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Dhumal SN, Choudhari SK, Patankar S, Ghule SS, Jadhav YB, Masne S. Cancer Stem Cell Markers, CD44 and ALDH1, for Assessment of Cancer Risk in OPMDs and Lymph Node Metastasis in Oral Squamous Cell Carcinoma. Head Neck Pathol 2021; 16:453-465. [PMID: 34655409 PMCID: PMC9187836 DOI: 10.1007/s12105-021-01384-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Tumour heterogeneity in oral cancer is attributed to the presence of cancer stem cells (CSCs). CSCs are the most migratory and metastatic cellular subpopulation within tumours. Assessment of CSC markers as significant predictors of lymph node metastasis may prove valuable in the clinical setting. Furthermore, analysis of this panel of putative stem cell markers in oral dysplasia may additionally inform of the likelihood for oral potentially malignant disorders (OPMDs) to progress to oral squamous cell carcinoma (OSCC). The present study aims to assess the significance of CSC markers in the progression of OPMDs to OSCC and assessment of lymph node metastasis in OSCC. CD44 and ALDH1 were assessed immunohistochemically in 25 normal, 30 OPMDs, and 24 OSCCs. CD44 is a membranous marker and ALDH1 is a cytoplasmic marker. The immunohistochemical expression of these markers were compared between OPMDs with and without dysplasia, as well as between low-risk and high-risk dysplasias. Similarly, expression was compared between OSCC with and without lymph node metastasis and among grades of OSCC. Positive CD44 expression was seen in all normal mucosal tissues. The expression decreased from normal epithelium to OPMDs but increased in OSCC. CD44 expression was positive in 21 cases of OSCC (87.5%) and reduced from well-differentiated to poorly differentiated OSCC. CD44 staining index was higher in OSCC without lymph node metastasis (3.59) when compared with OSCC with lymph node metastasis (1.33). There was a statistically significant difference observed in the ALDH1 staining index among three groups (p < 0.05), with highest expression seen in OSCC. Within OPMDs, the ALDH1 staining index was statistically higher in OPMDs with dysplasia as compared to OPMDs without dysplasia. Furthermore, the expression was higher in OPMDs with high-risk dysplasia when compared with low-risk dysplasia, but this was not statistically significant (p = 0.82). In conclusion, The CD44 positive population possesses properties of CSCs in head and neck carcinoma, and continuous shedding could be found after CD44 down-regulation. The present study reports differences in ALDH1 expression between OPMDs with and without dysplasia, dysplastic and non-dysplastic epithelia, and low-risk and high-risk dysplasia. These findings may suggest ALDH1 as a specific marker for dysplasia. CD44 demonstrated a difference in staining index in OSCC without lymph node metastasis versus OSCC with lymph node metastasis. These findings may suggest CD44 as a marker for lymph node metastasis. Both proteins may play key roles in the tumorigenicity of CSCs in OPMDs and OSCC.
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Affiliation(s)
| | | | - Sangeeta Patankar
- YMT Dental College and Research Institute, Navi Mumbai, Maharashtra India
| | | | - Yogesh B. Jadhav
- YMT Dental College and Research Institute, Navi Mumbai, Maharashtra India
| | - Sneha Masne
- YMT Dental College and Research Institute, Navi Mumbai, Maharashtra India
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Shimizu T, Togo S, Kumamoto T, Makino H, Morita T, Tanaka K, Kubota T, Ichikawa Y, Nagasima Y, Okazaki Y, Hayashizaki Y, Shimada H. Gene expression during liver regeneration after partial hepatectomy in mice lacking type 1 tumor necrosis factor receptor. J Surg Res 2008; 152:178-88. [PMID: 18639250 DOI: 10.1016/j.jss.2007.12.785] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 12/10/2007] [Accepted: 12/27/2007] [Indexed: 12/13/2022]
Abstract
BACKGROUND To investigate the function of tumor necrosis factor-alpha (TNF-alpha) during hepatocyte proliferation, we studied liver regeneration following partial hepatectomy in mice lacking type 1 TNF receptor (TNFR-1). MATERIALS AND METHODS TNFR-1 knockout (KO) and wild-type mice were subjected to partial (two-thirds) hepatectomy. Liver regeneration was evaluated by assessing liver weights and Ki67 immunohistochemistry. Riken complementary DNA microarray analysis was performed for liver samples from mice undergoing partial hepatectomy to better compare different mouse partial hepatectomy models (TNFR-1 KO mice, KO group; and wild-type mice, W group). RESULTS Liver weight was regained after 14 days in the KO group, and after 7 days in the W group. Genes including lipopolysaccharide, toll-like receptor 4 precursor, mitogen-activated protein kinase kinase kinase 4, mitogen-activated protein kinase kinase kinase kinase 4, and mitogen-activated protein kinase 8-interacting protein were up-regulated in the KO group. As for the cell-cycle-regulated genes, the levels of cyclin D1, nuclear factor-kappa B light chain, and TNF receptor super family membrane 1a were down-regulated in the KO group. Microarray analysis showed decreased activities of the hexokinase- and phospho-fructokinase-related glycolytic pathways in the KO group. CONCLUSIONS These results contribute to the better understanding of the mechanisms of liver regeneration after partial hepatectomy in TNFR-1 KO mice.
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Affiliation(s)
- Tetsuya Shimizu
- Department of Gastroenterological Surgery, Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Abstract
In recent years, genome-wide detection of alternative splicing based on Expressed Sequence Tag (EST) sequence alignments with mRNA and genomic sequences has dramatically expanded our understanding of the role of alternative splicing in functional regulation. This chapter reviews the data, methodology, and technical challenges of these genome-wide analyses of alternative splicing, and briefly surveys some of the uses to which such alternative splicing databases have been put. For example, with proper alternative splicing database schema design, it is possible to query genome-wide for alternative splicing patterns that are specific to particular tissues, disease states (e.g., cancer), gender, or developmental stages. EST alignments can be used to estimate exon inclusion or exclusion level of alternatively spliced exons and evolutionary changes for various species can be inferred from exon inclusion level. Such databases can also help automate design of probes for RT-PCR and microarrays, enabling high throughput experimental measurement of alternative splicing.
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Konrad L, Scheiber JA, Völck-Badouin E, Keilani MM, Laible L, Brandt H, Schmidt A, Aumüller G, Hofmann R. Alternative splicing of TGF-betas and their high-affinity receptors T beta RI, T beta RII and T beta RIII (betaglycan) reveal new variants in human prostatic cells. BMC Genomics 2007; 8:318. [PMID: 17845732 PMCID: PMC2075524 DOI: 10.1186/1471-2164-8-318] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2007] [Accepted: 09/11/2007] [Indexed: 01/14/2023] Open
Abstract
Background The transforming growth factors (TGF)-β, TGF-β1, TGF-β2 and TGF-β3, and their receptors [TβRI, TβRII, TβRIII (betaglycan)] elicit pleiotropic functions in the prostate. Although expression of the ligands and receptors have been investigated, the splice variants have never been analyzed. We therefore have analyzed all ligands, the receptors and the splice variants TβRIB, TβRIIB and TGF-β2B in human prostatic cells. Results Interestingly, a novel human receptor transcript TβRIIC was identified, encoding additional 36 amino acids in the extracellular domain, that is expressed in the prostatic cancer cells PC-3, stromal hPCPs, and other human tissues. Furthermore, the receptor variant TβRIB with four additional amino acids was identified also in human. Expression of the variant TβRIIB was found in all prostate cell lines studied with a preferential localization in epithelial cells in some human prostatic glands. Similarly, we observed localization of TβRIIC and TGF-β2B mainly in the epithelial cells with a preferential localization of TGF-β2B in the apical cell compartment. Whereas in the androgen-independent hPCPs and PC-3 cells all TGF-β ligands and receptors are expressed, the androgen-dependent LNCaP cells failed to express all ligands. Additionally, stimulation of PC-3 cells with TGF-β2 resulted in a significant and strong increase in secretion of plasminogen activator inhibitor-1 (PAI-1) with a major participation of TβRII. Conclusion In general, expression of the splice variants was more heterogeneous in contrast to the well-known isoforms. The identification of the splice variants TβRIB and the novel isoform TβRIIC in man clearly contributes to the growing complexity of the TGF-β family.
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Affiliation(s)
- Lutz Konrad
- Department of Urology, Medical Faculty, 35033 Marburg, Germany
| | | | - Elke Völck-Badouin
- Department of Anatomy and Cell Biology, Medical Faculty, 35033 Marburg, Germany
| | | | - Leslie Laible
- Department of Urology, Medical Faculty, 35033 Marburg, Germany
| | - Heidrun Brandt
- Department of Urology, Medical Faculty, 35033 Marburg, Germany
| | - Ansgar Schmidt
- Department of Pathology, Medical Faculty, 35033 Marburg, Germany
| | - Gerhard Aumüller
- Department of Anatomy and Cell Biology, Medical Faculty, 35033 Marburg, Germany
| | - Rainer Hofmann
- Department of Urology, Medical Faculty, 35033 Marburg, Germany
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Konrad L, Lüers GH, Völck-Badouin E, Keilani MM, Laible L, Aumüller G, Hofmann R. Analysis of the mRNA expression of the TGF-Beta family in testicular cells and localization of the splice variant TGF-beta2B in testis. Mol Reprod Dev 2006; 73:1211-20. [PMID: 16868931 DOI: 10.1002/mrd.20399] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The transforming growth factors (TGF)-beta, TGF-beta1, TGF-beta2, and TGF-beta3, and their receptors [TbetaRI, TbetaRII, TbetaRIII (betaglycan)] elicit many functions in the testis, for example, they perturb the blood testis barrier (BTB). Although expression of the ligands and receptors have been investigated, the alternative splice variants are incompletely examined. We therefore have analyzed all ligands, the receptors, and the splice variants TbetaRIB, TbetaRIIB, and TGF-beta2B in testicular cells from rat and mouse. In mouse, the novel transcript variant TGF-beta2B was identified and was found in Leydig cells, spermatogonia, pachytene spermatocytes, and in the apical regions of the Sertoli cells in adult testis. Even though expression of the splice variant TbetaRIB could be shown in mouse and rat, we never found the isoform TbetaRIIB in the rat cell lines studied. Whereas in all testicular cells expression of all TGF-beta ligands could be shown, receptor mRNA expression was slightly more diverse. Furthermore, expression pattern of the splice variants was more heterogeneous, for example, TbetaRIB was not detectable in adult Sertoli cells, primary peritubular cells, and immortalized peritubular cells. The heterogeneous expression of the receptors and especially of the splice variants might provide possible clues for the different functions of the TGF-beta ligands in testicular cells.
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Affiliation(s)
- Lutz Konrad
- Department of Urology, Medical Faculty, Marburg, Germany.
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Takeda JI, Suzuki Y, Nakao M, Barrero RA, Koyanagi KO, Jin L, Motono C, Hata H, Isogai T, Nagai K, Otsuki T, Kuryshev V, Shionyu M, Yura K, Go M, Thierry-Mieg J, Thierry-Mieg D, Wiemann S, Nomura N, Sugano S, Gojobori T, Imanishi T. Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56,419 completely sequenced and manually annotated full-length cDNAs. Nucleic Acids Res 2006; 34:3917-28. [PMID: 16914452 PMCID: PMC1557807 DOI: 10.1093/nar/gkl507] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2006] [Revised: 07/03/2006] [Accepted: 07/03/2006] [Indexed: 11/12/2022] Open
Abstract
We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56,419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37,670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants.
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Affiliation(s)
- Jun-ichi Takeda
- Integrated Database Group, Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Mitsuteru Nakao
- Computational Biology Research Center, National Institute of Advanced Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Kazusa DNA Research Institute2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Roberto A. Barrero
- Center for Information Biology and DDBJ, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Kanako O. Koyanagi
- Graduate School of Information Science and Technology, Hokkaido UniversityNorth 14, West 9, Kita-ku, Sapporo, Hokkaido 060-0814, Japan
| | - Lihua Jin
- Center for Information Biology and DDBJ, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Chie Motono
- Computational Biology Research Center, National Institute of Advanced Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
| | - Hiroko Hata
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Takao Isogai
- Reverse Proteomics Research Institute, 2-6-7 Kazusa-KamatariKisarazu, Chiba 292-0818, Japan
- Helix Research Institute, Inc. 1532-3Yana, Kisarazu, Chiba 292-0812, Japan
| | - Keiichi Nagai
- Helix Research Institute, Inc. 1532-3Yana, Kisarazu, Chiba 292-0812, Japan
- Central Research Laboratory, Hitachi Ltd1-280, Higashi-koigakubo, Kokubunji-shi, Tokyo 185-8601, Japan
| | - Tetsuji Otsuki
- Helix Research Institute, Inc. 1532-3Yana, Kisarazu, Chiba 292-0812, Japan
| | - Vladimir Kuryshev
- Division of Molecular Genome Analysis, German Cancer Research CenterIm Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Masafumi Shionyu
- Faculty of Bio-Science, Nagahama Institute of Bio-Science and Technology1266 Tamura-cho, Nagahama, Shiga 526-0829, Japan
| | - Kei Yura
- Quantum Bioinformatics Team, Center for Computational Science and Engineering, Japan Atomic Energy Agency8-1 Umemidai, Kizu, Souraku, Kyoto 619-0215, Japan
- Core Research for Evolution Science and Technology, Japan Science and Technology AgencyJapan
| | - Mitiko Go
- Division of Molecular Genome Analysis, German Cancer Research CenterIm Neuenheimer Feld 580, D-69120 Heidelberg, Germany
- Ochanomizu University2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MD, USA
- Centre National de la Recherche Scientifique, Laboratoire de Physique MathematiqueMontpellier, France
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesda, MD, USA
- Centre National de la Recherche Scientifique, Laboratoire de Physique MathematiqueMontpellier, France
| | - Stefan Wiemann
- Division of Molecular Genome Analysis, German Cancer Research CenterIm Neuenheimer Feld 580, D-69120 Heidelberg, Germany
| | - Nobuo Nomura
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, the University of Tokyo5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan
| | - Takashi Gojobori
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Center for Information Biology and DDBJ, National Institute of Genetics1111 Yata, Mishima, Shizuoka 411-8540, Japan
| | - Tadashi Imanishi
- Biological Information Research Center, National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research BuildingAomi 2-42, Koto-ku, Tokyo 135-0064, Japan
- Graduate School of Information Science and Technology, Hokkaido UniversityNorth 14, West 9, Kita-ku, Sapporo, Hokkaido 060-0814, Japan
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Xing Y, Yu T, Wu YN, Roy M, Kim J, Lee C. An expectation-maximization algorithm for probabilistic reconstructions of full-length isoforms from splice graphs. Nucleic Acids Res 2006; 34:3150-60. [PMID: 16757580 PMCID: PMC1475746 DOI: 10.1093/nar/gkl396] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2006] [Revised: 04/13/2006] [Accepted: 05/10/2006] [Indexed: 11/13/2022] Open
Abstract
Reconstructing full-length transcript isoforms from sequence fragments (such as ESTs) is a major interest and challenge for bioinformatic analysis of pre-mRNA alternative splicing. This problem has been formulated as finding traversals across the splice graph, which is a directed acyclic graph (DAG) representation of gene structure and alternative splicing. In this manuscript we introduce a probabilistic formulation of the isoform reconstruction problem, and provide an expectation-maximization (EM) algorithm for its maximum likelihood solution. Using a series of simulated data and expressed sequences from real human genes, we demonstrate that our EM algorithm can correctly handle various situations of fragmentation and coupling in the input data. Our work establishes a general probabilistic framework for splice graph-based reconstructions of full-length isoforms.
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Affiliation(s)
- Yi Xing
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
| | - Tianwei Yu
- Department of Statistics, University of CaliforniaLos Angeles, USA
- Dental Research Institute, School of Dentistry, University of CaliforniaLos Angeles, USA
| | - Ying Nian Wu
- Department of Statistics, University of CaliforniaLos Angeles, USA
| | - Meenakshi Roy
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
| | - Joseph Kim
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
| | - Christopher Lee
- Molecular Biology Institute, Center for Computational Biology, Department of Chemistry and Biochemistry, University of CaliforniaLos Angeles, USA
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Le K, Mitsouras K, Roy M, Wang Q, Xu Q, Nelson SF, Lee C. Detecting tissue-specific regulation of alternative splicing as a qualitative change in microarray data. Nucleic Acids Res 2004; 32:e180. [PMID: 15598820 PMCID: PMC545471 DOI: 10.1093/nar/gnh173] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2004] [Revised: 11/22/2004] [Accepted: 11/22/2004] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing has recently emerged as a major mechanism of regulation in the human genome, occurring in perhaps 40-60% of human genes. Thus, microarray studies of functional regulation could, in principle, be extended to detect not only the changes in the overall expression of a gene, but also changes in its splicing pattern between different tissues. However, since changes in the total expression of a gene and changes in its alternative splicing can be mixed in complex ways among a set of samples, separating these effects can be difficult, and is essential for their accurate assessment. We present a simple and general approach for distinguishing changes in alternative splicing from changes in expression, based on detecting systematic anti-correlation between the log-ratios of two different samples versus a pool containing both samples. We have tested this analysis method on microarray data for five human tissues, generated using a standard microarray platform and experimental protocols shown previously to be sensitive to alternative splicing. Our automatic analysis was able to detect a wide variety of tissue-specific alternative splicing events, such as exon skipping,mutually exclusive exons, alternative 3' and alternative 5' splicing, alternative initiation and alternative termination, all of which were validated by independent reverse-transcriptase PCR experiments, with validation rates of 70-85%. Our analysis method also enables hierarchical clustering of genes and samples by the level of similarity to their alternative splicing patterns, revealing patterns of tissue-specific regulation that are distinct from those obtained by hierarchical clustering of gene expression from the same microarray data. Our data and analysis source code are available from http://www.bioinformatics.ucla.edu/ASAP.
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Affiliation(s)
- Keith Le
- Department of Chemistry and Biochemistry, Center for Genomics and Proteomics, Molecular Biology Institute, University of California, Los Angeles, CA 90095-1570, USA
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CLOE: identification of putative functional relationships among genes by comparison of expression profiles between two species. BMC Bioinformatics 2004; 5:179. [PMID: 15550177 PMCID: PMC535557 DOI: 10.1186/1471-2105-5-179] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2004] [Accepted: 11/19/2004] [Indexed: 11/22/2022] Open
Abstract
Background Public repositories of microarray data contain an incredible amount of information that is potentially relevant to explore functional relationships among genes by meta-analysis of expression profiles. However, the widespread use of this resource by the scientific community is at the moment limited by the limited availability of effective tools of analysis. We here describe CLOE, a simple cDNA microarray data mining strategy based on meta-analysis of datasets from pairs of species. The method consists in ranking EST probes in the datasets of the two species according to the similarity of their expression profiles with that of two EST probes from orthologous genes, and extracting orthologous EST pairs from a given top interval of the ranked lists. The Gene Ontology annotation of the obtained candidate partners is then analyzed for keywords overrepresentation. Results We demonstrate the capabilities of the approach by testing its predictive power on three proteomically-defined mammalian protein complexes, in comparison with single and multiple species meta-analysis approaches. Our results show that CLOE can find candidate partners for a greater number of genes, if compared to multiple species co-expression analysis, but retains a comparable specificity even when applied to species as close as mouse and human. On the other hand, it is much more specific than single organisms co-expression analysis, strongly reducing the number of potential candidate partners for a given gene of interest. Conclusions CLOE represents a simple and effective data mining approach that can be easily used for meta-analysis of cDNA microarray experiments characterized by very heterogeneous coverage. Importantly, it produces for genes of interest an average number of high confidence putative partners that is in the range of standard experimental validation techniques.
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Kitamura-Abe S, Itoh H, Washio T, Tsutsumi A, Tomita M. Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs. J Bioinform Comput Biol 2004; 2:309-31. [PMID: 15297984 DOI: 10.1142/s0219720004000570] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2003] [Revised: 11/17/2003] [Accepted: 11/17/2003] [Indexed: 11/18/2022]
Abstract
For the purpose of analyzing the relation between the splice sites and the order of introns, we conducted the following analysis for the GT-AG and GC-AG splice site groups. First, the pre-mRNAs of H. sapiens, M. musculus, D. melanogaster, A. thaliana and O. sativa were sampled by mapping the full-length cDNA to the genomes. Next, the consensus sequences at different regions of pre-mRNAs were analyzed in the five species. We also investigated the mononucleotide and dinucleotide frequencies in the extensive regions around the 5' splice sites (5'ss) and 3' splice sites (3'ss). As a result, differential frequencies of nucleotides at the first 5'ss in both the GT-AG and GC-AG splice site groups were observed in A. thaliana and O. sativa pre-mRNAs. The trend, which indicates that GC 5'ss possess strong consensus sequences, was observed not only in mammalian pre-mRNAs but also in the pre-mRNAs of D. melanogaster, A. thaliana and O. sativa. Furthermore, we examined the consensus sequences of the constitutive and alternative splice sites. It was suggested that in the case of the alternative GC-AG introns, the tendency to have a weak consensus sequence at 5'ss is different between H. sapiens and M. musculus pre-mRNAs.
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Affiliation(s)
- Sumie Kitamura-Abe
- Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan.
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Zhou Y, Zhou C, Ye L, Dong J, Xu H, Cai L, Zhang L, Wei L. Database and analyses of known alternatively spliced genes in plants. Genomics 2004; 82:584-95. [PMID: 14611800 DOI: 10.1016/s0888-7543(03)00204-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Alternative splicing is an important cellular mechanism that increases the diversity of gene products. The number of alternatively spliced genes reported so far in plants is much smaller than that in mammals, but is increasing as a result of the explosive growth of available EST and genomic sequences. We have searched for all alternatively spliced genes reported in GenBank and PubMed in all plant species under Viridiplantae. After careful merging and manual review of the search results, we obtained a comprehensive, high-quality collection of 168 genes reported to be alternatively spliced in plants, spanning 44 plant species (March 22, 2003 update). We developed a relational database with Web-based user interface to store and present the data, named the Plant Alternative Splicing Database (PASDB), freely available at http://pasdb.genomics.org.cn. We analyzed the functional categories that these genes belong to using the Gene Ontology. We also analyzed in detail the biological roles and gene structures of the four genes that are known to be alternatively spliced in more than one plant species. Finally, we studied the structural features of the splice sites in the alternatively spliced genes.
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Affiliation(s)
- Yan Zhou
- Hangzhou Genomics Institute, Key Laboratory of Bioinformatics of Zhejiang Province, Zhejiang University, Hangzhou, Zhejiang 310007, China
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Itoh H, Washio T, Tomita M. Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA (NEW YORK, N.Y.) 2004; 10:1005-18. [PMID: 15208437 PMCID: PMC1370592 DOI: 10.1261/rna.5221604] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2003] [Accepted: 04/21/2004] [Indexed: 05/09/2023]
Abstract
We previously reported a computational approach to infer alternative splicing patterns from Mus musculus full-length cDNA clones and microarray data. Although we predicted a large number of unreported splice variants, the general mechanisms regulating alternative splicing were yet unknown. In the present study, we compared alternative exons and constitutive exons in terms of splice-site strength and frequency of potential regulatory sequences. These regulatory features were further compared among five different species: Homo sapiens, M. musculus, Arabidopsis thaliana, Oryza sativa, and Drosophila melanogaster. Solid statistical validations of our comparative analyses indicated that alternative exons have (1) weaker splice sites and (2) more potential regulatory sequences than constitutive exons. Based on our observations, we propose a combinatorial model of alternative splicing mechanisms, which suggests that alternative exons contain weak splice sites regulated alternatively by potential regulatory sequences on the exons.
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Affiliation(s)
- Hitomi Itoh
- Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan
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Castle J, Garrett-Engele P, Armour CD, Duenwald SJ, Loerch PM, Meyer MR, Schadt EE, Stoughton R, Parrish ML, Shoemaker DD, Johnson JM. Optimization of oligonucleotide arrays and RNA amplification protocols for analysis of transcript structure and alternative splicing. Genome Biol 2003; 4:R66. [PMID: 14519201 PMCID: PMC328455 DOI: 10.1186/gb-2003-4-10-r66] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2003] [Revised: 07/25/2003] [Accepted: 08/15/2003] [Indexed: 11/26/2022] Open
Abstract
A novel, unbiased amplification protocol has been developed that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. Microarrays offer a high-resolution means for monitoring pre-mRNA splicing on a genomic scale. We have developed a novel, unbiased amplification protocol that permits labeling of entire transcripts. Also, hybridization conditions, probe characteristics, and analysis algorithms were optimized for detection of exons, exon-intron edges, and exon junctions. These optimized protocols can be used to detect small variations and isoform mixtures, map the tissue specificity of known human alternative isoforms, and provide a robust, scalable platform for high-throughput discovery of alternative splicing.
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Affiliation(s)
- John Castle
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Phil Garrett-Engele
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Christopher D Armour
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Sven J Duenwald
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Patrick M Loerch
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Michael R Meyer
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Eric E Schadt
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Roland Stoughton
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Mark L Parrish
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Daniel D Shoemaker
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
| | - Jason M Johnson
- Rosetta Inpharmatics, Merck & Co. Inc., 12040 115th Ave NE, Kirkland, Washington 98034, USA
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14
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Carninci P, Waki K, Shiraki T, Konno H, Shibata K, Itoh M, Aizawa K, Arakawa T, Ishii Y, Sasaki D, Bono H, Kondo S, Sugahara Y, Saito R, Osato N, Fukuda S, Sato K, Watahiki A, Hirozane-Kishikawa T, Nakamura M, Shibata Y, Yasunishi A, Kikuchi N, Yoshiki A, Kusakabe M, Gustincich S, Beisel K, Pavan W, Aidinis V, Nakagawara A, Held WA, Iwata H, Kono T, Nakauchi H, Lyons P, Wells C, Hume DA, Fagiolini M, Hensch TK, Brinkmeier M, Camper S, Hirota J, Mombaerts P, Muramatsu M, Okazaki Y, Kawai J, Hayashizaki Y. Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res 2003; 13:1273-89. [PMID: 12819125 PMCID: PMC403712 DOI: 10.1101/gr.1119703] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs were enriched in full-length by Cap-Trapper,and in most cases,aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC),which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project,which also include non-protein-coding RNAs,and the lower gene number estimation of genome annotations. Altogether,5'-end clusters identify regions that are potential promoters for 8637 known genes and 5'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.
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Affiliation(s)
- Piero Carninci
- Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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15
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2447381 DOI: 10.1002/cfg.226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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16
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Kan Z, States D, Gish W. Selecting for functional alternative splices in ESTs. Genome Res 2002; 12:1837-45. [PMID: 12466287 PMCID: PMC187565 DOI: 10.1101/gr.764102] [Citation(s) in RCA: 141] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2002] [Accepted: 09/30/2002] [Indexed: 11/24/2022]
Abstract
The expressed sequence tag (EST) collection in dbEST provides an extensive resource for detecting alternative splicing on a genomic scale. Using genomically aligned ESTs, a computational tool (TAP) was used to identify alternative splice patterns for 6400 known human genes from the RefSeq database. With sufficient EST coverage, one or more alternatively spliced forms could be detected for nearly all genes examined. To identify high (>95%) confidence observations of alternative splicing, splice variants were clustered on the basis of having mutually exclusive structures, and sample statistics were then applied. Through this selection, alternative splices expected at a frequency of >5% within their respective clusters were seen for only 17%-28% of genes. Although intron retention events (potentially unspliced messages) had been seen for 36% of the genes overall, the same statistical selection yielded reliable cases of intron retention for <5% of genes. For high-confidence alternative splices in the human ESTs, we also noted significantly higher rates both of cross-species conservation in mouse ESTs and of validation in the GenBank mRNA collection. We suggest quantitative analytical approaches such as these can aid in selecting useful targets for further experimental characterization and in so doing may help elucidate the mechanisms and biological implications of alternative splicing.
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Affiliation(s)
- Zhengyan Kan
- Department of Genetics, Washington University, St. Louis, Missouri 63110, USA
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