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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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Li L, Wang Y, Song G, Zhang X, Gao S, Liu H. HOX cluster-embedded antisense long non-coding RNAs in lung cancer. Cancer Lett 2019; 450:14-21. [PMID: 30807784 DOI: 10.1016/j.canlet.2019.02.036] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/30/2019] [Accepted: 02/19/2019] [Indexed: 12/11/2022]
Abstract
Homeobox (HOX) genes play vital roles in embryonic development and oncogenesis. In humans, there are 39 HOX genes found in four clusters that are located on different chromosomes. The HOX clusters also contain numerous non-protein-coding RNAs, including some lncRNAs. The HOX cluster-embedded lncRNAs (HOX-lncRNAs), most notably, HOTTIP and HOTAIR play a major role in the regulation of their adjacent coding genes. Recently, most HOX-lncRNAs have been shown to impact tumorigenesis and cancer progression. Several HOX-lncRNAs, including HOTTIP, HOXA11-AS, HOTAIRM1, HOXA-AS3, HOXA10-AS, HOTAIR, and HAGLR, are dysregulated in lung cancer. Moreover, their expression levels are correlated with the clinical features of this disease. These HOX-lncRNAs regulate the proliferation, invasion, migration, and chemo-resistance of lung cancer cells through various molecular mechanisms. Although lncRNAs have received much attention lately, the functions of some HOX-lncRNAs in the development of cancer are unclear. Thus, HOX-embedded lncRNAs should be widely investigated in cancer. Here, we review the functions of HOX-lncRNAs in lung cancer.
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Affiliation(s)
- Lianlian Li
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China.
| | - Yong Wang
- Shandong Xinchuang Biotechnology Co., LTD, Jinan, 250102, China
| | | | - Xiaoyu Zhang
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Shan Gao
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China
| | - Hongyan Liu
- Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, China.
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Paralogous HOX13 Genes in Human Cancers. Cancers (Basel) 2019; 11:cancers11050699. [PMID: 31137568 PMCID: PMC6562813 DOI: 10.3390/cancers11050699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/17/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Hox genes (HOX in humans), an evolutionary preserved gene family, are key determinants of embryonic development and cell memory gene program. Hox genes are organized in four clusters on four chromosomal loci aligned in 13 paralogous groups based on sequence homology (Hox gene network). During development Hox genes are transcribed, according to the rule of “spatio-temporal collinearity”, with early regulators of anterior body regions located at the 3’ end of each Hox cluster and the later regulators of posterior body regions placed at the distal 5’ end. The onset of 3’ Hox gene activation is determined by Wingless-type MMTV integration site family (Wnt) signaling, whereas 5’ Hox activation is due to paralogous group 13 genes, which act as posterior-inhibitors of more anterior Hox proteins (posterior prevalence). Deregulation of HOX genes is associated with developmental abnormalities and different human diseases. Paralogous HOX13 genes (HOX A13, HOX B13, HOX C13 and HOX D13) also play a relevant role in tumor development and progression. In this review, we will discuss the role of paralogous HOX13 genes regarding their regulatory mechanisms during carcinogenesis and tumor progression and their use as biomarkers for cancer diagnosis and treatment.
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de Almeida BP, Apolónio JD, Binnie A, Castelo-Branco P. Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. BMC Cancer 2019; 19:219. [PMID: 30866861 PMCID: PMC6416975 DOI: 10.1186/s12885-019-5403-0] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Breast cancer is a highly heterogeneous disease resulting in diverse clinical behaviours and therapeutic responses. DNA methylation is a major epigenetic alteration that is commonly perturbed in cancers. The aim of this study is to characterize the relationship between DNA methylation and aberrant gene expression in breast cancer. METHODS We analysed DNA methylation and gene expression profiles from breast cancer tissue and matched normal tissue in The Cancer Genome Atlas (TCGA). Genome-wide differential methylation analysis and methylation-gene expression correlation was performed. Gene expression changes were subsequently validated in the METABRIC dataset. The Oncoscore tool was used to identify genes that had previously been associated with cancer in the literature. A subset of genes that had not previously been studied in cancer was chosen for further analysis. RESULTS We identified 368 CpGs that were differentially methylated between tumor and normal breast tissue (∆β > 0.4). Hypermethylated CpGs were overrepresented in tumor tissue and were found predominantly (56%) in upstream promoter regions. Conversely, hypomethylated CpG sites were found primarily in the gene body (66%). Expression analysis revealed that 209 of the differentially-methylated CpGs were located in 169 genes that were differently expressed between normal and breast tumor tissue. Methylation-expression correlations were predominantly negative (70%) for promoter CpG sites and positive (74%) for gene body CpG sites. Among these differentially-methylated and differentially-expressed genes, we identified 7 that had not previously been studied in any form of cancer. Three of these, TDRD10, PRAC2 and TMEM132C, contained CpG sites that showed diagnostic and prognostic value in breast cancer, particularly in estrogen-receptor (ER)-positive samples. A pan-cancer analysis confirmed differential expression of these genes together with diagnostic and prognostic value of their respective CpG sites in multiple cancer types. CONCLUSION We have identified 368 DNA methylation changes that characterize breast cancer tumor tissue, of which 209 are associated with genes that are differentially-expressed in the same samples. Novel DNA methylation markers were identified, of which cg12374721 (PRAC2), cg18081940 (TDRD10) and cg04475027 (TMEM132C) show promise as diagnostic and prognostic markers in breast cancer as well as other cancer types.
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Affiliation(s)
- Bernardo P. de Almeida
- Institute of Molecular Medicine, Faculty of Medicine, University of Lisbon, 1649-028 Lisbon, Portugal
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Present address: Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Vienna, Austria
| | - Joana Dias Apolónio
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
| | - Alexandra Binnie
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
- William Osler Health System, Brampton, ON Canada
| | - Pedro Castelo-Branco
- Department of Biomedical Sciences and Medicine, University of Algarve, Campus Gambelas, Bld. 2 - Ala Norte, 8005-139 Faro, Portugal
- Centre for Biomedical Research (CBMR), University of Algarve, 8005-139 Faro, Portugal
- Algarve Biomedical Center, Campus Gambelas, 8005-139 Faro, Portugal
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Xiong Y, Kuang W, Lu S, Guo H, Wu M, Ye M, Wu L. Long noncoding RNA HOXB13-AS1 regulates HOXB13 gene methylation by interacting with EZH2 in glioma. Cancer Med 2018; 7:4718-4728. [PMID: 30105866 PMCID: PMC6144250 DOI: 10.1002/cam4.1718] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 12/30/2022] Open
Abstract
Dysregulation of long noncoding RNAs (lncRNAs) has been implicated in human diseases, in particular, cancers. In this study, we determined the expression of an lncRNA, HOXB13‐AS1, involving in glioma. We showed that HOXB13‐AS1 was significantly upregulated in glioma tissues and cells and was negatively correlated with its surrounding gene HOXB13 levels. Functional experiments in vitro and in vivo revealed that high level of HOXB13‐AS1 increased cell proliferation and tumor growth by promoting cell cycle progression. Conversely, knockdown of HOXB13‐AS1 resulted in decreased cell proliferation and tumor growth. Mechanistically, we showed that HOXB13‐AS1 overexpression increased DNMT3B‐mediated methylation of adjacent gene HOXB13 promoter by binding with the enhancer of zeste homolog 2 (EZH2) using bisulfite sequencing PCR (BSP), epigenetically suppressing HOXB13 expression. Additionally, the interaction between HOXB13‐AS1 and HOXB13 was validated by RNA immunoprecipitation (RIP) and chromatin immunoprecipitation (ChIP) assays using antibody against to EZH2. Taken together, our study indicated that HOXB13‐AS1 could regulate HOXB13 gene expression by methylation HOXB13 promoter and acts as an epigenetic oncogenic in glioma.
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Affiliation(s)
- Yu Xiong
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Kuang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shigang Lu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hua Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Miaojing Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Minhua Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lei Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Genome-wide study to detect single nucleotide polymorphisms associated with visceral and subcutaneous fat deposition in Holstein dairy cows. Animal 2018; 13:487-494. [PMID: 29961431 DOI: 10.1017/s1751731118001519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Excessive abdominal fat might be associated with more severe metabolic disorders in Holstein cows. Our hypothesis was that there are genetic differences between cows with low and high abdominal fat deposition and a normal cover of subcutaneous adipose tissue. The objective of this study was to assess the genetic basis for variation in visceral adiposity in US Holstein cows. The study included adult Holstein cows sampled from a slaughterhouse (Green Bay, WI, USA) during September 2016. Only animals with a body condition score between 2.75 and 3.25 were considered. The extent of omental fat at the level of the insertion of the lesser omentum over the pylorus area was assessed. A group of 100 Holstein cows with an omental fold <5 mm in thickness and minimum fat deposition throughout the entire omentum, and the second group of 100 cows with an omental fold ⩾20 mm in thickness and with a marked fat deposition observed throughout the entire omentum were sampled. A small piece of muscle from the neck was collected from each cow into a sterile container for DNA extraction. Samples were submitted to a commercial laboratory for interrogation of genome-wide genomic variation using the Illumina BovineHD Beadchip. Genome-Wide association analysis was performed to test potential associations between fat deposition and genomic variation. A univariate mixed linear model analysis was performed using genome-wide efficient mixed model association to identify single nucleotide polymorphisms (SNPs) significantly associated with variation in a visceral fat deposition. The chip heritability was 0.686 and the estimated additive genetic and residual variance components were 0.427 and 0.074, respectively. In total, 11 SNPs defining four quantitative trait locus (QTL) regions were found to be significantly associated with visceral fat deposition (P<0.00001). Among them, two of the QTL were detected with four and five significantly associated SNPs, respectively; whereas, the QTLs detected on BTA12 and BTA19 were each detected with only one significantly associated SNP. No enriched gene ontology terms were found within the gene networks harboring these genes when supplied to DAVID using either the Bos taurus or human gene ontology databases. We conclude that excessive omental fat in Holstein cows with similar body condition scores is not caused by a single Mendelian locus and that the trait appears to be at least moderately heritable; consequently, selection to reduce excessive omental fat is potentially possible, but would require the generation of predicted transmitting abilities from larger and random samples of Holstein cattle.
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Perlman EJ, Gadd S, Arold ST, Radhakrishnan A, Gerhard DS, Jennings L, Huff V, Guidry Auvil JM, Davidsen TM, Dome JS, Meerzaman D, Hsu CH, Nguyen C, Anderson J, Ma Y, Mungall AJ, Moore RA, Marra MA, Mullighan CG, Ma J, Wheeler DA, Hampton OA, Gastier-Foster JM, Ross N, Smith MA. MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours. Nat Commun 2015; 6:10013. [PMID: 26635203 PMCID: PMC4686660 DOI: 10.1038/ncomms10013] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 10/23/2015] [Indexed: 12/11/2022] Open
Abstract
Wilms tumour is an embryonal tumour of childhood that closely resembles the developing kidney. Genomic changes responsible for the development of the majority of Wilms tumours remain largely unknown. Here we identify recurrent mutations within Wilms tumours that involve the highly conserved YEATS domain of MLLT1 (ENL), a gene known to be involved in transcriptional elongation during early development. The mutant MLLT1 protein shows altered binding to acetylated histone tails. Moreover, MLLT1-mutant tumours show an increase in MYC gene expression and HOX dysregulation. Patients with MLLT1-mutant tumours present at a younger age and have a high prevalence of precursor intralobar nephrogenic rests. These data support a model whereby activating MLLT1 mutations early in renal development result in the development of Wilms tumour.
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Affiliation(s)
- Elizabeth J. Perlman
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, 225 E. Chicago Ave, Chicago, Illinosis 60611, USA
| | - Samantha Gadd
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, 225 E. Chicago Ave, Chicago, Illinosis 60611, USA
| | - Stefan T. Arold
- King Abdullah University of Science and Technology, Department of Biochemistry and Molecular Biology, Division of Biological and Environmental Sciences and Engineering, Computational Bioscience Research Center, Thuwal 23955, Saudi Arabia
| | - Anand Radhakrishnan
- King Abdullah University of Science and Technology, Department of Biochemistry and Molecular Biology, Division of Biological and Environmental Sciences and Engineering, Computational Bioscience Research Center, Thuwal 23955, Saudi Arabia
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, 31 Center Drive, Bethesda, Maryland 20892, USA
| | - Lawrence Jennings
- Department of Pathology, Ann & Robert H. Lurie Children's Hospital of Chicago, Northwestern University's Feinberg School of Medicine, 225 E. Chicago Ave, Chicago, Illinosis 60611, USA
| | - Vicki Huff
- Department of Genetics, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, Texas 77030, USA
| | - Jaime M. Guidry Auvil
- Office of Cancer Genomics, National Cancer Institute, 31 Center Drive, Bethesda, Maryland 20892, USA
| | - Tanja M. Davidsen
- Office of Cancer Genomics, National Cancer Institute, 31 Center Drive, Bethesda, Maryland 20892, USA
| | - Jeffrey S. Dome
- Department of Pediatrics, Division of Pediatric Hematology/Oncology, Children's National Medical Center, 111 Michigan Avenue, NW, Washington DC 20010, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, Maryland 20892, USA
| | - Chih Hao Hsu
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, Maryland 20892, USA
| | - Cu Nguyen
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, National Institutes of Health, 9609 Medical Center Drive, Bethesda, Maryland 20892, USA
| | - James Anderson
- Frontier Science and Technology Research Foundation, 505 S. Rosa Rd #100, Madison, Wisconsin 53719, USA
| | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Richard A. Moore
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada V5Z 4S6
| | - Charles G. Mullighan
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, Tennessee 38105, USA
| | - Jing Ma
- Department of Pathology, St Jude Children's Research Hospital, 262 Danny Thomas Place, Mail Stop 342, Memphis, Tennessee 38105, USA
| | - David A. Wheeler
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio 43205, USA
| | - Oliver A. Hampton
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio 43205, USA
| | - Julie M. Gastier-Foster
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Departments of Pathology and Pediatrics, Ohio State University College of Medicine, 700 Children's Drive, Columbus, Ohio 43205, USA
| | - Nicole Ross
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Malcolm A. Smith
- Cancer Therapy Evaluation Program, National Cancer Institute, 9609 Medical Center Drive, RM 5-W414, MSC 9737, Bethesda, Maryland 20892, USA
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Koestler DC, Li J, Baron JA, Tsongalis GJ, Butterly LF, Goodrich M, Lesseur C, Karagas MR, Marsit CJ, Moore JH, Andrew AS, Srivastava A. Distinct patterns of DNA methylation in conventional adenomas involving the right and left colon. Mod Pathol 2014; 27:145-55. [PMID: 23868178 PMCID: PMC3880603 DOI: 10.1038/modpathol.2013.104] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 05/05/2013] [Accepted: 05/11/2013] [Indexed: 12/17/2022]
Abstract
Recent studies have shown two distinct non-CIMP methylation clusters in colorectal cancer, raising the possibility that DNA methylation, involving non-CIMP genes, may play a role in the conventional adenoma-carcinoma pathway. A total of 135 adenomas (65 left colon and 70 right colon) were profiled for epigenome-wide DNA methylation using the Illumina HumanMethylation450 BeadChip. A principal components analysis was performed to examine the association between variability in DNA methylation and adenoma location. Linear regression and linear mixed effects models were used to identify locus-specific differential DNA methylation in adenomas of right and left colon. A significant association was present between the first principal component and adenoma location (P=0.007), even after adjustment for subject age and gender (P=0.009). A total of 168 CpG sites were differentially methylated between right- and left-colon adenomas and these loci demonstrated enrichment of homeobox genes (P=3.0 × 10(-12)). None of the 168 probes were associated with CIMP genes. Among CpG loci with the largest difference in methylation between right- and left-colon adenomas, probes associated with PRAC (prostate cancer susceptibility candidate) gene showed hypermethylation in right-colon adenomas whereas those associated with CDX2 (caudal type homeobox transcription factor 2) showed hypermethylation in left-colon adenomas. A subgroup of left-colon adenomas enriched for current smokers (OR=6.1, P=0.004) exhibited a methylation profile similar to right-colon adenomas. In summary, our results indicate distinct patterns of DNA methylation, independent of CIMP genes, in adenomas of the right and left colon.
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Affiliation(s)
- Devin C Koestler
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Jing Li
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - John A Baron
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Gregory J Tsongalis
- Department of Pathology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Lynn F Butterly
- Department of Gastroenterology, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Martha Goodrich
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Corina Lesseur
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Margaret R Karagas
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Carmen J Marsit
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA,Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth College, Hanover, NH, USA
| | - Jason H Moore
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA,Department of Genetics, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
| | - Angeline S Andrew
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth College, Lebanon, NH, USA
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Lenka G, Weng WH, Chuang CK, Ng KF, Pang ST. Aberrant expression of the PRAC gene in prostate cancer. Int J Oncol 2013; 43:1960-6. [PMID: 24100630 DOI: 10.3892/ijo.2013.2117] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/23/2013] [Indexed: 11/06/2022] Open
Abstract
Identification of aberrant expression patterns of genes in prostate cancer (PCa) is a key step towards the development of effective therapies. Prostate-specific antigen (PSA) levels are commonly measured for the early detection of PCa, but which itself is still not an ideal biomarker. We analysed the expression patterns of prostate cancer susceptibility candidate (PRAC) in prostate cancer. The PRAC gene is known to be commonly expressed in prostate tissue, rectum and colon. To provide clear insights into the expression patterns of PRAC in PCa, we examined the gene expression by quantitative real-time PCR (qRT-PCR), western blot analysis and immunohistochemistry (IHC). The results showed that PRAC expression levels in androgen‑insensitive cells (DU145 and PC3) are lower than those in androgen-sensitive cell lines (LNCaP, LNCaP-R and CW22R). However, treatment of the LNCaP cell line with androgen and anti-androgen demonstrated that PRAC is expressed in an androgen-independent manner. Further, PRAC expression was restored upon treatment of DU145 and PC3 cells with the methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5-aza-CdR), which indicates the effect of methylation in the control of PRAC expression. In addition, IHC analysis revealed a significantly decreased immunoreactivity of PRAC protein in PCa tissues compared to benign prostatic hyperplasia (BPH) (p<0.0001). Thus, our findings suggest that the pathogenesis of PCa may be due to the expression levels of PRAC protein, and this protein can serve as a potential biomarker for the management of PCa.
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Affiliation(s)
- Govinda Lenka
- Department of Chemical Engineering and Biotechnology, Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan, R.O.C
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10
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Gascoigne DK, Cheetham SW, Cattenoz PB, Clark MB, Amaral PP, Taft RJ, Wilhelm D, Dinger ME, Mattick JS. Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes. Bioinformatics 2012; 28:3042-50. [PMID: 23044541 DOI: 10.1093/bioinformatics/bts582] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Comparing transcriptomic data with proteomic data to identify protein-coding sequences is a long-standing challenge in molecular biology, one that is exacerbated by the increasing size of high-throughput datasets. To address this challenge, and thereby to improve the quality of genome annotation and understanding of genome biology, we have developed an integrated suite of programs, called Pinstripe. We demonstrate its application, utility and discovery power using transcriptomic and proteomic data from publicly available datasets. RESULTS To demonstrate the efficacy of Pinstripe for large-scale analysis, we applied Pinstripe's reverse peptide mapping pipeline to a transcript library including de novo assembled transcriptomes from the human Illumina Body Atlas (IBA2) and GENCODE v10 gene annotations, and the EBI Proteomics Identifications Database (PRIDE) peptide database. This analysis identified 736 canonical open reading frames (ORFs) supported by three or more PRIDE peptide fragments that are positioned outside any known coding DNA sequence (CDS). Because of the unfiltered nature of the PRIDE database and high probability of false discovery, we further refined this list using independent evidence for translation, including the presence of a Kozak sequence or functional domains, synonymous/non-synonymous substitution ratios and ORF length. Using this integrative approach, we observed evidence of translation from a previously unknown let7e primary transcript, the archetypical lncRNA H19, and a homolog of RD3. Reciprocally, by exclusion of transcripts with mapped peptides or significant ORFs (>80 codon), we identify 32 187 loci with RNAs longer than 2000 nt that are unlikely to encode proteins. AVAILABILITY AND IMPLEMENTATION Pinstripe (pinstripe.matticklab.com) is freely available as source code or a Mono binary. Pinstripe is written in C# and runs under the Mono framework on Linux or Mac OS X, and both under Mono and .Net under Windows. CONTACT m.dinger@garvan.org.au or j.mattick@garvan.org.au SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Dennis K Gascoigne
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Brisbane, Queensland 4072, Australia
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11
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Bera T, Lee B. Mining of Genome Sequence Databases to Identify New Targets for Prostate and Breast Cancer Therapy. Genomics 2008. [DOI: 10.3109/9781420067064-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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12
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Cooper CS, Campbell C, Jhavar S. Mechanisms of Disease: biomarkers and molecular targets from microarray gene expression studies in prostate cancer. ACTA ACUST UNITED AC 2007; 4:677-87. [DOI: 10.1038/ncpuro0946] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 08/24/2007] [Indexed: 11/09/2022]
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13
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Yue Y, Farcas R, Thiel G, Bommer C, Grossmann B, Galetzka D, Kelbova C, Küpferling P, Daser A, Zechner U, Haaf T. De novo t(12;17)(p13.3;q21.3) translocation with a breakpoint near the 5′ end of the HOXB gene cluster in a patient with developmental delay and skeletal malformations. Eur J Hum Genet 2007; 15:570-7. [PMID: 17327879 DOI: 10.1038/sj.ejhg.5201795] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
A boy with severe mental retardation, funnel chest, bell-shaped thorax, and hexadactyly of both feet was found to have a balanced de novo t(12;17)(p13.3;q21.3) translocation. FISH with BAC clones and long-range PCR products assessed in the human genome sequence localized the breakpoint on chromosome 17q21.3 to a 21-kb segment that lies <30 kb upstream of the HOXB gene cluster and immediately adjacent to the 3' end of the TTLL6 gene. The breakpoint on chromosome 12 occurred within telomeric hexamer repeats and, therefore, is not likely to affect gene function directly. We propose that juxtaposition of the HOXB cluster to a repetitive DNA domain and/or separation from required cis-regulatory elements gave rise to a position effect.
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Affiliation(s)
- Ying Yue
- Institute for Human Genetics, Johannes Gutenberg University Mainz, Mainz, Germany
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14
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Calvo A, Gonzalez-Moreno O, Yoon CY, Huh JI, Desai K, Nguyen QT, Green JE. Prostate cancer and the genomic revolution: Advances using microarray analyses. Mutat Res 2005; 576:66-79. [PMID: 15950992 DOI: 10.1016/j.mrfmmm.2004.08.019] [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] [Received: 10/30/2003] [Revised: 08/12/2004] [Accepted: 08/12/2004] [Indexed: 11/30/2022]
Abstract
The emerging technology of microarray analysis allows the establishment of molecular portraits of prostate cancer and the discovery of novel genes involved in the carcinogenesis process. Many novel genes have already been identified using this technique, and functional analyses of these genes are currently being tested. The combination of microarray analysis with other recently developed high-throughput techniques, such as proteomics, tissue arrays, and gene promoter-methylation, especially using tissue microdissection methods, will provide us with more comprehensive insights into how prostate cancer develops and responds to gene-targeted therapies. Animal models of prostate cancer are being characterized by high throughput techniques to better define the similarities and differences between those models and the human disease, and to determine whether particular models may be useful for specific targeted therapies in pre-clinical studies. Although profiling of mRNA expression provides important information of gene expression, the development of proteomic technologies will allow for an even more precise global insight into cellular signaling and structural alterations during prostate carcinogenesis. Not only will the "omic" revolution change basic science, but it will lead to a new era of molecular medicine.
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Affiliation(s)
- Alfonso Calvo
- Laboratory of Cell Regulation and Carcinogenesis, National Cancer Institute, NIH, Building 41, Bethesda, MD 20892, USA
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15
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Edwards S, Campbell C, Flohr P, Shipley J, Giddings I, te-Poele R, Dodson A, Foster C, Clark J, Jhavar S, Kovacs G, Cooper CS. Expression analysis onto microarrays of randomly selected cDNA clones highlights HOXB13 as a marker of human prostate cancer. Br J Cancer 2005; 92:376-81. [PMID: 15583692 PMCID: PMC2361840 DOI: 10.1038/sj.bjc.6602261] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In a strategy aimed at identifying novel markers of human prostate cancer, we performed expression analysis using microarrays of clones randomly selected from a cDNA library prepared from the LNCaP prostate cancer cell line. Comparisons of expression profiles in primary human prostate cancer, adjacent normal prostate tissue, and a selection of other (nonprostate) normal human tissues, led to the identification of a set of clones that were judged as the best candidate markers of normal and/or malignant prostate tissue. DNA sequencing of the selected clones revealed that they included 10 genes that had previously been established as prostate markers: NKX3.1, KLK2, KLK3 (PSA), FOLH1 (PSMA), STEAP2, PSGR, PRAC, RDH11, Prostein and FASN. Following analysis of the expression patterns of all selected and sequenced genes through interrogation of SAGE databases, a further three genes from our clone set, HOXB13, SPON2 and NCAM2, emerged as additional candidate markers of human prostate cancer. Quantitative RT-PCR demonstrated the specificity of expression of HOXB13 in prostate tissue and revealed its ubiquitous expression in a series of 37 primary prostate cancers and 20 normal prostates. These results demonstrate the utility of this expression-microarray approach in hunting for new markers of individual human cancer types.
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Affiliation(s)
- S Edwards
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - C Campbell
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TR, UK
| | - P Flohr
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - J Shipley
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - I Giddings
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - R te-Poele
- CRUK Centre for Cancer Therapeutics, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - A Dodson
- Department of Pathology & Molecular Genetics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C Foster
- Department of Pathology & Molecular Genetics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - J Clark
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - S Jhavar
- Section of Cancer Genetics, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - G Kovacs
- Laboratory of Molecular Oncology, University Surgical Hospital, Im Neuenheimer Feld 365, Heidelberg 69120, Germany
| | - C S Cooper
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK. E-mail:
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16
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Strausberg RL, Simpson AJG, Old LJ, Riggins GJ. Oncogenomics and the development of new cancer therapies. Nature 2004; 429:469-74. [PMID: 15164073 DOI: 10.1038/nature02627] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Scientists have sequenced the human genome and identified most of its genes. Now it is time to use these genomic data, and the high-throughput technology developed to generate them, to tackle major health problems such as cancer. To accelerate our understanding of this disease and to produce targeted therapies, further basic mutational and functional genomic information is required. A systematic and coordinated approach, with the results freely available, should speed up progress. This will best be accomplished through an international academic and pharmaceutical oncogenomics initiative.
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Affiliation(s)
- Robert L Strausberg
- Department of Mammalian Genomics, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 2085, USA.
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