FANCP/SLX4

Fanconi anemia (FA) is a rare genetic disease characterized by congenital abnormalities, bone marrow failure and heightened cancer susceptibility. The FA proteins are known to function in the cellular defense against DNA interstrand crosslinks (ICLs), a process that remains poorly understood. A recent spate of discoveries has led to the identification of one new FA gene, FANCP/SLX4, and two strong candidate FA genes, FAN1 and RAD51C. In this perspective we describe the discovery of FANCP/SLX4 and discuss how these new findings collectively refine our understanding of DNA ICL repair.     

Nuclease Delivery: Versatile Functions of SLX4/FANCP in Genome Maintenance

As a scaffold, SLX4/FANCP interacts with multiple proteins involved in genome integrity. Although not having recognizable catalytic domains, SLX4 participates in diverse genome maintenance pathways by delivering nucleases where they are needed, and promoting their cooperative execution to prevent genomic instabilities. Physiological importance of SLX4 is emphasized by the identification of causative mutations of SLX4 genes in patients diagnosed with Fanconi anemia (FA), a rare recessive genetic disorder characterized by genomic instability and predisposition to cancers. Recent progress in understanding functional roles of SLX4 has greatly expanded our knowledge in the repair of DNA interstrand crosslinks (ICLs), Holliday junction (HJ) resolution, telomere homeostasis and regulation of DNA damage response induced by replication stress. Here, these diverse functions of SLX4 are reviewed in detail.     

FANCP/SLX4: A Swiss army knife of DNA interstrand crosslink repair

Fanconi anemia (FA) is a rare genetic disease characterized by congenital abnormalities, bone marrow failure and heightened cancer susceptibility. The FA proteins are known to function in the cellular defense against DNA interstrand crosslinks (ICLs), a process that remains poorly understood. A recent spate of discoveries has led to the identification of one new FA gene, FANCP/SLX4, and two strong candidate FA genes, FAN1 and RAD51C. In this perspective we describe the discovery of FANCP/SLX4 and discuss how these new findings collectively refine our understanding of DNA ICL repair.Key words: Fanconi anemia, DNA repair, ubiquitin, FANCP/SLX4, DNA interstrand crosslink repair     

Genetic heterogeneity of early-onset familial breast cancer

Summary A gene for early-onset familial breast cancer has recently been mapped to the chromosome 17q12–23 region. In order to confirm the gene location, we have tested an extensive early-onset breast cancer family with 4 markers in this chromosome region. Linkage was negative with all 4 markers. This study suggests that there is genetic heterogeneity among early-onset breast cancer families.     

Mutational analysis of breast/ovarian cancer hereditary predisposition gene BRCA1 in Tunisian women

BRCA1 is a breast cancer susceptibility gene. Germline mutations in BRCA1 gene are found in 5 to 10% of breast cancer. The aim of this study is to screen the tunisian women with familial or sporadic breast cancer for BRCA1 gene mutations. The authors used the Protein Truncation Test (PTT) and DNA sequencing to detect BRCA1 gene mutations in 12 tunisian families with breast cancer and the Allele Specific Oligonucleotide-PCR (ASO-PCR) to detect the 185delAG and 1294del40 mutations in 150 tunisian women with sporadic breast cancer. A nonsens mutation was found, by PTT, in exon 11 of BRCA1 gene in one case of familial breast cancer. No mutation in the rest of exons was found by the DNA sequencing. The BRCA1 1294del40 mutation was found only in a patient with non familial breast cancer. The 185delAG mutation was absent in all cases of breast cancer. These data suggest that the germline mutation of BRCA1 is implicated in breast cancer in Tunisia and that the 185delAG mutation is absent in arab tunisian women.     

The genetics of breast cancer, population and familial research and segregation analysis

The data on clinico-genealogy studies of 1046 probands with breast cancer and their relatives are presented. The nature of inheritance corresponded to the Mendelian model. As to other families, there is no strong evidence for the monogene model both with complete and incomplete penetrance of mutant homo- and heterozygotes. Penetrance of homozygotes was 7.9-30.5%, this being 2.0-7.3% for heterozygotes. The conclusion is drawn that it is necessary to consider the regularities of inheritance of breast cancer in the light of the multifactorial model.     

Compartmentalization of the SUMO/RNF4 pathway by SLX4 drives DNA repair

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Assessment of SLX4 Mutations in Hereditary Breast Cancers

Background

SLX4 encodes a DNA repair protein that regulates three structure-specific endonucleases and is necessary for resistance to DNA crosslinking agents, topoisomerase I and poly (ADP-ribose) polymerase (PARP) inhibitors. Recent studies have reported mutations in SLX4 in a new subtype of Fanconi anemia (FA), FA-P. Monoallelic defects in several FA genes are known to confer susceptibility to breast and ovarian cancers.

Methods and Results

To determine if SLX4 is involved in breast cancer susceptibility, we sequenced the entire SLX4 coding region in 738 (270 Jewish and 468 non-Jewish) breast cancer patients with 2 or more family members affected by breast cancer and no known BRCA1 or BRCA2 mutations. We found a novel nonsense (c.2469G>A, p.W823*) mutation in one patient. In addition, we also found 51 missense variants [13 novel, 23 rare (MAF<0.1%), and 15 common (MAF>1%)], of which 22 (5 novel and 17 rare) were predicted to be damaging by Polyphen2 (score = 0.65–1). We performed functional complementation studies using p.W823* and 5 SLX4 variants (4 novel and 1 rare) cDNAs in a human SLX4-null fibroblast cell line, RA3331. While wild type SLX4 and all the other variants fully rescued the sensitivity to mitomycin C (MMC), campthothecin (CPT), and PARP inhibitor (Olaparib) the p.W823* SLX4 mutant failed to do so.

Conclusion

Loss-of-function mutations in SLX4 may contribute to the development of breast cancer in very rare cases.     

CYP21/C4 gene organisation in Italian 21-hydroxylase deficiency families

Summary A total of 33 Italian 21-hydroxylase (21-OH) deficiency families were investigated using a combination of short and long range restriction mapping of the CYP21/C4 gene cluster. The analyses revealed that large-scale length polymorphism in this gene cluster strictly conformed to a compound variable number of tandem repeats (VNTR) plus insertion system with between one and four CYP21 + C4 units and seven BssHII restriction fragment length polymorphisms (RFLPs) (75kb, 80kb, 105kb, 110kb, 135kb, 140kb and 180kb). A total of 9/66 disease haplotypes, but only 1/61 nondisease haplotypes, showed evidence of gene addition by exhibiting three or more CYP21 + C4 repeat units. Of these, two were identified in one 21-OH deficiency patient who has a total of eight CYP21 + C4 units, being homozygous for the HLA haplotype DR2 DQ2 B5 A28. This haplotype carries four CYP21 + C4 units, three of which contain CYP21A-like genes and one of which contains a CYP21B-like gene that presumably carries a pathological point mutation. Of the other gene addition haplotypes associated with 21-OH deficiency, four show three CYP21 + C4 units flanked by HLA-DR1 and HLA-B14 markers. Although such haplotypes have commonly been associated with non-classical 21-OH deficiency, three examples in the present study are unexpectedly found in two salt-wasting patients, who are respectively homozygous or heterozygous for this haplotype. Only 7/66 disease haplotypes showed evidence of a CYP21B gene deletion.     

Prevalence of widespread BRCA1 gene mutations in patients with familial breast cancer from St. Petersburg

Ten variants different from the canonical nucleotide sequence (GenBank, U14680) has been identified when studying the mutation spectrum in gene BRCA1. Six of them (5382insC, 2963del10, 3819de15, 3875del4, 2274insA, and R1203X) cause premature termination of protein synthesis, thus predisposing to breast cancer. A missense mutation E1250K is presumed to be a factor of predisposition to cancer. We classified three variants of nucleotide sequence found in some patients as DNA polymorphisms S694S, L771L, and E1038G. The 5382insC and 3819de15 mutations have been detected in four and two families, respectively. Five of the mutations detected have not been found in Russia before. However, all mutations except for 2963del10 have been found in other populations of the world, which indicates their long evolutionary history. Two mutations found in patients from St. Petersburg (5382insC and 3875de14) have also been found in oncological patients from other regions of the Russian Federation.     

Network analysis of gene lists for finding reproducible prognostic breast cancer gene signatures

Many genome-scale studies in molecular biology deliver results in the form of a ranked list of gene names, accordingly to some scoring method. There is always the question how many top-ranked genes to consider for further analysis, for example, in order creating a diagnostic or predictive gene signature for a disease. This question is usually approached from a statistical point of view, without considering any biological properties of top-ranked genes or how they are related to each other functionally. Here we suggest a new method for selecting a number of genes in a ranked gene list such that this set forms the Optimally Functionally Enriched Network (OFTEN), formed by known physical interactions between genes or their products. The method allows associating a network with the gene list, providing easier interpretation of the results and classifying the genes or proteins accordingly to their position in the resulting network. We demonstrate the method on four breast cancer datasets and show that 1) the resulting gene signatures are more reproducible from one dataset to another compared to standard statistical procedures and 2) the overlap of these signatures has significant prognostic potential. The method is implemented in BiNoM Cytoscape plugin (http://binom.curie.fr).     

Pathway analysis reveals functional convergence of gene expression profiles in breast cancer

Background

Angiotensin I-converting enzyme (ACE) plays an important role in cardiovascular homeostasis. There is evidence from different ethnic groups that circulating ACE levels are influenced by a quantitative trait locus (QTL) at the ACE gene on chromosome 17. The finding of significant residual familial correlations in different ethnic groups, after accounting for this QTL, and the finding of support for linkage to a locus on chromosome 4 in Mexican-American families strongly suggest that there may well be QTLs for ACE unlinked to the ACE gene.

Methods

A genome-wide panel of microsatellite markers, and a panel of biallelic polymorphisms in the ACE gene were typed in Nigerian families. Single locus models with fixed parameters were used to test for linkage to circulating ACE with and without adjustment for the effects of the ACE gene polymorphisms.

Results

Strong evidence was found for D17S2193 (Z_max = 3.5); other nearby markers on chromosome 17 also showed modest support. After adjustment for the effects of the ACE gene locus, evidence of "suggestive linkage" to circulating ACE was found for D4S1629 (Z_max = 2.2); this marker is very close to a locus previously shown to be linked to circulating ACE levels in Mexican-American families.

Conclusion

In this report we have provided further support for the notion that there are QTLs for ACE unlinked to the ACE gene; our findings for chromosome 4, which appear to replicate the findings of a previous independent study, should be considered strong grounds for a more detailed examination of this region in the search for genes/variants which influence ACE levels. The poor yields, thus far, in defining the genetic determinants of hypertension risk suggest a need to look beyond simple relationships between genotypes and the ultimate phenotype. In addition to incorporating information on important environmental exposures, a better understanding of the factors which influence the building blocks of the blood pressure homeostatic network is also required. Detailed studies of the genetic determinants of ACE, an important component of the renin-angiotensin system, have the potential to contribute to this strategic objective.     

Coupled two-way clustering analysis of breast cancer and colon cancer gene expression data

We present and review coupled two-way clustering, a method designed to mine gene expression data. The method identifies submatrices of the total expression matrix, whose clustering analysis reveals partitions of samples (and genes) into biologically relevant classes. We demonstrate, on data from colon and breast cancer, that we are able to identify partitions that elude standard clustering analysis. AVAILABILITY: Free, at http://ctwc.weizmann.ac.il.. SUPPLEMENTARY INFORMATION: http://www.weizmann.ac.il/physics/complex/compphys/bioinfo2/     

ARLTS1, MDM2 and RAD51 gene variations are associated with familial breast cancer

Genetic factors that contribute to the risk of breast cancer are largely not known and association studies have revealed several genes with low penetrance risk alleles for breast cancer. Analysis of these genes may provide important information on the risk factors affecting carcinogenesis. Variations in the ARLTS1, RAD51 and MDM2 genes have been associated with increased risk of different cancer types but for breast cancer the results are not consistent. In this study we investigated the role of the allelic variants in candidate genes acting in the tumor suppressor, DNA repair and p53 pathways as risk factors for familial breast cancer in 147 patients displaying characteristics of familial disease. Presence of the polymorphic variants were investigated by amplification of the corresponding regions and restriction fragment length polymorphism analysis. Genotype and allele frequencies in the patients were significantly different for all three variants. Our results indicate that the polymorphic variants might affect individual susceptibility towards breast cancer.     

Disease-specific gene repositioning in breast cancer

Genomes are nonrandomly organized within the three-dimensional space of the cell nucleus. Here, we have identified several genes whose nuclear positions are altered in human invasive breast cancer compared with normal breast tissue. The changes in positioning are gene specific and are not a reflection of genomic instability within the cancer tissue. Repositioning events are specific to cancer and do not generally occur in noncancerous breast disease. Moreover, we show that the spatial positions of genes are highly consistent between individuals. Our data indicate that cancer cells have disease-specific gene distributions. These interphase gene positioning patterns may be used to identify cancer tissues.