Identification of New Genes Involved in Germline Predisposition to Early-Onset Gastric Cancer

Cristina Herrera-Pariente, Roser Capó-García, Marcos Díaz-Gay, Sabela Carballal, Jenifer Muñoz, Joan Llach, Ariadna Sánchez, Laia Bonjoch, Coral Arnau-Collell, Yasmin Soares de Lima, Mariano Golubicki, Gerhard Jung, Juan José Lozano, Antoni Castells, Francesc Balaguer, Luis Bujanda, Sergi Castellví-Bel, Leticia Moreira, Cristina Herrera-Pariente, Roser Capó-García, Marcos Díaz-Gay, Sabela Carballal, Jenifer Muñoz, Joan Llach, Ariadna Sánchez, Laia Bonjoch, Coral Arnau-Collell, Yasmin Soares de Lima, Mariano Golubicki, Gerhard Jung, Juan José Lozano, Antoni Castells, Francesc Balaguer, Luis Bujanda, Sergi Castellví-Bel, Leticia Moreira

Abstract

The genetic cause for several families with gastric cancer (GC) aggregation is unclear, with marked relevance in early-onset patients. We aimed to identify new candidate genes involved in GC germline predisposition. Whole-exome sequencing (WES) of germline samples was performed in 20 early-onset GC patients without previous germline mutation identified. WES was also performed in nine tumor samples to analyze the somatic profile using SigProfilerExtractor tool. Sequencing germline data were filtered to select those variants with plausible pathogenicity, rare frequency and previously involved in cancer. Then, a manual filtering was performed to prioritize genes according to current knowledge and function. These genetic variants were prevalidated with Integrative Genomics Viewer 2.8.2 (IGV). Subsequently, a further selection step was carried out according to function and information obtained from tumor samples. After IGV and selection step, 58 genetic variants in 52 different candidate genes were validated by Sanger sequencing. Among them, APC, FAT4, CTNND1 and TLR2 seem to be the most promising genes because of their role in hereditary cancer syndromes, tumor suppression, cell adhesion and Helicobacter pylori recognition, respectively. These encouraging results represent the open door to the identification of new genes involved in GC germline predisposition.

Keywords: early-onset; gastric cancer; germline predisposition; next-generation sequencing; somatic profiling; whole-exome sequencing.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Somatic mutational profile analysis performed with SigProfilerExtractor in nine GC tumor samples. (a) tumor mutational burden (number of mutations per megabase). (b) single base substitution (SBS) signatures contribution in each sample. (c) indel signatures contribution in each sample. Pt, patient; Mb, megabase; ID, small insertions and deletions.
Figure 2
Figure 2
Scheme of the germline data analysis after whole-exome sequencing. Germline analysis pipeline characteristics can be found in Figure S1 in Supplementary Materials.
Figure 3
Figure 3
Example of prevalidation and Sanger sequencing of recessive and dominant candidate variants. (a) prevalidation by Integrative Genomics Viewer 2.8.2 (IGV) and validation by Sanger sequencing of homozygous TLR2 variant (c.1232C>T) of control (up) and patient from family 4 (down). (b) prevalidation by IGV and validation by Sanger sequencing of heterozygous RNF43 variant (c.1504A>G) of control (up) and patient from family 4 (down).
Figure 4
Figure 4
Gastric cancer predisposition candidate genes classify by function or involvement in hereditary cancer.

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