Identification of a novel PTEN intronic deletion in Li-Fraumeni syndrome and its effect on RNA processing

Li-Fraumeni syndrome heterogeneity

Clinical variability is commonly seen in Li-Fraumeni syndrome. Phenotypic heterogeneity is present among different families affected by the same pathogenic variant in TP53 gene and among members of the same family. However, causes of this huge clinical spectrum have not been studied in depth. TP53 type mutation, polymorphic variants in TP53 gene or in TP53-related genes, copy number variations in particular regions, and/or epigenetic deregulation of TP53 expression might be responsible for clinical heterogeneity. In this review, recent advances in the understanding of genetic and epigenetic aspects influencing Li-Fraumeni phenotype are discussed.

TP53 and CDKN1A mutation analysis in families with Li-Fraumeni and Li-Fraumeni like syndromes

Li-Fraumeni and Li-Fraumeni like syndromes (LFS/LFL) represent rare cancer-prone conditions associated mostly with sarcomas, breast cancer, brain tumors, and adrenocortical carcinomas. TP53 germline mutations are present in up to 80 % of families with classic Li-Fraumeni syndrome, and in 20-60 % of families with Li-Fraumeni like phenotypes. The frequency of LFS/LFL families with no TP53 mutations detected suggests the involvement of other genes in the syndrome. In this study, we searched for mutations in TP53 in 39 probands from families with criteria for LFS/LFL. We also searched for mutations in the gene encoding the main mediator of p53 in cell cycle arrest, CDKN1A/p21, in all patients with no mutations in TP53. Eight probands carried germline disease-causing mutations in TP53: six missense mutations and two partial gene deletions. No mutations in CDKN1A coding region were detected. TP53 partial deletions in our cohort represented 25 % (2/8) of the mutations found, a much higher frequency than usually reported, emphasizing the need to search for TP53 rearrangements in patients with LFS/LFL phenotypes. Two benign tumors were detected in two TP53 mutation carriers: an adrenocortical adenoma and a neurofibroma, which raises a question about the possible implication of TP53 mutations on the development of such lesions.

p53 and hereditary cancer

The roles of p53 as "guardian of the genome" are extensive, encompassing regulation of the cell cycle, DNA repair, apoptosis, cellular metabolism, and senescence - ultimately steering cells through a balance of death and proliferation. The majority of sporadic cancers exhibit loss of p53 activity due to mutations or deletions of TP53, and alterations in its signaling pathway. Germline TP53 mutations have been identified in a group of families exhibiting a rare but highly penetrant familial cancer syndrome, called the Li-Fraumeni syndrome (LFS). Between 60-80% of 'classic' LFS families carry mutant Trp53. The most frequent cancers observed are premenopausal breast cancer, bone and soft-tissue sarcomas, adrenal cortical carcinomas, and brain tumors. Penetrance is nearly 100% by age 70. Although TP53 is currently the only validated susceptibility locus recognized for LFS, recent studies have focused on the identification of genetic modifiers that may explain the wide phenotypic variability observed in LFS patients. Analyses of single nucleotide polymorphisms (SNPs), genome-wide copy number and telomere length have provided greater insight into the potential genetic modifiers of LFS. Moreover, the study of Trp53 mutant heterozygous mouse models has elucidated novel functions of p53, and offers insight into the mechanisms governing tumorigenesis in LFS. The key findings outlined in this chapter provide an overview of the molecular basis of LFS and the role of p53 in this unique heritable cancer syndrome.

Li-fraumeni syndrome

Li-Fraumeni syndrome (LFS) is a classic cancer predisposition disorder that is commonly associated with germline mutations of the p53 tumor suppressor gene. Examination of the wide spectrum of adult-onset and childhood cancers and the distribution of p53 mutations has led to a greater understanding of cancer genotype-phenotype correlations. However, the complex LFS phenotype is not readily explained by the simple identification of germline p53 mutations in affected individuals. Recent work has identified genetic events that modify the LFS phenotype. These include intragenic polymorphisms, mutations/polymorphisms of genes in the p53 regulatory pathway, as well as more global events such as aberrant copy number variation and telomere attrition. These genetic events may, in part, explain the breadth of tumor histiotypes within and across LFS families, the apparent accelerated age of onset within families, and the range of clinical outcomes among affected family members. This review will examine the clinical and genetic definitions of LFS and offer insight into how lessons learned from the study of this rare disorder may inform similar questions in other familial cancer syndromes.

Hereditary tumor syndromes and gliomas

Several congenital syndromes caused by germline mutations in tumor suppressor genes predispose to the development of glial tumors. In the last few decades our knowledge about the molecular functions of these genes and the pathogenesis of hereditary tumor syndromes has greatly increased. The most common syndromes are the neurofibromatoses (type 1 and type 2) and the tuberous scleroses complex. There are interesting overlaps in the molecular pathogen-esis. Deregulation of Ras or downstream Ras pathways including MEK/ERK and AKT/ mTOR plays an important role in these three syndromes. Other rare syndromes include Li-Fraumeni, melanoma-astrocytoma, and Turcot syndrome involving cell cycle regulators and DNA repair genes. The genes and pathways involved in the pathogenesis of these syndromes also play an important role in the development of sporadic tumors. Therefore research on hereditary syndromes contributes substantially to our understanding of tumor formation.

The contribution of CHEK2 to the TP53-negative Li-Fraumeni phenotype

BACKGROUND

CHEK2 has previously been excluded as a major cause of Li-Fraumeni syndrome (LFS). One particular CHEK2 germline mutation, c.1100delC, has been shown to be associated with elevated breast cancer risk. The prevalence of CHEK2*1100delC differs between populations and has been found to be relatively high in the Netherlands. The question remains nevertheless whether CHEK2 germline mutations contribute to the Li-Fraumeni phenotype.

METHODS

We have screened 65 Dutch TP53-negative LFS/LFL candidate patients for CHEK2 germline mutations to determine their contribution to the LFS/LFL phenotype.

RESULTS

We identified six index patients with a CHEK2 sequence variant, four with the c.1100delC variant and two sequence variants of unknown significance, p.Phe328Ser and c.1096-?_1629+?del.

CONCLUSION

Our data show that CHEK2 is not a major LFS susceptibility gene in the Dutch population. However, CHEK2 might be a factor contributing to individual tumour development in TP53-negative cancer-prone families.

Mutation analysis of five candidate genes in familial breast cancer

Most of the known breast cancer susceptibility genes (BRCA1, BRCA2, CHEK2 and ATM) are involved in the damage response pathway. Other members of this pathway are therefore good candidates for additional breast cancer susceptibility genes. ATR, along with ATM, plays a central role in DNA damage recognition and Chk1 relays checkpoint signals from both ATR and ATM. PPP2R1B and PPP2R5B code for subunits of protein phosphatase 2A (PP2A), which regulates autophosphorylation of ATM. In addition, EIF2S6/Int-6, which was originally identified as a common integration site for the mouse mammary tumour virus in virally induced mouse mammary tumours, is a candidate breast cancer susceptibility gene because of its putative role in maintaining chromosome stability. To investigate the role of ATR, CHK1, PPP2R1B, PPP2R5B and EIF2S6/Int-6, we carried out mutation analysis of these genes in the index cases from non-BRCA1/BRCA2 breast cancer families. We also screened sporadic breast tumours for somatic mutations in PPP2R1B and PPP2R5B. Although we identified many novel variants, we found no evidence that highly penetrant germline mutations in these five genes contribute to familial breast cancer susceptibility.

Evaluation of germline PTEN mutations in endometrial cancer patients

BACKGROUND AND OBJECTIVE

Cowden Syndrome is a rare autosomal dominant disorder characterized by multiple hamartomas, increased risks of breast and thyroid cancers, and possibly endometrial carcinoma. Susceptibility to Cowden syndrome is conferred by germline mutation of the PTEN tumor suppressor gene, and somatic mutations of PTEN are common in sporadic endometrial carcinomas. The aim of this study was to test whether a substantial proportion of endometrial cancers are associated with germline mutations of the PTEN gene, not necessarily in association with clinically overt Cowden syndrome.

METHODS

A retrospective cohort of 240 consecutive patients with pathologically confirmed endometrial carcinoma diagnosed at our institution from 1999 to 2002 was ascertained for study. Genomic DNA was isolated from peripheral blood lymphocytes and the entire PTEN coding region and exon-intron junctions were screened for mutations by single strand conformation polymorphism analysis. Potential variants were subjected to direct sequence analysis.

RESULTS

No clearly deleterious PTEN sequence variant was identified in this screened cohort of endometrial cancer patients. One patient harbored a 5-bp deletion in the intronic region adjacent to the splice acceptor site of PTEN exon 4, but this variant has been previously classified as a rare polymorphism.

CONCLUSIONS

Although these data do not preclude the possibility of an increased risk of endometrial cancer in association with the Cowden syndrome, they indicate that germline PTEN mutations do not account for a significant proportion of genetic attributable risk for endometrial carcinoma.

Germ Line BAX Alterations Are Infrequent in Li-Fraumeni Syndrome

Multiple early-onset tumors, frequently associated with germ line TP53 mutations characterize the Li-Fraumeni familial cancer syndrome (LFS). LFS-like (LFS-L) families have lower rates of germ line TP53 alteration and do not meet the strict definition of LFS. This study examined 7 LFS cell lines and 30 LFS and 36 LFS-L primary leukocyte samples for mutations in the proapoptotic p53-regulated gene BAX. No germ line BAX mutations were found. A known BAX polymorphism was observed, yet there was no correlation between polymorphism frequency and TP53 status in either LFS or LFS-L. In summary, alterations of BAX are not responsible for cancers in TP53 wild-type LFS or LFS-L families.

Germline TP53 mutations and Li-Fraumeni syndrome

There are now reports of nearly 250 independent germline TP53 (p53) mutations in over 100 publications. Such mutations are typically associated with Li-Fraumeni or Li-Fraumeni-like syndrome, although many have been identified in cohorts of patients with tumors considered to be typical of LFS. In general, the spectrum of mutations that has been detected in the germline reflects that found in tumors, although there are some notable exceptions in certain tumor types. Detailed knowledge of the pedigrees allows a comprehensive analysis of genotype-phenotype correlations and an understanding of the tumors that are associated with germline TP53 mutations. This review will discuss the spectrum of mutations and the methods for mutation detection, the tumors associated with inheritance of a germline mutation, and some of the ethical and clinical problems in patients with a germline TP53 mutation.

Screening for TP53 rearrangements in families with the Li-Fraumeni syndrome reveals a complete deletion of the TP53 gene

The absence of detectable germline TP53 mutations in a fraction of families with Li-Fraumeni syndrome (LFS) has suggested the involvement of other genes, but this hypothesis remains controversial. The density of Alu repeats within the TP53 gene led us to search genomic rearrangements of TP53 in families without detectable TP53 mutation. To this aim, we adapted the quantitative multiplex PCR of short fluorescent fragments (QMPSF) method to the analysis of the 11 exons of TP53. We analysed 98 families, either fulfilling (six families) or partially meeting (92 families) the criteria for LFS, and in which classical methods had failed to reveal TP53 alterations. We identified, in a large family fulfilling the criteria for LFS, a complete heterozygous deletion of TP53. Additional QMPSF analyses indicated that this deletion, which partially removed the centromeric FLJ10385 locus, covered approximately 45 kb. This deletion was shown to result from a complex rearrangement involving two distinct Alu-mediated recombinations. We conclude that TP53 germline rearrangements occur as rare events, but must be considered in LFS families without detectable point TP53 mutation.

A novel, de novo germline TP53 mutation in a rare presentation of the Li-Fraumeni syndrome in the maxilla

We undertook the genetic analysis of a classic Li-Fraumeni syndrome (LFS) family with clustering of primary tumours including two maxillary sarcomas, a rare LFS site of tumour occurrence. Our aim was to investigate the presence of a specific type of TP53 mutation that could be associated with this unusual predilection of site for cancer occurrence. Mutational screening of the coding region of TP53 revealed an A>T transversion in codon 144 of exon 5 (CAG>CTG, Gln>Leu) in the germline of one of the three affected members, with loss of heterozygosity (LOH) in the tumour tissue. All other affected members were negative for germline or somatic TP53 mutations. TP53 immunohistochemistry was uninformative. The mutation we report is a de novo constitutional TP53 mutation that has not been previously described in the literature. It could explain the more burdened phenotype of the affected patient (died at 21 months). Alternative mechanisms to explain the overall family phenotype are discussed.