Concurrent RB1 loss and BRCA-deficiency predicts enhanced immunological response and long-term survival in tubo-ovarian high-grade serous carcinoma

• Authors: Susan J. Ramus, University of NSW Sydney; David D. L. Bowtell, Peter MacCallum Cancer Centre; Dale W. Garsed, Peter MacCallum Cancer Centre; Flurina A. M. Saner, Peter MacCallum Cancer Centre; Kazuaki Takahashi, Peter MacCallum Cancer Centre; Timothy Budden, University of NSW Sydney; Ahwan Pandey, Peter MacCallum Cancer Centre; Dinuka Ariyaratne, Peter MacCallum Cancer Centre; Tibor A. Zwinpfer, Peter MacCallum Cancer Centre; Nicola S. Meagher, University of NSW Sydney; Sian Fereday, Peter MacCallum Cancer Centre; Laura Twomey, Peter MacCallum Cancer Centre; Kathleen I. Pishas, Peter MacCallum Cancer Centre; Therese Hoang, Peter MacCallum Cancer Centre; Adelyn Bolithon, University of NSW Sydney; Nadia Traficante, Peter MacCallum Cancer Centre; Kathryn Alsop, Peter MacCallum Cancer Centre; Elizabeth L. Christie, Peter MacCallum Cancer Centre; Eun-Young Kang, University of Calgary; Gregg S. Nelson, University of Calgary; Prafull Ghatage, University of Calgary; Cheng-Han Lee, University of Alberta; Marjorie J. Riggan, Duke University; Jennifer Alsop, University of Cambridge; Matthias W. Beckmann, University Hospital Erlangen; Jessica Boros, Westmead Institute for Medical Research; Alison H. Brand, Westmead Hospital; Angela Brooks-Wilson, Canada’s Michael Smith Genome Sciences Centre; Michael E. Carney, University of Hawaii; Penny Coulson, Institute of Cancer Research; Madeleine Courtney-Brooks, University of Pittsburgh; Kara L. Cushing-Haugen, Fred Hutchinson Cancer Center; Cezary Cybulski, Pomeranian Medical University; Mona A. El-Bahrawy, Imperial College London; Esther Elishaev, University of Pittsburgh; Ramona Erber, University Hospital Erlangen; Simon A. Gayther, Cedars-Sinai Medical Center; Aleksandra Gentry-Maharaj, University College London; C. Blake Gilks, University of British Columbia; Paul R. Harnett, University of Sydney; Holly R. Harris, Fred Hutchinson Cancer Center; Arndt Hartmann, University Hospital Erlangen; Alexander Hein, University Hospital Erlangen; Joy Hendley, Peter MacCallum Cancer Centre; Brenda Y. Hernandez, University of Hawaii; Anna Jakubowska, Pomeranian Medical University; Mercedes Jimenez-Linan, Addenbrooke’s Hospital; Michael E. Jones, Institute of Cancer Research; Scott H. Kaufmann, Mayo Clinic, Rochester; Catherine J. Kennedy, Westmead Institute for Medical Research; Tomasz Kluz, Medical College of Rzeszow University; Jennifer M. Koziak, Alberta Health Services-Cancer Care; Bjorg Kristjansdottir, University of Gothenburg; Nhu D. Le, BC Cancer Agency; Marcin Lener, Pomeranian Medical University in Szczecin; Jenny Lester, University of California Los Angeles; Jan Lubinski, Pomeranian Medical University; Constantina Mateoiu, University of Gothenburg; Sandra Orsulic, University of California Los Angeles; Matthias Ruebner, University Hospital Erlangen; Minouk J. Schoemaker, University of Pittsburgh; Mitul Shah, University of Cambridge; Raghwa Sharma, Westmead Hospital; Mark E. Sherman, Mayo Clinic, Jacksonville; Yurii B. Shvetsov, University of Hawaii; Naveena Singh, University of British Columbia; T. Rinda Soong, University of Pittsburgh; Helen Steed, University of Alberta; Paniti Sukumvanich, University of Pittsburgh; Aline Talhouk, University of British Columbia; Sarah E. Taylor, University of Pittsburgh; Robert A. Vierkant, Mayo Clinic, Rochester; Chen Wang, Mayo Clinic, Rochester; Martin Widschwendter, University of Innsbruck; Lynne R. Wilkens, University of Hawaii; Stacey J. Winham, Mayo Clinic, Rochester; Michael S. Anglesio, University of British Columbia; Andrew Berchuck, Duke University; James D. Brenton, University of Cambridge; Ian Campbell, Peter MacCallum Cancer Centre; Linda S. Cook, University of Colorado; Jennifer A. Doherty, University of Utah; Peter A. Fasching, University Hospital Erlangen; Renee T. Fortner, German Cancer Research Center; Marc T. Goodman, Cedars-Sinai Medical Center; Jacek Gronwald, Pomeranian Medical University; David G. Huntsman, University of British Columbia; Beth Y. Karlan, University of California Los Angeles; Linda E. Kelemen, South Carolina Department of Health & Environmental Control; Usha Menon, University College London; Francesmary Modugno, University of Pittsburgh; Paul D. P. Pharoah, University of Cambridge; Joellen Martha Schildkraut, Emory University; Karin Sundfeldt, University of Gothenburg; Anthony J. Swerdlow, Institute of Cancer Research; Ellen L. Goode, Mayo Clinic, Rochester; Anna DeFazio, University of Sydney; Martin Kobel, University of Calgary
• Journal Title: medRxiv
• Publisher: NIH | 2023-11-10
• Type of Work: Article | Preprint: Prior to Peer Review
• Publisher DOI: http://doi.org/10.1101/2023.11.09.23298321
• Subjects: Biology, Genetics; Health Sciences, Oncology
• Keywords: tumor suppressor; RB1; tubo-ovarian high-grade serous carcinoma; HGSC; co-occurance; homologous recombination DNA repair genes; BRCA1; BRCA2

Abstract

Background: Somatic loss of the tumour suppressor RB1 is a common event in tubo-ovarian high-grade serous carcinoma (HGSC), which frequently co-occurs with alterations in homologous recombination DNA repair genes including BRCA1 and BRCA2 (BRCA). We examined whether tumour expression of RB1 was associated with survival across ovarian cancer histotypes (HGSC, endometrioid (ENOC), clear cell (CCOC), mucinous (MOC), low-grade serous carcinoma (LGSC)), and how co-occurrence of germline BRCA pathogenic variants and RB1 loss influences long-term survival in a large series of HGSC. Patients and methods: RB1 protein expression patterns were classified by immunohistochemistry in epithelial ovarian carcinomas of 7436 patients from 20 studies participating in the Ovarian Tumor Tissue Analysis consortium and assessed for associations with overall survival (OS), accounting for patient age at diagnosis and FIGO stage. We examined RB1 expression and germline BRCA status in a subset of 1134 HGSC, and related genotype to survival, tumour infiltrating CD8+ lymphocyte counts and transcriptomic subtypes. Using CRISPR-Cas9, we deleted RB1 in HGSC cell lines with and without BRCA1 mutations to model co-loss with treatment response. We also performed genomic analyses on 126 primary HGSC to explore the molecular characteristics of concurrent homologous recombination deficiency and RB1 loss. Results: RB1 protein loss was most frequent in HGSC (16.4%) and was highly correlated with RB1 mRNA expression. RB1 loss was associated with longer OS in HGSC (hazard ratio [HR] 0.74, 95% confidence interval [CI] 0.66–0.83, P = 6.8 ×10−7), but with poorer prognosis in ENOC (HR 2.17, 95% CI 1.17–4.03, P = 0.0140). Germline BRCA mutations and RB1 loss co-occurred in HGSC (P < 0.0001). Patients with both RB1 loss and germline BRCA mutations had a superior OS (HR 0.38, 95% CI 0.25–0.58, P = 5.2 ×10−6) compared to patients with either alteration alone, and their median OS was three times longer than non-carriers whose tumours retained RB1 expression (9.3 years vs. 3.1 years). Enhanced sensitivity to cisplatin (P < 0.01) and paclitaxel (P < 0.05) was seen in BRCA1 mutated cell lines with RB1 knockout. Among 126 patients with whole-genome and transcriptome sequence data, combined RB1 loss and genomic evidence of homologous recombination deficiency was correlated with transcriptional markers of enhanced interferon response, cell cycle deregulation, and reduced epithelial-mesenchymal transition in primary HGSC. CD8+ lymphocytes were most prevalent in BRCA-deficient HGSC with co-loss of RB1. Conclusions: Co-occurrence of RB1 loss and BRCA mutation was associated with exceptionally long survival in patients with HGSC, potentially due to better treatment response and immune stimulation.