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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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Barker HE, Lim R, Carmagnac A, Vandenberg C, Ratnayake G, Dall G, Milesi B, Komiti A, O'Grady E, Tram J, Stewart KP, Bedo J, Penington J, Vissers J, Grimmond S, Wakefield M, Papenfuss T, Scott C. Abstract PO037: Identifying effective combinations of targeted therapies, using novel pre-clinical models, to improve treatment options for high-grade serous endometrial cancer. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.endomet20-po037] [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
High-grade serous endometrial carcinoma (HGSEC) accounts for just 10% of endometrial cancer (EC) cases but is responsible for at least 40% of all EC-related deaths. It typically arises in post-menopausal women, with 70% of patients presenting with stage III or IV disease, does not respond to hormone therapy unlike the less aggressive forms of EC, and has a lower overall survival rate of just 18-27%, which has not improved over the past two decades. The primary treatment for HGSEC is surgery, followed by a combination of standard chemotherapies (platinum and taxane) with or without localised radiotherapy. However, recurrent HGSEC is less responsive to chemotherapy than are other subtypes of EC and even initial responses to chemotherapy are poor. Therefore, there is a great unmet clinical need to find better treatment options for women with this aggressive cancer. Apart from TP53 (mutated in up to 90% of cases), the other most frequently mutated genes in HGSEC are PPP2R1A (31%), PIK3CA (22%), FBXW7 (28%), CHD4 (17%) and BRCA2 (12%). Focal amplifications of the genes MYC, ERBB2, CCNE1, FGFR3 and SOX17 are also common. The presence of ERBB2 amplification and/or HER2 over-expression in around 30% of HGSEC suggests these patients may respond to HER2-targeting drugs, such as trastuzumab. However, only modest benefit has so far been seen for single-agent HER2-targeted therapies (ie trastuzumab or lapatinib) against HGSEC, suggesting resistance mechanisms are present. Another feature of HGSEC that could be exploited therapeutically is homologous recombination deficiency (HRD), which may be targeted with PARP inhibitors (PARPi). It is not clear what proportion of HGSEC are HRD and neither HER2-targeting drugs or PARPi have been approved for the treatment of HGSEC. Due to its rarity and a lack of pre-clinical models, HGSEC has so far been understudied, resulting in a lack of effective treatment options. We currently have 33 HGSEC patients consented to the WEHI-Stafford Fox Rare Cancer Program and have developed pre-clinical models from fresh patient tumour samples received (4 patient-derived xenograft (PDX) models validated, with 3 pending). Preliminary molecular analysis of whole-genome sequencing (5 samples, one of which gave rise to a PDX model), whole-exome sequencing (4 samples), and cancer panel sequencing (3 samples, 2 of which gave rise to PDX models; one harbouring ERBB2 amplification and one harbouring an AKT mutation) data from our HGSEC cohort has been performed. This has identified potential treatment targets, including ERBB2 amplifications and mutations in HR genes. I am using the PDX models for initial in vivo therapeutic characterization studies and to develop organoid models for use in high-throughput drug assays in vitro. This will guide subsequent novel drug combination testing in our PDX models. By combining specific targeted drugs I hope to overcome de novo resistance mechanisms and prevent acquired resistance. Results from this study will guide future decisions about therapeutic strategies to improve survival of women with HGSEC.
Citation Format: Holly E. Barker, Ratana Lim, Amandine Carmagnac, Cassandra Vandenberg, Gayanie Ratnayake, Genevieve Dall, Briony Milesi, Angela Komiti, Emily O'Grady, Joshua Tram, Kym Pham Stewart, Justin Bedo, Jocelyn Penington, Joep Vissers, Sean Grimmond, Matthew Wakefield, Tony Papenfuss, Clare Scott. Identifying effective combinations of targeted therapies, using novel pre-clinical models, to improve treatment options for high-grade serous endometrial cancer [abstract]. In: Proceedings of the AACR Virtual Special Conference: Endometrial Cancer: New Biology Driving Research and Treatment; 2020 Nov 9-10. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(3_Suppl):Abstract nr PO037.
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Affiliation(s)
- Holly E. Barker
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Ratana Lim
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Amandine Carmagnac
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Cassandra Vandenberg
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | | | - Genevieve Dall
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Briony Milesi
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Angela Komiti
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Emily O'Grady
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Joshua Tram
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | | | - Justin Bedo
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Jocelyn Penington
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Joep Vissers
- 3The University of Melbourne, Melbourne, VIC, Australia
| | - Sean Grimmond
- 3The University of Melbourne, Melbourne, VIC, Australia
| | - Matthew Wakefield
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Tony Papenfuss
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
| | - Clare Scott
- 1The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia,
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Dall G, Vandenberg C, Carmagnac A, Lim R, Milesi B, Komiti A, O'Grady E, Tram J, Ratnayake G, Stewart KP, Bedo J, Penington J, Vissers J, Olesen I, Grimmond S, Barker H, Papenfuss T, Scott C. Abstract PO021: Developing pre-clinical models of uterine leiomyosarcoma. Clin Cancer Res 2021. [DOI: 10.1158/1557-3265.endomet20-po021] [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
Uterine sarcomas make up 1-4% of uterine malignancies. Of these 60% are classified as leiomyosarcoma (uLMS). The 5-year survival rate of uLMS is 35-65.2% for tumours that have not spread beyond the uterus. However, women are often diagnosed at a late stage due to a lack of screening options by which time the tumour has often spread to adjacent and distant tissues. Current standard of care for uLMS patients is surgical de-bulking followed by adjuvant chemotherapy, but significant improvement in progression free survival and overall survival is not consistently observed. The lack of advances for the treatment and screening of uLMS is due in part to the scarcity of appropriate research resources for this rare disease. Genetic analyses have been performed but on relatively small samples and there are just 14 reported patient-derived xenograft (PDX) models of uLMS in the literature to date. Through the WEHI Stafford Fox Rare Cancer Program, as well as collaborations (facilitated by ANZGOG) throughout the country and internationally, we have access to a large biobank of uLMS tissue. We have received 8 fresh uLMS samples in the laboratory, 2 of which have established PDX lines that were validated as uLMS by our anatomical pathologist. All fresh samples received into the laboratory are snap frozen for whole-genome sequencing as well as viably frozen to enable regeneration of the tissue for future applications. One application is organoid culturing, which allows the tissue to retain its 3D growth properties and is significantly cheaper than growing tissue as a PDX. Organoid culturing also allows for higher throughput of samples in drug screening assays, enabling us to fast-track the selection of drugs for validation in our PDX models. In addition to these fresh samples we also have 23 archival uLMS samples (formalin fixed, paraffin embedded) that can be used for lower coverage genetic analysis, and protein expression by immunohistochemistry. This unique biobank of uLMS tissue is the first of its kind in Australia and with it we will endeavour to gain a comprehensive understanding of this disease. Through our PDX modelling we also have the opportunity to predict resistance to therapy and test emerging therapies in a clinically relevant context. We believe this biobank will provide a critical resource which will ultimately lead to better outcomes for uLMS patients.
Citation Format: Genevieve Dall, Cassandra Vandenberg, Amandine Carmagnac, Ratana Lim, Briony Milesi, Angela Komiti, Emily O'Grady, Joshua Tram, Gayanie Ratnayake, Kym Pham Stewart, Justin Bedo, Jocelyn Penington, Joep Vissers, Inger Olesen, Sean Grimmond, Holly Barker, Tony Papenfuss, Clare Scott. Developing pre-clinical models of uterine leiomyosarcoma [abstract]. In: Proceedings of the AACR Virtual Special Conference: Endometrial Cancer: New Biology Driving Research and Treatment; 2020 Nov 9-10. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(3_Suppl):Abstract nr PO021.
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Affiliation(s)
- Genevieve Dall
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Cassandra Vandenberg
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Amandine Carmagnac
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Ratana Lim
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Briony Milesi
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Angela Komiti
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Emily O'Grady
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Joshua Tram
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | | | | | - Justin Bedo
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Jocelyn Penington
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Joep Vissers
- 3University of Melbourne, Parkville, VIC, Australia
| | - Inger Olesen
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | | | - Holly Barker
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Tony Papenfuss
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
| | - Clare Scott
- 1Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia,
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