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Ring A, Campo D, Porras TB, Kaur P, Forte VA, Tripathy D, Lu J, Kang I, Press MF, Jeong YJ, Snow A, Zhu Y, Zada G, Wagle N, Lang JE. Circulating Tumor Cell Transcriptomics as Biopsy Surrogates in Metastatic Breast Cancer. Ann Surg Oncol 2022; 29:2882-2894. [PMID: 35000083 PMCID: PMC8989945 DOI: 10.1245/s10434-021-11135-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/11/2021] [Indexed: 01/28/2023]
Abstract
BACKGROUND Metastatic breast cancer (MBC) and the circulating tumor cells (CTCs) leading to macrometastases are inherently different than primary breast cancer. We evaluated whether whole transcriptome RNA-Seq of CTCs isolated via an epitope-independent approach may serve as a surrogate for biopsies of macrometastases. METHODS We performed RNA-Seq on fresh metastatic tumor biopsies, CTCs, and peripheral blood (PB) from 19 newly diagnosed MBC patients. CTCs were harvested using the ANGLE Parsortix microfluidics system to isolate cells based on size and deformability, independent of a priori knowledge of cell surface marker expression. RESULTS Gene expression separated CTCs, metastatic biopsies, and PB into distinct groups despite heterogeneity between patients and sample types. CTCs showed higher expression of immune oncology targets compared with corresponding metastases and PB. Predictive biomarker (n = 64) expression was highly concordant for CTCs and metastases. Repeat observation data post-treatment demonstrated changes in the activation of different biological pathways. Somatic single nucleotide variant analysis showed increasing mutational complexity over time. CONCLUSION We demonstrate that RNA-Seq of CTCs could serve as a surrogate biomarker for breast cancer macrometastasis and yield clinically relevant insights into disease biology and clinically actionable targets.
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Affiliation(s)
- Alexander Ring
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA ,Present Address: Department of Hematology and Medical Oncology, University Hospital Zurich, Zurich, Switzerland
| | - Daniel Campo
- Department of Biological Sciences, University of Southern California, Los Angeles, CA USA
| | - Tania B. Porras
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Pushpinder Kaur
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Victoria A. Forte
- Division of Medical Oncology, Department of Medicine, SUNY Downstate Medical Center, New York, NY USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, UT MD Anderson Cancer Center, Houston, TX USA
| | - Janice Lu
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Irene Kang
- Department of Pathology and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Michael F. Press
- Department of Pathology and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Young Ju Jeong
- Department of Surgery, Catholic University of Daegu School of Medicine, Daegu, Republic of Korea
| | - Anson Snow
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Yue Zhu
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Gabriel Zada
- Department of Neurosurgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Naveed Wagle
- Division of Medical Oncology, Department of Medicine and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA
| | - Julie E. Lang
- Division of Surgical Oncology, Department of Surgery and University of Southern California Norris Cancer Center, University of Southern California, Los Angeles, CA USA ,Present Address: Division of Breast Services, Department of General Surgery, Cleveland Clinic Breast Cancer Program, Cleveland, Ohio USA
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Yashiro M, Ohya M, Mima T, Ueda Y, Nakashima Y, Kawakami K, Ishizawa Y, Yamamoto S, Kobayashi S, Yano T, Tanaka Y, Okuda K, Sonou T, Shoshihara T, Iwashita Y, Iwashita Y, Tatsuta K, Matoba R, Negi S, Shigematsu T. FGF23 modulates the effects of erythropoietin on gene expression in renal epithelial cells. Int J Nephrol Renovasc Dis 2018; 11:125-136. [PMID: 29670389 PMCID: PMC5894721 DOI: 10.2147/ijnrd.s158422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background FGF23 plays an important role in calcium–phosphorus metabolism. Other roles of FGF23 have recently been reported, such as commitment to myocardium enlargement and immunological roles in the spleen. In this study, we aimed to identify the roles of FGF23 in the kidneys other than calcium–phosphorus metabolism. Methods DNA microarrays and bioinformatics tools were used to analyze gene expression in mIMCD3 mouse renal tubule cells following treatment with FGF23, erythropoietin and/or an inhibitor of ERK. Results Three protein-coding genes were upregulated and 12 were downregulated in response to FGF23. Following bioinformatics analysis of these genes, PPARγ and STAT3 were identified as candidate transcript factors for mediating their upregulation, and STAT1 as a candidate for mediating their downregulation. Because STAT1 and STAT3 also mediate erythropoietin signaling, we investigated whether FGF23 and erythropoietin might show interactive effects in these cells. Of the 15 genes regulated by FGF23, 11 were upregulated by erythropoietin; 10 of these were downregulated following cotreatment with FGF23. Inhibition of ERK, an intracellular mediator of FGF23, reversed the effects of FGF23. However, FGF23 did not influence STAT1 phosphorylation, suggesting that it impinges on erythropoietin signaling through other mechanisms. Conclusion Our results suggest cross talk between erythropoietin and FGF23 signaling in the regulation of renal epithelial cells.
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Affiliation(s)
- Mitsuru Yashiro
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Masaki Ohya
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Toru Mima
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Yumi Ueda
- DNA Chip Research Inc., Minato, Japan
| | - Yuri Nakashima
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Kazuki Kawakami
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | | | - Shuto Yamamoto
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Sou Kobayashi
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Takurou Yano
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Yusuke Tanaka
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Kouji Okuda
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Tomohiro Sonou
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | | | - Yuko Iwashita
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Yu Iwashita
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | - Kouichi Tatsuta
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
| | | | - Shigeo Negi
- Department of Nephrology, Wakayama Medical University, Wakayama, Japan
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Pellegrina DVDS, Severino P, Machado MC, Pinheiro da Silva F, Reis EM. Microarray gene expression analysis of neutrophils from elderly septic patients. GENOMICS DATA 2015; 6:51-3. [PMID: 26697331 PMCID: PMC4664687 DOI: 10.1016/j.gdata.2015.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 08/07/2015] [Accepted: 08/10/2015] [Indexed: 11/27/2022]
Affiliation(s)
| | - Patricia Severino
- Instituto Israelita de Ensino e Pesquisa, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Marcel Cerqueira Machado
- Departamento de Emergências Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Fabiano Pinheiro da Silva
- Departamento de Emergências Clínicas, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil
| | - Eduardo Moraes Reis
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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Oberthuer A, Juraeva D, Li L, Kahlert Y, Westermann F, Eils R, Berthold F, Shi L, Wolfinger RD, Fischer M, Brors B. Comparison of performance of one-color and two-color gene-expression analyses in predicting clinical endpoints of neuroblastoma patients. THE PHARMACOGENOMICS JOURNAL 2010; 10:258-66. [PMID: 20676065 PMCID: PMC2920066 DOI: 10.1038/tpj.2010.53] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microarray-based prediction of clinical endpoints may be performed using either a one-color approach reflecting mRNA abundance in absolute intensity values or a two-color approach yielding ratios of fluorescent intensities. In this study, as part of the MAQC-II project, we systematically compared the classification performance resulting from one- and two-color gene-expression profiles of 478 neuroblastoma samples. In total, 196 classification models were applied to these measurements to predict four clinical endpoints, and classification performances were compared in terms of accuracy, area under the curve, Matthews correlation coefficient and root mean-squared error. Whereas prediction performance varied with distinct clinical endpoints and classification models, equivalent performance metrics were observed for one- and two-color measurements in both internal and external validation. Furthermore, overlap of selected signature genes correlated inversely with endpoint prediction difficulty. In summary, our data strongly substantiate that the choice of platform is not a primary factor for successful gene expression based-prediction of clinical endpoints.
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Affiliation(s)
- A Oberthuer
- Department of Pediatric Oncology and Hematology, Children's Hospital, and Center for Molecular Medicine Cologne (ZMMK), University of Cologne, Köln, Germany
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Development of a common oligonucleotide reference standard for microarray data normalization and comparison across different microbial communities. Appl Environ Microbiol 2009; 76:1088-94. [PMID: 20038701 DOI: 10.1128/aem.02749-09] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
High-density functional gene arrays have become a powerful tool for environmental microbial detection and characterization. However, microarray data normalization and comparison for this type of microarray remain a challenge in environmental microbiology studies because some commonly used normalization methods (e.g., genomic DNA) for the study of pure cultures are not applicable. In this study, we developed a common oligonucleotide reference standard (CORS) method to address this problem. A unique 50-mer reference oligonucleotide probe was selected to co-spot with gene probes for each array feature. The complementary sequence was synthesized and labeled for use as the reference target, which was then spiked and cohybridized with each sample. The signal intensity of this reference target was used for microarray data normalization and comparison. The optimal amount or concentration were determined to be ca. 0.5 to 2.5% of a gene probe for the reference probe and ca. 0.25 to 1.25 fmol/microl for the reference target based on our evaluation with a pilot array. The CORS method was then compared to dye swap and genomic DNA normalization methods using the Desulfovibrio vulgaris whole-genome microarray, and significant linear correlations were observed. This method was then applied to a functional gene array to analyze soil microbial communities, and the results demonstrated that the variation of signal intensities among replicates based on the CORS method was significantly lower than the total intensity normalization method. The developed CORS provides a useful approach for microarray data normalization and comparison for studies of complex microbial communities.
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Millard AD, Tiwari B. Oligonucleotide microarrays for bacteriophage expression studies. Methods Mol Biol 2009; 502:193-226. [PMID: 19082558 DOI: 10.1007/978-1-60327-565-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Gene expression microarrays offer the ability to monitor the expression of all phage genes over an infection cycle. However, there are relatively few reports to date of microarrays being used to investigate phage biology. This chapter aims to provide an overview of how to design and implement a microarray experiment to investigate phage biology. Given the nature of microarrays being specific to an organism, each will provide a number of unique issues. In this chapter, we outline the basic theory behind microarrays and provide details on how to implement a microarray experiment from the design of oligonucleotide probes through to the hybridisation of microarrays. The matter of designing oligonucleotide probes will be discussed with regards to how probe length, secondary structure, free energy, probe orientation and amplification all have to be taken into account. As means of an example, the conditions used for the hybridisation of an array designed to be specific to the cyanophage S-PM2 is detailed.
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Affiliation(s)
- Andrew D Millard
- Department of Biological Sciences, University of Warwick, Coventry, UK
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7
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Ponzielli R, Boutros PC, Katz S, Stojanova A, Hanley AP, Khosravi F, Bros C, Jurisica I, Penn LZ. Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic Acids Res 2008; 36:e144. [PMID: 18940864 PMCID: PMC2588500 DOI: 10.1093/nar/gkn735] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
High-throughput, microarray-based chromatin immunoprecipitation (ChIP-chip) technology allows in vivo elucidation of transcriptional networks. However this complex is not yet readily accessible, in part because its many parameters have not been systematically evaluated and optimized. We address this gap by systematically assessing experimental-design parameters including antibody purity, dye-bias, array-batch, inter-day hybridization bias, amplification method and choice of hybridization control. The combined performance of these optimized parameters shows a 90% validation rate in ChIP-chip analysis of Myc genomic binding in HL60 cells using two different microarray platforms. Increased sensitivity and decreased noise in ChIP-chip assays will enable wider use of this methodology to accurately and affordably elucidate transcriptional networks.
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Affiliation(s)
- Romina Ponzielli
- Division of Cancer Genomics and Proteomics, Ontario Cancer Institute, University Health Network, University of Toronto, Toronto, ON, Canada
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Nakaya HI, Beckedorff FC, Baldini ML, Fachel AA, Reis EM, Verjovski-Almeida S. Splice variants of TLE family genes and up-regulation of a TLE3 isoform in prostate tumors. Biochem Biophys Res Commun 2007; 364:918-23. [PMID: 18273443 DOI: 10.1016/j.bbrc.2007.10.097] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Accepted: 10/17/2007] [Indexed: 10/22/2022]
Abstract
The TLE genes constitute a family of important transcriptional co-repressors involved in many cellular processes. We found evidence of alternatively spliced mRNAs for human TLE1-4 containing premature stop codons, thus encoding putative shortened proteins. Microarray experiments and Real-time RT-PCR assays showed that alternatively spliced isoforms of TLE1, TLE2 an d TLE3 were preferentially expressed in prostate in comparison to liver and kidney tissues. We identified by orientation-specific R T-PCR an antisense partially intronic non-coding RNA that overlaps a novel exon of the TLE3 gene, raising the possibility of regulation of alternative splicing by this non-coding transcript. The alternatively spliced isoform of TLE3 was up-regulated (6- to 17-fo ld) in prostate tumors in comparison to matched non-tumor adjacent tissue from 7 out of 11 (64%) patients and in four prostate tumor cell lines in comparison to a normal prostate cell line. These results demonstrate that different isoforms of TLE genes are commonly transcribed in human tissues and suggest that TLE3 could be involved in prostate cancer development.
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Affiliation(s)
- Helder I Nakaya
- Departamento de Bioquimica, Instituto de Quimica, Universidade de Sao Paulo, 05508-900 Sao Pau lo, SP, Brazil
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9
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Bai X, Wu J, Zhang Q, Alesci S, Manoli I, Blackman MR, Chrousos GP, Goldstein AL, Rennert OM, Su YA. Third-generation human mitochondria-focused cDNA microarray and its bioinformatic tools for analysis of gene expression. Biotechniques 2007; 42:365-75. [PMID: 17390543 DOI: 10.2144/000112388] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
To facilitate profiling mitochondrial transcriptomes, we developed a third-generation human mitochondria-focused cDNA microarray (hMitChip3) and its bioinformatic tools. hMitChip3 consists of the 37 mitochondrial DNA-encoded genes, 1098 nuclear DNA-encoded and mitochondria-related genes, and 225 controls, each in triplicate. The bioinformatic tools included data analysis procedures and customized database for interpretation of results. The database associated 645 molecular functions with 946 hMitChip3 genes, 612 biological processes with 930 genes, 172 cellular components with 869 genes, 107 biological chemistry pathways with 476 genes, 23 reactome events with 227 genes, 320 genetic disorders with 237 genes, and 87 drugs targets with 55 genes. To test these tools, hMitChip3 was used to compare expression profiles between human melanoma cell lines UACC903 (rapidly dividing) and UACC903(+6) (slowly dividing). Our results demonstrated internal gene-set consistency (correlation R > or = 0.980 +/- 0.005) and interexperimental reproducibility (R > or = 0.931 +/- 0.013). Expression patterns of 16 genes, involved in DNA, RNA, or protein biosyntheses in mitochondrial and other organelles, were consistent with the proliferation rates of both cell lines, and the patterns of 6 tested genes were verified by quantitative reverse transcription PCR (RT-PCR). Thus, hMitChip3 and its bioinformatics software provide an integrated tool for profiling mitochondria-focused gene expression.
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Affiliation(s)
- Xueyan Bai
- The George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA
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10
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Louro R, Nakaya HI, Amaral PP, Festa F, Sogayar MC, da Silva AM, Verjovski-Almeida S, Reis EM. Androgen responsive intronic non-coding RNAs. BMC Biol 2007; 5:4. [PMID: 17263875 PMCID: PMC1800835 DOI: 10.1186/1741-7007-5-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 01/30/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. RESULTS Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5-5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. CONCLUSION Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program.
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Affiliation(s)
- Rodrigo Louro
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Helder I Nakaya
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Paulo P Amaral
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Fernanda Festa
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Mari C Sogayar
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Aline M da Silva
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Sergio Verjovski-Almeida
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
| | - Eduardo M Reis
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, Brazil
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Nakaya HI, Amaral PP, Louro R, Lopes A, Fachel AA, Moreira YB, El-Jundi TA, da Silva AM, Reis EM, Verjovski-Almeida S. Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription. Genome Biol 2007; 8:R43. [PMID: 17386095 PMCID: PMC1868932 DOI: 10.1186/gb-2007-8-3-r43] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 01/17/2007] [Accepted: 03/26/2007] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND RNAs transcribed from intronic regions of genes are involved in a number of processes related to post-transcriptional control of gene expression. However, the complement of human genes in which introns are transcribed, and the number of intronic transcriptional units and their tissue expression patterns are not known. RESULTS A survey of mRNA and EST public databases revealed more than 55,000 totally intronic noncoding (TIN) RNAs transcribed from the introns of 74% of all unique RefSeq genes. Guided by this information, we designed an oligoarray platform containing sense and antisense probes for each of 7,135 randomly selected TIN transcripts plus the corresponding protein-coding genes. We identified exonic and intronic tissue-specific expression signatures for human liver, prostate and kidney. The most highly expressed antisense TIN RNAs were transcribed from introns of protein-coding genes significantly enriched (p = 0.002 to 0.022) in the 'Regulation of transcription' Gene Ontology category. RNA polymerase II inhibition resulted in increased expression of a fraction of intronic RNAs in cell cultures, suggesting that other RNA polymerases may be involved in their biosynthesis. Members of a subset of intronic and protein-coding signatures transcribed from the same genomic loci have correlated expression patterns, suggesting that intronic RNAs regulate the abundance or the pattern of exon usage in protein-coding messages. CONCLUSION We have identified diverse intronic RNA expression patterns, pointing to distinct regulatory roles. This gene-oriented approach, using a combined intron-exon oligoarray, should permit further comparative analysis of intronic transcription under various physiological and pathological conditions, thus advancing current knowledge about the biological functions of these noncoding RNAs.
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Affiliation(s)
- Helder I Nakaya
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Paulo P Amaral
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Rodrigo Louro
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - André Lopes
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Angela A Fachel
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Yuri B Moreira
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Tarik A El-Jundi
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Aline M da Silva
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Eduardo M Reis
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
| | - Sergio Verjovski-Almeida
- Departamento de Bioquimica, Instituto de Quimica, Universidade de São Paulo, 05508-900 São Paulo, SP, Brazil
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DeMarco R, Oliveira KC, Venancio TM, Verjovski-Almeida S. Gender biased differential alternative splicing patterns of the transcriptional cofactor CA150 gene in Schistosoma mansoni. Mol Biochem Parasitol 2006; 150:123-31. [PMID: 16904200 DOI: 10.1016/j.molbiopara.2006.07.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 07/05/2006] [Accepted: 07/06/2006] [Indexed: 11/19/2022]
Abstract
The complex molecular systems involved in the process of sex-differentiation and fertility in Schistosoma mansoni have not yet been completely described. Using a 4608-element cDNA microarray, we have now determined 90 and 139 genes with significantly (q-value</=0.06) higher expression levels in adult males and females, respectively. Eight out of eleven (73%) selected transcripts had their differential expression levels validated by real-time RT-PCR. One of these transcripts was extended by RT-PCR and was shown to span the intronic region between exons 9 and 11 of the S. mansoni CA150 gene, a transcriptional cofactor known in humans to interact with both RNA polymerase II and the spliceosome complex. The longer transcript probably represents a novel isoform of S. mansoni CA150. Additionally, we obtained full-length sequences for three other isoforms of the SmCA150 gene, coding for proteins of different lengths and domain compositions. Semi-quantitative RT-PCR showed different expression ratios among these isoforms between male and female. Due to the role of CA150 in RNA transcription and processing, we hypothesize that these differential expression events may be important in the generation and maintenance of the different phenotypes between male and female.
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Affiliation(s)
- Ricardo DeMarco
- Laboratory of Gene Expression in Eukaryotes, Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Brazil
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