Comprehensive characterization of CRC with germline mutations reveals a distinct somatic mutational landscape and elevated cancer risk in the Chinese population.

OBJECTIVE: Hereditary colorectal cancer (CRC) accounts for approximately 5%-10% of all CRC cases. The full profile of CRC-related germline mutations and the corresponding somatic mutational profile have not been fully determined in the Chinese population. METHODS: We performed the first population study investigating the germline mutation status in more than 1,000 (n = 1,923) Chinese patients with CRC and examined their relationship with the somatic mutational landscape. Germline alterations were examined with a 58-gene next-generation sequencing panel, and somatic alterations were examined with a 605-gene panel. RESULTS: A total of 92 pathogenic (P) mutations were identified in 85 patients, and 81 likely pathogenic (LP) germline mutations were identified in 62 patients, accounting for 7.6% (147/1,923) of all patients. MSH2 and APC was the most mutated gene in the Lynch syndrome and non-Lynch syndrome groups, respectively. Patients with P/LP mutations had a significantly higher ratio of microsatellite instability, highly deficient mismatch repair, family history of CRC, and lower age. The somatic mutational landscape revealed a significantly higher mutational frequency in the P group and a trend toward higher copy number variations in the non-P group. The Lynch syndrome group had a significantly higher mutational frequency and tumor mutational burden than the non-Lynch syndrome group. Clustering analysis revealed that the Notch signaling pathway was uniquely clustered in the Lynch syndrome group, and the MAPK and cAMP signaling pathways were uniquely clustered in the non-Lynch syndrome group. Population risk analysis indicated that the overall odds ratio was 11.13 (95% CI: 8.289-15.44) for the P group and 20.68 (95% CI: 12.89-33.18) for the LP group. CONCLUSIONS: Distinct features were revealed in Chinese patients with CRC with germline mutations. The Notch signaling pathway was uniquely clustered in the Lynch syndrome group, and the MAPK and cAMP signaling pathways were uniquely clustered in the non-Lynch syndrome group. Patients with P/LP germline mutations exhibited higher CRC risk.

The contribution of hereditary cancer-related germline mutations to lung cancer susceptibility.

BACKGROUND: Germline variations may contribute to lung cancer susceptibility besides environmental factors. The influence of germline mutations on lung cancer susceptibility and their correlation with somatic mutations has not been systematically investigated. METHODS: In this study, germline mutations from 1,026 non-small cell lung cancer (NSCLC) patients were analyzed with a 58-gene next-generation sequencing (NGS) panel containing known hereditary cancer-related genes, and were categorized based on American College of Medical Genetics and Genomics (ACMG) guidelines in pathogenicity, and the corresponding somatic mutations were analyzed using a 605-gene NGS panel containing known cancer-related genes. RESULTS: Plausible genetic susceptibility was found in 4.7% of lung cancer patients, in which 14 patients with pathogenic mutations (P group) and 34 patients with likely-pathogenic mutations (LP group) were identified. The ratio of the first degree relatives with lung cancer history of the P groups was significantly higher than the Non-P group (P=0.009). The ratio of lung cancer patients with history of other cancers was higher in P (P=0.0007) or LP (P=0.017) group than the Non-P group. Pathogenic mutations fell most commonly in BRCA2, followed by CHEK2 and ATM. Likely-pathogenic mutations fell most commonly in NTRK1 and EXT2, followed by BRIP1 and PALB2. These genes are involved in DNA repair, cell cycle regulation and tumor suppression. By comparing the germline mutation frequency from this study with that from the whole population or East Asian population (gnomAD database), we found that the overall odds ratio (OR) for P or LP group was 17.93 and 15.86, respectively, when compared with the whole population, and was 2.88 and 3.80, respectively, when compared with the East Asian population, suggesting the germline mutations of the P and LP groups were risk factors for lung cancer. Somatic mutation analysis revealed no significant difference in tumor mutation burden (TMB) among the groups, although a trend of lower TMB in the pathogenic group was found. The SNV/INDEL mutation frequency of TP53 in the P group was significantly lower than the other two groups, and the copy number variation (CNV) mutation frequency of PIK3CA and MET was significantly higher than the Non-P group. Pathway enrichment analysis found no significant difference in aberrant pathways among the three groups. CONCLUSIONS: A proportion of 4.7% of patients carrying germline variants may be potentially linked to increased susceptibility to lung cancer. Patients with pathogenic germline mutations exhibited stronger family history and higher lung cancer risk.

Identification of a novel germline frameshift mutation p.D300fs of PMS1 in a patient with hepatocellular carcinoma: A case report and literature review.

RATIONALE: PMS1 is one of the mismatch repair (MMR) genes with potential crucial roles in carcinogenesis. Very few reports have been identified on germline PMS1 mutations with definite disease phenotype. Here we report a case of hepatocellular carcinoma (HCC) with a novel potential pathogenic germline PMS1 mutation. PATIENT CONCERNS: A 46-year-old Chinese male with Hepatitis B infection history presented a single cancerous nodule (10×12×10 mm) at the left lobe of liver. The nodule was considered malignant by type-B ultrasonic and computed tomography (CT) examinations. DIAGNOSIS AND INTERVENTION: Liver lobectomy was performed to remove the liver cancerous nodule and postoperative TACE was performed for recurrence prevention. Pathological examination on resected tumor tissue confirmed the diagnosis of HCC. Whole-exome sequencing (WES) identified the c.900delT (p.D300fs) heterozygous germline mutation of PMS1, along with 253 nonsynonymous single nucleotide variations (SNVs), 14 Insertion or deletion mutations (INDELs) and 21 genes with copy number variations (CNVs). Three-dimensional prediction of protein tertiary structure suggested that the conformation of the enzyme active site and the ligand binding site might be changed due to the protein truncation. OUTCOMES: The patient was still alive in good condition with no sign of recurrence in 12 months follow-up period. LESSONS: The affected pathways in this case were unique from previously reported HCC patients with no PMS1 germline mutations. The novel PMS1 germline mutation may increase cancer risk. The roles of PMS1 germline mutations in carcinogenesis need further investigation.

The ESR1 gene in unexplained recurrent spontaneous abortion.

Recurrent spontaneous abortion (RSA) is a health problem that affects nearly 1% of fertile couples. However, the underlying etiology and mechanism(s) remain elusive. The aim of this study was to investigate estrogen receptor (ESR) 1 gene polymorphisms for risk association of unexplained recurrent spontaneous abortion (URSA) in the Chinese Han population. The entire coding region of the ESR1 gene was sequenced from 129 URSA patients and 183 healthy controls. There was a significant difference between the G allele and GG genotype distributions, of the ESR1 gene (XbaI) polymorphism, between the URSA and the control groups (χ(2) = 14.93, df = 1, p < 0.001, OR = 2.01 95% CI: 1.41-2.88 by allele; χ(2) = 12.24, df = 2, p = 0.002 by genotype). The PvuII polymorphism, C allele frequency was higher in RSA than in controls (41.9% vs. 34.7%, respectively). Women carrying C-G haplotype were associated with an increased risk of URSA in this population (permutation test p value = 0.016, OR = 1.76 95% CI: 1.19-2.59). Estrogen receptor 1 gene PvuII and XbaI polymorphisms were associated with URSA in a Chinese Han population. However, independent replication of these associations are necessary to assure veracity.

The HHEX gene is not related to congenital heart disease in 296 Chinese patients.

BACKGROUND: The hematopoietically expressed homeobox (HHEX) gene is an important determinant of mammalian heart development. This study aimed to identify the potential mutations of the gene in Chinese patients with congenital heart disease (CHD). METHODS: We collected 296 CHD patients and 200 controls, and classified the cardiac deformities. Then we conducted sequence analyses of the HHEX gene in those patients. RESULTS: In all the CHD patients, we did not find any causative mutations in the coding region of the HHEX gene. CONCLUSION: To our knowledge, this is the first study to examine the HHEX gene in non-symptomatic CHD cases, and this has expanded our knowledge about its etiology.

Association analysis between HOXD9 genes and the development of developmental dysplasia of the hip in Chinese female Han population.

BACKGROUND: Developmental dysplasia of the hip (DDH) is a congenital or acquired deformation or misalignment of the hip joint which affects mainly females. We hypothesized that HOXD9 gene could be regulated in acetabular size or shape and related in DDH developing. METHODS: Two hundred and nine Chinese Han female DDH patients and 173 ethnic, age matched healthy female controls were genotyped for HOXD9 two tag SNPs using sequenom method. RESULTS: One of the two tag SNPs, rs711822, was not shown significantly differences in genotypic or allelic distribution between case and control group. Comparing the genotypic distribution of rs711819, there was significant differences between DDH patients group and control group (χ² = 7.54, df =2, P =0.023), and the association to DDH developing reached significance (P =0.045, OR =1.79, 95 % CI: 1.01-3.17 by dominant mode). CONCLUSION: In conclusion, the association between one tag SNP of HOXD9 gene and the development of DDH reach significant in our study population, this result indicate the positive correlation between HOXD9 gene and DDH developing. Further study in larger sample size and different population as well as functional studies will help to understand the pathogenesis of DDH.

Polymorphisms in the presumptive promoter region of the SLC2A9 gene are associated with gout in a Chinese male population.

BACKGROUND: Glucose transporter 9 (GLUT9) is a high-capacity/low-affinity urate transporter. To date, several recent genome-wide association studies (GWAS) and follow-up studies have identified genetic variants of SLC2A9 associated with urate concentrations and susceptibility to gout. We therefore investigated associations between gout and polymorphisms and haplotypes in the presumptive promoter region of GLUT9 in Chinese males. METHODOLOGY/PRINCIPAL FINDINGS: The approximately 2000 bp presumptive promoter region upstream of the start site of exon 1 of GLUT9 was sequenced and subjected to genetic analysis. A genotype-phenotype correlation was performed and polymorphisms-induced changes in transcription factor binding sites were predicted. Of 21 SNPs identified in GLUT9, five had not been previously reported. Two of the SNPs (rs13124007 and rs6850166) were associated with susceptibility to gout (p = 0.009 and p = 0.042, respectively). The C allele of rs13124007 appeared to be the risk allele for predisposition to gout (p = 0.006, OR 1.709 [95% CI 1.162-2.514]). For rs6850166, an increased risk of gout was associated with the A allele (p = 0.029, OR 1.645 [95% CI 1.050-2.577]). After Bonferroni correction, there was statistically difference in rs13124007 allele frequencies between gout cases and controls (P = 0.042). Haplotype analyses showed that haplotype GG was a protective haplotype (p = 0.0053) and haplotype CA was associated with increased risk of gout (p = 0.0326). Genotype-phenotype analysis among gout patients revealed an association of rs13124007 with serum triglycerides levels (P = 0.001). The C to G substitution in polymorphism rs13124007 resulted in a loss of a binding site for transcription factor interferon regulatory factor 1 (IRF-1). CONCLUSIONS/SIGNIFICANCE: Polymorphisms rs13124007 and rs6850166 are associated with susceptibility to gout in Chinese males.

Mutation analysis of the WNT4 gene in Han Chinese women with premature ovarian failure.

BACKGROUND: The WNT4 gene plays an important role in female sex determination and differentiation. It also contributes to maintaining of the ovaries and the survival of follicles. METHODS: We sequenced the coding region and splice sites of WNT4 in 145 Han Chinese women with premature ovarian failure (POF) and 200 healthy controls. RESULTS: Only one novel variation, in Exon 2 (195C > T), was detected among the women with POF. However, this synonymous variation did not result in a change in amino acid sequence (65 Asp > Asp). No further variants were found in any of the samples. CONCLUSION: Although we cannot provide any evidence that it is a possible disease-causing gene, this study is the first attempt to investigate the possible role of WNT4 in Han Chinese women with POF.

Haplotype analysis of chemokine CXCL12 polymorphisms and susceptibility to premature ovarian failure in Chinese women.

BACKGROUND Chemokine (C-X-C motif) ligand 12 (CXCL12/stromal cell-derived factor 1) has been suggested to play an essential role in primordial germ cell migration, colonization and survival, and in the primordial to primary follicle transition. This study was performed to investigate an association of polymorphisms in CXCL12 with the risk of premature ovarian failure (POF) in Chinese patients. METHODS Tagging single nucleotide polymorphisms (SNPs) were selected using the Chinese HapMap database. Five SNPs (rs4948878, rs1801157, rs266087, rs266093 and rs1029153) were genotyped by direct sequencing in 111 patients with POF and 183 healthy controls recruited from the First Affiliated Hospital, Anhui Medical University, China. RESULTS Compared with controls, there were significantly higher frequencies of the rs1801157 A allele and haplotype C-T-A-T-T in cases with POF [P = 6.38E-07, odds ratio (OR) = 3.10, 95% confidence interval (CI) 1.955-4.890 by allele; P = 7.0E-04, OR = 2.39, 95% CI 1.43-3.97 by haplotype]. No differences were observed for the other four SNPs between POF cases and controls. CONCLUSIONS A strong association between a CXCL12 polymorphism and POF was established in Chinese patients, suggesting that CXCL12 might be a new candidate gene involved in POF. The A allele of CXCL12 polymorphism rs1801157 is a possible risk factor for developing POF. However, further independent studies are necessary to confirm our findings.

Genetic association between BDNF gene polymorphisms and phobic disorders: a case-control study among mainland Han Chinese.

INTRODUCTION: Phobic disorders are a common group of syndromes comprising persistently recurring, irrational severe anxiety of specific objects, activities, or situations with avoidance behavior of the phobic stimulus. The present study investigated the association between whole region polymorphisms, (including the Val66Met variant), in the BDNF gene and phobic disorders among Han Chinese young adults. METHODS: We conducted a case-control study to investigate the genetic association between BDNF polymorphisms and phobic disorders among mainland Chinese. One hundred and twenty young adults with phobic disorders and 267 matched controls were recruited. Three tag SNPs of BDNF were successfully genotyped by using PCR-based ligase detection reaction (PCR-LDR). RESULTS: We found significant differences in allele distributions of SNP rs10835210 (P<0.001) between the experimental and the control groups. In the haplotype analysis based on linkage-disequilibrium across this gene locus, we demonstrated significant association between phobic disorders and BDNF haplotype CAC (P=0.004). Association was significant after 10(4) permutation tests (P<0.001). CONCLUSION: To the best of our knowledge, this is the first study showing that the BDNF gene may play a significant role in the etiology of phobic disorders in the Han Chinese population.

New candidate gene POU5F1 associated with premature ovarian failure in Chinese patients.

Premature ovarian failure (POF) is defined as a cessation of ovarian function in women before the age of 40 years. POU5F1 has a critical role in regulating pluripotency in embryonic development and POU5F1 transcription factor is down-regulated more than 30-fold in the POF candidate gene Nobox knockout ovaries. In order to identify the potential correlation between POU5F1 and the development of POF, the exon regions of POU5F1 were amplified and sequenced in 115 POF patients and 149 healthy controls. One non-synonymous variant of POU5F1 (c. C37A, p. Pro13Thr) was identified and confirmed in one of the POF patients. The substitution replacing a hydrophobic amino acid, proline, with a hydrophilic amino acid, threonine. As far as is known, the present study is the first to identify a potential association between POU5F1 and the development of POF.

A novel GJA8 mutation (p.I31T) causing autosomal dominant congenital cataract in a Chinese family.

PURPOSE: To identify the genetic defect associated with autosomal dominant congenital nuclear cataract in a Chinese family. METHODS: Family history and clinical data were recorded. The genomic DNA was extracted from peripheral blood leukocytes. All the members were genotyped with microsatellite markers at loci considered to be associated with cataracts. Two-point logarithm of odds (LOD) scores were calculated by using the Linkage software after genotyping. Mutations were detected by DNA sequence analysis of the candidate genes. Effects of amino acid changes on the structure and function of proteins were predicted by bioinformatics analysis. RESULTS: Evidence of a linkage was obtained at markers D1S514 (LOD score [Z]=3.48, recombination fraction [theta]=0.0) and D1S1595 (Z=2.49, theta=0.0). Haplotype analysis indicated that the cataract gene was close to these two markers. Sequencing of the connexin 50 (GJA8) gene revealed a T>C transition at nucleotide position c.92. This nucleotide change resulted in the substitution of highly conserved isoleucine by threonine at codon 31(I31T). This mutation co-segregated with all affected individuals and was not observed in unaffected or 110 normal unrelated individuals. Bioinformatics analysis showed that a highly conserved region was located at Ile31, and the mutation was predicted to affect the function and secondary structure of the GJA8 protein. CONCLUSION: A novel mutation in GJA8 was detected in a Chinese family with autosomal dominant congenital nuclear cataract, providing clear evidence of a relationship between the genotype and the corresponding cataract phenotype.