Integrated Genomic and Immunophenotypic Classification of Pancreatic Cancer Reveals Three Distinct Subtypes with Prognostic/Predictive Significance

Abstract

Current clinical classification of pancreatic ductal adenocarcinoma (PDAC) is unable to predict prognosis or response to chemo- or immunotherapy and does not take into account the host reaction to PDAC cells. Our aim is to classify PDAC according to host- and tumor-related factors into clinically/biologically relevant subtypes by integrating molecular and microenvironmental findings. A well-characterized PDAC cohort ( = 110) underwent next-generation sequencing with a hot spot cancer panel while next-generation tissue microarrays were immunostained for CD3, CD4, CD8, CD20, PD-L1, p63, hyaluronan-mediated motility receptor (RHAMM), and DNA mismatch repair proteins. Previous data on FOXP3 were integrated. Immune cell counts and protein expression were correlated with tumor-derived driver mutations, clinicopathologic features (TNM 8th edition, 2017), survival, and epithelial-mesenchymal transition (EMT)-like tumor budding. Three PDAC subtypes were identified: the "immune escape" (54%), poor in T and B cells and enriched in FOXP3 regulatory T cells (Treg), with high-grade budding, frequent ,, and mutations, and poor outcome; the "immune rich" (35%), rich in T and B cells and poorer in FOXP3 Tregs, with infrequent budding, lower and mutation rate, and better outcome and a subpopulation with tertiary lymphoid tissue (TLT), mutations in DNA damage response genes ( and ), and the best outcome; and the "immune exhausted" (11%), with immunogenic microenvironment and two subpopulations-one with PD-L1 expression and a high mutation rate and a microsatellite-unstable subpopulation with a high prevalence of mutations. The combination of low budding, low stromal FOXP3 counts, presence of TLTs, and absence of mutations confers significant survival advantage in patients with PDAC. Immune host responses correlate with tumor characteristics, leading to morphologically recognizable PDAC subtypes with prognostic/predictive significance. .

Comprehensive characterisation of pancreatic ductal adenocarcinoma with microsatellite instability: histology, molecular pathology and clinical implications

“…44 Regarding the presence of any potential specific driver genes in MSI/dMMR PDAC, we found a bi-univocal correspondence regarding genes belonging to the JAK/STAT pathway and those of KMT2 family. Indeed, these have been described as frequently mutated in MSI/dMMR cancers of different extrapancreatic sites 45 46 ; the review of all molecular data of MSI/ dMMR PDAC showed the involvement of the JAK/STAT pathway also in MSI/dMMR PDAC, given that the paper by Wartenberg et al, 39 reported a higher mutation rate of JAK3 specifically in this genetic subgroup (3/5 MSI/dMMR cases vs 4/105 microsatellite-stable PDAC, p<0.01, Fisher's exact test; all these cases were KRAS mutated), and in the paper by Singhi et al, two of the three reported MSI/dMMR PDAC harboured a JAK1 mutation (2/3 MSI/dMMR PDAC vs 0/608 microsatellitestable PDAC with actionable targets, p<0.01, Fisher's exact test). 44 Furthermore, we found that alterations affecting the KMT2 family were involved as well, since 3/3 MSI/dMMR cases described by Singhi et al harboured KMT2 mutations (two cases with KMT2D and one case KMT2C mutation; 3/3 KMT2 mutated MSI/dMMR PDAC vs 32/608 KMT2 mutated microsatellite-stable PDAC with actionable targets, p<0.01, Fisher's exact test; the MSI/dMMR and KMT2 mutated cases were KRAS wild type).…”

Prognostic and predictive factors in pancreatic cancer

“…The presence of tumor budding in surgical samples has been clearly described to be related to advanced pT classification, lymphatic invasion, decreased disease-free and overall survival (DFS; OS) [13]. A correlation between the grade of tumor budding and the immune system invasion has been reported, with high grade of tumor budding being associated with FOXP3+ regulatory T cells invasion and worse prognosis [19].…”

Integrated clinicomolecular characterization identifies RAS activation and CDKN2A deletion as independent adverse prognostic factors in cancer of unknown primary

“…Deletion of CDKN2A and KRAS mutations were reported as adverse prognostic markers throughout a plethora of diverse malignancies . Thus, poor prognosis associated with CDKN2A deletion and KRAS activation appears as a recurrent feature of a broad spectrum of malignancies.…”

“…12 Deletion of CDKN2A and KRAS mutations were reported as adverse prognostic markers throughout a plethora of diverse malignancies. [21][22][23][24][25][26][27][28][29] Thus, poor prognosis associated with CDKN2A deletion and KRAS activation appears as a recurrent feature of a broad spectrum of malignancies. As CUP may arise from any organ site, it is plausible that these negative prognostic effects observed in other cancer entities are also reflected in CUP.…”