Genetic testing in four Indian families with suspected Stickler syndrome

Purpose:

Stickler syndrome is associated with the development of rhegmatogenous retinal detachment (RRD), and often presents with ocular, auditory, skeletal, and orofacial abnormalities. Molecular analysis has proven effective in diagnosis, confirmation and classification of the disease. We aimed to describe the utility of next-generation sequencing (NGS) in genetic analysis of four Indian families with suspected Stickler syndrome.

Methods:

The index cases presented with retinal detachment with family history. Genetic analysis in the index case was performed by next-generation sequencing of inherited retinal degeneration genes, and validated by Sanger sequencing followed by co-segregation analysis in the other family members.

Results:

Twenty patients were included for the genetic analysis (15 males and 5 females from four families). Clinical details were available for 15 patients (30 eyes). Fourteen eyes (11 patients) developed RRD. In the 16 eyes without RRD, 8 underwent barrage laser to lattice degeneration and 8 were under observation. Disease segregating heterozygous mutations with pathogenic/likely pathogenic effect was identified in COL2A1 (c.4318-1G>A, c.141G>A, c.1221+1G>A for 3 families) and COL11A1 (c.1737+1 G>A for 1 family) gene. In addition to the mutation in the COL2A1 gene, a pathogenic heterozygous variant associated with risk for arrhythmogenic right ventricular cardiomyopathy (ARVC) was identified in one member.

Conclusion:

NGS testing confirmed the presence of the causative gene for Stickler syndrome in the index case followed by evaluation of family members and confirmation of genetic and ocular findings. We believe that this may be the first such report of families with RRD from India.

Leber hereditary optic neuropathy-new insights and old challenges

Leber hereditary optic neuropathy (LHON) is the most common primary mitochondrial DNA (mtDNA) disorder with the majority of patients harboring one of three primary mtDNA point mutations, namely, m.3460G>A (MTND1), m.11778G>A (MTND4), and m.14484T>C (MTND6). LHON is characterized by bilateral subacute loss of vision due to the preferential loss of retinal ganglion cells (RGCs) within the inner retina, resulting in optic nerve degeneration. This review describes the clinical features associated with mtDNA LHON mutations and recent insights gained into the disease mechanisms contributing to RGC loss in this mitochondrial disorder. Although treatment options remain limited, LHON research has now entered an active translational phase with ongoing clinical trials, including gene therapy to correct the underlying pathogenic mtDNA mutation.

Economic Impact Of India-China Trade War: Future Directions

The growing trade war among India and China is creating imbalance in the among developing countries. Both countries are affecting in their business prospects. India is basically importing raw material for export of good and services. Growing tension leads to unnecessary growth impetus which affects industry growth, loss of employment opportunities and other trade related problems. India has considerable potential for reducing its trade deficit with China, as we can see from Made-in-China products sold on the Indian market. Most of them are low- and mid-range products. India can make these things itself. The value tune to the cores of rupees is loss for the both counties; it will create far reaching impact in Indian business environment. These papers highlight the possible causes and consequences of trade war between to Asian giants and suggest how to promote regional growth prospects for speedy development of economics.

Screening for mutation hotspots in Bardet-Biedl syndrome patients from India

Background & objectives:

Bardet–Biedl syndrome (BBS) is a genetically heterogeneous autosomal recessive disorder characterized by multiple organ defects involving retina, kidney, liver and brain. Disease-causing mutations in BBS genes narrowed down by homozygosity mapping in small consanguineous and non-consanguineous pedigrees were reported in 80 per cent of the study population. This study was aimed to screen these genes (BBS3, BBS10) and specific exons of BBS genes (BBS1, BBS5, MKKS, BBS9, BBS11 and BBS12) for recurrent mutations in a selected sample of BBS patients.

Methods:

The recurrent mutations in BBS genes were screened in the BBS affected individuals by PCR based direct sequencing. The pathogenicity of the observed mutations were confirmed by co-segregation analysis, screening of healthy unrelated controls and in silico analysis.

Results:

In the 64 BBS patients (44 males, 20 females) were studied, mutations were predominant in BBS10 and ARL6 genes; the c.272T>C; p.(I91T) mutation in ARL6 gene was a recurrent mutation. One novel non-sense mutation c.425T>G; p(L142^*) was obtained in BBS5 gene (family BSI-31).

Interpretation & conclusions:

BBS10 gene mutations clustered in exon 2 of the gene suggesting the exon as a probable hotspot for mutations in Indian population. A cost- and time-effective strategy for the molecular diagnosis of BBS was designed based on these results.

IFT88 mutations identified in individuals with non-syndromic recessive retinal degeneration result in abnormal ciliogenesis

Whole genome sequencing (WGS) was performed to identify the variants responsible for inherited retinal degeneration (IRD) in a Caucasian family. Segregation analysis of selected rare variants with pathogenic potential identified a set of compound heterozygous changes p.Arg266*:c.796C>T and p.Ala568Thr:c.1702G>A in the intraflagellar transport protein-88 (IFT88) gene segregating with IRD. Expression of IFT88 with the p.Arg266* and p.Ala568Thr mutations in mIMDC3 cells by transient transfection and in HeLa cells by introducing the mutations using CRISPR-cas9 system suggested that both mutations result in the formation of abnormal ciliary structures. The introduction of the IFT88 p.Arg266* variant in the homozygous state in HeLa cells by CRISPR-Cas9 genome-editing revealed that the mutant transcript undergoes nonsense-mediated decay leading to a significant depletion of IFT88 transcript. Additionally, abnormal ciliogenesis was observed in these cells. These observations suggest that the rare and unique combination of IFT88 alleles observed in this study provide insight into the physiological role of IFT88 in humans and the likely mechanism underlying retinal pathology in the pedigree with IRD.

Genetic association study of exfoliation syndrome identifies a protective rare variant at LOXL1 and five new susceptibility loci

Exfoliation syndrome (XFS) is the most common known risk factor for secondary glaucoma and a major cause of blindness worldwide. Variants in two genes, LOXL1 and CACNA1A, have previously been associated with XFS. To further elucidate the genetic basis of XFS, we collected a global sample of XFS cases to refine the association at LOXL1, which previously showed inconsistent results across populations, and to identify new variants associated with XFS. We identified a rare protective allele at LOXL1 (p.Phe407, odds ratio (OR) = 25, P = 2.9 × 10^-14) through deep resequencing of XFS cases and controls from nine countries. A genome-wide association study (GWAS) of XFS cases and controls from 24 countries followed by replication in 18 countries identified seven genome-wide significant loci (P < 5 × 10^-8). We identified association signals at 13q12 (POMP), 11q23.3 (TMEM136), 6p21 (AGPAT1), 3p24 (RBMS3) and 5q23 (near SEMA6A). These findings provide biological insights into the pathology of XFS and highlight a potential role for naturally occurring rare LOXL1 variants in disease biology.

Genetic association of SNPs near ATOH7, CARD10, CDKN2B, CDC7 and SIX1/SIX6 with the endophenotypes of primary open angle glaucoma in Indian population

Primary open angle glaucoma (POAG) belonging to a group of optic neuropathies, result from interaction between genetic and environmental factors. Study of associations with quantitative traits (QTs) is one of the successful strategies to understand the complex genetics of POAG. The current study attempts to explore the association of variations near/in genes like ATOH7, SIX1/SIX6 complex, CDKN2B, CARD10, and CDC7 with POAG and its QTs including vertical cup to disc ratio (VCDR), central corneal thickness (CCT), intra ocular pressure (IOP), and axial length (AL). Case-control study design was carried out in a sample size of 97 POAG cases and 371 controls from South India. Model-based (additive, recessive, dominant) association of the genotypes and their interaction was carried out between cases and controls using chi-square, linear and logistic regression methods. Nominal significance (P<0.05) was observed for QTs like i) VCDR with SNPs rs1900004 (ATOH7); rs1192415 (CDC7); rs10483727 (SIX1/SIX6), rs9607469 (CARD10); ii) CCT with rs1192415; iii) IOP with rs1900004 and iv) AL with rs1900004 and rs1063192 (CDKN2B). We were able to replicate previously known interactions between ATOH7-SIX6 and SIX6-CDKN2B along with few novel interactions between ATOH7—CDC7 and SIX6 with genes including CARD10 and CDC7. In summary, our results suggest that a probable interaction among the candidate genes for QTs, play a major role in determining the individual’s susceptibility to POAG.

Combinatorial Screening of Anode and Cathode Electrocatalysts for Direct Methanol Fuel Cells

Progress in several important electrochemical technologies, including batteries, fuel cells, sensors, and electrosynthesis, is currently materials-limited. A common feature of all electrode reactions is the imbalance (i.e., loss or generation) of ions at the electrode surface. We describe in this paper a method by which excess ions in the electrode diffusion layer can be imaged, and used to identify the best electrode materials from a combinatorial array of compositions.

Although in principle this method can be applied to many electrochemical problems, we have focused on finding better electrocatalysts for direct methanol fuel cells (DMFCs). The DMFC performs two half-cell reactions: oxidation of methanol, and reduction of oxygen. Two of the most important problems in DMFCs are the poor performance of the electrocatalysts, and the crossover of methanol from the anode to the cathode side of the cell. An ideal situation would be the simultaneous development of two new catalysts: an anode that oxidizes methanol at low overpotential, and a “methanol-tolerant” cathode that reduces oxygen without oxidizing methanol.

Based on previously developed rules for predicting the activity of ternary alloy catalysts (Ley, et al., J. Electrochem. Soc. 1997, 144, 1543), we began searching quaternary combinations of noble metals for the anode, and ruthenium selenide-type materials for the cathode reaction. The anode and cathode reactions generate and consume protons, respectively, creating a substantial pH gradient at the electrode surface. Changes in local pH are imaged by means of an appropriate fluorescent indicator: Ni-PTP for the anode and Eosin Y for the cathode. DMFC testing confirms the utility of the screening method, in that a Pt/Ru/Os/Ir quaternary catalyst was substantially superior to the best binary and ternary catalysts prepared under similar conditions.

Combinatorial electrochemistry: A highly parallel, optical screening method for discovery of better electrocatalysts

Combinatorial screening of electrochemical catalysts by current-voltage methods can be unwieldy for large sample sizes. By converting the ions generated in an electrochemical half-cell reaction to a fluorescence signal, the most active compositions in a large electrode array have been identified. A fluorescent acid-base indicator was used to image high concentrations of hydrogen ions, which were generated in the electrooxidation of methanol. A 645-member electrode array containing five elements (platinum, ruthenium, osmium, iridium, and rhodium), 80 binary, 280 ternary, and 280 quaternary combinations was screened to identify the most active regions of phase space. Subsequent "zoom" screens pinpointed several very active compositions, some in ternary and quaternary regions that were bounded by rather inactive binaries. The best catalyst, platinum(44)/ruthenium(41)/osmium(10)/iridium(5) (numbers in parentheses are atomic percent), was significantly more active than platinum(50)/ruthenium(50) in a direct methanol fuel cell operating at 60 degreesC, even though the latter catalyst had about twice the surface area of the former.

An improved model for bacterial encrustation studies

A comparative evaluation of various biomaterials for their resistance to bacterial colonization and encrustation in infected urine is an important area in urological biomaterials research. This article describes an in vitro dynamic perfusion system that allows four reactors containing 24 1-in. catheter samples (6 per reactor) to be simultaneously perfused at a constant flow rate by synthetic urine. A common urease-producing urinary pathogen, Proteus mirabilis, was maintained at a level of 10(6) colony-forming units/mL for 7 days in the dynamic perfusion reactors. The pH and bacterial population were monitored every 24 h and the percentage of encrustation on latex and hydrogel-coated commercial catheter materials gave reproducible results in three different runs, 15.2 +/- 3.65% and 13.8 +/- 2.58%, respectively. A major issue of inlet clogging due to ascending bacteria or ammonia has been rectified using a dismountable inlet assembly. An incubator coupled with a cooling system allowed accurate temperature maintenance of 37 degrees C in all four reactors. Results from scanning electron microscopy of some latex samples are also presented.

In vitro and in vivo testing of an electrocatalytic glucose sensor

A prerequisite for the development of an implantable artificial pancreas is the availability of a stable, long-life glucose sensor. Platinum (Pt) catalyzed electrodes have been demonstrated in vitro to show high sensitivity to glucose and long cycle life but are more sensitive to co-reactants compared with enzymatic methods. The authors developed a special data processing method (compensated net charge ratio, or CNCR) in which the measured electrode response is very sensitive to glucose, completely insensitive to urea, and only moderately sensitive to amino acids. Other endogenous and exogenous co-reactants show only minor interferences. The CNCR method involves the determination of the ratio of net oxidation charge to total charge during one complete cycle of a cyclic voltammogram. Prototype electrodes tested in vitro in spiked plasma have shown typical sensitivities of greater than 2 x 10(-4) CNCR units per 1 mg/dl change in glucose concentration, with linear response up to 400 mg/dl. For in vivo testing, a modified 5 F vascular catheter with membrane covered surface mounted electrodes was used at a vena cava site in swine. Several sensor designs were tested in vivo, with sensitivities of 1-5 x 10(-4) CNCR units (mg/dl).