Dynamic Mutations Research Articles

A highly mutable GST is essential for bract colouration in Euphorbia pulcherrima Willd. Ex Klotsch

BackgroundMutation breeding is an extraordinary tool in plant breeding to increase the genetic variability, where mutations in anthocyanin biosynthesis are targets to generate distinctive phenotypes in ornamental species. In poinsettia, ionizing radiation is routinely applied in breeding programs to obtaining a range of colours, with nearly all pink and white varieties being obtained after γ- or X-ray mutagenesis of red varieties. In the present study we performed a thorough characterization of a potential mutagenesis target gene as the main responsible for the ‘white paradox’ in poinsettia.ResultsWe identified a GST gene in poinsettia (Bract1) as an essential factor for the expression of anthocyanin-based red colouration of bracts, which presents a high phylogenetic similarity to known anthocyanin-related GSTs. Red poinsettia varieties and white mutants generated from these varieties by X-ray were analysed for polymorphisms related to the ‘white paradox’ in the species. A 4 bp mutation in a short repeat within the coding region of Bract1 is most likely responsible for the appearance of white phenotypes upon irradiation treatment. The polymorphism between wild-type and mutant alleles co-segregates with the phenotype in progeny from heterozygous red and white parents. Moreover, overexpression of Bract1 wild-type allele in Arabidopsis tt19 mutants restored the anthocyanin phenotype, while the Bract1 mutated allele showed to be non-functional.ConclusionsThe identified repeat seems to be highly unstable, since mutated plants can be easily detected among fewer than 200 shoots derived from 10 mutated plants. Our data indicate that particular short repeat sequences, similar to microsatellite sequences or so-called dynamic mutations, might be hot spots for genetic variability. Moreover, the identification of the Bract1 mutation fills a gap on the understanding on the molecular mechanism of colour formation in poinsettia.

Challenges in Clinicogenetic Correlations: One Gene - Many Phenotypes.

ABSTRACTBackgroundProgress in genetics – particularly the advent of next‐generation sequencing (NGS) – has enabled an unparalleled gene discovery and revealed unmatched complexity of genotype–phenotype correlations in movement disorders. Among other things, it has emerged that mutations in one and the same gene can cause multiple, often markedly different phenotypes. Consequently, movement disorder specialists have increasingly experienced challenges in clinicogenetic correlations.ObjectivesTo deconstruct biological phenomena and mechanistic bases of phenotypic heterogeneity in monogenic movement disorders and neurodegenerative diseases. To discuss the evolving role of movement disorder specialists in reshaping disease phenotypes in the NGS era.MethodsThis scoping review details phenomena contributing to phenotypic heterogeneity and their underlying mechanisms.ResultsThree phenomena contribute to phenotypic heterogeneity, namely incomplete penetrance, variable expressivity and pleiotropy. Their underlying mechanisms, which are often shared across phenomena and non‐mutually exclusive, are not fully elucidated. They involve genetic factors (ie, different mutation types, dynamic mutations, somatic mosaicism, intragenic intra‐ and inter‐allelic interactions, modifiers and epistatic genes, mitochondrial heteroplasmy), epigenetic factors (ie, genomic imprinting, X‐chromosome inactivation, modulation of genetic and chromosomal defects), and environmental factors.ConclusionMovement disorders is unique in its reliance on clinical judgment to accurately define disease phenotypes. This has been reaffirmed by the NGS revolution, which provides ever‐growing sequencing data and fuels challenges in variant pathogenicity assertions for such clinically heterogeneous disorders. Deep phenotyping, with characterization and continual updating of “core” phenotypes, and comprehension of determinants of genotype–phenotype complex relationships are crucial for clinicogenetic correlations and have implications for the diagnosis, treatment and counseling.

Rapid Molecular Screen of Spinocerebellar Ataxia Types 1, 2, and 3 by Triplet-Primed PCR and Melting Curve Analysis

The autosomal-dominantly inherited spinocerebellar ataxias (SCAs) can be caused by dynamic mutations of short tandem repeats within various genes. Due to the significant clinical overlap among the various SCA types, molecular screening of multiple genetic loci by fluorescent PCR and capillary electrophoresis is necessary to identify the causative repeat expansion. We describe a simple, rapid, and inexpensive strategy to screen for CAG repeat expansion mutations at the ATXN1, ATXN2, and ATXN3 loci using melting curve analysis (MCA) of triplet-primed PCR products. Plasmid DNAs of known repeat sizes were used to generate threshold melt peak temperatures, which rapidly and effectively distinguish samples carrying an expanded allele from those carrying non-expanded alleles. MCA-positive samples were confirmed by capillary electrophoresis sizing of the triplet-primed PCR products. All three assays achieved 100% sensitivity with 95% confidence intervals (CI) of 67.86-100 (SCA1), 74.65-100 (SCA2), and 91.58-100 (SCA3). The SCA1 assay also achieved 100% specificity (95% CI: 97.52-100), while the SCA2 and SCA3 assays achieved specificity of 99.46% (95% CI: 96.56-99.97) and 99.32% (95% CI: 95.70-99.96), respectively. These screening assays provide robust and highly accurate detection of expanded alleles and are amenable to large-scale screening while minimizing the need for capillary electrophoresis sizing for every sample.

Evolution of a Record-Setting AT-Rich Genome: Indel Mutation, Recombination, and Substitution Bias.

Genome-wide nucleotide composition varies widely among species. Despite extensive research, the source of genome-wide nucleotide composition diversity remains elusive. Yeast mitochondrial genomes (mitogenomes) are highly A + T rich, and they provide a unique opportunity to study the evolution of AT-biased landscape. In this study, we sequenced ten complete mitogenomes of the Saccharomycodes ludwigii yeast with 8% G + C content, the lowest genome-wide %(G + C) in all published genomes to date. The S. ludwigii mitogenomes have high densities of short tandem repeats but severely underrepresented mononucleotide repeats. Comparative population genomics of these record-setting A + T-rich genomes shows dynamic indel mutations and strong mutation bias toward A/T. Indel mutations play a greater role in genomic variation among very closely related strains than nucleotide substitutions. Indels have resulted in presence–absence polymorphism of tRNAArg (ACG) among S. ludwigii mitogenomes. Interestingly, these mitogenomes have undergone recombination, a genetic process that can increase G + C content by GC-biased gene conversion. Finally, the expected equilibrium G + C content under mutation pressure alone is higher than observed G + C content, suggesting existence of mechanisms other than AT-biased mutation operating to increase A/T. Together, our findings shed new lights on mechanisms driving extremely AT-rich genomes.

Mutational mechanism for DAB1 (ATTTC)n insertion in SCA37: ATTTT repeat lengthening and nucleotide substitution.

Dynamic mutations by microsatellite instability are the molecular basis of a growing number of neuromuscular and neurodegenerative diseases. Repetitive stretches in the human genome may drive pathogenicity, either by expansion above a given threshold, or by insertion of abnormal tracts in nonpathogenic polymorphic repetitive regions, as is the case in spinocerebellar ataxia type 37 (SCA37). We have recently established that this neurodegenerative disease is caused by an (ATTTC)n insertion within an (ATTTT)n in a noncoding region of DAB1. We now investigated the mutational mechanism that originated the (ATTTC)n insertion within an ancestral (ATTTT)n . Approximately 3% of nonpathogenic (ATTTT)n alleles are interspersed by AT-rich motifs, contrarily to mutant alleles that are composed of pure (ATTTT)n and (ATTTC)n stretches. Haplotype studies in unaffected chromosomes suggested that the primary mutational mechanism, leading to the (ATTTC)n insertion, was likely one or more T>C substitutions in an (ATTTT)n pure allele of approximately 200 repeats. Then, the (ATTTC)n expanded in size, originating a deleterious allele in DAB1 that leads to SCA37. This is likely the mutational mechanism in three similar (TTTCA)n insertions responsible for familial myoclonic epilepsy. Because (ATTTT)n tracts are frequent in the human genome, many loci could be at risk for this mutational process.

Screening for FMR1 expanded alleles in patients with Autism Spectrum Disorders in Manaus, Northern Brazil.

Fragile X Syndrome (FXS) is a neurodevelopmental disorder caused by dynamic mutations of a CGG repetition segment in an X chromosome's single gene. It is considered the leading hereditary cause of both Autism Spectrum Disorders and Intellectual Disability. Some authors suggest that all individuals diagnosed with some of these latter conditions to be clinically and molecularly trialled for FXS due to the high levels of comorbidity between both conditions and also due to the variable expressiveness of this syndrome. This study has focused on verifying the presence of FMR1 expanded alleles since there is a lack of information about this kind of mutation in autism patients from the northern region of Brazil. The presence of large alleles for this gene could offer new therapeutic or pharmacological methods for the treatment of these patients. Both the presence and the frequency of CGG expansions were verified in 90 autism males by molecular analysis. Four of them had intermediate alleles and four others presented premutated alleles. Premutation carriers are on the propensity of developing the late onset Fragile X-associated tremor/ataxia syndrome. No full mutation alleles were found. Further studies are necessary to obtain more accurate statistical data about this kind of dynamic mutation.

Next Generation Myelofibrosis Risk Analysis in the Electronic Health Record

Background: Myelofibrosis (MF) is a devastating myeloproliferative neoplasm that is hallmarked by marrow fibrosis, symptomatic extramedullary hematopoiesis, and risk of leukemic transformation, most commonly driven by janus kinase 2 (JAK2) pathway mutations. MF risk classification systems guide prognosis, decisions regarding allogeneic stem cell transplantation, and disease modifying agents. Key systems include the Dynamic International Prognostic Scoring System (DIPSS) 2009, DIPSS plus 2010, Genetics-Based Prognostic Scoring System (GPSS) 2014, and Mutation-Enhanced International Prognostic Scoring System (MIPSS) 2014. System contributions include dynamic scoring (DIPSS), cytogenetics (DIPSS Plus), and high risk molecular mutations (GPSS and MIPSS). To power the next generation of MF risk prognostication, and ascertain new prognostic factors, large scale electronic health record (EHR) and genomic data will need integration. As a proof of concept, we leveraged our de-identified research EHR (2.9 million records) and linked genomic biobank (288,000 patients) to develop an all-inclusive phenotype-genotype-prognostic system for MF and recapitulate DIPSS, DIPSS Plus, GPSS and MIPSS.Methods: Our previously described methods (Bejan et al. AACR 2018) utilized natural language processing to algorithmically identify 306 MF patients. A subset (N=125) had available DNA for genotyping. We automatically extracted: age greater than 65, leukocyte count (WBC) greater than 25x109/L, hemoglobin (Hgb) less than 10g/dL, platelets (PLT) less than 100 x 109/L, circulating myeloid blasts ≥ 1%, and 10% weight loss compared to baseline as a proxy for constitutional symptoms. Transfusion data was not included. Karyotype data was manually reviewed. Next generation sequencing (NGS) was performed on biobanked peripheral blood DNA with the Trusight Myeloid Panel (Illumina®). Genotyped samples were restricted to dates after MF diagnosis. Multivariate Cox proportional hazard analysis was performed on all clinical and genomic variables. DIPSS plus was calculated without adjustment but lacked transfusion data. DIPSS, GPSS and MIPSS scores were calculated by published methods.Results: Multivariate Cox proportional hazard regression identified Hgb (HR=6.4; P=0.006), myeloid blasts (HR=3.8; P=0.03), and ASXL1 (HR=5.2; P=0.02) as significant in our cohort with regard to overall survival (OS). We noted a strong trend for high risk karyotype (HR=5.6; P=0.07). Our DIPSS model median survival (N=120) for each subgroup; low risk (median survival not met), intermediate-1 (108 months), intermediate-2 (47 months) and high risk (6 months) P=0.0002 (Figure 1a). DIPSS Plus (N=122) integrated karyotype data and PLT count with similar survival with the exception of high risk (4 months) P=0.00003 (Figure 1b). The percentage of patients with driver mutations in JAK2V617F (57%), CALR (3%) and MPLW515 (7.2%); JAK2WT, CALRWT and MPLWT triple negative (34%); high molecular risk ASXL1 (15%), EZH2 (6%), IDH1/2 (7%), SRFS2 (17%); other variants of interest TET2 (9.6%), TP53 (29%) and DNMT3A (16.8%). MIPSS (N=125; 48 months follow up) noted low risk, intermediate-1, and intermediate-2 (median survival not met) and high risk (32 months) P=0.0001 (Figure 1c). GPSS (N=125; 48 months follow up) did not demonstrate statistical separation among groups (Figure 1d).Discussion: This proof of concept transformed raw EHR records into clinical risk scores for MF. The addition of retrospective DNA analysis via NGS opens the possibility of multi-institutional EHR-biobank studies to most accurately create a system to define MF risk. Our sample size limited the significance of age, PLTs, poor risk mutations and other variables previously shown to impact OS. Likewise, we lacked the capacity to track transfusion dependence, previously shown to have prognostic relevance. Still, prognostication via the EHR mimics common scoring systems in MF and supports correct MF case selection, accurate laboratory extraction and reproducible genotyping of biobanked samples. Similar to the original GPSS report, our low risk cohort was small (N=2) and will benefit from expansion of genotyping underway. Finally, this phenotype-genotype-prognostic paradigm represents a technical advance and a unique opportunity to deploy patient specific comorbidities from lifetime EHR records to further refine risk across all myeloid disease. [Display omitted] DisclosuresSavona:Boehringer Ingelheim: Consultancy; Celgene: Consultancy, Membership on an entity's Board of Directors or advisory committees; Incyte: Membership on an entity's Board of Directors or advisory committees, Research Funding.

Experimental DNA- or RNA-Directed Therapies for Trinucleotide Repeat Disease

Dynamic mutations involve expansion of the number of repeat units consisting of three or more nucleotides in tandem (i.e., adjacent to one another), present in a gene or in its neighborhood. Depending on expansion size, unaffected individuals can be carriers of a pre-mutation. Instability of triplet repeats can lead to gradual expansion through generations and accumulation of a certain number of repeats can lead to the consequent development of disease. The increase in the number of triplet repeats from one generation to the next, resulting from repeat instability, leads to the reduction in the age of disease onset and worsening of symptoms in affected individuals in successive generations. There is still no treatment for this type of diseases, however, several strategies are under study. This work describes treatment approaches for triplet repeat expansion diseases that have been developed during the last years, having as target DNA or RNA molecules. Some of these strategies might be used in the future as gene therapy of trinucleotide repeat disorders.

Dynamic Variation and Reversion in the Signature Amino Acids of H7N9 Virus During Human Infection.

Signature amino acids of H7N9 influenza A virus play critical roles in human adaption and pathogenesis, but their dynamic variation is unknown during disease development. We sequentially collected respiratory samples from H7N9 patients at different timepoints and applied next-generation sequencing (NGS) to the whole genome of the H7N9 virus to investigate the variation at signature sites. A total of 11 patients were involved, from whom 29 samples were successfully sequenced, including samples from multiple timepoints in 9 patients. Neuraminidase (NA) R292K, basic polymerase 2 (PB2) E627K, and D701N were the 3 most dynamic mutations. The oseltamivir resistance-related NA R292K mutation was present in 9 samples from 5 patients, including 1 sample obtained before antiviral therapy. In all patients with the NA 292K mutation, the oseltamivir-sensitive 292R genotype persisted and was not eliminated by antiviral treatment. The PB2 E627K substitution was present in 18 samples from 8 patients, among which 12 samples demonstrated a mixture of E/K and the 627K frequency exhibited dynamic variation. Dual D701N and E627K mutations emerged but failed to achieve predominance in any of the samples. Signature amino acids in PB2 and NA demonstrated high polymorphism and dynamic variation within individual patients during H7N9 virus infection.

Automatic mutation feature identification from well logging curves based on sliding t test algorithm

The mutation detection is an effective identification method of well logging curves, which can be utilized to detect mutations of the correlation time series by a sliding window technology. The computational complexity and accuracy of mutation detection are very important for detecting the series change points, however, some of the existing calculation methods take none of these into account. By sliding window technology, in the present paper we put forward a new method, the sliding t test for detecting a series of dynamic mutations. The principle is that mutation morphology of the spontaneous potential curve and microelectrode that are related to sandstone recognition contrast layers are described. In order to prove the performance of the method, the mutation analyses of time series are carried out by selecting different sliding windows. The test results are shown that the method can quickly and accurately detect the mutation change points and intervals. It has robust stability, and depends less on the sliding window length, which has some advantages in the large data processing. Finally, the method is utilized to detect the mutation of numerous experiments in well logging curves. The experimental results indicate that the mutation interval is consistent with the abrupt change, which further is verified the validity of the method.

Evidence for a relatively high proportion of DM2 mutations in a large group of Polish patients

IntroductionMyotonic dystrophies (DMs) type 1 (DM1) and type 2 (DM2) are autosomal dominant, multisystem disorders, considered the most common dystrophies in adults. DM1 and DM2 are caused by dynamic mutations in the DMPK and CNBP genes, respectively. MethodsMolecular analyses were performed by PCR and the modified RP-PCR in patients, in their at-risk relatives and prenatal cases. ResultsThe analysis of Polish controls revealed the range of 5-31 CTG repeats for DM1 and 110-228 bp alleles for DM2. Among 318 confirmed probands - 196 (62%) were DM1 and 122 (38%) – DM2. Within DM1families, 10 subjects carried a low expanded CTG tract (< 100 repeats), which resulted in a full mutation in subsequent generations. Two related individuals had unstable alleles–188 bp and 196 bp without common interruptions. ConclusionThe relative frequencies of DM1/DM2 among Polish patients were 68% and 32%, respectively, with a relatively high proportion of DM2 mutations (1.6:1).

Emergence and Adaptation of a Novel Highly Pathogenic H7N9 Influenza Virus in Birds and Humans from a 2013 Human-Infecting Low-Pathogenic Ancestor.

Since its emergence in 2013, the H7N9 low-pathogenic avian influenza virus (LPAIV) has been circulating in domestic poultry in China, causing five waves of human infections. A novel H7N9 highly pathogenic avian influenza virus (HPAIV) variant possessing multiple basic amino acids at the cleavage site of the hemagglutinin (HA) protein was first reported in two cases of human infection in January 2017. More seriously, those novel H7N9 HPAIV variants have been transmitted and caused outbreaks on poultry farms in eight provinces in China. Herein, we demonstrate the presence of three different amino acid motifs at the cleavage sites of these HPAIV variants which were isolated from chickens and humans and likely evolved from the preexisting LPAIVs. Animal experiments showed that these novel H7N9 HPAIV variants are both highly pathogenic in chickens and lethal to mice. Notably, human-origin viruses were more pathogenic in mice than avian viruses, and the mutations in the PB2 gene associated with adaptation to mammals (E627K, A588V, and D701N) were identified by next-generation sequencing (NGS) and Sanger sequencing of the isolates from infected mice. No polymorphisms in the key amino acid substitutions of PB2 and HA in isolates from infected chicken lungs were detected by NGS. In sum, these results highlight the high degree of pathogenicity and the valid transmissibility of this new H7N9 variant in chickens and the quick adaptation of this new H7N9 variant to mammals, so the risk should be evaluated and more attention should be paid to this variant.IMPORTANCE Due to the recent increased numbers of zoonotic infections in poultry and persistent human infections in China, influenza A(H7N9) virus has remained a public health threat. Most of the influenza A(H7N9) viruses reported previously have been of low pathogenicity. Now, these novel H7N9 HPAIV variants have caused human infections in three provinces and outbreaks on poultry farms in eight provinces in China. We analyzed the molecular features and compared the relative characteristics of one H7N9 LPAIV and two H7N9 HPAIVs isolated from chickens and two human-origin H7N9 HPAIVs in chicken and mouse models. We found that all HPAIVs both are highly pathogenic and have valid transmissibility in chickens. Strikingly, the human-origin viruses were more highly pathogenic than the avian-origin viruses in mice, and dynamic mutations were confirmed by NGS and Sanger sequencing. Our findings offer important insight into the origin, adaptation, pathogenicity, and transmissibility of these viruses to both poultry and mammals.

Application of moving cut data-wavelet transformation analysis in dynamic structure mutation testing

The scaling exponent is an effective nonlinear dynamic index, which can be used to detect the dynamic structure mutations of the correlation time series by the moving cut a fixed window technology. The immediacy and accuracy of scaling exponent is very important for detecting the series change points, however, some of the existing scale index calculation methods (such as rescaled range analysis and rescaled variance analysis) take none of these into account. Wavelet transform analysis can quickly decompose the sequence on different scales, and then the scaling index can be calculated by analyzing the scaling relation of wavelet coefficients on different scales, which has the characteristics of fast calculation speed and good convergence and memory saving. By moving cut window technology, in the present paper we put forward a new method, i. e., the moving cut data-wavelet transformation for detecting a series of dynamic structure mutations. The principle is that the removal of the data has little effect on the estimation of the scaling exponents of the correlation time series with the same dynamical properties. In order to test the performance of the method, first of all, the dynamic structure mutation analyses of linear ideal time series and nonlinear ideal time series are carried out by selecting different moving cut fixed windows. The test results show that the method can quickly and accurately detect the dynamic structure change points and intervals both in linear time series and nonlinear time series, besides, its calculation speed is obviously better than the moving cut data-rescaled range analysis and the moving cut data-rescaled variance analysis. It has strong stability, and depends less on the moving cut window length, which will have some advantages in the large data processing. At the same time, in order to detect the influence of noise on the method, the linear and nonlinear ideal time series are added to the white Gaussian noise (SNR=20, 25, 30 dB), respectively, and the results show that the method has a strong anti-noise ability with different moving cut window lengths, can still quickly and accurately detect the mutation point or interval in different noise additions. Finally, the method is used to detect the dynamic structure mutation of measured daily maximum temperature data of Foping station in Wei basin, the experimental results indicate that the mutation interval is consistent with the abrupt change in 1970's on a global scale, which further verifies the validity of the method.

Clinical features of Chinese patients with Gerstmann–Sträussler–Scheinker identified by targeted next-generation sequencing

Gerstmann–Sträussler–Scheinker (GSS) is an autosomal dominant neurodegenerative disease due to mutations within prion protein (PRNP) gene. Clinically, it is not easy to distinguish GSS from spinocerebellar ataxia (SCA), especially in the early stage of disease. We aimed to identify genetic mutations in 8 Chinese pedigrees with dominant ataxia but excluded dynamic mutations of SCA genes. Targeted next-generation sequencing was performed in the 8 probands. A customized panel was designed to capture 24 known causative genes, including 15 autosomal dominant SCA genes and 9 dementia-related genes. A 2-year follow-up was performed in these patients who harbored mutation. Of the 8 probands, 5 were identified to harbor the p.P102L mutation within PRNP. All these 5 cases had progressive ataxia with age at onset ranging from 48 to 52 years (49.5 ± 4.51). Remarkable phenotypic heterogeneity was observed in them. Cognitive decline was found in 4/5 probands. The average duration from initial symptoms to cognitive decline is 32.5 months, ranging from 22 to 48 months. In this study, we presented the detailed clinical features of 5 GSS pedigrees with PRNP p.P102L mutation. The variable phenotypes among these GSS patients indicated other genetic or environmental factors might be involved in the phenotypic heterogeneity of GSS. Our findings also support the proposal that screening of PRNP mutations should be performed for the patients with dominant ataxia if dynamic mutations of SCA genes were excluded.

Role of dynamic and mitochondrial mutations in neurodegenerative diseases with ataxia: lower repeats and LNAs at multiple loci as alternative pathogenesis.

Spinocerebellar ataxia is a growing group of hereditary neurodegenerative diseases for which ≥30 different genetic loci have been identified. In this study, we assessed the repeats at eight spinocerebellar ataxia (SCA) loci in 188 clinical SCA patients and 100 individuals without any neurological signs. Results from the present study were able to identify 16/188 (8.5%) clinical ataxia patients with repeat expansions in the pathological range of SCA genes, with the majority having expansion at the SCA1, 2, and 3 loci. The present study further evaluated two mitochondrial mutations associated with ataxia, i.e., T8993G and A8344G. Six patients were identified with A8344G mutation and none had the mutation in ATPase 6 gene; however, G8994A variation was found in three cases. Overall, three cases had triplet repeat expansions as well as mitochondrial (mt) mutations, which indicates potential association of triplet repeat expansions and mitochondrial mutations. Both the molecular analysis of several SCA loci and two relevant mt mutations indicated that the majority of ataxia cases were still undiagnosed; hence, the following hypotheses were proposed and tested based on available data: (i) lower repeats than normal range and (ii) large normal alleles (LNAs) at multiple loci may be an alternative basis for disease pathogenesis.

Effect of lovastatin on behavior in children and adults with fragile X syndrome: An open‐label study

Fragile X syndrome (FXS) results from dynamic mutations leading ultimately to the absence of expression of the Fragile X Mental Retardation Protein (FMRP). It is characterized by synaptic upregulated protein synthesis and immature dendritic spines associated with altered brain plasticity and cognitive functions. Recent work in Fmr1 knockout mice has shown that lovastatin, an inhibitor of Ras-ERK1/2, normalized hippocampus protein synthesis. We hypothesize that lovastatin, as a disease-modifying drug, would counterweigh the absence of FMRP and improve behavior. Here we report a phase I study to assess the safety and efficacy of lovastatin in individuals with FXS. A total of 15 patients (13 males, 6-31 years old) were treated with escalating doses of lovastatin (up to 40 mg) for three months. Their behavior were assessed before and after treatment using the Aberrant Behavioral Checklist--Community (ABC-C) total score (primary outcome), as well as domains of the FXS validated version of the ABC-C (secondary outcomes). The treatment was well tolerated and minimal side effects were reported. Significant improvement in the primary outcome (P<0.005), as well as in secondary outcomes, were observed in the majority of the subjects (12/15). We think that long-term sustained treatment with diseased-modifying drugs would be necessary in order to improve behavior and ultimately learning. Lovastatin, well known for its long-term security profile, would be a good candidate for that purposes. Our study showing reassuring safety data along with potential functional benefit emphasizes the need of a placebo-controlled trial to ascertain lovastatin efficacy in FXS individuals.

Disabilities caused by unstable mutations in Costa Rica

Motonic dystrophy and fragile X syndrome are two genetically determined relatively common disabilities. Both are examples of a new type of mutation mechanism called unstable or dynamic mutations, triple repeats expansions or DNA amplification. Fragile X syndrome is recognized as the main cause of hereditary mental retardation and myotonic dystrophy is considered the most common muscular dystrophy of adults. This is a prospective non randomized study of clinically affected people, in order to confirm the diagnosis with molecular techniques (Southern blot and PCR) and to perform cascade screening of the rest of the family to offer them adequate genetic counseling. We were able to corroborate the initial diagnosis in most clinical cases of myotonic dystrophy, but in the cases of mental retardation more than half studies were negative for fragile X syndrome, stressing the difficulties encountered by medical practitioners to diagnose this syndrome. The reasons for this are several; probable the main culprit is the subtle and unspecific clinical picture affected individuals exhibit, particularly children before puberty. Cascade screening, genetic counseling and selective abortion are the only tools available to prevent these disabling diseases for the moment.

FRA2A is a CGG repeat expansion associated with silencing of AFF3.

Folate-sensitive fragile sites (FSFS) are a rare cytogenetically visible subset of dynamic mutations. Of the eight molecularly characterized FSFS, four are associated with intellectual disability (ID). Cytogenetic expression results from CGG tri-nucleotide-repeat expansion mutation associated with local CpG hypermethylation and transcriptional silencing. The best studied is the FRAXA site in the FMR1 gene, where large expansions cause fragile X syndrome, the most common inherited ID syndrome. Here we studied three families with FRA2A expression at 2q11 associated with a wide spectrum of neurodevelopmental phenotypes. We identified a polymorphic CGG repeat in a conserved, brain-active alternative promoter of the AFF3 gene, an autosomal homolog of the X-linked AFF2/FMR2 gene: Expansion of the AFF2 CGG repeat causes FRAXE ID. We found that FRA2A-expressing individuals have mosaic expansions of the AFF3 CGG repeat in the range of several hundred repeat units. Moreover, bisulfite sequencing and pyrosequencing both suggest AFF3 promoter hypermethylation. cSNP-analysis demonstrates monoallelic expression of the AFF3 gene in FRA2A carriers thus predicting that FRA2A expression results in functional haploinsufficiency for AFF3 at least in a subset of tissues. By whole-mount in situ hybridization the mouse AFF3 ortholog shows strong regional expression in the developing brain, somites and limb buds in 9.5–12.5dpc mouse embryos. Our data suggest that there may be an association between FRA2A and a delay in the acquisition of motor and language skills in the families studied here. However, additional cases are required to firmly establish a causal relationship.

Biophysical Underpinnings of the Repeat Length Dependence of Polyglutamine Amyloid Formation

There are now 10 expanded CAG repeat diseases in which both disease risk and age of onset are strongly dependent on the repeat length of the polyglutamine (polyQ) sequence in the disease protein. Large, polyQ-rich inclusions in patient brains and in cell and animal models are consistent with the involvement of polyQ aggregation in the disease mechanism. This possibility is reinforced by studies showing strong repeat length dependence to the aggregation process, qualitatively mirroring the repeat length dependence of disease risk. Our understanding of the underlying biophysical principles that mediate the repeat length dependence of aggregation, however, is far from complete. A previous study of simple polyQ peptides showed that N*, the size of the critical nucleus that controls onset of aggregation, decreases from unfavorable tetramer to favorable monomer over the range Q23 to Q26. These data, however, do not explain why, for all peptides exhibiting N* ∼ 1, spontaneous aggregation rates continue to increase with increasing repeat length. Here we describe a novel kinetics analyses that maps out the nonlinear dependence with repeat length of a nucleation efficiency term that is likely related to aspects of nucleus structure. This trend accounts for why nucleus size increases to tetrameric at repeat lengths of Q23 or below. Intriguingly, both aggregation and age of onset trend with repeat length in similar ways, exhibiting large changes per added Gln at low repeat lengths and small changes per added Gln at relatively long repeat lengths. Fibril stability also increases with repeat length in a nonlinear fashion.

Application of moving cut data-rescaled variance analysis in dynamic structure mutation testing

Scaling exponent is a valid nonlinear dynamics index, and can effectively detect the dynamic structure mutations in the correlation time series by means of moving a fixed widow and the moving cut a fixed window technique. When there is short-term correlation, sequence with short-term correlation and the calculation result of scaling exponent with rescaled range will be influenced to a certain degree, resulting in a certain deviation for the scaling exponent calculation of a moving cut window sequence, and some false mutations point and mutations range for abrupt change detection. In view of this, we present a new method of the dynamic structure mutation detection-moving cut data-rescaled variance analysis. The numerical testing of ideal time series shows that the moving cut data-rescaled variance analysis has strong stability and accuracy, which is much better than the moving rescaled variance and the moving approximate entropy. The test results have not false mutation point and interval when the moving window is small. The further application to practically measured data validates the reliability of the new method.