chronic phase of Chagas disease are asymptomatic (indeterminate form). Every year 2-3% of these individuals develop severe clinical manifestations (cardiac and digestive forms). In this study a Trypanosoma cruzi DNA microarray was used to compare the transcript profiles of six human isolates: three from asymptomatic and three from cardiac patients. Seven signals were expressed differentially between the two classes of isolates, including tryparedoxin, surface protease GP63, cyclophilin, some hypothetical proteins and the pre-edited maxicircle gene NADH dehydrogenase subunit 7 (ND7). The approximately 30-fold greater signal in cardiac strains for ND7 was the most pronounced of the group, and differential levels of pre-edited ND7 transcript confirmed the microarray analysis. The ND7 gene from asymptomatic isolates showed a deletion of 455bp from nt 222 to nt 677 relative to ND7 of the CL Brener reference strain. The ND7 gene structure correlated with disease manifestation for 20 isolates from clinically characterised, chronic phase patients. The ND7 lesion produces a truncated product that could impair the function of mitochondrial complex I. Possible links between the integrity of the electron transport chain and symptom presentation are discussed. We propose that ND7 and other genes of the pathway constitute valuable targets for PCR assays in the differential diagnosis of the infective T. cruzi strain. While this hypothesis requires validation by the examination of additional recent parasite isolates from patients with defined pathologies, the identification of specific molecular markers represents a promising advance in the association between parasite genetics and disease pathology.
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Affiliation(s)
- Cassio S Baptista
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes, 748 CEP 05508-000, São Paulo, SP, Brazil
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Vêncio RZN, Patrão DFC, Baptista CS, Pereira CAB, Zingales B. BayBoots: a model-free Bayesian tool to identify class markers from gene expression data. Genet Mol Res 2006; 5:138-42. [PMID: 16755505] [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: 05/10/2023]
Abstract
One of the goals of gene expression experiments is the identification of differentially expressed genes among populations that could be used as markers. For this purpose, we implemented a model-free Bayesian approach in a user-friendly and freely available web-based tool called BayBoots. In spite of a common misunderstanding that Bayesian and model-free approaches are incompatible, we merged them in the BayBoots implementation using the Kernel density estimator and Rubin 's Bayesian Bootstrap. We used the Bayes error rate (BER) instead of the usual P values as an alternative statistical index to rank a class marker's discriminative potential, since it can be visualized by a simple graphical representation and has an intuitive interpretation. Subsequently, Bayesian Bootstrap was used to assess BER 's credibility. We tested BayBoots on microarray data to look for markers for Trypanosoma cruzi strains isolated from cardiac and asymptomatic patients. We found that the three most frequently used methods in microarray analysis: t-test, non-parametric Wilcoxon test and correlation methods, yielded several markers that were discarded by a time-consuming visual check. On the other hand, the BayBoots graphical output and ranking was able to automatically identify markers for which classification performance was consistent. BayBoots is available at: http://www.vision.ime.usp.br/~rvencio/BayBoots.
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Affiliation(s)
- Ricardo Z N Vêncio
- BIOINFO-USP Departamento de Estatística, Instituto de Matemática e Estatística, Universidade de São Paulo, 05508-090 São Paulo, SP, Brazil.
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Koide T, Salem-Izacc SM, Gomes SL, Vêncio RZN. SpotWhatR: a user-friendly microarray data analysis system. Genet Mol Res 2006; 5:93-107. [PMID: 16755501] [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: 05/10/2023]
Abstract
SpotWhatR is a user-friendly microarray data analysis tool that runs under a widely and freely available R statistical language (http://www.r-project.org) for Windows and Linux operational systems. The aim of SpotWhatR is to help the researcher to analyze microarray data by providing basic tools for data visualization, normalization, determination of differentially expressed genes, summarization by Gene Ontology terms, and clustering analysis. SpotWhatR allows researchers who are not familiar with computational programming to choose the most suitable analysis for their microarray dataset. Along with well-known procedures used in microarray data analysis, we have introduced a stand-alone implementation of the HTself method, especially designed to find differentially expressed genes in low-replication contexts. This approach is more compatible with our local reality than the usual statistical methods. We provide several examples derived from the Blastocladiella emersonii and Xylella fastidiosa Microarray Projects. SpotWhatR is freely available at http://blasto.iq.usp.br/~tkoide/SpotWhatR, in English and Portuguese versions. In addition, the user can choose between "single experiment" and "batch processing" versions.
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Affiliation(s)
- Tie Koide
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
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Ribichich KF, Salem-Izacc SM, Georg RC, Vêncio RZN, Navarro LD, Gomes SL. Gene discovery and expression profile analysis through sequencing of expressed sequence tags from different developmental stages of the chytridiomycete Blastocladiella emersonii. Eukaryot Cell 2005; 4:455-64. [PMID: 15701807 PMCID: PMC549328 DOI: 10.1128/ec.4.2.455-464.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Blastocladiella emersonii is an aquatic fungus of the chytridiomycete class which diverged early from the fungal lineage and is notable for the morphogenetic processes which occur during its life cycle. Its particular taxonomic position makes this fungus an interesting system to be considered when investigating phylogenetic relationships and studying the biology of lower fungi. To contribute to the understanding of the complexity of the B. emersonii genome, we present here a survey of expressed sequence tags (ESTs) from various stages of the fungal development. Nearly 20,000 cDNA clones from 10 different libraries were partially sequenced from their 5' end, yielding 16,984 high-quality ESTs. These ESTs were assembled into 4,873 putative transcripts, of which 48% presented no matches with existing sequences in public databases. As a result of Gene Ontology (GO) project annotation, 1,680 ESTs (35%) were classified into biological processes of the GO structure, with transcription and RNA processing, protein biosynthesis, and transport as prevalent processes. We also report full-length sequences, useful for construction of molecular phylogenies, and several ESTs that showed high similarity with known proteins, some of which were not previously described in fungi. Furthermore, we analyzed the expression profile (digital Northern analysis) of each transcript throughout the life cycle of the fungus using Bayesian statistics. The in silico approach was validated by Northern blot analysis with good agreement between the two methodologies.
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Affiliation(s)
- Karina F Ribichich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, 05508-000, São Paulo, SP, Brazil
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Pashalidis S, Moreira LM, Zaini PA, Campanharo JC, Alves LMC, Ciapina LP, Vêncio RZN, Lemos EGM, Da Silva AM, Da Silva ACR. Whole-genome expression profiling of Xylella fastidiosa in response to growth on glucose. OMICS 2005; 9:77-90. [PMID: 15805779 DOI: 10.1089/omi.2005.9.77] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Xylella fastidiosa is the etiologic agent of diseases in a wide range of economically important crops including citrus variegated chlorosis, a major threat to the Brazilian citrus industry. The genomes of several strains of this phytopathogen have been completely sequenced enabling large-scale functional studies. In this work we used whole-genome DNA microarrays to investigate the transcription profile of X. fastidiosa grown in defined media with different glucose concentrations. Our analysis revealed that while transcripts related to fastidian gum production were unaffected, colicin-V-like and fimbria precursors were induced in high glucose medium. Based on these results, we suggest a model for colicin-defense mechanism in X. fastidiosa.
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Affiliation(s)
- Stefano Pashalidis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
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Baptista CS, Vêncio RZN, Abdala S, Valadares MP, Martins C, de Bragança Pereira CA, Zingales B. DNA microarrays for comparative genomics and analysis of gene expression in Trypanosoma cruzi. Mol Biochem Parasitol 2005; 138:183-94. [PMID: 15555730 DOI: 10.1016/j.molbiopara.2004.06.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2003] [Revised: 05/25/2004] [Accepted: 06/09/2004] [Indexed: 11/27/2022]
Abstract
Trypanosoma cruzi presents high genetic diversity and parasite isolates show remarkable differences in biological parameters. In this study, we evaluated whether DNA microarrays containing CL Brener cDNAs can be used for comparative genomics and for the analysis of gene expression in T. cruzi. We constructed a prototype microarray with 710 expression sequence tags of CL Brener and 20 sequences of T. cruzi strains. These probes represent 665 unique genes. Results from four hybridisations with genomic DNA of Silvio (T. cruzi I) and CL Brener (hybrid genotype) identified 9.3% of the probes (68/730) differentially represented in the two genomes. Data from eight hybridisations with cDNA obtained from three independent parasite harvests of Silvio and CL Brener disclosed 84 sequences of 730 (11.5%) that showed statistical significant (P < or = 0.01) changes in expression (1.6-6.5-fold). Some of the array-identified sequences were confirmed by Southern and Northern blot analysis. Only 20% of the probes with increased expression in Silvio or CL Brener presented higher hybridisation with genomic DNA of either strain. Approximately 2.5% (18/730) and 9.0% (65/730) of the probes were differentially expressed (P < or = 0.01), respectively, in epimastigotes and metacyclic trypomastigotes of two T. cruzi II strains isolated from chronic chagasic patients. Microarrays identified several sequences for which differences in gene copy number and/or in the levels of RNA transcripts were previously demonstrated by different approaches. The data indicate that DNA microarrays are a useful tool for comparative studies between strains and provide further evidence for a high level of post-transcriptional regulation of RNA abundance in T. cruzi.
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Affiliation(s)
- Cassio Silva Baptista
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Avenida Professor Lineu Prestes 748, CEP 05508-000 São Paulo, SP, Brazil
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Abstract
MOTIVATION Statistical methods usually used to perform Serial Analysis of Gene Expression (SAGE) analysis are based on hypothesis testing. They answer the biologist's question: 'what are the genes with differential expression greater than r with P-value smaller than P?'. Another useful and not yet explored question is: 'what is the uncertainty in differential expression ratio of a gene?'. RESULTS We have used Bayesian model for SAGE differential gene expression ratios as a more informative alternative to hypothesis tests since it provides credibility intervals. AVAILABILITY The model is implemented in R statistical language script and is available under GNU/GLP copyleft at supplemental web site. SUPPLEMENTARY INFORMATION http://www.ime.usp.br/~rvencio/SAGEci/
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Affiliation(s)
- Ricardo Z N Vêncio
- Departamento de Estatística, Instituto de Matemática e Estatística da Universidade de São Paulo, São Paulo 04601-003, Brazil, Fundação Antônio Prudente, São Paulo 01509-900, Brazil.
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Koide T, Zaini PA, Moreira LM, Vêncio RZN, Matsukuma AY, Durham AM, Teixeira DC, El-Dorry H, Monteiro PB, da Silva ACR, Verjovski-Almeida S, da Silva AM, Gomes SL. DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence. J Bacteriol 2004; 186:5442-9. [PMID: 15292146 PMCID: PMC490883 DOI: 10.1128/jb.186.16.5442-5449.2004] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2004] [Accepted: 03/22/2004] [Indexed: 12/15/2022] Open
Abstract
Xylella fastidiosa is a phytopathogenic bacterium that causes serious diseases in a wide range of economically important crops. Despite extensive comparative analyses of genome sequences of Xylella pathogenic strains from different plant hosts, nonpathogenic strains have not been studied. In this report, we show that X. fastidiosa strain J1a12, associated with citrus variegated chlorosis (CVC), is nonpathogenic when injected into citrus and tobacco plants. Furthermore, a DNA microarray-based comparison of J1a12 with 9a5c, a CVC strain that is highly pathogenic and had its genome completely sequenced, revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. Among them, we found an arginase and a fimbrial adhesin precursor of type III pilus, which were confirmed to be absent in the nonpathogenic strain by PCR and DNA sequencing. The absence of arginase can be correlated to the inability of J1a12 to multiply in host plants. This enzyme has been recently shown to act as a bacterial survival mechanism by down-regulating host nitric oxide production. The lack of the adhesin precursor gene is in accordance with the less aggregated phenotype observed for J1a12 cells growing in vitro. Thus, the absence of both genes can be associated with the failure of the J1a12 strain to establish and spread in citrus and tobacco plants. These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of X. fastidiosa, constituting an important step towards understanding the molecular basis of the disease.
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Affiliation(s)
- Tie Koide
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
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