Genetic analysis of Japanese patients with small bowel adenocarcinoma using next-generation sequencing

Abstract

Background Small bowel adenocarcinomas (SBAs) are rare and there is little comprehensive data on SBA genomic alterations for Asian patients. This study aimed to profile genomic alterations of SBA in Japanese patients using targeted next-generation sequencing (NGS). Methods We examined 22 surgical resections from patients with primary SBA. SBA genomic alterations were analyzed by NGS. Mismatch repair (MMR) status was determined by immunohistochemical analysis. Mucin phenotypes were classified as gastric (G), intestinal (I), gastrointestinal (GI), and null (N) types on MUC2, MUC5AC, MUC6, and CD10 immunostaining. Results The most common genomic alterations found in SBA tumors were TP53 (n = 16), followed by KRAS (n = 6), APC (n = 5), PIK3CA (n = 4), CTNNB1 (n = 3), KIT (n = 2), BRAF (n = 2), CDKN2A (n = 2), and PTEN (n = 2). Deficient MMR tumors were observed in 6 out of 22 patients. Tumor mucin phenotypes included 2 in G-type, 12 in I-type, 3 in GI-type, and 5 in N-type. APC and CTNNB1 mutations were not found in G-type and GI-type tumors. KRAS mutations were found in all tumor types except for G-type tumors. TP53 mutations were found in all tumor types. Although no single gene mutation was associated with overall survival (OS), we found that KRAS mutations were associated with significant worse OS in patients with proficient MMR tumors. Conclusions SBA genomic alterations in Japanese patients do not differ significantly from those reports in Western countries. Tumor localization, mucin phenotype, and MMR status all appear to impact SBA gene mutations.

Relationship Between Immunophenotypes, Genetic Profiles, and Clinicopathologic Characteristics in Small Bowel Adenocarcinoma

“…Genetic profiles indicate that the mutation rates of KRAS, APC, and CTNNB1 are lower in gastric-type SBA, although these are more commonly observed in intestinal-type SBA, suggesting that the characteristics of intestinal-type SBA resembles those of colorectal cancer. 15 In contrast, gastric-type SBA had fewer mutations, with the exception of GNAS mutations, implying that its characteristics are distinguishable from those of colorectal cancer. It has been reported that gastric phenotype is inversely associated with Wnt-signaling abnormalities, which is consistent with our results.…”

“…DNA extraction, NGS, and mutation calling were performed as described previously. 15,28 In brief, ~10 ng of DNA per sample was amplified using multiplex polymerase chain reaction (PCR) with the Ion AmpliSeq Cancer Hotspot Panel v2 (Thermo Fisher Scientific), which was designed to amplify 207 amplicons covering the 2849 Catalogue of Somatic Mutations in Cancer (COSMIC; http://cancer.sanger.ac.uk/cosmic) mutations in hotspot regions for the 50 most commonly reported oncogenes and tumor suppressor genes. Pooled and barcoded libraries were clonally amplified on Ion Sphere particles using emulsion PCR with the Ion Chef system and Ion PGM HI-Q View Chef Kit (Thermo Fisher Scientific).…”

“…13,14 Our own studies have shown that mutations of APC and CTNNB1 have an inverse relationship with gastric-type markers, but it remains to be determined whether gastric-type and intestinal-type SBAs have different clinicopathologic characteristics. 15 Only a few studies have been reported that classified SBA into gastric and intestinal types and that examined clinicopathologic differences using immunostaining for phenotype markers. [16][17][18][19] Although immunostaining for CK7/20, CD10, CDX2, and various mucins has already been investigated on their own in a number of SBA studies, there has been no investigation to date that has brought all of these markers under one study for comprehensive analyses.…”

Molecular genetic positioning of small intestine and papilla of Vater carcinomas including clinicopathological classification

“…Furthermore, there have been several reports of genomic analysis using formalin‐fixed, paraffin‐embedded (FFPE) samples in comparison with adjacent organ carcinomas 7,8 . However, few studies have reported genomic analysis, including gene expression analysis, using fresh‐frozen samples 2,3,9 …”

“…7,8 However, few studies have reported genomic analysis, including gene expression analysis, using fresh-frozen samples. 2,3,9 PVC was included as a SIC in the 4th edition of the World Health Organization (WHO) classification of tumors of the digestive system. 10 It was reclassified as an independent disease from small intestine, gastric, colorectal, and bile duct carcinomas since 2019 in the 5th edition, similar to the Union for International Cancer Control (UICC) classification.…”