Spatial profiling of gastric cancer patient-matched primary and locoregional metastases reveals principles of tumour dissemination

Abstract

Objective Endoscopic mucosal biopsies of primary gastric cancers (GCs) are used to guide diagnosis, biomarker testing and treatment. Spatial intratumoural heterogeneity (ITH) may influence biopsy-derived information. We aimed to study ITH of primary GCs and matched lymph node metastasis (LNmet). Design GC resection samples were annotated to identify primary tumour superficial (PTsup), primary tumour deep (PTdeep) and LN met subregions. For each subregion, we determined (1) transcriptomic profiles (NanoString 'PanCancer Progression Panel', 770 genes); (2) next-generation sequencing (NGS, 225 gastrointestinal cancer-related genes); (3) DNA copy number profiles by multiplex ligation-dependent probe amplification (MLPA, 16 genes); and (4) histomorphological phenotypes. Results NanoString profiling of 64 GCs revealed no differences between PT sup1 and PT (sup2), while 43% of genes were differentially expressed between PT sup versus PTdeep and 38% in PT (sup) versus LNmet. Only 16% of genes were differently expressed between PTdeep and LNmet. Several genes with therapeutic potential (eg IGF1, PIK3CD and TGFB1) were overexpressed in LNmet and PTdeep compared with PT sup. NGS data revealed orthogonal support of NanoString results with 40% mutations present in PT deep and/or LNmet, but not in PT (sup). Conversely, only 6% of mutations were present in PT sup and were absent in PTdeep and LNmet. MLPA demonstrated significant ITH between subregions and progressive genomic changes from PTsup to PTdeep/LN met. Conclusion In GC, regional lymph node metastases are likely to originate from deeper subregions of the primary tumour. Future clinical trials of novel targeted therapies must consider assessment of deeper subregions of the primary tumour and/or metastases as several therapeutically relevant genes are only mutated, overexpressed or amplified in these regions.