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Gu K, Mok L, Wakefield MJ, Chong MMW. Non-canonical RNA substrates of Drosha lack many of the conserved features found in primary microRNA stem-loops. Sci Rep 2024; 14:6713. [PMID: 38509178 PMCID: PMC10954719 DOI: 10.1038/s41598-024-57330-5] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 03/18/2024] [Indexed: 03/22/2024] Open
Abstract
The RNase III enzyme Drosha has a central role in microRNA (miRNA) biogenesis, where it is required to release the stem-loop intermediate from primary (pri)-miRNA transcripts. However, it can also cleave stem-loops embedded within messenger (m)RNAs. This destabilizes the mRNA causing target gene repression and appears to occur primarily in stem cells. While pri-miRNA stem-loops have been extensively studied, such non-canonical substrates of Drosha have yet to be characterized in detail. In this study, we employed high-throughput sequencing to capture all polyA-tailed RNAs that are cleaved by Drosha in mouse embryonic stem cells (ESCs) and compared the features of non-canonical versus miRNA stem-loop substrates. mRNA substrates are less efficiently processed than miRNA stem-loops. Sequence and structural analyses revealed that these mRNA substrates are also less stable and more likely to fold into alternative structures than miRNA stem-loops. Moreover, they lack the sequence and structural motifs found in miRNA stem-loops that are required for precise cleavage. Notably, we discovered a non-canonical Drosha substrate that is cleaved in an inverse manner, which is a process that is normally inhibited by features in miRNA stem-loops. Our study thus provides valuable insights into the recognition of non-canonical targets by Drosha.
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Affiliation(s)
- Karen Gu
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia
| | - Lawrence Mok
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Mark M W Chong
- St Vincent's Institute of Medical Research, Fitzroy, VIC, 3065, Australia.
- Department of Medicine (St Vincent's), University of Melbourne, Fitzroy, VIC, 3065, Australia.
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2
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Geissler F, Nesic K, Kondrashova O, Dobrovic A, Swisher EM, Scott CL, J. Wakefield M. The role of aberrant DNA methylation in cancer initiation and clinical impacts. Ther Adv Med Oncol 2024; 16:17588359231220511. [PMID: 38293277 PMCID: PMC10826407 DOI: 10.1177/17588359231220511] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 11/21/2023] [Indexed: 02/01/2024] Open
Abstract
Epigenetic alterations, including aberrant DNA methylation, are now recognized as bone fide hallmarks of cancer, which can contribute to cancer initiation, progression, therapy responses and therapy resistance. Methylation of gene promoters can have a range of impacts on cancer risk, clinical stratification and therapeutic outcomes. We provide several important examples of genes, which can be silenced or activated by promoter methylation and highlight their clinical implications. These include the mismatch DNA repair genes MLH1 and MSH2, homologous recombination DNA repair genes BRCA1 and RAD51C, the TERT oncogene and genes within the P15/P16/RB1/E2F tumour suppressor axis. We also discuss how these methylation changes might occur in the first place - whether in the context of the CpG island methylator phenotype or constitutional DNA methylation. The choice of assay used to measure methylation can have a significant impact on interpretation of methylation states, and some examples where this can influence clinical decision-making are presented. Aberrant DNA methylation patterns in circulating tumour DNA (ctDNA) are also showing great promise in the context of non-invasive cancer detection and monitoring using liquid biopsies; however, caution must be taken in interpreting these results in cases where constitutional methylation may be present. Thus, this review aims to provide researchers and clinicians with a comprehensive summary of this broad, but important subject, illustrating the potentials and pitfalls of assessing aberrant DNA methylation in cancer.
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Affiliation(s)
- Franziska Geissler
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, VIC, Australia
| | | | - Clare L. Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Matthew J. Wakefield
- Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
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3
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Ho GY, Vandenberg CJ, Lim R, Christie EL, Garsed DW, Lieschke E, Nesic K, Kondrashova O, Ratnayake G, Radke M, Penington JS, Carmagnac A, Heong V, Kyran EL, Zhang F, Traficante N, Huang R, Dobrovic A, Swisher EM, McNally O, Kee D, Wakefield MJ, Papenfuss AT, Bowtell DDL, Barker HE, Scott CL. The microtubule inhibitor eribulin demonstrates efficacy in platinum-resistant and refractory high-grade serous ovarian cancer patient-derived xenograft models. Ther Adv Med Oncol 2023; 15:17588359231208674. [PMID: 38028140 PMCID: PMC10666702 DOI: 10.1177/17588359231208674] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023] Open
Abstract
Background Despite initial response to platinum-based chemotherapy and PARP inhibitor therapy (PARPi), nearly all recurrent high-grade serous ovarian cancer (HGSC) will acquire lethal drug resistance; indeed, ~15% of individuals have de novo platinum-refractory disease. Objectives To determine the potential of anti-microtubule agent (AMA) therapy (paclitaxel, vinorelbine and eribulin) in platinum-resistant or refractory (PRR) HGSC by assessing response in patient-derived xenograft (PDX) models of HGSC. Design and methods Of 13 PRR HGSC PDX, six were primary PRR, derived from chemotherapy-naïve samples (one was BRCA2 mutant) and seven were from samples obtained following chemotherapy treatment in the clinic (five were mutant for either BRCA1 or BRCA2 (BRCA1/2), four with prior PARPi exposure), recapitulating the population of individuals with aggressive treatment-resistant HGSC in the clinic. Molecular analyses and in vivo treatment studies were undertaken. Results Seven out of thirteen PRR PDX (54%) were sensitive to treatment with the AMA, eribulin (time to progressive disease (PD) ⩾100 days from the start of treatment) and 11 out of 13 PDX (85%) derived significant benefit from eribulin [time to harvest (TTH) for each PDX with p < 0.002]. In 5 out of 10 platinum-refractory HGSC PDX (50%) and one out of three platinum-resistant PDX (33%), eribulin was more efficacious than was cisplatin, with longer time to PD and significantly extended TTH (each PDX p < 0.02). Furthermore, four of these models were extremely sensitive to all three AMA tested, maintaining response until the end of the experiment (120d post-treatment start). Despite harbouring secondary BRCA2 mutations, two BRCA2-mutant PDX models derived from heavily pre-treated individuals were sensitive to AMA. PRR HGSC PDX models showing greater sensitivity to AMA had high proliferative indices and oncogene expression. Two PDX models, both with prior chemotherapy and/or PARPi exposure, were refractory to all AMA, one of which harboured the SLC25A40-ABCB1 fusion, known to upregulate drug efflux via MDR1. Conclusion The efficacy observed for eribulin in PRR HGSC PDX was similar to that observed for paclitaxel, which transformed ovarian cancer clinical practice. Eribulin is therefore worthy of further consideration in clinical trials, particularly in ovarian carcinoma with early failure of carboplatin/paclitaxel chemotherapy.
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Affiliation(s)
- Gwo Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- The Royal Women’s Hospital, Parkville, VIC, Australia
- School of Clinical Sciences, Monash University, Clayton Road, Clayton, VIC 3168, Australia
| | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Ratana Lim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Elizabeth L. Christie
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Dale W. Garsed
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- QIMR Berghofer Medical Research Institute, Herston, QLD, Australia
| | | | - Marc Radke
- University of Washington, Seattle, WA, USA
| | - Jocelyn S. Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Amandine Carmagnac
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Valerie Heong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Elizabeth L. Kyran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Fan Zhang
- Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | | | | | - Alexander Dobrovic
- Department of Surgery, Austin Health, University of Melbourne, Heidelberg, VIC, Australia
| | | | - Orla McNally
- The Royal Women’s Hospital, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
| | - Damien Kee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Medical Oncology, Austin Hospital, Heidelberg, VIC, Australia
| | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
| | - Anthony T. Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - David D. L. Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- The Royal Women’s Hospital, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, Australia
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Nesic K, Krais JJ, Vandenberg CJ, Wang Y, Patel P, Cai KQ, Kwan T, Lieschke E, Ho GY, Barker HE, Bedo J, Casadei S, Farrell A, Radke M, Shield-Artin K, Penington JS, Geissler F, Kyran E, Zhang F, Dobrovic A, Olesen I, Kristeleit R, Oza A, Ratnayake G, Traficante N, DeFazio A, Bowtell DDL, Harding TC, Lin K, Swisher EM, Kondrashova O, Scott CL, Johnson N, Wakefield MJ. BRCA1 secondary splice-site mutations drive exon-skipping and PARP inhibitor resistance. medRxiv 2023:2023.03.20.23287465. [PMID: 36993400 PMCID: PMC10055590 DOI: 10.1101/2023.03.20.23287465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
BRCA1 splice isoforms Δ11 and Δ11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out the mutation-containing exon, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers of BRCA1 exon skipping remain undetermined. We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with BRCA1 exon 11 frameshift mutations for exon skipping and therapy response, including a matched PDX pair derived from a patient pre- and post-chemotherapy/PARPi. BRCA1 exon 11 skipping was elevated in PARPi resistant PDX tumors. Two independent PDX models acquired secondary BRCA1 splice site mutations (SSMs), predicted in silico to drive exon skipping. Predictions were confirmed using qRT-PCR, RNA sequencing, western blots and BRCA1 minigene modelling. SSMs were also enriched in post-PARPi ovarian cancer patient cohorts from the ARIEL2 and ARIEL4 clinical trials. We demonstrate that SSMs drive BRCA1 exon 11 skipping and PARPi resistance, and should be clinically monitored, along with frame-restoring secondary mutations.
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Affiliation(s)
- Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | | | | | - Tanya Kwan
- Clovis Oncology Inc., San Francisco, CA, USA
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Gwo-Yaw Ho
- School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Justin Bedo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | | | - Andrew Farrell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Marc Radke
- University of Washington, Seattle, WA, USA
| | - Kristy Shield-Artin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Jocelyn S. Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Franziska Geissler
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Elizabeth Kyran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Fan Zhang
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, Victoria, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Health, Heidelberg, Victoria, Australia
| | - Inger Olesen
- The Andrew Love Cancer Centre, Barwon Health, Geelong, Victoria, Australia
| | - Rebecca Kristeleit
- Department of Oncology, Guys and St Thomas’ NHS Foundation Trust, London, UK
- National Institute for Health Research, University College London Hospitals Clinical Research Facility, London, UK
| | - Amit Oza
- Princess Margaret Cancer Center, Toronto, ON, Canada
| | | | - Nadia Traficante
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | | | - Anna DeFazio
- The Daffodil Centre, The University of Sydney, a joint venture with Cancer Council New South Wales, Sydney, New South Wales, Australia
- The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
- Department of Gynecological Oncology, Westmead Hospital, Western Sydney Local Health District, New South Wales, Australia
| | - David D. L. Bowtell
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
| | | | - Kevin Lin
- Clovis Oncology Inc., San Francisco, CA, USA
| | | | - Olga Kondrashova
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Royal Women’s Hospital, Parkville, VIC, Australia
- Sir Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, VIC, Australia
| | | | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
- Department of Obstetrics and Gynecology, University of Melbourne, Parkville, VIC, Australia
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5
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Marks ZRC, Campbell NK, Mangan NE, Vandenberg CJ, Gearing LJ, Matthews AY, Gould JA, Tate MD, Wray-McCann G, Ying L, Rosli S, Brockwell N, Parker BS, Lim SS, Bilandzic M, Christie EL, Stephens AN, de Geus E, Wakefield MJ, Ho GY, McNally O, McNeish IA, Bowtell DDL, de Weerd NA, Scott CL, Bourke NM, Hertzog PJ. Interferon-ε is a tumour suppressor and restricts ovarian cancer. Nature 2023; 620:1063-1070. [PMID: 37587335 DOI: 10.1038/s41586-023-06421-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [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: 08/09/2018] [Accepted: 07/11/2023] [Indexed: 08/18/2023]
Abstract
High-grade serous ovarian cancers have low survival rates because of their late presentation with extensive peritoneal metastases and frequent chemoresistance1, and require new treatments guided by novel insights into pathogenesis. Here we describe the intrinsic tumour-suppressive activities of interferon-ε (IFNε). IFNε is constitutively expressed in epithelial cells of the fallopian tube, the cell of origin of high-grade serous ovarian cancers, and is then lost during development of these tumours. We characterize its anti-tumour activity in several preclinical models: ovarian cancer patient-derived xenografts, orthotopic and disseminated syngeneic models, and tumour cell lines with or without mutations in Trp53 and Brca genes. We use manipulation of the IFNε receptor IFNAR1 in different cell compartments, differential exposure status to IFNε and global measures of IFN signalling to show that the mechanism of the anti-tumour activity of IFNε involves direct action on tumour cells and, crucially, activation of anti-tumour immunity. IFNε activated anti-tumour T and natural killer cells and prevented the accumulation and activation of myeloid-derived suppressor cells and regulatory T cells. Thus, we demonstrate that IFNε is an intrinsic tumour suppressor in the female reproductive tract whose activities in models of established and advanced ovarian cancer, distinct from other type I IFNs, are compelling indications of potential new therapeutic approaches for ovarian cancer.
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Affiliation(s)
- Zoe R C Marks
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Nicole K Campbell
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Niamh E Mangan
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Cassandra J Vandenberg
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Linden J Gearing
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Antony Y Matthews
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Jodee A Gould
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Michelle D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Georgie Wray-McCann
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Le Ying
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Sarah Rosli
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Natasha Brockwell
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Belinda S Parker
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - San S Lim
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Maree Bilandzic
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | | | - Andrew N Stephens
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
- Centre for Cancer Research, Hudson Institute of Medical Research, Clayton, Victoria, Australia
| | - Eveline de Geus
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- School of Clinical Sciences, Monash University, Clayton, Victoria, Australia
| | - Orla McNally
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
- Royal Women's Hospital, Parkville, Victoria, Australia
| | - Iain A McNeish
- Ovarian Cancer Action Research Centre, Division of Cancer, Department of Surgery and Cancer, Imperial College London, London, UK
| | - David D L Bowtell
- Research Division, Peter McCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Nicole A de Weerd
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Royal Women's Hospital, Parkville, Victoria, Australia
| | - Nollaig M Bourke
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia
- Department of Medical Gerontology, School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Paul J Hertzog
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.
- Department of Molecular and Translational Science, Monash University, Clayton, Victoria, Australia.
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6
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Dall G, Vandenberg CJ, Nesic K, Ratnayake G, Zhu W, Vissers JHA, Bedő J, Penington J, Wakefield MJ, Kee D, Carmagnac A, Lim R, Shield-Artin K, Milesi B, Lobley A, Kyran EL, O'Grady E, Tram J, Zhou W, Nugawela D, Stewart KP, Caldwell R, Papadopoulos L, Ng AP, Dobrovic A, Fox SB, McNally O, Power JD, Meniawy T, Tan TH, Collins IM, Klein O, Barnett S, Olesen I, Hamilton A, Hofmann O, Grimmond S, Papenfuss AT, Scott CL, Barker HE. Targeting homologous recombination deficiency in uterine leiomyosarcoma. J Exp Clin Cancer Res 2023; 42:112. [PMID: 37143137 PMCID: PMC10157936 DOI: 10.1186/s13046-023-02687-0] [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: 02/14/2023] [Accepted: 04/25/2023] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Uterine leiomyosarcoma (uLMS) is a rare and aggressive gynaecological malignancy, with individuals with advanced uLMS having a five-year survival of < 10%. Mutations in the homologous recombination (HR) DNA repair pathway have been observed in ~ 10% of uLMS cases, with reports of some individuals benefiting from poly (ADP-ribose) polymerase (PARP) inhibitor (PARPi) therapy, which targets this DNA repair defect. In this report, we screened individuals with uLMS, accrued nationally, for mutations in the HR repair pathway and explored new approaches to therapeutic targeting. METHODS A cohort of 58 individuals with uLMS were screened for HR Deficiency (HRD) using whole genome sequencing (WGS), whole exome sequencing (WES) or NGS panel testing. Individuals identified to have HRD uLMS were offered PARPi therapy and clinical outcome details collected. Patient-derived xenografts (PDX) were generated for therapeutic targeting. RESULTS All 13 uLMS samples analysed by WGS had a dominant COSMIC mutational signature 3; 11 of these had high genome-wide loss of heterozygosity (LOH) (> 0.2) but only two samples had a CHORD score > 50%, one of which had a homozygous pathogenic alteration in an HR gene (deletion in BRCA2). A further three samples harboured homozygous HRD alterations (all deletions in BRCA2), detected by WES or panel sequencing, with 5/58 (9%) individuals having HRD uLMS. All five individuals gained access to PARPi therapy. Two of three individuals with mature clinical follow up achieved a complete response or durable partial response (PR) with the subsequent addition of platinum to PARPi upon minor progression during initial PR on PARPi. Corresponding PDX responses were most rapid, complete and sustained with the PARP1-specific PARPi, AZD5305, compared with either olaparib alone or olaparib plus cisplatin, even in a paired sample of a BRCA2-deleted PDX, derived following PARPi therapy in the patient, which had developed PARPi-resistance mutations in PRKDC, encoding DNA-PKcs. CONCLUSIONS Our work demonstrates the value of identifying HRD for therapeutic targeting by PARPi and platinum in individuals with the aggressive rare malignancy, uLMS and suggests that individuals with HRD uLMS should be included in trials of PARP1-specific PARPi.
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Affiliation(s)
- Genevieve Dall
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Cassandra J Vandenberg
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Ksenija Nesic
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | | | - Wenying Zhu
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Joseph H A Vissers
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Justin Bedő
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Computing and Information Systems, the University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jocelyn Penington
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Damien Kee
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- Austin Health, Heidelberg, VIC, 3084, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Amandine Carmagnac
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Ratana Lim
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Kristy Shield-Artin
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Briony Milesi
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Amanda Lobley
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Elizabeth L Kyran
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Emily O'Grady
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Joshua Tram
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Warren Zhou
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Devindee Nugawela
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Kym Pham Stewart
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Reece Caldwell
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
| | - Lia Papadopoulos
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
| | - Ashley P Ng
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
| | | | - Stephen B Fox
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Orla McNally
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jeremy D Power
- Launceston General Hospital, Launceston, TAS, 7250, Australia
| | - Tarek Meniawy
- University of Western Australia, Perth, WA, 6009, Australia
| | - Teng Han Tan
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Ian M Collins
- SouthWest Healthcare, Warrnambool, VIC, 3280, Australia
- Faculty of Health, School of Medicine, Deakin University, Warrnambool, VIC, 3280, Australia
| | - Oliver Klein
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- Austin Health, Heidelberg, VIC, 3084, Australia
| | - Stephen Barnett
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
- Western Hospital, Footscray, VIC, 3011, Australia
| | - Inger Olesen
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- University Hospital Geelong, Geelong, VIC, 3220, Australia
| | - Anne Hamilton
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Oliver Hofmann
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Anthony T Papenfuss
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Australian Rare Cancer Portal, BioGrid Australia, Melbourne Health, Parkville, VIC, 3052, Australia
- Peter MacCallum Cancer Centre and Sir Peter MacCallum Department of Oncology, The University of Melbourne, Victoria, 3010, Australia
- Royal Melbourne Hospital, Parkville, VIC, 3052, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Holly E Barker
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3052, Australia
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7
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Veneziani AC, Scott C, Wakefield MJ, Tinker AV, Lheureux S. Fighting resistance: post-PARP inhibitor treatment strategies in ovarian cancer. Ther Adv Med Oncol 2023; 15:17588359231157644. [PMID: 36872947 PMCID: PMC9983116 DOI: 10.1177/17588359231157644] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a therapeutic milestone in the management of epithelial ovarian cancer. The concept of 'synthetic lethality' is exploited by PARPi in tumors with defects in DNA repair pathways, particularly homologous recombination deficiency. The use of PARPis has been increasing since its approval as maintenance therapy, particularly in the first-line setting. Therefore, resistance to PARPi is an emerging issue in clinical practice. It brings an urgent need to elucidate and identify the mechanisms of PARPi resistance. Ongoing studies address this challenge and investigate potential therapeutic strategies to prevent, overcome, or re-sensitize tumor cells to PARPi. This review aims to summarize the mechanisms of resistance to PARPi, discuss emerging strategies to treat patients post-PARPi progression, and discuss potential biomarkers of resistance.
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Affiliation(s)
- Ana C Veneziani
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Clare Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Royal Women's Hospital, Parkville, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Anna V Tinker
- BC Cancer Agency, Medical Oncology Vancouver, Canada
| | - Stephanie Lheureux
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5B 2M9, Canada
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8
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Ho GY, Kyran EL, Bedo J, Wakefield MJ, Ennis DP, Mirza HB, Vandenberg CJ, Lieschke E, Farrell A, Hadla A, Lim R, Dall G, Vince JE, Chua NK, Kondrashova O, Upstill-Goddard R, Bailey UM, Dowson S, Roxburgh P, Glasspool RM, Bryson G, Biankin AV, Cooke SL, Ratnayake G, McNally O, Traficante N, DeFazio A, Weroha SJ, Bowtell DD, McNeish IA, Papenfuss AT, Scott CL, Barker HE. Epithelial-to-Mesenchymal Transition Supports Ovarian Carcinosarcoma Tumorigenesis and Confers Sensitivity to Microtubule Targeting with Eribulin. Cancer Res 2022; 82:4457-4473. [PMID: 36206301 PMCID: PMC9716257 DOI: 10.1158/0008-5472.can-21-4012] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 01/24/2023]
Abstract
Ovarian carcinosarcoma (OCS) is an aggressive and rare tumor type with limited treatment options. OCS is hypothesized to develop via the combination theory, with a single progenitor resulting in carcinomatous and sarcomatous components, or alternatively via the conversion theory, with the sarcomatous component developing from the carcinomatous component through epithelial-to-mesenchymal transition (EMT). In this study, we analyzed DNA variants from isolated carcinoma and sarcoma components to show that OCS from 18 women is monoclonal. RNA sequencing indicated that the carcinoma components were more mesenchymal when compared with pure epithelial ovarian carcinomas, supporting the conversion theory and suggesting that EMT is important in the formation of these tumors. Preclinical OCS models were used to test the efficacy of microtubule-targeting drugs, including eribulin, which has previously been shown to reverse EMT characteristics in breast cancers and induce differentiation in sarcomas. Vinorelbine and eribulin more effectively inhibited OCS growth than standard-of-care platinum-based chemotherapy, and treatment with eribulin reduced mesenchymal characteristics and N-MYC expression in OCS patient-derived xenografts. Eribulin treatment resulted in an accumulation of intracellular cholesterol in OCS cells, which triggered a downregulation of the mevalonate pathway and prevented further cholesterol biosynthesis. Finally, eribulin increased expression of genes related to immune activation and increased the intratumoral accumulation of CD8+ T cells, supporting exploration of immunotherapy combinations in the clinic. Together, these data indicate that EMT plays a key role in OCS tumorigenesis and support the conversion theory for OCS histogenesis. Targeting EMT using eribulin could help improve OCS patient outcomes. SIGNIFICANCE Genomic analyses and preclinical models of ovarian carcinosarcoma support the conversion theory for disease development and indicate that microtubule inhibitors could be used to suppress EMT and stimulate antitumor immunity.
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Affiliation(s)
- Gwo Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- The Royal Women's Hospital, Parkville, Victoria, Australia
| | - Elizabeth L. Kyran
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Cancer Research UK Cambridge Institute, Cambridge, United Kingdom
| | - Justin Bedo
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- School of Computing and Information Systems, the University of Melbourne, Parkville, Victoria, Australia
| | - Matthew J. Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
| | - Darren P. Ennis
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Hasan B. Mirza
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Cassandra J. Vandenberg
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Farrell
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Anthony Hadla
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ratana Lim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Genevieve Dall
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - James E. Vince
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - Ngee Kiat Chua
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Rosanna Upstill-Goddard
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Ulla-Maja Bailey
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Suzanne Dowson
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | - Patricia Roxburgh
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Rosalind M. Glasspool
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Gareth Bryson
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, United Kingdom
| | - Andrew V. Biankin
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | - Susanna L. Cooke
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
| | | | - Orla McNally
- The Royal Women's Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Nadia Traficante
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, Australia
- The Daffodil Centre, The University of Sydney, A Joint Venture with Cancer Council NSW, Sydney, Australia
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, Australia
| | - S. John Weroha
- Department of Oncology, Mayo Clinic, Rochester, Minnesota
| | - David D. Bowtell
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Iain A. McNeish
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
- Institute of Cancer Sciences, Wolfson Wohl Cancer Research Centre, University of Glasgow, Glasgow, United Kingdom
- Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Anthony T. Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
- The Royal Women's Hospital, Parkville, Victoria, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, Victoria, Australia
- Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
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9
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Nesic K, Kondrashova O, Hurley RM, McGehee CD, Vandenberg CJ, Ho GY, Lieschke E, Dall G, Bound N, Shield-Artin K, Radke M, Musafer A, Chai ZQ, Eftekhariyan Ghamsari MR, Harrell MI, Kee D, Olesen I, McNally O, Traficante N, Cancer Study AO, DeFazio A, Bowtell DDL, Swisher EM, Weroha SJ, Nones K, Waddell N, Kaufmann SH, Dobrovic A, Wakefield MJ, Scott CL. Acquired RAD51C promoter methylation loss causes PARP inhibitor resistance in high grade serous ovarian carcinoma. Cancer Res 2021; 81:4709-4722. [PMID: 34321239 DOI: 10.1158/0008-5472.can-21-0774] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/10/2021] [Accepted: 07/07/2021] [Indexed: 11/16/2022]
Abstract
In high-grade serous ovarian carcinoma (HGSC), deleterious mutations in DNA repair gene RAD51C are established drivers of defective homologous recombination and are emerging biomarkers of PARP inhibitor (PARPi) sensitivity. RAD51C promoter methylation (meRAD51C) is detected at similar frequencies to mutations, yet its effects on PARPi responses remain unresolved. In this study, three HGSC patient-derived xenograft (PDX) models with methylation at most or all examined CpG sites in the RAD51C promoter show responses to PARPi. Both complete and heterogeneous methylation patterns were associated with RAD51C gene silencing and homologous recombination deficiency (HRD). PDX models lost meRAD51C following treatment with PARPi rucaparib or niraparib, where a single unmethylated copy of RAD51C was sufficient to drive PARPi resistance. Genomic copy number profiling of one of the PDX models using SNP arrays revealed that this resistance was acquired independently in two genetically distinct lineages. In a cohort of 11 patients with RAD51C-methylated HGSC, various patterns of meRAD51C were associated with genomic 'scarring', indicative of HRD history, but exhibited no clear correlations with clinical outcome. Differences in methylation stability under treatment pressure were also observed between patients, where one HGSC was found to maintain meRAD51C after 6 lines of therapy (4 platinum-based), whilst another HGSC sample was found to have heterozygous meRAD51C and elevated RAD51C gene expression (relative to homozygous meRAD51C controls) after only neo-adjuvant chemotherapy. As meRAD51C loss in a single gene copy was sufficient to cause PARPi resistance in PDX, methylation zygosity should be carefully assessed in previously treated patients when considering PARPi therapy.
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Affiliation(s)
- Ksenija Nesic
- Cancer Biology and Stem Cells, Walter and Eliza Hall Institute of Medical Research
| | - Olga Kondrashova
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute
| | | | | | | | - Gwo-Yaw Ho
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | - Elizabeth Lieschke
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | | | | | - Kristy Shield-Artin
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | - Marc Radke
- Obstetrics and Gynecology, University of Washington Medical Center
| | - Ashan Musafer
- Translational Genomics and Epigenomics Group, Olivia Newton-John Cancer Wellness & Research Centre
| | - Zi Qing Chai
- Olivia Newton-John Cancer Wellness & Research Centre
| | | | - Maria I Harrell
- Obstetrics and Gynecology, University of Washington Medical Center
| | | | | | - Orla McNally
- Department of Obstetrics and Gynaecology, Royal Women's Hospital
| | - Nadia Traficante
- Cancer Genetics and Genomics Laboratory and Australian Ovarian Cancer Study, Peter MacCallum Cancer Centre
| | | | - Anna DeFazio
- Centre for Cancer Research, University of Sydney, Westmead Institute for Medical Research
| | - David D L Bowtell
- Cancer Genetics and Genomics Laboratory and Austrialian Ovarian Cancer Study, Peter MacCallum Cancer Centre
| | | | | | - Katia Nones
- Cell and Molecular Biology, QIMR Berghofer Medical Research Institute
| | - Nicola Waddell
- Medical Genomics Laboratory, QIMR Berghofer Medical Research Institute
| | | | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, University of Melbourne
| | - Matthew J Wakefield
- Stem Cells and Cancer Division, Walter and Eliza Hall Institute of Medical Research
| | - Clare L Scott
- Cancer Biology and Stem Cells Division Division, Walter and Eliza Hall Institute of Medical Research
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10
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Hurley RM, McGehee CD, Nesic K, Correia C, Weiskittel TM, Kelly RL, Venkatachalam A, Hou X, Pathoulas NM, Meng XW, Kondrashova O, Radke MR, Schneider PA, Flatten KS, Peterson KL, Becker MA, Wong EM, Southey MS, Dobrovic A, Lin KK, Harding TC, McNeish I, Ross CA, Wagner JM, Wakefield MJ, Scott CL, Haluska P, Wahner Hendrickson AE, Karnitz LM, Swisher EM, Li H, Weroha SJ, Kaufmann SH. Characterization of a RAD51C-silenced high-grade serous ovarian cancer model during development of PARP inhibitor resistance. NAR Cancer 2021; 3:zcab028. [PMID: 34316715 PMCID: PMC8271218 DOI: 10.1093/narcan/zcab028] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 01/31/2021] [Revised: 05/28/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Acquired PARP inhibitor (PARPi) resistance in BRCA1- or BRCA2-mutant ovarian cancer often results from secondary mutations that restore expression of functional protein. RAD51C is a less commonly studied ovarian cancer susceptibility gene whose promoter is sometimes methylated, leading to homologous recombination (HR) deficiency and PARPi sensitivity. For this study, the PARPi-sensitive patient-derived ovarian cancer xenograft PH039, which lacks HR gene mutations but harbors RAD51C promoter methylation, was selected for PARPi resistance by cyclical niraparib treatment in vivo. PH039 acquired PARPi resistance by the third treatment cycle and grew through subsequent treatment with either niraparib or rucaparib. Transcriptional profiling throughout the course of resistance development showed widespread pathway level changes along with a marked increase in RAD51C mRNA, which reflected loss of RAD51C promoter methylation. Analysis of ovarian cancer samples from the ARIEL2 Part 1 clinical trial of rucaparib monotherapy likewise indicated an association between loss of RAD51C methylation prior to on-study biopsy and limited response. Interestingly, the PARPi resistant PH039 model remained platinum sensitive. Collectively, these results not only indicate that PARPi treatment pressure can reverse RAD51C methylation and restore RAD51C expression, but also provide a model for studying the clinical observation that PARPi and platinum sensitivity are sometimes dissociated.
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Affiliation(s)
- Rachel M Hurley
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Cordelia D McGehee
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Cristina Correia
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Taylor M Weiskittel
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Rebecca L Kelly
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Annapoorna Venkatachalam
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Xiaonan Hou
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | | | - X Wei Meng
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Marc R Radke
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA 98195, USA
| | | | - Karen S Flatten
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905 USA
| | - Kevin L Peterson
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905 USA
| | - Marc A Becker
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria 3800, Australia
| | - Melissa S Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Victoria 3800, Australia
| | - Alexander Dobrovic
- University of Melbourne Department of Surgery, Austin Hospital, Heidelberg, Victoria 3084, Australia
| | - Kevin K Lin
- Clovis Oncology, San Francisco, CA 94158, USA
| | | | - Iain McNeish
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Hammersmith Campus, London, W12 0NN United Kingdom
| | - Christian A Ross
- Division of Information Technology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jill M Wagner
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Paul Haluska
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | | | - Larry M Karnitz
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - Elizabeth M Swisher
- Department of Obstetrics & Gynecology, University of Washington, Seattle, WA 98195, USA
| | - Hu Li
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
| | - S John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905 USA
| | - Scott H Kaufmann
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905 USA
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11
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Nesic K, Vandenberg CJ, Kondrashova O, Krais JJ, Johnson N, Swisher EM, Wakefield MJ, Scott CL. Abstract 2057: BRCA1 D11q isoform expression impacts PARP inhibitor responses in high grade serous ovarian carcinoma patient derived xenografts. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: Acquired PARP inhibitor (PARPi) resistance in High Grade Serous Ovarian Carcinoma (HGSOC) commonly occurs via restored homologous recombination DNA repair due to secondary mutations in BRCA1/2. However, overexpression of certain BRCA1 splice isoforms can also contribute to PARPi resistance in HGSOC. This includes the D11q isoform of BRCA1, where deleterious mutations in the 11q region of BRCA1 (exon 10) can be spliced out resulting in a truncated but partially functional BRCA1 protein. Here we describe four HGSOC Patient Derived Xenografts (PDX) with primary BRCA1 11q mutations, where D11q isoform expression has been shown to correlate with platinum and PARPi responses in vivo.
Methods: PDX were derived from chemo-naive and pre-treated patients (Table 1). PDX were treated with PARPi rucaparib (300mg/kg) and cisplatin (4mg/kg). D11q isoform expression was assessed using two-step RT-qPCR. DNA sequencing was performed using the BROCA Cancer Risk Panel.
Results: PARPi resistant PDX #1032 and #1049 had high D11q expression relative to D11q-high cell line UWB1.289 and the PARPi-responsive models (Table 1). Interestingly, PDX #1049 harboured a second BRCA1 exon 11 donor splice site mutation, shown previously to enhance splicing and increase abundance of the D11q isoform. Indeed, other proximal splice site mutations have been found following relapse in patients with BRCA1 11q mutations post-PARPi.
Conclusions: Our work in PDX provides additional functional evidence that BRCA1 D11q expression impacts on PARPi and platinum responses, and is a clinically relevant mechanism of PARPi resistance in a subset of patients with BRCA1 mutations. Whilst high D11q expression can be associated with secondary BRCA1 splice site mutations (PDX #1049), it can also occur in their absence (PDX #1032). Thus, BRCA1 D11q isoform expression should be considered a potential mechanism of PARP-resistance in patients with BRCA1 11q mutations.
Table 1.Summary of results.PDX modelPrimary BRCA1 mutationBRCA1 D11q isoform expressionSecondary BRCA1 mutationsOther mutations (BROCA)PDX platinum responsePDX PARPi responsePatient treatments prior to PDX generation#1049Germline BRCA1: c.2475delCVery highBRCA1: c.4096+3A>C (33%) - splice site mutation known to cause increased D11q expressionTP53: c.428_429insCAStable diseaseNon-responsive - progressive disease3 lines of platinum chemotherapy and PARPi#1032Somatic BRCA1: c.1251delTHighNone detectedTP53: c.97-1_97-6del; FANCA: c.3788_3790delResistant - progressive diseaseNon-responsive - progressive disease3 lines of platinum chemotherapy and PARPi#56Germline BRCA1: c.894_895delTGModerateNone detectedNone detectedSensitive - complete responseMixed responsesNo prior treatment#206Germline BRCA1: c.3817C>TLowNone in PDX, one found in post-PARPi patient biopsy: BRCA1:c.3746_4081delTP53:c.451C>T; BLM rearrangementSensitive - complete responseResponsive - complete response1 line of platinum chemotherapy
Citation Format: Ksenija Nesic, Cassandra J. Vandenberg, Olga Kondrashova, John J. Krais, Neil Johnson, Elizabeth M. Swisher, Matthew J. Wakefield, Clare L. Scott. BRCA1 D11q isoform expression impacts PARP inhibitor responses in high grade serous ovarian carcinoma patient derived xenografts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2057.
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Affiliation(s)
| | | | - Olga Kondrashova
- 2QIMR Berghofer Medical Research Institute, Melbourne, Australia
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12
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Grohmann C, Walker F, Devlin M, Luo MX, Chüeh AC, Doherty J, Vaillant F, Ho GY, Wakefield MJ, Weeden CE, Kamili A, Murray J, Po'uha ST, Weinstock J, Kane SR, Faux MC, Broekhuizen E, Zheng Y, Shield-Artin K, Kershaw NJ, Tan CW, Witchard HM, Ebert G, Charman SA, Street I, Kavallaris M, Haber M, Fletcher JI, Asselin-Labat ML, Scott CL, Visvader JE, Lindeman GJ, Watson KG, Burgess AW, Lessene G. Preclinical small molecule WEHI-7326 overcomes drug resistance and elicits response in patient-derived xenograft models of human treatment-refractory tumors. Cell Death Dis 2021; 12:268. [PMID: 33712556 PMCID: PMC7955127 DOI: 10.1038/s41419-020-03269-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 10/01/2020] [Accepted: 10/02/2020] [Indexed: 12/29/2022]
Abstract
Targeting cell division by chemotherapy is a highly effective strategy to treat a wide range of cancers. However, there are limitations of many standard-of-care chemotherapies: undesirable drug toxicity, side-effects, resistance and high cost. New small molecules which kill a wide range of cancer subtypes, with good therapeutic window in vivo, have the potential to complement the current arsenal of anti-cancer agents and deliver improved safety profiles for cancer patients. We describe results with a new anti-cancer small molecule, WEHI-7326, which causes cell cycle arrest in G2/M, cell death in vitro, and displays efficacious anti-tumor activity in vivo. WEHI-7326 induces cell death in a broad range of cancer cell lines, including taxane-resistant cells, and inhibits growth of human colon, brain, lung, prostate and breast tumors in mice xenografts. Importantly, the compound elicits tumor responses as a single agent in patient-derived xenografts of clinically aggressive, treatment-refractory neuroblastoma, breast, lung and ovarian cancer. In combination with standard-of-care, WEHI-7326 induces a remarkable complete response in a mouse model of high-risk neuroblastoma. WEHI-7326 is mechanistically distinct from known microtubule-targeting agents and blocks cells early in mitosis to inhibit cell division, ultimately leading to apoptotic cell death. The compound is simple to produce and possesses favorable pharmacokinetic and toxicity profiles in rodents. It represents a novel class of anti-cancer therapeutics with excellent potential for further development due to the ease of synthesis, simple formulation, moderate side effects and potent in vivo activity. WEHI-7326 has the potential to complement current frontline anti-cancer drugs and to overcome drug resistance in a wide range of cancers.
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Affiliation(s)
- Christoph Grohmann
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia.
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia.
| | - Francesca Walker
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia
| | - Mark Devlin
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - Meng-Xiao Luo
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Anderly C Chüeh
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - Judy Doherty
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - François Vaillant
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- The University of Melbourne, Department of Obstetrics and Gynaecology, Parkville, VIC, 3050, Australia
| | - Clare E Weeden
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Alvin Kamili
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, 2052, Australia
| | - Jayne Murray
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
| | - Sela T Po'uha
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
| | - Janet Weinstock
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia
| | - Serena R Kane
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Maree C Faux
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Esmee Broekhuizen
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Ye Zheng
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Kristy Shield-Artin
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Nadia J Kershaw
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia
| | - Chin Wee Tan
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Helen M Witchard
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
| | - Gregor Ebert
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Susan A Charman
- Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Clayton, VIC, 3052, Australia
| | - Ian Street
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- Cancer Therapeutics CRC, Melbourne, VIC, 3000, Australia
| | - Maria Kavallaris
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- ARC Centre of Excellence in Convergent Bionano Science and Technology, Australian Centre for Nanomedicine, UNSW, Sydney, NSW, 2052, Australia
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW, Sydney, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW, Sydney, NSW, 2052, Australia
| | - Marie-Liesse Asselin-Labat
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- The University of Melbourne, Department of Obstetrics and Gynaecology, Parkville, VIC, 3050, Australia
| | - Jane E Visvader
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Geoffrey J Lindeman
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre building, Melbourne, 3000, Australia
- The University of Melbourne, Department of Medicine, Parkville, VIC, 3000, Australia
| | - Keith G Watson
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia
| | - Antony W Burgess
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia.
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia.
- Ludwig Institute for Cancer Research, Melbourne, VIC, 3000, Australia.
| | - Guillaume Lessene
- Walter and Eliza Hall Institute, Parkville, VIC, 3052, Australia.
- The University of Melbourne, Department of Medical Biology, Parkville, VIC, 3050, Australia.
- The University of Melbourne, Department of Pharmacology and Therapeutics, Parkville, VIC, 3050, Australia.
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13
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Kang EY, Cheasley D, LePage C, Wakefield MJ, da Cunha Torres M, Rowley S, Salazar C, Xing Z, Allan P, Bowtell DDL, Mes-Masson AM, Provencher DM, Rahimi K, Kelemen LE, Fasching PA, Doherty JA, Goodman MT, Goode EL, Deen S, Pharoah PDP, Brenton JD, Sieh W, Mateoiu C, Sundfeldt K, Cook LS, Le ND, Anglesio MS, Gilks CB, Huntsman DG, Kennedy CJ, Traficante N, DeFazio A, Kaufmann S, Churchman M, Gourley C, Stephens AN, Meagher NS, Ramus SJ, Antill YC, Campbell I, Scott CL, Köbel M, Gorringe KL. Refined cut-off for TP53 immunohistochemistry improves prediction of TP53 mutation status in ovarian mucinous tumors: implications for outcome analyses. Mod Pathol 2021; 34:194-206. [PMID: 32724153 PMCID: PMC9704519 DOI: 10.1038/s41379-020-0618-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [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: 05/13/2020] [Revised: 06/15/2020] [Accepted: 06/19/2020] [Indexed: 11/09/2022]
Abstract
TP53 mutations are implicated in the progression of mucinous borderline tumors (MBOT) to mucinous ovarian carcinomas (MOC). Optimized immunohistochemistry (IHC) for TP53 has been established as a proxy for the TP53 mutation status in other ovarian tumor types. We aimed to confirm the ability of TP53 IHC to predict TP53 mutation status in ovarian mucinous tumors and to evaluate the association of TP53 mutation status with survival among patients with MBOT and MOC. Tumor tissue from an initial cohort of 113 women with MBOT/MOC was stained with optimized IHC for TP53 using tissue microarrays (75.2%) or full sections (24.8%) and interpreted using established criteria as normal or abnormal (overexpression, complete absence, or cytoplasmic). Cases were considered concordant if abnormal IHC staining predicted deleterious TP53 mutations. Discordant tissue microarray cases were re-evaluated on full sections and interpretational criteria were refined. The initial cohort was expanded to a total of 165 MBOT and 424 MOC for the examination of the association of survival with TP53 mutation status, assessed either by TP53 IHC and/or sequencing. Initially, 82/113 (72.6%) cases were concordant using the established criteria. Refined criteria for overexpression to account for intratumoral heterogeneity and terminal differentiation improved concordance to 93.8% (106/113). In the expanded cohort, 19.4% (32/165) of MBOT showed evidence for TP53 mutation and this was associated with a higher risk of recurrence, disease-specific death, and all-cause mortality (overall survival: HR = 4.6, 95% CI 1.5-14.3, p = 0.0087). Within MOC, 61.1% (259/424) harbored a TP53 mutation, but this was not associated with survival (overall survival, p = 0.77). TP53 IHC is an accurate proxy for TP53 mutation status with refined interpretation criteria accounting for intratumoral heterogeneity and terminal differentiation in ovarian mucinous tumors. TP53 mutation status is an important biomarker to identify MBOT with a higher risk of mortality.
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MESH Headings
- Adult
- Australia
- Biomarkers, Tumor/genetics
- DNA Mutational Analysis
- Female
- Humans
- Immunohistochemistry
- Middle Aged
- Mutation
- Neoplasms, Cystic, Mucinous, and Serous/genetics
- Neoplasms, Cystic, Mucinous, and Serous/mortality
- Neoplasms, Cystic, Mucinous, and Serous/pathology
- Neoplasms, Cystic, Mucinous, and Serous/therapy
- North America
- Observer Variation
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/mortality
- Ovarian Neoplasms/pathology
- Ovarian Neoplasms/therapy
- Predictive Value of Tests
- Prognosis
- Reproducibility of Results
- Risk Assessment
- Risk Factors
- Tissue Array Analysis
- Tumor Suppressor Protein p53/genetics
- United Kingdom
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Affiliation(s)
- Eun Young Kang
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Dane Cheasley
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Cecile LePage
- Centre de recherche du Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
- Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Michelle da Cunha Torres
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Simone Rowley
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Carolina Salazar
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Zhongyue Xing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Prue Allan
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
- Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Diane M Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
- Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Kurosh Rahimi
- Centre de recherche du Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
- Centre hospitalier de l'Université de Montréal, Montréal, QC, Canada
| | - Linda E Kelemen
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Peter A Fasching
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center ER-EMN, University Hospital Erlangen, Friedrich-Alexander-University Erlangen-Nuremberg, Erlangen, Germany
| | - Jennifer A Doherty
- Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA
| | - Marc T Goodman
- Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ellen L Goode
- Department of Health Sciences Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA
| | - Suha Deen
- Department of Histopathology, Queen's Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Weiva Sieh
- Department of Genetics and Genomic Sciences, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Constantina Mateoiu
- Department of Pathology and Cytology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Karin Sundfeldt
- Department of Obstetrics and Gynecology, Institute of Clinical Sciences, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Sahlgrenska Cancer Center, University of Gothenburg, Gothenburg, Sweden
| | - Linda S Cook
- University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, NM, USA
| | - Nhu D Le
- Cancer Control Research, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Michael S Anglesio
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - C Blake Gilks
- Cancer Control Research, BC Cancer Research Centre, Vancouver, BC, Canada
- British Columbia's Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - David G Huntsman
- Cancer Control Research, BC Cancer Research Centre, Vancouver, BC, Canada
- British Columbia's Ovarian Cancer Research (OVCARE) Program, Vancouver General Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Catherine J Kennedy
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | - Nadia Traficante
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Anna DeFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney, Westmead, NSW, Australia
| | - Scott Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Nicola S Meagher
- School of Women's and Children's Health, Faculty of Medicine, University of NSW Sydney, Sydney, NSW, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, NSW, Australia
| | - Susan J Ramus
- School of Women's and Children's Health, Faculty of Medicine, University of NSW Sydney, Sydney, NSW, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, NSW, Australia
| | - Yoland C Antill
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC, Australia
- Cabrini Health, Malvern, VIC, Australia
- Frankston Hospital, Frankston, VIC, Australia
| | - Ian Campbell
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
| | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- The Royal Women's Hospital, Parkville, VIC, Australia
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada.
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC, Australia
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14
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Kommoss FKF, Cheasley D, Wakefield MJ, Scott CL, Campbell IG, Gilks CB, Gorringe K. Primary mucinous ovarian neoplasms rarely show germ cell histogenesis. Histopathology 2020; 78:640-642. [PMID: 33151585 DOI: 10.1111/his.14297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Felix K F Kommoss
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Matthew J Wakefield
- Walter and Eliza Hall Institute, Parkville, Australia.,University of Melbourne, Parkville, Australia
| | - Clare L Scott
- Peter MacCallum Cancer Centre, Melbourne, Australia.,Walter and Eliza Hall Institute, Parkville, Australia.,University of Melbourne, Parkville, Australia
| | - Ian G Campbell
- Peter MacCallum Cancer Centre, Melbourne, Australia.,University of Melbourne, Parkville, Australia
| | - C Blake Gilks
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Kylie Gorringe
- Peter MacCallum Cancer Centre, Melbourne, Australia.,University of Melbourne, Parkville, Australia
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15
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Sanij E, Hannan K, Xuan J, Yan S, Ahern JA, Trigos AS, Brajanovski N, Son J, Chan KT, Kondrashova O, Lieschke E, Wakefield MJ, Ellis S, Cullinane C, Poortinga G, Khanna KK, Mileshkin L, McArthur GA, Soong J, Berns EM, Hannan RD, Scott CL, Sheppard KE, Pearson RB. Abstract PR13: Inhibition of RNA polymerase I transcription activates targeted DNA damage response and enhances the efficacy of PARP inhibitors in high-grade serous ovarian cancer. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.ovca19-pr13] [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
Introduction: PARP inhibitors (PARPi) have revolutionized disease management of patients with homologous recombination (HR) DNA repair-deficient high-grade serous ovarian cancer (HGSOC). However, acquired resistance to PARPi is a major challenge in the clinic. The specific inhibitor of RNA polymerase I (Pol I) transcription of ribosomal RNA genes (rDNA) has demonstrated single-agent antitumor activity in p53 wild-type and p53-mutant hematologic malignancies (first-in-human trial, dose escalation study of CX-5461 at Peter MacCallum Cancer Centre) (Khot et al., Cancer Discov 2019). CX-5461 has also been reported to exhibit synthetic lethality with BRCA1/2 deficiency through stabilization of G-quadruplex DNA (GQ) structures. Here, we investigate the efficacy of CX-5461 in treating HGSOC.
Experimental Design: The mechanisms by which CX-5461 induces DNA damage response (DDR) and displays synthetic lethality in HR-deficient HGSOC cells are explored. We present in vivo data of mice bearing two functionally and genomically profiled HGSOC-patient-derived xenograft (PDX)s treated with CX-5461 and olaparib, alone and in combination. We also investigate CX-5461-sensitivity gene expression signatures in primary and relapsed HGSOC.
Results: Utilizing ovarian cancer cell lines, we demonstrate that sensitivity to CX-5461 is associated with “BRCA1 mutation” and “MYC targets” gene expression signatures. In addition, sensitivity to CX-5461 is associated with high basal rates of Pol I transcription. Importantly, we demonstrate a novel mechanism for CX-5461 synthetic lethal interaction with HR deficiency mediated through the induction of replication stress at rDNA repeats. Our data reveal CX-5461-mediated DDR in HR-deficient cells does not involve stabilization of GQ structures as previously proposed. On the contrary, we show definitively that CX-5461 inhibits Pol I recruitment leading to rDNA chromatin defects including stabilization of R-loops, single-stranded DNA, and replication stress at the rDNA. Mechanistically, we demonstrate CX-5461 leads to replication-dependent DNA damage involving MRE11-dependent degradation of replication forks. Importantly, CX-5461 has a different sensitivity spectrum to olaparib and cooperates with PARPi in exacerbating replication stress, leading to enhanced therapeutic efficacy in HR-deficient HGSOC-PDX in vivo compared to single-agent treatment of both drugs. Further, CX-5461 exhibits single-agent efficacy in olaparib-resistant HGSOC-PDX overcoming PARPi-resistance mechanisms involving fork protection. Importantly, we identify CX-5461-sensitivity gene expression signatures in primary and relapsed HGSOC.
Conclusions: CX-5461 is a promising therapy alone and in combination therapy with PARPi in HR-deficient HGSOC. CX-5461 also has exciting potential as a treatment option for patients with relapsed HGSOC tumors that have high MYC activity and poor clinical outcome; these patients currently have very limited effective treatment options.
This abstract is also being presented as Poster A71.
Citation Format: Elaine Sanij, Katherine Hannan, Jiachen Xuan, Shunfei Yan, Jessica A. Ahern, Anna S. Trigos, Natalie Brajanovski, Jinbae Son, Keefe T. Chan, Olga Kondrashova, Elizabeth Lieschke, Matthew J. Wakefield, Sarah Ellis, Carleen Cullinane, Gretchen Poortinga, Kum Kum Khanna, Linda Mileshkin, Grant A. McArthur, John Soong, Els M. Berns, Ross D. Hannan, Clare L. Scott, Karen E. Sheppard, Richard B. Pearson. Inhibition of RNA polymerase I transcription activates targeted DNA damage response and enhances the efficacy of PARP inhibitors in high-grade serous ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr PR13.
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Affiliation(s)
- Elaine Sanij
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | - Katherine Hannan
- 2The John Curtin School of Medical Research, Canberra, ACT, Australia,
| | - Jiachen Xuan
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | - Shunfei Yan
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | | | - Anna S. Trigos
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | | | - Jinbae Son
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | - Keefe T. Chan
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | - Olga Kondrashova
- 3The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Elizabeth Lieschke
- 3The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Matthew J. Wakefield
- 3The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Sarah Ellis
- 1Peter MacCallum Cancer Centre, Melbourne, VIC, Australia,
| | | | | | - Kum Kum Khanna
- 4QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia,
| | | | | | - John Soong
- 5Senhwa Biosciences, Virginia Commonwealth University School of Medicine, Richmond, VA,
| | - Els M. Berns
- 6Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ross D. Hannan
- 2The John Curtin School of Medical Research, Canberra, ACT, Australia,
| | - Clare L. Scott
- 3The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
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16
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Sanij E, Hannan KM, Xuan J, Yan S, Ahern JE, Trigos AS, Brajanovski N, Son J, Chan KT, Kondrashova O, Lieschke E, Wakefield MJ, Frank D, Ellis S, Cullinane C, Kang J, Poortinga G, Nag P, Deans AJ, Khanna KK, Mileshkin L, McArthur GA, Soong J, Berns EMJJ, Hannan RD, Scott CL, Sheppard KE, Pearson RB. CX-5461 activates the DNA damage response and demonstrates therapeutic efficacy in high-grade serous ovarian cancer. Nat Commun 2020; 11:2641. [PMID: 32457376 PMCID: PMC7251123 DOI: 10.1038/s41467-020-16393-4] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [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: 06/28/2019] [Accepted: 04/30/2020] [Indexed: 02/06/2023] Open
Abstract
Acquired resistance to PARP inhibitors (PARPi) is a major challenge for the clinical management of high grade serous ovarian cancer (HGSOC). Here, we demonstrate CX-5461, the first-in-class inhibitor of RNA polymerase I transcription of ribosomal RNA genes (rDNA), induces replication stress and activates the DNA damage response. CX-5461 co-operates with PARPi in exacerbating replication stress and enhances therapeutic efficacy against homologous recombination (HR) DNA repair-deficient HGSOC-patient-derived xenograft (PDX) in vivo. We demonstrate CX-5461 has a different sensitivity spectrum to PARPi involving MRE11-dependent degradation of replication forks. Importantly, CX-5461 exhibits in vivo single agent efficacy in a HGSOC-PDX with reduced sensitivity to PARPi by overcoming replication fork protection. Further, we identify CX-5461-sensitivity gene expression signatures in primary and relapsed HGSOC. We propose CX-5461 is a promising therapy in combination with PARPi in HR-deficient HGSOC and also as a single agent for the treatment of relapsed disease.
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Affiliation(s)
- Elaine Sanij
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Katherine M Hannan
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton, 2601, Australia Capital Territory, Australia.
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
| | - Jiachen Xuan
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Shunfei Yan
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jessica E Ahern
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Anna S Trigos
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Natalie Brajanovski
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Jinbae Son
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Keefe T Chan
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Melbourne Bioinformatics, University of Melbourne, Victoria, 3010, Australia
| | - Daniel Frank
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Sarah Ellis
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Carleen Cullinane
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jian Kang
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
| | - Gretchen Poortinga
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Purba Nag
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Environment and Sciences, Griffith University, Nathan, Brisbane, QLD, 4111, Australia
| | - Andrew J Deans
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Parkville, VIC, 3010, Australia
- Genome Stability Unit, St Vincent's Institute, Fitzroy, VIC, 3065, Australia
| | - Kum Kum Khanna
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Grant A McArthur
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, VIC, 3010, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Medicine, St. Vincent's Hospital, University of Melbourne, Parkville, VIC, 3010, Australia
| | - John Soong
- Senhwa Biosciences, Virginia Commonwealth University School of Medicine, San Diego, CA, USA
| | - Els M J J Berns
- Department of Medical Oncology, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Ross D Hannan
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, Australian National University, Acton, 2601, Australia Capital Territory, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, 4072, Australia
| | - Clare L Scott
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Karen E Sheppard
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Richard B Pearson
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, VIC, 3000, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia.
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3800, Australia.
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Jung M, Gao J, Cheung L, Bongers A, Somers K, Clifton M, Ramsay EE, Russell AJ, Valli E, Gifford AJ, George J, Kennedy CJ, Wakefield MJ, Topp M, Ho GY, Scott CL, Bowtell DD, deFazio A, Norris MD, Haber M, Henderson MJ. ABCC4/MRP4 contributes to the aggressiveness of Myc-associated epithelial ovarian cancer. Int J Cancer 2020; 147:2225-2238. [PMID: 32277480 DOI: 10.1002/ijc.33005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 01/12/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/24/2022]
Abstract
Epithelial ovarian cancer (EOC) is a complex disease comprising discrete histological and molecular subtypes, for which survival rates remain unacceptably low. Tailored approaches for this deadly heterogeneous disease are urgently needed. Efflux pumps belonging to the ATP-binding cassette (ABC) family of transporters are known for roles in both drug resistance and cancer biology and are also highly targetable. Here we have investigated the association of ABCC4/MRP4 expression to clinical outcome and its biological function in endometrioid and serous tumors, common histological subtypes of EOC. We found high expression of ABCC4/MRP4, previously shown to be directly regulated by c-Myc/N-Myc, was associated with poor prognosis in endometrioid EOC (P = .001) as well as in a subset of serous EOC with a "high-MYCN" profile (C5/proliferative; P = .019). Transient siRNA-mediated suppression of MRP4 in EOC cells led to reduced growth, migration and invasion, with the effects being most pronounced in endometrioid and C5-like serous cells compared to non-C5 serous EOC cells. Sustained knockdown of MRP4 also sensitized endometrioid cells to MRP4 substrate drugs. Furthermore, suppression of MRP4 decreased the growth of patient-derived EOC cells in vivo. Together, our findings provide the first evidence that MRP4 plays an important role in the biology of Myc-associated ovarian tumors and highlight this transporter as a potential therapeutic target for EOC.
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Affiliation(s)
- Moonsun Jung
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia.,School of Women's and Children's Health, UNSW Australia, Kensington, New South Wales, Australia
| | - Jixuan Gao
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia
| | - Leanna Cheung
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia
| | - Angelika Bongers
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia
| | - Klaartje Somers
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia.,School of Women's and Children's Health, UNSW Australia, Kensington, New South Wales, Australia
| | - Molly Clifton
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia
| | - Emma E Ramsay
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia
| | - Amanda J Russell
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia
| | - Emanuele Valli
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia
| | - Andrew J Gifford
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia.,Department of Anatomical Pathology, Prince of Wales Hospital, Randwick, New South Wales, Australia
| | - Joshy George
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Catherine J Kennedy
- Department of Gynecological Oncology, Westmead Hospital and Centre for Cancer Research, The Westmead Millennium Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Monique Topp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Gwo-Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | -
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - David D Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Anna deFazio
- Department of Gynecological Oncology, Westmead Hospital and Centre for Cancer Research, The Westmead Millennium Institute for Medical Research, The University of Sydney, Sydney, New South Wales, Australia
| | - Murray D Norris
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia.,School of Women's and Children's Health, UNSW Australia, Kensington, New South Wales, Australia.,University of New South Wales Centre for Childhood Cancer Research, UNSW Australia, Kensington, New South Wales, Australia
| | - Michelle Haber
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia.,School of Women's and Children's Health, UNSW Australia, Kensington, New South Wales, Australia
| | - Michelle J Henderson
- Children's Cancer Institute Australia, Lowy Cancer Research Centre, UNSW Australia, Kensington, New South Wales, Australia.,School of Women's and Children's Health, UNSW Australia, Kensington, New South Wales, Australia
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18
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Gorringe KL, Cheasley D, Wakefield MJ, Ryland GL, Allan PE, Alsop K, Amarasinghe KC, Ananda S, Bowtell DDL, Christie M, Chiew YE, Churchman M, DeFazio A, Fereday S, Gilks CB, Gourley C, Hadley AM, Hendley J, Hunter SM, Kaufmann SH, Kennedy CJ, Köbel M, Le Page C, Li J, Lupat R, McNally OM, McAlpine JN, Pyman J, Rowley SM, Salazar C, Saunders H, Semple T, Stephens AN, Thio N, Torres MC, Traficante N, Zethoven M, Antill YC, Campbell IG, Scott CL. Therapeutic options for mucinous ovarian carcinoma. Gynecol Oncol 2020; 156:552-560. [PMID: 31902686 PMCID: PMC7056511 DOI: 10.1016/j.ygyno.2019.12.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/18/2019] [Accepted: 12/15/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Mucinous ovarian carcinoma (MOC) is an uncommon ovarian cancer histotype that responds poorly to conventional chemotherapy regimens. Although long overall survival outcomes can occur with early detection and optimal surgical resection, recurrent and advanced disease are associated with extremely poor survival. There are no current guidelines specifically for the systemic management of recurrent MOC. We analyzed data from a large cohort of women with MOC to evaluate the potential for clinical utility from a range of systemic agents. METHODS We analyzed gene copy number (n = 191) and DNA sequencing data (n = 184) from primary MOC to evaluate signatures of mismatch repair deficiency and homologous recombination deficiency, and other genetic events. Immunohistochemistry data were collated for ER, CK7, CK20, CDX2, HER2, PAX8 and p16 (n = 117-166). RESULTS Molecular aberrations noted in MOC that suggest a match with current targeted therapies include amplification of ERBB2 (26.7%) and BRAF mutation (9%). Observed genetic events that suggest potential efficacy for agents currently in clinical trials include: KRAS/NRAS mutations (66%), TP53 missense mutation (49%), RNF43 mutation (11%), ARID1A mutation (10%), and PIK3CA/PTEN mutation (9%). Therapies exploiting homologous recombination deficiency (HRD) may not be effective in MOC, as only 1/191 had a high HRD score. Mismatch repair deficiency was similarly rare (1/184). CONCLUSIONS Although genetically diverse, MOC has several potential therapeutic targets. Importantly, the lack of response to platinum-based therapy observed clinically corresponds to the lack of a genomic signature associated with HRD, and MOC are thus also unlikely to respond to PARP inhibition.
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Affiliation(s)
- Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia.
| | - Dane Cheasley
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - Matthew J Wakefield
- The University of Melbourne, Melbourne, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia
| | | | - Prue E Allan
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | | | - Sumitra Ananda
- Peter MacCallum Cancer Centre, Melbourne, Australia; Western Health, St. Albans, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - Michael Christie
- The University of Melbourne, Melbourne, Australia; Royal Melbourne Hospital, Parkville, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, Australia; The Westmead Institute for Medical Research, Sydney, Australia
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, University of Edinburgh, UK
| | - Anna DeFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, Australia; The Westmead Institute for Medical Research, Sydney, Australia; The University of Sydney, Sydney, Australia
| | - Sian Fereday
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | | | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, University of Edinburgh, UK
| | | | - Joy Hendley
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | | | | | | | - Jason Li
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Orla M McNally
- Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Royal Womens Hospital, Parkville, Australia
| | | | - Jan Pyman
- Royal Womens Hospital, Parkville, Australia; Royal Children's Hospital, Flemington, Australia
| | | | | | | | | | | | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Nadia Traficante
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | | | - Yoland C Antill
- Cabrini Health, Malvern, Australia; Frankston Hospital, Frankston, Australia
| | - Ian G Campbell
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia
| | - Clare L Scott
- Peter MacCallum Cancer Centre, Melbourne, Australia; The University of Melbourne, Melbourne, Australia; Walter and Eliza Hall Institute of Medical Research, Parkville, Australia; Royal Melbourne Hospital, Parkville, Australia; Royal Womens Hospital, Parkville, Australia
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19
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Kondrashova O, Ho GY, Au-Yeung G, Leas L, Boughtwood T, Alsop K, Zapparoli G, Dobrovic A, Ko YA, Hsu AL, Love CJ, Lunke S, Wakefield MJ, McNally O, Quinn M, Ananda S, Neesham D, Hamilton A, Grossi M, Freimund A, Kanjanapan Y, Rischin D, Traficante N, Bowtell D, Scott CL, Christie M, Taylor GR, Mileshkin L, Waring PM. Clinical Utility of Real-Time Targeted Molecular Profiling in the Clinical Management of Ovarian Cancer: The ALLOCATE Study. JCO Precis Oncol 2019; 3:1-18. [DOI: 10.1200/po.19.00019] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE The ALLOCATE study was designed as a pilot to demonstrate the feasibility and clinical utility of real-time targeted molecular profiling of patients with recurrent or advanced ovarian cancer for identification of potential targeted therapies. PATIENTS AND METHODS A total of 113 patients with ovarian cancer of varying histologies were recruited from two tertiary hospitals, with 99 patient cases suitable for prospective analysis. Targeted molecular and methylation profiling of fresh biopsy and archived tumor samples were performed by screening for mutations or copy-number variations in 44 genes and for promoter methylation of BRCA1 and RAD51C. RESULTS Somatic genomic or methylation events were identified in 85% of all patient cases, with potentially actionable events with defined targeted therapies (including four resistance events) detected in 60% of all patient cases. On the basis of these findings, six patients received molecularly guided therapy, three patients had unsuspected germline cancer–associated BRCA1/ 2 mutations and were referred for genetic counseling, and two intermediate differentiated (grade 2) serous ovarian carcinomas were reclassified as low grade, leading to changes in clinical management. Additionally, secondary reversion mutations in BRCA1/ 2 were identified in fresh biopsy samples of two patients, consistent with clinical platinum/poly (ADP-ribose) polymerase inhibitor resistance. Timely reporting of results if molecular testing is done at disease recurrence, as well as early referral for patients with platinum-resistant cancers, were identified as factors that could improve the clinical utility of molecular profiling. CONCLUSION ALLOCATE molecular profiling identified known genomic and methylation alterations of the different ovarian cancer subtypes and was deemed feasible and useful in routine clinical practice. Better patient selection and access to a wider range of targeted therapies or clinical trials will further enhance the clinical utility of molecular profiling.
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Affiliation(s)
- Olga Kondrashova
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- QIMR Berghofer Medical Research Institute, Queensland, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - George Au-Yeung
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Leakhena Leas
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Giada Zapparoli
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - Alexander Dobrovic
- University of Melbourne, Melbourne, Victoria, Australia
- Olivia Newton-John Cancer Research Institute, Heidelberg, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - Yi-An Ko
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Arthur L. Hsu
- University of Melbourne, Melbourne, Victoria, Australia
| | - Clare J. Love
- University of Melbourne, Melbourne, Victoria, Australia
| | | | - Matthew J. Wakefield
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Orla McNally
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
| | - Michael Quinn
- Royal Women’s Hospital, Parkville, Victoria, Australia
| | - Sumitra Ananda
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - Anne Hamilton
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Marisa Grossi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Alison Freimund
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Yada Kanjanapan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Danny Rischin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | | | - David Bowtell
- University of Melbourne, Melbourne, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Clare L. Scott
- University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Royal Women’s Hospital, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Michael Christie
- University of Melbourne, Melbourne, Victoria, Australia
- Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Graham R. Taylor
- University of Melbourne, Melbourne, Victoria, Australia
- King’s College London, London, United Kingdom
| | - Linda Mileshkin
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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20
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Cheasley D, Wakefield MJ, Ryland GL, Allan PE, Alsop K, Amarasinghe KC, Ananda S, Anglesio MS, Au-Yeung G, Böhm M, Bowtell DDL, Brand A, Chenevix-Trench G, Christie M, Chiew YE, Churchman M, DeFazio A, Demeo R, Dudley R, Fairweather N, Fedele CG, Fereday S, Fox SB, Gilks CB, Gourley C, Hacker NF, Hadley AM, Hendley J, Ho GY, Hughes S, Hunstman DG, Hunter SM, Jobling TW, Kalli KR, Kaufmann SH, Kennedy CJ, Köbel M, Le Page C, Li J, Lupat R, McNally OM, McAlpine JN, Mes-Masson AM, Mileshkin L, Provencher DM, Pyman J, Rahimi K, Rowley SM, Salazar C, Samimi G, Saunders H, Semple T, Sharma R, Sharpe AJ, Stephens AN, Thio N, Torres MC, Traficante N, Xing Z, Zethoven M, Antill YC, Scott CL, Campbell IG, Gorringe KL. The molecular origin and taxonomy of mucinous ovarian carcinoma. Nat Commun 2019; 10:3935. [PMID: 31477716 PMCID: PMC6718426 DOI: 10.1038/s41467-019-11862-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 08/07/2019] [Indexed: 02/03/2023] Open
Abstract
Mucinous ovarian carcinoma (MOC) is a unique subtype of ovarian cancer with an uncertain etiology, including whether it genuinely arises at the ovary or is metastatic disease from other organs. In addition, the molecular drivers of invasive progression, high-grade and metastatic disease are poorly defined. We perform genetic analysis of MOC across all histological grades, including benign and borderline mucinous ovarian tumors, and compare these to tumors from other potential extra-ovarian sites of origin. Here we show that MOC is distinct from tumors from other sites and supports a progressive model of evolution from borderline precursors to high-grade invasive MOC. Key drivers of progression identified are TP53 mutation and copy number aberrations, including a notable amplicon on 9p13. High copy number aberration burden is associated with worse prognosis in MOC. Our data conclusively demonstrate that MOC arise from benign and borderline precursors at the ovary and are not extra-ovarian metastases.
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Affiliation(s)
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute, Parkville, Australia
- The University of Melbourne, Melbourne, Australia
| | | | - Prue E Allan
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | | | - Sumitra Ananda
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Western Health, St. Albans, Australia
| | | | - George Au-Yeung
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | - Maret Böhm
- Kinghorn Cancer Centre and Garvan Institute of Medical Research, Darlinghurst, Australia
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | - Alison Brand
- Westmead Hospital, University of Sydney, Sydney, Australia
| | | | - Michael Christie
- The University of Melbourne, Melbourne, Australia
- Royal Melbourne Hospital, Parkville, Australia
| | - Yoke-Eng Chiew
- Westmead Hospital, University of Sydney, Sydney, Australia
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Anna DeFazio
- Westmead Hospital, University of Sydney, Sydney, Australia
| | - Renee Demeo
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | | | - Clare G Fedele
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | - Sian Fereday
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | | | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | | | | | - Joy Hendley
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute, Parkville, Australia
| | | | | | | | | | | | | | | | | | | | - Jason Li
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Orla M McNally
- The University of Melbourne, Melbourne, Australia
- Royal Womens Hospital, Parkville, Australia
| | | | | | | | - Diane M Provencher
- CRCHUM, Montreal, Canada
- Centre Hospitalier de L'Université de Montreal, Montreal, Canada
| | - Jan Pyman
- Royal Womens Hospital, Parkville, Australia
- Royal Children's Hospital, Flemington, Australia
| | - Kurosh Rahimi
- CRCHUM, Montreal, Canada
- Centre Hospitalier de L'Université de Montreal, Montreal, Canada
| | | | | | - Goli Samimi
- Kinghorn Cancer Centre and Garvan Institute of Medical Research, Darlinghurst, Australia
| | | | | | - Ragwha Sharma
- Westmead Hospital, University of Sydney, Sydney, Australia
- NSW Health Pathology, Sydney, Australia
| | | | | | - Niko Thio
- Peter MacCallum Cancer Centre, Melbourne, Australia
| | | | - Nadia Traficante
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | | | | | - Yoland C Antill
- Cabrini Health, Malvern, Australia
- Frankston Hospital, Frankston, Australia
| | - Clare L Scott
- Peter MacCallum Cancer Centre, Melbourne, Australia
- Walter and Eliza Hall Institute, Parkville, Australia
- The University of Melbourne, Melbourne, Australia
- Royal Melbourne Hospital, Parkville, Australia
| | - Ian G Campbell
- Peter MacCallum Cancer Centre, Melbourne, Australia
- The University of Melbourne, Melbourne, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, Melbourne, Australia.
- The University of Melbourne, Melbourne, Australia.
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21
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Fisicaro N, Salvaris EJ, Philip GK, Wakefield MJ, Nottle MB, Hawthorne WJ, Cowan PJ. Fok
I‐dCas9 mediates high‐fidelity genome editing in pigs. Xenotransplantation 2019; 27:e12551. [DOI: 10.1111/xen.12551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 07/02/2019] [Accepted: 07/24/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Nella Fisicaro
- Immunology Research Centre St Vincent’s Hospital Melbourne Melbourne Vic. Australia
| | - Evelyn J. Salvaris
- Immunology Research Centre St Vincent’s Hospital Melbourne Melbourne Vic. Australia
| | - Gayle K. Philip
- Melbourne Bioinformatics University of Melbourne Melbourne Vic. Australia
| | - Matthew J. Wakefield
- Melbourne Bioinformatics University of Melbourne Melbourne Vic. Australia
- Walter and Eliza Hall Institute Melbourne Vic. Australia
| | - Mark B. Nottle
- Robinson Research Institute & Adelaide Medical School University of Adelaide Adelaide SA Australia
| | - Wayne J. Hawthorne
- Department of Surgery, Westmead Clinical School Westmead Hospital, University of Sydney Sydney NSW Australia
- The Centre for Transplant and Renal Research Westmead Institute for Medical Research Westmead NSW Australia
| | - Peter J. Cowan
- Immunology Research Centre St Vincent’s Hospital Melbourne Melbourne Vic. Australia
- Department of Medicine University of Melbourne Melbourne Vic. Australia
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22
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Chan WH, Komada M, Fukushima T, Southard-Smith EM, Anderson CR, Wakefield MJ. RNA-seq of Isolated Chromaffin Cells Highlights the Role of Sex-Linked and Imprinted Genes in Adrenal Medulla Development. Sci Rep 2019; 9:3929. [PMID: 30850723 PMCID: PMC6408553 DOI: 10.1038/s41598-019-40501-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 09/13/2018] [Accepted: 02/15/2019] [Indexed: 12/20/2022] Open
Abstract
Adrenal chromaffin cells and sympathetic neurons synthesize and release catecholamines, and both cell types are derived from neural crest precursors. However, they have different developmental histories, with sympathetic neurons derived directly from neural crest precursors while adrenal chromaffin cells arise from neural crest-derived cells that express Schwann cell markers. We have sought to identify the genes, including imprinted genes, which regulate the development of the two cell types in mice. We developed a method of separating the two cell types as early as E12.5, using differences in expression of enhanced yellow fluorescent protein driven from the tyrosine hydroxylase gene, and then used RNA sequencing to confirm the characteristic molecular signatures of the two cell types. We identified genes differentially expressed by adrenal chromaffin cells and sympathetic neurons. Deletion of a gene highly expressed by adrenal chromaffin cells, NIK-related kinase, a gene on the X-chromosome, results in reduced expression of adrenaline-synthesizing enzyme, phenyl-N-methyl transferase, by adrenal chromaffin cells and changes in cell cycle dynamics. Finally, many imprinted genes are up-regulated in chromaffin cells and may play key roles in their development.
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Affiliation(s)
- Wing Hei Chan
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia.
| | - Masayuki Komada
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | - Toshiaki Fukushima
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
| | | | - Colin R Anderson
- Department of Anatomy and Neuroscience, University of Melbourne, Melbourne, Australia
| | - Matthew J Wakefield
- Melbourne Bioinformatics, University of Melbourne, Melbourne, Australia. .,Walter and Eliza Hall Institute, Parkville, Australia.
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23
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Kondrashova O, Topp M, Nesic K, Lieschke E, Ho GY, Harrell MI, Zapparoli GV, Hadley A, Holian R, Boehm E, Heong V, Sanij E, Pearson RB, Krais JJ, Johnson N, McNally O, Ananda S, Alsop K, Hutt KJ, Kaufmann SH, Lin KK, Harding TC, Traficante N, deFazio A, McNeish IA, Bowtell DD, Swisher EM, Dobrovic A, Wakefield MJ, Scott CL. Methylation of all BRCA1 copies predicts response to the PARP inhibitor rucaparib in ovarian carcinoma. Nat Commun 2018; 9:3970. [PMID: 30266954 PMCID: PMC6162272 DOI: 10.1038/s41467-018-05564-z] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 06/25/2018] [Indexed: 01/17/2023] Open
Abstract
Accurately identifying patients with high-grade serous ovarian carcinoma (HGSOC) who respond to poly(ADP-ribose) polymerase inhibitor (PARPi) therapy is of great clinical importance. Here we show that quantitative BRCA1 methylation analysis provides new insight into PARPi response in preclinical models and ovarian cancer patients. The response of 12 HGSOC patient-derived xenografts (PDX) to the PARPi rucaparib was assessed, with variable dose-dependent responses observed in chemo-naive BRCA1/2-mutated PDX, and no responses in PDX lacking DNA repair pathway defects. Among BRCA1-methylated PDX, silencing of all BRCA1 copies predicts rucaparib response, whilst heterozygous methylation is associated with resistance. Analysis of 21 BRCA1-methylated platinum-sensitive recurrent HGSOC (ARIEL2 Part 1 trial) confirmed that homozygous or hemizygous BRCA1 methylation predicts rucaparib clinical response, and that methylation loss can occur after exposure to chemotherapy. Accordingly, quantitative BRCA1 methylation analysis in a pre-treatment biopsy could allow identification of patients most likely to benefit, and facilitate tailoring of PARPi therapy.
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Affiliation(s)
- Olga Kondrashova
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Monique Topp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Ksenija Nesic
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Elizabeth Lieschke
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
| | - Gwo-Yaw Ho
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
| | - Maria I Harrell
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Giada V Zapparoli
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Alison Hadley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Robert Holian
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Medicine, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Emma Boehm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- School of Medicine, University of Melbourne, Parkville, VIC, 3052, Australia
| | - Valerie Heong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | - Elaine Sanij
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Richard B Pearson
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, VIC, 3010, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, 3168, Australia
| | - John J Krais
- Fox Chase Cancer Centre, Philadelphia, PA, 19111, USA
| | - Neil Johnson
- Fox Chase Cancer Centre, Philadelphia, PA, 19111, USA
| | - Orla McNally
- Royal Women's Hospital, Parkville, VIC, 3052, Australia
| | | | - Kathryn Alsop
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
| | - Karla J Hutt
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacology, Mayo Clinic, Rochester, MN, 55905, USA
| | | | | | - Nadia Traficante
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney Medical School, The University of Sydney and Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, 2145, Australia
| | - Iain A McNeish
- Division of Cancer, Department of Surgery and Cancer, Imperial College London, Kensington, London, SW7 2AZ, United Kingdom
| | - David D Bowtell
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Elizabeth M Swisher
- Department of Obstetrics and Gynecology, University of Washington, Seattle, WA, 98195, USA
| | - Alexander Dobrovic
- Olivia Newton-John Cancer Research Institute, Heidelberg, VIC, 3084, Australia
- School of Cancer Medicine, La Trobe University, Bundoora, VIC, 3086, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia
- Melbourne Bioinformatics, University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3052, Australia.
- Department of Medicine and Health Sciences, Monash University, Clayton, VIC, 3168, Australia.
- Research Division, Peter MacCallum Cancer Centre, Grattan Street, Parkville, VIC, 3010, Australia.
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24
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Janic A, Valente LJ, Wakefield MJ, Di Stefano L, Milla L, Wilcox S, Yang H, Tai L, Vandenberg CJ, Kueh AJ, Mizutani S, Brennan MS, Schenk RL, Lindqvist LM, Papenfuss AT, O’Connor L, Strasser A, Herold MJ. DNA repair processes are critical mediators of p53-dependent tumor suppression. Nat Med 2018; 24:947-953. [DOI: 10.1038/s41591-018-0043-5] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/27/2018] [Indexed: 01/08/2023]
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Kondrashova O, Nguyen M, Shield-Artin K, Tinker AV, Teng NNH, Harrell MI, Kuiper MJ, Ho GY, Barker H, Jasin M, Prakash R, Kass EM, Sullivan MR, Brunette GJ, Bernstein KA, Coleman RL, Floquet A, Friedlander M, Kichenadasse G, O'Malley DM, Oza A, Sun J, Robillard L, Maloney L, Bowtell D, Giordano H, Wakefield MJ, Kaufmann SH, Simmons AD, Harding TC, Raponi M, McNeish IA, Swisher EM, Lin KK, Scott CL. Secondary Somatic Mutations Restoring RAD51C and RAD51D Associated with Acquired Resistance to the PARP Inhibitor Rucaparib in High-Grade Ovarian Carcinoma. Cancer Discov 2017; 7:984-998. [PMID: 28588062 PMCID: PMC5612362 DOI: 10.1158/2159-8290.cd-17-0419] [Citation(s) in RCA: 278] [Impact Index Per Article: 39.7] [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: 04/21/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 11/16/2022]
Abstract
High-grade epithelial ovarian carcinomas containing mutated BRCA1 or BRCA2 (BRCA1/2) homologous recombination (HR) genes are sensitive to platinum-based chemotherapy and PARP inhibitors (PARPi), while restoration of HR function due to secondary mutations in BRCA1/2 has been recognized as an important resistance mechanism. We sequenced core HR pathway genes in 12 pairs of pretreatment and postprogression tumor biopsy samples collected from patients in ARIEL2 Part 1, a phase II study of the PARPi rucaparib as treatment for platinum-sensitive, relapsed ovarian carcinoma. In 6 of 12 pretreatment biopsies, a truncation mutation in BRCA1, RAD51C, or RAD51D was identified. In five of six paired postprogression biopsies, one or more secondary mutations restored the open reading frame. Four distinct secondary mutations and spatial heterogeneity were observed for RAD51CIn vitro complementation assays and a patient-derived xenograft, as well as predictive molecular modeling, confirmed that resistance to rucaparib was associated with secondary mutations.Significance: Analyses of primary and secondary mutations in RAD51C and RAD51D provide evidence for these primary mutations in conferring PARPi sensitivity and secondary mutations as a mechanism of acquired PARPi resistance. PARPi resistance due to secondary mutations underpins the need for early delivery of PARPi therapy and for combination strategies. Cancer Discov; 7(9); 984-98. ©2017 AACR.See related commentary by Domchek, p. 937See related article by Quigley et al., p. 999See related article by Goodall et al., p. 1006This article is highlighted in the In This Issue feature, p. 920.
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Affiliation(s)
- Olga Kondrashova
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | | | - Kristy Shield-Artin
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Anna V Tinker
- British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Michael J Kuiper
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Gwo-Yaw Ho
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Holly Barker
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Meghan R Sullivan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Gregory J Brunette
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Kara A Bernstein
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Robert L Coleman
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Michael Friedlander
- University of New South Wales and Prince of Wales Hospital, Sydney, New South Wales, Australia
| | | | | | - Amit Oza
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - James Sun
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | | | | | | | | | - Iain A McNeish
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Clare L Scott
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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Scott CL, Ho GY, Lieschke EE, Kondrashova O, Drapkin R, Bowtell D, Wakefield MJ. Abstract 4798: Genetically engineered mouse models of proliferative C5 high grade serous ovarian cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-4798] [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
Introduction: High-grade serous ovarian cancer (HGSOC) can be divided into four subgroups based on molecular characteristics1,2. The proliferative/C5 subgroup is defined by MYCN-pathway activation and may be associated with stem cell-like behavior3. The majority of HGSOC originate from the secretory cells of the fallopian tube (FT), with both tumours and secretory cells characterised by PAX8 expression4. We have developed pre-malignant C5 sub-type Genetically Engineered Mouse Models (GEMM) to characterise key molecular events in the initiation of this sub-type and to provide an immune-competent model for testing therapeutics.
Methods: We have generated independent GEMM with p53 dysfunction (p53lsl-R172H knock-in5) and over-expression of the MYCN-pathway, using either lsl-MYCN or lsl-lin28b transgenes6 directed by the doxycycline-inducible PAX8 promoter. Murine FT were harvested following two-weeks of transgene activation. One FT was harvested en bloc and paraffin embedded for analysis by H&E and immunohistochemistry for the presence of pre-malignant tubal lesions. The contralateral FT was macro-dissected into distal/mid-FT, which were snap frozen for analysis of gene expression by qRT-PCR and RNAseq. As mice with PAX8-directed expression of oncogenes (±MYCN/lin28b overexpression) developed enlarged kidneys due to renal tubular adenomata, for alternate mice, the mid/distal FT tissue was implanted into the bursae of wild-type CBA/nu mice for observation and later analysis.
Results: FT were harvested from twelve p53lsl-R172H/lsl-lin28b mice and from ten p53lsl-R172H/lsl-MYCN mice (including relevant control mice). Dysplastic lesions were observed in a subset of p53lsl-R172H/lsl-MYCN or lsl-lin28b FT and not in controls. MYCN pathway activation was demonstrated by qRT-PCR analysis.
Conclusion: Over-expression of the MYCN-pathway can drive FT epithelial dysplasia in the presence of p53 dysfunction. RNASeq analysis is being performed to elucidate early genetic events in dysplastic FT. Mice are now being harvested after eight-weeks of doxycycline activation to determine whether more advanced pre-malignant change occurs. CRISPR guides deleting relevant genes including p53, PTEN, Nf1 or Rb1 were generated to delete additional genes in MYCN pathway-transgenic FT, followed by implantation for observation of tumourigenesis.
Note: This abstract was not presented at the meeting.
Citation Format: Clare L. Scott, Gwo Y. Ho, Elizabeth E. Lieschke, Olga Kondrashova, Ronny Drapkin, David Bowtell, Matthew J. Wakefield. Genetically engineered mouse models of proliferative C5 high grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4798. doi:10.1158/1538-7445.AM2017-4798
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Affiliation(s)
- Clare L. Scott
- 1Walter & Eliza Hall Inst. of Med. Research, Parkville, Australia
| | - Gwo Y. Ho
- 1Walter & Eliza Hall Inst. of Med. Research, Parkville, Australia
| | | | - Olga Kondrashova
- 1Walter & Eliza Hall Inst. of Med. Research, Parkville, Australia
| | - Ronny Drapkin
- 2University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - David Bowtell
- 3Peter MacCallum Cancer Centre, Parkville, Australia
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Liddelow SA, Dziegielewska KM, Ek CJ, Habgood MD, Bauer H, Bauer HC, Lindsay H, Wakefield MJ, Strazielle N, Kratzer I, Møllgård K, Ghersi-Egea JF, Saunders NR. Correction: Mechanisms That Determine the Internal Environment of the Developing Brain: A Transcriptomic, Functional and Ultrastructural Approach. PLoS One 2016; 11:e0147680. [PMID: 26783757 PMCID: PMC4718702 DOI: 10.1371/journal.pone.0147680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Wakefield MJ, Armitage WJ, Jones MNA, Kaye SB, Larkin DFP, Tole D, Prydal J. The impact of donor age and endothelial cell density on graft survival following penetrating keratoplasty. Br J Ophthalmol 2015; 100:986-989. [PMID: 26567026 DOI: 10.1136/bjophthalmol-2015-306871] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 03/10/2015] [Revised: 07/22/2015] [Accepted: 10/13/2015] [Indexed: 01/27/2023]
Abstract
PURPOSE To determine if donor age and preoperative endothelial cell density (ECD) affect corneal endothelial failure following penetrating keratoplasty (PK). METHODS Preoperative and postoperative data for PKs performed in the UK between April 1999 and March 2012 were analysed. Donor age was split into three groups (0-60, 61-75 and >75 years) and donor ECD was split into three groups (≤2400, 2401-2600 and >2600 cells/mm2). Cox proportional hazards regression was used to determine whether the selected subgroups of donor age and donor ECD have an impact on endothelial failure and a systematic analysis of the interaction between donor ECD and donor age was conducted. The analysis was stratified for primary corneal diagnosis (Fuchs endothelial dystrophy (FED), pseudophakic bullous keratopathy (PBK) and other) and corrected for potentially confounding factors (human leukocyte antigen matching, donor trephine diameter, deep vascularisation, the occurrence of reversible rejection episodes and receipt of systemic antiviral medication, long-term steroids or other immunosuppressive agents). RESULTS A total of 9415 patients, from the National Health Service Blood and Transplant UK Transplant Registry, who received their first PK for visual reasons were included in this study. The overall 5-year graft survival rate due to endothelial failure was 89%. Survival rates in recipients with FED, PBK and 'all other indications' were 95%, 83% and 89%, respectively. Our analysis shows that donor ECD did not affect outcome following corneal graft within the preselected categories, irrespective of diagnosis and after allowing for any potential confounding factors. Furthermore, HRs for each level of donor ECD, relative to >2600 cells/mm2, for each combination of age group and indication, were not statistically significant. CONCLUSIONS We were unable to detect a significant effect of donor age, up to 90 years, and preoperative donor ECD, above the lower limit of 2200 cells/mm2, on endothelial failure at 5 years following PK.
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Affiliation(s)
- M J Wakefield
- Department of Ophthalmology, Leicester Royal Infirmary, Leicester, UK
| | - W J Armitage
- National Health Service Blood and Transplant, Bristol Eye Bank, Bristol, UK.,School of Clinical Sciences, University of Bristol, Bristol, UK
| | - M N A Jones
- National Health Service Blood and Transplant, Bristol, UK
| | - S B Kaye
- St. Paul's Eye Unit, Royal Liverpool University Hospital, Liverpool, UK
| | | | - D Tole
- National Health Service Blood and Transplant, Bristol, UK.,Bristol Eye Hospital, Bristol, UK
| | - J Prydal
- Department of Ophthalmology, Leicester Royal Infirmary, Leicester, UK
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Saunders NR, Dziegielewska KM, Møllgård K, Habgood MD, Wakefield MJ, Lindsay H, Stratzielle N, Ghersi-Egea JF, Liddelow SA. Influx mechanisms in the embryonic and adult rat choroid plexus: a transcriptome study. Front Neurosci 2015; 9:123. [PMID: 25972776 PMCID: PMC4412010 DOI: 10.3389/fnins.2015.00123] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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: 12/24/2014] [Accepted: 03/24/2015] [Indexed: 11/13/2022] Open
Abstract
The transcriptome of embryonic and adult rat lateral ventricular choroid plexus, using a combination of RNA-Sequencing and microarray data, was analyzed by functional groups of influx transporters, particularly solute carrier (SLC) transporters. RNA-Seq was performed at embryonic day (E) 15 and adult with additional data obtained at intermediate ages from microarray analysis. The largest represented functional group in the embryo was amino acid transporters (twelve) with expression levels 2–98 times greater than in the adult. In contrast, in the adult only six amino acid transporters were up-regulated compared to the embryo and at more modest enrichment levels (<5-fold enrichment above E15). In E15 plexus five glucose transporters, in particular Glut-1, and only one monocarboxylate transporter were enriched compared to the adult, whereas only two glucose transporters but six monocarboxylate transporters in the adult plexus were expressed at higher levels than in embryos. These results are compared with earlier published physiological studies of amino acid and monocarboxylate transport in developing rodents. This comparison shows correlation of high expression of some transporters in the developing brain with higher amino acid transport activity reported previously. Data for divalent metal transporters are also considered. Immunohistochemistry of several transporters (e.g., Slc16a10, a thyroid hormone transporter) gene products was carried out to confirm translational activity and to define cellular distribution of the proteins. Overall the results show that there is substantial expression of numerous influx transporters in the embryonic choroid plexus, many at higher levels than in the adult. This, together with immunohistochemical evidence and data from published physiological transport studies suggests that the choroid plexus in embryonic brain plays a major role in supplying the developing brain with essential nutrients.
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Affiliation(s)
- Norman R Saunders
- Department of Pharmacology and Therapeutics, University of Melbourne Parkville, VIC, Australia
| | | | - Kjeld Møllgård
- Department of Cellular and Molecular Medicine, University of Copenhagen Copenhagen, Denmark
| | - Mark D Habgood
- Department of Pharmacology and Therapeutics, University of Melbourne Parkville, VIC, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research Parkville, VIC, Australia
| | - Helen Lindsay
- Institute of Molecular Life Sciences, University of Zurich Zurich, Switzerland
| | - Nathalie Stratzielle
- Lyon Neuroscience Research Center, INSERM U1028, Centre National de la Recherche Scientifique UMR5292, Université Lyon 1 Lyon, France
| | - Jean-Francois Ghersi-Egea
- Lyon Neuroscience Research Center, INSERM U1028, Centre National de la Recherche Scientifique UMR5292, Université Lyon 1 Lyon, France
| | - Shane A Liddelow
- Department of Pharmacology and Therapeutics, University of Melbourne Parkville, VIC, Australia ; Department of Neurobiology, Stanford University Stanford, CA, USA
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Saunders NR, Noor NM, Dziegielewska KM, Wheaton BJ, Liddelow SA, Steer DL, Ek CJ, Habgood MD, Wakefield MJ, Lindsay H, Truettner J, Miller RD, Smith AI, Dietrich WD. Age-dependent transcriptome and proteome following transection of neonatal spinal cord of Monodelphis domestica (South American grey short-tailed opossum). PLoS One 2014; 9:e99080. [PMID: 24914927 PMCID: PMC4051688 DOI: 10.1371/journal.pone.0099080] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [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: 12/04/2013] [Accepted: 05/09/2014] [Indexed: 01/08/2023] Open
Abstract
This study describes a combined transcriptome and proteome analysis of Monodelphis domestica response to spinal cord injury at two different postnatal ages. Previously we showed that complete transection at postnatal day 7 (P7) is followed by profuse axon growth across the lesion with near-normal locomotion and swimming when adult. In contrast, at P28 there is no axon growth across the lesion, the animals exhibit weight-bearing locomotion, but cannot use hind limbs when swimming. Here we examined changes in gene and protein expression in the segment of spinal cord rostral to the lesion at 24 h after transection at P7 and at P28. Following injury at P7 only forty genes changed (all increased expression); most were immune/inflammatory genes. Following injury at P28 many more genes changed their expression and the magnitude of change for some genes was strikingly greater. Again many were associated with the immune/inflammation response. In functional groups known to be inhibitory to regeneration in adult cords the expression changes were generally muted, in some cases opposite to that required to account for neurite inhibition. For example myelin basic protein expression was reduced following injury at P28 both at the gene and protein levels. Only four genes from families with extracellular matrix functions thought to influence neurite outgrowth in adult injured cords showed substantial changes in expression following injury at P28: Olfactomedin 4 (Olfm4, 480 fold compared to controls), matrix metallopeptidase (Mmp1, 104 fold), papilin (Papln, 152 fold) and integrin α4 (Itga4, 57 fold). These data provide a resource for investigation of a priori hypotheses in future studies of mechanisms of spinal cord regeneration in immature animals compared to lack of regeneration at more mature stages.
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Affiliation(s)
- Norman R. Saunders
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
- * E-mail:
| | - Natassya M. Noor
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
| | | | - Benjamin J. Wheaton
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
| | - Shane A. Liddelow
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
- Department of Neurobiology, Stanford University, Stanford, California, United States of America
| | - David L. Steer
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - C. Joakim Ek
- Department of Neuroscience and Physiology, University of Gothenburg, Gothenburg, Sweden
| | - Mark D. Habgood
- Department of Pharmacology & Therapeutics, The University of Melbourne, Victoria, Australia
| | - Matthew J. Wakefield
- Walter & Eliza Hall Institute of Medical Research, Victoria, Australia
- Department of Genetics, The University of Melbourne, Victoria, Australia
| | - Helen Lindsay
- Walter & Eliza Hall Institute of Medical Research, Victoria, Australia
- Institute of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Jessie Truettner
- The Miami Project to Cure Paralysis, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
| | - Robert D. Miller
- Center for Evolutionary & Theoretical Immunology, Department of Biology, University of New Mexico, Albuquerque, New Mexico, United States of America
| | - A. Ian Smith
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - W. Dalton Dietrich
- The Miami Project to Cure Paralysis, University of Miami, Miller School of Medicine, Miami, Florida, United States of America
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Bannister NP, Wakefield MJ, Tatham A, Bugby SL, Molyneux PM, Prydal JI. Spectroscopic measurements in scleritis: bluish-red or deep red? Br J Ophthalmol 2014; 98:1761-4. [PMID: 24795332 DOI: 10.1136/bjophthalmol-2013-304086] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
PURPOSE To design a slit-lamp mountable spectrometer for the assessment of ophthalmic patients and to illustrate a potential clinical application by measuring the spectral characteristics of inflamed eyes of differing aetiologies. METHODS A slit lamp mountable instrument was designed and built, and methods for data analysis developed. Reflectance spectra were recorded from two patients with scleritis, three with non-scleritic red eyes and from two controls with non-inflamed eyes. RESULTS Measurements were reproducible and demonstrated statistically significant differences in the spectral characteristics between the three groups. Spectra from scleritic eyes revealed a relative increase in intensity of long wavelength red light, 650-740 nm, compared with non-scleritic red eyes. These longer wavelengths will be appreciated as dark red. There was no increase in relative intensity in the blue part of the spectrum in scleritic eyes. CONCLUSIONS Reproducible measurements of the eye were made using an innovative, slit-lamp mountable spectrometer and its functionality demonstrated by differentiating the spectra from eyes with differing pathologies. While intending only to illustrate one potential application; for the cases examined, our results indicate that inflamed scleritic eyes exhibit a longer wavelength red light with no increase in shorter wavelength blue light. Thus our measurements would seem to confirm that the perceived redness of scleritis differs from other red eyes. However, it is a deeper darker red and not a bluish one as traditionally described.
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Affiliation(s)
- N P Bannister
- Department of Physics and Astronomy, University of Leicester, Leicester, UK
| | - M J Wakefield
- Department of Ophthalmology, Leicester Royal Infirmary, Leicester, UK
| | - A Tatham
- Princess Alexandra Eye Pavilion, Edinburgh, UK
| | - S L Bugby
- Department of Physics and Astronomy, University of Leicester, Leicester, UK
| | - P M Molyneux
- Department of Physics and Astronomy, University of Leicester, Leicester, UK
| | - J I Prydal
- Department of Ophthalmology, Leicester Royal Infirmary, Leicester, UK
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Topp MD, Hartley L, Cook M, Heong V, Boehm E, McShane L, Pyman J, McNally O, Ananda S, Harrell M, Etemadmoghadam D, Galletta L, Alsop K, Mitchell G, Fox SB, Kerr JB, Hutt KJ, Kaufmann SH, Swisher EM, Bowtell DD, Wakefield MJ, Scott CL. Molecular correlates of platinum response in human high-grade serous ovarian cancer patient-derived xenografts. Mol Oncol 2014; 8:656-68. [PMID: 24560445 DOI: 10.1016/j.molonc.2014.01.008] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/20/2013] [Accepted: 01/14/2014] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Improvement in the ability to target underlying drivers and vulnerabilities of high-grade serous ovarian cancer (HG-SOC) requires the development of molecularly annotated pre-clinical models reflective of clinical responses. METHODS We generated patient-derived xenografts (PDXs) from consecutive, chemotherapy-naïve, human HG-SOC by transplanting fresh human HG-SOC fragments into subcutaneous and intra-ovarian bursal sites of NOD/SCID IL2Rγ(null) recipient mice, completed molecular annotation and assessed platinum sensitivity. RESULTS The success rate of xenografting was 83%. Of ten HG-SOC PDXs, all contained mutations in TP53, two were mutated for BRCA1, three for BRCA2, and in two, BRCA1 was methylated. In vivo cisplatin response, determined as platinum sensitive (progression-free interval ≥ 100 d, n = 4), resistant (progression-free interval <100 d, n = 3) or refractory (n = 3), was largely consistent with patient outcome. Three of four platinum sensitive HG-SOC PDXs contained DNA repair gene mutations, and the fourth was methylated for BRCA1. In contrast, all three platinum refractory PDXs overexpressed dominant oncogenes (CCNE1, LIN28B and/or BCL2). CONCLUSIONS Because PDX platinum response reflected clinical outcome, these annotated PDXs will provide a unique model system for preclinical testing of novel therapies for HG-SOC.
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Affiliation(s)
- Monique D Topp
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medicine and Health Sciences, Monash University, Clayton, Victoria 3168, Australia
| | - Lynne Hartley
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Michele Cook
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Valerie Heong
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Royal Women's Hospital, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia
| | - Emma Boehm
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Lauren McShane
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Jan Pyman
- Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Orla McNally
- Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | - Sumitra Ananda
- Royal Women's Hospital, Parkville, Victoria 3052, Australia
| | | | - Dariush Etemadmoghadam
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 8006, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Laura Galletta
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 8006, Australia
| | - Kathryn Alsop
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 8006, Australia
| | - Gillian Mitchell
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 8006, Australia
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 8006, Australia; Department of Pathology, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Jeffrey B Kerr
- Department of Medicine and Health Sciences, Monash University, Clayton, Victoria 3168, Australia
| | - Karla J Hutt
- Department of Medicine and Health Sciences, Monash University, Clayton, Victoria 3168, Australia; Prince Henry's Institute of Medical Research, Clayton, Victoria 3168, Australia
| | | | | | - David D Bowtell
- Peter MacCallum Cancer Centre, East Melbourne, Victoria 8006, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria 3010, Australia; Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria 8006, Australia
| | - Matthew J Wakefield
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia; Department of Genetics, University of Melbourne, Melbourne, Victoria 8006, Australia
| | - Clare L Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Royal Women's Hospital, Parkville, Victoria 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, Victoria 3052, Australia.
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Srikhanta YN, Hocking DM, Wakefield MJ, Higginson E, Robins-Browne RM, Yang J, Tauschek M. Control of bacterial virulence by the RalR regulator of the rabbit-specific enteropathogenic Escherichia coli strain E22. Infect Immun 2013; 81:4232-43. [PMID: 24002063 PMCID: PMC3811808 DOI: 10.1128/iai.00710-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 06/06/2013] [Accepted: 08/24/2013] [Indexed: 11/20/2022] Open
Abstract
Atypical enteropathogenic Escherichia coli (aEPEC) causes endemic diarrhea, diarrheal outbreaks, and persistent diarrhea in humans, but the mechanism by which aEPEC causes disease is incompletely understood. Virulence regulators and their associated regulons, which often include adhesins, play key roles in the expression of virulence factors in enteric pathogenic bacteria. In this study we identified a transcriptional regulator, RalR, in the rabbit-specific aEPEC strain, E22 (O103:H2) and examined its involvement in the regulation of virulence. Microarray analysis and quantitative real-time reverse transcription-PCR demonstrated that RalR enhances the expression of a number of genes encoding virulence-associated factors, including the Ral fimbria, the Aap dispersin, and its associated transport system, and downregulates several housekeeping genes, including fliC. These observations were confirmed by proteomic analysis of secreted and heat-extracted surface-associated proteins and by adherence and motility assays. To investigate the mechanism of RalR-mediated activation, we focused on its most highly upregulated target operons, ralCDEFGHI and aap. By using primer extension, electrophoretic mobility shift assay, and mutational analysis, we identified the promoter and operator sequences for these two operons. By employing promoter-lacZ reporter systems, we demonstrated that RalR activates the expression of its target genes by binding to one or more 8-bp palindromic sequences (with the consensus of TGTGCACA) located immediately upstream of the promoter core regions. Importantly, we also demonstrated that RalR is essential for virulence since infection of rabbits with E22 carrying a knockout mutation in the ralR gene completely abolished its ability to cause disease.
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Affiliation(s)
- Yogitha N. Srikhanta
- Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia
| | - Dianna M. Hocking
- Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia
| | - Matthew J. Wakefield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Genetics, The University of Melbourne, Victoria, Australia
| | - Ellen Higginson
- Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia
| | - Roy M. Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia
- Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Ji Yang
- Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia
| | - Marija Tauschek
- Department of Microbiology and Immunology, The University of Melbourne, Victoria, Australia
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Affiliation(s)
- M J Wakefield
- Ophthalmology Department, Leicester Royal Infirmary, Leicestershire, UK
| | - P Kumar
- Ophthalmology Department, Leicester Royal Infirmary, Leicestershire, UK
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Liddelow SA, Dziegielewska KM, Ek CJ, Habgood MD, Bauer H, Bauer HC, Lindsay H, Wakefield MJ, Strazielle N, Kratzer I, Møllgård K, Ghersi-Egea JF, Saunders NR. Mechanisms that determine the internal environment of the developing brain: a transcriptomic, functional and ultrastructural approach. PLoS One 2013; 8:e65629. [PMID: 23843944 PMCID: PMC3699566 DOI: 10.1371/journal.pone.0065629] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [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: 02/10/2013] [Accepted: 04/25/2013] [Indexed: 01/04/2023] Open
Abstract
We provide comprehensive identification of embryonic (E15) and adult rat lateral ventricular choroid plexus transcriptome, with focus on junction-associated proteins, ionic influx transporters and channels. Additionally, these data are related to new structural and previously published permeability studies. Results reveal that most genes associated with intercellular junctions are expressed at similar levels at both ages. In total, 32 molecules known to be associated with brain barrier interfaces were identified. Nine claudins showed unaltered expression, while two claudins (6 and 8) were expressed at higher levels in the embryo. Expression levels for most cytoplasmic/regulatory adaptors (10 of 12) were similar at the two ages. A few junctional genes displayed lower expression in embryos, including 5 claudins, occludin and one junctional adhesion molecule. Three gap junction genes were enriched in the embryo. The functional effectiveness of these junctions was assessed using blood-delivered water-soluble tracers at both the light and electron microscopic level: embryo and adult junctions halted movement of both 286Da and 3kDa molecules into the cerebrospinal fluid (CSF). The molecular identities of many ion channel and transporter genes previously reported as important for CSF formation and secretion in the adult were demonstrated in the embryonic choroid plexus (and validated with immunohistochemistry of protein products), but with some major age-related differences in expression. In addition, a large number of previously unidentified ion channel and transporter genes were identified for the first time in plexus epithelium. These results, in addition to data obtained from electron microscopical and physiological permeability experiments in immature brains, indicate that exchange between blood and CSF is mainly transcellular, as well-formed tight junctions restrict movement of small water-soluble molecules from early in development. These data strongly indicate the brain develops within a well-protected internal environment and the exchange between the blood, brain and CSF is transcellular and not through incomplete barriers.
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Affiliation(s)
- Shane A Liddelow
- Department of Pharmacology, the University of Melbourne, Victoria, Australia.
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Cheng C, Wakefield MJ, Yang J, Tauschek M, Robins-Browne RM. Genome-wide analysis of the Pho regulon in a pstCA mutant of Citrobacter rodentium. PLoS One 2012; 7:e50682. [PMID: 23226353 PMCID: PMC3511308 DOI: 10.1371/journal.pone.0050682] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 09/13/2012] [Accepted: 10/26/2012] [Indexed: 11/19/2022] Open
Abstract
The phosphate-specific transport operon, pstSCAB-phoU, of Gram-negative bacteria is an essential part of the Pho regulon. Its key roles are to encode a high-affinity inorganic phosphate transport system and to prevent activation of PhoB in phosphate-rich environments. In general, mutations in pstSCAB-phoU lead to the constitutive expression of the Pho regulon. Previously, we constructed a pstCA deletion mutant of Citrobacter rodentium and found it to be attenuated for virulence in mice, its natural host. This attenuation was dependent on PhoB or PhoB-regulated gene(s) because a phoB mutation restored virulence for mice to the pstCA mutant. To investigate how downstream genes may contribute to the virulence of C. rodentium, we used microarray analysis to investigate global gene expression of C. rodentium strain ICC169 and its isogenic pstCA mutant when grown in phosphate-rich medium. Overall 323 genes of the pstCA mutant were differentially expressed by at least 1.5-fold compared to the wild-type C. rodentium. Of these 145 were up-regulated and 178 were down-regulated. Differentially expressed genes included some involved in phosphate homoeostasis, cellular metabolism and protein metabolism. A large number of genes involved in stress responses and of unknown function were also differentially expressed, as were some virulence-associated genes. Up-regulated virulence-associated genes in the pstCA mutant included that for DegP, a serine protease, which appeared to be directly regulated by PhoB. Down-regulated genes included those for the production of the urease, flagella, NleG8 (a type III-secreted protein) and the tad focus (which encodes type IVb pili in Yersinia enterocolitica). Infection studies using C57/BL6 mice showed that DegP and NleG8 play a role in bacterial virulence. Overall, our study provides evidence that Pho is a global regulator of gene expression in C. rodentium and indicates the presence of at least two previously unrecognized virulence determinants of C. rodentium, namely, DegP and NleG8.
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Affiliation(s)
- Catherine Cheng
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Matthew J. Wakefield
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Genetics, The University of Melbourne, Parkville, Victoria, Australia
| | - Ji Yang
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Marija Tauschek
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
| | - Roy M. Robins-Browne
- Department of Microbiology and Immunology, The University of Melbourne, Parkville, Victoria, Australia
- Murdoch Childrens Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
- * E-mail:
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011; 12:R81. [PMID: 21854559 PMCID: PMC3277949 DOI: 10.1186/gb-2011-12-8-r81] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2011] [Revised: 07/22/2011] [Accepted: 08/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We present the genome sequence of the tammar wallaby, Macropus eugenii, which is a member of the kangaroo family and the first representative of the iconic hopping mammals that symbolize Australia to be sequenced. The tammar has many unusual biological characteristics, including the longest period of embryonic diapause of any mammal, extremely synchronized seasonal breeding and prolonged and sophisticated lactation within a well-defined pouch. Like other marsupials, it gives birth to highly altricial young, and has a small number of very large chromosomes, making it a valuable model for genomics, reproduction and development. RESULTS The genome has been sequenced to 2 × coverage using Sanger sequencing, enhanced with additional next generation sequencing and the integration of extensive physical and linkage maps to build the genome assembly. We also sequenced the tammar transcriptome across many tissues and developmental time points. Our analyses of these data shed light on mammalian reproduction, development and genome evolution: there is innovation in reproductive and lactational genes, rapid evolution of germ cell genes, and incomplete, locus-specific X inactivation. We also observe novel retrotransposons and a highly rearranged major histocompatibility complex, with many class I genes located outside the complex. Novel microRNAs in the tammar HOX clusters uncover new potential mammalian HOX regulatory elements. CONCLUSIONS Analyses of these resources enhance our understanding of marsupial gene evolution, identify marsupial-specific conserved non-coding elements and critical genes across a range of biological systems, including reproduction, development and immunity, and provide new insight into marsupial and mammalian biology and genome evolution.
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Affiliation(s)
- Marilyn B Renfree
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Anthony T Papenfuss
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Mathematics and Statistics, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Janine E Deakin
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - James Lindsay
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Thomas Heider
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Katherine Belov
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Willem Rens
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Paul D Waters
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Elizabeth A Pharo
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Geoff Shaw
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Emily SW Wong
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Christophe M Lefèvre
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Kevin R Nicholas
- Institute for Technology Research and Innovation, Deakin University, Geelong, Victoria, 3214, Australia
| | - Yoko Kuroki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Matthew J Wakefield
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Kyall R Zenger
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
- School of Marine and Tropical Biology, James Cook University, Townsville, Queensland 4811, Australia
| | - Chenwei Wang
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Malcolm Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge, CB3 0ES, UK
| | - Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Danielle Hickford
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hongshi Yu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kirsty R Short
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Hannah V Siddle
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Stephen R Frankenberg
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Keng Yih Chew
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Brandon R Menzies
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, Berlin 10315, Germany
| | - Jessica M Stringer
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Shunsuke Suzuki
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Timothy A Hore
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Laboratory of Developmental Genetics and Imprinting, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Margaret L Delbridge
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Amir Mohammadi
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Nanette Y Schneider
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - Yanqiu Hu
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - William O'Hara
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Shafagh Al Nadaf
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Chen Wu
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW 2006, Australia
| | - Zhi-Ping Feng
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Benjamin G Cocks
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Jianghui Wang
- Biosciences Research Division, Department of Primary Industries, Victoria, 1 Park Drive, Bundoora 3083, Australia
| | - Paul Flicek
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephen MJ Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Susan Fairley
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Kathryn Beal
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Javier Herrero
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Dawn M Carone
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Yutaka Suzuki
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Sumio Sugano
- Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8560, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
| | - Yoshiyuki Sakaki
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shinji Kondo
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Yuichiro Nishida
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Shoji Tatsumoto
- RIKEN Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Ion Mandiou
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269, USA
| | - Arthur Hsu
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Kaighin A McColl
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Benjamin Lansdell
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - George Weinstock
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Elizabeth Kuczek
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
- Westmead Institute for Cancer Research, University of Sydney, Westmead, New South Wales 2145, Australia
| | - Annette McGrath
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Peter Wilson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Artem Men
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Mehlika Hazar-Rethinam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Allison Hall
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - John Davis
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - David Wood
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Sarah Williams
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yogi Sundaravadanam
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Donna M Muzny
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lora R Lewis
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret B Morgan
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Geoffrey O Okwuonu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - San Juana Ruiz
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jireh Santibanez
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lynne Nazareth
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Andrew Cree
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Gerald Fowler
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Christie L Kovar
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Huyen H Dinh
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandita Joshi
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Chyn Jing
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Fremiet Lara
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Rebecca Thornton
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Lei Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Jixin Deng
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Yue Liu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua Y Shen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Xing-Zhi Song
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Janette Edson
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Carmen Troon
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Daniel Thomas
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Amber Stephens
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lankesha Yapa
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Tanya Levchenko
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Richard A Gibbs
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
| | - Desmond W Cooper
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Terence P Speed
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia
| | - Asao Fujiyama
- National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan
- National Institute of Informatics, 2-1-2 Hitotsubashi, Chiyoda-ku, Tokyo 101-8430, Japan
| | - Jennifer A M Graves
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Rachel J O'Neill
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Andrew J Pask
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Department of Zoology, The University of Melbourne, Melbourne, Victoria 3010, Australia
- Department of Molecular and Cell Biology, Center for Applied Genetics and Technology, University of Connecticut, Storrs, CT 06269, USA
| | - Susan M Forrest
- The Australian Research Council Centre of Excellence in Kangaroo Genomics, Australia
- Australian Genome Research Facility, Melbourne, Victoria, 3052 and the University of Queensland, St Lucia, Queensland 4072, Australia
| | - Kim C Worley
- Human Genome Sequencing Center, Department of Molecular and Human Genetics Baylor College of Medicine, Houston, TX 77030, USA
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Wang C, Webley L, Wei KJ, Wakefield MJ, Patel HR, Deakin JE, Alsop A, Marshall Graves JA, Cooper DW, Nicholas FW, Zenger KR. A second-generation anchored genetic linkage map of the tammar wallaby (Macropus eugenii). BMC Genet 2011; 12:72. [PMID: 21854616 PMCID: PMC3176194 DOI: 10.1186/1471-2156-12-72] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [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: 09/09/2010] [Accepted: 08/19/2011] [Indexed: 11/13/2022] Open
Abstract
Background The tammar wallaby, Macropus eugenii, a small kangaroo used for decades for studies of reproduction and metabolism, is the model Australian marsupial for genome sequencing and genetic investigations. The production of a more comprehensive cytogenetically-anchored genetic linkage map will significantly contribute to the deciphering of the tammar wallaby genome. It has great value as a resource to identify novel genes and for comparative studies, and is vital for the ongoing genome sequence assembly and gene ordering in this species. Results A second-generation anchored tammar wallaby genetic linkage map has been constructed based on a total of 148 loci. The linkage map contains the original 64 loci included in the first-generation map, plus an additional 84 microsatellite loci that were chosen specifically to increase coverage and assist with the anchoring and orientation of linkage groups to chromosomes. These additional loci were derived from (a) sequenced BAC clones that had been previously mapped to tammar wallaby chromosomes by fluorescence in situ hybridization (FISH), (b) End sequence from BACs subsequently FISH-mapped to tammar wallaby chromosomes, and (c) tammar wallaby genes orthologous to opossum genes predicted to fill gaps in the tammar wallaby linkage map as well as three X-linked markers from a published study. Based on these 148 loci, eight linkage groups were formed. These linkage groups were assigned (via FISH-mapped markers) to all seven autosomes and the X chromosome. The sex-pooled map size is 1402.4 cM, which is estimated to provide 82.6% total coverage of the genome, with an average interval distance of 10.9 cM between adjacent markers. The overall ratio of female/male map length is 0.84, which is comparable to the ratio of 0.78 obtained for the first-generation map. Conclusions Construction of this second-generation genetic linkage map is a significant step towards complete coverage of the tammar wallaby genome and considerably extends that of the first-generation map. It will be a valuable resource for ongoing tammar wallaby genetic research and assembling the genome sequence. The sex-pooled map is available online at http://compldb.angis.org.au/.
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Affiliation(s)
- Chenwei Wang
- Reprogen, Faculty of Veterinary Science, The University of Sydney, Sydney, NSW 2006, Australia.
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Young MD, Willson TA, Wakefield MJ, Trounson E, Hilton DJ, Blewitt ME, Oshlack A, Majewski IJ. ChIP-seq analysis reveals distinct H3K27me3 profiles that correlate with transcriptional activity. Nucleic Acids Res 2011; 39:7415-27. [PMID: 21652639 PMCID: PMC3177187 DOI: 10.1093/nar/gkr416] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Transcriptional control is dependent on a vast network of epigenetic modifications. One epigenetic mark of particular interest is tri-methylation of lysine 27 on histone H3 (H3K27me3), which is catalysed and maintained by Polycomb Repressive Complex 2 (PRC2). Although this histone mark is studied widely, the precise relationship between its local pattern of enrichment and regulation of gene expression is currently unclear. We have used ChIP-seq to generate genome-wide maps of H3K27me3 enrichment, and have identified three enrichment profiles with distinct regulatory consequences. First, a broad domain of H3K27me3 enrichment across the body of genes corresponds to the canonical view of H3K27me3 as inhibitory to transcription. Second, a peak of enrichment around the transcription start site (TSS) is commonly associated with ‘bivalent’ genes, where H3K4me3 also marks the TSS. Finally and most surprisingly, we identified an enrichment profile with a peak in the promoter of genes that is associated with active transcription. Genes with each of these three profiles were found in different proportions in each of the cell types studied. The data analysis techniques developed here will be useful for the identification of common enrichment profiles for other histone modifications that have important consequences for transcriptional regulation.
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Affiliation(s)
- Matthew D Young
- Walter and Eliza Hall Institute, 1G Royal Parade, Parkville 3052, Australia
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Renfree MB, Papenfuss AT, Deakin JE, Lindsay J, Heider T, Belov K, Rens W, Waters PD, Pharo EA, Shaw G, Wong ESW, Lefèvre CM, Nicholas KR, Kuroki Y, Wakefield MJ, Zenger KR, Wang C, Ferguson-Smith M, Nicholas FW, Hickford D, Yu H, Short KR, Siddle HV, Frankenberg SR, Chew KY, Menzies BR, Stringer JM, Suzuki S, Hore TA, Delbridge ML, Patel H, Mohammadi A, Schneider NY, Hu Y, O'Hara W, Al Nadaf S, Wu C, Feng ZP, Cocks BG, Wang J, Flicek P, Searle SMJ, Fairley S, Beal K, Herrero J, Carone DM, Suzuki Y, Sugano S, Toyoda A, Sakaki Y, Kondo S, Nishida Y, Tatsumoto S, Mandiou I, Hsu A, McColl KA, Lansdell B, Weinstock G, Kuczek E, McGrath A, Wilson P, Men A, Hazar-Rethinam M, Hall A, Davis J, Wood D, Williams S, Sundaravadanam Y, Muzny DM, Jhangiani SN, Lewis LR, Morgan MB, Okwuonu GO, Ruiz SJ, Santibanez J, Nazareth L, Cree A, Fowler G, Kovar CL, Dinh HH, Joshi V, Jing C, Lara F, Thornton R, Chen L, Deng J, Liu Y, Shen JY, Song XZ, Edson J, Troon C, Thomas D, Stephens A, Yapa L, Levchenko T, Gibbs RA, Cooper DW, Speed TP, Fujiyama A, M Graves JA, O'Neill RJ, Pask AJ, Forrest SM, Worley KC. Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol 2011. [PMCID: PMC3334613 DOI: 10.1186/gb-2011-12-12-414] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
Significant histological overlap exists between fibro-osseous lesions and diagnosis is made on a clinicopathological basis. Ossifying fibroma is a benign fibro-osseous neoplasm of the jaw and craniofacial complex that has generated a degree of controversy regarding diagnosis and classification, especially with respect to the psammomatoid variant. Orbital lesions mainly arise from the paranasal sinuses affecting the medial or inferior orbital wall. Lateral orbital wall ossifying fibroma is, therefore, a rare condition with only a single previous case report. We present a second case of lateral orbital wall ossifying fibroma and a review of the associated literature.
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Affiliation(s)
- M J Wakefield
- Department of Ophthalmology, Lincoln County Hospital, Greetwell Road, Lincoln, UK.
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Abstract
We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology.
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Affiliation(s)
- Matthew D Young
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3052, Australia
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Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol 2010; 11:R14. [PMID: 20132535 PMCID: PMC2872874 DOI: 10.1186/gb-2010-11-2-r14] [Citation(s) in RCA: 4212] [Impact Index Per Article: 300.9] [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: 12/01/2009] [Revised: 01/14/2010] [Accepted: 02/04/2010] [Indexed: 12/13/2022] Open
Abstract
GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq We present GOseq, an application for performing Gene Ontology (GO) analysis on RNA-seq data. GO analysis is widely used to reduce complexity and highlight biological processes in genome-wide expression studies, but standard methods give biased results on RNA-seq data due to over-detection of differential expression for long and highly expressed transcripts. Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology.
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Affiliation(s)
- Matthew D Young
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville 3052, Australia
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Abstract
Background Several recent studies have demonstrated the effectiveness of deep sequencing for transcriptome analysis (RNA-seq) in mammals. As RNA-seq becomes more affordable, whole genome transcriptional profiling is likely to become the platform of choice for species with good genomic sequences. As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data. Results We investigated the effect of transcript length bias in RNA-seq data using three different published data sets. For standard analyses using aggregated tag counts for each gene, the ability to call differentially expressed genes between samples is strongly associated with the length of the transcript. Conclusion Transcript length bias for calling differentially expressed genes is a general feature of current protocols for RNA-seq technology. This has implications for the ranking of differentially expressed genes, and in particular may introduce bias in gene set testing for pathway analysis and other multi-gene systems biology analyses. Reviewers This article was reviewed by Rohan Williams (nominated by Gavin Huttley), Nicole Cloonan (nominated by Mark Ragan) and James Bullard (nominated by Sandrine Dudoit).
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Affiliation(s)
- Alicia Oshlack
- Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia.
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45
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Deakin JE, Koina E, Waters PD, Doherty R, Patel VS, Delbridge ML, Dobson B, Fong J, Hu Y, van den Hurk C, Pask AJ, Shaw G, Smith C, Thompson K, Wakefield MJ, Yu H, Renfree MB, Graves JAM. Physical map of two tammar wallaby chromosomes: a strategy for mapping in non-model mammals. Chromosome Res 2008; 16:1159-75. [PMID: 18987984 DOI: 10.1007/s10577-008-1266-y] [Citation(s) in RCA: 48] [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: 07/30/2008] [Revised: 09/02/2008] [Accepted: 09/02/2008] [Indexed: 01/20/2023]
Abstract
Marsupials are especially valuable for comparative genomic studies of mammals. Two distantly related model marsupials have been sequenced: the South American opossum (Monodelphis domestica) and the tammar wallaby (Macropus eugenii), which last shared a common ancestor about 70 Mya. The six-fold opossum genome sequence has been assembled and assigned to chromosomes with the help of a cytogenetic map. A good cytogenetic map will be even more essential for assembly and anchoring of the two-fold wallaby genome. As a start to generating a physical map of gene locations on wallaby chromosomes, we focused on two chromosomes sharing homology with the human X, wallaby chromosomes X and 5. We devised an efficient strategy for mapping large conserved synteny blocks in non-model mammals, and applied this to generate dense maps of the X and 'neo-X' regions and to determine the arrangement of large conserved synteny blocks on chromosome 5. Comparisons between the wallaby and opossum chromosome maps revealed many rearrangements, highlighting the need for comparative gene mapping between South American and Australian marsupials. Frequent rearrangement of the X, along with the absence of a marsupial XIST gene, suggests that inactivation of the marsupial X chromosome does not depend on a whole-chromosome repression by a control locus.
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Affiliation(s)
- Janine E Deakin
- ARC Centre of Excellence for Kangaroo Genomics, Research School of Biological Sciences, The Australian National University, Canberra, ACT 0200, Australia.
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46
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Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AFA, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ESW, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Nefedov M, de Jong PJ, Renfree MB, Mardis ER, Wilson RK. Genome analysis of the platypus reveals unique signatures of evolution. Nature 2008; 453:175-83. [PMID: 18464734 PMCID: PMC2803040 DOI: 10.1038/nature06936] [Citation(s) in RCA: 475] [Impact Index Per Article: 29.7] [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: 09/14/2007] [Accepted: 03/25/2008] [Indexed: 12/18/2022]
Abstract
We present a draft genome sequence of the platypus, Ornithorhynchus anatinus. This monotreme exhibits a fascinating combination of reptilian and mammalian characters. For example, platypuses have a coat of fur adapted to an aquatic lifestyle; platypus females lactate, yet lay eggs; and males are equipped with venom similar to that of reptiles. Analysis of the first monotreme genome aligned these features with genetic innovations. We find that reptile and platypus venom proteins have been co-opted independently from the same gene families; milk protein genes are conserved despite platypuses laying eggs; and immune gene family expansions are directly related to platypus biology. Expansions of protein, non-protein-coding RNA and microRNA families, as well as repeat elements, are identified. Sequencing of this genome now provides a valuable resource for deep mammalian comparative analyses, as well as for monotreme biology and conservation.
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Affiliation(s)
- Wesley C Warren
- Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.
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47
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Knight R, Maxwell P, Birmingham A, Carnes J, Caporaso JG, Easton BC, Eaton M, Hamady M, Lindsay H, Liu Z, Lozupone C, McDonald D, Robeson M, Sammut R, Smit S, Wakefield MJ, Widmann J, Wikman S, Wilson S, Ying H, Huttley GA. PyCogent: a toolkit for making sense from sequence. Genome Biol 2008; 8:R171. [PMID: 17708774 PMCID: PMC2375001 DOI: 10.1186/gb-2007-8-8-r171] [Citation(s) in RCA: 147] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2007] [Revised: 08/13/2007] [Accepted: 08/21/2007] [Indexed: 12/30/2022] Open
Abstract
The COmparative GENomic Toolkit, a framework for probabilistic analyses of biological sequences, devising workflows and generating publication quality graphics, has been implemented in Python. We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from .
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Affiliation(s)
- Rob Knight
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Peter Maxwell
- Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | | | - Jason Carnes
- Seattle Biomedical Research Institute, Seattle, Washington, USA
| | - J Gregory Caporaso
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, Colorado, USA
| | - Brett C Easton
- Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Michael Eaton
- Science Applications International Corporation, Englewood, Colorado, USA
| | - Micah Hamady
- Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Helen Lindsay
- Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Zongzhi Liu
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Catherine Lozupone
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Daniel McDonald
- Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Michael Robeson
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Raymond Sammut
- Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Sandra Smit
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Matthew J Wakefield
- Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
- Walter and Eliza Hall Institute, Melbourne, Victoria, Australia
| | - Jeremy Widmann
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Shandy Wikman
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Stephanie Wilson
- Department of Computer Science, University of Colorado, Boulder, Colorado, USA
| | - Hua Ying
- Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Gavin A Huttley
- Computational Genomics Laboratory, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
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48
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Gentles AJ, Wakefield MJ, Kohany O, Gu W, Batzer MA, Pollock DD, Jurka J. Evolutionary dynamics of transposable elements in the short-tailed opossum Monodelphis domestica. Genome Res 2007; 17:992-1004. [PMID: 17495012 PMCID: PMC1899126 DOI: 10.1101/gr.6070707] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The genome of the gray short-tailed opossum Monodelphis domestica is notable for its large size ( approximately 3.6 Gb). We characterized nearly 500 families of interspersed repeats from the Monodelphis. They cover approximately 52% of the genome, higher than in any other amniotic lineage studied to date, and may account for the unusually large genome size. In comparison to other mammals, Monodelphis is significantly rich in non-LTR retrotransposons from the LINE-1, CR1, and RTE families, with >29% of the genome sequence comprised of copies of these elements. Monodelphis has at least four families of RTE, and we report support for horizontal transfer of this non-LTR retrotransposon. In addition to short interspersed elements (SINEs) mobilized by L1, we found several families of SINEs that appear to use RTE elements for mobilization. In contrast to L1-mobilized SINEs, the RTE-mobilized SINEs in Monodelphis appear to shift from G+C-rich to G+C-low regions with time. Endogenous retroviruses have colonized approximately 10% of the opossum genome. We found that their density is enhanced in centromeric and/or telomeric regions of most Monodelphis chromosomes. We identified 83 new families of ancient repeats that are highly conserved across amniotic lineages, including 14 LINE-derived repeats; and a novel SINE element, MER131, that may have been exapted as a highly conserved functional noncoding RNA, and whose emergence dates back to approximately 300 million years ago. Many of these conserved repeats are also present in human, and are highly over-represented in predicted cis-regulatory modules. Seventy-six of the 83 families are present in chicken in addition to mammals.
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Affiliation(s)
- Andrew J. Gentles
- Department of Radiology, School of Medicine, Stanford University, Stanford, California 94305, USA
- Genetic Information Research Institute, Mountain View, California 94043, USA
- Corresponding authors.E-mail ; fax (650) 723-5795.E-mail ; fax (650) 961-4473
| | - Matthew J. Wakefield
- ARC Centre for Kangaroo Genomics, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3050, Australia
| | - Oleksiy Kohany
- Genetic Information Research Institute, Mountain View, California 94043, USA
| | - Wanjun Gu
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora 80045, Colorado, USA
| | - Mark A. Batzer
- Department of Biological Sciences, Biological Computation and Visualization Center, Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - David D. Pollock
- Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora 80045, Colorado, USA
| | - Jerzy Jurka
- Genetic Information Research Institute, Mountain View, California 94043, USA
- Corresponding authors.E-mail ; fax (650) 723-5795.E-mail ; fax (650) 961-4473
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49
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Abstract
Accurate estimation of any phylogeny is important as a framework for evolutionary analysis of form and function at all levels of organization from sequence to whole organism. Using alignments of nonrepetitive components of opossum, human, mouse, rat, and dog genomes we evaluated two alternative tree topologies for eutherian evolution. We show with very high confidence that there is a basal split between rodents (as represented by the mouse and rat) and a branch joining primates (as represented by humans) and carnivores (as represented by dogs), consistent with some but not the most widely accepted mammalian phylogenies. The result was robust to substitution model choice with equivalent inference returned from a spectrum of models ranging from a general time reversible model, a model that treated nucleotides as either purines and pyrimidines, and variants of these that incorporated rate heterogeneity among sites. By determining this particular branching order we are able to show that the rate of molecular evolution is almost identical in rodent and carnivore lineages and that sequences evolve approximately 11%-14% faster in these lineages than in the primate lineage. In addition by applying the chicken as outgroup the analyses suggested that the rate of evolution in all eutherian lineages is approximately 30% slower than in the opossum lineage. This pattern of relative rates is inconsistent with the hypothesis that generation time is an important determinant of substitution rates and, by implication, mutation rates. Possible factors causing rate differences between the lineages include differences in DNA repair and replication enzymology, and shifts in nucleotide pools. Our analysis demonstrates the importance of using multiple sequences from across the genome to estimate phylogeny and relative evolutionary rate in order to reduce the influence of distorting local effects evident even in relatively long sequences.
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Affiliation(s)
- Gavin A Huttley
- John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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50
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Mikkelsen TS, Wakefield MJ, Aken B, Amemiya CT, Chang JL, Duke S, Garber M, Gentles AJ, Goodstadt L, Heger A, Jurka J, Kamal M, Mauceli E, Searle SMJ, Sharpe T, Baker ML, Batzer MA, Benos PV, Belov K, Clamp M, Cook A, Cuff J, Das R, Davidow L, Deakin JE, Fazzari MJ, Glass JL, Grabherr M, Greally JM, Gu W, Hore TA, Huttley GA, Kleber M, Jirtle RL, Koina E, Lee JT, Mahony S, Marra MA, Miller RD, Nicholls RD, Oda M, Papenfuss AT, Parra ZE, Pollock DD, Ray DA, Schein JE, Speed TP, Thompson K, VandeBerg JL, Wade CM, Walker JA, Waters PD, Webber C, Weidman JR, Xie X, Zody MC, Graves JAM, Ponting CP, Breen M, Samollow PB, Lander ES, Lindblad-Toh K. Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature 2007; 447:167-77. [PMID: 17495919 DOI: 10.1038/nature05805] [Citation(s) in RCA: 592] [Impact Index Per Article: 34.8] [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: 12/05/2006] [Accepted: 04/03/2007] [Indexed: 12/15/2022]
Abstract
We report a high-quality draft of the genome sequence of the grey, short-tailed opossum (Monodelphis domestica). As the first metatherian ('marsupial') species to be sequenced, the opossum provides a unique perspective on the organization and evolution of mammalian genomes. Distinctive features of the opossum chromosomes provide support for recent theories about genome evolution and function, including a strong influence of biased gene conversion on nucleotide sequence composition, and a relationship between chromosomal characteristics and X chromosome inactivation. Comparison of opossum and eutherian genomes also reveals a sharp difference in evolutionary innovation between protein-coding and non-coding functional elements. True innovation in protein-coding genes seems to be relatively rare, with lineage-specific differences being largely due to diversification and rapid turnover in gene families involved in environmental interactions. In contrast, about 20% of eutherian conserved non-coding elements (CNEs) are recent inventions that postdate the divergence of Eutheria and Metatheria. A substantial proportion of these eutherian-specific CNEs arose from sequence inserted by transposable elements, pointing to transposons as a major creative force in the evolution of mammalian gene regulation.
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Affiliation(s)
- Tarjei S Mikkelsen
- Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
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