FACC gene mutations and early prenatal diagnosis of Fanconi's anaemia

A comprehensive molecular study identified 12 complementation groups with 56 novel FANC gene variants in Indian Fanconi anemia subjects

Fanconi anemia (FA) is a rare autosomal or X-linked genetic disorder characterized by chromosomal breakages, congenital abnormalities, bone marrow failure (BMF), and cancer. There has been a discovery of 22 FANC genes known to be involved in the FA pathway. This wide number of pathway components makes molecular diagnosis challenging for FA. We present here the most comprehensive molecular diagnosis of FA subjects from India. We observed a high frequency (4.42 ± 1.5 breaks/metaphase) of chromosomal breakages in 181 FA subjects. The major clinical abnormalities observed were skin pigmentation (70.2%), short stature (46.4%), and skeletal abnormalities (43.1%), along with a few minor clinical abnormalities. The combination of Sanger sequencing and Next Generation Sequencing could molecularly characterize 164 (90.6%) FA patients and identified 12 different complementation groups [FANCA (56.10%), FANCG (16.46%), FANCL (12.80%), FANCD2 (4.88%), FANCJ (2.44%), FANCE (1.22%), FANCF (1.22%), FANCI (1.22%), FANCN (1.22%), FANCC (1.22%), FANCD1 (0.61%) and FANCB (0.61%)]. A total of 56 novel variants were identified in our cohort, including a hotspot variant: a deletion of exon 27 in the FANCA gene and a nonsense variant at c.787 C>T in the FANCG gene. Our comprehensive molecular findings can aid in the stratification of molecular investigation in the diagnosis and management of FA patients.

Two truncating variants in FANCC and breast cancer risk

Fanconi anemia (FA) is a genetically heterogeneous disorder with 22 disease-causing genes reported to date. In some FA genes, monoallelic mutations have been found to be associated with breast cancer risk, while the risk associations of others remain unknown. The gene for FA type C, FANCC, has been proposed as a breast cancer susceptibility gene based on epidemiological and sequencing studies. We used the Oncoarray project to genotype two truncating FANCC variants (p.R185X and p.R548X) in 64,760 breast cancer cases and 49,793 controls of European descent. FANCC mutations were observed in 25 cases (14 with p.R185X, 11 with p.R548X) and 26 controls (18 with p.R185X, 8 with p.R548X). There was no evidence of an association with the risk of breast cancer, neither overall (odds ratio 0.77, 95%CI 0.44-1.33, p = 0.4) nor by histology, hormone receptor status, age or family history. We conclude that the breast cancer risk association of these two FANCC variants, if any, is much smaller than for BRCA1, BRCA2 or PALB2 mutations. If this applies to all truncating variants in FANCC it would suggest there are differences between FA genes in their roles on breast cancer risk and demonstrates the merit of large consortia for clarifying risk associations of rare variants.

Prenatal exclusion/confirmation of Fanconi anemia via flow cytometry: a pilot study

OBJECTIVE

To explore the potential of flow cytometry in the prenatal exclusion or confirmation of Fanconi anemia (FA).

METHODS

Indications for prenatal diagnosis were (1) FA-negative family history, but suspicious ultrasound findings such as radial ray aplasia, (2) FA-positive family history, but without knowledge of the affected gene and/or mutation. Amniotic fluid (AF) cell cultures and umbilical cord (UC) blood cultures were assayed for typical cell cycle changes (G2-phase accumulations) without and with mitomycin C (MMC) treatments using single- and dual-parameter (BrdU-Hoechst) flow cytometry.

RESULTS

Single-parameter flow cytometry correctly identified 2 positive and 9 negative cases on the basis of MMC sensitivity of cultivated AF cells. Likewise, 8 negative and 2 positive cases were correctly predicted using bivariate flow cytometry of 72-hour UC blood cultures. In contrast, bivariate flow cytometry applied to AF cells grown in the presence of bromodeoxyuridine (BrdU) yielded false-positive and false-negative results.

CONCLUSIONS

Single-parameter flow cytometry of AF cell cultures and bivariate flow cytometry of UC cell cultures have the potential to correctly predict the affected status in cases at risk for FA, whereas bivariate flow cytometry proved unreliable when applied to BrdU-substituted AF cell cultures. Cases with a low a priori risk (e.g. sonographic finding of radial ray abnormalities and negative family history) would benefit most from flow cytometry as a rapid and economical prenatal screening procedure.

The IVS4 + 4 A to T mutation of the Fanconi anemia geneFANCC is not associated with a severe phenotype in Japanese patients

Fanconi anemia (FA) is an autosomal recessive disease characterized by congenital anomalies, aplastic anemia, and a susceptibility to leukemia. There are at least 8 complementation groups (A through H). Extensive analyses of the FA group C gene FANCC in Western countries revealed that 10% to 15% of FA patients have mutations of this gene. The most common mutation is IVS4 + 4 A to T (IVS4), a splice mutation in intron 4, which has been found only in patients of Ashkenazi Jewish ancestry. When we screened 29 Japanese patients (20 unrelated patients and 4 families) using polymerase chain reaction–single strand conformation polymorphism, we found 8 unrelated patients homozygous for IVS4. This is apparently the first non–Ashkenazi-Jewish population for whom this mutation has been detected. The Ashkenazi Jewish patients homozygous for IVS4 have a severe phenotype, in comparison with other FA patients. Our analyses of Japanese patients indicate no significant difference between IVS4 homozygotes and other patients with regard to severity of a clinical phenotype. Thus, ethnic background may have a significant effect on a clinical phenotype in FA patients carrying the same mutation.

Mutations of the Fanconi anemia group A gene (FAA) in Italian patients

Fanconi anemia (FA) is an autosomal recessive disease characterized by progressive pancytopenia, congenital malformations, and predisposition to acute myeloid leukemia. At least five complementation groups (FA-A-FA-E) have been identified. The relative prevalence of FA-A has been estimated at an average of approximately 65% but may widely vary according to ethnic background. In Italy, 11 of 12 patients analyzed by cell-fusion studies were assigned to group FA-A, suggesting an unusually high relative prevalence of this FA subtype in patients of Italian ancestry. We have screened the 43 exons of the FAA gene and their flanking intronic sequences in 38 Italian FA patients, using RNA-SSCP. Ten different mutations were detected: three nonsense and one missense substitutions, four putative splice mutations, an insertion, and a duplication. Most of the mutations are expected to cause a premature termination of the FAA protein at various sites throughout the molecule. Four protein variants were also found, three of which were polymorphisms. The missense mutation D1359Y, not found in chromosomes from healthy unrelated individuals, was responsible for a local alteration of hydrophobicity in the FAA protein, and it was likely to be pathogenic. Thus, the mutations so far encountered in the FAA gene are essentially all different. Since screening based on the analysis of single exons by genomic DNA amplification apparently detects only a minority of the mutations, methods designed to detect alterations in the genomic structure of the gene or in the FAA polypeptide may be helpful in the identification of FAA mutations.

Phenotypic Consequences of Mutations in the Fanconi Anemia FAC Gene: An International Fanconi Anemia Registry Study

Fanconi anemia (FA) is a genetically and phenotypically heterogeneous disorder defined by cellular hypersensitivity to DNA cross-linking agents; mutations in the gene defective in FA complementation group C, FAC, are responsible for the syndrome in a subset of patients. We have performed an analysis of the clinical effects of specific mutations in the FAC gene. Using the amplification refractory mutation system assays that we developed to rapidly detect FAC mutations, at least one mutated copy of the FAC gene was identified in 59 FA patients from the International Fanconi Anemia Registry (IFAR). This represents 15% of the 397 FA patients tested. FA-C patients were divided into three subgroups based on results of a genotype-phenotype analysis using the Cox proportional hazards model: (1) patients with the IVS4 mutation (n = 26); (2) patients with at least one exon 14 mutation (R548X or L554P) (n = 16); and (3) patients with at least one exon 1 mutation (322delG or Q13X) and no known exon 14 mutation (n = 17). Kaplan-Meier analysis shows that IVS4 or exon 14 mutations define poor risk subgroups, as they are associated with significantly earlier onset of hematologic abnormalities and poorer survival compared to exon 1 patients and to the non-FA-C IFAR population. There was no direct correlation between the degree of cellular hypersensitivity to the clastogenic effect of diepoxybutane and severity of clinical phenotype. Sixteen of the 59 FA-C patients (27%) have developed acute myelogenous leukemia. Thirteen of these patients have died; AML was the cause of death in 46% of the expired FA-C patients. This study enables us to define this clinically heterogeneous disorder genotypically to better predict clinical outcome and aid decision-making regarding major therapeutic modalities for a subset of FA patients.

Phenotypic Consequences of Mutations in the Fanconi Anemia FAC Gene: An International Fanconi Anemia Registry Study

Fanconi anemia (FA) is a genetically and phenotypically heterogeneous disorder defined by cellular hypersensitivity to DNA cross-linking agents; mutations in the gene defective in FA complementation group C, FAC, are responsible for the syndrome in a subset of patients. We have performed an analysis of the clinical effects of specific mutations in the FAC gene. Using the amplification refractory mutation system assays that we developed to rapidly detect FAC mutations, at least one mutated copy of the FAC gene was identified in 59 FA patients from the International Fanconi Anemia Registry (IFAR). This represents 15% of the 397 FA patients tested. FA-C patients were divided into three subgroups based on results of a genotype-phenotype analysis using the Cox proportional hazards model: (1) patients with the IVS4 mutation (n = 26); (2) patients with at least one exon 14 mutation (R548X or L554P) (n = 16); and (3) patients with at least one exon 1 mutation (322delG or Q13X) and no known exon 14 mutation (n = 17). Kaplan-Meier analysis shows that IVS4 or exon 14 mutations define poor risk subgroups, as they are associated with significantly earlier onset of hematologic abnormalities and poorer survival compared to exon 1 patients and to the non-FA-C IFAR population. There was no direct correlation between the degree of cellular hypersensitivity to the clastogenic effect of diepoxybutane and severity of clinical phenotype. Sixteen of the 59 FA-C patients (27%) have developed acute myelogenous leukemia. Thirteen of these patients have died; AML was the cause of death in 46% of the expired FA-C patients. This study enables us to define this clinically heterogeneous disorder genotypically to better predict clinical outcome and aid decision-making regarding major therapeutic modalities for a subset of FA patients.

Cytoplasmic localization of FAC is essential for the correction of a prerepair defect in Fanconi anemia group C cells

Mutations in the gene defective in Fanconi anemia complementation group C, FAC, are responsible for a subset of Fanconi anemia, a group of autosomal recessive disorders characterized by chromosomal instability, hypersensitivity to cross-linking agents, and cancer susceptibility. Although abnormalities in DNA repair have been suspected, localization of the FAC gene product to the cytoplasm has cast doubt on such a mechanism. Monitoring of interstrand DNA cross-linking shows that the predominant defect in group C cells is in the initial induction of cross-links, not in repair synthesis. Both the cross-linking defect and the enhanced cytotoxicity of cross-linkers on Fanconi anemia group C cells are corrected completely by cytoplasmic isoforms of the FAC protein, but not by an isoform targeted to the nucleus. The ability of FAC to correct these phenotypic abnormalities reaches a maximum threshold despite overexpression leading to higher levels of cytosolic protein. These results demonstrate that cytoplasmic localization is essential for the intracellular activity of the FAC protein. It is proposed that this activity is coupled to a cytoplasmic defense mechanism against a specific class of genotoxic agents.

Early prenatal diagnosis of Fanconi anaemia in a twin pregnancy, using DNA analysis

We present a case of prenatal diagnosis of Fanconi anaemia (FA) in a pair of twins at 14 weeks of gestation. The parents had previously had two children: a healthy boy and a boy with FA belonging to complementation group C (FAC). The FA patient is a compound heterozygote, carrying a 322delG and a IVS4+4A-->T mutation in the FAC gene. Prenatal DNA analysis showed that both fetuses were heterozygous for different mutations in the FAC gene. Both fetuses had normal male karyotypes. At 36 weeks the twins were born. They did not show congenital anomalies.

Induction of Fanconi anemia cellular phenotype in human 293 cells by overexpression of a mutant FAC allele

The polypeptide encoded by the Fanconi anemia (FA) complementation group C gene, FAC, binds to a group of cytoplasmic proteins in vitro and may form a multimeric complex. A known mutant allele of FAC resulting from the substitution of Pro for Leu at codon 554 fails to correct the sensitivity of FA group C cells to mitomycin C. We reasoned that overexpression of the mutant protein in a wild-type cellular background might induce the FA phenotype by competing with endogenous FAC for binding to the accessory proteins. After stable transfection of 293 cells with wild-type and a mutant FAC allele containing the L554P substitution, four independent clones that expressed four-to-fifteen fold higher levels of transcript from the mutant transgene relative to the endogenous FAC gene showed hypersensitivity to mitomycin C. By contrast, both parental and FAC-overexpressing cells maintained their relative resistance to mitomycin C. No differences in the biosynthesis, subcellular localization and protein interactions of the normal and mutant proteins were detected. The induction of the FA phenotype in this system is compatible with the competition hypothesis and provides support for a functional role of the FAC-binding proteins in vivo.

Novel mutations and polymorphisms in the Fanconi anemia group C gene

Fanconi anemia (FA) is an autosomal recessive disorder associated with hypersensitivity to DNA cross-linking agents and bone marrow failure. At least four complementation groups have been defined, and the FA group C gene (FAC) has been cloned. We have screened 76 unrelated FA patients of diverse ethnic and geographic origins and from unknown complementation groups for mutations in the FAC gene either by chemical cleavage mismatch analysis or by single-strand conformational polymorphism (SSCP). Five mutations were detected in four patients (5.3%), including two novel mutations (W22X and L496R). Nine polymorphisms were detected, seven of which have not been described previously (663A-->G, L190F, IVS6 + 30C-->T, I312V, V449M, Q465R, and 1974G-->A). Six of the nine polymorphisms occurred in patients or controls from the Tswana or Sotho chiefdoms of South Africa and were not found in 50 unrelated European controls. Restriction site assays were established for all 8 pathogenic mutations identified in the FAC gene to date and used to screen a total of 94 unrelated FA patients. This identified only one other group C patient, who was homozygons for the mutation IVS4 + 4A-->T. This study indicates that the proportion of FA patients from complementation group C is generally likely to be less than 10%. Guidelines for the selection of FA patients for FAC mutation screening are proposed.

Fanconi anaemia research: current status and prospects

Fanconi anaemia (FA) is an autosomal recessive disease featuring diverse clinical symptoms in addition to chromosomal instability and hypersensitivity to crosslinking agents. The much increased risk of FA patients developing leukaemia and squamous cell carcinomas makes FA an important model disease for cancer predisposition. Studies documenting the characteristics of FA cells and their response to environmental toxins have failed thus far to disclose the basic cellular process that is primarily disturbed in FA cells. Complementation analysis suggests that mutations in at least four different genes can cause FA (complementation groups FA-A to FA-D). The cDNA for FA-C has been cloned and found to encode a novel protein that localises to the cytoplasmic compartment of cells. Even though the protein's function is still unknown at present, research has now reached the point from where rapid progress to a detailed understanding of this syndrome may be foreseen.