Ovarian cancer mutational processes drive site-specific immune evasion

Abstract

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability1–4 patterned by distinct mutational processes5,6, tumour heterogeneity7–9 and intraperitoneal spread7,8,10. Immunotherapies have had limited efficacy in HGSOC11–13, highlighting an unmet need to assess how mutational processes and the anatomical sites of tumour foci determine the immunological states of the tumour microenvironment. Here we carried out an integrative analysis of whole-genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumour sites from 42 treatment-naive patients with HGSOC. Homologous recombination-deficient HRD-Dup (BRCA1 mutant-like) and HRD-Del (BRCA2 mutant-like) tumours harboured inflammatory signalling and ongoing immunoediting, reflected in loss of HLA diversity and tumour infiltration with highly differentiated dysfunctional CD8+ T cells. By contrast, foldback-inversion-bearing tumours exhibited elevated immunosuppressive TGFβ signalling and immune exclusion, with predominantly naive/stem-like and memory T cells. Phenotypic state associations were specific to anatomical sites, highlighting compositional, topological and functional differences between adnexal tumours and distal peritoneal foci. Our findings implicate anatomical sites and mutational processes as determinants of evolutionary phenotypic divergence and immune resistance mechanisms in HGSOC. Our study provides a multi-omic cellular phenotype data substrate from which to develop and interpret future personalized immunotherapeutic approaches and early detection research.

Exploiting allele-specific transcriptional effects of subclonal copy number alterations for genotype-phenotype mapping in cancer cell populations

“…We next investigated TreeAlign’s performance on real-world patient derived data from high grade serous ovarian cancer (HGSC). We first applied TreeAlign on single cell sequencing data from a HGSC patient (patient 022) 7 . Tumor samples were obtained from both left and right adnexa sites of the patient.…”

“…Samples were collected under Memorial Sloan Kettering Cancer Center’s institutional IRB protocol 15-200 and 06-107. Single cell suspensions from surgically excised tissues were generated and flow sorted on CD45 to separate the immune component as previously described 7 . CD45 negative fractions were then sequenced using the DLP+ platform as previously described 1,30,38 .…”

“…scRNA data were processed as previously described 7 . Read alignment and barcode filtering were performed by CellRanger v.3.1.0.…”

“…We obtained matched scRNA and scDNA from two HGSC patients (patient 022 and patient 081) from the MSK SPECTRUM cohort 7 . Samples were collected under Memorial Sloan Kettering Cancer Center's institutional IRB protocol 15-200 and 06-107.…”

“…Recent reports on the extent of cell-to-cell variation of CNAs in tumors (including in well understood oncogenes) 1 raises the critical question of how granular subpopulations are phenotypically impacted by subclonal CNAs. Importantly, phenotypic impact of subclonal CNAs can have cell intrinsic effects and act as cell-extrinsic determinants of the tumor microenvironment 7 , further illustrating the importance of dissecting how CNAs modulate intra-tumor heterogeneity.…”