Comprehensive analysis of the transcriptional landscape of the human FMR1 gene reveals two new long noncoding RNAs differentially expressed in Fragile X syndrome and Fragile X-associated tremor/ataxia syndrome

The majority of the human genome is transcribed but not translated, giving rise to noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs, >200 nt) that perform a wide range of functions in gene regulation. The Fragile X mental retardation 1 (FMR1) gene is a microsatellite locus that in the general population contains <55 CGG repeats in its 5′-untranslated region. Expansion of this repeat region to a size of 55-200 CGG repeats, known as premutation, is associated with Fragile X tremor and ataxia syndrome (FXTAS). Further expansion beyond 200 CGG repeats, or full mutation, leads to FMR1 gene silencing and results in Fragile X syndrome (FXS). Using a novel technology called “Deep-RACE”, which combines rapid amplification of cDNA ends (RACE) with next generation sequencing, we systematically interrogated the FMR1 gene locus for the occurrence of novel lncRNAs. We discovered two transcripts, FMR5 and FMR6. FMR5 is a sense lncRNA transcribed upstream of the FMR1 promoter, whereas FMR6 is an antisense transcript overlapping the 3′ region of FMR1. FMR5 was expressed in several human brain regions from unaffected individuals and from full and premutation patients. FMR6 was silenced in full mutation and, unexpectedly, in premutation carriers suggesting abnormal transcription and/or chromatin remodeling prior to transition to the full mutation. These lncRNAs may thus be useful as biomarkers, allowing for early detection and therapeutic intervention in FXS and FXTAS. Finally we show that FMR5 and FMR6 are expressed in peripheral blood leukocytes and propose future studies that correlate lncRNA expression with clinical outcomes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00439-013-1356-6) contains supplementary material, which is available to authorized users

Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7

PURPOSE: Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts. METHODS: We performed exome, targeted capture, and Sanger sequencing of patients with undiagnosed developmental disorders, in multiple independent diagnostic or research centers. Phenotypic and mutational comparisons were facilitated through data exchange platforms. Whole-transcriptome sequencing was performed on RNA from patient- and control-derived fibroblasts. RESULTS: We identified heterozygous missense variants in TRAF7 as the cause of a developmental delay-malformation syndrome in 45 patients. Major features include a recognizable facial gestalt (characterized in particular by blepharophimosis), short neck, pectus carinatum, digital deviations, and patent ductus arteriosus. Almost all variants occur in the WD40 repeats and most are recurrent. Several differentially expressed genes were identified in patient fibroblasts. CONCLUSION: We provide the first large-scale analysis of the clinical and mutational spectrum associated with the TRAF7 developmental syndrome, and we shed light on its molecular etiology through transcriptome studies

Early-Onset Marfan Syndrome: A Case Series

Mutations in fibrillin 1 cause Marfan syndrome (MFS), an autosomal dominant disorder of the connective tissue, with multisystem manifestations. In early-onset MFS, the physical characteristics are expressed much earlier than the classical MFS. Those affected by this form generally have their mutations restricted to the gene “hotspot” region of exons 24 to 32. Historically, affected individuals usually die within the first few years of life due to heart failure secondary to severe valvular insufficiency. We report three patients with early-onset MFS, whose clinical evolution has been remarkably positive, when compared with other reported cases in the literature

Patient management problem-preferred responses

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Causes of Death in 184 Patients with Type 1 Gaucher Disease From the United States Who Were Never Treated with Enzyme Replacement Therapy

Abstract Abstract 3128 Type 1 Gaucher disease (GD1) is caused by deficient lysosomal glucocerebrosidase activity with resultant accumulation of glucosylceramide predominantly within hepatic, splenic, pulmonary and bone marrow macrophages. Intravenous recombinant glucocerebrosidase (ERT) is generally safe and effective in decreasing morbidity due to the heterogeneous manifestations of GD1: hematological cytopenias, hepatosplenomegaly, bone pain, osteonecrosis, osteopenia and fractures. There are other complications whose responsiveness to conventional treatment is yet undetermined: atypical Parkinsonism and an increased risk for cancer (CA), particularly plasma cell and other hematological and lymphoid malignancies and hepatocellular carcinoma. Because of the widespread use of ERT during the past 20 years and attrition of older medical records, a phenotypically representative control group of untreated symptomatic patients for study of these late outcome events is hard to find. From 1961–97, one of us (REL) collected information on 395 US patients with GD1. We determined through public records that 217 died from 1950–2010 of whom 184 never received ERT. Here, we report confirmed causes of death (COD) for the untreated GD1 patients compared to COD reported for this time period in an age comparable overall US population. Methods: After IRB approval, COD recorded in death certificates were accessed via the National Death Index for available years 1979–2008. COD prior to 1979 were determined based on autopsy or physician communication with REL and, where possible, by death certificates obtained from State Bureaus of Vital Records. Information on COD (1950–2008) for the general US population is from US National Vital Statistics Reports. The analysis included descriptive statistics, calculation of proportional mortality ratios (PMR), and 2-tailed Fisher exact test calculations based on absolute death numbers in the GD1 and general populations. Results: COD is unknown for 9 patients who died before 1979. 111 pts were male (60.3%); 124 (67.4%) were Ashkenazi Jewish. Median age at death was 66y (2–97y). Median age at GD1 diagnosis (N=102): 39y (1–83y). Spleen status: Splenectomy 94 (51.1%); Intact 56 (30.4%); Unknown 34 (18.5%). Median age at splenectomy: 36y (1.3–78y). Symptomatic bone disease was present in 74 (40.2%), absent in 7 (3.8%) and undocumented for 103 (60.0%). COD for which the PMR was significantly increased (P<0.01): malignant neoplasms (PMR 1.57), suicide/drug overdose (PMR 3.86), chronic liver disease (PMR 4.76) and septicemia (PMR 9.22). Other COD that were disproportionately high included CNS and gastrointestinal bleeding, post-splenectomy complications, pulmonary hypertension (PHT), and Parkinsonism. Heart disease/atherosclerosis was the only COD for which PMR was very significantly decreased (0.33). PMR for cerebrovascular disease was 0.48 (P=0.027). For 57 pts with a CA COD, PMRs for myeloma (9.66), kidney CA (4.63), liver CA (4.36), NHL (4.13), and all leukemia (3.19) were significantly elevated (P<0.01). Conversely, the PMR for lung CA was 0.32 (P=0.002). There was 1 death from breast CA and none from gynecological CA. PMR for colorectal, pancreatic and prostate CA were not divergent from expected. Compared to the control population, the age distribution of deaths was identical for heart disease, septicemia, and suicide. Age at death was not younger than expected in pts with myeloma but there was a tendency for death at a younger age for GD pts with NHL, chronic liver disease and Parkinsonism. COD significantly more prevalent in surgically asplenic pts included chronic liver disease, septicemia, GI bleeding, PHT and post-splenectomy complications. Spleen status was statistically irrelevant to CA deaths including myeloma except for hepatocellular CA (splenectomy) and CLL (intact spleen). Conclusions: With earlier diagnosis, improved risk assessment and phase-out of splenectomy, COD that we encountered (chronic liver disease, GI bleeding, septicemia, PHT, suicide and drug dependency) should be increasingly rare with timely institution of appropriate treatment. Our study population of untreated pts (estimated at 5% of all US GD1 deaths from 1950–2008 but a substantially greater percentage of GD1 deaths over age 60y), should serve as a valuable control for future studies of the effect of GD1 treatment on mortality due to malignancy or other later course events. Disclosures: Weinreb: Genzyme Corporation: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Shire HGT: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding, Speakers Bureau; Actelion Corporation: Speakers Bureau

Klinefelter Syndrome in Association with Tetralogy of Fallot and Congenital Diaphragmatic Hernia

Klinefelter syndrome (KS) is the most common sex chromosomal aneuploidy in males. Major cardiovascular and diaphragmatic anomalies are uncommon in this syndrome. Here we report an infant with KS who had tetralogy of Fallot and congenital diaphragmatic hernia, all of which were identified prenatally and managed successfully after birth. Microarray analysis did not reveal any deletions or duplications other than the additional X-chromosome, to account for the additional abnormalities in this infant. To the authors' knowledge, this is the first such report of major cardiac and diaphragm anomaly occurring together, in an infant with KS