Variants Within TSC2 Exons 25 and 31 Are Very Unlikely to Cause Clinically Diagnosable Tuberous Sclerosis.

Inactivating mutations in TSC1 and TSC2 cause tuberous sclerosis complex (TSC). The 2012 international consensus meeting on TSC diagnosis and management agreed that the identification of a pathogenic TSC1 or TSC2 variant establishes a diagnosis of TSC, even in the absence of clinical signs. However, exons 25 and 31 of TSC2 are subject to alternative splicing. No variants causing clinically diagnosed TSC have been reported in these exons, raising the possibility that such variants would not cause TSC. We present truncating and in-frame variants in exons 25 and 31 in three individuals unlikely to fulfil TSC diagnostic criteria and examine the importance of these exons in TSC using different approaches. Amino acid conservation analysis suggests significantly less conservation in these exons compared with the majority of TSC2 exons, and TSC2 expression data demonstrates that the majority of TSC2 transcripts lack exons 25 and/or 31 in many human adult tissues. In vitro assay of both exons shows that neither exon is essential for TSC complex function. Our evidence suggests that variants in TSC2 exons 25 or 31 are very unlikely to cause classical TSC, although a role for these exons in tissue/stage specific development cannot be excluded.

Monoallelic germline TSC1 mutations are permissive for T lymphocyte development and homeostasis in tuberous sclerosis complex individuals.

Germline and somatic biallelic mutations of the Tuberous sclerosis complex (TSC) 1 and TSC2 gene products cause TSC, an autosomal dominant multifocal hamartomatosis with variable neurological manifestations. The consequences of TSC1 or TSC2 loss in cells of hematopoietic origin have recently started to be unveiled in mice and showed to hinder the development of proper T cell immunity. To date, the consequences of germline TSC1 mutations and/or its loss in mature human T cells remain to be determined. To address these issues, we analyzed subset representation, phenotype and responsiveness to mitogens in T cells from patients with inherited monoallelic TSC1 mutations, and induced shRNA-mediated TSC1 down-regulation in primary and transformed human T cells. We report that, the distribution of peripheral CD4 and CD8 T cell subsets, their cytokine-secretion profile, and responsiveness to in vitro stimulation were largely preserved in TSC subjects with monoallelic TSC1 germline mutations when compared to healthy controls. Sufficient levels of hamartin and tuberin and proper control of mTOR-dependent signaling in primary T cells from TSC subjects best explained this. In contrast, shRNA-induced down-regulation of TSC1, likely mimicking biallelic inactivation of TSC1, compromised hamartin and tuberin expression and mTORC2/AKT/FoxO1/3 signaling causing both primary and transformed T cells to die by apoptosis. Thus, our results indicate that, while one functional TSC1 allele preserves human T lymphocytes development and homeostasis, TSC1 acute down-regulation is detrimental to the survival of both primary and transformed T cells.

Missense mutations in the AFG3L2 proteolytic domain account for ∼1.5% of European autosomal dominant cerebellar ataxias.

Spinocerebellar ataxia type 28 is an autosomal dominant form of cerebellar ataxia (ADCA) caused by mutations in AFG3L2, a gene that encodes a subunit of the mitochondrial m-AAA protease. We screened 366 primarily Caucasian ADCA families, negative for the most common triplet expansions, for point mutations in AFG3L2 using DHPLC. Whole-gene deletions were excluded in 300 of the patients, and duplications were excluded in 129 patients. We found six missense mutations in nine unrelated index cases (9/366, 2.6%): c.1961C>T (p.Thr654Ile) in exon 15, c.1996A>G (p.Met666Val), c.1997T>G (p.Met666Arg), c.1997T>C (p.Met666Thr), c.2011G>A (p.Gly671Arg), and c.2012G>A (p.Gly671Glu) in exon 16. All mutated amino acids were located in the C-terminal proteolytic domain. In available cases, we demonstrated the mutations segregated with the disease. Mutated amino acids are highly conserved, and bioinformatic analysis indicates the substitutions are likely deleterious. This investigation demonstrates that SCA28 accounts for ∼3% of ADCA Caucasian cases negative for triplet expansions and, in extenso, to ∼1.5% of all ADCA. We further confirm both the involvement of AFG3L2 gene in SCA28 and the presence of a mutational hotspot in exons 15-16. Screening for SCA28, is warranted in patients who test negative for more common SCAs and present with a slowly progressive cerebellar ataxia accompanied by oculomotor signs.

Large genomic mutations within the ATM gene detected by MLPA, including a duplication of 41 kb from exon 4 to 20.

Mutation detection remains problematic for large genes, primarily because PCR-based methodology fails to detect heterozygous deletions and any duplication. In the ATM gene only a handful of multi-exon deletions have been described to date, and this type of mutation has been considered rare. To address this issue we tested a new MLPA (Multiplex Ligation Probe Amplification) kit that covers 33 of the 66 ATM exons, using for controls two previously characterized genomic deletions in addition to three A-T patients, taken from a survey of nine, who had missing four mutations unidentified after conventional mutation screening. We identified for the first time: 1) a approximately 41 kb genomic duplication spanning exons 4-20 (c.-30_2816dup41kb)(a.k.a., ATM dup 41 kb); 2) a novel genomic deletion including exon 31, and 3) in hemizygosis a point mutation in the non-deleted exon 31. In this study we extended mutation detection to nine new Italian A-T patients, using a combined approach of haplotype analysis, DHPLC and MLPA. Overall we achieved a mutation detection rate of >97%, and can now define a spectrum of ATM mutations based on twenty-one consecutive Italian families with A-T.

Intractable epilepsy in hemimegalencephaly and tuberous sclerosis complex.

Hemimegalencephaly is a rare brain malformation consisting of the enlargement of 1 hemisphere, often associated with abnormal cortical gyration, thick cortex, large neurons, and increased astrocytes. Cranial asymmetry is the first clinical sign usually present at birth; in the most severe cases, hemimegalencephaly may be evident during pregnancy. Hemiparesis, intractable epilepsy, and developmental delay are the typical clinical manifestations. Tuberous Sclerosis Complex is an autosomal dominant disorder affecting about 1 in 6000 live births; the number of spontaneous mutations is remarkable. It is characterized by the development of hamartias, or nongrowing lesions, and hamartomas, which grow as benign tumors and rarely progress to malignancy. These lesions most frequently involve the brain, skin, kidneys, eyes, and heart. The rare association of hemimegalencephaly and tuberous sclerosis complex has been reported in a few cases. The authors report the case of a 4-year-old boy with left hemimegalencephaly, tuberous sclerosis complex genetically confirmed, and intractable epilepsy originating from the nonhemimegalencephalic hemisphere.

ATM mutations in Italian families with ataxia telangiectasia include two distinct large genomic deletions.

In patients affected by Ataxia-Telangiectasia (A-T), mutations in the ATM gene lead to loss-of-function alleles. Nonsense, splice-site variants, small insertions or deletions (frameshifts) and missense are the most commonly found mutations. Large genomic deletions (LGDs) are rare (approximately 1%) but can lead to the same phenotype. In compound heterozygotes, deletions are not detected by most screening strategies. We analysed the ATM gene in 12 unrelated Italian A-T patients and identified all 24 mutated alleles. Twelve mutations were novel. Standardized SNP and STR haplotyping followed by DHPLC screening of genomic DNA, allowed all but three mutations to be detected (approximately 87.5%). The remaining mutations required RT-PCR analysis of ATM transcript and Southern blotting of genomic DNA. We found three LGDs: one of 8.5 and two identical of 18 kb spanning exons 32-36 and 21-29, respectively. The breakpoints of these deletions were sequenced in an attempt to understand the mechanisms of mutations; both deletions involved regions rich in repeated elements.

An enhanced polymerase chain reaction assay to detect pre- and full mutation alleles of the fragile X mental retardation 1 gene.

Several diagnostic strategies have been applied to the detection of FMR1 gene repeat expansions in fragile X syndrome. Here, we report a novel polymerase chain reaction-based strategy using the Expand Long Template PCR System (Roche Diagnostics, Mannheim, Germany) and the osmolyte betaine. Repeat expansions up to approximately 330 CGGs in males and up to at least approximately 160 CGGs in carrier women could be easily visualized on ethidium bromide agarose gels. We also demonstrated that fluorescence analysis of polymerase chain reaction products was a reliable tool to verify the presence of premutation and full mutation alleles both in males and in females. This technique, primarily designed to detect premutation alleles, can be used as a routine first screen for expanded FMR1 alleles.

Six novel ATM mutations in Italian patients with classical ataxia-telangiectasia.

Mutations in the ATM gene are responsible for the autosomal recessive syndrome Ataxia Telangiectasia (AT). In a group of 26 classical AT Italian patients studied by protein truncation test (PTT), we identified six new mutations, never reported so far. Mutations -spread over the entire ATM coding sequence with not clear "hot-spot"- are four frameshifts (2192_2193insA, 3110delC, 7150delA, 8368delA), one splice site alteration (8850G>T, causing exon 63 skipping) and one nonsense change (6913C>T, Q2305X). The identification of ATM gene mutations is important for understanding the molecular basis of the disease, and is essential for diagnosis and genetic counseling.

The endophilin-CIN85-Cbl complex mediates ligand-dependent downregulation of c-Met.

Ligand-dependent downregulation of tyrosine kinase receptors is a critical step for modulating their activity. Upon ligand binding, hepatocyte growth factor (HGF) receptor (Met) is polyubiquitinated and degraded; however, the mechanisms underlying HGF receptor endocytosis are not yet known. Here we demonstrate that a complex involving endophilins, CIN85 and Cbl controls this process. Endophilins are regulatory components of clathrin-coated vesicle formation. Through their acyl-transferase activity they are thought to modify the membrane phospholipids and induce negative curvature and invagination of the plasma membrane during the early steps of endocytosis. Furthermore, by means of their Src-homology 3 domains, endophilins are able to bind CIN85, a recently identified protein that interacts with the Cbl proto-oncogene. Cbl, in turn, binds and ubiquitinates activated HGF receptor, and by recruiting the endophilin-CIN85 complex, it regulates receptor internalization. Inhibition of complex formation is sufficient to block HGF receptor internalization and to enhance HGF-induced signal transduction and biological responses. These data provide further evidence of a relationship between receptor-mediated signalling and endocytosis, and disclose a novel functional role for Cbl in HGF receptor signalling.