A 60-year-old man presented to surgical oncology out patient with complaints of epigastric pain and melena for 1 month, patient had a history of colon cancer for which he had undergone extended right hemicolectomy 16 years back. The earlier colonic cancer was microsatellite (MSI) stable and mismatch repair (MMR) intact, with low tumour mutation burden (TMB) and no reported mutations on NGS. On clinical examination, ECOG performance status was 1, general examination was unremarkable, on abdominal examination, there was tenderness in the epigastrium however no mass/lump was palpable. There was no ascites, or organomegaly, rectal examination was unremarkable.

Routine haematology and biochemistry were within normal limits, contrast enhanced computed tomography (CECT) scan showed asymmetric eccentric gastric wall thickening, with few polypoidal lesions noted in gastroesophageal (GE) junction and antro-pyloric region with multiple sub centimetric lymph nodes along the lesser curvature and common hepatic artery, the plane with pancreas was obliterated (Fig. 1), the lesion was close to previous anastomotic site, however colon was free. An upper gastro intestinal endoscopy (UGI) showed a large ulceroproliferative growth (UPG) at gastro oesophageal junction extending to cardia of stomach, and another UPG at antro-pyloric area was seen with overlying unhealthy mucosa, a biopsy was taken. Keeping in mind his history of colonic cancer, a colonoscopy was performed that showed healthy anastomotic site with normal vascularity and mucosal pattern. Histopathology of the gastric biopsy suggested adenocarcinoma, immunohistochemistry (IHC) showed CDX2 and CD 20 positivity suggesting it to be intestinal type of adenocarcinoma. Positron emission tomography showed two FDG avid lesions in stomach one of which was close to previous anastomosis, there was no other lesion.

Contrast enhanced computerized tomography and PET scan showing lesions at cardia (A, B) and pylorus (C, D)

With an initial diagnosis of gastric metastasis from colon cancer, patient was started on oxaliplatin (100 mg/m2 3 weekly), capecitabine (1000 mg/m2 twice a day, for 14 days with 1 week break), and bevacizumab (7.5 mg/m2 3 weekly) as per institutional protocol. After 3 cycles of chemotherapy, repeat CECT showed a partial response and as patient developed features of peripheral neuritis oxaliplatin was stopped and he continued capecitabine and bevacizumab (CapBeva). After 7 cycles patient developed gastric outlet obstruction. Repeat imaging showed near complete obstruction of the pylorus with minimal residual disease, the plane with pancreas was still not clear (Fig. 2). Patient was taken up for surgery, intra operatively 3 × 3 cm lesion was seen with serosal involvement in gastroesophageal junction and cardia, another lesion was seen along the lesser curvature of stomach with serosal involvement, enlarged lymph nodes were seen in station 1 to 11. A total gastrectomy with D2 lymphadenectomy and Roux-en-Y oesophageao-jejunal pouch anastomosis was done. Postoperative period was uneventful, final histopathology showed moderately differentiated adenocarcinoma, intestinal type pT3N2. Patient was discharged on 10th postoperative day without any complications.

Contrast enhanced computerized tomography and PET scan showing pyloric obstruction (A, B), grossly distended stomach (C)

On IHC, HER2 was equivocal and amplification was negative on fluorescent in situ hybridization (FISH), PD-1 was immunoreactive with score 1 + in tumour infiltrating immune cells (IC), score 0 in tumour cells (TC), with ≥ 1% IC/TC-PDL1 (SP142 Ventana) expression. On NGS analysis, 3 novel mutations were identified. A missense mutation in exon 27 of KMT2A gene (p.Leu2824Pro) with mutant allelic burden 63%. A frame deletion in exon 7 of LTK gene (p.Ala321_Gly330del), with 29% mutant allelic burden, and another missense mutation in exon 17 of MST1R gene (p.His1206Arg) with mutant allelic burden of 40%. No targetable gene variants were detected, The TMB was low, and MMR, MI were stable.

After the surgery, the option of adjuvant chemotherapy was discussed with the patient however he refused further therapy due to weakness. He is alive and well 18 months after the surgery and has gained 7 kg weight.

To investigate the significance of mutations bioinformatic analysis was done using WEB-based Gene Set Analysis Toolkit (WebGestalt) (http://www.webgestalt.org/) to perform Gene Ontology (GO) and Functional pathway analysis. The p < 0.05 was chosen as the cut-off. NetworkAnalyst (http://www.networkanalyst.ca.) was used to construct a protein–protein interaction network and a signalling network among the stomach cancer-specific genes. GeneMania (https://genemania.org/) tool was utilized to construct a gene–gene interaction network.

The results of GO enrichment analysis were categorized into three functional categories, i.e., biological process (BP), molecular functions (MF), and cellular components (CC) (Fig. 3A–C). Three most common BP identified through these genes are metabolic process, development process, and response to stimulus; three most common CC are protein containing complexes and cellular membrane; and three most common MF are protein binding, transferase activity, and ion binding.

Gene Ontology through Webgestalt tool showing A biological process, b cellular components, and C molecular functions

Reactome pathway enrichment analysis through webgestalt tool based on false discovery rate (FDR) showed eight positive and two negative categories (Table 1). The genes which are significantly enriched were KMT2A and MST1R gene.

Protein–protein Interaction network through NetworkAnalyst using plugin IMEx Interactome created, with 3 significant genes, had 3 nodes and 116 edges (Fig. 4), further signaling interaction network created through network analyst tool for all 3 genes separately through plugin Signor had 18 edges and 21 nodes (Fig. 5). Several hub genes exhibiting co-expression, predicted and physical and genetic interaction with other genes were identified, and a network was constructed through the gene mania tool (Fig. 6), Gene-miRNA Interaction network was prepared through NetworkAnalyst with miRTarBasev 8.0 with 2 genes, i.e., KMT2A and LTK with 113 nodes and 112 edges (Fig. 7).

Protein–protein Interaction network through NetworkAnalyst using plugin IMEx Interactome showing network for KTM2A, LTK and MST1R genes

Signaling Interaction network through NetworkAnalyst showing network for KTM2A, LTK, and MST1R

Gene–gene Interaction network through GeneMania

Gene-miRNA Interaction network through NetworkAnalyst for KTM2A and LTK gene showing interaction with number of miRNAs