1
|
Bartonicek N, Clark MB, Quek XC, Torpy JR, Pritchard AL, Maag JLV, Gloss BS, Crawford J, Taft RJ, Hayward NK, Montgomery GW, Mattick JS, Mercer TR, Dinger ME. Intergenic disease-associated regions are abundant in novel transcripts. Genome Biol 2017; 18:241. [PMID: 29284497 PMCID: PMC5747244 DOI: 10.1186/s13059-017-1363-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genotyping of large populations through genome-wide association studies (GWAS) has successfully identified many genomic variants associated with traits or disease risk. Unexpectedly, a large proportion of GWAS single nucleotide polymorphisms (SNPs) and associated haplotype blocks are in intronic and intergenic regions, hindering their functional evaluation. While some of these risk-susceptibility regions encompass cis-regulatory sites, their transcriptional potential has never been systematically explored. RESULTS To detect rare tissue-specific expression, we employed the transcript-enrichment method CaptureSeq on 21 human tissues to identify 1775 multi-exonic transcripts from 561 intronic and intergenic haploblocks associated with 392 traits and diseases, covering 73.9 Mb (2.2%) of the human genome. We show that a large proportion (85%) of disease-associated haploblocks express novel multi-exonic non-coding transcripts that are tissue-specific and enriched for GWAS SNPs as well as epigenetic markers of active transcription and enhancer activity. Similarly, we captured transcriptomes from 13 melanomas, targeting nine melanoma-associated haploblocks, and characterized 31 novel melanoma-specific transcripts that include fusion proteins, novel exons and non-coding RNAs, one-third of which showed allelically imbalanced expression. CONCLUSIONS This resource of previously unreported transcripts in disease-associated regions ( http://gwas-captureseq.dingerlab.org ) should provide an important starting point for the translational community in search of novel biomarkers, disease mechanisms, and drug targets.
Collapse
Affiliation(s)
- N Bartonicek
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - M B Clark
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Psychiatry, University of Oxford, Warneford Hospital, Oxford, UK
| | - X C Quek
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - J R Torpy
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - A L Pritchard
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - J L V Maag
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - B S Gloss
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - J Crawford
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - R J Taft
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
- Illumina, Inc., San Diego, CA, USA
| | - N K Hayward
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - G W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - J S Mattick
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - T R Mercer
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
- Altius Institute for Biomedical Sciences, Seattle, USA
| | - M E Dinger
- Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia.
| |
Collapse
|
2
|
O'Brien PM, Davies MJ, Scurry JP, Smith AN, Barton CA, Henderson MJ, Saunders DN, Gloss BS, Patterson KI, Clancy JL, Heinzelmann-Schwarz VA, Murali R, Scolyer RA, Zeng Y, Williams ED, Scurr L, DeFazio A, Quinn D, Watts CKW, Hacker NF, Henshall SM, Sutherland RL. Erratum: The E3 ubiquitin ligase EDD is an adverse prognostic factor for serous epithelial ovarian cancer and modulates cisplatin resistance in vitro. Br J Cancer 2008. [PMCID: PMC2410105 DOI: 10.1038/sj.bjc.6604419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
|
3
|
O'Brien PM, Davies MJ, Scurry JP, Smith AN, Barton CA, Henderson MJ, Saunders DN, Gloss BS, Patterson KI, Clancy JL, Heinzelmann-Schwarz VA, Murali R, Scolyer RA, Zeng Y, Williams ED, Scurr L, Defazio A, Quinn DI, Watts CKW, Hacker NF, Henshall SM, Sutherland RL. The E3 ubiquitin ligase EDD is an adverse prognostic factor for serous epithelial ovarian cancer and modulates cisplatin resistance in vitro. Br J Cancer 2008; 98:1085-93. [PMID: 18349819 PMCID: PMC2275489 DOI: 10.1038/sj.bjc.6604281] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Despite a high initial response rate to first-line platinum/paclitaxel chemotherapy, most women with epithelial ovarian cancer relapse with recurrent disease that becomes refractory to further cytotoxic treatment. We have previously shown that the E3 ubiquitin ligase, EDD, a regulator of DNA damage responses, is amplified and overexpressed in serous ovarian carcinoma. Given that DNA damage pathways are linked to platinum resistance, the aim of this study was to determine if EDD expression was associated with disease recurrence and platinum sensitivity in serous ovarian cancer. High nuclear EDD expression, as determined by immunohistochemistry in a cohort of 151 women with serous ovarian carcinoma, was associated with an approximately two-fold increased risk of disease recurrence and death in patients who initially responded to first-line chemotherapy, independently of disease stage and suboptimal debulking. Although EDD expression was not directly correlated with relative cisplatin sensitivity of ovarian cancer cell lines, sensitivity to cisplatin was partially restored in platinum-resistant A2780-cp70 ovarian cancer cells following siRNA-mediated knockdown of EDD expression. These results identify EDD as a new independent prognostic marker for outcome in serous ovarian cancer, and suggest that pathways involving EDD, including DNA damage responses, may represent new therapeutic targets for chemoresistant ovarian cancer.
Collapse
Affiliation(s)
- P M O'Brien
- Garvan Institute of Medical Research, Darlinghurst, Sydney, New South Wales 2010, Australia .
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|