Exome Sequencing Revealed a Novel Splice Site Variant in the CRB2 Gene Underlying Nephrotic Syndrome.

Background and Objectives: Nephrotic syndrome (NS) is a kidney disease where the patient has a classic triad of signs and symptoms including hypercholesterolemia, hypoalbuminemia, proteinuria (>3.5 g/24 h), and peripheral edema. In case of NS, the damaged nephrons (structural and functional unit of the kidney) filter unwanted blood contents to make urine. Thus, the urine contains unwanted proteins (proteinuria) and blood cells (hematuria), while the bloodstream lacks enough protein albumin (hypoalbuminemia). Nephrotic syndrome is divided into two types, primary NS, and secondary NS. Primary NS, also known as primary glomerulonephrosis, is the result of a glomerular disease that is limited to the kidney, while secondary NS is a condition that affects the kidney and other parts of the body. The main causes of primary NS are minimal change disease, membranous glomerulonephritis, and focal segmental glomerulosclerosis. In the present study we recruited a family segregating primary NS with the aim to identify the underlying genetic etiology. Such type of study is important in children because it allows counseling of other family members who may be at risk of developing NS, predicts risk of recurrent disease phenotypes after kidney transplant, and predicts response to immunosuppressive therapy. Materials and Methods: All affected individuals were clinically evaluated. Clinical examination, results of laboratory tests, and biopsy investigations led us to the diagnosis. The next-generation sequencing technique (whole-exome sequencing) followed by Sanger sequencing identified a novel homozygous splice site variant (NM_173689.7: c.941-3C>T) in the CRB2 gene. The variant was present in a homozygous state in the affected individuals, while in a heterozygous state in phenotypically normal parents. Results: The study expanded the spectrum of the mutations in the gene CRB2 responsible for causing NS. Conclusions: In addition, the study will also help in genetic counseling, carrier testing, and prenatal and/or postnatal early diagnosis of the disease in the affected family.

Exome sequencing reveals the first intragenic deletion in ABCA5 underlying autosomal recessive hypertrichosis.

BACKGROUND: Hereditary hypertrichosis (HH) is characterized by excessive hair growth on various body areas, which is independent of the individual's age. This rare hair disorder has been classified by its origin (genetic or acquired), age of onset, breadth of hair distribution (universal or localized) and the affected body areas. HH is often linked to several additional congenital abnormalities involving teeth, heart and bones. Human HH is associated with heterozygous genomic duplications and deletions in the chromosomal region 17q24.2-q24.3, containing genes such as ABCA5, ABCA6, ABCA10 and MAP2K6. Recently, a homozygous splice-site variant in ABCA5 has been reported to cause autosomal recessive congenital generalized hypertrichosis terminalis (CGHT; OMIM 135400). AIM: To investigate the clinical and genetic basis of autosomal recessive hypertrichosis in a large consanguineous Pakistani family. METHODS: In the present study, we characterized a family of Pakistani origin segregating CGHT in an autosomal recessive pattern, using whole exome sequencing followed by Sanger sequencing. RESULTS: We identified a novel 2-bp intragenic deletion [NM_172232.4(ABCA5);c.977_978delAT] causing a frameshift variant (p.His326ArgfsTer5) in ABCA5. CONCLUSIONS: To our knowledge, this is the first intragenic deletion in ABCA5 underlying CGHT. The findings further validate the involvement of ABCA5 in hair development. The study will facilitate genetic counselling of families carrying CGHT-related features in Pakistani and other populations.

Sequence variants in three genes underlying leukodystrophy in Pakistani families.

Leukodystrophies (LDs) are a heterogeneous group of rare and progressive genetic diseases that affect brain, spinal cord, and often the peripheral nerves. They are characterized by abnormal development or destruction of the myelin sheath of the brain. This study was aimed to search for the causative variants in three unrelated consanguineous families presented with LD. Detailed clinical investigations were carried out on probands in three unrelated consanguineous families of Pakistani origin. Targeted gene sequencing and Whole Exome Sequencing (WES) were performed for variant identification. Candidate variants were checked for co-segregation with the phenotype using Sanger sequencing. Public databases including ExAC, gnomAD, dbSNP, and the 1,000 Genome Project were searched to determine frequencies of the alleles. Conservation of the missense variants was ensured by aligning orthologous protein sequences from diverse vertebrate species. Targeted gene sequencing identified a novel homozygous missense mutation [c.2135G > A, p.(Arg712His) in the ATP Binding Cassette Subfamily D Member 1 (ABCD1; OMIM# 300371) in three affected siblings in family A.WES followed by validation by Sanger sequencing revealed previously reported homozygous missense variants [c.162C > A; p.(Asn54Lys)] in ASPA (OMIM# 608034) in family B and [c.361G > C,p.(Gly121Arg)] in ARSA (OMIM# 607574) in family C. Investigation of three families underlies importance of WES as an amazing diagnostic tool for conclusive determination of a specific type of LD. Further, the study would assist in carrier testing and prenatal diagnosis of the affected families. In addition, searching for common variants in the genes causing LD would help in designing low-cost targeted variation testing in patients.

Zinc source modulates zootechnical characteristics, intestinal features, humoral response, and paraoxonase (PON1) activity in broilers.

The current experiment was performed to find the potential effect of inorganic and organic forms of zinc (Zn) on growth, intestinal histomorphology, immune response, and paraoxonase (PON1) activity in broiler. In this experiment, a total of 450 broiler chickens were assigned to four experimental and control groups. The birds received organic Zn at the rate of 50 mg/kg (OZ-50) and 60 mg/kg (OZ-60) or inorganic Zn at the rate of 50 mg/kg (IZ-50) and 60 mg/kg (IZ-60) for an experimental period of 30 days. Significantly (P < 0.05) higher feed consumption, body weight, feed conversion ratio, and production efficiency factor (PEF) were recorded in OZ-50. Similarly, antibody titer against infectious bronchitis (IB) and PON1 activity was higher (P < 0.05) in OZ-50 compared with the control group. In addition, significantly (P < 0.05) higher villus dimensions and goblet cell count were recorded for the group OZ-50 compared with other treatments. It was concluded that the organic form of Zn was superior in improving the growth, histological features of intestines, humoral response, and PON1 activity in broiler.

Two dimensional gel electrophoresis (2-DE) for high-throughput proteome analyses of Mycoplasma bovis.

Expression proteomics approaches do not only directly confirm protein coding genes of sequenced genomes but also facilitate resolution of minute qualitative protein differences and improve the quality of genome annotation. Despite development of many tools, use of 2-DE coupled with MS in proteomics is not uncommon. With an accelerated trend of genome sequencing of microorganisms, proteome analysis of animal pathogens with 2-DE has gained more attention in the last decade. Therefore, in this study primarily the protein extraction, sample preparation and loading, IPG strip rehydration, IEF, and SDS-PAGE conditions were improved for high throughput resolution and reproducible 2-DE map of proteins of Mycoplasma bovis HB0801 (M. bovis HB0801- Chinese Strain), a pneumonia pathogen in feedlot cattle, and its attenuated strains. Literally, higher amount of proteins was extracted exploiting the French pressure cell coupled with TCA precipitation when compared to the sonication method. Total protein concentration was determined using a 2D quant Kit. About 330-380 µg TCA treated protein sample, solubilized in calibrated rehydration solution, loaded on 17 cm IPG gel strip (pH 3-10 NL) followed by active rehydration at 50V and isoelectric focusing at final 10 000 Volt (33 uA/gel strip) for 80kVh had revealed well resolved proteins spots on 10% gel stained by CBB R250 (0.15%), representing 83-89% of the total protein coding genes of M. bovis HB0801, estimated by PD Quest (Bio-Rad, USA). Conclusively, this effort attempted to provide more precise 2-DE platform and suitable conditions, after extensive calibration, for future comprehensive proteome and immunoproteome analyses and future research on the elucidation of factors related to pathogenesis of M. bovis in cattle.