In silico - funkcijska analiza genskih polimorfizmov, povezanih z nesindromskimi orofacialnimi shizami

Rožič, Tjaša (avtor), Karas Kuželički, Nataša (mentor)

Orofacialne shize (OFC) so ena najpogostejših prirojenih razvojnih nepravilnosti obraza. Incidenca se v svetu v zadnjih letih giblje okrog 1,7 na 1000 živorojenih otrok. Delimo jih lahko na sindromske in nesindromske, ki predstavljajo kar 70 % vseh OFC. Nesindromske shize so definirane kot shize, pri katerih gre za nepopolno združitev tkiv, ki tvorijo zgornjo ustnico, čeljustni greben in nebo, ter niso povezane z nobeno drugo anomalijo izven anatomske regije shiz. Poleg okolijskih dejavnikov in demografskih dejavnikov tveganja lahko tveganje za nastanek nesindromskih OFC pri potomcih povečajo tudi genetski polimorfizmi. Študije primerov in kontrol po celem svetu so odkrile ogromno polimorfizmov, ki naj bi bili povezani z OFC. Za večino omenjenih polimorfizmov pa niso bile izvedene funkcijske študije, ki bi mehanistično razložile oziroma dokazale povezavo med določenim polimorfizmom in OFC. Za oceno patološkega potenciala posameznega polimorfizma lahko uporabimo različna bioinformacijska orodja. Namen magistrske naloge je bil z uporabo omenjenih orodij preučiti polimorfizme, ki so bili v genetskih študijah primerov in kontrol povezani z OFC. V nalogi smo preučili 141 polimorfizmov. Najprej smo izmed vseh 141 polimorfizmov s pomočjo spletnega orodja Ensembl izločili tiste polimorfizme, ki se nahajajo izven kodirajočih regij, in polimorfizme intronskih regij, ki so več kot 40 baznih parov oddaljeni od prvega eksona. Našli smo 10 takšnih polimorfizmov posameznega nukleotida (SNP). Ti polimorfizmi so rs7552, rs698, rs9277934, rs357564, rs17563, rs3746101, rs1800471, rs1994798, rs1476413 in rs10498038. Za vseh 10 SNP smo preučili funkcijo gena, v katerem se nahajajo v podatkovni bazi GeneCards. Sledila je analiza polimorfizmov v bazi Ensembl. Na koncu smo in silico ovrednotili vpliv SNP na proteinski produkt gena in njihov patogeni potencial z uporabo bioinformacijskih orodij Variant Effect Predictor v sklopu baze Ensembl. Za polimorfizma rs9277934 in rs357564 smo z in silico analizo dokazali vpliv na proteinski produkt ter patogeni potencial, vendar za rs357564 nismo našli direktne povezave z OFC. Polimorfizme rs7552, rs9277934, rs17563 in rs3746101 smo na podlagi podatkovnih baz lahko povezali z OFC, vendar smo, kot že omenjeno, patogeni potencial zaznali samo pri rs9277934. Čeprav pri rs698, rs1994798 in rs1476413 v podatkovnih bazah nismo našli direktne povezave z OFC, bi lahko napake v genih, v katerih se ti polimorfizmi nahajajo, povezali z ostalimi dejavniki tveganja, kot sta uživanje alkohola in homocisteinemija.

• Jezik: Slovenski jezik
• Ključne besede: in silico funkcijska analiza, SNP, orofacialne shize, Ensembl, Variant Effect Predictor
• Vrsta gradiva: Magistrsko delo/naloga
• Organizacija: FFA - Fakulteta za farmacijo
• Leto izida: 2022
• PID: 20.500.12556/RUL-137481
• Datum objave v RUL: 18.06.2022

Sekundarni jezik

• Jezik: Angleški jezik
• Naslov: In silico functional analysis of genetic polymorphisms associated with non-syndromic orofacial clefts

Izvleček

Orofacial clefts (OFC) are one of the most common congenital facial malformations. The world incidence is around 1.7 per 1,000 live-born children. OFCs can be divided into syndromic and non-syndromic, which represent up to 70% of all OFCs. Non-syndromic clefts are defined as the clefts that involve the incomplete union of the tissues that form the upper lip, jawbone, and palate and are not associated with any other anomaly outside the anatomical region of the cleft. In addition to an environmental and demographic risk factors, genetic polymorphisms may also increase the risk of developing non-syndromic OFC in offspring. Case - control studies around the world have established a large number of polymorphisms that are thought to be associated with OFC. However, no functional studies, that would mechanistically explain or prove the connection between a particular polymorphism and OFC, have been performed for most of the mentioned polymorphisms. Different bioinformatic tools can be used to assess the pathological potential of an individual polymorphism. The purpose of the master's thesis was to study polymorphisms that were associated with OFC in genetic case - control studies using these tools. 141 polymorphisms were included in the study. First, we used the online tool Ensembl to exclude polymorphisms that are located outside the coding regions and polymorphisms of intron regions that are more than 40 base pairs away from the nearest exon. We identified 10 such single nucleotide polymorphisms (SNP). These polymorphisms are rs7552, rs698, rs9277934, rs357564, rs17563, rs3746101, rs1800471, rs1994798, rs1476413 and rs10498038. We examined the function of the gene in which they are located for all those 10 SNPs in the GeneCards database. An analysis of polymorphisms in the Ensembl database was followed, and finally we evaluated in silico the influence of SNPs on the protein product of the gene and their pathogenic potential using bioinformatic tool Variant Effect Predictor within the Ensembl database. We demonstrated the effect on protein product and pathogenic potential by in silico analysis for the rs9277934 and rs357564 polymorphisms, but no direct association with OFC was found for rs357564. Polymorphisms rs7552, rs9277934, rs17563 and rs3746101 could be associated with OFC based on databases, but as previously mentioned, pathogenic potential was detected only in rs9277934. Although no direct association with OFC was found in rs698, rs1994798, and rs1476413 in the databases, defects in the genes in which these polymorphisms are found, could be associated with other risk factors such as alcohol consumption and homocysteinemia.

• Ključne besede: in silico functional analysis, SNP, orofacial clefts, Ensembl, Variant Effect Predictor