Investigation of Genes Responsible for Diaphragmatic Developmental Defects with Next Generation Sequencing Technologies.


Thesis Type: Doctorate

Institution Of The Thesis: Istanbul University, Health Sciences Institute, İstanbul Tıp Fakültesi Bölümü, Turkey

Approval Date: 2023

Thesis Language: Turkish

Student: SOMAYYEH HEIDARGHOLIZADEH

Principal Supervisor (For Co-Supervisor Theses): Birsen Karaman

Co-Supervisor: Çağrı Güleç

Abstract:

A thin skeletal muscle located between the abdominal and the thoracic cavity, the diaphragm, is necessary for the continuity of respiratory function. Congenital Diaphragmatic Hernias (CDH) that occur as a result of defects in the development of the diaphragm is identified as a severe anomaly with high mortality and requiring surgical intervention. CDH, could be as an isolated or syndromic types and is characterized by herniation of abdominal contents into the thoracic cavity that may result in pulmonary hypoplasia or pulmonary hypertension. CDH, where genetic and environmental factors play a role in its etiology, has been shown to be associated with numerous chromosomal anomalies, copy number variations (CNVs) and gene sequence variants, although these changes were insufficient to explain the etiology of all CDH cases. It is thought that more genes and factors play a role in the etiology of CDH and studies conducted for this purpose have shown the importance of retinoic acid (RA) signaling pathway and related genes in particular. However, because of many other processes such as cell migration, cytoskeleton organization, and myogenesis involved in diaphragmatic development, genes with pathogenic variants responsible for CDH are not limited to RA signaling pathway genes. It is expected that the use of methods such as NGS-based whole-exome sequencing (WES) will be effective in investigation of the genetic basis of CDH, in which many genes are thought to play a role in its etiology. In order to identify new candidate genes responsible for CDH, within the scope of this project, trio-WES analysis was performed in eight fetuses and their parents, and solo-WES analysis was performed in ten fetus with excluded CNVs by chromosome analysis and a-CGH study. As a result of the bioinformatics analysis, pathogenic variants have been identified in the genes that were directly associated with CDH (NR2F2, ZFPM2, ARID1A, CREBBP, PLAT, POGZ and RARB) and in candidate genes that their association with CDH may be found based on their functions, databases and literature data (CDKL4, STAB2, NEIL2, SETD5, TAF4, ZBTB38, ZNF423, COL11A1, PCSK5 and RBM8A). In summary, the results of the project study support the notion that a single gene or variant is not responsible for the majority of CDH cases. The functional effects of the new variants detected in different genes in our cases and their clinical relevance should be supported by functional or animal model studies. However, the findings of our study have the potential to become a resource for similar studies in the future and thus contribute to the literature on the genes and the variants that play a role in the etiology of CDH.