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.

Fiber gene based molecular and biological characterization of hydropericardium-hepatitis syndrome associated avian adenoviruses

This study was designed to perform biological and molecular characterization of avian adenoviruses (AAVs) recovered from suspected cases of hydropericardium-hepatitis syndrome (HHS) in commercial poultry. Initially the samples were screened by Agar Gel Precipitation Test (AGPT) for the presence of AAVs followed by its confirmation and typing through polymerase chain reaction (PCR) focusing on already reported serotypes AAV-4, AAV-8 and AAV-10 elsewhere. These PCR-positive samples were further subjected to amplification of fiber gene, followed by conducting restriction fragment length polymorphism (RFLP) using restriction enzyme Alu. The selected isolates were further propagated through cell culture and pathogenic potential of selected isolates was determined by infecting chickens. In this study, out of a total 190 samples, 57.8% of suspected cases were found positive for AAV presence through AGPT while sub-type identification using PCR revealed 46.3% for these viruses belonging to AAV-4, 41.8% to AAV-8 and 11.8% showed co-infection of AAV-4 and AAV-8. AAV-10 was not detected in any of the tested samples. On the basis of RFLP pattern, AAV-4 isolates were further divided into four sub-groups (A-D) while AAV-8 isolates had identical RFLP pattern. To further evaluate the pathogenic potential of these sub-groups of AAV-4 isolates, specific pathogen free (SPF) chicks were challenged with selected isolates belonging to each of the sub-groups, resulting in variable pattern of pathogenicity. It is concluded that any variation in the fiber gene of AAV-4 isolates may affect its pathogenicity and eventually specificity of the vaccines used against such infections. Therefore, regular monitoring of the circulating AAV serotypes may be helpful in understanding the pathogenic potential of emerging AAVs, which may lead to development of more effective response strategies accordingly.

Health Related Quality of Life in Children with Nephrotic Syndrome in Bangladesh

Outcome of children with nephrotic syndrome has continued to improve over time. However minimal data exist to describe health-related quality of life in children with nephrotic syndrome. This cross sectional study was conducted over a period of six months to assess the health related quality of life in children with nephrotic syndrome in the Department of Pediatric Nephrology, Dhaka Medical College Hospital, Bangladesh. Fifty children (age ranged 2-12 years) with nephrotic syndrome who had three or more relapses diagnosed at least one year back receiving treatment and on follow up were included in this study. Quality of Life scores were collected using Bengali translated instruments- the Pediatric Quality of Life Inventory™ (PedsQL™) version 4.0 Generic Scale and the Pediatric Quality of Life Questionnaire for Nephrotic Syndrome proxy-report from parents. Medical data and Demographic data were collected from medical records, and from parents in outpatient department or hospital ward. Interviews of eligible guardians were performed individually to collect quality of life (QoL) scores. Among 50 children, mean±SD age of the children was 7±2.92 years. Most children were male (58%). Female parents respondent during interview were 62%, most parents (48%) were very poor in socioeconomic condition. Most children had frequent relapses (60%). Median time since diagnosis was 2 years. Regarding PedsQL scores, child age with physical summary score (p value <0.001), child age with social summary score (p value 0.003), frequent relapse with kidney disease summary score (p value 0.04) and time since diagnosis (p value <0.001) were statistically significant. In conclusion physical and social summary score were worst. Frequent relapse found to be an important factor in impaired QoL. Prolonged duration of the disease activity was associated with significant impairment of QoL.

Role of nitric oxide modified DNA in the etiopathogenesis of systemic lupus erythematosus

The role of the nitric oxide(NO) radicalin systemic lupus erythematosus(SLE) pathogenesishas been investigated in the present study. The binding characteristics of SLE autoantibodies with native calf thymus DNA, native and NO-modified plasmid DNA were assessed. Binding characteristics and specificity of antibodies were analysed by direct binding and inhibition ELISA, gel retardation assay and quantitativeprecipitin titration.The data shows preferentialbinding of SLE autoantibodiesto NO-modified plasmid DNA (NO-DNA) in comparison with native plasmid DNA. Inhibition ELISA reiterates the direct binding results. Gel retardation assay further substantiated the enhanced recognition of NO-DNA by anti-DNA autoantibodies. The binding affinity of modified and native plasmid DNA with one of the SLE IgGs was calculated, using the Langmuir plot. The apparent association constant for NO-plasmid DNA was found to be highest, followed by native calf thymus DNA and native plasmid DNA. The results suggest that the NO radical modification of plasmid DNA causes perturbations, resulting in the generation of neo-epitopes, and making it a potential immunogen. The DNA modified with the NO radical may be one of the factors for the induction of circulating SLE anti-DNA autoantibodies.

Amelioration of Benzo[a]pyrene-induced oxidative stress and pulmonary toxicity by Naringenin in Wistar rats: A plausible role of COX-2 and NF-κB

Naringenin is a naturally occurring flavanones and has been found to exhibit free radical scavenging, enzyme inhibition, antioxidants, anti-inflammatory, and anticancer activities. Present study was designed to evaluate the protective role of naringenin against benzo[a]pyrene (B[a]P)-induced oxidative stress and pulmonary toxicity. Rats were treated with naringenin at a dose of 100 mg/kg body weight (b. wt.), by oral gavage. B[a]P in a single dose of 50 mg/kg b. wt. was given intraperitoneally. Total protein, total cell counts, lactate dehydrogenase, lipid peroxidation, reduced glutathione, antioxidant enzymes activities, lung histology and expression of nuclear factor kappa B (NF-κB), and cyclo-oxygenase-2 (COX-2) was assessed to evaluate protective effects of naringenin. Histopathological and immunohistochemical studies were also carried out to observe lung toxicity and inflammation. B[a]P administration enhanced the levels of lung injury markers and reduced antioxidant enzymes activities. Naringenin treatment attenuated the levels of oxidative stress by restoring antioxidant enzymes, further improved lung histological damage and significant decrease in inflammatory responses. Naringenin also effectively decreased the expression of NF-κB, and COX-2 induced by B[a]P. These findings suggest that naringenin supplementation is beneficial in maintaining the integrity of alveoli and the epithelium that may be used as a protective agent in B[a]P-induced oxidative stress and lung damage. However, further studies are warranted to elucidate the potential mechanism of action of naringenin.

Implementation of objective activity monitoring to supplement the interpretation of ambulatory esophageal PH investigations

Conventional catheter-based systems used for ambulatory esophageal pH monitoring have been reported to affect patient behavior. As physical activity has been associated with gastroesophageal reflux disease (GERD), there is a risk that abnormal behavior will degrade the value of this diagnostic investigation and consequent management strategies. The aim of this study was to quantify the effect of conventional pH monitoring on behavior and to investigate the temporal association between activity and reflux. A total of 20 patients listed for 24 hours pH monitoring underwent activity monitoring using a lightweight ear-worn accelerometer (e-AR sensor, Imperial College London) 2 days prior to, and during their investigation. PH was measured and recorded using a conventional nasogastric catheter and waist-worn receiver. Daily activity levels, including subject-specific activity intensity quartiles, were calculated and compared. Physical activity was added to the standard pH output to supplement interpretation. Average patient activity levels decreased by 26.5% during pH monitoring (range -4.5 to 51.0%, P = 0.036). High-intensity activity decreased by 24.4% (range -4.0 to 75.6%, P = 0.036), and restful activity increased on average by 34% although this failed to reach statistical significance (-24.0 to 289.2%, P = 0.161). Some patients exhibited consistent associations between bouts of activity and acidic episodes. The results of this study support the previously reported reduction in activity during ambulatory esophageal pH monitoring, with the added reliability of objective data. In the absence of more pervasive pH monitoring systems (e.g. wireless), quantifying activity changes in the setting of activity-induced reflux might guide the physicians' interpretation of patient DeMeester scores resulting in more appropriate management of GERD.

Influence of step faceting on the enantiospecific decomposition of aspartic acid on chiral Cu surfaces vicinal to Cu{111}

The crystallographic orientation of chiral step facets created by l-aspartic acid adsorption dictates enantioselectivity on chiral surfaces vicinal to Cu{111}.