Functional Homologous Recombination Assay on FFPE Specimens of Advanced High-Grade Serous Ovarian Cancer Predicts Clinical Outcomes

Abstract

Purpose: Deficiency in homologous recombination (HR) repair of DNA damage is characteristic of many high-grade serous ovarian cancers (HGSC). It is imperative to identify patients with homologous recombination deficient (HRD) tumors as they are most likely to benefit from platinum-based chemotherapy and PARP inhibitors (PARPi). Existing methods measure historical, not necessarily current HRD, and/or require high tumor cell content which is not achievable for many patients. We set out to develop a clinically feasible assay for identifying functionally HRD tumors that can predict clinical outcomes. Experimental Design: We quantified RAD51, a key HR protein, in immunostained FFPE tumor samples obtained from both chemotherapy-naïve and neoadjuvant chemotherapy (NACT) treated HGSC patients. We defined cut-offs for functional HRD separately for these sample types, classified the patients accordingly as HR-deficient or HR-proficient, and analyzed correlations with clinical outcomes. From the same specimens, genomics-based HRD estimates (HR gene mutations, genomic signatures and genomic scars) were also determined, and compared with functional HR status. Results: Functional HR status significantly predicted several clinical outcomes, including progression-free survival (PFS) and overall survival (OS), when determined from chemo-naïve (PFS p<0.0001; OS p<0.0001) as well as NACT-treated (PFS p<0.0001; OS p=0.0033) tumor specimens. The functional HR test also identified as HRD those PARPi-at-recurrence -treated patients with longer OS (p=0.0188). Conclusions: We developed a functional HR assay performed on routine FFPE specimens, obtained from either chemo-naïve or NACT-treated HGSC patients, that can significantly predict real-world platinum-based chemotherapy and PARPi response.

Patient-derived functional immuno-oncology platform identifies responders to ATR inhibitor and immunotherapy combinations in ovarian cancer

“…However, somatic alterations analysis of the #C218 resistant tumor through WES revealed a deletion spanning from intron 6 to 7 to the middle of exon 10 on chromosome 17 (chr17:g.43092980-43102933del) both in tumor and iPDCs, causing a potential in frame transcript and restoration of BRCA1 activity. In addition, functional HRD test ( 32 ) based on RAD51 foci on the formalin fixed tissue samples of these three tumors showed that the olaparib resistant #C218 sample was HRP while other two samples were found to be HRD, supporting the notion of HR restoration in #C218. Together, the results from scRNA-seq and WES showing enrichment of pathways related to cell cycle, proliferation, and drug resistance, combined with restoration of HR proficiency suggest possible mechanisms of therapy resistance leading to progressive disease in olaparib resistant patient #C218.…”

Chemotherapy induces myeloid-driven spatial T-cell exhaustion in ovarian cancer

“…In addition to newly produced scRNA-seq data from 25 tumors, the scRNA-seq cohort contains data from three clinical specimens originally published in 33 , 21 specimens originally published in 16 , and two specimens originally published in 67 . Genomic HRD annotations were previously published in 24,68,69 , and bulk RNAseq in 70 . The DECIDER study was approved by the Ethics Committee of the Hospital District of Southwest Finland (ETMK 145/1801/2015).…”

Treatment of Ovarian Cancer Beyond PARP Inhibition: Current and Future Options

“…This can be performed on treatment-naive as well as post-chemotherapy specimens with low tumour content, thereby providing dynamic HRD monitoring. Although the assay predicted response to platinum therapy, it lacks prospective validation and predictive value for PARPi therapy [ 28 ].…”