Daniela Toniolo

Mutations in the gene encoding lamin A/C cause autosomal dominant Emery-Dreifuss muscular dystrophy

Emery-Dreifuss muscular dystrophy (EDMD) is characterized by early contractures of elbows and Achilles tendons, slowly progressive muscle wasting and weakness, and a cardiomyopathy with conduction blocks which is life-threatening. Two modes of inheritance exist, X-linked (OMIM 310300) and autosomal dominant (EDMD-AD; OMIM 181350). EDMD-AD is clinically identical to the X-linked forms of the disease. Mutations in EMD, the gene encoding emerin, are responsible for the X-linked form. We have mapped the locus for EDMD-AD to an 8-cM interval on chromosome 1q11-q23 in a large French pedigree, and found that the EMD phenotype in four other small families was potentially linked to this locus. This region contains the lamin A/C gene (LMNA), a candidate gene encoding two proteins of the nuclear lamina, lamins A and C, produced by alternative splicing. We identified four mutations in LMNA that co-segregate with the disease phenotype in the five families: one nonsense mutation and three missense mutations. These results are the first identification of mutations in a component of the nuclear lamina as a cause of inherited muscle disorder. Together with mutations in EMD (Refs 5,6), they underscore the potential importance of the nuclear envelope components in the pathogenesis of neuromuscular disorders.

Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis (vol 5, 4926, 2014)

Corrigendum: Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis

Different mutations in the LMNA gene cause autosomal dominant and autosomal recessive Emery-Dreifuss muscular dystrophy.

Emery-Dreifuss muscular dystrophy (EMD) is a condition characterized by the clinical triad of early-onset contractures, progressive weakness in humeroperoneal muscles, and cardiomyopathy with conduction block. The disease was described for the first time as an X-linked muscular dystrophy, but autosomal dominant and autosomal recessive forms were reported. The genes for X-linked EMD and autosomal dominant EMD (AD-EMD) were identified. We report here that heterozygote mutations in LMNA, the gene for AD-EMD, may cause diverse phenotypes ranging from typical EMD to no phenotypic effect. Our results show that LMNA mutations are also responsible for the recessive form of the disease. Our results give further support to the notion that different genetic forms of EMD have a common pathophysiological background. The distribution of the mutations in AD-EMD patients (in the tail and in the 2A rod domain) suggests that unique interactions between lamin A/C and other nuclear components exist that have an important role in cardiac and skeletal muscle function.

Genetic Structure of Europeans: A View from the North–East

Using principal component (PC) analysis, we studied the genetic constitution of 3,112 individuals from Europe as portrayed by more than 270,000 single nucleotide polymorphisms (SNPs) genotyped with the Illumina Infinium platform. In cohorts where the sample size was >100, one hundred randomly chosen samples were used for analysis to minimize the sample size effect, resulting in a total of 1,564 samples. This analysis revealed that the genetic structure of the European population correlates closely with geography. The first two PCs highlight the genetic diversity corresponding to the northwest to southeast gradient and position the populations according to their approximate geographic origin. The resulting genetic map forms a triangular structure with a) Finland, b) the Baltic region, Poland and Western Russia, and c) Italy as its vertexes, and with d) Central- and Western Europe in its centre. Inter- and intra- population genetic differences were quantified by the inflation factor lambda (λ) (ranging from 1.00 to 4.21), fixation index (Fst) (ranging from 0.000 to 0.023), and by the number of markers exhibiting significant allele frequency differences in pair-wise population comparisons. The estimated lambda was used to assess the real diminishing impact to association statistics when two distinct populations are merged directly in an analysis. When the PC analysis was confined to the 1,019 Estonian individuals (0.1% of the Estonian population), a fine structure emerged that correlated with the geography of individual counties. With at least two cohorts available from several countries, genetic substructures were investigated in Czech, Finnish, German, Estonian and Italian populations. Together with previously published data, our results allow the creation of a comprehensive European genetic map that will greatly facilitate inter-population genetic studies including genome wide association studies (GWAS).

Mutations in GDI1 are responsible for X-linked non-specific mental retardation.

Rab GDP-dissociation inhibitors (GDI) are evolutionarily conserved proteins that play an essential role in the recycling of Rab GTPases required for vesicular transport through the secretory pathway. We have found mutations in the GDI1 gene (which encodes αGDI) in two families affected with X-linked non-specific mental retardation. One of the mutations caused a non-conservative substitution (L92P) which reduced binding and recycling of RAB3A, the second was a null mutation. Our results show that both functional and developmental alterations in the neuron may account for the severe impairment of learning abilities as a consequence of mutations in GDI1, emphasizing its critical role in development of human intellectual and learning abilities.

A Mutation in the Rett Syndrome Gene, MECP2, Causes X-Linked Mental Retardation and Progressive Spasticity in Males

Heterozygous mutations in the X-linked MECP2 gene cause Rett syndrome, a severe neurodevelopmental disorder of young females. Only one male presenting an MECP2 mutation has been reported; he survived only to age 1 year, suggesting that mutations in MECP2 are male lethal. Here we report a three-generation family in which two affected males showed severe mental retardation and progressive spasticity, previously mapped in Xq27.2-qter. Two obligate carrier females showed either normal or borderline intelligence, simulating an X-linked recessive trait. The two males and the two obligate carrier females presented a mutation in the MECP2 gene, demonstrating that, in males, MECP2 can be responsible for severe mental retardation associated with neurological disorders.

A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness

Many existing cohorts contain a range of relatedness between genotyped individuals, either by design or by chance. Haplotype estimation in such cohorts is a central step in many downstream analyses. Using genotypes from six cohorts from isolated populations and two cohorts from non-isolated populations, we have investigated the performance of different phasing methods designed for nominally ‘unrelated’ individuals. We find that SHAPEIT2 produces much lower switch error rates in all cohorts compared to other methods, including those designed specifically for isolated populations. In particular, when large amounts of IBD sharing is present, SHAPEIT2 infers close to perfect haplotypes. Based on these results we have developed a general strategy for phasing cohorts with any level of implicit or explicit relatedness between individuals. First SHAPEIT2 is run ignoring all explicit family information. We then apply a novel HMM method (duoHMM) to combine the SHAPEIT2 haplotypes with any family information to infer the inheritance pattern of each meiosis at all sites across each chromosome. This allows the correction of switch errors, detection of recombination events and genotyping errors. We show that the method detects numbers of recombination events that align very well with expectations based on genetic maps, and that it infers far fewer spurious recombination events than Merlin. The method can also detect genotyping errors and infer recombination events in otherwise uninformative families, such as trios and duos. The detected recombination events can be used in association scans for recombination phenotypes. The method provides a simple and unified approach to haplotype estimation, that will be of interest to researchers in the fields of human, animal and plant genetics.

Structural analysis of the X-linked gene encoding human glucose 6-phosphate dehydrogenase.

We report the isolation and analysis of human genomic DNA clones spanning about 100 kb of the X chromosome and comprising the entire gene coding for the enzyme glucose 6‐phosphate dehydrogenase (G6PD). The G6PD gene is 18 kb long and consists of 13 exons: the protein‐coding region is divided into 12 segments ranging in size from 12 to 236 bp; an intron is present in the 5′ untranslated region. Mature G6PD mRNA has a single polyadenylation site in HeLa cells. The major 5′ end of mature G6PD mRNA in several cell lines is located 177 bp upstream of the translation initiating codon; longer mRNA molecules extending further in the 5′ direction could be identified by S1 mapping and by comparing genomic and cDNA sequences. The DNA sequence around the major mRNA start is very GC rich; as to putative transcription regulatory sequences, a non‐canonical TATA box and 9 CCGCCC elements are present, but no CAAT element could be identified. The genomic DNA we have isolated includes another ubiquitously transcribed region, provisionally named the GdX gene. Although the function of GdX is as yet unknown, we have established that this gene is located about 40 kb downstream of G6PD and is transcribed in the same direction. A comparative analysis of the promoter region of G6PD and 10 other housekeeping enzyme genes has confirmed the presence of a number of common features. In particular, in the eight cases in which a ‘TATA’ box is present, a conserved sequence of 25 bp is seen immediately downstream.

The immunoglobulin gene repertoire of low-count chronic lymphocytic leukemia (CLL)-like monoclonal B lymphocytosis is different from CLL: diagnostic implications for clinical monitoring.

In the revised National Cancer Institute Working Group (NCI-WG)/International Workshop on Chronic Lymphocytic Leukemia (IWCLL) guidelines for CLL, CLL-like monoclonal B lymphocytosis (MBL) is defined as the presence of less than 5 x 10(9)/L B lymphocytes in the peripheral blood. However, the concentration of MBL in the blood is extremely variable. MBL in subjects with lymphocytosis require treatment at a rate of 1.1% per year and present immunoglobulin (IG) gene features and similar to good prognosis CLL. Little is known about low-count MBL cases, accidentally found in the general population. We analyzed IGHV-D-J rearrangements in 51 CLL-like MBL cases from healthy individuals, characterized by few clonal B cells. Seventy percent of the IGHV genes were mutated. The most frequent IGHV gene was IGHV4-59/61, rarely used in CLL, whereas the IGHV1-69 gene was lacking and the IGHV4-34 gene was infrequent. Only 2 of 51 (3.9%) MBL cases expressed a CLL-specific stereotyped HCDR3. Therefore, the IG gene repertoire in low-count MBL differs from both mutated and unmutated CLL, suggesting that the detection of MBL in an otherwise healthy subject is not always equivalent to a preleukemic state. Detailed IG analysis of individual MBL may help to identify cases that necessitate continuous clinical monitoring to anticipate disease progression.

Clinical Relevance of Atrial Fibrillation/Flutter, Stroke, Pacemaker Implant, and Heart Failure in Emery-Dreifuss Muscular Dystrophy A Long-Term Longitudinal Study

Background and Purpose— Emery-Dreifuss muscular dystrophy (EDMD) is a rare inherited disorder associated with cardiac involvement. We investigated the spectrum and relevance of the cardiac manifestations of EDMD, focusing on bradyarrhythmias and tachyarrhythmias (including atrial fibrillation/flutter), embolic stroke, and heart failure. Methods and Results— Eighteen patients (age 42.8±19.6 years) with genetically confirmed X-linked (n=10, including 3 carriers) or autosomal dominant (n=8) EDMD were followed for a period ranging from 1 to 30 years in a research center for neuromuscular diseases and in a university cardiological department. Pacemakers were required by 10 of 18 (56%) patients for bradyarrhythmia, and related complications occurred in 3 of 10 (30%) cases. Atrial fibrillation/flutter developed in 11 of 18 (61%) patients, with atrial standstill subsequently occurring in 5 of 11 (45%) cases and embolic stroke (most often disabling) in 4 of 11 (36%). Heart failure requiring transplantation occurred in 1 of 18 (6%) patients, and asymptomatic left ventricular dysfunction in a further 3 (17%). No relationship was evident between neuromuscular impairment and cardiac involvement. Conclusions— Both X-linked and autosomal dominant EDMD patients risk not only bradyarrhythmia (requiring pacemaker implant) but also atrial fibrillation/flutter, which often anticipates atrial standstill and can cause disabling embolic stroke at a relatively young age. Antithromboembolic prophylaxis has to be recommended in EDMD patients with atrial fibrillation/flutter or atrial standstill. With careful monitoring, survival after pacemaker implant may be long. Heart failure, which seems to occur only in a minority of patients, may be severe.