Myeloid cell states determine reinstatement of original immune environments in recurrent ovarian cancer

Immunotherapy has produced disappointing results in recurrent ovarian cancer (OC). However, the prognostic value of tumour-infiltrating lymphocytes (TILs) is grounded on the analysis of treatment-naive tumours. To understand the immunobiology of recurrent cancers, and their evolution, we profiled 170 patient-matched primary-recurrent OC samples from 69 patients of two independent cohorts. By capturing heterogeneous TIL distributions, we identified four immune phenotypes associated with differential prognosis, TILs states and TILs:myeloid networks, which dictate malignant evolution after chemotherapy and recurrence. Notably, recurrent tumours recapitulate the immunogenic patterns of original cancers. Mirroring inflamed human OC, preclinical recurrent Brca1mut tumours maintained activated TILs:dendritic cells (DCs) niches and immunostimulatory tumour-associated macrophages (TAMs). Conversely, recurrent Brca1wt tumours displayed loss of TILs:DCs niches and accumulated immunosuppressive myeloid networks featuring Trem2/ApoEhigh TAMs and Nduf4l2high/Galectin3high malignant states. Our study highlights that persistent immunogenicity in recurrent OC is governed by the crosstalk between dissimilar myeloid cells and TILs, which is BRCA-dependent. scRNA-seq of mouse ovarian cancer models: Trp53-/- Brca1-/- (hereby referred as Brca1mut) or Trp53-/- Brca1+/+ (or Brca1wt). We characterized solid tumors at baseline (referred as primary tumors) and relapse after chemotherapy treatment (referred as recurrent tumors). Therefore, the experiment included 4 arms and the single-cell samples belonging to each arm are assigned below: Brca1wt primary: group BRCA-A (mice A1-A5 and A_pooled) and group BRCA-B (mice B7-B10 and B_pooled). Brca1wt recurrent: group BRCAP1 (mice P1_3, P1_13, and P1_pooled) and group BRCAP2 (mice P2_1, P2_47, and P2_pooled). Brca1mut primary: group BRCA-C (mice C11-C15 and C_pooled) and group BRCA-D (mice D16-D20 and D_pooled). Brca1mut recurrent: group BRCAB1 (mice B1_21, B1_23, and B1_pooled) and group BRCAB2 (mice B2_28, B2_29, and B2_pooled). Note: This represents a multiplexed sc RNAseq assay (see methods). Most cells were successfully de-multiplexed to individual mice. Unassigned cells from each group of the corresponding experimental arm were grouped as additional "pooled" sc samples.