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Lechpammer M, Todd A, Tang V, Morningstar T, Borowsky A, Shahlaie K, Kintner JA, McPherson JD, Bishop JW, Fereidouni F, Harmany ZT, Coley N, Zagzag D, Wong JWH, Tao J, Hesson LB, Burnett L, Levenson R. Neuropathological Applications of Microscopy with Ultraviolet Surface Excitation (MUSE): A Concordance Study of Human Primary and Metastatic Brain Tumors. Brain Sci 2024; 14:108. [PMID: 38275528 PMCID: PMC10813539 DOI: 10.3390/brainsci14010108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/10/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Whereas traditional histology and light microscopy require multiple steps of formalin fixation, paraffin embedding, and sectioning to generate images for pathologic diagnosis, Microscopy using Ultraviolet Surface Excitation (MUSE) operates through UV excitation on the cut surface of tissue, generating images of high resolution without the need to fix or section tissue and allowing for potential use for downstream molecular tests. Here, we present the first study of the use and suitability of MUSE microscopy for neuropathological samples. MUSE images were generated from surgical biopsy samples of primary and metastatic brain tumor biopsy samples (n = 27), and blinded assessments of diagnoses, tumor grades, and cellular features were compared to corresponding hematoxylin and eosin (H&E) images. A set of MUSE-treated samples subsequently underwent exome and targeted sequencing, and quality metrics were compared to those from fresh frozen specimens. Diagnostic accuracy was relatively high, and DNA and RNA integrity appeared to be preserved for this cohort. This suggests that MUSE may be a reliable method of generating high-quality diagnostic-grade histologic images for neuropathology on a rapid and sample-sparing basis and for subsequent molecular analysis of DNA and RNA.
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Affiliation(s)
- Mirna Lechpammer
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
- Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, New York, NY 10016, USA
- Pathology and Laboratory Operations, Foundation Medicine, Inc., Cambridge, MA 02141, USA
| | - Austin Todd
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - Vivian Tang
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - Taryn Morningstar
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - Alexander Borowsky
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - Kiarash Shahlaie
- Department of Neurosurgery, University of California Davis Health, Sacramento, CA 95817, USA;
| | - John A. Kintner
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - John D. McPherson
- Department of Biochemistry and Molecular Medicine, University of California Davis Health, Sacramento, CA 95817, USA;
| | - John W. Bishop
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - Farzad Fereidouni
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - Zachary T. Harmany
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - Nicholas Coley
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
| | - David Zagzag
- Departments of Pathology and Neurosurgery, New York University Langone Medical Center, New York, NY 10016, USA;
| | - Jason W. H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China;
| | - Jiang Tao
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst NSW 2010, Australia; (J.T.); (L.B.H.); (L.B.)
- School of Clinical Medicine, University of New South Wales Sydney, St Vincent’s Healthcare Clinical Campus, Darlinghurst NSW 2010, Australia
| | - Luke B. Hesson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst NSW 2010, Australia; (J.T.); (L.B.H.); (L.B.)
- Department of Molecular Genetics, Douglass Hanly Moir Pathology, Macquarie Park NSW 2113, Australia
- School of Clinical Medicine, University of New South Wales Sydney, Randwick NSW 2052, Australia
| | - Leslie Burnett
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst NSW 2010, Australia; (J.T.); (L.B.H.); (L.B.)
- School of Clinical Medicine, University of New South Wales Sydney, St Vincent’s Healthcare Clinical Campus, Darlinghurst NSW 2010, Australia
| | - Richard Levenson
- Department of Pathology and Laboratory Medicine, University of California Davis Health, Sacramento, CA 95817, USA; (A.T.); (V.T.); (T.M.); (A.B.); (J.A.K.); (J.W.B.); (F.F.); (Z.T.H.); (N.C.); (R.L.)
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Saya S, Chondros P, Abela A, Mihalopolous C, Chatterton ML, Gunn J, Chen TF, Polasek TM, Dettmann E, Brooks R, King M, Spencer L, Alphonse P, Milton S, Ramsay G, Siviour Z, Liew J, Ly P, Thoenig M, Seychell R, La Rocca F, Hesson LB, Mejias N, Sivertsen T, Galea MA, Bousman C, Emery J. The PRESIDE (PhaRmacogEnomicS In DEpression) Trial: a double-blind randomised controlled trial of pharmacogenomic-informed prescribing of antidepressants on depression outcomes in patients with major depressive disorder in primary care. Trials 2023; 24:342. [PMID: 37208772 DOI: 10.1186/s13063-023-07361-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 05/06/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND The evidence for the clinical utility of pharmacogenomic (PGx) testing is growing, and guidelines exist for the use of PGx testing to inform prescribing of 13 antidepressants. Although previous randomised controlled trials of PGx testing for antidepressant prescribing have shown an association with remission of depression in clinical psychiatric settings, few trials have focused on the primary care setting, where most antidepressant prescribing occurs. METHODS The PRESIDE Trial is a stratified double-blinded randomised controlled superiority trial that aims to evaluate the impact of a PGx-informed antidepressant prescribing report (compared with standard prescribing using the Australian Therapeutic Guidelines) on depressive symptoms after 12 weeks, when delivered in primary care. Six hundred seventy-two patients aged 18-65 years of general practitioners (GPs) in Victoria with moderate to severe depressive symptoms, measured using the Patient Health Questionnaire-9 (PHQ-9), will be randomly allocated 1:1 to each arm using a computer-generated sequence. Participants and GPs will be blinded to the study arm. The primary outcome is a difference between arms in the change of depressive symptoms, measured using the PHQ-9 after 12 weeks. Secondary outcomes include a difference between the arms in change in PHQ-9 score at 4, 8 and 26 weeks, proportion in remission at 12 weeks, a change in side effect profile of antidepressant medications, adherence to antidepressant medications, change in quality of life and cost-effectiveness of the intervention. DISCUSSION This trial will provide evidence as to whether PGx-informed antidepressant prescribing is clinically efficacious and cost-effective. It will inform national and international policy and guidelines about the use of PGx to select antidepressants for people with moderate to severe depressive symptoms presenting in primary care. TRIAL REGISTRATION Australian and New Zealand Clinical Trial Registry ACTRN12621000181808. Registered on 22 February 2021.
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Affiliation(s)
- Sibel Saya
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia.
| | - Patty Chondros
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
| | - Anastasia Abela
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Cathrine Mihalopolous
- School of Public Health and Preventive Medicine, Monash University Health Economics Group, Monash University, Melbourne, VIC, Australia
| | - Mary Lou Chatterton
- School of Public Health and Preventive Medicine, Monash University Health Economics Group, Monash University, Melbourne, VIC, Australia
| | - Jane Gunn
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
| | - Timothy F Chen
- Sydney Pharmacy School, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Thomas M Polasek
- , Certara, Princeton, NJ, USA
- Centre for Medicine Use and Safety, Monash University, Melbourne, Australia
| | - Elise Dettmann
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
| | - Rachel Brooks
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Michelle King
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Luke Spencer
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Pavithran Alphonse
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Shakira Milton
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Georgia Ramsay
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Zoe Siviour
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Jamie Liew
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Philip Ly
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Matthew Thoenig
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Raushaan Seychell
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Floriana La Rocca
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
| | - Luke B Hesson
- Genetics Department, Douglass Hanly Moir Pathology, Sonic Healthcare, Sydney, NSW, Australia
- School of Clinical Medicine, Faculty of Medicine, UNSW Sydney, Randwick, NSW, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | | | - Terri Sivertsen
- Genetics Department, Douglass Hanly Moir Pathology, Sonic Healthcare, Sydney, NSW, Australia
| | - Melanie Anne Galea
- Genetics Department, Douglass Hanly Moir Pathology, Sonic Healthcare, Sydney, NSW, Australia
| | - Chad Bousman
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Jon Emery
- Department of General Practice and Primary Care, Melbourne Medical School, University of Melbourne, Melbourne, Australia
- Centre for Cancer Research, University of Melbourne, Melbourne, Australia
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Yeola A, Subramanian S, Oliver RA, Lucas CA, Thoms JAI, Yan F, Olivier J, Chacon D, Tursky ML, Srivastava P, Potas JR, Hung T, Power C, Hardy P, Ma DD, Kilian KA, McCarroll J, Kavallaris M, Hesson LB, Beck D, Curtis DJ, Wong JWH, Hardeman EC, Walsh WR, Mobbs R, Chandrakanthan V, Pimanda JE. Induction of muscle-regenerative multipotent stem cells from human adipocytes by PDGF-AB and 5-azacytidine. Sci Adv 2021; 7:7/3/eabd1929. [PMID: 33523875 PMCID: PMC7806226 DOI: 10.1126/sciadv.abd1929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 11/23/2020] [Indexed: 06/12/2023]
Abstract
Terminally differentiated murine osteocytes and adipocytes can be reprogrammed using platelet-derived growth factor-AB and 5-azacytidine into multipotent stem cells with stromal cell characteristics. We have now optimized culture conditions to reprogram human adipocytes into induced multipotent stem (iMS) cells and characterized their molecular and functional properties. Although the basal transcriptomes of adipocyte-derived iMS cells and adipose tissue-derived mesenchymal stem cells were similar, there were changes in histone modifications and CpG methylation at cis-regulatory regions consistent with an epigenetic landscape that was primed for tissue development and differentiation. In a non-specific tissue injury xenograft model, iMS cells contributed directly to muscle, bone, cartilage, and blood vessels, with no evidence of teratogenic potential. In a cardiotoxin muscle injury model, iMS cells contributed specifically to satellite cells and myofibers without ectopic tissue formation. Together, human adipocyte-derived iMS cells regenerate tissues in a context-dependent manner without ectopic or neoplastic growth.
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Affiliation(s)
- Avani Yeola
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Shruthi Subramanian
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Rema A Oliver
- Surgical and Orthopaedic Research Laboratories, Prince of Wales Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Christine A Lucas
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Julie A I Thoms
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Feng Yan
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Jake Olivier
- School of Mathematics and Statistics, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Diego Chacon
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - Melinda L Tursky
- St. Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney and St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Pallavi Srivastava
- School of Material Sciences and Engineering, School of Chemistry, Australian Centre for Nanomedicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Jason R Potas
- Translational Neuroscience Facility, School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Tzongtyng Hung
- Biological Resources Imaging Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Carl Power
- Biological Resources Imaging Laboratory, Mark Wainwright Analytical Centre, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - David D Ma
- St. Vincent's Centre for Applied Medical Research, St Vincent's Hospital Sydney and St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2010, Australia
| | - Kristopher A Kilian
- School of Material Sciences and Engineering, School of Chemistry, Australian Centre for Nanomedicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Joshua McCarroll
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales Sydney, Sydney, NSW, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Australian Centre for Nanomedicine, UNSW Sydney, Sydney, NSW 2052, Australia
- School of Women's and Children's Health, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Luke B Hesson
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Dominik Beck
- School of Biomedical Engineering, University of Technology Sydney, Sydney, NSW 2007, Australia
| | - David J Curtis
- Australian Centre for Blood Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Department of Clinical Haematology, Alfred Health, Melbourne, VIC, Australia
| | - Jason W H Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region
| | - Edna C Hardeman
- Cellular and Genetic Medicine Unit, School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | - William R Walsh
- Surgical and Orthopaedic Research Laboratories, Prince of Wales Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Ralph Mobbs
- Surgical and Orthopaedic Research Laboratories, Prince of Wales Clinical School, UNSW Sydney, Sydney, NSW 2052, Australia
- Department of Neurosurgery, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Vashe Chandrakanthan
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia.
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - John E Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW 2052, Australia.
- School of Medical Sciences, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
- Prince of Wales Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
- Department of Haematology, Prince of Wales Hospital, Randwick, NSW 2031, Australia
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Morris MJ, Hesson LB, Youngson NA. Non-CpG methylation biases bisulphite PCR towards low or unmethylated mitochondrial DNA: recommendations for the field. Environ Epigenet 2020; 6:dvaa001. [PMID: 32154030 PMCID: PMC7055202 DOI: 10.1093/eep/dvaa001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/31/2020] [Accepted: 02/03/2020] [Indexed: 05/04/2023]
Abstract
Mitochondrial DNA (mtDNA) is a circular genome of 16 kb that is present in multiple copies in mitochondria. mtDNA codes for genes that contribute to mitochondrial structure and function. A long-standing question has asked whether mtDNA is epigenetically regulated similarly to the nuclear genome. Recently published data suggest that unlike the nuclear genome where CpG methylation is the norm, mtDNA is methylated predominantly at non-CpG cytosines. This raises important methodological considerations for future investigations. In particular, existing bisulphite PCR techniques may be unsuitable due to primers being biased towards amplification from unmethylated mtDNA. Here, we describe how this may have led to previous studies underestimating the level of mtDNA methylation and reiterate methodological strategies for its accurate assessment.
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Affiliation(s)
| | - Luke B Hesson
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, NSW 2052, Australia
| | - Neil A Youngson
- School of Medical Sciences, UNSW Sydney, NSW 2052, Australia
- The Institute of Hepatology, Foundation for Liver Research, London, SE5 9NT, UK
- Faculty of Life Sciences and Medicine, King’s College London, London, UK
- Correspondence address. The Institute of Hepatology, Foundation for Liver Research, London, UK. Tel : +44 (0)20 7255 9835; E-mail:
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Poulos RC, Perera D, Packham D, Shah A, Janitz C, Pimanda JE, Hawkins N, Ward RL, Hesson LB, Wong JWH. Scarcity of Recurrent Regulatory Driver Mutations in Colorectal Cancer Revealed by Targeted Deep Sequencing. JNCI Cancer Spectr 2019; 3:pkz012. [PMID: 31360895 PMCID: PMC6649856 DOI: 10.1093/jncics/pkz012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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] [Received: 09/26/2018] [Revised: 02/07/2019] [Accepted: 02/22/2019] [Indexed: 11/18/2022] Open
Abstract
Background Genetic testing of cancer samples primarily focuses on protein-coding regions, despite most mutations arising in noncoding DNA. Noncoding mutations can be pathogenic if they disrupt gene regulation, but the benefits of assessing promoter mutations in driver genes by panel testing has not yet been established. This is especially the case in colorectal cancer, for which few putative driver variants at regulatory elements have been reported. Methods We designed a unique target capture sequencing panel of 39 colorectal cancer driver genes and their promoters, together with more than 35 megabases of regulatory elements focusing on gene promoters. Using this panel, we sequenced 95 colorectal cancer and matched normal samples at high depth, averaging 170× and 82× coverage, respectively. Results Our target capture sequencing design enabled improved coverage and variant detection across captured regions. We found cases with hereditary defects in mismatch and base excision repair due to deleterious germline coding variants, and we identified mutational spectra consistent with these repair deficiencies. Focusing on gene promoters and other regulatory regions, we found little evidence for base or region-specific recurrence of functional somatic mutations. Promoter elements, including TERT, harbored few mutations, with none showing strong functional evidence. Recurrent regulatory mutations were rare in our sequenced regions in colorectal cancer, though we highlight some candidate mutations for future functional studies. Conclusions Our study supports recent findings that regulatory driver mutations are rare in many cancer types and suggests that the inclusion of promoter regions into cancer panel testing is currently likely to have limited clinical utility in colorectal cancer.
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Affiliation(s)
- Rebecca C Poulos
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.,Children's Medical Research Institute, Faculty of Medicine and Health The University of Sydney, Westmead, NSW, Australia
| | - Dilmi Perera
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Deborah Packham
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Anushi Shah
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Caroline Janitz
- Next-Generation Sequencing Facility, Office of the Deputy Vice-Chancellor (R&D), Western Sydney University, Penrith, NSW, Australia
| | - John E Pimanda
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.,Department of Haematology, Prince of Wales Hospital, Sydney, NSW, Australia.,School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia
| | - Nicholas Hawkins
- School of Medical Sciences, UNSW Sydney, Sydney, NSW, Australia.,Faculty of Medicine, The University of Queensland, Herston, QLD, Australia
| | - Robyn L Ward
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.,Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Luke B Hesson
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia
| | - Jason W H Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW, Australia.,School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
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Hesson LB, Pritchard AL. Genetics and Epigenetics: A Historical Overview. Clin Epigenetics 2019. [DOI: 10.1007/978-981-13-8958-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Morris MJ, Hesson LB, Poulos RC, Ward RL, Wong JWH, Youngson NA. Reduced nuclear DNA methylation and mitochondrial transcript changes in adenomas do not associate with mtDNA methylation. Biomark Res 2018; 6:37. [PMID: 30619609 PMCID: PMC6311003 DOI: 10.1186/s40364-018-0151-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/28/2018] [Indexed: 12/15/2022] Open
Abstract
Background Altered mitochondrial function and large-scale changes to DNA methylation patterns in the nuclear genome are both hallmarks of colorectal cancer (CRC). Mitochondria have multiple copies of a 16 kb circular genome that contains genes that are vital for their function. While DNA methylation is known to alter the nuclear genome in CRC, it is not clear whether it could have a similar influence in mtDNA; indeed, currently, the issue of whether mitochondrial genome (mtDNA) methylation occurs is controversial. Thus our goal here was to determine whether the methylation state of mtDNA is linked to mitochondrial gene transcription in colorectal adenomas, and to assess its suitability as a biomarker in CRC. Methods To investigate the relationship between DNA methylation and mitochondrial transcripts in adenomas, we performed RNA-sequencing and Whole Genome Bisulphite Sequencing (WGBS) of mtDNA-enriched DNA from normal mucosa and paired adenoma patient samples. Results Transcriptional profiling indicated that adenomas had reduced mitochondrial proton transport versus normal mucosa, consistent with altered mitochondrial function. The expression of 3 tRNAs that are transcribed from mtDNA were also decreased in adenoma. Overall methylation of CG dinucleotides in the nuclear genome was reduced in adenomas (68%) compared to normal mucosa (75%, P < 0.01). Methylation in mtDNA was low (1%) in both normal and adenoma tissue but we observed clusters of higher methylation at the ribosomal RNA genes. Levels of methylation within these regions did not differ between normal and adenoma tissue. Conclusions We provide evidence that low-level methylation of specific sites does exist in the mitochondrial genome but that it is not associated with mitochondrial gene transcription changes in adenomas. Furthermore, as no large scale changes to mtDNA methylation were observed it is unlikely to be a suitable biomarker for early-stage CRC. Electronic supplementary material The online version of this article (10.1186/s40364-018-0151-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M J Morris
- 1Department of Pharmacology, School of Medical Sciences, UNSW Sydney, Sydney, NSW Australia
| | - L B Hesson
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia
| | - R C Poulos
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia.,3Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, NSW Australia
| | - R L Ward
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia.,4Office of the Deputy Vice-Chancellor (Research), University of Queensland, QLD, Brisbane, Australia
| | - J W H Wong
- 2Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Sydney, Sydney, NSW Australia.,5School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong, Special Administrative Region of China
| | - N A Youngson
- 1Department of Pharmacology, School of Medical Sciences, UNSW Sydney, Sydney, NSW Australia
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8
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Liu Q, Thoms JAI, Nunez AC, Huang Y, Knezevic K, Packham D, Poulos RC, Williams R, Beck D, Hawkins NJ, Ward RL, Wong JWH, Hesson LB, Sloane MA, Pimanda JE. Disruption of a -35 kb Enhancer Impairs CTCF Binding and MLH1 Expression in Colorectal Cells. Clin Cancer Res 2018; 24:4602-4611. [PMID: 29898989 DOI: 10.1158/1078-0432.ccr-17-3678] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 04/17/2018] [Accepted: 06/06/2018] [Indexed: 11/16/2022]
Abstract
Purpose:MLH1 is a major tumor suppressor gene involved in the pathogenesis of Lynch syndrome and various sporadic cancers. Despite their potential pathogenic importance, genomic regions capable of regulating MLH1 expression over long distances have yet to be identified.Experimental Design: Here, we use chromosome conformation capture (3C) to screen a 650-kb region flanking the MLH1 locus to identify interactions between the MLH1 promoter and distal regions in MLH1-expressing and nonexpressing cells. Putative enhancers were functionally validated using luciferase reporter assays, chromatin immunoprecipitation, and CRISPR-Cas9-mediated deletion of endogenous regions. To evaluate whether germline variants in the enhancer might contribute to impaired MLH1 expression in patients with suspected Lynch syndrome, we also screened germline DNA from a cohort of 74 patients with no known coding mutations or epimutations at the MLH1 promoter.Results: A 1.8-kb DNA fragment, 35 kb upstream of the MLH1 transcription start site enhances MLH1 gene expression in colorectal cells. The enhancer was bound by CTCF and CRISPR-Cas9-mediated deletion of a core binding region impairs endogenous MLH1 expression. A total of 5.4% of suspected Lynch syndrome patients have a rare single-nucleotide variant (G > A; rs143969848; 2.5% in gnomAD European, non-Finnish) within a highly conserved CTCF-binding motif, which disrupts enhancer activity in SW620 colorectal carcinoma cells.Conclusions: A CTCF-bound region within the MLH1-35 enhancer regulates MLH1 expression in colorectal cells and is worthy of scrutiny in future genetic screening strategies for suspected Lynch syndrome associated with loss of MLH1 expression. Clin Cancer Res; 24(18); 4602-11. ©2018 AACR.
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Affiliation(s)
- Qing Liu
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Julie A I Thoms
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
- School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Yizhou Huang
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, New South Wales, Australia
| | - Kathy Knezevic
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Deborah Packham
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Rebecca C Poulos
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Rachel Williams
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Dominik Beck
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, New South Wales, Australia
| | - Nicholas J Hawkins
- School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
| | - Robyn L Ward
- School of Medicine, The University of Queensland, Brisbane, Queensland, Australia
- Level 3, Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland, Australia
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia.
- Genome.One, Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia.
- Australian Museum, Sydney, New South Wales, Australia
| | - John E Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia.
- School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia
- Department of Haematology, Prince of Wales Hospital, Randwick, New South Wales, Australia
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9
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Unnikrishnan A, Vo ANQ, Pickford R, Raftery MJ, Nunez AC, Verma A, Hesson LB, Pimanda JE. AZA-MS: a novel multiparameter mass spectrometry method to determine the intracellular dynamics of azacitidine therapy in vivo. Leukemia 2017; 32:900-910. [PMID: 29249821 PMCID: PMC5886051 DOI: 10.1038/leu.2017.340] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 01/19/2023]
Abstract
The cytidine analogue, 5-azacytidine (AZA; 5-AZA-cR), is the primary treatment for myelodysplastic syndrome and chronic myelomonocytic leukaemia. However, only ~50% of treated patients will respond to AZA and the drivers of AZA resistance in vivo are poorly understood. To better understand the intracellular dynamics of AZA upon therapy and decipher the molecular basis for AZA resistance, we have developed a novel, multiparameter, quantitative mass spectrometry method (AZA-MS). Using AZA-MS, we have accurately quantified the abundance of the ribonucleoside (5-AZA-cR) and deoxyribonucleoside (5-AZA-CdR) forms of AZA in RNA, DNA and the cytoplasm within the same sample using nanogram quantities of input material. We report that although AZA induces DNA demethylation in a dose-dependent manner, it has no corresponding effect on RNA methylation. By applying AZA-MS to primary bone marrow samples from patients undergoing AZA therapy, we have identified that responders accumulate more 5-AZA-CdR in their DNA compared with nonresponders. AZA resistance was not a result of impaired AZA metabolism or intracellular accumulation. Furthermore, AZA-MS has helped to uncover different modes of AZA resistance. Whereas some nonresponders fail to incorporate sufficient 5-AZA-CdR into DNA, others incorporate 5-AZA-CdR and effect DNA demethylation like AZA responders, but show no clinical benefit.
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Affiliation(s)
- A Unnikrishnan
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - A N Q Vo
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - R Pickford
- Bioanalytical Mass Spectrometry Facility, UNSW Sydney, Sydney, New South Wales, Australia
| | - M J Raftery
- Bioanalytical Mass Spectrometry Facility, UNSW Sydney, Sydney, New South Wales, Australia
| | - A C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - A Verma
- Climate Change Cluster, University of Technology Sydney, Sydney, New South Wales, Australia
| | - L B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - J E Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Sydney, New South Wales, Australia.,Prince of Wales Clinical School, UNSW Sydney, Sydney, New South Wales, Australia.,Department of Pathology, School of Medical Sciences, UNSW Sydney, Sydney, New South Wales, Australia.,Haematology Department, Prince of Wales Hospital, Randwick, New South Wales, Australia
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10
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Luo A, Leach ST, Barres R, Hesson LB, Grimm MC, Simar D. The Microbiota and Epigenetic Regulation of T Helper 17/Regulatory T Cells: In Search of a Balanced Immune System. Front Immunol 2017; 8:417. [PMID: 28443096 PMCID: PMC5385369 DOI: 10.3389/fimmu.2017.00417] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
Immune cells not only affect tissue homeostasis at the site of inflammation but also exert systemic effects contributing to multiple chronic conditions. Recent evidence clearly supports an altered T helper 17/regulatory T cell (Th17/Treg) balance leading to the development and progression of inflammatory diseases that not only affect the gastrointestinal tract but also have whole-body manifestations, including insulin resistance. Epigenetic mechanisms are amenable to both environmental and circulating factors and contribute to determining the T cell landscape. The recently identified participation of the gut microbiota in the remodeling of the epigenome of immune cells has triggered a paradigm shift in our understanding of the etiology of various inflammatory diseases and opened new paths toward therapeutic strategies. In this review, we provide an overview of the contribution of the Th17/Treg balance in the development and progression of inflammatory bowel diseases and metabolic diseases. We discuss the involvement of epigenetic mechanisms in the regulation of T cell function in the particular context of dysbiosis. Finally, we examine the potential for nutritional interventions affecting the gut microbiota to reshape the T cell epigenome and address the inflammatory component of various diseases.
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Affiliation(s)
- Annie Luo
- St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Steven T Leach
- School of Women and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Romain Barres
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Michael C Grimm
- St George and Sutherland Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - David Simar
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Mechanisms of Disease and Translational Research, School of Medical Sciences, University of New South Wales, Sydney, NSW, Australia
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11
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Youngson NA, Lecomte V, Maloney CA, Leung P, Liu J, Hesson LB, Luciani F, Krause L, Morris MJ. Obesity-induced sperm DNA methylation changes at satellite repeats are reprogrammed in rat offspring. Asian J Androl 2016; 18:930-936. [PMID: 26608942 PMCID: PMC5109891 DOI: 10.4103/1008-682x.163190] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 05/21/2015] [Accepted: 07/15/2015] [Indexed: 12/29/2022] Open
Abstract
There is now strong evidence that the paternal contribution to offspring phenotype at fertilisation is more than just DNA. However, the identity and mechanisms of this nongenetic inheritance are poorly understood. One of the more important questions in this research area is: do changes in sperm DNA methylation have phenotypic consequences for offspring? We have previously reported that offspring of obese male rats have altered glucose metabolism compared with controls and that this effect was inherited through nongenetic means. Here, we describe investigations into sperm DNA methylation in a new cohort using the same protocol. Male rats on a high-fat diet were 30% heavier than control-fed males at the time of mating (16-19 weeks old, n = 14/14). A small (0.25%) increase in total 5-methyl-2Ͳ-deoxycytidine was detected in obese rat spermatozoa by liquid chromatography tandem mass spectrometry. Examination of the repetitive fraction of the genome with methyl-CpG binding domain protein-enriched genome sequencing (MBD-Seq) and pyrosequencing revealed that retrotransposon DNA methylation states in spermatozoa were not affected by obesity, but methylation at satellite repeats throughout the genome was increased. However, examination of muscle, liver, and spermatozoa from male 27-week-old offspring from obese and control fathers (both groups from n = 8 fathers) revealed that normal DNA methylation levels were restored during offspring development. Furthermore, no changes were found in three genomic imprints in obese rat spermatozoa. Our findings have implications for transgenerational epigenetic reprogramming. They suggest that postfertilization mechanisms exist for normalising some environmentally-induced DNA methylation changes in sperm cells.
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Affiliation(s)
- Neil A Youngson
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Virginie Lecomte
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Christopher A Maloney
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Preston Leung
- Inflammation and Infection Research, School of Medical Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Jia Liu
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, NSW 2052, Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- Inflammation and Infection Research, School of Medical Sciences, UNSW Australia, Sydney, NSW 2052, Australia
| | - Lutz Krause
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Queensland 4006, Australia
- University of Queensland Diamantina Institute, Translational Research Institute, University of Queensland, 37 Kent Street Woolloongabba, Queensland 4102, Australia
| | - Margaret J Morris
- Department of Pharmacology, School of Medical Sciences, UNSW Australia, Sydney, NSW 2052, Australia
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12
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Ma SSQ, Henry CE, Llamosas E, Higgins R, Daniels B, Hesson LB, Hawkins NJ, Ward RL, Ford CE. Erratum to: Validation of specificity of antibodies for immunohistochemistry: the case of ROR2. Virchows Arch 2016; 469:717. [PMID: 27796585 DOI: 10.1007/s00428-016-2036-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/07/2016] [Accepted: 09/01/2016] [Indexed: 11/25/2022]
Affiliation(s)
- Sean S Q Ma
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Claire E Henry
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Estelle Llamosas
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rupert Higgins
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Benjamin Daniels
- Faculty of Medicine, Medicines Policy Research Unit, Centre for Big Data Research in Health, UNSW, Sydney, Australia
| | - Luke B Hesson
- Colorectal Cancer Group, Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | | | | | - Caroline E Ford
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia.
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13
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Liu Q, Hesson LB, Nunez AC, Packham D, Hawkins NJ, Ward RL, Sloane MA. Pathogenic germline MCM9 variants are rare in Australian Lynch-like syndrome patients. Cancer Genet 2016; 209:497-500. [DOI: 10.1016/j.cancergen.2016.10.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 12/21/2022]
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14
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Hesson LB, Ng B, Zarzour P, Srivastava S, Kwok CT, Packham D, Nunez AC, Beck D, Ryan R, Dower A, Ford CE, Pimanda JE, Sloane MA, Hawkins NJ, Bourke MJ, Wong JWH, Ward RL. Integrated Genetic, Epigenetic, and Transcriptional Profiling Identifies Molecular Pathways in the Development of Laterally Spreading Tumors. Mol Cancer Res 2016; 14:1217-1228. [PMID: 27671336 DOI: 10.1158/1541-7786.mcr-16-0175] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 08/15/2016] [Accepted: 09/07/2016] [Indexed: 11/16/2022]
Abstract
Laterally spreading tumors (LST) are colorectal adenomas that develop into extremely large lesions with predominantly slow progression to cancer, depending on lesion subtype. Comparing and contrasting the molecular profiles of LSTs and colorectal cancers offers an opportunity to delineate key molecular alterations that drive malignant transformation in the colorectum. In a discovery cohort of 11 LSTs and paired normal mucosa, we performed a comprehensive and unbiased screen of the genome, epigenome, and transcriptome followed by bioinformatics integration of these data and validation in an additional 84 large, benign colorectal lesions. Mutation rates in LSTs were comparable with microsatellite-stable colorectal cancers (2.4 vs. 2.6 mutations per megabase); however, copy number alterations were infrequent (averaging only 1.5 per LST). Frequent genetic, epigenetic, and transcriptional alterations were identified in genes not previously implicated in colorectal neoplasia (ANO5, MED12L, EPB41L4A, RGMB, SLITRK1, SLITRK5, NRXN1, ANK2). Alterations to pathways commonly mutated in colorectal cancers, namely, the p53, PI3K, and TGFβ pathways, were rare. Instead, LST-altered genes converged on axonal guidance, Wnt, and actin cytoskeleton signaling. These integrated omics data identify molecular features associated with noncancerous LSTs and highlight that mutation load, which is relatively high in LSTs, is a poor predictor of invasive potential. IMPLICATIONS The novel genetic, epigenetic, and transcriptional changes associated with LST development reveal important insights into why some adenomas do not progress to cancer. The finding that LSTs exhibit a mutational load similar to colorectal carcinomas has implications for the validity of molecular biomarkers for assessing cancer risk. Mol Cancer Res; 14(12); 1217-28. ©2016 AACR.
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Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia.
| | - Benedict Ng
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Peter Zarzour
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Sameer Srivastava
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia.,Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Chau-To Kwok
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Deborah Packham
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Dominik Beck
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Regina Ryan
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Ashraf Dower
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Caroline E Ford
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - John E Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Nicholas J Hawkins
- School of Medical Sciences, UNSW Australia, Kensington, Sydney, Australia
| | - Michael J Bourke
- Department of Gastroenterology, Westmead Hospital, Sydney, New South Wales, Australia
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia. .,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland, Australia
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15
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Ma SSQ, Henry CE, Llamosas E, Higgins R, Daniels B, Hesson LB, Hawkins NJ, Ward RL, Ford CE. Validation of specificity of antibodies for immunohistochemistry: the case of ROR2. Virchows Arch 2016; 470:99-108. [PMID: 27631337 DOI: 10.1007/s00428-016-2019-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Revised: 08/07/2016] [Accepted: 09/01/2016] [Indexed: 02/06/2023]
Abstract
The Wnt signalling receptor receptor tyrosine kinase-like orphan receptor 2 (ROR2) is implicated in numerous human cancers. However, there have been conflicting reports regarding ROR2 expression, some studies showing upregulation and others downregulation of ROR2 in the same cancer type. The majority of these studies used immunohistochemistry (IHC) to detect ROR2 protein, without validation of the used antibodies. There appears to be currently no consensus on the antibody best suited for ROR2 detection or how ROR2 expression changes in various cancer types. We examined three commercially available ROR2 antibodies and found that only one bound specifically to ROR2. Another antibody cross-reacted with other proteins, and the third failed to detect ROR2 at all. ROR2 detection by IHC on 107 patient samples using the ROR2 specific antibody showed that the majority of colorectal cancers show loss of ROR2 protein. We found no association between ROR2 staining and poor patient survival, as had been previously reported. These results question the previously reported association between ROR2 and poor patient survival in colorectal cancer. Future studies should use fully validated antibodies when detecting ROR2 protein, as non-specific staining can lead to irrelevant observations and misinterpretations.
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Affiliation(s)
- Sean S Q Ma
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Claire E Henry
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Estelle Llamosas
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Rupert Higgins
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Benjamin Daniels
- Faculty of Medicine, Medicines Policy Research Unit, Centre for Big Data Research in Health, UNSW, Sydney, Australia
| | - Luke B Hesson
- Colorectal Cancer Group, Adult Cancer Program, Lowy Cancer Research Centre, UNSW, Sydney, Australia
| | | | | | - Caroline E Ford
- Adult Cancer Program, Level 2, Metastasis Research Group, Lowy Cancer Research Centre and School of Women's and Children's Health, University of New South Wales, Sydney, NSW, 2052, Australia.
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16
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Abstract
With the advent of high-throughput and relatively inexpensive whole-genome sequencing technology, the focus of cancer research has begun to shift toward analyses of somatic mutations in non-coding cis-regulatory elements of the cancer genome. Cis-regulatory elements play an important role in gene regulation, with mutations in these elements potentially resulting in changes to the expression of linked genes. The recent discoveries of recurrent TERT promoter mutations in melanoma, and recurrent mutations that create a super-enhancer regulating TAL1 expression in T-cell acute lymphoblastic leukaemia (T-ALL), have sparked significant interest in the search for other somatic cis-regulatory mutations driving cancer development. In this review, we look more closely at the TERT promoter and TAL1 enhancer alterations and use these examples to ask whether other cis-regulatory mutations may play a role in cancer susceptibility. In doing so, we make observations from the data emerging from recent research in this field, and describe the experimental and analytical approaches which could be adopted in the hope of better uncovering the true functional significance of somatic cis-regulatory mutations in cancer.
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Affiliation(s)
- Rebecca C Poulos
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Australia, Sydney, Australia
| | - Mathew A Sloane
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Australia, Sydney, Australia
| | - Luke B Hesson
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Australia, Sydney, Australia
| | - Jason W H Wong
- Prince of Wales Clinical School and Lowy Cancer Research Centre, UNSW Australia, Sydney, Australia
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17
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Abstract
The use of epigenetic biomarkers in cancer management relies on the availability of robust assays and evidence that these markers are able to segregate clinically significant groups of patients. While many cancers are characterized by genetic and epigenetic modifications, it is far simpler to develop molecular tests that detect genetic rather than epigenetic changes. In this special report, we will describe the challenges associated with developing epigenetic assays and the practical issues that must be overcome before they can be used in the clinic.
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Affiliation(s)
- Peter Zarzour
- Adult Cancer Program, Lowy Cancer Research Centre & Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales 2052, Australia
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18
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Abstract
In the January 2016 issue of Clinical Epigenetics, Quiñonez-Silva et al. (Clin Epigenetics 8:1, 2016) described a possible constitutional epimutation of the RB1 gene as a cause of hereditary predisposition to retinoblastoma. The term constitutional epimutation describes an epigenetic aberration in normal tissues that predisposes to disease. The data presented by Quiñonez-Silva et al. are interesting, but further analysis is required to demonstrate a constitutional epimutation in this family. Here, we define the criteria and describe the experimental approach necessary to identify an epigenetic aberration as a constitutional epimutation.
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Affiliation(s)
- Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Kensington, Sydney, New South Wales 2052 Australia
| | - Robyn L Ward
- The University of Queensland, Level 3 Brian Wilson Chancellery, Brisbane, Queensland 4072 Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Kensington, Sydney, New South Wales 2052 Australia
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19
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Sloane MA, Nunez AC, Packham D, Kwok CT, Suthers G, Hesson LB, Ward RL. Mosaic Epigenetic Inheritance as a Cause of Early-Onset Colorectal Cancer. JAMA Oncol 2016; 1:953-7. [PMID: 26181641 DOI: 10.1001/jamaoncol.2015.1484] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Constitutional hypermethylation of 1 allele throughout the soma (constitutional epimutation) is an accepted mechanism of cancer predisposition. Understanding the origin and inheritance of epimutations is important for assessing cancer risk in affected families. OBSERVATIONS We report a 29-year-old man with early-onset colorectal cancer who showed a constitutional MLH1 epimutation (approximately 50% of alleles methylated and allele-specific loss of MLH1 expression) that was stable over a 16-year period. The epimutation was inherited without a genetic alteration from his asymptomatic mother. She showed methylation on the same allele but in less than 5% of her somatic cells. CONCLUSIONS AND RELEVANCE These findings indicate that low-level somatic mosaicism for an epimutation in an asymptomatic parent can produce a nonmosaic constitutional epimutation in a child. Asymptomatic low-level methylation in some individuals may be associated with substantial cancer risk to their offspring.
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Affiliation(s)
- Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Deborah Packham
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Chau-To Kwok
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Graeme Suthers
- Department of Paediatrics, University of Adelaide, South Australia, Australia3Sonic Healthcare, Macquarie Park, New South Wales, Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia4Brian Wilson Chancellery, University of Queensland, Brisbane, Queensland, Australia
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Srivastava S, Ludwig AK, Wong JWH, Hesson LB. An investigation of the potential for epigenetic inactivation by transcription read-through in a sporadic colorectal cancer. Gene 2016; 585:154-158. [PMID: 27016300 DOI: 10.1016/j.gene.2016.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 03/20/2016] [Indexed: 01/05/2023]
Abstract
Aberrant transcription read-through of a gene promoter as a result of genetic structural rearrangements can cause the epigenetic inactivation of a neighbouring gene. All reported cases have involved copy number alterations that remove the 3' poly(A) transcription terminator sequence of a gene leading to transcription read-through (TRT) and methylation of the gene promoter of a downstream gene. We aimed to determine whether deletion of poly (A) transcription terminator sequences was associated with the methylation of neighbouring genes in a CRC with extensive copy number alterations. We performed a high resolution CGH array and methylation analysis on a CRC specimen to identify such alterations. Analysis of the CRC using high-resolution CGH identified 6 genes with deletions in the 3' part of the gene that encompassed the poly(A) transcription terminator sequence. Bisulphite sequencing of the promoter region of neighbouring (affected) genes at these six regions showed all candidate genes were unmethylated. Considering the fact that six TRT affected genes in a CRC with multiple deletions show no signs of hypermethylated promoters, it would be fairly appropriate to suggest that epigenetic inactivation by TRT might be a rare phenomenon in sporadic CRCs.
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Affiliation(s)
- Sameer Srivastava
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia; Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India.
| | - Anne K Ludwig
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia; Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
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Liu Q, Thompson BA, Ward RL, Hesson LB, Sloane MA. Understanding the Pathogenicity of Noncoding Mismatch Repair Gene Promoter Variants in Lynch Syndrome. Hum Mutat 2016; 37:417-26. [DOI: 10.1002/humu.22971] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 02/05/2016] [Indexed: 01/04/2023]
Affiliation(s)
- Qing Liu
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Bryony A. Thompson
- Huntsman Cancer Institute; University of Utah; Salt Lake City Utah
- Centre for Epidemiology and Biostatistics; Melbourne School of Population and Global Health; University of Melbourne; Melbourne Victoria Australia
| | - Robyn L. Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
- Level 3 Brian Wilson Chancellery; The University of Queensland; Brisbane Queensland Australia
| | - Luke B. Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
| | - Mathew A. Sloane
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; UNSW Australia; Sydney New South Wales Australia
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Liu Q, Hesson LB, Nunez AC, Packham D, Williams R, Ward RL, Sloane MA. A cryptic paracentric inversion of MSH2 exons 2-6 causes Lynch syndrome. Carcinogenesis 2015; 37:10-17. [PMID: 26498247 DOI: 10.1093/carcin/bgv154] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 12/28/2022] Open
Abstract
Lynch syndrome is an autosomal dominant disorder that predisposes carriers of DNA mismatch repair (MMR) gene mutations to early-onset cancer. Germline testing screens exons and splice sites for mutations, but does not examine introns or RNA transcripts for alterations. Pathogenic mutations have not been detected in ~30% of suspected Lynch syndrome cases with standard screening practices. We present a 38-year-old male with a clinicopathological and family history consistent with Lynch syndrome, including loss of MSH2 expression in his tumor. Germline testing revealed normal MSH2 coding sequence, splice sites and exon copy number, however, cDNA sequencing identified an aberrant MSH2 transcript lacking exons 2-6. An inversion PCR on germline DNA identified an ~18kb unbalanced, paracentric inversion within MSH2, with breakpoints in a long terminal repeat in intron 1 and an Alu repeat in intron 6. The 3' end of the inversion had a 1.2 kb deletion and an 8 bp insertion at the junction with intron 6. Screening of 55 additional Australian patients presenting with MSH2-deficient tumors who were negative in germline genetic tests for MSH2 mutations identified another inversion-positive patient. We propose an Alu-mediated recombination model to explain the origin of the inversion. Our study illustrates the potential value of cDNA screening to identify patients with cryptic MMR gene rearrangements, clarifies why standard testing may not detect some pathogenic alterations, and provides a genetic test for screening individuals with suspected Lynch syndrome that present with unexplained MSH2-deficient tumors.
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Affiliation(s)
- Qing Liu
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Luke B Hesson
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Andrea C Nunez
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Deborah Packham
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Rachel Williams
- Hereditary Cancer Clinic , Prince of Wales Hospital , Randwick, New South Wales 2031 , Australia and
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney New South Wales 2052, Australia.,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mathew A Sloane
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
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Hesson LB, Sloane MA, Wong JW, Nunez AC, Srivastava S, Ng B, Hawkins NJ, Bourke MJ, Ward RL. Altered promoter nucleosome positioning is an early event in gene silencing. Epigenetics 2015; 9:1422-30. [PMID: 25437056 DOI: 10.4161/15592294.2014.970077] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DNA methylation, and gene expression in the early stages of gene silencing. Genome-wide gene expression correlated with highly positioned nucleosomes upstream and downstream of a nucleosome-depleted transcription start site (TSS). Hypermethylated promoters displayed increased nucleosome occupancy, specifically at the TSS. We investigated 2 genes, CDH1 and CDKN2B, which were silenced in adenomas but lacked promoter hypermethylation. Instead, silencing correlated with loss of nucleosomes from the -2 position upstream of the TSS relative to normal mucosa. In contrast, permanent CDH1 silencing in carcinoma cells was characterized by promoter hypermethylation and dense nucleosome occupancy. Our findings suggest that silenced genes transition through an intermediary stage involving altered promoter nucleosome positioning, before permanent silencing by hypermethylation and dense nucleosome occupancy.
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Affiliation(s)
- Luke B Hesson
- a Adult Cancer Program; Lowy Cancer Research Center and Prince of Wales Clinical School; UNSW ; Sydney , Australia
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Hesson LB, Packham D, Kwok CT, Nunez AC, Ng B, Schmidt C, Fields M, Wong JWH, Sloane MA, Ward RL. Lynch syndrome associated with two MLH1 promoter variants and allelic imbalance of MLH1 expression. Hum Mutat 2015; 36:622-30. [PMID: 25762362 PMCID: PMC4682451 DOI: 10.1002/humu.22785] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 03/03/2015] [Indexed: 12/27/2022]
Abstract
Lynch syndrome is a hereditary cancer syndrome caused by a constitutional mutation in one of the mismatch repair genes. The implementation of predictive testing and targeted preventative surveillance is hindered by the frequent finding of sequence variants of uncertain significance in these genes. We aimed to determine the pathogenicity of previously reported variants (c.-28A>G and c.-7C>T) within the MLH1 5′untranslated region (UTR) in two individuals from unrelated suspected Lynch syndrome families. We investigated whether these variants were associated with other pathogenic alterations using targeted high-throughput sequencing of the MLH1 locus. We also determined their relationship to gene expression and epigenetic alterations at the promoter. Sequencing revealed that the c.-28A>G and c.-7C>T variants were the only potentially pathogenic alterations within the MLH1 gene. In both individuals, the levels of transcription from the variant allele were reduced to 50% compared with the wild-type allele. Partial loss of expression occurred in the absence of constitutional epigenetic alterations within the MLH1 promoter. We propose that these variants may be pathogenic due to constitutional partial loss of MLH1 expression, and that this may be associated with intermediate penetrance of a Lynch syndrome phenotype. Our findings provide further evidence of the potential importance of noncoding variants in the MLH1 5′UTR in the pathogenesis of Lynch syndrome.
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Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Deborah Packham
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Chau-To Kwok
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Benedict Ng
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Christa Schmidt
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim
| | - Michael Fields
- Royal North Shore Hospital, Sydney, New South Wales, Australia
| | - Jason W H Wong
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney, New South Wales, Australia.,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland, Australia
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25
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Zarzour P, Boelen L, Luciani F, Beck D, Sakthianandeswaren A, Mouradov D, Sieber OM, Hawkins NJ, Hesson LB, Ward RL, Wong JWH. Single nucleotide polymorphism array profiling identifies distinct chromosomal aberration patterns across colorectal adenomas and carcinomas. Genes Chromosomes Cancer 2015; 54:303-14. [PMID: 25726927 DOI: 10.1002/gcc.22243] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/11/2015] [Indexed: 11/07/2022] Open
Abstract
The progression of benign colorectal adenomas into cancer is associated with the accumulation of chromosomal aberrations. Even though patterns and frequencies of chromosomal aberrations have been well established in colorectal carcinomas, corresponding patterns of aberrations in adenomas are less well documented. The aim of this study was to profile chromosomal aberrations across colorectal adenomas and carcinomas to provide a better insight into key changes during tumor initiation and progression. Single nucleotide polymorphism array analysis was performed on 216 colorectal tumor/normal matched pairs, comprising 60 adenomas and 156 carcinomas. While many chromosomal aberrations were specific to carcinomas, those with the highest frequency in carcinomas (amplification of chromosome 7, 13q, and 20q; deletion of 17p and chromosome 18; LOH of 1p, chromosome 4, 5q, 8p, 17p, chromosome 18, and 20p) were also identified in adenomas. Hierarchical clustering using chromosomal aberrations revealed three distinct subtypes. Interestingly, these subtypes were only partially dependent on tumor staging. A cluster of colorectal cancer patients with frequent chromosomal deletions had the least favorable prognosis, and a number of adenomas (n = 9) were also present in the cluster suggesting that, at least in some tumors, the chromosomal aberration pattern is determined at a very early stage of tumor formation. Finally, analysis of LOH events revealed that copy-neutral/gain LOH (CN/G-LOH) is frequent (>10%) in carcinomas at 5q, 11q, 15q, 17p, chromosome 18, 20p, and 22q. Deletion of the corresponding region is sometimes present in adenomas, suggesting that LOH at these loci may play an important role in tumor initiation.
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Affiliation(s)
- Peter Zarzour
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, UNSW, Sydney, NSW 2052, Australia
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Hesson LB, Ward RL. The importance of distinguishing pseudogenes from parental genes. Clin Epigenetics 2015; 6:90. [PMID: 25553138 PMCID: PMC4280768 DOI: 10.1186/s13148-014-0033-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 11/28/2014] [Indexed: 12/03/2022] Open
Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW, Sydney, Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW, Sydney, Australia
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Sloane MA, Hesson LB, Nunez AC, Thompson BA, Ward RL. Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients. Clin Epigenetics 2014; 6:32. [PMID: 25530820 PMCID: PMC4272815 DOI: 10.1186/s13148-014-0032-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/28/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Splicing is more efficient when coupled with transcription and it has been proposed that nucleosomes enriched in exons are important for splice site recognition. Lynch syndrome is a familial cancer syndrome that can be caused by the autosomal dominant inheritance of splice site mutations in the MutL homolog 1 (MLH1) gene. To better understand the role of nucleosomes in splicing, we used MLH1 splice site mutations in Lynch syndrome cases as a model to investigate if abnormal splicing was associated with altered nucleosome positioning at exon-intron boundaries. FINDINGS Nucleosome Occupancy and Methylome sequencing (NOMe-seq) was used to determine the allele-specific positioning of nucleosomes around heterozygous splice site mutations in lymphoblastoid cells lines (LCLs) derived from six Lynch syndrome patients. These mutations were previously shown to cause exon skipping in five of the six patients. Allele-specific high-resolution nucleosome mapping across exons and exon-intron boundaries revealed high levels of nucleosomes across all regions examined. Alleles containing donor or acceptor splice site mutations showed no consistent alteration in nucleosome positioning or occupancy. CONCLUSION Nucleosomes were enriched at MLH1 exons in LCLs derived from Lynch syndrome patients, and in this model system the positioning of nucleosomes was unaltered at exon-intron boundaries containing splice site mutations. Thus, these splice site mutations alone do not significantly change the local organisation of nucleosomes.
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Affiliation(s)
- Mathew A Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Andrea C Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
| | - Bryony A Thompson
- Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, QLD Australia
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW Australia
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Sloane MA, Wong JWH, Perera D, Nunez AC, Pimanda JE, Hawkins NJ, Sieber OM, Bourke MJ, Hesson LB, Ward RL. Epigenetic inactivation of the candidate tumor suppressor USP44 is a frequent and early event in colorectal neoplasia. Epigenetics 2014; 9:1092-100. [PMID: 24837038 DOI: 10.4161/epi.29222] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In mouse models, loss of the candidate tumor suppressor gene Ubiquitin Specific Protease 44 (USP44) is associated with aneuploidy and cancer. USP44 is also transcriptionally silenced in human cancers. Here we investigated the molecular mechanism of USP44 silencing and whether this correlated with aneuploidy in colorectal adenomas. DNA methylation at the USP44 CpG island (CGI) promoter was measured using combined bisulfite restriction analysis (COBRA) in colorectal cancer (CRC) cell lines (n = 18), and with COBRA and bisulfite sequencing in colorectal adenomas (n = 89) and matched normal colonic mucosa (n = 51). The USP44 CGI was hypermethylated in all CRC cell lines, in most colorectal adenomas (79 of 89, 89%) but rarely in normal mucosa samples (3 of 51, 6%). USP44 expression was also compared between normal mucosa and paired hypermethylated adenomas in six patients using qRT-PCR. Hypermethylation of the USP44 CGI in adenomas was associated with a 1.8 to 5.5-fold reduction in expression compared with paired normal mucosa. Treatment of CRC cell lines with the DNA hypomethylating agent decitabine resulted in a 14 to 270-fold increase in USP44 expression. Whole genome SNP array data showed that gain or loss of individual chromosomes occurred in adenomas, but hypermethylation did not correlate with more aneuploidy. In summary, our data shows that USP44 is epigenetically inactivated in colorectal adenomas, but this alone is not sufficient to cause aneuploidy in colorectal neoplasia.
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Affiliation(s)
- Mathew A Sloane
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia
| | - Jason W H Wong
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia
| | - Dilmi Perera
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia
| | - Andrea C Nunez
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia
| | - John E Pimanda
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia
| | - Nicholas J Hawkins
- School of Medical Sciences; University of New South Wales; Sydney, NSW Australia
| | - Oliver M Sieber
- Colorectal Cancer Genetics Laboratory; Systems Biology and Personalised Medicine Division; Walter and Eliza Hall Institute of Medial Research; Parkville, VIC Australia; Faculty of Medicine, Dentistry and Health Sciences; Department of Medical Biology; University of Melbourne; Parkville, VIC Australia
| | - Michael J Bourke
- Department of Gastroenterology and Hepatology; Westmead Hospital; Sydney, NSW Australia
| | - Luke B Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia
| | - Robyn L Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; Sydney, NSW Australia
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Abstract
In mammalian genomes, the methylation of cytosine residues within CpG dinucleotides is crucial to normal development and cell differentiation. However, methylation of cytosines in the contexts of CpA, CpT, and CpC (non-CpG methylation) has been reported for decades, yet remains poorly understood. In recent years, whole genome bisulphite sequencing (WGBS) has confirmed significant levels of non-CpG methylation in specific tissues and cell types. Non-CpG methylation has several properties that distinguish it from CpG methylation. Here we review the literature describing non-CpG methylation in mammalian cells, describe the important characteristics that distinguish it from CpG methylation, and discuss its functional importance.
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Affiliation(s)
- Vibha Patil
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; University of New South Wales; Sydney, NSW Australia
| | - Robyn L Ward
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; University of New South Wales; Sydney, NSW Australia
| | - Luke B Hesson
- Adult Cancer Program; Lowy Cancer Research Centre and Prince of Wales Clinical School; University of New South Wales; Sydney, NSW Australia
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Abstract
Determining the methylation status of genes with pseudogenes can be technically challenging due to sequence homology. High sequence homology can result in the amplification of both pseudogene and parental gene alleles, potentially leading to data misinterpretation. Allelic bisulfite sequencing allows for detection of the methylation status of individual alleles at nucleotide resolution and represents the most reliable method for discriminating pseudogene and parental gene sequences. Here, we discuss important points that should be considered when investigating pseudogene and parental gene methylation status and we describe the method of allelic bisulfite sequencing, including assay design.
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Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Kensington, Sydney, NSW, 2227, Australia,
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Sloane MA, Hesson LB, Nunez AC, Thompson BA, Ward RL. Nucleosome positioning is unaltered at MLH1 splice site mutations in cells derived from Lynch syndrome patients. Clin Epigenetics 2014. [DOI: 10.1186/preaccept-1571082317134727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Hesson LB, Patil V, Sloane MA, Nunez AC, Liu J, Pimanda JE, Ward RL. Reassembly of nucleosomes at the MLH1 promoter initiates resilencing following decitabine exposure. PLoS Genet 2013; 9:e1003636. [PMID: 23935509 PMCID: PMC3723495 DOI: 10.1371/journal.pgen.1003636] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 05/31/2013] [Indexed: 01/01/2023] Open
Abstract
Hypomethylating agents reactivate tumor suppressor genes that are epigenetically silenced in cancer. Inevitably these genes are resilenced, leading to drug resistance. Using the MLH1 tumor suppressor gene as a model, we showed that decitabine-induced re-expression was dependent upon demethylation and eviction of promoter nucleosomes. Following decitabine withdrawal, MLH1 was rapidly resilenced despite persistent promoter demethylation. Single molecule analysis at multiple time points showed that gene resilencing was initiated by nucleosome reassembly on demethylated DNA and only then was followed by remethylation and stable silencing. Taken together, these data establish the importance of nucleosome positioning in mediating resilencing of drug-induced gene reactivation and suggest a role for therapeutic targeting of nucleosome assembly as a mechanism to overcome drug resistance. Hypomethylating agents are emerging as effective cancer therapies. However, their therapeutic effects are transient and drug resistance inevitably develops. While resistance is associated with resilencing of genes initially demethylated by the drug, the mechanism underlying this resilencing is unknown. We provide evidence that the rapid reassembly of nucleosomes at transcription start sites initiates resilencing and is a prerequisite for promoter remethylation. This finding shows reassembly of nucleosomes at the promoter of critical genes is a potential early marker of resistance to hypomethylating agents. Our findings have implications for the treatment of cancer using epigenetic therapies that target DNA methylation alone, and suggest that overcoming drug resistance will require therapeutic strategies which prevent nucleosome deposition.
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Affiliation(s)
- Luke B. Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: (LBH); (RLW)
| | - Vibha Patil
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Mathew A. Sloane
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Andrea C. Nunez
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Jia Liu
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - John E. Pimanda
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Robyn L. Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
- * E-mail: (LBH); (RLW)
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Patil V, Sloane MA, Wong JW, Liu J, Ward RL, Hesson LB. Abstract 2983: Gene resilencing following decitabine therapy is initiated by nucleosome reoccupancy and is related to CpG island shore methylation. Cancer Res 2013. [DOI: 10.1158/1538-7445.am2013-2983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Decitabine is a front line therapy for myelogenous leukaemias and is in clinical trials for various solid tumour types. This DNA demethylating agent reactivates genes silenced by promoter hypermethylation in cancer. However upon drug withdrawal reexpressed genes undergo remethylation (resilencing) which may underlie drug resistance and presents a barrier to effective therapy. We aimed to define the ordered sequence of epigenetic events associated with resilencing. Using biallelically methylated MLH1 as a model gene, we profiled epigenetic changes at the MLH1 promoter associated with reexpression and resilencing in a colorectal cancer cell line before, during and after Decitabine treatment. In contrast to the closed chromatin structure observed before treatment, Decitabine induced increased MLH1 expression and 54% decreased promoter methylation. We show that gene resilencing, which occurs 6-8 days following removal of therapy, is not due to promoter remethylation but is initiated by reoccupancy of nucleosomes to demethylated promoter alleles. Furthermore, long-term monitoring of cells following treatment showed MLH1 expression never reverts to pretreatment levels with low-level expression and demethylated promoter alleles persisting up to 118 days after withdrawal of Decitabine. Genome-wide methylation profiling was used to categorise promoter CpG Islands (CGI) based on their degree of demethylation after treatment. This revealed that CGIs with persistence of demethylated promoter alleles after long-term recovery (n=108) showed significantly lower levels of CGI shore methylation (p=0.0231). Our findings suggest a role for shore methylation in susceptibility to CGI remethylation and that therapeutic targeting of nucleosome assembly may provide a novel strategy to prevent gene resilencing.
Citation Format: Vibha Patil, Mathew A. Sloane, Jason Wh Wong, Jia Liu, Robyn L. Ward, Luke B. Hesson. Gene resilencing following decitabine therapy is initiated by nucleosome reoccupancy and is related to CpG island shore methylation. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2983. doi:10.1158/1538-7445.AM2013-2983
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Affiliation(s)
- Vibha Patil
- Lowy Cancer Research Ctr., Kensington, Australia
| | | | | | - Jia Liu
- Lowy Cancer Research Ctr., Kensington, Australia
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Lau DT, Hesson LB, Norris MD, Marshall G, Haber M, Ashton LJ. Abstract 68: Beyond GWAS: The prognostic significance of promoter DNA methylation in patients with neuroblastoma. Cancer Epidemiol Biomarkers Prev 2012. [DOI: 10.1158/1055-9965.gwas-68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Background: Neuroblastoma is a genetically heterogenic tumor diagnosed in childhood which exhibits broad clinical diversity ranging from rapid disease progression to spontaneous regression. Although amplification of the MYCN oncogene is one of the most prominent prognostic markers of this disease it is only present in around 25% of patients. Hence, additional molecular markers are needed for patients lacking MYCN amplification to enable better stratification of patient risk groups.
To date, genome wide association studies have identified few gene candidates in neuroblastoma patients that can be further developed for prognostic use in the clinic. DNA methylation is a major epigenetic mechanism for gene silencing in a wide range of human cancers and methylation sites may reveal new prognostic targets in neuroblastoma. Recent studies have suggested that the methylation status of specific gene promoters may be useful for clinically discriminating subgroups of children diagnosed with neuroblastoma. To date, these investigations have assessed DNA methylation using variable techniques; focused on small numbers of candidate genes and; examined few primary tumor samples. The aims of our study were to characterize the clinical significance of promoter methylation in a large cohort of primary neuroblastoma tumors and investigate the association between DNA methylation and clinical outcome.
Methods: A customized Illumina GoldenGate methylation assay was used to assess methylation status of 96 CpG sites within 48 candidate genes in primary neuroblastoma tumors obtained from 131 children diagnosed in Australia between 1985 and 2000. Candidate genes were selected on the basis of previous reports of altered DNA methylation in embryonal cancers. Levels of DNA methylation were quantified and confirmed in a subset of 48 patient samples using combined bisulphite restriction analysis (CoBRA). A Cox proportional hazards model was used to investigate the association between promoter hypermethylation and the risk of relapse or death within 5 years of diagnosis, while adjusting for known prognostic cofactors such as MYCN amplification, age and stage at diagnosis.
Results: The level of promoter methylation of DNAJC15, NTRK1 and TNFRSF10D were significantly higher in older patients at diagnosis (p<0.01), while higher levels of promoter methylation of DNAJC15, NTRK1 and PYCARD were observed in patients with MYCN amplification (p<0.001). In multivariate analysis, promoter hypermethylation of FOLH1, MYOD1 and THBS1 remained significant independent predictors of poorer clinical outcome, after adjusting for MYCN amplification, age at diagnosis and tumor stage (p≤0.017). Around a third of patients displayed promoter hypermethylation in 2 or more of these genes and were almost 3 times more likely to relapse or die than those who did not display promoter hypermethylation (HR=2.72; 95%C1=1.55-4.78; p=0.001).
Conclusion: DNA methylation of FOLH1, MYOD1 and THBS1 appears to have independent prognostic value in children diagnosed with neuroblastoma. While the functional consequences of promoter hypermethylation in individual neuroblastoma patients remains to be fully determined, these investigations show how epigenetic profiling of tumor tissue can provide additional genetic markers for predicting treatment response in the clinical setting and has the potential to reveal important new therapeutic targets for selected patient subsets.
Citation Format: Diana T. Lau, Luke B. Hesson, Murray D. Norris, Glenn Marshall, Michelle Haber, Lesley J. Ashton. Beyond GWAS: The prognostic significance of promoter DNA methylation in patients with neuroblastoma. [abstract]. In: Proceedings of the AACR Special Conference on Post-GWAS Horizons in Molecular Epidemiology: Digging Deeper into the Environment; 2012 Nov 11-14; Hollywood, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2012;21(11 Suppl):Abstract nr 68.
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Affiliation(s)
- Diana T. Lau
- 1Children's Cancer Institute Australia, Randwick, Australia, 2Lowy Cancer Research Centre, Randwick, Australia
| | - Luke B. Hesson
- 1Children's Cancer Institute Australia, Randwick, Australia, 2Lowy Cancer Research Centre, Randwick, Australia
| | - Murray D. Norris
- 1Children's Cancer Institute Australia, Randwick, Australia, 2Lowy Cancer Research Centre, Randwick, Australia
| | - Glenn Marshall
- 1Children's Cancer Institute Australia, Randwick, Australia, 2Lowy Cancer Research Centre, Randwick, Australia
| | - Michelle Haber
- 1Children's Cancer Institute Australia, Randwick, Australia, 2Lowy Cancer Research Centre, Randwick, Australia
| | - Lesley J. Ashton
- 1Children's Cancer Institute Australia, Randwick, Australia, 2Lowy Cancer Research Centre, Randwick, Australia
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Lau DT, Hesson LB, Norris MD, Marshall GM, Haber M, Ashton LJ. Prognostic significance of promoter DNA methylation in patients with childhood neuroblastoma. Clin Cancer Res 2012; 18:5690-700. [PMID: 22929802 DOI: 10.1158/1078-0432.ccr-12-0294] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To characterize the clinical significance of promoter methylation in a cohort of primary neuroblastoma tumors and investigate the association between DNA methylation and clinical outcome. EXPERIMENTAL DESIGN A customized Illumina GoldenGate methylation assay was used to assess methylation status of 96 CpG sites within 48 candidate genes in primary neuroblastoma tumors obtained from 131 children diagnosed in Australia. Genes were selected on the basis of previous reports of altered DNA methylation in embryonal cancers. Levels of DNA methylation were validated in a subset of 48 patient samples using combined bisulfite restriction analysis (CoBRA) and bisulfite sequencing. A Cox proportional hazards model was used to investigate the association between promoter hypermethylation and the risk of relapse/death within 5 years of diagnosis, while adjusting for known prognostic factors including MYCN amplification, age, and stage at diagnosis. RESULTS Levels of promoter methylation of DNAJC15, neurotrophic tyrosine kinase receptor 1 or TrkA (NTRK1), and tumor necrosis factor receptor superfamily, member 10D (TNFRSF10D), were higher in older patients at diagnosis (P < 0.01), whereas higher levels of methylation of DNAJC15, NTRK1, and PYCARD were observed in patients with MYCN amplification (P < 0.001). In multivariate analysis, hypermethylation of folate hydrolase (FOLH1), myogenic differentiation-1 (MYOD1), and thrombospondin-1 (THBS1) remained significant independent predictors of poorer clinical outcome after adjusting for known prognostic factors (P ≤ 0.017). Moreover, more than 30% of patients displayed hypermethylation in 2 genes or more and were at least 2 times more likely to relapse or die (HR = 2.72, 95% confidence interval = 1.55-4.78, P = 0.001), independent of MYCN status, age, and stage at diagnosis. CONCLUSIONS Our findings highlight the potential use of methylation profiling to identify additional prognostic markers and detect new therapeutic targets for selected patient subsets.
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Affiliation(s)
- Diana T Lau
- Children's Cancer Institute Australia for Medical Research, Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW, Australia
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Liu J, Hesson LB, Meagher AP, Bourke MJ, Hawkins NJ, Rand KN, Molloy PL, Pimanda JE, Ward RL. Relative distribution of folate species is associated with global DNA methylation in human colorectal mucosa. Cancer Prev Res (Phila) 2012; 5:921-9. [PMID: 22609762 DOI: 10.1158/1940-6207.capr-11-0577] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Folate exists as functionally diverse species within cells. Although folate deficiency may contribute to DNA hypomethylation in colorectal cancer, findings on the association between total folate concentration and global DNA methylation have been inconsistent. This study determined global, LINE-1, and Alu DNA methylation in blood and colon of healthy and colorectal cancer patients and their relationship to folate distribution. Blood and normal mucosa from 112 colorectal cancer patients and 114 healthy people were analyzed for global DNA methylation and folate species distribution using liquid chromatography tandem mass spectrometry. Repeat element methylation was determined using end-specific PCR. Colorectal mucosa had lower global and repeat element DNA methylation compared with peripheral blood (P < 0.0001). After adjusting for age, sex and smoking history, global but not repeat element methylation was marginally higher in normal mucosa from colorectal cancer patients compared with healthy individuals. Colorectal mucosa from colorectal cancer subjects had lower 5-methyltetrahydrofolate and higher tetrahydrofolate and formyltetrahydrofolate levels than blood from the same individual. Blood folate levels should not be used as a surrogate for the levels in colorectal mucosa because there are marked differences in folate species distribution between the two tissues. Similarly, repeat element methylation is not a good surrogate measure of global DNA methylation in both blood and colonic mucosa. There was no evidence that mucosal global DNA methylation or folate distribution was related to the presence of cancer per se, suggesting that if abnormalities exist, they are confined to individual cells rather than the entire colon.
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Affiliation(s)
- Jia Liu
- Lowy Cancer Research Centre and Prince of Wales Clinical School, Australia
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Liu J, Hesson LB, Meagher AP, Bourke MJ, Hawkins NJ, Rand KN, Molloy PL, Pimanda JE, Ward RL. Abstract 3125: Relative distribution of folate species is associated with global DNA methylation in human colorectal mucosa. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-3125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Folate, an important cellular methyl donor, exists as functionally diverse species within cells. Folate deficiency is thought to contribute to DNA hypomethylation in colorectal cancer (CRC) however findings on the relationship between total folate concentration and global DNA methylation have been inconsistent. The aim of this study was to determine if global DNA methylation in blood and colorectal mucosa from healthy and CRC patients is related to folate species distribution. Blood and colorectal mucosa was collected from 112 CRC patients, 114 healthy individuals and 82 low folate individuals. Global methylation and folate was determined using liquid chromatography tandem mass spectrometry and repeat element methylation was determined using end-specific polymerase chain reaction. In colorectal mucosa mean global methylation was 8% lower compared to blood while LINE-1 and Alu elements were 3.3-fold and 1.9-fold hypomethylated respectively (P <0.0001). After adjusting for age and smoking, statistically significant but small (2.2%) differences in global but not repeat methylation were found in normal colorectal mucosa from CRC patients compared to healthy individuals. Low folate patients had 18% lower blood 5-methyltetrahydrofolate distribution (P <0.0001) and global (P =0.001) and LINE-1 demethylation (P <0.0001) compared to healthy individuals. The colorectal mucosa from cancer and healthy patients had an altered distribution of folate species (lower 5-methyltetrahydrofolate) similar to the folate distribution found in the blood of low folate individuals. On a background of tissue specific hypomethylation, global methylation of the normal mucosa of CRC patients is similar to healthy individuals. The level of global and repeat element hypomethylation may reflect the underlying distribution of folate species rather than total folate concentration. Future studies on the relationship between methylation and folate should consider folate species distribution, and how genetic or other factors may alter this balance in different tissue types and in neoplasia.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3125. doi:1538-7445.AM2012-3125
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Affiliation(s)
- Jia Liu
- 1University of New South Wales, Australia, Sydney, Australia
| | - Luke B. Hesson
- 1University of New South Wales, Australia, Sydney, Australia
| | | | | | | | - Keith N. Rand
- 4CSIRO Food and Nutritional Sciences, North Ryde, Australia
| | | | - John E. Pimanda
- 1University of New South Wales, Australia, Sydney, Australia
| | - Robyn L. Ward
- 1University of New South Wales, Australia, Sydney, Australia
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Hesson LB, Wong JW, Sloane MA, Pimanda JE, Bourke MJ, Hawkins NJ, Ward RL. Abstract 990: Nucleosome occupancy at unmethylated promoter CpG islands represents a novel mechanism of epigenetic gene silencing in cancer. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Promoter CpG island (CGI) hypermethylation is an established mechanism of silencing gene expression in cancer. Although the silenced state is thought to be consolidated by the recruitment of nucleosomes across the promoter, this has been observed in only a limited number of genes. Here we performed genome-wide MBD-Seq, MNase-Seq and RNA-Seq to investigate the relationship between CGI methylation, nucleosome occupancy around the transcription start site (TSS) and gene expression in a premalignant colorectal adenoma and matched normal mucosa. Analysis of RNA-seq data identified 1987 silent genes that were not expressed in the normal or adenoma tissues. Of these 1987 genes, 1401 (70.51%) showed either methylation in both the normal and adenoma tissues or nucleosome occupancy across the TSS, with 524 (26.37%) of genes showing both, suggestive of a consolidated silenced state. Our RNA-Seq data also revealed that 2010 genes were downregulated >2-fold in the adenoma when compared to paired normal mucosa. Of these 2010 genes, only 67 (3.33%) genes showed aberrant CGI hypermethylation, and of these 67 genes, only six (8.96%) showed nucleosome occupancy across the TSS. Therefore, the presence of both CGI hypermethylation and nucleosome occupancy across the TSS of downregulated genes is significantly lower than at silent genes (p<0.0001). Interestingly, 272 of the remaining 1966 (13.84%) genes that were downregulated in the absence of aberrant CGI hypermethylation showed clear evidence of nucleosome occupancy across the TSS, including the important cancer-related genes CDH1 and CDKN2B. Only seven of these 272 genes (2.57%) have previously been described as frequent targets of hypermethylation in cancer, suggesting nucleosome recruitment represents an alternative mechanism of inactivation of these genes. In summary, we identified some of the earliest epigenetic events in colorectal neoplasia by profiling the transcriptome and epigenetic landscape of a premalignant colorectal adenoma. Our data show that for the majority of genes showing adenoma-specific downregulation and aberrant CGI hypermethylation, nucleosomes are not recruited to the promoter. Moreover, our data reveals a potential novel mechanism of epigenetic gene inactivation in the absence of promoter hypermethylation, through physical occlusion of transcription by nucleosome occupancy at the TSS.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 990. doi:1538-7445.AM2012-990
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Lau DT, Hesson LB, Norris MD, Haber M, Marshall GM, Ashton LJ. Abstract 1425: Prognostic significance of promoter DNA methylation in patients with neuroblastoma. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-1425] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Neuroblastoma is a genetically heterogenic tumor diagnosed in childhood which exhibits broad clinical diversity ranging from rapid disease progression to spontaneous regression. One of the most prominent prognostic markers of this disease is the amplification of the MYCN oncogene, which occurs in approximately 25% of patients. However, additional molecular markers are needed for patients lacking MYCN amplification to enable better stratification of patient risk groups. DNA methylation is a major epigenetic mechanism for gene silencing in a wide range of human cancers, including neuroblastoma. Recent studies have suggested that the methylation status of specific gene promoters may be useful for clinically discriminating subgroups of children diagnosed with neuroblastoma. To date, these investigations have assessed DNA methylation using variable techniques; focused on small numbers of candidate genes and; examined few primary tumor samples. The aims of our study were to characterize the clinical significance of promoter methylation in a large cohort of primary neuroblastoma tumors and investigate the association between DNA methylation and clinical outcome. Methods: A customized Illumina GoldenGate methylation assay was used to assess methylation status of 96 CpG sites within 48 candidate genes in primary neuroblastoma tumors obtained from 131 children diagnosed in Australia between 1985 and 2000. Candidate genes were selected on the basis of previous reports of altered DNA methylation in embryonal cancers. Levels of DNA methylation were quantified and confirmed in a subset of 48 patient samples using combined bisulphite restriction analysis (CoBRA). A Cox proportional hazards model was used to investigate the association between promoter hypermethylation and the risk of relapse or death within 5 years of diagnosis, while adjusting for known prognostic cofactors such as MYCN amplification, age and stage at diagnosis. Results: The level of promoter methylation of DNAJC15, NTRK1 and TNFRSF10D were significantly higher in older patients at diagnosis (p<0.01), while higher levels of promoter methylation of DNAJC15, NTRK1 and PYCARD were observed in patients with MYCN amplification (p<0.001). In multivariate analysis, promoter hypermethylation of FOLH1, MTRR, MYOD1 and THBS1 remained significant independent predictors of poorer clinical outcome, after adjusting for MYCN amplification, age at diagnosis, and tumor stage (p≤0.009). Moreover, over 40% of patients displayed promoter hypermethylation in 2 or more of these genes and were 3 times more likely to relapse or die than those who did not display promoter hypermethylation (HR=3.08; 95%C1=1.71-5.54; p<0.001). Conclusion: DNA methylation of FOLH1, MTRR, MYOD1 and THBS1 appears to have independent prognostic value in children diagnosed with neuroblastoma and highlights important new therapeutic targets for selected patient subsets.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1425. doi:1538-7445.AM2012-1425
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Affiliation(s)
- Diana T. Lau
- 1Children's Cancer Institute Australia, Sydney, Australia
| | - Luke B. Hesson
- 2Lowy Cancer Research Centre, University of NSW, Sydney, Australia
| | | | - Michelle Haber
- 1Children's Cancer Institute Australia, Sydney, Australia
| | - Glenn M. Marshall
- 3Centre for Children's Cancer and Blood Disorders, Sydney Children's Hospital, Sydney, Australia
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Hesson LB, Packham D, Pontzer E, Funchain P, Eng C, Ward RL. A reinvestigation of somatic hypermethylation at the PTEN CpG island in cancer cell lines. Biol Proced Online 2012; 14:5. [PMID: 22490388 PMCID: PMC3342897 DOI: 10.1186/1480-9222-14-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 04/10/2012] [Indexed: 12/15/2022] Open
Abstract
Background PTEN is an important tumour suppressor gene that is mutated in Cowden syndrome as well as various sporadic cancers. CpG island hypermethylation is another route to tumour suppressor gene inactivation, however, the literature regarding PTEN hypermethylation in cancer is controversial. Furthermore, investigation of the methylation status of the PTEN CpG island is challenging due to sequence homology with the PTEN pseudogene, PTENP1. PTEN shares a CpG island promoter with another gene known as KLLN. Here we present a thorough reinvestigation of the methylation status of the PTEN CpG island in DNA from colorectal, breast, ovarian, glioma, lung and haematological cancer cell lines. Results Using a range of bisulphite-based PCR assays we investigated 6 regions across the PTEN CpG island. We found that regions 1-4 were not methylated in cancer cell lines (0/36). By allelic bisulphite sequencing and pyrosequencing methylation was detected in regions 5 and 6 in colorectal, breast and haematological cancer cell lines. However, methylation detected in this region was associated with the PTENP1 promoter and not the PTEN CpG island. Conclusions We show that methylation of the PTEN CpG island is a rare event in cancer cell lines and that apparent methylation most likely originates from homologous regions of the PTENP1 pseudogene promoter. Future studies should utilize assays that reliably discriminate between PTEN and PTENP1 to avoid data misinterpretation.
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Affiliation(s)
- Luke B Hesson
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2052, Australia.
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Hesson LB, Patil V, Sloane M, Ward RL. Abstract 2000: Investigation of the molecular events associated with gene resilencing following withdrawal of epigenetic therapies. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-2000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Epigenetic therapies are a potential new class of anticancer medication for the treatment of solid tumors as well as haematological malignancies. These therapies reverse changes to DNA methylation and histone modifications allowing re-expression of epigenetically inactivated genes. However, upon drug withdrawal reactivated genes undergo re-silencing. This study investigates the mechanism of gene re-silencing following withdrawal of epigenetic therapies, in an effort to identify strategies which deliver a permanent re-expression of epigenetically inactivated genes. Using the mismatch repair gene MLH1 as a model we investigated the molecular events associated with the re-silencing process in the colorectal cancer cell line RKO. These cells lack MLH1 expression due to biallelic promoter DNA hypermethylation. We treated RKO cells for 72hrs with a combination of 2.56µM 5-aza-2’deoxycytidine (a DNA methyltransferase (DNMT) inhibitor) and 19nM Trichostatin A (a histone deacetylase (HDAC) inhibitor). We observed MLH1 re-expression by quantitative RT-PCR, concomitant with de-methylation at the MLH1 promoter as determined by bisulphite sequencing. Methylation at the MLH1 promoter decreased from 90.9% in mock-treated cells to 74.7, 61.7, 62.4 and 65.9% at 0, 3, 5 and 7 days after drug withdrawal, respectively. We observed a reproducible re-silencing of MLH1 gene expression, which began three days after drug withdrawal and was complete by 120 days. We further demonstrate the recruitment of a nucleosome, located immediately upstream of the transcription start site, prior to the re-silencing of MLH1 expression that remained high whilst MLH1 transcript levels decreased. We propose that the recruitment of promoter nucleosomes precedes a reduction in transcriptional output and the re-methylation of promoter DNA. Ongoing work aims to dissect the re-silencing process further by investigating the dynamics of RNApolII occupancy and histone modifications at the MLH1 promoter. This study provides important information on the molecular events associated with gene re-silencing by addressing the temporal relationship between changes to gene expression, nucleosomal occupancy and DNA methylation.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2000. doi:10.1158/1538-7445.AM2011-2000
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Affiliation(s)
- Luke B. Hesson
- 1Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Vibha Patil
- 1Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Mathew Sloane
- 1Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
| | - Robyn L. Ward
- 1Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Sydney, Australia
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Hesson LB, Hitchins MP, Ward RL. Epimutations and cancer predisposition: importance and mechanisms. Curr Opin Genet Dev 2010; 20:290-8. [PMID: 20359882 DOI: 10.1016/j.gde.2010.02.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 01/31/2010] [Accepted: 02/20/2010] [Indexed: 01/24/2023]
Abstract
Germline sequence mutations in tumour suppressor genes can cause cancer predisposition syndromes. More recently, epimutations have also been proposed to cause at least one such syndrome, hereditary non-polyposis colorectal cancer (HNPCC). 'Epigenetic predisposition', is defined as an inherited propensity to an altered epigenetic state in normal tissues that confers a predisposition to disease. Genetic sequence variations acting in cis or trans may contribute to epigenetic variations. Understanding the origin of epimutations will inform cancer risk assessment and will also aid the design and application of new therapies that target the epigenome.
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Affiliation(s)
- Luke B Hesson
- Lowy Cancer Research Centre and Prince of Wales Clinical School, University of New South Wales, Kensington, New South Wales, Australia
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Hesson LB, Dunwell TL, Cooper WN, Catchpoole D, Brini AT, Chiaramonte R, Griffiths M, Chalmers AD, Maher ER, Latif F. The novel RASSF6 and RASSF10 candidate tumour suppressor genes are frequently epigenetically inactivated in childhood leukaemias. Mol Cancer 2009; 8:42. [PMID: 19570220 PMCID: PMC2711046 DOI: 10.1186/1476-4598-8-42] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2009] [Accepted: 07/01/2009] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The Ras-association family (RASSF) of tumour suppressor genes (TSGs) contains 10 members that encode proteins containing Ras-association (RA) domains. Several members of the RASSF family are frequently epigenetically inactivated in cancer, however, their role in leukaemia has remained largely uninvestigated. Also, RASSF10 is a predicted gene yet to be experimentally verified. Here we cloned, characterised and demonstrated expression of RASSF10 in normal human bone marrow. We also determined the methylation status of CpG islands associated with RASSF1-10 in a series of childhood acute lymphocytic leukaemias (ALL) and normal blood and bone marrow samples. RESULTS COBRA and bisulphite sequencing revealed RASSF6 and RASSF10 were the only RASSF members with a high frequency of leukaemia-specific methylation. RASSF6 was methylated in 94% (48/51) B-ALL and 41% (12/29) T-ALL, whilst RASSF10 was methylated in 16% (8/51) B-ALL and 88% (23/26) T-ALL. RASSF6 and RASSF10 expression inversely correlated with methylation which was restored by treatment with 5-aza-2'deoxycytidine (5azaDC). CONCLUSION This study shows the hypermethylation profile of RASSF genes in leukaemias is distinct from that of solid tumours and represents the first report of inactivation of RASSF6 or RASSF10 in cancer. These data show epigenetic inactivation of the candidate TSGs RASSF6 and RASSF10 is an extremely frequent event in the pathogenesis of childhood leukaemia. This study also warrants further investigation of the newly identified RASSF member RASSF10 and its potential role in leukaemia.
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Affiliation(s)
- Luke B Hesson
- Department of Medical and Molecular Genetics, Institute of Biomedical Research, Medical School, University of Birmingham, Edgbaston, B15 2TT, UK.
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Dallol A, Hesson LB, Matallanas D, Cooper WN, O'Neill E, Maher ER, Kolch W, Latif F. RAN GTPase Is a RASSF1A Effector Involved in Controlling Microtubule Organization. Curr Biol 2009; 19:1227-32. [DOI: 10.1016/j.cub.2009.05.064] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Revised: 05/21/2009] [Accepted: 05/22/2009] [Indexed: 12/21/2022]
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Dunwell TL, Hesson LB, Pavlova T, Zabarovska V, Kashuba V, Catchpoole D, Chiaramonte R, Brini AT, Griffiths M, Maher ER, Zabarovsky E, Latif F. Epigenetic analysis of childhood acute lymphoblastic leukemia. Epigenetics 2009; 4:185-93. [PMID: 19430199 DOI: 10.4161/epi.4.3.8752] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
We used a chromosome 3 wide NotI microarray for identification of epigenetically inactivated genes in childhood acute lymphoblastic leukemia (ALL). Three novel genes demonstrated frequent methylation in childhood ALL. PPP2R3A (protein phosphatase 2, regulatory subunit B", alpha) was frequently methylated in T (69%) and B (82%)-ALL. Whilst FBLN2 (fibulin 2) and THRB (thyroid hormone receptor, beta) showed frequent methylation in B-ALL (58%; 56% respectively), but were less frequently methylated in T-ALL (17% for both genes). Recently it was demonstrated that BNC1 (Basonuclin 1) and MSX1 (msh homeobox 1) were frequently methylated across common epithelial cancers. In our series of childhood ALL BNC1 was frequently methylated in both T (77%) and B-ALL (79%), whilst MSX1 showed T-ALL (25%) specific methylation. The methylation of the above five genes was cancer specific and expression of the genes could be restored in methylated leukemia cell lines treated with 5-aza-2'-deoxycytidine. This is the first report demonstrating frequent epigenetic inactivation of PPP2R3A, FBLN2, THRB, BNC1 and MSX1 in leukemia. The identification of frequently methylated genes showing cancer specific methylation will be useful in developing early cancer detection screens and for targeted epigenetic therapies.
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Affiliation(s)
- Thomas L Dunwell
- Institute of Biomedical Research, Medical School, University of Birmingham, Edgbaston, Birmingham, UK
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Abstract
Gliomas represent the most common CNS cancers in adults. Prognosis for patients harboring malignant gliomas is particularly dismal and, despite current treatment strategies comprising surgery, radiotherapy and chemotherapy, the median survival time after diagnosis is still in the range of just 12 months. In recent years, there has been an increased effort to identify tumor biomarkers that can be used as diagnostic tools, or markers for predicting therapeutic response and prognosis. Investigation of genetic changes has identified several such markers that have shown some success in predicting the most effective therapy. In recent years, however, it has become apparent that the biology of many cancers of the CNS is determined not only by their genetic profile but also their epigenetic profile. Epigenetic biomarkers show great potential in effectively predicting patient prognosis and response to therapy. The eventual application of epigenetic profiling of tumors may help to indicate the most effective tailored therapy for individual patients.
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Affiliation(s)
- Luke B Hesson
- Department of Reproductive and Child Health, Institute of Biomedical Research, Medical School, University of Birmingham, Edgbaston, B15 2TT, UK.
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Cooper WN, Dickinson RE, Dallol A, Hesson LB, Bieche I, Clark GJ, Maher ER, Zabarovsky ER, Latif F. RASSF2 can suppress the growth of breast cancer cell lines and is epigenetically inactivated in breast tumours. Breast Cancer Res 2008. [PMCID: PMC3300712 DOI: 10.1186/bcr1893] [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: 11/10/2022] Open
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48
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Cooper WN, Dickinson RE, Dallol A, Grigorieva EV, Pavlova TV, Hesson LB, Bieche I, Broggini M, Maher ER, Zabarovsky ER, Clark GJ, Latif F. Epigenetic regulation of the ras effector/tumour suppressor RASSF2 in breast and lung cancer. Oncogene 2008; 27:1805-11. [PMID: 17891178 PMCID: PMC2948550 DOI: 10.1038/sj.onc.1210805] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2007] [Revised: 08/18/2007] [Accepted: 08/20/2007] [Indexed: 12/30/2022]
Abstract
RASSF2 is a recently identified member of a class of novel tumour suppressor genes, all containing a ras-association domain. RASSF2 resides at 20p13, a region frequently lost in human cancers. In this report we investigated methylation status of the RASSF2 promoter CpG island in a series of breast, ovarian and non-small cell lung cancers (NSCLC). RASSF2 was frequently methylated in breast tumour cell lines (65%, 13/20) and in primary breast tumours (38%, 15/40). RASSF2 expression could be switched back on in methylated breast tumour cell lines after treatment with 5'-aza-2'deoxycytidine. RASSF2 was also frequently methylated in NSCLC tumours (44%, (22/50). The small number of corresponding normal breast and lung tissue DNA samples analysed were unmethylated. We also did not detect RASSF2 methylation in ovarian tumours (0/17). Furthermore no mutations were found in the coding region of RASSF2 in these ovarian tumours. We identified a highly conserved putative bipartite nuclear localization signal (NLS) and demonstrated that endogenous RASSF2 localized to the nucleus. Mutation of the putative NLS abolished the nuclear localization. RASSF2 suppressed breast tumour cell growth in vitro and in vivo, while the ability of NLS-mutant RASSF2 to suppress growth was much diminished. Hence we demonstrate that RASSF2 has a functional NLS that is important for its tumour suppressor gene function. Our data from this and a previous report indicate that RASSF2 is frequently methylated in colorectal, breast and NSCLC tumours. We have identified RASSF2 as a novel methylation marker for multiple malignancies and it has the potential to be developed into a valuable marker for screening several cancers in parallel using promoter hypermethylation profiles.
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Affiliation(s)
- W N Cooper
- Department of Medical and Molecular Genetics, Division of Reproductive and Child Health, Institute of Biomedical Research, University of Birmingham, Edgbaston, Birmingham, UK
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Abstract
Deletions of the 3p21.3 region are a frequent and early event in the formation of lung, breast, kidney and other cancers. Intense investigation of allelic losses and the discovery of overlapping homozygous deletions in lung and breast tumour-cell lines have defined a minimal critical 120 kb deletion region containing eight genes and likely to harbor one or more tumour-suppressor genes (TSGs). The candidate genes are HYAL2, FUS1, Ras-associated factor 1 (RASSF1), BLU/ZMYND10, NPR2L, 101F6, PL6 and CACNA2D2. Recent research indicates that several of these genes can suppress the growth of lung and other tumour cells. Furthermore, some genes (RASSF1A and BLU/ZMYND10) are very frequently inactivated by non-classical mechanisms such as promoter hypermethylation resulting in loss of expression. These data indicate that the 120 kb critical deletion region at 3p21.3 may represent a TSG cluster with preferential inactivation of particular genes depending on tumour type. The eight genes within this region and their potential role in cancer will be the focus of this review.
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Affiliation(s)
- L B Hesson
- Department of Medical and Molecular Genetics, MRC Protein Phosphorylation Unit, College of Life Sciences, Sir James Black Centre, Dow Street, University of Dundee, Dundee, UK.
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50
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Abstract
Tumour suppressor gene inactivation is critical to the pathogenesis of cancers; such loss of function may be mediated by irreversible processes such as gene deletion or mutation. Alternatively tumour suppressor genes may be inactivated via epigenetic processes a reversible mechanism that promises to be more amenable to treatment by therapeutic agents. The CpG dinucleotide is under-represented in the genome, but it is found in clusters within the promoters of some genes, and methylation of these CpG islands play a critical role in the control of gene expression. Inhibitors of the DNA methyltransferases DNMT1 and DNMT3b have been used in a clinical setting, these nucleotide analogues lack specificity but the side effects of low dose treatments were minimal and in 2004 Vidaza (5-azacitidine) was licensed for use in myelodysplastic syndrome. Methylation inhibitors are also entering trials in conjunction with another class of epigenetic modifiers, the histone deacetylase inhibitors and this epigenetic double bullet offers hope of improved treatment regimes. Recently there has been a plethora of reports demonstrating epigenetic inactivation of genes that play important roles in development of cancer, including Ras-association domain family of genes. Epigenetic inactivation of RASSF1A (Ras-association domain family 1, isoform A) is one of the most common molecular changes in cancer. Hypermethylation of the RASSF1A promoter CpG island silences expression of the gene in many cancers including lung, breast, prostate, glioma, neuroblastoma and kidney cancer. Several recent studies have illustrated the diagnostic and prognostic potential of RASSF1A methylation. This presents RASSF1A methylation as an attractive biomarker for early cancer detection which, for most cancers, results in improved clinical outcome. DNA methylation analysis is applicable to a range of body fluids including serum, urine, bronchioalveolar lavage and sputum. The ease with which these body fluids can be acquired negates the need for invasive procedures to obtain biopsy material. This review will discuss the feasibility of using RASSF1A methylation as a diagnostic and prognostic marker in cancer management.
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Affiliation(s)
- Luke B. Hesson
- Section of Medical and Molecular GeneticsDivision of Reproductive and Child HealthInstitute of Biomedical ResearchUniversity of BirminghamEdgbastonBirminghamUK
- MRC Protein Phosphorylation UnitSchool of Life SciencesMSI/WTB ComplexDow StreetUniversity of DundeeDundeeScotlandUK
| | - Wendy N. Cooper
- Section of Medical and Molecular GeneticsDivision of Reproductive and Child HealthInstitute of Biomedical ResearchUniversity of BirminghamEdgbastonBirminghamUK
| | - Farida Latif
- Section of Medical and Molecular GeneticsDivision of Reproductive and Child HealthInstitute of Biomedical ResearchUniversity of BirminghamEdgbastonBirminghamUK
- *Farida Latif:
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