Defining novel immune biomarkers of prognosis and immunotherapy sensitivity in gastro-oesophageal and colorectal cancers

Abstract

Background Gastro-oesophageal adenocarcinomas (GOAs) frequently recur after resection; prognostic and predictive markers are absent. Mismatch repair-deficient (MMRd) GOAs have high mutational burden, are frequently immunogenic but may acquire immune-evasion mechanisms. T-cell infiltrates have been validated as prognostic markers in colorectal carcinomas (CRCs) and MMRd CRCs are typically highly immunogenic. Outcomes in early-stage MMRd CRCs are more favourable than MMR-proficient (MMRp), whereas late-stage MMRd and MMRp CRC outcomes are similar, suggesting acquisition of immune-evasion mechanisms.

Methods Multi-omic computational analysis of whole exome and target panel DNA- and RNA-sequencing, multicolour immunofluorescence and immunohistochemistry data was performed on cohorts of GOAs and MMRd CRCs respectively.

Results TMA cohorts of surgically-resected, chemotherapy-naïve gastric carcinomas (GCs) were analysed. CD45RO-cell and FOXP3-cell densities predicted Cancer Specific survival (CSS), independent of stage in multivariable analysis and when combined into the Stomach Cancer Immune Score groups, showed highly statistically significant differences. A small subgroup of highly immunogenic GCs showed particularly good CSS. T-cell infiltrates were highest in EBV-positive but similar in MMRd and MMRp GCs. GOAs treated with oxaliplatin, flourouracil, leucovorin, docetaxel and avelumab (FLOT-A) within the ICONIC clinical trial demonstrated treatment efficacy in association with increased PDL-L1 (CPS >5) and increased mutation burden metrics. CD8 T-cell localisation within tumour compartments was predictive of pathological responses to FLOT-A and of progression free survival (PFS). Tumour compartment densities of regulatory T-cells and activated CD8 T-cells were also associated with clinical and pathological outcomes, which is hypothesised to reflect immune-modulation of IFNγ responses and of TGFβ pathways by upregulated BMP7 expression.

POLEM clinical trial and archival cohorts of MMRd CRCs identified high truncal mutation burden and pervasive intratumour heterogenity. WNT/Catenin, MAPk and TGF receptor family genes were almost always truncal. Immune evasion (IE) drivers, such as inactivation of genes involved in antigen presentation or IFNγ signalling, were predominantly subclonal and showed parallel evolution. Phylogenetic analysis identified three distinct patterns of IE driver evolution: pan-tumour evolution, subclonal evolution and evolutionary stasis that significantly correlated with T-cell densities, which were used as a surrogate marker of tumour immunogenicity. PD-L1 was expressed in the tumour microenvironment in most samples and correlated with T-cell densities. However, PD-L1 expression in cancer cells was independent of T-cell densities but strongly associated with loss of the intestinal homeobox transcription factor CDX2, which explains infrequent PD-L1 expression by cancer cells and may contribute to a higher recurrence risk of MMRd CRCs with impaired CDX2 expression.

Conclusion Multi-omic analysis of GOAs and MMRd CRCs has identified immune biomarkers that are hypothesised to predict immunotherapy responses. These should now be tested within larger and on-going clinical trials.