Mapping Genes Causing Syndromic and Non- Syndromic Human Hereditary Skin Disorders

Abstract

Genetic defects in complex processes of embryonic development and postnatal maintenance of the skin and its appendages result in clinically and genetically heterogeneous group of skin disorders. Due to nonspecific presentation, variable clinical manifestations and highly overlapping phenotypes, the diagnosis of skin disorders is a challenging job for the clinicians and geneticists. However, recent advances in molecular biology technologies notably whole exome sequencing (WES) and microarray have incredibly accelerated identification of genes involved in inherited diseases. The research work, presented in this dissertation, described clinical and molecular characterization of seventeen families of Pakistani origin (A-Q) segregating various forms of syndromic and non-syndromic skin disorders. This included one with palmoplantar hyperkeratosis (A), three with nail disorders (B-D), one with xeroderma pigmentosum (E), two with non-photosensitive trichothiodystrophy and mitral regurgitation (F-G), three with different types of ichthyosis (H-J), two with epidermolysis bullosa (K-L), and five with different types of hair abnormalities (M-Q). In all seventeen families, combination of at least two or three techniques, including microsatellite/SNP genotyping and Sanger/Exome sequencing, led to the establishment of linkage on human chromosomes and detection of potential disease causing variants in different genes. This included fourteen novel variants in 13 different genes (SLURP1, SLCO2A1, ERRC5, MPLKIP, KRT83, ALDH3A2, ABHD5, PLEC, BTAF1, C3orf52, MTUS1, SGSM1, DCAF1) and previously reported three variants in 3 genes (RSPO4, FZD6, KRT14). Disease causing variants, identified in six genes (KRT83, SLCO2A1, BTAF1, MTUS1, C3orf52, SGSM1), are the first report of involvement of such genes in causing skin disorders. Pathogenicity of disease causing variants were tested and verified by various bioinformatics tools (SIFT, PolyPhen, MutationTaster, MutationAssessor, GERP++, phyloP). Non-polymorphic nature of the variants was validated by screening large number of ethnically matched control individuals and by searching various databases. In a couple of cases, qPCR was used to monitor effect of the variants on expression of other genes. In addition, where necessary, protein modelling studies were Abstract Mapping Genes Causing Syndromic and Non-Syndromic Human Hereditary Skin Disorders XIV performed to identify location of the mutations in the protein and its possible effect on structure and functions of the protein. The work presented in the dissertation resulted in the following publications. 1. Shah K, Ansar M, Khan FS, Ahmad W, Ferrara TM, Spritz RA (2017). Recessive progressive symmetric erythrokeratoderma results from a homozygous loss-of-function mutation of KRT83 and is allelic with dominant monilethrix. Journal of Medical Genetics 54: 186-189. 2. Shah K, Ferrara TM, Jan A, Umair M, Khan S, Ahmad W, Spritz RA. Homozygous SLCO2A1 translation initiation codon mutation in a Pakistani family with recessive isolated congenital nail clubbing (ICNC) (2017). British Journal of Dermatology. doi: 10.1111/bjd.15094. 3. Shah K, Ali RH, Ansar M, Lee K, Chishti MS, Abbe I, Li B, Smith JD, Nickerson DA, Shendure J, Coucke PJ, Leal SM, Ahmad W (2016). Mitral regurgitation as a phenotypic manifestation of nonphotosensitive trichothiodystrophy due to a splice variant in MPLKIP. BMC Medical Genetics 17: 13. 4. Shah K, Nasir A, Shahzad S, Khan S, Ahmad W (2016). A novel homozygous mutation disrupting the initiation codon in the SLURP1 gene underlies mal de Meleda in a consanguineous family. Clinical and Experimental Dermatology. 41: 675-679. 5. Raza SI, Navid AK, Noor Z, Shah K, Dar NR, Ahmad W, Rashid S (2017). GLY67ARG substitution in RSPO4 disrupts the WNT signaling pathway due to an abnormal binding pattern with LGRs leading to anonychia. RSC Advances 7:17357- 17366. 6. Shah K, Mehmood S, Jan A, Abbe I, Ali RH, Khan A, Chishti MS, Lee K, Ahmad F, Ansar M, University of Washington Center for Mendelian Genomics, Nickerson DA, Bamshad MJ, Coucke PJ, Santos‐Cortez RL, Spritz RA, Leal SM, Ahmad W (2017). Sequence Variants in Nine Different Genes Underlying Rare Skin Disorders in Ten Consanguineous Families. International Journal of Dermatology (Under Review). 7. Ahmad F, Shah K, Muhammad D, Basit S, Wakil SM, Umair M, Ramzand K, Ahmad W (2017). Novel autosomal recessive LAMA3 and PLEC1 mutations underlie non-hertz junctional epidermolysis bullosa and epidermolysis bullosa simplex with Abstract Mapping Genes Causing Syndromic and Non-Syndromic Human Hereditary Skin Disorders XV muscular dystrophy in two consanguineous families. Clinical and Experimental Dermatology (Under Review). 8. Shah K, Jan A, Ahmad W, Umair M, Irfanullah, Basit S, Ahmad W. A novel start loss variant in DCAF17 underlies Woodhouse-Sakati Syndrome phenotypes in a large consanguineous family (In Preparation). 9. Shah K, Umair M, Ahmad F, Ali G, Nawaz G, Jhon P, Ferrara TM, Spritz RA, Ahmad W. A heterozygous missense sequence variant in BTAF1 gene miss-regulate transcription and results in progressive patchy hair loss from the scalp (In Preparation). 10. Shah K, Ali G, Jhon P, Irfanullah, Ahmad F, Basit S, Ahmad W. C3orf52 is a probable candidate gene for autosomal recessive hypotrichosis in large Pakistani family. (In Preparation). 11. Shah K, Hussain S, Raza SI, Basit S, Ahmad W. Missense sequence variant in SGSM1 gene underlies unexplored phenotypes of hypertrichosis, macrocephaly, facial deformities, cardiac and urinary defects in Pakistani kindred. (In Preparation). 12. Shah k, Irfanullah, Ahmad F, Umair M, Basit S, Ahmad W. Complete hair loss in large consanguineous Pakistani family results from mutation in MTUS1 gene in a large consanguineous family. (In Preparation).