Predominance of pathogenic missense variants in the RAD51C gene occurring in breast and ovarian cancer families

RAD51C was defined by Meindl et al. in 2010 as a high-risk gene involved in hereditary breast and ovarian cancers. Although this role seems to be clear, nowadays there is controversy about the indication of including the gene in routine clinical genetic testing, due to the lower prevalence or the absence of mutations found in subsequent studies. Here, we present the results of a comprehensive mutational screening of the RAD51C gene in a large series of 785 Spanish breast and/or ovarian cancer families, which, in contrast to the various subsequent studies published to date, includes the functional characterization of suspicious missense variants as reported in the initial study. We have detected 1.3% mutations of RAD51C in breast and ovarian cancer families, while mutations in breast cancer only families seem to be very rare. More than half of the deleterious variants detected were of missense type, which highlights their significance in the gene, and suggest that RAD51C mutations may have been so far partially disregarded and their prevalence underestimated due to the lack of functional complementation assays. Our results provide new evidences, suggesting that the genetic testing of RAD51C should be considered for inclusion into the clinical setting, at least for breast and ovarian cancer families, and encourage re-evaluating its role incorporating functional assays.     

Truncating mutations of TP53AIP1 gene predispose to cutaneous melanoma

Genetic predisposition to cutaneous malignant melanoma (CMM) involves highly penetrant predisposing genes and low and intermediate penetrant predisposing alleles. However, the missing heritability in (CMM) is still high. For such and in order to identify new genetic factors for CMM, we conducted an exome sequencing study in high‐risk CMM patients. Two rounds of exome sequencing were successively performed in 33 and 27 high‐risk patients. We focused on genes carrying rare nonsense, frameshift, and splice variants (allelic frequency <1%) that were present in both series of exomes. An extension study was then conducted in a large cohort (1 079 CMM patients and 1 230 Caucasian ethnically matched healthy controls), and the inactivating variants frequency was compared between groups using two‐sided Fisher exact test. Two TP53AIP1 truncating mutations were identified in four patients: a frameshift c.63_64insG, p.Q22Afs*81 in two patients from the same family and in the proband of a second family; and a nonsense mutation c.95 C > A, p.Ser32Stop in a patient with multiple CMMs. In all patients, TP53AIP1 truncating variants were strongly associated with CMM risk (two‐sided Fisher exact test = 0.004, OR = 3.3[1.3‐8.5]). Additionally, we showed that TP53AIP1 mRNA was strongly down‐regulated throughout different phases of melanoma progression. TP53AIP1 gene is a TP53 target which plays a key role by inducting apoptosis in response to UV‐induced DNA damage. Constitutional mutations of TP53AIP1 had previously been involved in susceptibility to prostate cancer. Our results show that constitutional truncating TP53AIP1 mutations predispose to CMM in the French population. Replication studies in other populations should be performed.     

The ATPase motif in RAD51D is required for resistance to DNA interstrand crosslinking agents and interaction with RAD51C

Homologous recombination (HR) is a mechanism for repairing DNAinterstrand crosslinks and double-strand breaks. In mammals,HR requires the activities of the RAD51 family (RAD51, RAD51B,RAD51C, RAD51D, XRCC2, XRCC3 and DMC1), each of which containsconserved ATP binding sequences (Walker Motifs A and B). RAD51Dis a DNA-stimulated ATPase that interacts directly with RAD51Cand XRCC2. To test the hypothesis that ATP binding and hydrolysisby RAD51D are required for the repair of interstrand crosslinks,site-directed mutations in Walker Motif A were generated, andcomplementation studies were performed in Rad51d-deficient mouseembryonic fibroblasts. The K113R and K113A mutants demonstrateda respective 96 and 83% decrease in repair capacity relativeto wild-type. Further examination of these mutants, by yeasttwo-hybrid analyses, revealed an 8-fold reduction in the abilityto associate with RAD51C whereas interaction with XRCC2 wasretained at a level similar to the S111T control. These cell-basedstudies are the first evidence that ATP binding and hydrolysisby RAD51D are required for efficient HR repair of DNA interstrandcrosslinks. ² Present address: Genentech, Inc., South San Francisco, CA, USA ³ Present address: University of California, Davis, Sacramento,CA, USA ^* To whom correspondence should be addressed at Department of Physiology and Cardiovascular Genomics, Medical University of Ohio, Block Health Science Building, 3035 Arlington Avenue, Toledo, OH 43614-5804, USA. Tel: +1 419 383 4370; Fax: +1 419 383 6168; Email: dpittman{at}meduohio.edu.      

TP53 status and gene amplification in human colorectal carcinomas

Gene amplification is one of the characteristics of cancer cells. In vitro studies suggested that alterations of the TP53 gene might be responsible for gene amplification. We have examined the presence of TP53 mutations and looked for cytogenetic evidence of gene amplification in a series of 79 primary colorectal carcinomas. Other parameters such as the pattern of cytogenetic alterations, microsatellite instability, tumor site, and histological staging were also considered. A multiparametric study supported by statistical analyses suggests the existence of two major pathways of colorectal carcinogenesis. No relationships could be established between the presence of TP53 alterations and gene amplification.     

Absence of TP53 alterations in pheochromocytomas and medullary thyroid carcinomas

The role of the TP53 gene in the development of inherited and sporadic pheochromocytomas and medullary thyroid carcinomas (MTC) has not been clarified because of conflicting reports and limitations in the assays used to detect mutations. To determine the frequency of TP53 alterations in these tumors, 22 pheochromocytomas and 29 MTCs were screened for loss of heterozygosity (LOH) on 17p with four markers. Single-strand-conformation-variant (SSCV) analysis of exons 4–9 of the TP53 gene was performed in 20 of the pheochromocytomas and in 22 of the MTCs. The expression of p53 was determined by immunohistochemistry in 19 pheochromocytomas and in 17 MTCs using two antibodies (D01 and D07) on frozen and paraffin-embedded tissues. Four of the 22 pheochromocytomas and none of the MTCs showed LOH on 17p. No mutations were detected in any of the tumors screened by SSCV analysis. Immunohistochemical staining of frozen and paraffin-embedded tumor sections did not show p53 overexpression in any of the tumors examined. Our findings indicate that mutations in the TP53 gene are an uncommon event in the tumorigenesis of pheochromocytomas and medullary thyroid carcinomas. Genes Chromosom. Cancer 20:24–29, 1997. © 1997 Wiley-Liss, Inc.     

Common polymorphisms in TP53 and MDM2 and the relationship to TP53 mutations and clinical outcomes in women with ovarian and peritoneal carcinomas

The importance of somatic TP53 mutations and germline TP53 codon 72 genotype in the survival of women with epithelial ovarian cancer is controversial. Recent data suggest that a promoter polymorphism in the MDM2 gene may influence age of cancer onset in a gender-specific fashion. We sought to determine the relationship between somatic TP53 mutations, germline genotypes at TP53 codon 72 and MDM2 SNP309, and overall survival and response to chemotherapy in a large series of patients with ovarian and peritoneal carcinomas. Of the 188 cancers, 103 (54.8%) had a TP53 mutation, of which 71% were missense mutations and 29% were null mutations. TP53 mutation status and mutation type (null vs. missense) did not influence response to therapy or overall survival. Women with the codon 72 Pro/Pro had a decreased overall survival (median, 29 months) compared with women with one or two arginine alleles (median, 49 months; P=0.04). Somatic mutation or deletion was equally common for either codon 72 allele. Age of diagnosis was not influenced by codon 72 but showed a trend for younger age in women with somatic TP53 mutations and the MDM2 G/G genotype.     

The clinical significance of RAD51 G135C polymorphysm and p53 mutation in non-small cell lung cancer

目的 探讨RAD51基因G135C多态性与肺癌发病风险、病理特点及p53基因突变的相关性.方法 选择80例肺癌患者为病例组,40例非肿瘤肺疾病患者为对照组.以PCR-RFLP技术检测病例组和对照组的RAD51基因型,比较不同基因型与肺癌危险性以及肺癌病理特点的关系;并采用免疫组化法对病例组进行p53突变的检测.结果 (1)RAD51基因型G/G、G/C和C/C在病例组的分布频率分别为77.5%、15.0%和1.3%,在对照组的分布频率分别为92.5%、7.5%和0.与携带G/G的个体相比,携带RAD51变异基因型(G/C和C/C)的个体具有更高的患癌风险(P＜0.05);(2)RAD51基因型与肺癌的病理学类型及组织学分级无相关性;(3)RAD51 G135C基因型在不同p53基因突变状态肺癌中的分布频率差异无显著性(P＞0.05).结论 RAD51基因多态性与肺癌发病风险有关,携带RAD51变异基因型(G/C和C/C)的个体易患肺癌.     

RAD51基因G135C单核苷酸多态性及p53突变在肺癌中的意义

目的探讨RAD51基因G135C多态性与肺癌发病风险、病理特点及p53基因突变的相关性。方法选择80例肺癌患者为病例组,40例非肿瘤肺疾病患者为对照组。以PCR-RFLP技术检测病例组和对照组的RAD51基因型,比较不同基因型与肺癌危险性以及肺癌病理特点的关系;并采用免疫组化法对病例组进行p53突变的检测。结果 (1)RAD51基因型G/G、G/C和C/C在病例组的分布频率分别为77.5%、15.0%和1.3%,在对照组的分布频率分别为92.5%、7.5%和0。与携带G/G的个体相比,携带RAD51变异基因型(G/C和C/C)的个体具有更高的患癌风险(P<0.05);(2)RAD51基因型与肺癌的病理学类型及组织学分级无相关性;(3)RAD51 G135C基因型在不同p53基因突变状态肺癌中的分布频率差异无显著性(P>0.05)。结论 RAD51基因多态性与肺癌发病风险有关,携带RAD51变异基因型(G/C和C/C)的个体易患肺癌。     

A quantitative model to predict pathogenicity of missense variants in the TP53 gene

Germline pathogenic variants in the TP53 gene cause Li‐Fraumeni syndrome, a condition that predisposes individuals to a wide range of cancer types. Identification of individuals carrying a TP53 pathogenic variant is linked to clinical management decisions, such as the avoidance of radiotherapy and use of high‐intensity screening programs. The aim of this study was to develop an evidence‐based quantitative model that integrates independent in silico data (Align‐GVGD and BayesDel) and somatic to germline ratio (SGR), to assign pathogenicity to every possible missense variant in the TP53 gene. To do this, a likelihood ratio for pathogenicity (LR) was derived from each component calibrated using reference sets of assumed pathogenic and benign missense variants. A posterior probability of pathogenicity was generated by combining LRs, and algorithm outputs were validated using different approaches. A total of 730 TP53 missense variants could be assigned to a clinically interpretable class. The outputs of the model correlated well with existing clinical information, functional data, and ClinVar classifications. In conclusion, these quantitative outputs provide the basis for individualized assessment of cancer risk useful for clinical interpretation. In addition, we propose the value of the novel SGR approach for use within the ACMG/AMP guidelines for variant classification.     

How wild-type TP53 is inactivated in undifferentiated-type gastric carcinomas: analyses of intratumoral heterogeneity in deletion and mutation of TP53.

OBJECTIVE: In undifferentiated-type gastric carcinoma (UGC), inactivation of TP53 is infrequent at early stages and comparable to tubular adenocarcinomas (TUBs) at advanced stages. To clarify how TP53 inactivation relates to histogenesis of UGCs, we examined p53 alterations in multiple samples of individual UGCs. METHODS: We used 27 UGCs including 12 mixed types with minor tubular component (TC) and 16 with a layered structure (LS), a histological remnant of incipient signet ring cell carcinoma (SIG). We examined p53 expression immunohistochemically and analyzed loss of heterozygosity (LOH) with four microsatellite markers within 17p13.1 in multiple microdissected samples. DNA sequence of mutation hot spots in TP53 was determined in representative samples of each tumor. RESULTS: In the mixed-type UGCs, 5 and 1 of the 8 tumors without LS showed global and regional loss of wild-type TP53, respectively, through mutation and LOH, and one fourth of the tumors with LS showed the regional loss. In the tumors with the mutation, the mutation pattern was identical between TC and poorly differentiated major component. CONCLUSION: The inactivation of wild-type TP53 is an earlier event before dedifferentiation of TUB to mixed-type UGC, but is less frequent and a later event in a subset of mixed-type UGC deriving from SIG. .     

Higher‐than‐expected population prevalence of potentially pathogenic germline TP53 variants in individuals unselected for cancer history

Li–Fraumeni syndrome (LFS) is an autosomal‐dominant cancer predisposition disorder associated with pathogenic germline variants in TP53, with a high penetrance over an individual's lifetime. The actual population prevalence of pathogenic germline TP53 mutations is still unclear, most likely due to biased selection of cancer affected families. The aim of this study was to estimate the population prevalence of potentially pathogenic TP53 exonic variants in three sequencing databases, totaling 63,983 unrelated individuals. Potential pathogenicity was defined using an original algorithm combining bioinformatic prediction tools, suggested clinical significance, and functional data. We identified 34 different potentially pathogenic TP53 variants in 131 out of 63,983 individuals (0.2%). Twenty‐eight (82%) of these variants fell within the DNA‐binding domain of TP53, with an enrichment for specific variants that were not previously identified as LFS mutation hotspots, such as the p.R290H and p.N235S variants. Our findings reveal that the population prevalence of potentially pathogenic TP53 variants may be up to 10 times higher than previously estimated from family‐based studies. These results point to the need for further studies aimed at evaluating cancer penetrance modifiers as well as the risk associated between cancer and rare TP53 variants.     

Genetic testing for RAD51C mutations: in the clinic and community

Much of the observed familial clustering of breast and ovarian cancer cannot be explained by mutations in BRCA1 and BRCA2. Several other cancer susceptibility genes have been identified, but their value in routine clinical genetic testing is still unclear. Germline mutations in RAD51C have been identified in about 1% of hereditary breast and ovarian cancer families. RAD51C mutations are predominantly found in families with a history of ovarian cancer and are rare in families with a history of breast cancer alone. RAD51C is primarily an ovarian cancer susceptibility gene. A mutation is present in approximately 1% of unselected ovarian cancers. Among mutation carriers, the lifetime risk of ovarian cancer is approximately 9%. The average age at onset is approximately 60 years; this suggests that preventive oophorectomy can be delayed until after natural menopause. Under current guidelines, genetic testing for RAD51C is expected to have a limited impact on ovarian cancer incidence at a population level. This is because the penetrance is 9% to age 80; the great majority of families with mutations would be represented by a single case of ovarian cancer, these are potentially preventable through population screening but not through screening of established ovarian cancer families.     

Analysis of human papillomavirus prevalence and TP53 polymorphism in head and neck squamous cell carcinomas

Head and neck squamous cell carcinoma is a disease associated with tobacco and alcohol abuse. There is evidence that the oncogenic human papillomavirus (HPV) may also be a risk for upper aerodigestive tract cancers. High-risk HPVs encode two early proteins, E6 and E7, that can bind to p53 and pRb, respectively, and induce its degradation or inactivation. The TP53 gene has a single polymorphism at codon 72 of exon 4 that encodes either arginine (Arg) or proline (Pro). The purpose of this study was to evaluate the role of HPV infection and TP53 polymorphism in head and neck cancer. We analyzed 50 tumors, as well swabs of oral mucosa from 142 control individuals, with a polymerase chain reaction technique. The prevalence of HPV in controls was 10.6% and in cancer specimens 16%. The frequency distribution of genotypes in controls was 50% Arg/Arg, 43% Arg/Pro and 7% Pro/Pro; in tumors, it was 52% Arg/Arg, 32% Arg/Pro, and 16% Pro/Pro. Contrary to the results of some studies on cervical cancer, no association between any TP53 genotype or allele and the development of head and neck cancer was observed, regardless of HPV status, except for the Pro/Pro genotype, which is associated with the absence of HPV. The arginine allele appears to protect against head and neck cancers. Also, the data showed that HPV infection results in no increased risk of developing head and neck tumors.     

Mutational analysis of hSNF5/INI1 and TP53 genes in choroid plexus carcinomas

We report here the mutational analysis of hSNF5/INI1 and TP53 genes performed on 11 specimens of choroid plexus carcinomas (CPC) in which a large number of abnormalities has been detected by molecular biology techniques. Loss of heterozygosity (LOH) analysis performed on six tumors revealed losses on chromosomes 1, 3, 5, 9, 10, 13, 16, 18, and 22. However, there were no abnormalities on 17p and mutations of the TP53 gene have been observed for two tumors comprising exons 5 and 7, respectively. Exon 4 of hSNF5/INI1 was mutated in one tumor with LOH restricted to the hSNF5/INI1 locus. There was no coexistence of mutations in both analyzed genes. Our analysis confirms the presence of the hSNF5/INI1 mutations and proves involvement of TP53 mutations in sporadic cases of CPC.