Genetic Perspectives of Inherited Skin Disorders in Pakistani Population

MUHAMMAD NASIR, . (2015) Genetic Perspectives of Inherited Skin Disorders in Pakistani Population. Doctoral thesis, Quaid-i-Azam University, Islamabad.

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Abstract

Genodermatoses are one of the major causes of long-term morbidity including crippling deformities and mortality worldwide. Though, the last twenty years have witnessed incredible advancements in the field of genodermatoses but it mainly remained limited to the western populations. Unfortunately, the human genetic research in developing countries including Pakistan is not up to the mark. Highly conserved and genetically diverse ethnic groups quite different from Caucasians are the major contributors of Pakistani population. Continuous practice of consanguinity in these highly conserved groups has left large numbers of Pakistani families suffering from variety of hereditary disorders including genodermatoses and hence, holds great potential for genetic studies. To address the issue, seventeen families suffering from different types of genodermatoses including xeroderma pigmentosum (XP), lipoid proteinosis (LP) and different form of ichthyosis were clinically and genetically characterized. Traditional linkage analysis and high-throughput next-generation sequencing approaches were utilized to establish molecular basis of these genodermatoses. Several bioinformatics parameters as well as functional studies were also opted to assess impact of functional variants on skin phenotypes. </BR> Genetic characterization of a family with typical phenotypes of XP including severe sunburn, blisters, and ulcers on different parts of the body revealed a novel homozygous c.654delA deletion in the XPA gene. Deletion not only substituted lysine with asparagine (p.L218A) but also resulted in premature termination of XPA protein just 5 residues downstream from the point of deletion (p.K218NfsX5). Comparative protein structure modeling and analysis predicted incomplete synthesis of XPA protein product as a pathogenic cause of XP in this family. </BR> Ethnically diverse four LP families with hoarse voice, limited tongue mobility, waxy papules along the margins of both eyelids and thick yellowish skin revealed same homozygous nonsense c.742G>T transversion in the ECM1 gene. Mutation resulted in transformation of glutamic acid into premature termination codon (p.E248X). ECM1 sequence analysis and comparative structure modeling predicted synthesis of 65% shorter mutant protein lacking functional domains that might have badly distorted ECM1 activities and led to the LP pathogenesis in these families. </BR> Genetic Perspectives of Inherited Skin Disorders in Pakistani Population Page XV In the present study, twelve Pakistani families including ten with non-syndromic autosomal recessive congenital ichthyosis (ARCI) and two with syndromic ichthyosis were studied. For the identification of candidate gene, families were subjected to targeted as well as whole exome sequencing (WES). Affected subjects from ARCI families displayed significant clinical heterogeneity ranging from affected individuals with fine, whitish scales on marked erythematic background to those with severe brown, plate-like scaling without visible erythema. Palmoplantar keratoderma was demonstrated only in affected subjects from one of the ARCI families. Likewise, most of the affected subjects with ARCI were premature collodion babies but still others were born at full term without involvement of collodion membrane. Two ARCI families revealed same c.527C>A mutation in exon 4 of the NIPAL4 gene that caused homozygous substitution of alanine to aspartic acid (p.A176D). Identification of this recurrent mutation in Pakistani as well as other distinct populations suggested the site a hotspot for NIPAL4 mutations. Four ARCI Pakistani families revealed two novel pathogenic variations in the ALOXE3 gene; a homozygous c.950G>C missense change led to the replacement of serine with threonine (p.S317T) and second homozygous nonsense mutation c.2026C>T caused substitution of serine with stop codon (p.Q676*). Targeted exome sequencing of another ARCI family with clinical characteristics of lamellar ichthyosis (LI) uncovered previously reported homozygous 3'splice site variation (c.2226-2A>G) in the TGM1 gene. Genetic change might have resulted in abnormal splice variants of TGase-1 protein and hence, contributed to LI pathogenesis. Whole exome sequencing analysis of a family suffering from autosomal recessive ichthyosis with hypotrichosis (ARIH) syndrome revealed two homozygous sequence variations in the ST14 gene. A previously reported single nucleotide polymorphism c.661C>T (rs758176034) caused substitution of arginine with cysteine (p.R221C), whereas a novel missense mutation c.737G>C led to the conversion of tryptophan into serine (p.W246S). Bioinformatics evaluation of both variations for their functional impact on ST14 protein and sequence conservation favored p.W246S change for being highly pathogenic and conserved across different species. An affected subject from non-consanguineous family with keratitis-ichthyosisdeafness (KID) syndrome revealed de novo dominant 3 bp deletion (c.85_87delTTC) Genetic Perspectives of Inherited Skin Disorders in Pakistani Population in the GJB2 gene. Mutation resulted in removal of a highly conserved phenylalanine (p.F29del) from GJB2 led to the KID syndrome. Histological studies of in vitro generated mutant transgenic skin (keratinocytes + HA- GJB2-F29del) demonstrated hyper-proliferated epidermis along with incomplete, disrupted morphology. Observed features were consistent with findings from patient's skin biopsy and hence, established the genotype-phenotype correlation in the patient. Identification of recurrent as well as novel pathogenic variations from this study will not only help in quick and accurate molecular diagnosis but also improve our knowledge in understanding the mechanism and biochemical pathways operating behind these life-long disorders.

Item Type: Thesis (Doctoral)
Uncontrolled Keywords: Genetic,Perspectives,Inherited, Skin Disorders ,Population
Subjects: Q Science > Q Science (General)
Depositing User: Unnamed user with email bkhan@hec.gov.pk
Date Deposited: 27 Oct 2017 04:53
Last Modified: 27 Oct 2017 04:53
URI: http://eprints.hec.gov.pk/id/eprint/6957

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