Clinical and Molecular Characterization of Various Types of Hereditary Skin and Immunological Disorders Segregating in Families of Pakistani Origin

Abstract

The research work, presented in the dissertation, describes the genetic and clinical characterization of sixteen families showing various types of hereditary skin and twelve other families of immunological disorders. The families with skin disorders were collected from remote areas in Pakistan and those with disrupted immune system from local government and non-government hospitals in capital Islamabad. Following clinical characterization, search for the disease-causing variants was performed via various techniques, including genotyping microsatellite markers, exome sequencing, and Sanger sequencing. Various bioinformatics tools were used to test pathogenicity of the selected variants. Segregation analysis, using DNA of all available members, was employed to test association of the selected sequence variants with the disorder in each family. In selected cases protein modelling was employed to determine effect of the sequence variants on structural and functional aspects of the proteins. Clinical examination of affected members revealed various types of skin disorders in sixteen families. This included hypertrichosis, non-syndromic/syndromic hypotrichosis, autosomal recessive congenital ichthyosis (ARCI), and nail dysplasia. Analysis of the sequencing data helped in the identification of a novel gene HDAC7 on chromosome 12q13.11 involved in causing ichthyosis. Since it is the first report of a disease-causing variant in the HDAC7, further evidence is required to substantiate the findings. Also, the study provided first evidence of involvement of CDH23 in causing scalp hair loss in a family. In total, seven novel disease-causing variants were identified in previously reported genes. The genes included ABCA5 for congenital generalized hypertrichosis terminalis (CGHT), KRT25 for wooly hair/hypotrichosis and dental anomalies, CDH23 for syndromic hypotrichosis, ATP2A2 for Darier disease, and HDAC7, SULT2B1 and SDR9C7 for ARCI. In addition, previously reported skin disorder causative variants were found in six other genes including LPAR6, LIPH, CDH3, DSP, NIPAL4 and X-chromosome deletion [5892715-7843604]. Clinical evaluation of families with immunological disorders, leukocyte adhesion deficiency type 1 (LAD-1) was found in eleven and OTULIN-related auto-inflammatory syndrome (ORAS) in one family. Genetic evaluation revealed three novels and four previously reported DRSML QAU Abstract Clinical and Genetic Characterization of Various Types of Hereditary Skin and Immunological Disorders Segregating in Families of Pakistani Origin XX disease-causing variants in ITGB2 gene in families segregating LAD-1. In addition, exome sequencing/Sanger sequencing identified a novel variant in OTULIN gene in a family segregating ORAS. The research work presented here contributed in the publication of the following articles. 1. Rubab Raza, Asmat Ullah, Nighat Hiader, Jai Krishin, Muqadar Shah, Abdullah, Kifayat Ullah, Torben Hansen, Syed Irfan Raza, Sulman Basit, Wasim Ahmad (2022). Exome sequencing revealed the first intragenic deletion in ABCA5 underlying autosomal recessive hypertrichosis. Clinical and Experimental Dermatology [Epub ahead of print] doi: 10.1111/ced.15128. 2. Rubab Raza, Gagan Chhabra, Muhammad Bilal, Mary A. Ndiaye, Khurram Liaqat, Shoaib Nawaz, Jean-Yves Sgro, Ivan Rayment, Wasim Ahmad, and Nihal Ahmad (2022). A Homozygous Missense Variant in K25 Underlying Overlapping Phenotype with Woolly Hair and Dental Anomalies. Journal of Investigative Dermatology 143(1):173-176.e3. doi: 10.1016/j.jid.2022.07.010. 3. Rubab Raza, Raul Jimenez-Heredia, Atteaya Zaman, Muhammad Zeeshan Anwar, Muhammad Akram Shahzad Khokhar, Asmat Ullah, Ayisha Zia, Sajid Rashid, Wasim Ahmad, Ana Krolo, Kaan Boztug, Syed Irfan Raza (2021). Whole exome sequencing revealed a novel sequence variant in the OTULIN underlying auto inflammatory syndrome. doi: 10.21203/rs.3.rs-164929/v1. 4. Rubab Raza, Zara Khalid, Sadaf Jafar, Momin Iqbal, Atteaya Zaman, Wasim Ahmad, Syed Irfan Raza (2022). Sequence variants in the ITGB2 gene underlying leukocyte adhesion deficiency Type-1 in four consanguineous families. Gene Reports 29: 101699. doi: 10.1016/j.genrep.2022.101699. 5. Hamid Nawaz Tipu, Rubab Raza, Sadaf Jaffar, Alamgir Khan, Muhammad Zeeshan Anwar, Wasim Ahmad, Syed Irfan Raza (2020). β2 integrin gene (ITGB2) mutation spectra in Pakistani families with leukocyte adhesion deficiency type 1 (LAD1). Immunobiology 225(3): 151938. doi: 10.1016/j.imbio.2020.151938