The tumor microenvironment and immune infiltration landscape of KRAS mutant pancreatic ductal adenocarcinomas (PDAC) compared to colorectal adenocarcinomas (CRC).
Authors: Lou Emil , Xiu Joanne , Baca Yasmine , Walker Phillip , Manji Gulam Abbas , Gholami Sepideh , Saeed Anwaar , Philip Philip Agop , Prakash Ajay , Astsaturov Igor A. , Botta Greg , Abushahin Laith I. , Sohal Davendra , Lenz Heinz-Josef , Shields Anthony Frank , Nabhan Chadi , El-Deiry Wafik S. , Seeber Andreas , Korn Wolfgang Michael 
Published: June 2022

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Background: The composition of the tumor microenvironment (TME) in PDACs is more heavily driven by mutant (mt) KRAS than any other cancer. How genomic alterations of PDAC including KRAS status affect the immune cell (IC) landscape remains unclear. Thus, we characterized IC types and the prevalence of immuno-oncologic (IO) biomarkers in PDAC by genomic and transcriptomic analysis, and investigated associations of mt KRAS with IC estimates in the TME. Our findings were compared to our previous study in CRC. Methods: A total of 4,142 PDAC and 3,727 CRC with KRAS- mts were analyzed using next-generation DNA sequencing (NextSeq, 592 gene panel or NovaSeq, WES), IHC, and whole transcriptome RNA sequencing (NovaSeq) (Caris Life Sciences, Phoenix, AZ). MSI/MMR was tested by FA, IHC and NGS. TMB-H was classified based on a cut-off of >10 mutations per MB. ICs were estimated by QuantiSeq (Finotello 2019, Genome Medicine) or MCP counter (Betcht 2016, Genome Biology). Significance was determined by X2 and Fisher-Exact and p-adjusted for multiple comparisons (q<0.05). Results: Mutant KRAS was seen in 81% of PDAC and in 48% of CRC. The most common variant was G12D, comprising 43% and 32% of all PDAC and CRC KRAS variants, respectively. The therapeutically actionable KRAS G12C variant comprises 2% and 7% of PDAC and CRC in this cohort, respectively. In PDAC, KRAS mt was associated with lower prevalence of MSI-H/dMMR than KRAS-wildtype (wt); 0.9% vs 1.9%, p=0.027). PDL1 expression was significantly lower in KRAS wt (12%) compared to G12D (19%) and G13X (33%), similar to previous observations in CRC. However, when considering TMB, in PDAC, G12D (1%), G12V (1%) and Q61 (1%) mutations had significantly lower TMB-H than RAS wt tumors (4%); in contradiction to CRC. The immune cell environment of KRAS mt PDAC showed significantly higher infiltration with M1 macrophages and cancer-associated fibroblasts (CAFs), as well as lower M2 macrophages, CD4+ & CD8+ T cells, T-reg, NK, myeloid dendritic and endothelial cells compared to KRAS wt. In CRC, a similar pattern was observed but more pronounced in PDAC. Immune-regulatory markers, were among multiple genes downregulated in KRAS-mt PDAC, including CTLA-4 and LAG3. Overall changes were most pronounced in cases harboring KRAS G12D, G12V, Q61, and rare KRAS variants. Conclusions: The TME of KRAS mt PDAC shows IC patterns similar to KRAS mt CRC. Actionable IO-targets, such as PDL1, are enriched in tumors harboring specific variants of KRAS mt PDAC including the targetable G12C variant. If G12D becomes druggable, it could be targetable in 35% patients with PDAC or 15% in CRC. These results demonstrate that the TME of PDAC and CRC shows immune-cold features. Tailored immunotherapeutic strategies would have to overcome these barriers in KRAS mt PDAC and CRC, possibly in combination with molecularly targeted treatment strategies.