Minigene-based splicing analysis and ACMG/AMP-based tentative classification of 56 ATM variants.

The ataxia telangiectasia-mutated (ATM) protein is a major coordinator of the DNA damage response pathway. ATM loss-of-function variants are associated with 2-fold increased breast cancer risk. We aimed at identifying and classifying spliceogenic ATM variants detected in subjects of the large-scale sequencing project BRIDGES. A total of 381 variants at the intron-exon boundaries were identified, 128 of which were predicted to be spliceogenic. After further filtering, we ended up selecting 56 variants for splicing analysis. Four functional minigenes (mgATM) spanning exons 4-9, 11-17, 25-29, and 49-52 were constructed in the splicing plasmid pSAD. Selected variants were genetically engineered into the four constructs and assayed in MCF-7/HeLa cells. Forty-eight variants (85.7%) impaired splicing, 32 of which did not show any trace of the full-length (FL) transcript. A total of 43 transcripts were identified where the most prevalent event was exon/multi-exon skipping. Twenty-seven transcripts were predicted to truncate the ATM protein. A tentative ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology)-based classification scheme that integrates mgATM data allowed us to classify 29 ATM variants as pathogenic/likely pathogenic and seven variants as likely benign. Interestingly, the likely pathogenic variant c.1898+2T>G generated 13% of the minigene FL-transcript due to the use of a noncanonical GG-5'-splice-site (0.014% of human donor sites). Circumstantial evidence in three ATM variants (leakiness uncovered by our mgATM analysis together with clinical data) provides some support for a dosage-sensitive expression model in which variants producing ≥30% of FL-transcripts would be predicted benign, while variants producing ≤13% of FL-transcripts might be pathogenic. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

The complex clinical and genetic classification of inherited ataxias. II. Autosomal recessive ataxias.

Autosomal recessive ataxias are a heterogeneous group of rare neurodegenerative diseases characterized by early onset cerebellar ataxia associated with various neurologic, ophthalmologic and systemic signs. In comparison with autosomal dominant ataxias, the group of recessive ataxias is less extensively characterized. In fact, only a few conditions have been genetically characterized. The pathogenesis of these forms is associated with a "loss of function" of specific cellular proteins involved in metabolic homeostasis, cell cycle, and DNA repair/protection processing. The two most common autosomal recessive ataxias, in European countries, are Friedreich's ataxia and ataxia telangiectasia. Other forms are much less frequent, and include ataxia with vitamin E deficiency, abetalipoproteinemia. Refsum's disease, spastic ataxia, infantile onset spinocerebellar ataxia, and ataxia with oculomotor apraxia. These pathological conditions, although extremely rare, have nevertheless to be carefully considered in differential diagnosis, not only for correct nosographical classification, but particularly, for specific prognostic and therapeutic implications. Some of these diseases exhibit a peculiar regional distribution. An updated review of the clinical, genetic, and pathogenic aspects of recessive ataxias is presented. Specific management problems with respect to diagnosis and genetic counseling are discussed.

Positional cloning and functional analysis of the gene responsible for Nijmegen breakage syndrome, NBS1.

Nijmegen breakage syndrome (NBS) is a rare autosomal recessive disorder characterized by microcephaly, combined immunodeficiency, and a high incidence of lymphoid tumor. Cells from NBS patients show chromosomal instability, hypersensitivity to ionizing radiation and abnormal p53-mediated cell cycle regulation. We cloned the underlying gene for NBS, designated NBS1, by complementation-assisted positional cloning from the candidate region 8q21. Large genomic sequencing, as well as a search using computer programs, provides a powerful approach for identifying the underlying gene for a disease. The NBS1 gene encodes a protein of 754 amino acids that has FHA and BRCT domains which often are conserved in cell-cycle checkpoint proteins. The gene has weak homology to the yeast (Saccharomyces cerevisiae) Xrs2 protein in the N-terminus region. Like yeast Xrs2, the NBS1 protein forms a complex with hRAD50/hMRE11, and the complex is condensed as foci in the nucleus after irradiation, indicative that this triple-complex is a crucial factor in DNA repair. Functional analysis of the NBS1 protein is in progress and it should provide further clues to understanding the repair mechanism of radiation-induced DNA double-strand breaks.

Mutations associated with variant phenotypes in ataxia-telangiectasia.

We have identified 14 families with ataxia-telangiectasia (A-T) in which mutation of the ATM gene is associated with a less severe clinical and cellular phenotype (approximately 10%-15% of A-T families identified in the United Kingdom). In 10 of these families, all the homozygotes have a 137-bp insertion in their cDNA caused by a point mutation in a sequence resembling a splice-donor site. The second A-T allele has a different mutation in each patient. We show that the less severe phenotype in these patients is caused by some degree of normal splicing, which occurs as an alternative product from the insertion-containing allele. The level of the 137-bp PCR product containing the insertion was lowest in two patients who showed a later onset of cerebellar ataxia. A further four families who do not have this insertion have been identified. Mutations detected in two of four of these are missense mutations, normally rare in A-T patients. The demonstration of mutations giving rise to a slightly milder phenotype in A-T raises the interesting question of what range of phenotypes might occur in individuals in whom both mutations are milder. One possibility might be that individuals who are compound heterozygotes for ATM mutations are more common than we realize.

Nucleotide sequence analysis of a candidate gene for ataxia-telangiectasia group D (ATDC).

A radioresistant cell clone (1B3) was previously isolated after transfection of an ataxia-telangiectasia (AT) group D cell line with a human cosmid library. A cosmid rescued from the integration site in 1B3 contained human DNA from chromosome position 11q23, the same region shown by both genetic linkage and chromosome transfer to contain the genes for AT complementation groups A/B, C, and D. A gene within the cosmid (ATDC) was found to produce mRNAs of different sizes. A cDNA for one of the most abundant mRNAs (3.0 kb) was isolated from a HeLa cell library. In the present study, we sequenced the 3.0-kb cDNA and the surrounding intron DNA in the cosmids. We used polymerase chain reaction, with primers in the introns, to confirm the number of exons and to analyze DNA from AT group D cells for mutations within this gene. Although no mutations were found, we do not rule out the possibility that mutations may be present within the regulatory sequences or coding sequences found in other mRNAs specific for this gene. From the sequence analysis, we found that the ATDC gene product is one of a group of proteins that share multiple zinc finger motifs and an adjacent leucine zipper motif. These proteins have been proposed to form homo- or heterodimers involved in nucleic acid binding, consistent with the fact that many of these proteins appear to be transcriptional regulatory factors involved in carcinogenesis and/or differentiation. The likelihood that the ATDC gene product is involved in transcriptional regulation could explain the pleiomorphic characteristics of AT, including abnormal cell cycle regulation.

Ataxia without telangiectasia.

Ataxia telangiectasia (AT) is an autosomal recessive hereditary disorder characterized by onset in infancy or childhood of a cerebellar and later extrapyramidal disorder associated with telangiectasias and an immune deficit. Only a handful of cases have been described in which the features were not stereotypic. This report describes a case that is classic except for the absence of telangiectasias through age 17. This and other cases suggest that a new, more inclusive term be used to describe the syndrome of ataxia with immune deficit until the genetic abnormalities in these disorders become identifiable.

Ataxia-telangiectasia

El síndrome de ataxia telangiectasia antes llamado síndrome de Louis-Bar fue descrito en 1941. La enfermedad es autosómica recesiva y se cree que la anormalidad se localiza en la banda 11 del brazo corto de los cromosomas 22-23 (11a 22-23) en donde se sitúa el gen que codifica la proteína esencial en la recombinación utilizada por los genes de la familia de las inmunoglobulinas. El síndrome se caracteriza por ataxia cerebelar progresiva, telangiectasias óculo-cutáneas, enfermedad sinu-bronquial crónica, inmunodeficiencia variable y alta incidencia de tumores como leucemia, adenomas y linfoma no-Hodgkin. A continuación se describe un caso de ataxia-telangiectásica que consultó a nuestra institución.