E-Poster Presentation 33rd Lorne Cancer Conference 2021

Whole genome and exome sequencing of a rare ovarian carcinosarcoma identify tumour neoantigens that are targetable with CD8+ T cytotoxic cells. (#168)

Gwo Yaw Ho 1 2 3 , Jessica Wu 2 , Holly Barker 3 4 , Tu Nguyen-Dumont 2 5 , Janet Chang 2 , Peter Eggenhuizen 2 , Jason Stein 2 5 , Tom Manolitsas 1 , Sophia Frentzas 1 , Stafford Fox Rare Cancer 3 , Justin Bedo 3 6 , Cassandra Vandenberg 3 4 , Tony Papenfuss 3 4 , Clare Scott 3 4 , Eva Segelov 1 2 , Joshua Ooi 2
  1. Monash Health, Clayton, VIC, Australia
  2. School of Clinical Sciences, Monash University, Clayton , Victoria
  3. Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
  4. Department of Medical Biology, University of Melbourne, Parkville
  5. Department of Clinical Pathology, University of Melbourne, Parkville
  6. Department of Computing and Information Systems, University of Melbourne, Parkville

Ovarian carcinosarcoma (OCS) are rare, aggressive cancers with poor prognosis due to limited effective treatments1. OCS tumorigenesis is thought to be based on the “conversion hypothesis” of sarcomatous transformation of a differentiated cancer cell-type (carcinoma) into undifferentiated (sarcomatous) malignancy2. It is generally accepted that the transformation is not driven by somatic mutation, but via reprogramming of gene expression. Therefore, the tumour mutation burden (TMB) is often low, with these tumours being relatively non-responsive to single agent immunotherapy, i.e. immunologically “cold”.

Here we describe an OCS pre-clinical model, SFRC01177, where the baseline chemonaïve and recurrent post-adjuvant chemotherapy tumours were initially established subcutaneously in NOD-scid IL2Rgammanull (NSG) mice and then re-established in NSG MHCnull mice. The NSG MHCnull mice are deficient in MHC class I/II expression, thus lacking acute graft-versus-host disease following injection of human peripheral mononuclear cells3. The tumour in vivo platinum-refractory response was consistent with the patient’s clinical outcome.

Whole genome sequencing was performed on the baseline tumour. Whole exome sequencing (WES) and RNA sequencing (RNAseq) were performed on both the baseline and the recurrent tumours for tumour neoantigen (TNA) discovery. Despite a low TMB of <4 mutations/Mb, 2871 predicted neoantigens have been identified in-silico to bind to the patient’s human leukocyte antigen (HLA) class I complexes and thus presented to CD8+ T-cytotoxic cells. The stability of the neoantigen expression will be confirmed by comparing WES/RNAseq data between the baseline and the recurrent tumour. This TNA expression profile will be crucial for TNA selection to be used as cancer-specific markers to direct CD8+ T-cell activity.

Utilising newly developed single-cell T-cell receptor (TCR) sequencing protocols, high affinity TCRs will be identified and lentivirally transduced onto CD8+ T cells. The cytotoxic capability of these genetically modified CD8+ T-cells will be assessed using the OCS NSG MHCnull PDX model. This approach, using the TNA to manufacture tumour-specific CD8+ T-cells, offers a novel personalised cell-based therapy to treat immunologically “cold” tumours.

  1. Rauh-Hain, J.A., Birrer, M. & Del Carmen, M.G. "Carcinosarcoma of the ovary, fallopian tube, and peritoneum: Prognostic factors and treatment modalities". Gynecol Oncol 142, 248-254 (2016).
  2. Zhao, S., et al. Mutational landscape of uterine and ovarian carcinosarcomas implicates histone genes in epithelial-mesenchymal transition. Proc Natl Acad Sci U S A 113, 12238-12243 (2016).
  3. Brehm, M.A., et al. Lack of acute xenogeneic graft- versus-host disease, but retention of T-cell function following engraftment of human peripheral blood mononuclear cells in NSG mice deficient in MHC class I and II expression. FASEB J 33, 3137-3151 (2019).