Bridging genomics and phenomics of gastric carcinoma

Abstract

Genetic alterations are the starting point leading to numerous changes in clinical and pathologic features (phenotypes) of individual cancers; however, their inter‐relationships in gastric cancers (GC) are unclear. We performed massive parallel sequencing of 381 cancer‐related genes and compared the results with clinical and pathologic findings in 330 GC. High tumor mutation burden (TMB) accounted for 11% of GC (n = 37) and all 19 MSI‐H GCs were high TMB. High TMB was significantly more frequent in intestinal‐type by Lauren, tumor with higher host cellular immune response, earlier AJCC stage and favorable prognosis. The most significantly mutated genes were TP53 (54%), ARID1A (23%), CDH1 (22%), PIK3CA (12%), RNF43 (10%) and KRAS (9%). For receptor tyrosine kinases, amplifications detected by immunohistochemistry were higher than sequencing (HER2, 9.1% vs. 5.8%; EGFR, 11.2% vs. 6.1%; FGFR2, 4.6% vs. 3.9%, c‐MET, 3.4% vs. 0.9%). PTEN protein loss (22%) correlated well with underlying PTEN alterations while ATM loss (27%) was not significantly correlated with genetic alterations of ATM. p53 protein expression predicted alterations of TP53 with high sensitivity (97.8%) and low (15.9%) specificity. The poorly cohesive histology/CDH1‐mutant GC subgroup showed the worst survival (p < 0.001). PD‐L1 expression was significantly associated with MSI‐H, MLH1 loss, ATM loss, MET positivity, higher host immune response, and genetic alterations of ARID1A, BRD3, PIK3CA, KRAS, MAP3K13, CDH2, PTEN and ESR1. The merged clinical, pathology and genomics of GC provide a better understanding of GC and new insights into the treatment of GC.

Tumor Mutational Burden Determined by Panel Sequencing Predicts Survival After Immunotherapy in Patients With Advanced Gastric Cancer

“…For mismatch repair protein immunohistochemistry, antibodies against MLH1 (clone ES05; 1:100 dilution; Novocastra) and MSH2 (clone G219-1129; 1:500 dilution; Cell Marque) were used, as previously reported (23).…”

“…However, most studies determining TMB by panel-based sequencing were performed in patients with non-small-cell lung cancer or melanoma (13,16,20). Although several studies evaluated TMB in gastric cancer, most studies proposed cut-off points for TMB and their relevance to survival (21)(22)(23), and only two studies included patients treated with ICB, in which TMB was measured by whole exome sequencing (18) and custom-designed large-sized panels (14). Moreover, despite efforts to standardize the TMB from multiple different genomic profiling panels (24), the cutoff value for TMB is not consistent and the associations with other biomarkers have not been fully defined in gastric cancer.…”

CDH1 mutations in gastric cancers are not influenced by family history

“…of GC cases [16][17][18][19][20][21][22] and are highly prevalent in sporadic EODGC (53.2% of cases). Somatic CDH1 mutation has also been suggested as a poor prognostic marker in diffuse-type GC [17,22,23]. The previously reported germline and somatic CDH1 mutations detected in patients with gastric cancer by various technologies are summarized in Table 4.…”

“…Genomic DNA (~ 250 ng) from each tissue was sheared in a Covaris S220 ultrasonicator (Covaris, Woburn, MA, USA) and used with CancerSCAN™ probes and a SureSelect XT reagent kit HSQ (Agilent Technologies) for construction of a library according to the manufacturer's protocol. This panel is designed to enrich 381 exons, covering 366.2 kb of the human genome [23]. After enriched exome libraries were multiplexed, the libraries were sequenced on a HiSeq 2500 sequencing platform (Illumina).…”

“…With NGS, somatic mutations of CDH1 are found in 9%~36% of GC cases [16][17][18][19][20][21][22] and are highly prevalent in sporadic early-onset diffuse-type GC (EODGC) (53.2% of cases) [17]. Somatic mutations of CDH1 have been suggested as a poor prognostic marker in diffuse-type GC [22,23]. Although a few studies have investigated the frequency and impact of CDH1 mutations in HDGC and EODGC [9,10,17,24] the incidence of CDH1 mutations in sporadic GC with or without family history has not been studied.…”