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Alser M, Lawlor B, Abdill RJ, Waymost S, Ayyala R, Rajkumar N, LaPierre N, Brito J, Ribeiro-Dos-Santos AM, Almadhoun N, Sarwal V, Firtina C, Osinski T, Eskin E, Hu Q, Strong D, Kim BDBD, Abedalthagafi MS, Mutlu O, Mangul S. Packaging and containerization of computational methods. Nat Protoc 2024; 19:2529-2539. [PMID: 38565959 DOI: 10.1038/s41596-024-00986-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 02/12/2024] [Indexed: 04/04/2024]
Abstract
Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.
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Affiliation(s)
- Mohammed Alser
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Brendan Lawlor
- Department of Computer Science, Munster Technological University, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Richard J Abdill
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Sharon Waymost
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ram Ayyala
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | - Neha Rajkumar
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nathan LaPierre
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Jaqueline Brito
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA
| | | | - Nour Almadhoun
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Varuni Sarwal
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
| | - Can Firtina
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Tomasz Osinski
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Eleazar Eskin
- Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, University of California, Los Angeles, CA, USA
| | - Qiyang Hu
- Office of Advanced Research Computing, University of California, Los Angeles, CA, USA
| | - Derek Strong
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Byoung-Do B D Kim
- Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA
| | - Malak S Abedalthagafi
- Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA
- King Salman Center for Disability Research, Riyadh, Saudi Arabia
| | - Onur Mutlu
- Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland
| | - Serghei Mangul
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
- Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
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2
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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] [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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3
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Abdelmogod A, Papadopoulos L, Riordan S, Wong M, Weltman M, Lim R, McEvoy C, Fellowes A, Fox S, Bedő J, Penington J, Pham K, Hofmann O, Vissers JHA, Grimmond S, Ratnayake G, Christie M, Mitchell C, Murray WK, McClymont K, Luk P, Papenfuss AT, Kee D, Scott CL, Goldstein D, Barker HE. A Matched Molecular and Clinical Analysis of the Epithelioid Haemangioendothelioma Cohort in the Stafford Fox Rare Cancer Program and Contextual Literature Review. Cancers (Basel) 2023; 15:4378. [PMID: 37686662 PMCID: PMC10487006 DOI: 10.3390/cancers15174378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/21/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
BACKGROUND Epithelioid haemangioendothelioma (EHE) is an ultra-rare malignant vascular tumour with a prevalence of 1 per 1,000,000. It is typically molecularly characterised by a WWTR1::CAMTA1 gene fusion in approximately 90% of cases, or a YAP1::TFE3 gene fusion in approximately 10% of cases. EHE cases are typically refractory to therapies, and no anticancer agents are reimbursed for EHE in Australia. METHODS We report a cohort of nine EHE cases with comprehensive histologic and molecular profiling from the Walter and Eliza Hall Institute of Medical Research Stafford Fox Rare Cancer Program (WEHI-SFRCP) collated via nation-wide referral to the Australian Rare Cancer (ARC) Portal. The diagnoses of EHE were confirmed by histopathological and immunohistochemical (IHC) examination. Molecular profiling was performed using the TruSight Oncology 500 assay, the TruSight RNA fusion panel, whole genome sequencing (WGS), or whole exome sequencing (WES). RESULTS Molecular analysis of RNA, DNA or both was possible in seven of nine cases. The WWTR1::CAMTA1 fusion was identified in five cases. The YAP1::TFE3 fusion was identified in one case, demonstrating unique morphology compared to cases with the more common WWTR1::CAMTA1 fusion. All tumours expressed typical endothelial markers CD31, ERG, and CD34 and were negative for pan-cytokeratin. Cases with a WWTR1::CAMTA1 fusion displayed high expression of CAMTA1 and the single case with a YAP1::TFE3 fusion displayed high expression of TFE3. Survival was highly variable and unrelated to molecular profile. CONCLUSIONS This cohort of EHE cases provides molecular and histopathological characterisation and matching clinical information that emphasises the molecular patterns and variable clinical outcomes and adds to our knowledge of this ultra-rare cancer. Such information from multiple studies will advance our understanding, potentially improving treatment options.
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Affiliation(s)
- Arwa Abdelmogod
- Limestone Coast Local Health Network, Flinders University, Bedford Park, SA 5042, Australia;
| | - Lia Papadopoulos
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- Eastern Health Clinical School, Monash University, Box Hill, VIC 3128, Australia
| | - Stephen Riordan
- Prince of Wales Clinical School, University of NSW, Randwick, NSW 2031, Australia;
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Melvin Wong
- Radiology Department, Prince of Wales Hospital, Randwick, NSW 2031, Australia;
| | - Martin Weltman
- Department of Gastroenterology, Nepean Hospital, Kingswood, NSW 2747, Australia;
| | - Ratana Lim
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
| | - Christopher McEvoy
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (A.F.)
| | - Andrew Fellowes
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (A.F.)
| | - Stephen Fox
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (A.F.)
| | - Justin Bedő
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
| | - Jocelyn Penington
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
| | - Kym Pham
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | - Oliver Hofmann
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | - Joseph H. A. Vissers
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | - Sean Grimmond
- Centre for Cancer Research and Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia; (K.P.); (O.H.); (J.H.A.V.); (S.G.)
| | | | | | - Catherine Mitchell
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (W.K.M.)
| | - William K. Murray
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (C.M.); (W.K.M.)
| | - Kelly McClymont
- Sullivan Nicolaides Pathology, Brisbane, QLD 4000, Australia;
| | - Peter Luk
- Royal Prince Alfred Hospital, Camperdown, NSW 2050, Australia;
| | - Anthony T. Papenfuss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- Department of Gastroenterology, Nepean Hospital, Kingswood, NSW 2747, Australia;
- Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, VIC 3000, Australia
| | - Damien Kee
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, VIC 3000, Australia
- Austin Health, Heidelberg, VIC 3084, Australia
| | - Clare L. Scott
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- The Royal Womens’ Hospital, Parkville, VIC 3052, Australia;
- Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, VIC 3000, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Obstetrics and Gynaecology, University of Melbourne, Parkville, VIC 3010, Australia
| | - David Goldstein
- The Australian Rare Cancer Portal, BioGrid, Parkville, VIC 3051, Australia;
- Eastern Health Clinical School, Monash University, Box Hill, VIC 3128, Australia
- Nelune Center, Prince of Wales Hospital, Randwick, NSW 2031, Australia
| | - Holly E. Barker
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; (L.P.); (R.L.); (J.B.); (J.P.); (A.T.P.); (D.K.); (C.L.S.)
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, 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 : THE PREPRINT SERVER FOR HEALTH SCIENCES 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] [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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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: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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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Vallet N, Michonneau D, Tournier S. Toward practical transparent verifiable and long-term reproducible research using Guix. Sci Data 2022; 9:597. [PMID: 36195618 PMCID: PMC9532446 DOI: 10.1038/s41597-022-01720-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 09/26/2022] [Indexed: 11/09/2022] Open
Abstract
Reproducibility crisis urge scientists to promote transparency which allows peers to draw same conclusions after performing identical steps from hypothesis to results. Growing resources are developed to open the access to methods, data and source codes. Still, the computational environment, an interface between data and source code running analyses, is not addressed. Environments are usually described with software and library names associated with version labels or provided as an opaque container image. This is not enough to describe the complexity of the dependencies on which they rely to operate on. We describe this issue and illustrate how open tools like Guix can be used by any scientist to share their environment and allow peers to reproduce it. Some steps of research might not be fully reproducible, but at least, transparency for computation is technically addressable. These tools should be considered by scientists willing to promote transparency and open science.
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Affiliation(s)
- Nicolas Vallet
- Université de Paris, INSERM U976, F-75010, Paris, France.
| | - David Michonneau
- Université de Paris, INSERM U976, F-75010, Paris, France.,Hematology Transplantation, Saint Louis hospital, 1 avenue Claude Vellefaux, 75010, Paris, France
| | - Simon Tournier
- Université de Paris, INSERM US53, CNRS UAR 2030, Saint Louis Research Institute, 1 avenue Claude Vellefaux, 75010, Paris, France
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Ioannidis JP. Pre-registration of mathematical models. Math Biosci 2022; 345:108782. [DOI: 10.1016/j.mbs.2022.108782] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/13/2022] [Accepted: 01/13/2022] [Indexed: 11/28/2022]
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Bedő J, Di Stefano L, Papenfuss AT. Unifying package managers, workflow engines, and containers: Computational reproducibility with BioNix. Gigascience 2020; 9:giaa121. [PMID: 33205815 PMCID: PMC7672450 DOI: 10.1093/gigascience/giaa121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 04/10/2020] [Indexed: 01/22/2023] Open
Abstract
MOTIVATION A challenge for computational biologists is to make our analyses reproducible-i.e. to rerun, combine, and share, with the assurance that equivalent runs will generate identical results. Current best practice aims at this using a combination of package managers, workflow engines, and containers. RESULTS We present BioNix, a lightweight library built on the Nix deployment system. BioNix manages software dependencies, computational environments, and workflow stages together using a single abstraction: pure functions. This lets users specify workflows in a clean, uniform way, with strong reproducibility guarantees. AVAILABILITY AND IMPLEMENTATION BioNix is implemented in the Nix expression language and is released on GitHub under the 3-clause BSD license: https://github.com/PapenfussLab/bionix (biotools:BioNix) (BioNix, RRID:SCR_017662).
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Affiliation(s)
- Justin Bedő
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde., Parkville, VIC 3052, Australia
- School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leon Di Stefano
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde., Parkville, VIC 3052, Australia
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, 615 N. Wolfe Street, Baltimore, Maryland, U.S.A
| | - Anthony T Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, 1G Royal Pde., Parkville, VIC 3052, Australia
- Peter MacCallum Cancer Centre, 305 Grattan St., Melbourne, VIC 3000, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC 3010, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
- School of Mathematics and Statistics, University of Melbourne, Melbourne, VIC 3010, Australia
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