Clinical genomics expands the morbid genome of intellectual disability and offers a high diagnostic yield

Intellectual disability (ID) is a measurable phenotypic consequence of genetic and environmental factors. In this study, we prospectively assessed the diagnostic yield of genomic tools (molecular karyotyping, multi-gene panel and exome sequencing) in a cohort of 337 ID subjects as a first-tier test and compared it with a standard clinical evaluation performed in parallel. Standard clinical evaluation suggested a diagnosis in 16% of cases (54/337) but only 70% of these (38/54) were subsequently confirmed. On the other hand, the genomic approach revealed a likely diagnosis in 58% (n=196). These included copy number variants in 14% (n=54, 15% are novel), and point mutations revealed by multi-gene panel and exome sequencing in the remaining 43% (1% were found to have Fragile-X). The identified point mutations were mostly recessive (n=117, 81%), consistent with the high consanguinity of the study cohort, but also X-linked (n=8, 6%) and de novo dominant (n=19, 13%). When applied directly on all cases with negative molecular karyotyping, the diagnostic yield of exome sequencing was 60% (77/129). Exome sequencing also identified likely pathogenic variants in three novel candidate genes (DENND5A, NEMF and DNHD1) each of which harbored independent homozygous mutations in patients with overlapping phenotypes. In addition, exome sequencing revealed de novo and recessive variants in 32 genes (MAMDC2, TUBAL3, CPNE6, KLHL24, USP2, PIP5K1A, UBE4A, TP53TG5, ATOH1, C16ORF90, SLC39A14, TRERF1, RGL1, CDH11, SYDE2, HIRA, FEZF2, PROCA1, PIANP, PLK2, QRFPR, AP3B2, NUDT2, UFC1, BTN3A2, TADA1, ARFGEF3, FAM160B1, ZMYM5, SLC45A1, ARHGAP33 and CAPS2), which we highlight as potential candidates on the basis of several lines of evidence, and one of these genes (SLC39A14) was biallelically inactivated in a potentially treatable form of hypermanganesemia and neurodegeneration. Finally, likely causal variants in previously published candidate genes were identified (ASTN1, HELZ, THOC6, WDR45B, ADRA2B and CLIP1), thus supporting their involvement in ID pathogenesis. Our results expand the morbid genome of ID and support the adoption of genomics as a first-tier test for individuals with ID.

Enhancement of the Adsorption of Co(II) and Ni(II) Ions onto Peanut Hulls through Esterification Using Citric Acid

Peanut hulls were modified chemically by esterification with citric acid under conditions which yielded hulls rich in carboxyl content. The esterified products thus obtained were used in the removal of Co(II) and Ni(II) ions from aqueous solutions. The factors affecting the esterification reaction and the adsorption of the metal cations onto the peanut hulls before and after esterification were thoroughly investigated. The results obtained highlighted the following conclusions. The optimum conditions for esterification involve the treatment of peanut hulls (1 g) with 12.4 mmol citric acid in the presence of a very small amount of water for 2 h at 140°C. Similarly, the optimum pH for the adsorption of cobalt(II) ions onto the peanut hulls citrate was 7.0. The adsorption capacity, qe (mg/g), of Co(II) ions onto the peanut hulls citrate increased on increasing the extent of esterification, expressed as mequiv. —COOH/100 g sample. The maximum values for the adsorption capacity, qmax, were 28.7 mg/g and 270.3 mg/g on native and peanut hulls citrate, respectively. The qmax values for of Ni(II) ion adsorption were 5 mg/g and 175.4 mg/g on native and peanut hulls citrate, respectively. The equilibrium data were well fitted by the Langmuir and Freundlich adsorption models and showed the large capacity of peanut hulls citrate in the removal of Co(II) and Ni(II) ions from aqueous solutions.

γ-Induced Graft Copolymerization onto Cellulosic Fabric Waste for Cationic Dye Removal

Radiation grafting of itaconic acid (IA) onto cellulosic fabric in the presence of dimethylformamide (DMF) as a solvent by the mutual method is discussed. Factors affecting the radiation graft copolymerization were investigated. These factors include the radiation dosage, the monomer concentration and the solvent. The grafted samples were characterized using FT-IR spectroscopy, thermogravimetric analysis (TGA) and scanning electron microscopy (SEM). Utilization of the grafted cellulosic fabric waste in the removal of Methylene Blue (MB) from aqueous solution was examined. The adsorption data showed that the maximum adsorption capacity of Methylene Blue onto grafted cellulosic fabric waste was 38 mg/g. The adsorption data also obeyed the Langmuir and Freundlich isotherms.

Preparation and Characterization of Cationized Cellulose for the Removal of Anionic Dyes

The factors influencing the cationization of microcrystalline cellulose with 3-chloro-2-hydroxypropyl triethylammonium chloride in the presence of NaOH were investigated. The course of the reaction was followed by estimating the nitrogen content of the cationized product while its structural features were confirmed by IR analysis. The ability of cationized cellulose to adsorb anionic dyes, viz. Acid Orange 7, Direct Blue 75 and Direct Violet 31, was investigated at 25°C and 50°C. The equilibrium data obtained were fitted by the Langmuir and Freundlich isotherm models, allowing the corresponding adsorption parameters to be determined. The results showed that the adsorption capacity was dependent on the adsorbent, temperature, the nature of the dye and (to some extent) on van der Waals and hydrogen bonding. Cationized cellulose exhibited a much better adsorption capacity towards anionic dyes than cellulose.

ADAT3-related intellectual disability: Further delineation of the phenotype

ADAT3-related intellectual disability has been recently described in 24 individuals from eight Saudi families who had cognitive impairment and strabismus. Other common features included growth failure, microcephaly, tone abnormalities, epilepsy, and nonspecific brain abnormalities. A single homozygous founder mutation (c.382G>A:p.(V128M)) in the ADAT3 gene, which encodes a protein that functions in tRNA editing, was identified in all affected individuals. In this report, we present additional 15 individuals from 11 families (10 Saudis and 1 Emirati) who are homozygous for the same founder mutation. In addition to the universal findings of intellectual disability and strabismus, the majority exhibited microcephaly and growth failure. Additional features not reported in the original cohort include dysmorphic facial features (prominent forehead, up-slanted palpebral fissures, epicanthus, and depressed nasal bridge), behavioral problems (hyperactivity and aggressiveness), recurrent otitis media, and growth hormone deficiency. ADAT3-related intellectual disability is an important recognizable cause of intellectual disability in Arabia.

RTTN Mutations Cause Primary Microcephaly and Primordial Dwarfism in Humans

Primary microcephaly is a developmental brain anomaly that results from defective proliferation of neuroprogenitors in the germinal periventricular zone. More than a dozen genes are known to be mutated in autosomal-recessive primary microcephaly in isolation or in association with a more generalized growth deficiency (microcephalic primordial dwarfism), but the genetic heterogeneity is probably more extensive. In a research protocol involving autozygome mapping and exome sequencing, we recruited a multiplex consanguineous family who is affected by severe microcephalic primordial dwarfism and tested negative on clinical exome sequencing. Two candidate autozygous intervals were identified, and the second round of exome sequencing revealed a single intronic variant therein (c.2885+8A>G [p.Ser963(∗)] in RTTN exon 23). RT-PCR confirmed that this change creates a cryptic splice donor and thus causes retention of the intervening 7 bp of the intron and leads to premature truncation. On the basis of this finding, we reanalyzed the exome file of a second consanguineous family affected by a similar phenotype and identified another homozygous change in RTTN as the likely causal mutation. Combined linkage analysis of the two families confirmed that RTTN maps to the only significant linkage peak. Finally, through international collaboration, a Canadian multiplex family affected by microcephalic primordial dwarfism and biallelic mutation of RTTN was identified. Our results expand the phenotype of RTTN-related disorders, hitherto limited to polymicrogyria, to include microcephalic primordial dwarfism with a complex brain phenotype involving simplified gyration.

Identification of embryonic lethal genes in humans by autozygosity mapping and exome sequencing in consanguineous families

Background

Identifying genetic variants that lead to discernible phenotypes is the core of Mendelian genetics. An approach that considers embryonic lethality as a bona fide Mendelian phenotype has the potential to reveal novel genetic causes, which will further our understanding of early human development at a molecular level. Consanguineous families in which embryonic lethality segregates as a recessive Mendelian phenotype offer a unique opportunity for high throughput novel gene discovery as has been established for other recessive postnatal phenotypes.

Results

We have studied 24 eligible families using autozygosity mapping and whole-exome sequencing. In addition to revealing mutations in genes previously linked to embryonic lethality in severe cases, our approach revealed seven novel candidate genes (THSD1, PIGC, UBN1, MYOM1, DNAH14, GALNT14, and FZD6). A founder mutation in one of these genes, THSD1, which has been linked to vascular permeability, accounted for embryonic lethality in three of the study families. Unlike the other six candidate genes, we were able to identify a second mutation in THSD1 in a family with a less severe phenotype consisting of hydrops fetalis and persistent postnatal edema, which provides further support for the proposed link between this gene and embryonic lethality.

Conclusions

Our study represents an important step towards the systematic analysis of “embryonic lethal genes” in humans.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-015-0681-6) contains supplementary material, which is available to authorized users.

A founder CEP120 mutation in Jeune asphyxiating thoracic dystrophy expands the role of centriolar proteins in skeletal ciliopathies

Jeune asphyxiating thoracic dystrophy (JATD) is a skeletal dysplasia characterized by a small thoracic cage and a range of skeletal and extra-skeletal anomalies. JATD is genetically heterogeneous with at least nine genes identified, all encoding ciliary proteins, hence the classification of JATD as a skeletal ciliopathy. Consistent with the observation that the heterogeneous molecular basis of JATD has not been fully determined yet, we have identified two consanguineous Saudi families segregating JATD who share a single identical ancestral homozygous haplotype among the affected members. Whole-exome sequencing revealed a single novel variant within the disease haplotype in CEP120, which encodes a core centriolar protein. Subsequent targeted sequencing of CEP120 in Saudi and European JATD cohorts identified two additional families with the same missense mutation. Combining the four families in linkage analysis confirmed a significant genome-wide linkage signal at the CEP120 locus. This missense change alters a highly conserved amino acid within CEP120 (p.Ala199Pro). In addition, we show marked reduction of cilia and abnormal number of centrioles in fibroblasts from one affected individual. Inhibition of the CEP120 ortholog in zebrafish produced pleiotropic phenotypes characteristic of cilia defects including abnormal body curvature, hydrocephalus, otolith defects and abnormal renal, head and craniofacial development. We also demonstrate that in CEP120 morphants, cilia are shortened in the neural tube and disorganized in the pronephros. These results are consistent with aberrant CEP120 being implicated in the pathogenesis of JATD and expand the role of centriolar proteins in skeletal ciliopathies.

Identification of KLHL41 Mutations Implicates BTB-Kelch-Mediated Ubiquitination as an Alternate Pathway to Myofibrillar Disruption in Nemaline Myopathy

Nemaline myopathy (NM) is a rare congenital muscle disorder primarily affecting skeletal muscles that results in neonatal death in severe cases as a result of associated respiratory insufficiency. NM is thought to be a disease of sarcomeric thin filaments as six of eight known genes whose mutation can cause NM encode components of that structure, however, recent discoveries of mutations in non-thin filament genes has called this model in question. We performed whole-exome sequencing and have identified recessive small deletions and missense changes in the Kelch-like family member 41 gene (KLHL41) in four individuals from unrelated NM families. Sanger sequencing of 116 unrelated individuals with NM identified compound heterozygous changes in KLHL41 in a fifth family. Mutations in KLHL41 showed a clear phenotype-genotype correlation: Frameshift mutations resulted in severe phenotypes with neonatal death, whereas missense changes resulted in impaired motor function with survival into late childhood and/or early adulthood. Functional studies in zebrafish showed that loss of Klhl41 results in highly diminished motor function and myofibrillar disorganization, with nemaline body formation, the pathological hallmark of NM. These studies expand the genetic heterogeneity of NM and implicate a critical role of BTB-Kelch family members in maintenance of sarcomeric integrity in NM.

Mutation in ADAT3, encoding adenosine deaminase acting on transfer RNA, causes intellectual disability and strabismus

BACKGROUND

Intellectual disability (ID) is one of the most common forms of disability worldwide, displaying a wide range of aetiologies and affecting nearly 2% of the global population.

OBJECTIVE

To describe a novel autosomal recessive form of ID with strabismus and its underlying aetiology.

MATERIALS AND METHODS

Autozygosity mapping, linkage analysis and exome sequencing were performed in a large multiplex consanguineous family that segregates ID and strabismus. Exome sequencing was independently performed in three other consanguineous families segregating the same disease. Direct sequencing of the resulting candidate gene was performed in four additional families with the same phenotype.

RESULTS

A single missense mutation was identified in ADAT3 in all studied families on an ancient ancestral haplotype. This gene encodes one of two eukaryotic proteins that are necessary for the deamination of adenosine at position 34 to inosine in t-RNA. Our results show the first human mutation in the t-RNA editing machinery and expand the landscape of pathways involved in the pathogenesis of ID.

Preparation, Characterization and Utilization of Amidoximated Poly(AN/MAA)-grafted Alhagi Residues for the Removal of Zn(II) Ions from Aqueous Solution

Radiation grafting by the mutual method of methacrylic acid/acrylonitrile (MAA/AN) onto Alhagi residues in the presence of dimethylformamide (DMF) as a solvent is discussed. The factors affecting the radiation graft copolymerization were investigated. These included radiation dose, co-monomer composition and concentration. The grafted samples were characterized using FT-IR spectroscopy and scanning electron microscopy (SEM), as well as by the estimation of their nitrogen and carboxyl group contents. The grafted samples were then amidoximated by treatment with hydroxylamine hydrochloride in an alkaline medium. Such amidoximated poly(MAA/AN)-grafted Alhagi residues were utilized for the removal of Zn(II) ions from aqueous solution by adsorption and the factors affecting such adsorption processes were studied. These factors were the pH of the adsorbate solution, the adsorbent dosage, the contact time and the adsorption temperature.

The adsorption data obeyed the Langmuir and Freundlich isotherms. The Langmuir adsorption capacity (Qmax) of the amidoximated poly(MAA/AN)-grafted Alhagi residues towards Zn(II) ions was found to be 212.76 and 344.8 mg/g at 30 °C and 50 °C, respectively. Similarly, the Freundlich constants, KF and 1/n, at 30 °C were found to be 21.47 and 0.3489, respectively.

The study showed that amidoximated poly(MAA/AN)-grafted Alhagi residues were effective in the adsorption of Zn(II) ions from aqueous solutions. The thermodynamics parameters of the adsorption process, viz. ΔH0, ΔG0 and ΔS0, were evaluated. The results showed that the adsorption of Zn(II) ions onto amidoximated poly(MAA/AN)-grafted Alhagi residues was endothermic and spontaneous. The adsorption data followed second-order kinetics.

Treatment of Alhagi Residues with Tartaric Acid for the Removal of Zn(II) Ions from Aqueous Solution

Alhagi cellulose tartrate (ACT) with a high carboxyl group content was prepared by treatment of Alhagi residues (AR) with tartaric acid (TA) at high temperature. Factors influencing the reaction were investigated, viz. tartaric acid concentration, dehydration temperature, particle size and dehydration time. The prepared Alhagi cellulose tartrate samples were characterized using FT-IR spectroscopy and by estimation of the carboxyl group content. The esterified samples were utilized for the adsorptive removal of Zn(II) ions from aqueous solution with all the factors influencing the process being studied. These factors were the pH value of the adsorbate solution, the adsorbent concentration, agitation time and temperature.

The Langmuir and Freundlich models were applied to the data obtained from the adsorption studies. It was demonstrated that the Alhagi cellulose tartrate samples could be used effectively for the adsorption of Zn(II) ions from aqueous solutions. The thermodynamics constants of the adsorption process, viz. ΔH0, ΔS0 and ΔG0, were evaluated. The results showed that the adsorption of Zn(II) ions onto ACT was exothermic and spontaneous. The adsorption data followed second-order kinetics, with the equilibrium data being only satisfactorily described by the Langmuir isotherm.

Application of Some Starch Hydrogels for the Removal of Mercury(II) Ions from Aqueous Solutions

Three types of starch hydrogels were prepared via the graft polymerization of acrylonitrile, AN, onto maize starch using ceric ammonium nitrate, CAN, as the initiator, followed by saponification with sodium hydroxide. The prepared hydrogel samples were characterized by estimating their nitrogen and carboxy group contents, and by the application of FT-IR spectroscopy, thermogravimetric analysis (TGA) and scanning electron microscopy (SEM); in addition, their water retention values, WRVs, were also determined. The feasibility of using these hydrogels to remove Hg(II) ions from aqueous solutions was examined. Factors affecting the adsorption of Hg(II) ions onto the starch hydrogels were studied, including the pH value of the solution, the contact time and the concentrations of the adsorbent and adsorbate. The present study has shown that the prepared hydrogels could be used effectively for the adsorption of Hg(II) ions from aqueous solutions. The adsorption data obtained obeyed the Langmuir and Freundlich isotherms. The adsorption of Hg(II) ions onto the starch hydrogels followed second-order kinetics. An examination was made of the mechanism for the adsorption of Hg(II) ions onto the starch hydrogels.

53 EVALUATION OF NUCLEAR REPROGRAMMING IN CLONED MINIATURE PIG EMBRYOS USING GENES OF Oct-4 FAMILY

Xenotransplantation as a source of organs is a rapidly expanding field which can save thousands of human lives each year. Cloned miniature pigs have been considered as a model system for xenotransplantation. However, the efficiency of somatic cell nuclear transfer (SCNT) is extremely low, with most clones resulting in early lethality and several aberrancies. Possible explanation of the developmental failure of SCNT embryos is related to insufficient reprogramming of the somatic cell nucleus. In order to test this, we analyzed the reprogramming capacity of differentiated fibroblast cell nuclei and undifferentiated germ cell nuclei with Oct-4 and four Oct-4-related genes (Ndp5211, Dppa2, Dppa3, and Dppa5) as molecular markers using quantitative reverse transcription-polymerase chain reaction (RT-PCR). Oct-4 expression patterns were similar among IVF-derived embryos and cloned embryos derived from fibroblasts or germ cells during pre-implantation embryo development. However, the expression level was significantly lower (P < 0.05) in hatched blastocysts of fibroblast clones compared to other hatched blastocysts. Also, 9 of 13 cloned morulae and 12 of 40 cloned blastocysts failed to reactivate at least one of the five tested genes, whereas all of the germ cell clones and control embryos correctly expressed these genes. Analysis with miniature pig fetuses collected at Day 30 of gestation revealed that normal and cloned fetuses successfully expressed these genes. In conclusion, our results suggest that analysis of expression of Oct-4 and related genes could be a reliable marker for evaluating the reprogramming status of transplanted donor nuclei in cloned embryos. The reprogramming of fibroblast cloned embryos is highly error-prone. This may contribute to their embryonic lethality because cloned embryos that fail to reactivate the marker genes may fail to be successfully implanted. This study was supported by grants from the Ministry of Science and Technology (Top Scientist Fellowship), and the Biogreen 21-1000520030100000.

46 ANTI-APOPTOTIC EFFECT OF INSULIN-LIKE GROWTH FACTOR-1 AND ITS RECEPTOR ON DEVELOPMENT OF PORCINE PRE-IMPLANTATION EMBRYOS PRODUCED BY IN VITRO FERTILIZATION AND SOMATIC CELL NUCLEAR TRANSFER

Insulin-like growth factor (IGF)-I is a receptor-mediated autocrine and/or paracrine growth and/or survival factor for mammalian embryo development. It is known to promote the growth and development of mouse pre-implantation embryos. The present study was designed to investigate the effects of IGF-I (50 ng/mL), anti-IGF-I receptor (IGR-IR) antibody (0.05 �g/mL), and their combination on porcine pre-implantation embryo development. Furthermore, the mechanism underlying the embryotropic effects of IGF-I was evaluated by monitoring the incidence of apoptosis and expression of apoptosis-related genes. In both IVF and SCNT embryos, culturing with IGF-I increased the rate of blastocyst formation and this embryotropic effect was neutralized by culturing with IGF-I and anti-IGF-I receptor antibody. Significant effects on the development of blastocysts (P < 0.05) were found in IVF (16.9, 22.6, 9.3, and 13.5% for control, IGF-I, anti-IGF-IR antibody, and their combination, respectively) and SCNT (13.2, 21.0, 5.4, and 15.7%) embryos. Culturing IVF and SCNT embryos with IGF-I significantly increased the total number of cells in IVF blastocysts (58.3, 72.4, 41.1, and 55.2; P < 0.05), and SCNT blastocysts (49.2, 60.1, 35.2, and 43.1; P < 0.05), and it decreased the number of apoptotic nuclei in IVF blastocysts (3.9, 2.8, 5.5, and 3.9; P < 0.05) and SCNT blastocysts (4.6, 3.0, 6.1, and 4.9; P < 0.05). These effects of IGF-I were also neutralized by culturing with IGF-I along with anti-IGF-IR antibody. Expression of the anti-apoptotic Bcl-2 gene was increased, whereas expression of the pro-apoptotic Bax gene was decreased in both IVF and SCNT embryos cultured with IGF-I. In both IVF and SCNT embryos, anti-IGF-IR antibody along with IGF-I neutralized the effect of IGF-I on expression of Bcl-2 and Bax genes. In conclusion, the present study demonstrated that IGF-I through its specific receptors improved the developmental competence of IVF and SCNT embryos by decreasing the incidence of apoptosis and regulating apoptosis-related genes in porcine pre-implantation embryos. This study was supported by grants from the Korean MOST (Top Scientist Fellowship) and MAF (Biogreen 21 #20050301-034-443-026-01-00).

Plexopathy in a Heroin Addict

Muscle and peripheral nerve disorders are important complications in intravenous heroin abusers. Rhabdomyolysis and acute lumbosacral plexopathy are important in the differential diagnosis of patients developing muscle weakness in an intensive care unit after intravenous overdoses of heroin. A 25-year-old man developed rhabdomyolysis with neuromuscular involvement, and consistent clinical and electrodiagnostic features of lumbar plexus neuropathy after an intravenous injection of heroin. The improvement occured slowly, over months, in spite of intensive physiotherapy.