Skip to main content
Download PDF

Germline variants in patients from the Iranian hereditary colorectal cancer registry

Cancer Cell International volume 25, Article number: 140 (2025) Cite this article

Abstract

Background and aim

Hereditary cancer syndromes account for 6–10% of all colorectal cancer (CRC) cases and 20% of early-onset CRC. Identifying novel pathogenic germline variants can impact genetic testing, counseling, and surveillance. This study aimed to determine the prevalence of germline variants associated with hereditary CRC in the Iranian population.

Methods

Whole exome sequencing (WES) was conducted on DNA from 101 patients in the Iranian Hereditary Colorectal Cancer Registry (IHCCR). The cohort included 63 high-risk Lynch Syndrome (LS) patients and 38 colorectal polyposis patients. Germline variants and phenotype spectrum were assessed. Relatives of individuals with the mutations received counseling and cascade testing. Gene ontology and protein-protein interaction (PPI) analyses were conducted to elucidate gene roles on protein function.

Results

Pathogenic/likely pathogenic (P/LP) variants were identified in Lynch-related genes in 36.51% of patients. P/LP variants in non-Lynch genes (ATM, FH (mono-allelic), MSH3, PMS1, and TP53) were identified in 26.98% of patients. Among polyposis patients, 50% had P/LP variants in the APC gene, and 15.79% had P/LP variants in the MUTYH gene. Additionally, 7.89% carried P/LP variants in non-FAP/MAP genes (BLM, BRCA2, and PTEN). MLH1 variants were most common in exons 10 and 18, MSH2 in exon 12, and APC gene in exon 16. Cascade testing identified 50% of the tested relatives (40/80). Topology analysis of the protein-protein interaction networks in high-risk LS cases highlighted stronger connections among nodes for genes such as TP53, ATM, POLD1, CDH1, MUTYH, WRN, NOTCH1, SMAD4, ERCC4, ERCC1, and MSH3. These genes were associated with high penetrance in CRC. The protein-protein interaction analyses of polyposis patients indicated that genes like POLE, MSH6, MSH2, BRCA2, BRCA1, MLH1, TOPBP1, BLM, RAD50, MUTYH, MSH3, MLH3, PTEN, BRIP1, and POLK had a higher degree value and were also associated with high penetrance. Gene ontology and protein-protein interaction (PPI) analysis showed that some of the top-scoring non-Lynch genes were TP53, ATM, POLD1, CDH1, MUTYH, WRN, NOTCH1, SMAD4, ERCC4, ERCC1, and MSH3.

Conclusions

The study identified crucial germline variants for hereditary polyposis and non-polyposis CRC pathogenesis in the Iranian population. A selective strategy and cascade genetic testing are recommended for the diagnosis of hereditary colorectal cancer syndromes.

Introduction

Colorectal cancer (CRC) is among the five most common cancers worldwide [1]. It is the third most commonly diagnosed cancer and the second leading cause of cancer-related deaths [2]. Recent data from Iran’s National Cancer Registry (INCR) shows that CRC is the third most common cancer in males and the second in females [3, 4]. The age-standardized incidence rate of CRC has increased in recent years [4]. While most CRC cases are sporadic, up to 35% of the inherited variability is due to genetic factors [5, 6], including a family history of CRC, hereditary cancer syndromes, and common low-penetrance genetic variations. Although some studies have provided more insights into the molecular mechanisms driving CRC, revealing its highly heterogeneous nature at the molecular level, many genetic factors remain unidentified [7, 8]. Recent studies have indicated the involvement of one or more moderate and high-penetrance cancer susceptibility gene(s) in 9.9–15.5% of patients with CRC. In early-onset CRC, this number shows an increased range of 16–25% [9]. Lynch syndrome (LS), the most common hereditary CRC syndrome, is caused by germline variants in the mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2, and also in EPCAM, affecting one out of every 25 patients diagnosed with CRC [10]. Recent studies using next-generation sequencing (NGS) have revealed germline variants in cancer-predisposing genes other than Lynch-related genes, including NTHL1, GERM1, GALNT12, RNF43, RPS20, MLH3, and MSH3 [11, 12, 13, 14].

Other hereditary CRC syndromes related to gastrointestinal (GI) polyposis include familial adenomatous polyposis (FAP; associated with APC pathogenic variants) and MUTYH-associated polyposis (MAP; caused by biallelic MUTYH pathogenic variants). Recently, more genes have been implicated in the development of other forms of hereditary colonic polyposis, such as polymerase proofreading–associated polyposis (PPAP) caused by the pathogenic variants of POLE or POLD1, NTHL1-associated polyposis, adenomatous polyposis related to the biallelic inactivation of MMR genes (such as MSH3 and MLH3), GREM1-associated mixed polyposis, and RNF43-associated serrated polyposis. Other germline variants in genes such as STK11, PTEN, BMPR1A, and SMAD4 can also be responsible for rarer cases of GI polyposis [15].

Identifying CRC susceptibility genes or familial polyposis syndromes can direct clinical management, leading to lifesaving interventions. In Iran, about 20–25% of CRC patients have a familial background, and 15% have a strong family history [16, 17], of whom almost 5% fulfil the Amsterdam II criteria, and 10% have loss of MMR protein expression [16, 18].

There is no study on the genetic landscape of hereditary CRC in the Iranian population, with most studies being case reports [19, 20, 21]. This study used whole exome sequencing (WES) to identify the genetic susceptibility to CRC and colorectal polyposis from 101 high-risk patients from three referral clinics [22]. We report common and novel germline variants that might be important in the pathogenesis and predisposition to hereditary CRC and polyposis. The updated phenotypic and genetic map of hereditary CRC could help develop national policies and guidelines for the screening and management of hereditary CRCs in Iran.

Methods

Settings, participants, and eligibility criteria

This study included participants from the Iranian Hereditary Colorectal Cancer Registry, a program for detecting and monitoring patients at high risk of hereditary CRC [16, 23]. The program involves Mashhad, Tehran, and Isfahan University of Medical Sciences. Between January 2019 and December 2021, 101 probands were selected from 2,500 registered patients based on clinical assessments indicating a high risk for hereditary CRC. The inclusion criteria for this study included patients who met the Amsterdam II or revised Bethesda criteria for LS [24, 25], and patients diagnosed with colorectal polyposis, defined as having more than ten polyps in the colon and rectum. This group comprised 63 CRC patients at high risk for LS and 38 with colorectal polyposis. These probands were invited and consented to participate in the study for genetic evaluation using WES. Colon and rectal cancer were defined based on ICD codes, and non-FAP-MAP cases were defined as cases with over ten colon polyps and a family history of cancer but with no pathogenic germline variants in APC and/or MUTYH genes. Non-Lynch cases were defined as cases that fulfilled the Amsterdam II or Revised Bethesda criteria but with no pathogenic variants in MLH1, MSH2, MSH6, and PMS2 or EPCAM genes.

Demographic, clinical, and pathological characteristics, such as pathological grade, TNM staging system, tumor location, and molecular features, including MSI, MMR IHC, KRAS/NRAS, and BRAF variant analyses, were identified. Sex as a biological variable was analyzed. Family history up to the fourth generation was recorded, and pedigrees were drawn using the website familyhistory.invitae.com. Blood samples (10 ml) were collected for DNA extraction using the Blood DNA Isolation Kit (DENAzist Asia Co., Iran). Ethical approval was obtained, and participants provided written informed consent.

Immunohistochemistry

Expression of MMR proteins (MLH1, MSH2, MSH6, and PMS2) was assessed using IHC with primary monoclonal antibodies (Vitro SA, Master Diagnostica, Spain; RRID: AB_2140114). Tissue sections were prepared and visualized using Novolink Polymer Detection Systems (Leica Company, Wetzlar, Germany) and counterstained with hematoxylin and eosin. Two expert pathologists independently and blindly evaluated the results.

Whole-exome sequencing

Human whole exome enrichment was performed using the Agilent SureSelect V6 Target Enrichment Kit (RRID: SCR_01479), followed by NGS on the Illumina HiSeq4000 platform (RRID: SCR_016383) to yield an average coverage depth of approximately 100X. All exons and flanking 10 bp sequences were detected and analyzed. Quality control of sequencing data was performed on all samples before analysis using the fast QC software (RRID: SCR_014583) sequence pipeline (Illumina) to filter out low-quality reads. Sequenced reads were trimmed for adaptor sequences. The Burrows-Wheeler Aligner (BWA-MEM algorithm) was used for read mapping to the human reference genome (build hs37d5, based on NCBI GRCh37). PCR duplicates were discarded using the Mark Duplicates (Picard, Broad Institute, Cambridge, MA, USA) tool. We used the tools mentioned in the GATK (RRID: SCR_001876) Best Practices (The Haplotype Caller, MuTect2) pipeline for variant calling, and Strelka2 (Illumina) was used for SNV. Indel realignment and base quality score recalibration were performed (GATK, Broad Institute, Cambridge, MA, USA).

Finally, for variant annotation, we used the ANNOVAR tool (RRID: SCR_012821). Several databases were considered for variant annotation. Variants with a minor allele frequency (MAF) of ≥ 0.1% (for heterozygous variants) or ≥ 1% (for homozygous variants) were excluded using 1000 Genomes (Asian: RRID: SCR_008801), Iranom, and Gnomad. SIFT (prediction of damaging: RRID: SCR_012813), PolyPhen2 (HumVar prediction of probably damaging or possibly damaging), and CADD (Phred score ≥ 20) were used for pathogenicity prediction of missense variants. We also selected truncating (nonsense, splice site, and frameshift variants) or missense variants that fulfilled at least two of the three missense pathogenicity tools criteria. The clinical significance of these variants was classified for variant pathogenicity annotations according to Varsome and Gnomad per the Ambry five-tier variant classification protocol (pathogenic, likely pathogenic, variant of unknown significance, likely benign, and benign), which is based on guidelines published by the American College of Medical Genetics and Genomics, the Association for Molecular Pathology, and the International Agency for Research on Cancer. A pathogenic or likely pathogenic variant was defined as a variant that was predicted to result in a stop codon, a frameshift variant, a large duplication or deletion, or a missense variant in the coding region or splice site previously reported within the scientific literature and databases to be pathogenic or likely pathogenic. Particular attention was paid to genes known to be involved in predisposition to CRC and other neoplasms by reviewing data present on OMIM (Online Mendelian Inheritance in Man; http://www.omim.org/) and ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/; RRID: SCR_006169). The remaining rare non-synonymous variants were classified with reference from established databases such as ClinVar, Franklin, and Varsome. Variants classified as pathogenic or novel (not previously reported at the point of analysis) were assessed based on patients’ clinical presentations, family history, and reference to the available literature.

Gene ontology (GO) and protein-protein interaction (PPI) network analyses

GO analysis was conducted on critical genes from WES of CRC patients. Candidate genes included 47 for LS and 22 for polyposis. To analyze cellular components (CC), molecular function (MF), and biological processes (BP), ClueGO (version 2.5.8, RRID: SCR_005748) and Cytoscape application (version 3.9.1, RRID: SCR_003032) were used [26]. A significance level of p ≤ 0.05 was considered for gene ontology analyses.

Protein-protein interaction (PPI) networks were constructed using STRING (version 1.7.0; RRID: SCR_005223) and Network Analyzer (version 4.4.8) [27, 28] applications in Cytoscape networks as they play a significant role in interpreting biological processes [29] and protein functions. Additionally, interaction networks may reveal both the temporal and spatial aspects of forming functional cellular networks [30].

Cascade genetic testing and Sanger sequencing

Novel variants identified by WES were validated using Sanger sequencing (Codon Genetic Group, Iran). The sequencing results were analyzed using the SnapGene software (from Insightful Science; available at snapgene.com, (RRID: SCR_015052). Family members of mutation carriers received genetic counseling and were offered mutation testing. PCR and sequencing techniques were used to assess whether first-degree relatives (FDR) and second-degree relatives (SDR) carried the mutation. DNA sequencing was conducted on 80 family members, comprising 52 family members related to 14 probands with high-risk LS and 28 family members related to 11 probands with hereditary polyposis.

Statistical analysis and presentation of data

The primary outcome was the detection of pathogenic, likely pathogenic, and variant of unknown significance (VUS) variants in cancer susceptibility genes. Age at CRC diagnosis was analyzed as a continuous variable; other characteristics were categorical. Circos plots (RRID: SCR_011798) were created using the shinyCircos package in R data (RRID: SCR_021252) visualization. To visually present the data distribution and trends, GraphPad Prism version 8.0.0 for Windows (GraphPad Software, Boston, Massachusetts USA, www.graphpad.com) was used.

Results

Germline variants in patients at risk for Lynch syndrome

We categorized 63 CRC patients as high-risk for LS (Amsterdam II or revised Bethesda clinical criteria). WES showed that 36.51% (n = 23) carried pathogenic/likely pathogenic (P/LP) variants in one or more of Lynch-related genes, while 26.98% (n = 17) carried P/LP variants in non-Lynch genes (Fig. 1A). Among 23 patients with P/LP variants in Lynch-related genes, 11 had germline variants in MLH1, 10 in MSH2, 1 in MSH6, and 1 in PMS2 (Table S1). We found P/LP variants in 36 non-Lynch genes, such as ATM, ASXL1, FH, MSH3, PMS1, and TP53 (Table S1). No EPCAM gene deletion was found. Analysis of Lynch-related genes revealed that the most frequent P/LP variants in the MLH1 gene are missense, while the MSH6 gene showed a nonsense variant, and the PMS2 gene showed a frameshift variant (Fig. 1B). Sanger sequencing was performed to confirm variants identified by WES (Figure S1). Among 52 family members of 14 probands with high-risk Lynch syndrome, half had variants.

Fig. 1
figure 1

Germline variants in patients at risk for Lynch syndrome and colorectal polyposis. (A) Percentage of pathogenic/likely pathogenic (P/LP) variants and VUS in Lynch-related and non-Lynch genes of patients at risk for Lynch syndrome. (B) Number of different variants in four Lynch-related MLH1, PMS2, MSH2, and MSH6 genes. For example, in the MLH1 gene, from the P/LP variants, there is one nonsense, one frameshift, one splice donor variant, and five missense variants, while there is only one VUS frameshift variant. (C) Percentage of P/LP and VUS variants in patients with colorectal polyposis. (D) Number of different types of variants in two FAP/MAP genes of APC and MUTYH. MUTYHm: mono-allelic variants in the MUTYH gene; MUTYHb: bi-allelic variants in the MUTYH gene

Full size image

Twenty patients (31.75%) carried VUS: four in MLH1, MSH2, and MSH6 genes and 16 in non-Lynch genes (Fig. 1A), the most frequent in the BCR and GXYLT1 genes (with an allele frequency of 0.019) (Table S1). Variants in the MLH1 gene were mainly located in exons 10 and 18 and exon 12 of the MSH2 gene (Figure S2).

We found 26.98% of high-risk LS probands with P/LP variants in non-Lynch genes such as ATM, ASXL1, FH (mono-allelic), PMS1, MSH3 (mono-allelic), and TP53 (Fig. 1, Table S1). Gene ontology and PPI analysis showed top-scoring non-Lynch genes were TP53, ATM, POLD1, CDH1, and others (Figures S3 and S4, Table S2).

Germline variants in patients with colorectal polyposis

Thirty-eight patients had more than ten colorectal polyps (polyposis). WES revealed that 19 patients (50%) carried P/LP variants in APC and six patients (15.79%) carried P/LP variants in MUTYH (Fig. 1C). Variants in the APC gene were most commonly found in the exon 16 (Figure S5). Three patients had biallelic variants in the MUTYH gene and three patients (7.89%) carried P/LP variants in non-FAP/MAP genes, including BLM, BRCA2, and PTEN (Fig. 1C, D; Table S2). Most P/LP variants of polyposis patients were heterozygous. Sanger sequencing was performed for some samples to confirm variants identified by WES. In the families of 11 of the polyposis probands, 29 at-risk family members were tested; of these, 15 were carriers (Figure S1).

Most P/LP variants in the APC and MUTYH genes were frameshift (Fig. 1D), whereas all VUS in the APC and MUTYH genes were missense (Fig. 1D). Eight patients (21.05%) carried VUS, one in APC, one in MUTYH, and six in non-FAP/MAP genes, such as BRIP1, MSH3, MLH3, and TOPBP1 (Fig. 1C; Table S3).

Clinical characteristics of patients with pathogenic/likely pathogenic variants in Lynch-related and non-Lynch genes

Among patients with P/LP variants in Lynch-related genes, 78.26% (18/23) were identified with MSI high and/or dMMR (Table 1), whereas in patients with P/LP variants in non-Lynch genes, 47.05% (8/17) were MSI high and/or dMMR. Most (95.7%) of patients with P/LP variants in Lynch-related genes fulfilled the revised Bethesda criteria, while 69.56% fulfilled the Amsterdam II criteria. However, 82.35% and 47.05% of patients with P/LP variants in non-Lynch genes fulfilled the revised Bethesda and Amsterdam II criteria, respectively (Table 1). 65.22% and 58.83% of patients with P/LP variants in Lynch-related and non-Lynch genes were male, respectively (Table 1). The mean age of CRC diagnosis in patients with P/LP variants in Lynch-related genes was 44.7 years (ranging from 38 to 70 years), while for patients with non-Lynch genes was 45.8 years. While the majority of patients with P/LP variants in Lynch-related genes (73.91%) had early-onset (≤ 50 years) CRC, only 52.9% of patients with P/LP variants in non-Lynch genes were diagnosed with early-onset CRC (Table 1). The IHC loss of staining of both MLH1 and PMS2 was recorded in 16 out of 47 patients (Table 2).

Table 1 The clinic-pathological characteristics of CRC patients with dMMR
Full size table
Table 2 Comparison of germline mutations (WES) and immunohistochemical (IHC) staining of tumor tissues for MMR genes
Full size table

Two patients had a previous diagnosis of endometrial cancer before CRC. The location of CRC tumors was mainly in the proximal colon (62.21% of patients in this study) and 26.08% were of mucinous histology. Of patients with P/LP variants in Lynch-related genes, 34.78% had CRC at clinical stage II, whereas 35.29% of patients with P/LP variants in non-Lynch genes had stage III CRC (Table 1).

In this cohort, the most common cancers diagnosed in the relatives of LS patients were colorectal, stomach, breast, prostate, and endometrial (Fig. 2A). Of 11 probands with P/LP variants in the MLH1 gene, the mean age of CRC diagnosis was 40 years, and 9 (81.81%) fulfilled the Amsterdam II criteria (Fig. 2A), CRC was mainly in the proximal colon and mucinous type. One patient with a VUS in MLH1 (c.c380G p.s127w) was a 42-year-old male with distal CRC, dMMR (with loss of expression of MLH1/PMS2) who fulfilled the Amsterdam II and the revised Bethesda criteria and developed metachronous colorectal cancer in the rectum and transverse colon. He had a family history of gastric cancer and CRC in FDR.

Fig. 2
figure 2

The number of cancer cases observed in the family of patients at risk for Lynch syndrome and polyposis. (A) The number of cancer cases observed in the family of patients at risk for Lynch syndrome is categorized based on P/LP variants in MLH1, MSH2, MSH6, and PMS6 genes. The bottom panel shows the percentage of CRC and stomach cancers in FDR (first-degree relatives) and SDR (second-degree relatives) of patients with P/LP variants in MLH1, MSH2, Lynch-related genes, and non-Lynch genes. (B) The number of cancer cases observed in the family of patients with colon polyposis, categorized based on P/LP variants in APC, MUTYH, and non-FAP/MAP genes. The bottom panel shows the number of CRC, stomach, and breast cancers in FDR (first-degree relatives) and SDR (second-degree relatives) of patients with P/LP variants in APC, MUTYH, and non-FAP/MAP genes

Full size image

P/LP variants in the MSH2 gene were identified in 10 probands. The mean age of these patients for CRC diagnosis was 40 years. Among these patients, 7 (70%) fulfilled the Amsterdam II criteria, and 80% had dMMR CRC, mostly (60%) in the proximal colon (Fig. 3A; Table 1). Their family members had mostly colorectal, gastric, prostate, and breast cancers (Fig. 2A). All the known criteria of a typical case of LS (Amsterdam II criteria, dMMR proximal CRC) were identified in only four patients (out of 10) with P/LP variants in the MSH2 gene. One patient had a VUS in MSH2, a 48-year-old male with with loss of expression of MSH2/MSH6 in a synchronous CRC in the proximal and distal colon (Fig. 3A). He had a family history of gastric cancer in an SDR.

Fig. 3
figure 3

Circular visualization of clinical characteristics of patients with variants in Lynch-related and FAMP/MAP genes. (A) 27 patients had P (pathogenic)/LP (Likely Pathogenic) and VUS (variants of uncertain significance) variants in Lynch-related genes. Rectangles with green gradients represent the clinical characteristics of patients with the MSH2 variants. Rectangles with blue gradients represent the clinical characteristics of patients with the MLH1 variants. Rectangles with orange gradients represent the clinical characteristics of patients with the PMS2 variants. Rectangles with purple gradients represent the clinical characteristics of patients with the MSH6 variants. The white rectangles show unknown characteristics. The white rectangle in the center of the circle shows the characteristics of the rsID number for dbSNP, Mis-s: missense, Fram-sh: frameshift, Del: deletion, Ins: Insertion, Splice-D: splice donor, and Non-s: nonsense. The red words correspond to the novel variants. (B) 25 patients had P/LP/VUS variants in FAP/MAP genes in polyposis patients. Rectangles with purple gradients represent the clinical characteristics of patients with the APC variants, and rectangles with gold gradients represent the clinical characteristics of patients with the MUTYH variants

Full size image

One patient with P/LP variants in MSH6 was a 69-year-old male with loss of expression of MSH6/MSH2 in a distal CRC. He had a family history of breast cancer in an SDR. A 54-year-old male patient with a VUS in MSH6 met the Amsterdam II clinical criteria and had a proximal CRC. Interestingly, the IHC findings revealed MMR proficiency and a family history of gastric cancer in an FDR and 4 CRCs in SDR. We found one case with a pathogenic variant in PMS2, a 53-year-old male with loss of expression of PMS2 in a distal CRC, and a family history of prostate cancer in his father at age 76. Pathogenic variants in MSH6 and PMS2 are the most common in LS cases [31].

Clinical characteristics of polyposis patients with P/LP variants in FAP/MAP genes

In 38 patients with polyposis criteria and germline P/LP variants in FAP/MAP genes, 52.63% (n = 20) had over 100 polyps (Table 3), of whom 78.94% (15/19) had pathogenic APC germline variants (Fig. 3B). Of the ten patients who had CRC at the time of diagnosis, seven had P/LP variants in the APC gene, and two in the MUTYH gene (one monoallelic, and one biallelic). The mean age at the time of diagnosis of polyposis patients was 46.26 years (ranging from 21 to 73 years; 63.15% of them ≤ 50 years). The mean age at the time of diagnosis of polyposis patients with pathogenic variants of APC and MUTYH was 43.9 and 42.3 years, respectively. Most patients (11/19) with APC and MUTYH pathogenic variants had frameshift variants (Fig. 1D). Six probands were carriers of the MUTYH variants, four as biallelic and two as mono-allelic (Fig. 3B). Most of the CRC tumors in polyposis patients were at stages III and IV (Table 3).

Table 3 Clinic-pathological characteristics of polyposis patients
Full size table

The most common cancers in the relatives were CRC, breast, stomach, and brain cancers (Fig. 2B). Three cases with P/LP germline variants in the APC gene developed desmoid tumor, one patient with c.3921_3925del(p.I1307fs), one patient with the c.3389 del G(p.c1130fs), and another patient with the c.3180_3184del (p.I1060fs) (Fig. 3B). In the FDR of patients with P/LP variants in the APC and MUTYH genes, 7 and 3 cases of CRC were identified, respectively (Table 3).

Remarkably, a PTEN variant was found in a 40-year-old woman with rectosigmoid polyposis (20–50 polyps). Following screening, she was diagnosed with early-stage breast cancer. Additionally, we observed intriguing MSH3 monoallelic variants (c.214 C > T p.P72S) in a 37-year-old male with more than 50 colon polyps and a family history of cancer in a second-degree relative.

Two patients with VUS in APC were suggested to be classified as pathogenic: a 51-year-old male with more than 100 colon polyps and rectal cancer with a family history of CRC in his father; and a 72-year-old male with more than 100 colon polyps and a family history of endometrial cancer in FDR and CRC in SDR (Figure S8). We also found two patients with two different mono-allelic variants (compound heterozygote) in MUTYH, a 35-year-old female with 50–100 colon polyps and CRC in his brother, and a 44-year-old female with more than 100 colon polyps and distal CRC (Figure S9). For polyposis patients, the PPI network analysis identified 41 nodes and 120 edges (Figure S10). Genes like POLE, MSH6, MSH2, BRCA2, BRCA1, MLH1, TOPBP1, BLM, RAD50, MUTYH, MSH3, MLH3, PTEN, and BRIP1 genes had a higher degree value indicating high penetrance in colorectal cancer [11, 32] (Figure S10, Table S4). Analysis showed 62.5% of terms related to colon carcinoma, 25% to familial breast cancer, and 12.5% to endometrial carcinoma (Figure S10). Proposed biomarkers included PTEN, POLE, BRCA1/2, MSH2, MSH6, MLH3, and MSH3, as potential candidates associated with polyposis and colorectal cancer. However, further investigation is necessary to validate these findings and establish their clinical significance.

Discussion

In this study, we conducted WES germline analysis from 63 high-risk LS patients based on clinical criteria and 38 polyposis patients. We identified P/LP variants in Lynch-related and non-Lynch genes in 63.49% of high-risk LS proband (Fig. 1). 36.51% (23/63) had variants in Lynch-related genes, and 26.98% had variants in non-Lynch genes, including ATM, ASXL1, FH (mono-allelic), MSH3 (mono-allelic), PMS1, MUTYH (mono-allelic), WRN, and TP53. These findings align with other studies and may suggest that the known Lynch-related genes do not explain all inherited susceptibility to CRC in high-risk cases that fulfill clinical criteria [33, 34, 35, 36, 37]. These findings also indicate that a broader number of genes should be tested in affected patients and their relatives. In the polyposis cohort, 71% had P/LP germline variants in FAP/MAP- and non-FAP/MAP genes. Most of these variants were in APC and MUTYH (mono- and bi-allelic) genes, with three patients having PTEN, BRCA2, and BLM P/LP germline variants. These findings highlight the need for a comprehensive hereditary cancer risk assessment in CRC and polyposis with appropriate pre and post-test genetic counseling.

Previous studies have identified various germline variants predisposing individuals to cancer. The National Comprehensive Cancer Network (NCCN) recommends universal MMR deficiency screening for all colorectal and endometrial tumors, regardless of age [36]. However, in low-resource settings like Iran, selective strategies using clinical criteria such as Bethesda or Amsterdam II are more practical due to the limited access to genetic testing and financial constraints in identifying high-risk patients [32].

We identified P/LP variants in Lynch-related genes in 23 (36.51%) patients, of whom 18 were confirmed to be MMR-deficient by IHC. (Fig. 3A). Studies using universal screening for MMR deficiency in all CRC cases found lower germline variant rates. In Australia, screening of 813 CRC cases identified 11.1% with MMR deficiency and 5.2% with germline variants [33]. In China, screening of 4802 patients found 5.37% with MMR loss, with only 20% confirmed as Lynch families [38].

Using a selective strategy focusing on high-risk LS patients, this study showed higher rates of germline variants, similar to other low-resource countries, such as Brazil, where 41% of high-risk LS patients had MMR-deficient tumors and about half carried pathogenic germline variants [37]. Another study using WES on familial colorectal cancer type X identified 32 patients with cancer-associated variants. Sanger sequencing had previously confirmed the absence of germline MMR mutations in these patients, classifying them as FCCX cases. Interestingly, 4 patients were found to have MMR gene variants, suggesting a potential role of somatic or other mechanisms [39]. Our study, which focused on clinically high-risk individuals, showed higher germline variant rates than studies with broader CRC screenings.

An ATM mutation in a 52-year-old male with proximal adenocarcinoma emphasized the importance of including ATM in genetic testing for high-risk CRC patients [40]. Other variants found were: ASXL1 (c.2728 C > T; p.Q910X), FH (c.557G > A; p.S186N), pathogenic stop-gain variants of PMS1 (c.301 C > T; p.R101X), and a VUS (c.473 C > T; p.T158M). ASXL1 is associated with CRC progression (45) and FH gene variants are linked to hereditary leiomyomatosis and renal cell cancer (HLRCC) [41]. While PMS1 variants are rare in LS, some studies have identified germline PMS1 mutations in families with hereditary non-polyposis colorectal cancer (HNPCC), suggesting a potential, though limited, role in the disease [42].

MSH3 variants were identified in three families meeting Amsterdam criteria for LS and one with colon polyposis (Figure S6). While MSH3 deficiency is linked to genetic instability [43, 44, 45] and tumorigenesis, its exact role in CRC remains uncertain.

A germline variant (c.614G > A:p.R205H) in the TP53 gene was found in a patient with early-onset CRC, suggesting that early-onset CRC may be the first presentation of Li-Fraumeni Syndrome (LFS), warranting the inclusion of TP53 in CRC NGS panels. VUS found in MMR genes in families with a strong history of cancer are potential candidates to be reclassified as pathogenic or likely pathogenic. In this study, VUS variants were identified in MLH1 (c.621delA p.L207fs), MSH2 (c.2116G > A p.Val706Met), and MSH6 (c.64 A > G; p.K22E) (Table S1, Figure S7).

We also found VUS variants in non-Lynch genes such as in the breakpoint cluster region (BCR) gene, and GXYLT1 with the potential to be involved in the pathogenesis of LS (Table S1). BCR alterations are present in several cancers (56) and GXYLT1 variants promote CRC metastasis via the MAPK pathway (57). These findings warrant the need for further studies due to the complexity of genetic factors in CRC tumorigenesis and reinforce the importance of comprehensive genetic testing for high-risk populations.

Other studies have reported variants in non-Lynch genes, including BRCA1/2, APC, and biallelic MUTYH, CHEK2, TP53, PTEN, CDH1, and SMAD4 in individuals with clinical LS features [46]. In this study, we also found variants in the majority of these non-Lynch genes, including TP53 (:c.1010 C > T p.Arg337Trp), PTEN (:c.323 C > T p.Arg108Cys), CDH1 (c.1557T > G p.Val519Gly), and SMAD4 (c. T977T > C p. I326T).

Most LS variant carriers (32 patients) and non-LS variant carriers (26 patients) fulfilled the National Comprehensive Cancer Network (NCCN) criteria for LS. Thus, limited panel gene testing for MMR variants may miss the non-LS variants. Additionally, this study observed discordance between IHC results and genomic findings in 17.39% (4/23) of LS patients, consistent with recent studies that showed 15.2% of MSI and or IHC results for patients with MSH6 or PMS2 mutations were discordant, potentially leading to missed mutations without the use of multi-gene panel testing (MGPT) (64–67). This highlights the limitations of single gene testing based on IHC results and reinforces the need for comprehensive genetic testing to accurately identify pathogenic variants.

Germline variants in the APC and MUTYH genes were identified in 65% (25/38) of patients with over ten colorectal polyps and 68% (17/26) of patients with more than 100 colon polyps. These results aligned with previous studies showing APC variants in 33.5% and the MUTYH variant in 7.8% of adenoma cohorts [47]. The higher prevalence of APC and biallelic MUTYH variants in patients with over 100 polyps compared to previous studies [47, 48] might be due to differences in inclusion criteria and study population. Findings of WES revealed that 7% (3/38) of patients with 10–50 colon polyps had APC variants, and 5% (2/38) had MUTYH variants. These findings are consistent with previous findings showing a prevalence of 2.3-9% for variants in these genes in patients with a similar polyp burden [47, 48]. These results further emphasize the significance of genetic testing for patients with ten or more polyps and highlight the need for analyzing both polyposis and non-polyposis colorectal cancer genes in this population, as we have identified P/LP variants in the PTEN, BLM, BRCA2, and MSH3 genes. Consistent with a previous study [49], our findings suggest that MSH3 variants may represent a recessive subtype of colorectal adenomatous polyposis, providing further insights into the potential role of MSH3 in colon polyposis.

LS individuals should undergo regular colonoscopies and endometrial screening. A study of 1745 LS individuals showed that 16% had malignancies beyond colorectal and endometrial cancers, including breast, urinary bladder, and small bowel carcinoma [50]. We found gastric cancer as the second most common cancer and breast cancer as the third most common among LS probands. In another Iranian study, gastric cancer was the most common cancer in men and breast cancer in women, which should guide surveillance strategies [51].

The higher prevalence of gastric cancer in both Iranian and Japanese populations than in Western countries, suggests that environmental factors might also contribute, so endoscopic surveillance and H. pylori eradication are recommended in these populations (46, 47).

Evidence suggests breast cancer with medullary features as LS-related tumors [25], particularly for PMS2 variant carriers. A Canadian study highlighted 41 breast cancer cases in LS families, emphasizing the importance of intensified breast cancer surveillance in LS women [52]. Our findings support the potential association between LS and breast cancer, necessitating further investigation as well as long-term registry and follow-up of carrier cases.

This study had limitations, including a small size population, limited genomic coverage of WES, and reliance on Clinvar and Gnomad for variant classification due to the scarcity of data on subpopulations, such as Iranian. On the other hand, its strength lies in using a clinically selected cohort of high-risk LS cases to better correlate phenotype with genotype. We emphasize the limitations of target gene testing and the preference of using a broader gene panel for testing high-risk groups, to further incorporate them in genetic testing protocols for the Iranian population.

Finally, these results are consistent with other studies related to cascade testing [53]. Hampel et al. reported that cascade testing could find three carriers out of six family members tested [54]. This highlights the importance of cascade testing to identify carriers in probands.

Conclusion

Here we report the first assessment of the prevalence and type of germline variants associated with hereditary CRC and polyposis in the Iranian population. Since clinical criteria for LS analysis appear to identify many probands with unexpected P/LP variants in highly penetrant non-LS cancer susceptibility genes, and because of the growing reduction of WES costs, we suggest that comprehensive panel testing or even WES could eventually replace targeted genetic testing. A selective strategy followed by cascade genetic testing in FDR and SDR may potentially identify carriers with low cost, and help healthcare professionals indicate the most appropriate gene panels for testing. Finally, establishing a national registry for hereditary cancer syndromes, as the IHCCR, is the utmost need for under-resourced populations. This study might help develop national policies and guidelines for the screening and management of hereditary CRCs in Iran.

Data availability

No datasets were generated or analysed during the current study.

Abbreviations

INCR:

Iranian National Cancer Registry

CRC:

Colorectal cancer

GWASs:

Genome-wide association studies

LS:

Lynch syndrome

MMR:

Mismatch repair

FAP:

Familial adenomatous polyposis

MAP:

MUTYH-associated polyposis

NGS:

Next-generation sequencing

WES:

Whole exome sequencing

PPAP:

Polymerase proofreading–associated polyposis

IHCCR:

Iranian Hereditary Colorectal Cancer Registry

HNPCC:

Hereditary non-polyposis colorectal cancer

NCCN:

National Comprehensive Cancer Network

IHC:

Immunohistochemistry

MAF:

Minor allele frequency

GO:

Gene ontology

PPI:

Protein-protein interaction

CC:

Cellular component

MF:

Molecular function

BP:

Biological process

VUS:

Variations of uncertain significance

P:

Pathogenic variants

LP:

Likely pathogenic

SDR:

Second-degree relative

FDR:

First-degree relative

NCCN:

National Comprehensive Cancer Network

HRC:

High-risk colorectal cancer

MSI:

Microsatellite instability

EMAST:

Elevated microsatellite alterations at selected tetranucleotide repeats

LOH:

Loss of heterozygosity

EC:

Endometrial cancer

ED:

Exonuclease domain

NER:

Nucleotide excision repair

References

  1. Bray F, Ferlay J, Soerjomataram I, Siegel RL, Torre LA, Jemal A. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018;68:394–424. https://doiorg.publicaciones.saludcastillayleon.es/10.3322/caac.21492.

    Article  PubMed  Google Scholar 

  2. Morgan E, Arnold M, Gini A, Lorenzoni V, Cabasag CJ, Laversanne M, et al. Global burden of colorectal cancer in 2020 and 2040: incidence and mortality estimates from GLOBOCAN. Gut. 2023;72:338–44. https://doiorg.publicaciones.saludcastillayleon.es/10.1136/gutjnl-2022-327736.

    Article  PubMed  Google Scholar 

  3. Farhood B, Raei B, Malekzadeh R, Shirvani M, Najafi M, Mortezazadeh T. A review of incidence and mortality of colorectal, lung, liver, thyroid, and bladder cancers in Iran and compared to other countries. Contemp Oncol (Pozn). 2019;23:7–15. https://doiorg.publicaciones.saludcastillayleon.es/10.5114/wo.2019.84112.

    Article  PubMed  Google Scholar 

  4. Roshandel G, Ferlay J, Ghanbari-Motlagh A, Partovipour E, Salavati F, Aryan K, et al. Cancer in Iran 2008 to 2025: recent incidence trends and short-term predictions of the future burden. Int J Cancer. 2021;149:594–605. https://doiorg.publicaciones.saludcastillayleon.es/10.1002/ijc.33574.

    Article  CAS  PubMed  Google Scholar 

  5. Czene K, Lichtenstein P, Hemminki K. Environmental and heritable causes of cancer among 9.6 million individuals in the Swedish Family-Cancer database. Int J Cancer. 2002;99:260–6. https://doiorg.publicaciones.saludcastillayleon.es/10.1002/ijc.10332.

    Article  CAS  PubMed  Google Scholar 

  6. Wills C, Watts K, Houseman A, Maughan TS, Fisher D, Al-Tassan NA, et al. Relationship between inherited genetic variation and survival from colorectal cancer stratified by tumour location. Sci Rep. 2025;15:2423. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/s41598-024-77870-0.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Huyghe JR, Bien SA, Harrison TA, Kang HM, Chen S, Schmit SL, et al. Discovery of common and rare genetic risk variants for colorectal cancer. Nat Genet. 2019;51:76–87. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/s41588-018-0286-6.

    Article  CAS  PubMed  Google Scholar 

  8. Sadien ID, Davies RJ, Wheeler J. The genomics of sporadic and hereditary colorectal cancer. Ann R Coll Surg Engl. 2024;106:313–20. https://doiorg.publicaciones.saludcastillayleon.es/10.1308/rcsann.2024.0024.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Sinicrope FA. Increasing incidence of Early-Onset colorectal cancer. N Engl J Med. 2022;386:1547–58. https://doiorg.publicaciones.saludcastillayleon.es/10.1056/NEJMra2200869.

    Article  CAS  PubMed  Google Scholar 

  10. Pearlman R, Frankel WL, Swanson BJ, Jones D, Zhao W, Yilmaz A, et al. Prospective statewide study of universal screening for hereditary colorectal cancer: the Ohio colorectal cancer prevention initiative. JCO Precision Oncol. 2021;779–91. https://doiorg.publicaciones.saludcastillayleon.es/10.1200/PO.20.00525.

  11. Uson PLS, Riegert-Johnson JR, Boardman D, Kisiel L, Mountjoy J, Patel L. Germline cancer susceptibility gene testing in unselected patients with colorectal adenocarcinoma: A multicenter prospective study. Clin Gastroenterol Hepatol. 2022;20:e508–28. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.cgh.2021.04.013.

    Article  CAS  PubMed  Google Scholar 

  12. Yurgelun MB, Kulke MH, Fuchs CS, Allen BA, Uno H, Hornick JL, et al. Cancer susceptibility gene mutations in individuals with colorectal cancer. J Clin Oncol. 2017;35:1086–95. https://doiorg.publicaciones.saludcastillayleon.es/10.1200/JCO.2016.71.0012.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Magrin L, Fanale D, Brando C, Fiorino A, Corsini LR, Sciacchitano R, et al. POLE, POLD1, and NTHL1: the last but not the least hereditary cancer-predisposing genes. Oncogene. 2021;40:5893–901. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/s41388-021-01984-2.

    Article  CAS  PubMed  Google Scholar 

  14. Brinch HH, Byrjalsen A, Lohse Z, Rasmussen AØ, Karstensen JG, Kristiansen BS, Jelsig AM. Germline pathogenic variants in RNF43 in patients with and without serrated polyposis syndrome. Fam Cancer. 2024;24:3. https://doiorg.publicaciones.saludcastillayleon.es/10.1007/s10689-024-00428-6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Valle L, de Voer RM, Goldberg Y, Sjursen W, Försti A, Ruiz-Ponte C, et al. Update on genetic predisposition to colorectal cancer and polyposis. Mol Aspects Med. 2019;69:10–26. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.mam.2019.03.001.

    Article  CAS  PubMed  Google Scholar 

  16. Hoseini B, Rahmatinejad Z, Goshayeshi L, Bergquist R, Golabpour A, Ghaffarzadegan K, et al. Colorectal cancer in North-Eastern Iran: a retrospective, comparative study of early-onset and late-onset cases based on data from the Iranian hereditary colorectal cancer registry. BMC Cancer. 2022. https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12885-021-09132-5.

    Article  PubMed  PubMed Central  Google Scholar 

  17. Keivanlou M-H, Amini-Salehi E, Joukar F, Letafatkar N, Habibi A, Norouzi N, et al. Family history of cancer as a potential risk factor for colorectal cancer in EMRO countries: a systematic review and meta-analysis. Sci Rep. 2023;13:17457. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/s41598-023-44487-8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Goshayeshi L, Khooiee A, Ghaffarzadegan K, Rahmani Khorram M, Bishehsari F, Hoseini B, et al. Screening for Lynch syndrome in cases with colorectal carcinoma from Mashhad. Arch Iran Med. 2017;20:332–7.

    PubMed  Google Scholar 

  19. Zeinalian M, Emami MH, Salehi R, Naimi A, Kazemi M, Hashemzadeh-Chaleshtori M. Molecular analysis of Iranian colorectal cancer patients at risk for Lynch syndrome: a new molecular, clinicopathological feature. J Gastrointest Cancer. 2015;46:118–25. https://doiorg.publicaciones.saludcastillayleon.es/10.1007/s12029-015-9696-1.

    Article  CAS  PubMed  Google Scholar 

  20. Ghafouri-Fard S, Fardaei M, Lankarani KB, Miryounesi M. Segregation of a novel MLH1 mutation in an Iranian Lynch syndrome family. Gene. 2015;570:304–5. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.gene.2015.07.005.

    Article  CAS  PubMed  Google Scholar 

  21. Kashfi SMH, Behboudi Farahbakhsh F, Golmohammadi M, Nazemalhosseini Mojarad E, Azimzadeh P, Asadzadeh Aghdaie H. Frameshift mutations (Deletion at codon 1309 and codon 849) in the APC gene in Iranian FAP patients: a case series and review of the literature. Int J Mol Cell Med. 2014;3:196–202.

    PubMed  PubMed Central  Google Scholar 

  22. Ku C-S, Cooper DN, Wu M, Roukos DH, Pawitan Y, Soong R, Iacopetta B. Gene discovery in Familial cancer syndromes by exome sequencing: prospects for the Elucidation of Familial colorectal cancer type X. Mod Pathol. 2012;25:1055–68. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/modpathol.2012.62.

    Article  CAS  PubMed  Google Scholar 

  23. Rahmatinejad Z, Goshayeshi L, Bergquist R, Goshayeshi L, Golabpour A, Hoseini B. PTEN Hamartoma tumour syndrome: case report based on data from the Iranian hereditary colorectal cancer registry and literature review. Diagn Pathol. 2023;18:43. https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s13000-023-01331-x.

    Article  PubMed  PubMed Central  Google Scholar 

  24. Vasen HFA, Blanco I, Aktan-Collan K, Gopie JP, Alonso A, Aretz S, et al. Revised guidelines for the clinical management of Lynch syndrome (HNPCC): recommendations by a group of European experts. Gut. 2013;62:812–23. https://doiorg.publicaciones.saludcastillayleon.es/10.1136/gutjnl-2012-304356.

    Article  CAS  PubMed  Google Scholar 

  25. Umar A, Boland CR, Terdiman JP, Syngal S, Chapelle Adl, Ruschoff J, et al. Revised Bethesda guidelines for hereditary nonpolyposis colorectal cancer (Lynch Syndrome) and microsatellite instability. JNCI J Natl Cancer Inst. 2004;96:261–8. https://doiorg.publicaciones.saludcastillayleon.es/10.1093/jnci/djh034.

    Article  CAS  PubMed  Google Scholar 

  26. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a cytoscape plug-in to Decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25:1091–3. https://doiorg.publicaciones.saludcastillayleon.es/10.1093/bioinformatics/btp101.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Doncheva NT, Morris JH, Gorodkin J, Jensen LJ. Cytoscape StringApp: network analysis and visualization of proteomics data. J Proteome Res. 2019;18:623–32. https://doiorg.publicaciones.saludcastillayleon.es/10.1021/acs.jproteome.8b00702.

    Article  CAS  PubMed  Google Scholar 

  28. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13:2498–504. https://doiorg.publicaciones.saludcastillayleon.es/10.1101/gr.1239303.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Bakhshalizadeh S, Zerehdaran S, Javadmanesh A. Meta-analysis of genome-wide association studies and gene networks analysis for milk production traits in Holstein cows. Livest Sci. 2021;250:104605. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.livsci.2021.104605.

    Article  Google Scholar 

  30. Ge H, Walhout AJM, Vidal M. Integrating ‘omic’ information: a Bridge between genomics and systems biology. Trends Genet. 2003;19:551–60. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.tig.2003.08.009.

    Article  CAS  PubMed  Google Scholar 

  31. Park J, Karnati H, Rustgi SD, Hur C, Kong X-F, Kastrinos F. Impact of population screening for Lynch syndrome insights from the all of Us data. Nat Commun. 2025;16:523. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/s41467-024-52562-5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Mao R, Krautscheid P, Graham RP, Ganguly A, Shankar S, Ferber M, Hegde M. Genetic testing for inherited colorectal cancer and polyposis, 2021 revision: a technical standard of the American college of medical genetics and genomics (ACMG). Genet Med. 2021;23:1807–17. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/s41436-021-01207-9.

    Article  PubMed  Google Scholar 

  33. Buchanan DD, Clendenning M, Rosty C, Eriksen SV, Walsh MD, Walters RJ, et al. Tumor testing to identify Lynch syndrome in two Australian colorectal cancer cohorts. J Gastro Hepatol. 2017;32:427–38. https://doiorg.publicaciones.saludcastillayleon.es/10.1111/jgh.13468.

    Article  CAS  Google Scholar 

  34. Zhu L, Miao B, Dymerska D, Kuswik M, Bueno-Martínez E, Sanoguera-Miralles L, et al. Germline variants of CYBA and TRPM4 predispose to Familial colorectal cancer. Cancers (Basel). 2022;14:670. https://doiorg.publicaciones.saludcastillayleon.es/10.3390/cancers14030670.

    Article  CAS  PubMed  Google Scholar 

  35. Esteban-Jurado C, Vila-Casadesús M, Garre P, Lozano JJ, Pristoupilova A, Beltran S, et al. Whole-exome sequencing identifies rare pathogenic variants in new predisposition genes for Familial colorectal cancer. Genet Sci. 2015;17:131–42. https://doiorg.publicaciones.saludcastillayleon.es/10.1038/gim.2014.89.

    Article  CAS  Google Scholar 

  36. Djursby M, Madsen MB, Frederiksen JH, Berchtold LA, Therkildsen C, Willemoe GL, et al. New pathogenic germline variants in very early onset and Familial colorectal cancer patients. Front Genet. 2020. https://doiorg.publicaciones.saludcastillayleon.es/10.3389/fgene.2020.566266.

    Article  PubMed  PubMed Central  Google Scholar 

  37. de Paula AE, Galvão HCR, Bonatelli M, Sabato C, Fernandes GC, Berardinelli GN, et al. Clinicopathological and molecular characterization of Brazilian families at risk for Lynch syndrome. Cancer Genet. 2021;254–255:82–91. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.cancergen.2021.02.003.

    Article  CAS  PubMed  Google Scholar 

  38. Zhao G, Xiang G, Hu X, Qiao Y, Ma S, Tian Y, et al. Universal screening for Lynch syndrome in operated colorectal cancer by immunohistochemistry: a cohort of patients in Liaoning Province, China. Eur J Cancer Prev. 2023;32:337–47. https://doiorg.publicaciones.saludcastillayleon.es/10.1097/CEJ.0000000000000775.

    Article  CAS  PubMed  Google Scholar 

  39. Singh AK, Talseth-Palmer B, Xavier A, Scott RJ, Drabløs F, Sjursen W. Detection of germline variants with pathogenic potential in 48 patients with Familial colorectal cancer by using whole exome sequencing. BMC Med Genomics. 2023;16:126. https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12920-023-01562-3.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Choi M, Kipps T, Kurzrock R. ATM mutations in cancer: therapeutic implications. Mol Cancer Ther. 2016;15:1781–91. https://doiorg.publicaciones.saludcastillayleon.es/10.1158/1535-7163.MCT-15-0945.

    Article  CAS  PubMed  Google Scholar 

  41. Garg K, Rabban J. Hereditary leiomyomatosis and renal cell carcinoma syndrome associated uterine smooth muscle tumors: bridging morphology and clinical screening. Genes Chromosomes Cancer. 2021;60:210–6. https://doiorg.publicaciones.saludcastillayleon.es/10.1002/gcc.22905.

    Article  CAS  PubMed  Google Scholar 

  42. Wang Q, Lasset C, Desseigne F, Saurin JC, Maugard C, Navarro C, et al. Prevalence of germline mutations of hMLH1, hMSH2, hPMS1, hPMS2, and hMSH6 genes in 75 French kindreds with nonpolyposis colorectal cancer. Hum Genet. 1999;105:79–85. https://doiorg.publicaciones.saludcastillayleon.es/10.1007/s004399900064.

    Article  CAS  PubMed  Google Scholar 

  43. Harrington JM, Kolodner RD. Saccharomyces cerevisiae Msh2-Msh3 acts in repair of base-base mispairs. Mol Cell Biol. 2007;27:6546–54. https://doiorg.publicaciones.saludcastillayleon.es/10.1128/MCB.00855-07.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ohmiya N, Matsumoto S, Yamamoto H, Baranovskaya S, Malkhosyan SR, Perucho M. Germline and somatic mutations in hMSH6 and hMSH3 in Gastrointestinal cancers of the microsatellite mutator phenotype. Gene. 2001;272:301–13. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/s0378-1119(01)00517-0.

    Article  CAS  PubMed  Google Scholar 

  45. Haugen AC, Goel A, Yamada K, Marra G, Nguyen T-P, Nagasaka T, et al. Genetic instability caused by loss of MutS homologue 3 in human colorectal cancer. Cancer Res. 2008;68:8465–72. https://doiorg.publicaciones.saludcastillayleon.es/10.1158/0008-5472.CAN-08-0002.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Yurgelun MB, Allen B, Kaldate RR, Bowles KR, Judkins T, Kaushik P, et al. Identification of a variety of mutations in cancer predisposition genes in patients with suspected Lynch syndrome. Gastroenterology. 2015;149:604–e61320. https://doiorg.publicaciones.saludcastillayleon.es/10.1053/j.gastro.2015.05.006.

    Article  CAS  PubMed  Google Scholar 

  47. Stanich PP, Pearlman R, Hinton A, Gutierrez S, LaDuca H, Hampel H, Jasperson K. Prevalence of germline mutations in polyposis and colorectal Cancer-Associated genes in patients with multiple colorectal polyps. Clin Gastroenterol Hepatol. 2019;17:2008–e20153. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.cgh.2018.12.008.

    Article  CAS  PubMed  Google Scholar 

  48. Grover S, Kastrinos F, Steyerberg EW, Cook EF, Dewanwala A, Burbidge LA, et al. Prevalence and phenotypes of APC and MUTYH mutations in patients with multiple colorectal adenomas. JAMA. 2012;308:485–92. https://doiorg.publicaciones.saludcastillayleon.es/10.1001/jama.2012.8780.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Adam R, Spier I, Zhao B, Kloth M, Marquez J, Hinrichsen I, et al. Exome sequencing identifies biallelic MSH3 germline mutations as a recessive subtype of colorectal adenomatous polyposis. Am J Hum Genet. 2016;99:337–51. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.ajhg.2016.06.015.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Elze L, van der Post RS, Vos JR, Mensenkamp AR, de Hullu MSC, Nagtegaal ID, et al. Microsatellite instability in noncolorectal and nonendometrial malignancies in patients with Lynch syndrome. JNCI J Natl Cancer Inst. 2023;115:853–60. https://doiorg.publicaciones.saludcastillayleon.es/10.1093/jnci/djad063.

    Article  CAS  PubMed  Google Scholar 

  51. Mohammadi E, Aminorroaya A, Fattahi N, Azadnajafabad S, Rezaei N, Farzi Y, et al. Epidemiologic pattern of cancers in Iran; current knowledge and future perspective. J Diabetes Metab Disord. 2021;20:825–9. https://doiorg.publicaciones.saludcastillayleon.es/10.1007/s40200-020-00654-6.

    Article  PubMed  Google Scholar 

  52. Goldberg M, Bell K, Aronson M, Semotiuk K, Pond G, Gallinger S, Zbuk K. Association between the Lynch syndrome gene MSH2 and breast cancer susceptibility in a Canadian Familial cancer registry. J Med Genet. 2017;54:742–6. https://doiorg.publicaciones.saludcastillayleon.es/10.1136/jmedgenet-2017-104542.

    Article  CAS  PubMed  Google Scholar 

  53. Passero LE, Roberts MC. Challenges and opportunities for Lynch syndrome cascade testing in the united States. Fam Cancer. 2024;23:147–54. https://doiorg.publicaciones.saludcastillayleon.es/10.1007/s10689-024-00374-3.

    Article  PubMed  Google Scholar 

  54. Hampel H. Population screening for hereditary colorectal cancer. Surg Oncol Clin N Am. 2018;27:319–25. https://doiorg.publicaciones.saludcastillayleon.es/10.1016/j.soc.2017.11.006.

    Article  PubMed  Google Scholar 

Download references

Acknowledgements

We would like to thank Mashhad University of Medical Sciences, The Research Institute of Biotechnology of Ferdowsi University of Mashhad, and Professor Reza Malekzadeh for their support.

Funding

This study was supported by the National Institute for Medical Research Development (NIMAD) (grant number 978991) and Mashhad University of Medical Sciences (grant number 978991).

Author information

Authors and Affiliations

  1. Surgical Oncology Research Center, Imam Reza Hospital, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

    Lena Goshayeshi & Ladan Goshayeshi

  2. Stem Cell Biology and Regenerative Medicine Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Azadi Square, Mashhad, 91779-48974, Iran

    Lena Goshayeshi, Morteza Zahedi & Hesam Dehghani

  3. Department of Gastroenterology and Hepatology, Abu Ali Sina Hospital, Shiraz, Iran

    Saeed Hoorang

  4. Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran

    Benyamin Hoseini

  5. Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

    Mohammad Reza Abbaszadegan & Maliheh Alimardani

  6. Department of Gastroenterology and Hepatology, Faculty of Medicine, Neyshabur University of Medical Sciences, Mashhad, Iran

    Maryam Afrazeh

  7. Poursina Hakim Digestive Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran

    Fatemeh Maghool & Mohammad Hassan Emami

  8. Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands

    Milad Shademan

  9. Department of Genetics & Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran

    Mehrdad Zeinalian

  10. Department of Gastroenterology and Hepatology, Tehran University of Medical Sciences, Tehran, Iran

    Foroogh Alborzi & Nasser Ebrahimi Daryani

  11. Division of Colorectal Surgery, Department of Surgery, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran

    Mohammad Reza Keramati

  12. Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

    Ashkan Torshizian

  13. Department of Gastroenterology and Hepatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

    Hassan Vosoghinia & Ladan Goshayeshi

  14. Department of Radiology, Mashhad Branch, Islamic Azad University, Mashhad, Iran

    Farnood Rajabzadeh

  15. Hematology-Oncology Department, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran

    Alireza Bary

  16. Familial & Hereditary Cancers Institute, Tehran, Iran

    Massih Bahar

  17. Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran

    Ali Javadmanesh

  18. Industrial Biotechnology Research Group, Research Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran

    Ali Javadmanesh

  19. Centre for Molecular Pathology, Royal Marsden Hospital, Institue of Cancer Research, London, UK

    Jamshid Sorouri-Khorashad

  20. Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands

    Hans F.A. Vasen

  21. Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran

    Hesam Dehghani

Authors
  1. Lena Goshayeshi
    View author publications

    You can also search for this author inPubMed Google Scholar

  2. Saeed Hoorang
    View author publications

    You can also search for this author inPubMed Google Scholar

  3. Benyamin Hoseini
    View author publications

    You can also search for this author inPubMed Google Scholar

  4. Mohammad Reza Abbaszadegan
    View author publications

    You can also search for this author inPubMed Google Scholar

  5. Maryam Afrazeh
    View author publications

    You can also search for this author inPubMed Google Scholar

  6. Maliheh Alimardani
    View author publications

    You can also search for this author inPubMed Google Scholar

  7. Fatemeh Maghool
    View author publications

    You can also search for this author inPubMed Google Scholar

  8. Milad Shademan
    View author publications

    You can also search for this author inPubMed Google Scholar

  9. Morteza Zahedi
    View author publications

    You can also search for this author inPubMed Google Scholar

  10. Mehrdad Zeinalian
    View author publications

    You can also search for this author inPubMed Google Scholar

  11. Foroogh Alborzi
    View author publications

    You can also search for this author inPubMed Google Scholar

  12. Mohammad Reza Keramati
    View author publications

    You can also search for this author inPubMed Google Scholar

  13. Ashkan Torshizian
    View author publications

    You can also search for this author inPubMed Google Scholar

  14. Hassan Vosoghinia
    View author publications

    You can also search for this author inPubMed Google Scholar

  15. Farnood Rajabzadeh
    View author publications

    You can also search for this author inPubMed Google Scholar

  16. Alireza Bary
    View author publications

    You can also search for this author inPubMed Google Scholar

  17. Massih Bahar
    View author publications

    You can also search for this author inPubMed Google Scholar

  18. Ali Javadmanesh
    View author publications

    You can also search for this author inPubMed Google Scholar

  19. Jamshid Sorouri-Khorashad
    View author publications

    You can also search for this author inPubMed Google Scholar

  20. Mohammad Hassan Emami
    View author publications

    You can also search for this author inPubMed Google Scholar

  21. Nasser Ebrahimi Daryani
    View author publications

    You can also search for this author inPubMed Google Scholar

  22. Hans F.A. Vasen
    View author publications

    You can also search for this author inPubMed Google Scholar

  23. Ladan Goshayeshi
    View author publications

    You can also search for this author inPubMed Google Scholar

  24. Hesam Dehghani
    View author publications

    You can also search for this author inPubMed Google Scholar

Contributions

HD, LaG, and HanV designed the study. LeG, MRA, NED, JSK, MHE, AJ, FA, MS, FM, SH, AB, MehZ, MRK, MB, MA, FR, and HV were involved in the data gathering and interpreting the results. LaG, MA, MorZ, and LeG performed analyses. LeG, LaG, AT, BH, and HD wrote the first draft of the manuscript. HD, HanV, JSK, LaG, MRA, FR, and LeG edited the final version of the manuscript. All authors read and approved the final version of the manuscript.

Corresponding authors

Correspondence to Ladan Goshayeshi or Hesam Dehghani.

Ethics declarations

Ethics approval and consent to participate

This study was approved by the Ethics Committee of Mashhad University of Medical Sciences (ethics code: IR.MUMS.REC.1396.164) and conformed to the ethical principles in the Declaration of Helsinki. The participants signed an informed consent form before the study for experiments involving human participants (including tissue samples).

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Material 1

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License, which permits any non-commercial use, sharing, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if you modified the licensed material. You do not have permission under this licence to share adapted material derived from this article or parts of it. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by-nc-nd/4.0/.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Goshayeshi, L., Hoorang, S., Hoseini, B. et al. Germline variants in patients from the Iranian hereditary colorectal cancer registry. Cancer Cell Int 25, 140 (2025). https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12935-025-03773-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doiorg.publicaciones.saludcastillayleon.es/10.1186/s12935-025-03773-3

Keywords

Cancer Cell International

ISSN: 1475-2867

Contact us