Whole genome and transcriptome sequencing of matched primary and peritoneal metastatic gastric carcinoma

Abstract

Gastric cancer is one of the most aggressive cancers and is the second leading cause of cancer death worldwide. Approximately 40% of global gastric cancer cases occur in China, with peritoneal metastasis being the prevalent form of recurrence and metastasis in advanced disease. Currently, there are limited clinical approaches for predicting and treatment of peritoneal metastasis, resulting in a 6-month average survival time. By comprehensive genome analysis will uncover the pathogenesis of peritoneal metastasis. Here we describe a comprehensive whole-genome and transcriptome sequencing analysis of one advanced gastric cancer case, including non-cancerous mucosa, primary cancer and matched peritoneal metastatic cancer. The peripheral blood is used as normal control. We identified 27 mutated genes, of which 19 genes are reported in COSMIC database (ZNF208, CRNN, ATXN3, DCTN1, RP1L1, PRB4, PRB1, MUC4, HS6ST3, MUC17, JAM2, ITGAD, IREB2, IQUB, CORO1B, CCDC121, AKAP2, ACAN and ACADL), and eight genes have not previously been described in gastric cancer (CCDC178, ARMC4, TUBB6, PLIN4, PKLR, PDZD2, DMBT1and DAB1).Additionally,GPX4 and MPND in 19q13.3-13.4 region, is characterized as a novel fusion-gene. This study disclosed novel biological markers and tumorigenic pathways that would predict gastric cancer occurring peritoneal metastasis.

Figure 1. Clinical information of the patient.

(A) Schematic diagram of gastric cancer with peritoneal metastasis on mesocolon transversum drawn by Yu YY. (B) Left, CT scan shows that the tumor located on antrum with penetration of serosa (white arrow). The stomach is filled with liquid by pyloric obstruction. Right, the metastatic tumor is noticed on the surface of mesocolon transversum (white arrow). (C) Microscopic features of chronic gastritis (top), primary gastric cancer (middle) and metastatic tumor on mesocolon transversum (down) by hematoxilin and eosin (H&E) stain of the case.

Figure 2. Correlation of somatic mutations and gene expression of chronic gastritis, primary cancer and metastatic cancer tissues.

(A) Top panel shows a summary of all kinds of somatic mutations in chronic gastritis, primary cancer and metastatic cancer tissues. The matrix in the center of the figure represents individual mutations in each tissue. Blue represents single nucleotide variation. Left bar chart indicates number of mutations for each gene. Percentages represent the fraction of tumors harboring at least one mutation in the specified gene. (B) The bars show percentage of somatic SNVs identified by whole genome sequencing in chronic gastritis, primary cancer and metastatic cancer tissues, compared to peripheral blood. (C) Heatmap plot shows gene expression levels from RNA-seq for mutated genes in chronic gastritis, primary cancer and metastatic cancer tissues.

Figure 3. GPX4-MPND gene fusion.

(A) Circos plot of multiple fusion genes identidied in chronic gastritis (red inner lines), primary cancer (blue inner lines) and PM cancer (green inner lines). The arabic numbers represent chromesome numbers. The nemes of fusion genes labled outside the circs. (B) Schematic diagram of fusion site for GPX4 and MPND genes. Schematic of the predicted gene fusion illustrating RNA-seq evidence that support the fusion between exon 7 of GPX4 and exon 3 of MPND. Reads highlighted in red span across the fusion junction. The Sanger sequecing result of fusion junction is also provided. (C) Heatmap plot shows gene expression levels from RNA-seq for fusion genes identified in chronic gastritis, primary cancer and metastatic cancer tissues.

Figure 4. Differential expressed genes and involved pathways in chronic gastritis, primary cancer and PM cancer.

(A) The overview of up-regulated genes of primary cancer or PM cancer relative to chronic gastritis. (B) Pathway analysis of shared up-regulated genes in both primary cancer and PM cancer by GO enrichment. (C) The overview of down-regulated genes of primary cancer or PM cancer relative to chronic gastritis. (D) Pathway analysis of shared down-regulated genes in both primary cancer and PM cancer by GO enrichment.