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Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families

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Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families GENETIC ANALYSIS OF HUMAN HEREDITARY NAIL DYSPLASIA IN PAKISTANI FAMILIES by Anwar Kamal Khan Department of Biotechnology & Genetic Engineering Kohat University of Science and Technology, Kohat-26000 Khyber Pakhtunkhwa, Pakistan 2019 GENETIC ANALYSIS OF HUMAN HEREDITARY NAIL DYSPLASIA IN PAKISTANI FAMILIES Thesis submitted in partial fulfillment of the requirements for the degree of doctor of philosophy (PhD) in Biotechnology & Genetic Engineering by Anwar Kamal Khan (Registration No. BT420142001) Department of Biotechnology & Genetic Engineering Kohat University of Science and Technology, Kohat-26000 Khyber Pakhtunkhwa, Pakistan 2019 CERTIFICATION FROM THE SUPERVISORS This thesis entitled “GENETIC ANALYSIS OF HUMAN HEREDITARY NAIL DYSPLASIA IN PAKISTANI FAMILIES” submitted by ANWAR KAMAL KHAN to the Kohat University of Science & Technology, Kohat for the award of Doctor of Philosophy in Biotechnology & Genetic Engineering presents bonafide research work carried out under our supervision. This work (fully or in part) has not been submitted to any other Institution for the award of any degree/ diploma/certificate. Supervisor I: Dr. Saad Ullah Khan Assistant professor __________ Department of Biotechnology & Genetic Engineering, Signature Kohat University of Science and Technology, Kohat Supervisor II: Dr. Noor Muhammad Associate professor __________ Department of Biotechnology & Genetic Engineering, Signature Kohat University of Science and Technology, Kohat Contents CONTENTS Page No ACKNOWLEDGEMENTS I LIST OF FIGURES III LIST OF TABLES XI LIST OF ABBREVIATIONS XII ABSTRACT XV CHAPTER 1 1 1.1 INTRODUCTION & REVIEW OF LITERATURE 1 1.1.1 Nail Growth 3 1.1.2 Nail Development 3 1.1.3 Signaling Pathways Stimulating Nail Development 4 1.1.3.1 WNT Signaling 5 1.1.3.2 NOTCH Signaling 6 1.1.3.3 BMP Signaling 6 1.1.3.4 Keratin Regulators and Keratin Related Genes 7 1.1.3.5 Keratins 7 1.1.3.6 Enzymes Involved in Nail Morphogenesis 8 1.1.4 Isolated Hereditary Nail Disorders 9 1.1.4.1 Trachonychia (Nail Disorder, Nonsyndromic Congenital, 1) 9 Continued..... Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families Contents Continued from the previous page Page No 1.1.4.2 Nail Disorder, Nonsyndromic Congenital, 2 10 1.1.4.3 Nail Disorder, Nonsyndromic Congenital, 3 10 1.1.4.4 Nail Disorder, Nonsyndromic Congenital, 4 12 1.1.4.5 Nail Disorder, Nonsyndromic Congenital, 5 14 1.1.4.6 Nail disorder, nonsyndromic congenital, 6 14 1.1.4.7 Nail Disorder, Nonsyndromic Congenital, 7 15 1.1.4.8 Nail Disorder, Nonsyndromic Congenital, 8 15 1.1.4.9 Nail Disorder, Nonsyndromic Congenital, 9 16 1.1.4.10 Nail Disorder, Nonsyndromic Congenital, 10 17 1.1.5 Isolated Congenital Nail Clubbing (ICNC) 18 1.1.6 Ectodermal Dysplasia 20 1.1.7 Syndromic Nail Disorders 24 1.1.7.1 Primary Hypertrophic Osteoarthropathy 24 1.1.7.2 Witkop Syndrome 25 1.1.7.3 Nail Patella Syndrome 26 1.1.7.4 Nail Hypertrophy 27 1.1.8 Homozygosity and recent techniques of gene identification 28 1.1.9 Cousin Marriages in Pakistani Population 29 1.1.10 Hypothesis 30 1.1.11 Objectives 30 CHAPTER 2 31 2.1 MATERIALS AND METHODS 31 Continued..... Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families Contents Continued from the previous page Page No 2.1.1 Study Approval 31 2.1.2 Clinical Examination and Collection of Blood Samples 31 2.1.3 DNA Extraction from Blood Samples 31 2.1.3.1 Genomic DNA Extraction using Organic Method (Phenol-Chloroform 32 Method) 2.1.3.2 Genomic DNA Extraction via Gentra puregene Kit Method 33 2.1.4 Quantification of Extracted DNA and Polymerase Chain Reaction 34 2.1.5 Linkage Studies 34 2.1.5.1 Exclusion Mapping 34 2.1.5.2 Human Genome Scan 35 2.1.5.3 Exome and Sanger Sequencing 36 2.1.6 Agarose Gel Electrophoresis 37 2.1.7 Polyacrylamide Gel Electrophoresis (PAGE) 37 2.1.8 Statistical Analysis 37 2.1.9 Candidate Gene Sequencing 38 Continued..... Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families Contents Continued from the previous page Page No 2.1.10 Prediction of Mutation Effect 39 2.1.11 Protein Structure Prediction 40 CHAPTER 3 49 3.1 HEREDITARY NAIL DISORDERS 49 3.1.1 Family A 50 3.1.1.1 Clinical Features 50 3.1.1.2 Demarcating Genes Through Homozygosity Mapping in Family A 51 3.1.1.3 Exome and Sanger Sequencing 52 3.1.2 Family B 53 3.1.2.1 Clinical Features 53 3.1.2.2 Sequencing PLCD1 Gene in family B 53 3.1.2.3 Protein Structure Prediction for PLCD1 54 3.1.3 Family C 54 3.1.3.1 Clinical Features 54 3.1.3.2 Sequencing PLCD1 gene 55 3.1.4 FAMILY D 55 3.1.4.1 Clinical Features 55 3.1.5 FAMILY E 56 3.1.5.1 Clinical Features 56 3.1.5.2 Sequencing FZD6 Gene in Family D and E 56 Continued..... Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families Contents Continued from the previous page Page No 3.1.5.3 Protein Modeling for Family E 57 3.1.6 Family F 57 3.1.6.1 Clinical Features 57 3.1.6.2 Mapping of Candidate Genes Involved in Family F 58 3.1.7 Discussion 58 CHAPTER 4 92 4.1 Ectodermal dysplasia 92 4.1.1 FAMILY G 92 4.1.1.1 Clinical Features 92 4.1.1.2 Genotyping and Sequencing 93 4.1.1.3 Protein Modeling 94 4.1.1.2 Discussion 94 CHAPTER 5 102 5.1 Primary Hypertrophic Osteoarthropathy 102 5.1.1 Family H 102 5.1.1.1 Clinical Features 102 5.1.1.2 Genotyping and Sequencing HPGD Gene 103 5.1.1.3 Protein Modeling 104 5.1.2 Discussion 104 Continued..... Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families Contents Continued from the previous page Page No CONCLUSION AND RECOMMENDATIONS 115 CHAPTER 6 118 References 118 Appendices 150 Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families Acknowledgements ACKNOWLEDGEMENTS First and foremost, I would like to express my gratitude to ‘ALLAH’ Almighty who has been gracious and merciful and provided me with guidance and inspiration throughout my life. All regards, respects and blessings be upon the Holy Prophet Hazrat Muhammad (Sallallahu aliahi wa sallam), whose blessings and teachings flourished my thoughts and thrived my ambitions. I wish to express my greatest gratitude to everyone who has contributed to this thesis and helped me along the way. Especially, I would like to thank all the participated patients and their families, healthy controls, co-authors and collaborators for their active participation and scientific contributions. The credit also goes to the medical doctors for the clear diagnosis which is the key success in medical genetics. I am deeply indebted and grateful to my supervisor Dr. Saad Ullah Khan and my co supervisor Dr. Noor Muhammad, Department of Biotechnology and Genetic Engineering, Kohat University of Science & Technology, Kohat, for their support, guidance, patience and valuable feedback throughout my PhD studies. I wish to extend my gratitude to chairman Department of Biotechnology & Genetic Engineering Dr. Muhammad Daud Khan for promoting research friendly environment for the students in the department. I would like to acknowledge Dr. Sulman Basit and Dr. Khadim Shah specially, because without his help and cooperation in my work, though not possible, would be really difficult. I appreciate my lab juniors Sher Alam Khan, Niamat Ullah Khan, Adil Rehman, Mehran Khan, Nazif Khan, Haris Khan, Abdullah Khan, Gohar Khan, Usman Ullah Khan and Hamid Nawaz Khan for the respect they gave me and for their support. I Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families Acknowledgements I present heartiest thanks to my friends Asad Ullah, Pirzada Khan, Wajid Alim, Naqib Ullah Khan, Dr. Wahid Ullah Khan, Dr. Zia-u-Rehman, Dr. Niamat Khan, Dr. Aziz Uullah, Dr. Muhammad Jami and Muhammad Mudasir Aslam for their nice company and advice throughout my research work. The good time spent with them can never be erased from my memories. I am extremely grateful to my parents for their endless support, love and care. The love and special concern of my brothers Mir Saad Ullah Khan, Asghar Ali Khan and Akhtar Ali Khan will always be cherished. Finally, I wish to thank the Higher Education Commission (HEC), Islamabad Pakistan, for funding this project through research grants to my supervisor. Anwar Kamal Khan II Genetic Analysis of Human Hereditary Nail Dysplasia in Pakistani Families List of Figures LIST OF FIGURES Figure No. Title Page No. Pedigree drawing for four generations family A inheriting 3.1 65 autosomal recessive congenital nail dysplasia (ARCND). Filled squires and circles denote affected subjects, while the empty squires and circles designate normal individuals. Squires and circles with cross lines denote deceased individuals while double line connection between individuals denotes cousin marriage. The numbers characterized with stars designate those siblings who donated blood samples for genetic study Phenotypes of the patients in family A. Patient V-1 showing severe 3.2 66 hyperkeratotic thick nail plate, nail bed and swelled fingers (a). Affected subject V-2 showing keratotic lesions of the, middle and ring fingers in the right hand and keratotic left fingernails and normal left thumb (b). Patient V-4 (c) showing onychodystrophy, hyperkeratotic with minor erythema and swelling. Thick dystrophic nails with hyperkeratotic nail bed in patient V-5 (d). Patient V-6 revealing destructed nail plate and nail bed (e) 3.3 Haplotype of family A transmitting congenital nail dysplasia in 67 recessive form.
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