Chemotherapy resistance in ENKTCL is poorly understood. We hypothesized that integrated omics would uncover molecular drivers of refractoriness to therapy in a topographically diverse series of cases with distinct treatment responses.
We performed WGS(60x), WES(150-300x), and bulk RNA-seq on 52 FFPE tumors and 14 geographically representative healthy PBMCs. Among cases with data, 19 were chemo-sensitive and 18 refractory. Spatial transcriptomics(n=12) was performed using a custom designed 480-gene panel on the Xenium 10x platform, including ~20 EBV-related probes.
WGS and RNA-seq (n=16) revealed distinct genomic copy number alterations (gCNAs): chemo-sensitive (n=10) cases showed more frequent 17q CNAs than refractory (n=6) cases. We identified 67 differentially expressed genes between chemo-sensitive and refractory cases (BH p<0.05), including MYC overexpression in refractory cases (log2FC=1.18, BH p=0.024), increased expression of proliferation (FDR p=4.38e-04) and PI3K-AKT pathway genes (FDR p=0.033). WES showed recurrent JAK/STAT mutations: STAT3(29.8%), STAT5B(14.9%), JAK3(8.5%), and JAK1(4.3%). Mutated epigenetic regulators included KMT2D(25.5%), ARID1A(21.3%), BCOR(17.0%), KMT2C(14.9%), and TP53(21.3%). PI3K mutations were rare and restricted to mutated JAK/STAT cases. STAT3/STAT5B-mutated cases exhibited significantly higher PIK3R3 and PIK3CD expression versus wild-type(p=0.0077,0.034). The MMR pathway was upregulated in enrichment analysis in JAK/STAT-mutated cases (NES=2.88, FDRq-val<0.001).
Novel spatial analysis (n=12) identified 2,122,592 cells from 9 major lineages. EBV-infected NK, B, and mast cells were more abundant in patients with CR to chemotherapy. Tumor-associated macrophages were more abundant in PD and relapse cases.
Unique molecular signatures are linked with therapy response in a topographically diverse global set of endemic and non-endemic ENKTCL patients.
