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Germline likely pathogenic variants in ataxia-telangiectasia-mutated gene in an Iranian family with hereditary diffuse gastric cancer without CDH1 mutation

1 Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
2 Department of Genetics and Molecular Biology, School of Medicine, Dezful University of Medical Sciences, Dezful, Iran

Date of Submission18-May-2019
Date of Decision08-Jan-2020
Date of Acceptance12-Apr-2020
Date of Web Publication27-Apr-2021

Correspondence Address:
Abbas Moridnia,
Department of Genetics and Molecular Biology, School of Medicine, Dezful University of Medical Sciences, Dezful
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/jcrt.JCRT_344_19

 > Abstract 

Background: Gastric cancer (GC) is the fourth common cancer in the world and the second cause of cancer-related mortality. Germline mutations in the E-cadherin gene (CDH1) are the most common cause of hereditary diffuse GC (HDGC) and explain 25%–30% of cases. In HDGC families without the pathogenic CDH1 variant, there is poor management and therapeutic strategies, and detect other genetic defects in HDGC, except CDH1 gene will be useful for further clarification of the disease mechanisms and risk-reducing strategies. Here, we reported an Iranian pedigree with familial HDGC to assess the fundamental genetic causes by whole-exome sequencing (WES).
Materials and Methods: WES performed in an Iranian with a history of familial GC in whom no pathogenic variants or indels has been found in CDH1 and CTNNA1 genes with Sanger sequencing and multiplex ligation-dependent probe amplification methods.
Results: Prioritizing genes associate with HDGC recognized several variants include c.2572T>C, and c.3161C>G in ataxia-telangiectasia mutated (ATM), c.1114A>C in BRCA2, and finally c.1173A>G in PIK3CA. Protein function prediction software tools reveal that c.3161C>G in ATM is likely pathogen.
Conclusion: The results of this study suggested a role for the known cancer predisposition gene ATM in families with HDGC with no pathogenic variant in CDH1. Our results suggested that mutations in ATM and other genes, particularly the mutations found in this study, should be considered even in one case of positive familial status of HDGC disease. The presence of these mutations in patients with familial history raises important issues regarding genetic counseling.

Keywords: Ataxia-telangiectasia-mutated gene, diffuse gastric cancer, whole-exome sequencing

How to cite this URL:
Kheirollahi M, Saneipour M, Moridnia A. Germline likely pathogenic variants in ataxia-telangiectasia-mutated gene in an Iranian family with hereditary diffuse gastric cancer without CDH1 mutation. J Can Res Ther [Epub ahead of print] [cited 2021 Dec 6]. Available from: https://www.cancerjournal.net/preprintarticle.asp?id=314862

 > Introduction Top

Gastric cancer (GC) is one of the most common cancers in the world and the second cause of mortality among all cancers.[1] The GC is a common cause of cancer-related deaths in Iran and its prevalence rate is high, particularly in the North and Northwest.[1],[2] The sporadic form of GC is a dominant type, and the hereditary form of GC accounts for up to 10% of cases (HGC).[3] The GCs are categorized into two groups, consisting of intestinal and diffuse type, according to the Lauren histological classification.[4] Diffuse GC (DGC) accounts for approximately 30% of all GCs and has a poor prognosis, especially in young patients.[5] Hereditary DGC (HDGC) is an autosomal dominant hereditary form of DGC that defined on the basis of family history of DGC, poor prognosis, high penetrance, highly aggressive tumors, delayed clinical signs, and associated with lobular breast cancer (LBC).[6],[7] The CDH1 mutations are the most common cause of HDGC disease.[8] This gene located on 16q22.1 position and contains 16 exons that encode for E-cadherin protein, which has three domains including extracellular, transmembrane, and cytoplasmic that shows a substantial role in cell–cell adhesion and tumor suppression.[9]

Other than the CDH1, germline mutations of CTNNA1 (α-E-catenin)[10] and BRCA2, STK11, SDHB, PRSS1, ataxia-telangiectasia mutated (ATM), MSR1, and PALB2 genes have been reported in HDGC patients.[11] Furthermore, several somatic mutations, including LMTK3, RHOA, PIK3CA, MED1, ARID1A, and MCTP22 genes, were detected in the HDGC patients.[10] However, given the rarity of these variants, the associated risk of DGC is hard to quantify, and these variants are not used in routine clinical testing to aid the management of these families.

For families with HDGC and known pathogenic CDH1 mutations, guidelines exist for risk assessment, disease management, surveillance (including regular endoscopies), and risk-reducing therapies (including prophylactic gastrectomy). However, for families with no pathogenic variant in CDH1, the risk assessment is uncertain, therefore making decisions and assessing the efficacy of risk-reducing strategies is challenging. Here, we aimed to identify genetic variants for predisposition to HDGC in an Iranian with a positive family history of DGC without pathogenic CDH1 variants and recognized a rare, likely pathogenic variant in ATM gene.

 > Materials And Methods Top

Statement of ethics

The present study was approved by the Local Ethics Committee of Isfahan University of Medical Sciences (IRAN) and was in accordance with the ethical standards as laid down in the 1964 Declaration of Helsinki and its later amendments or comparable ethical standards. Informed consent form was completed for each participant in the study.

Patient's information

According to the International GC Linkage Consortium,[9] a family pedigree for HDGC with an autosomal dominant pattern of inheritance from Isfahan province (central of Iran) was selected [Figure 1]. The proband is a patient with HDGC diagnosed at 57 years and has a sister with LBC under 50 years old. Informed consent forms were completed by patients participating in the study or their families.
Figure 1: Familial pedigree of hereditary diffuse gastric cancer in the studied family. Age of affected family members is indicated by an Asterisk

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Genetic analysis

High-quality genomic DNA from peripheral blood samples was extracted of two affected sisters in whom no pathogenic variants or indels have been found in CDH1 and CTNNA1 genes with Sanger sequencing and multiplex ligation-dependent probe amplification methods using PrimePrep Genomic DNA Isolation Kit (Genet Bio, Korea). The whole-exome sequencing (WES) was performed using a custom-designed Nimbelgen chip capturing (Agilent Technologies, Inc., Santa Clara, CA, USA), followed by a paired-end, high-throughput sequencing using Illumina HiSeq 4000 with coverage ×100 mean depth (Macrogen Company, South Korea). All exons and 10 bp flanking were detected and analyzed. The detected variations included point mutations, deletion, and duplication (<250 bp). Briefly, the variant analysis has been done through mapping the text files of sequences read to the reference genome (UCSC hg19) using the Burrows–Wheeler Alignment software with default parameters. Following alignment, Genome Analysis Toolkit software library was used to identify the single-nucleotide polymorphism and insertion/deletion of WES data.[12] Then, applying public databases, including 1000 Genome Project, HapMap samples, and dbSNP, identified variants with frequency >1% and synonymous substitutions filtered out. Variants with a minor allele frequency <0.1% were filtered to downstream analysis. The resulting list of variants were annotated by Annovar software. Annotated variations were filtered according to their frequency, chromosomal location, functional consequences, inheritance pattern, and clinical history.

Cosegregation study through Sanger sequencing

Sanger sequencing was used to confirm the accuracy of detecting variants in the proband and her sister's affected. Segregation analysis of the variants in the proband's parents was performed by PCR and Sanger sequencing.

 > Results Top

Whole-exome sequencing results

The total number of variants of the proband in the final VCF file was 101,252. An in-house step-wise filtering process was performed to find the genetic cause of DGC disease, according to the genes reported in the DGC, pathogenicity, variant's effect, nonsynonymous, upstream/downstream, and exonic/intronic variants. Prioritizing genes that association with DGC identified several gene mutations include one T/C heterozygote substitution (c.2572T>C, p. Phe858 Leu) in exon 17, and C/G heterozygote substitution (c.3161C>G, p. Pro1054Arg) in exon 22 of ATM gene, A/C heterozygote substitution (c.1114A>C, p. Asn372His) in exon 10 of BRCA2 gene, and one A/G heterozygote substitution (c.1173A>G, p. Ile391Met) in exon 7 of PIK3CA gene [Table 1].
Table 1: Variants in the PIK3CA, BRCA2, and ATM genes in hereditary diffuse gastric cancer family

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The heterozygous C to G transversion for the c.3161C>G (p. Pro1054Arg (in exon 22 of ATM was predicted likely pathogenic by PolyPhen-2, SIFT, I-Mutant, Mutation Taster, PROVEAN, Mutation Assessor, PhD-SNP, and ConSurf software. Sanger sequencing results confirmed the detected variant in both affected family members [Table 2] and [Figure 2].
Figure 2: The Sanger sequencing electropherograms. (a) Heterozygous c.3161C>G mutation in forward strand. (b) Heterozygous c.3161C>G mutation in reverse strand

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Table 2: The effects of variants on protein function

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 > Discussion Top

Families with a deleterious genetic mutation are advised to have genetic counseling, clinical monitoring, and recommendations for prophylactic surgery. In spite of known mutations in the CDH1 gene as the most frequent etiology of HDGC, remarkably in up to 70% of HDGC families, the genetic etiology remains unknown.[13] In this condition, the next-generation sequencing (NGS) method permits to find novel genes and variants involved in genetic diseases such as cancer.[14],[15] WES is a new emerging method of NGS for the identification of causative genes in Mendelian disorders, even in the lack of enough information about the inheritance pattern or exact clinical diagnosis.[16] According to the catalog of somatic mutations in cancer, the top genes often mutated in GC that are identified by NGS technique include TP53, APC, CDH1, TRRAP, PIK3CA, MLL3, RNF213, KMT2D, MLL, CTNNB1, CREBBP, AKAP9, CACNA1D, MYH9, ZNF521, SETBP1, KRAS, CDH11, and ATM.[17] The several of cancer-related genes that frequently mutated in GC identified by the WES technique. In this regard, the frequent mutations were reported by Wang et al., including TP53, PTEN, ARID1A, APC, CTNNB1, and CDH1,[18] and by Zang et al., including TP53, PI3KCA, CTNNB1, ARID1A, KMT2C, and FAT4.[19]

Since the predictive testing in asymptomatic at risk individual of the pedigree is provided the inherited pathogenic mutations, in this study, WES was performed in the proband and then cosegregation of the detected variants in the pedigree followed by a stepwise in-house filtering process, and identified a likely pathogenic c.3161C>G heterozygote variant that produces p. Pro1054Arg in exon 22 of the ATM gene in an Iranian family with DGC disease. Furthermore, several variants detected in other genes include BRCA2 and PIK3CA. The previous studies demonstrated the effect of these genes in cancer, for example, PIK3CA mutations associated with bone metastasis recurrence[20] and reduced responsiveness to EGF-targeted therapies[21] and also BRCA2 mutations[11] reported as candidate genes in HDGC families.

 > Conclusion Top

Our study expands the spectrum of ATM likely pathogenic variants in DGC patients with a positive family history and confirms the utility of targeted NGS sequencing in genetic diagnosis. However, confirmation of the pathogenicity status of missense variants that mentioned above, will be recommended in future studies by several analyses such as determining variant frequencies in a healthy control population, co-segregation of the variants in the pedigree, recurrence of the variants in independent families, in silico predictions, and in vitro functional studies.


We sincerely thank the patients and the professional staff of the Alaa Cancer Control Center, a charity-based foundation for cancer patients in Isfahan, Iran.

Financial support and sponsorship

This study was conducted with the support of Isfahan University of Medical Sciences (IRAN) with grant number 394479.

Conflicts of interest

There are no conflicts of interest.

 > References Top

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  [Figure 1], [Figure 2]

  [Table 1], [Table 2]


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