Spatially restricted tumour-associated and host-associated immune drivers correlate with the recurrence sites of pancreatic cancer

Abstract

ObjectiveMost patients with pancreatic ductal adenocarcinoma (PDAC) will experience recurrence after resection. Here, we investigate spatially organised immune determinants of PDAC recurrence.DesignPDACs (n=284; discovery cohort) were classified according to recurrence site as liver (n=93/33%), lung (n=49/17%), local (n=31/11%), peritoneal (n=38/13%) and no-recurrence (n=73/26%). Spatial compartments were identified by fluorescent imaging as: pancytokeratin (PanCK)+CD45−(tumour cells); CD45+PanCK-(leucocytes) and PanCK-CD45-(stromal cells), followed by transcriptomic (72 genes) and proteomic analysis (51 proteins) for immune pathway targets. Results from next-generation sequencing (n=194) were integrated. Finally, 10 tumours from each group underwent immunophenotypic analysis by multiplex immunofluorescence. A validation cohort (n=109) was examined in parallel.ResultsNo-recurrent PDACs show high immunogenicity, adaptive immune responses and are rich in pro-inflammatory chemokines, granzyme B and alpha-smooth muscle actin+fibroblasts. PDACs with liver and/or peritoneal recurrences display low immunogenicity, stemness phenotype and innate immune responses, whereas those with peritoneal metastases are additionally rich in FAP+fibroblasts. PDACs with local and/or lung recurrences display interferon-gamma signalling and mixed adaptive and innate immune responses, but with different leading immune cell population. Tumours with local recurrences overexpress dendritic cell markers whereas those with lung recurrences neutrophilic markers. Except the exclusive presence ofRNF43mutations in the no-recurrence group, no genetic differences were seen. The no-recurrence group exhibited the best, whereas liver and peritoneal recurrences the poorest prognosis.ConclusionsOur findings demonstrate distinct inflammatory/stromal responses in each recurrence group, which might affect dissemination patterns and patient outcomes. These findings may help to inform personalised adjuvant/neoadjuvant and surveillance strategies in PDAC, including immunotherapeutic modalities.

Network dynamics and therapeutic aspects of mRNA and protein markers with the recurrence sites of pancreatic cancer

“…We focused on reported genes and proteins identified in Ref. [ 35 ]. In the Discovery data set, the FAP-alpha – SMA protein connection occurred in both PDACs with lung and no recurrences.…”

“…We have used publicly available data sets to perform the analysis. Gene expression, protein abundance, and clinical data constituted the cohorts we considered as Discovery and Validation 1, and were previously published [ 35 ]. The gene expression matrices employed in this study were obtained from GEO ( https://www.ncbi.nlm.nih.gov/gds/?term= ) and TCGA ( https://www.cancer.gov/ccg/research/genome-sequencing/tcga ) database repositories, and accessed on May 12, 2023 and May 29, 2023, respectively.…”

“…We used Spearman's rank correlation to explore associations between genes and proteins [ 35 ]. Reported genes (HLA-DQ, ITGAM, LY6E, CCL5, CD44, CXCL10 and PECAM1) and proteins (STING, CD66b, CD11c, α[SMA], FAP-alpha AND GZMB) with the highest discriminative ability across the PDAC recurrence groups from Ref.…”

“…Spatially organised multi-omics PDAC data sets with distinct recurrence patterns (including, liver, local, lung, peritoneal and no recurrence) were used in previous analyses and differential activation of immune pathway-related genes and unique stromal/inflammatory responses in the PDAC tumour microenvironment (TME) have were revealed as key players for distinct PDAC recurrence patterns [ [35] , [36] , [37] ]. However, the molecular mechanisms underpinning PDAC recurrence patterns are yet to be fully identified.…”

High‐resolution and quantitative spatial analysis reveal intra‐ductal phenotypic and functional diversification in pancreatic cancer

“…Bulk NGS and, more recently, single-cell sequencing, spatial profiling, and AI-based histology have revealed the complexity of human PDAC [2][3][4][5][6]20,[24][25][26][27][28][29][30], with an emphasis on transcriptomic subtypes and the tumour microenvironment (TME) with different CAF subtypes and immune-suppressive cells. However, we perceived a lack of in situ assessment of point mutations (in particular those of KRAS that were reported to be amplified in subsets of aggressive patient tumours [3,10,36]) and, beyond GATA6, reliable markers that captured the two consensus transcriptomic subtypes in situ.…”