Genetske spremembe, povezane z orofacialnimi shizami v slovenski populaciji

Slavec Janev, Lara (author), Geršak, Ksenija (mentor), Karas Kuželički, Nataša (co-mentor)

Orofacialne shize (OFS) oziroma razcepe ustnice, čeljustnega grebena in/ali neba štejemo med najpogostejše prirojene razvojne nepravilnosti. Delimo jih na nesindromske OFS, katerih etiologija je po navadi večfaktorska, in sindromske OFS, ki imajo pogosto znan monogenski vzrok nastanka. Namen doktorskega dela je bil identificirati genetske dejavnike tveganja za nastanek OFS v slovenski populaciji in odkriti optimalne laboratorijske diagnostične pristope za njihovo detekcijo. Najprej smo naredili sistematični pregled literature in metaanalizo, da bi identificirali gene, ki so povezani z nesindromskimi OFS, v kavkazijskih populacijah evropskega izvora. Vključili smo 84 populacijskih študij primerov in kontrol na kandidatnih genih, ki so proučevale več kot 700 genetskih sprememb, porazdeljenih po celotnem genomu. Na podlagi pridobljenih informacij smo izbrali 74 kandidatnih genov za proučevanje etiologije OFS v slovenski populaciji. V nadaljevanju smo izvedli študijo družin. Vključili smo 34 družin z dvema ali več člani z domnevno nesindromskimi OFS. Najprej smo s sekvenciranjem po Sangerju ali sekvenciranjem celotnega eksoma analizirali IRF6, GRHL3 in TBX22, da bi identificirali družine s sindromom Van der Woude (VWS1/VWS2) in X-vezanim razcepom neba z/brez ankiloglosije (CPX). Te sindrome je včasih namreč težko ločiti od nesindromskih OFS. V petih družinah smo odkrili štiri različne vzročne spremembe v IRF6 (NM_006147.4:c.134G>A; c.622C>T; c.687delG; c.1234C>T) (VWS1), v eni družini verjetno vzročno spremembo v GRHL3 (NM_198173.3:c.1285G>T) (VWS2) in v eni družini delecijo vseh kodirajočih eksonov TBX22 (CPX). Tri od omenjenih genetskih sprememb smo odkrili prvi. Nato smo v preostalih družinah pregledali še kandidatne gene, povezane z nesindromskimi OFS, ki smo jih izbrali s sistematičnim pregledom literature. V teh družinah smo odkrili še pet genetskih sprememb, toda njihove povezave z OFS nismo mogli zanesljivo opredeliti na podlagi razpoložljivih informacij. Naš pristop sekvenciranja je tako uporaben za razlikovanje med sindromskimi in nesindromskimi OFS. Nasprotno, s tem pristopom v slovenski populaciji nismo uspeli odkriti genetskega vzroka nastanka nesindromskih OFS.

• Language: Slovenian
• Keywords: genetske spremembe, nesindromske orofacialne shize, sindrom Van der Woude, X-vezan razcep neba z/brez ankiloglosije, metaanaliza, družinska študija, slovenska populacija
• Work type: Doctoral dissertation
• Organization: FFA - Faculty of Pharmacy
• Year: 2023
• PID: 20.500.12556/RUL-151205
• Publication date in RUL: 01.10.2023

Secondary language

• Language: English
• Title: Genetic variants associated with orofacial clefts in the Slovenian population

Abstract

Orofacial clefts (OFCs), i.e., cleft lip, alveolus and/or palate, are among the most common congenital developmental anomalies. They are divided into non-syndromic OFCs, usually with multifactorial aetiology, and syndromic OFCs, often with a known monogenic cause. The aim of the doctoral thesis was to identify genetic risk factors for OFCs in the Slovenian population and discover optimal laboratory diagnostic approaches for their detection. Initially, we conducted a systematic review and meta-analysis to identify genes associated with non-syndromic OFCs in populations of European ancestry. We included 84 population-based case-control studies on candidate genes, examining more than 700 genetic variants throughout the genome. Based on the acquired information, 74 candidate genes were selected for studying OFCs' aetiology in the Slovenian population. Subsequently, we conducted a family study, enrolling 34 families with two or more members with apparent non-syndromic OFCs. First, we analysed IRF6, GRHL3, and TBX22 by Sanger sequencing or whole-exome sequencing to identify families with Van der Woude syndrome (VWS1/VWS2) and X-linked cleft palate with or without ankyloglossia (CPX). Differentiating these syndromes from non-syndromic OFCs can be challenging. In five families we found four different causal variants in IRF6 (NM_006147.4:c.134G>A; c.622C>T; c.687delG; c.1234C>T) (VWS1), in one family a likely causal variant in GRHL3 (NM_198173.3:c.1285G>T) (VWS2) and in one family a deletion of all coding exons of TBX22 (CPX). Three of these genetic variants were discovered for the first time. In the remaining families, we then examined candidate genes associated with non-syndromic OFCs, selected through a systematic review. We found five additional genetic variants in these families, but could not reliably determine their association with OFCs based on available information. Our sequencing approach is thus useful for distinguishing between syndromic and non-syndromic OFCs. However, in the Slovenian population, we were unable to discover the genetic cause of non-syndromic OFCs using this approach.

• Keywords: genetic variants, non-syndromic orofacial clefts, Van der Woude syndrome, X-linked cleft palate with or without ankyloglossia, meta-analysis, family study, Slovenian population