JAMA sub-journal: Xu Ruihua/Qiu Miaozhen team of Sun Yat-sen University reveals for the first time the germline variation characteristics of patients with hereditary diffuse gastric cancer in China!

Gastric cancer is the fifth most common cancer worldwide and the third most common cause of cancer death, especially in East Asian populations [1,2].

Although most stomach cancers are sporadic, about 10% of cases show familial clustering
.
According to reports, 3%~5% of gastric cancer cases are related to hereditary gastric cancer susceptibility syndrome, including hereditary diffuse gastric cancer (HDGC), gastric adenocarcinoma, proximal gastric polyposis and familial intestinal gastric cancer [3,4].

HDGC is considered to be a kind of gastric cancer with genetic predisposition, and studies have shown that 25%~50% of HDGC cases carry germline variants on CDH1 or CTNNA1, but the genetic mechanism of 50%~75% of HGDC cases is still unclear [5], and the mutation rate of CDH1 in East Asian populations, especially Chinese
, is also unknown.

This requires Chinese scientists to solve this problem
.

Recently, a research team led by Xu Ruihua and Qiu Miaozhen of the Cancer Center of Sun Yat-sen University published important research results in JAMA Network Open [6].

They performed a retrospective cohort analysis of 284 white blood cell samples and paired 186 tumor samples from 284 HDGC patients with whole exons and targeted sequencing, and found that the germline mutation rate of CDH1 in Chinese HDGC patients was only 2.
8%, while the somatic mutation rate was 25.
3%.

They also found that some genes with higher germline mutation rates in Chinese HDGC patients were not consistent with previously reported genes, and that there may be an interaction of genetic and environmental factors during the onset of HDGC in Chinese
HDGC patients.

Screenshot of the paper

Xu Ruihua's team retrospectively analyzed 10,431 patients diagnosed with gastric cancer at the Sun Yat-sen University Cancer Center between January 1, 2002 and August 31, 2018, and finally included 284 HDGC cases (two HDGC patients were from Foshan First People's Hospital).

Most of the 284 HDGC patients were stage III or IV patients (190 patients, 66.
9%), and patients diagnosed with diffuse gastric cancer before the age of 40 with no family history (254 patients, 89.
4%)
.
The median age at diagnosis was 35 years, 161 (56.
7%) were female, and the median follow-up period was 21.
7 months
.
Only 8 (2.
8%) patients were infected with EBV, which is much lower than the previously reported rate
of EBV infection in gastric cancer patients.
The 5-year survival rate was 61.
4%, higher than the previously reported 44.
1%
of patients with sporadic gastric cancer.

Next, the research team performed whole exome sequencing
on white blood cell samples from 284 HDGC patients and paired 186 tumor samples.
They used sequencing data to identify germline and somatic variants
carried by patients.

Based on the germline variants detected, the team found that only 8 patients carried the variation on CDH1, which is quite different from previous studies, and the patients carried variants that had not been previously reported
.
This shows that Chinese HDGC patients have different genetic backgrounds and pathogenic mechanisms
.

Germline variation and somatic variation on CDH1

In addition, previous studies have suggested that mutations in CTNa1, BRCA2, STK11, SDHB, PRSS1, ATM, MSR1, PALB2, BRCA1, and RAD51C may be related to
susceptibility to CDH1 wild-type HDGC.
But Xu's team found that the mutation rate of these genes in Chinese HDGC patients is still low, and the mutations that occur are inconsistent
with previous reports.

Among Chinese HDGC patients, the genes with the highest germline mutation rates are MUC4 (19%), ABCA13 (10%), ZNF469 (10%), FCGBP (10%), IGFN1 (10%), RNF213 (10%), and SSPO (10%), which have not been
reported.
Among them, the gene with the highest mutation rate, MUC4, was mutated
in all 53 patients.
Studies have pointed out that MUC4 may cause fibroblast carcinogenesis in mice, so the overexpression of MUC4 may promote the malignancy
of gastric cancer through the ERBB2 pathway.

Germline variant mutation spectrum in Chinese HDGC patients

Using paired tumor samples, the team identified somatic variants in 186 HDGC patients, with the gene with the highest mutation rate being TP53 (32.
3%)
.
Interestingly, although the germline mutation rate of CDH1 is not high in Chinese HDGC patients, the somatic mutation mutation rate is as high as 25.
3%.

In addition, the research team also found that genes such as HRCT1 and KRTAP5-4 in Chinese HDGC patients are significantly mutated genes (driver genes).

Atlas of somatic variation in HDGC patients in China

Subsequently, Xu Ruihua's team compared the somatic variation burden of Chinese HDGC patients and TCGA sporadic diffuse gastric adenocarcinoma (D-STAD) patients, and found that the frequency of gene mutations in the two cohorts was significantly correlated (R=0.
24, P<2.
2×10-16), but in some genes, the mutation rate of Chinese HDGC patients was significantly lower than that of D-STAD patients, for example, MLLT4 mutation rate in D-STAD patients was 10%, compared with 0% in Chinese HDGC patients
。

The research team also compared the somatic mutation frequency of the two cohorts in pathways that play an important role in the development and progression of gastric cancer, such as PI3K-Akt, MAPK, Wnt, and TGF-β, and found that the mutation frequency of D-STAD patients was higher than that of Chinese HDGC patients
.

On the basis of somatic variation, the research team also analyzed the copy number variation in HDGC patients, and they found that 6p22.
2 and 19p13.
2 were high-frequency amplification regions, while 1q21.
2 and 10q21.
3 were high-frequency deletion regions
.
Specific to the gene level, the genes with higher frequency of copy number variation are PTK6 (44.
6%), ERBB3 (13.
4%) and PIK3CA (11.
8%), all of which are known oncogenes
in gastric cancer.

Areas with significantly higher frequency of copy number mutations in HDGC patients in China

To explore the etiology of HDGC patients in China, Xu's team analyzed the somatic variant characteristics of all samples and matched
them with the variant characteristics in the COSMIC database.
They found 3 main features, namely (named after the COSMIC feature): Characteristic 1 (spontaneous deamination of 5-methylcytosine), Characteristic 5 (cause unknown), Characteristic 24 (aflatoxin exposure).

It was shown that environmental factors also played a large role in the occurrence of HDGC, and there may be an interaction
between genetic and environmental factors.

Finally, Xu's team analyzed the variation
related to clinical prognosis.
Among germline variants, they found that seven genetic variants were associated with overall survival: SDK1, HSPG2, FSIP2, CUBN, NCKAP5, FLNB, and MUC16
.

Among somatic variants, a large number of genetic variants are associated with overall survival, among which the genes with higher frequency of mutation are FGFR3 (HR, 2.
2), ASPSCR1 (HR, 2.
2), CIC (HR, 2.
4), DGCR8 (HR, 2.
2), and LZTR1 (HR, 2.
5).

Pathway enrichment analysis found that these genes were enriched in interferon-related pathways
.

The research team also made clinical operability annotations
on somatic variants in Chinese HDGC patients by integrating multiple databases such as OncoKB and CIViC.
Finally, 263 single nucleotide variants in 125 patients and 338 copy number variants in 153 patients were annotated as potentially clinically actionable variants
.

In general, this retrospective cohort study describes for the first time the germline variation characteristics of Chinese HDGC patients, and shows that the germline variation characteristics of Chinese patients are quite different from those analyzed in other previous studies, and also proposes some potential clinically operable variant targets in Chinese HDGC patients, which can provide reference for future research in the field of HDGC
.

References:

[1] Ferlay J, Soerjomataram I, Dikshit R, et al.
Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012.
Int J Cancer.
2015; 136(5):E359-E386.
doi:10.
1002/ijc.
29210

[2] Chen W, Zheng R, Zeng H, Zhang S.
The updated incidences and mortalities of major cancers in China, 2011.
Chin J Cancer.
2015; 34(11):502-507.
Published 2015 Sep 14.
doi:10.
1186/s40880-015-0042-6

[3] Oliveira C, Pinheiro H, Figueiredo J, Seruca R, Carneiro F.
Familial gastric cancer: genetic susceptibility, pathology, and implications for management.
Lancet Oncol.
2015; 16(2):e60-e70.
doi:10.
1016/S1470-2045(14)71016-2

[4] Fitzgerald RC, Hardwick R, Huntsman D, et al.
Hereditary diffuse gastric cancer: updated consensus guidelines for clinical management and directions for future research.
J Med Genet.
2010; 47(7):436-444.
doi:10.
1136/jmg.
2009.
074237

[5] Blair VR, McLeod M, Carneiro F, et al.
Hereditary diffuse gastric cancer: updated clinical practice guidelines.
Lancet Oncol.
2020; 21(8):e386-e397.
doi:10.
1016/S1470-2045(20)30219-9

[6] Liu ZX, Zhang XL, Zhao Q, et al.
Whole-Exome Sequencing Among Chinese Patients With Hereditary Diffuse Gastric Cancer.
JAMA Netw Open.
2022; 5(12):e2245836.
Published 2022 Dec 1.
doi:10.
1001/jamanetworkopen.
2022.
45836