PODPISI IZRAŽANJA GENOV PRI PREDROJSTNI DIAGNOSTIKI ANEVPLOIDIJ

Volk, Marija (author), Peterlin, Borut (mentor)

Kromosomske bolezni predstavljajo pomemben zdravstveni problem, saj so v predrojstnem obdobju pogosto povezane z razvojnimi nepravilnostmi ali s spontano izgubo nosečnosti. Številčne kromosomske nepravilnosti avtosomov niso združljive z življenjem, razen trisomije kromosoma 21, 18 in 13 (T21, T18, T13). Multiomski pristop omogoča sestavljeno raziskovanje genoma in transkriptoma ter posledično prepoznavanje biooznačevalcev za različna patološka stanja, pri čemer nam kromosomski sindromi z dobro opredeljeno klinično sliko lahko služijo kot model patološkega stanja. Transkriptomske raziskave predrojstnih vzorcev s T21, T18 in T13 so pokazale spremembe v genskem izražanju, niso pa raziskovale diagnostičnih možnosti za napoved nosečnosti z visokimi tveganji za trisomijo, niti niso ugotavljale skupnih značilnosti v genskem izražanju pri trisomijah. Postavili smo hipotezo, da obstajajo razlike v genskem izražanju, ki jih lahko uporabimo kot diagnostični biooznačevalec za specifično trisomijo in da je del razlik v genskem izražanju skupen pri različnih trisomijah, kar lahko obravnavamo kot homeostatski odgovor. Opravili smo ekspresijske mikromrežne ekperimente na predrojstnih vzorcih gojenih amniocitov s T21 in T18 ter gojenih celic horionskih resic s T13, ki smo jih primerjali z ujemajočimi vzorci z normalnim kariotipom. V prvem delu smo opravili diferencialno gensko ekspresijo (DGE) za vse trisomije in prepoznali podpise izražanja genov, ki so bili najbolj statistično značilni za T21, 18 in T13. Napovedno zanesljivost izbranih podpisov genskega izražanja smo preverili na dostopnih objavljenih transkriptomskih raziskavah in potrdili, da izbrani biooznačevalci z visoko zanesljivostjo napovedo status trisomije 21, 18 in 13. V drugem delu raziskave smo primerjali podobnosti v DGE med vzorci s T21 in T18 ter ugotovili 6 genov s spremenjenim izražanjem, ki so skupni pri obeh trisomijah. Analiza obogatitve genskih setov in bioloških procesov sta pokazali obogatitev genov povezanih s PI3K/AKT signalno potjo, G2/M kontrolno točko pri DNA okvari in predvideno inhibicijo regulatorja TP53 ter obogatitev genov povezanih s celičnim ciklom, celično smrtjo in preživetjem, preživetjem organizma ter razvojem in delovanjem tkiv. Z raziskavo smo ugotovili specifične podpise izražanja genov, ki so za preiskovane trisomije značilni in jih lahko uporabimo kot bioznačevalec. Zaznali smo tudi določene skupne podobnosti v genskem izražanju pri T21 in T18, za katere menimo, da lahko odražajo genomski homeostatski odgovor na kromosomsko nepravilnost. Naši rezultati predstavljajo temelj za nadaljnje raziskave biooznačevalcev za nosečnosti z visokimi tveganji in za razumevanje mehanizmov s katerimi se trisomična celica upira kromosomski motnji.

• Language: Slovenian
• Keywords: podpis izražanja genov, ekspresijska mikromreže, predrojstna diagnostika, anevploidija, biooznačevalec, homeostatski mehanizmi
• Work type: Doctoral dissertation
• Organization: MF - Faculty of Medicine
• Year: 2019
• PID: 20.500.12556/RUL-106355
• COBISS.SI-ID: 299133952
• Publication date in RUL: 20.02.2019

Secondary language

• Language: English
• Title: GENE EXPRESSION SIGNATURES IN PRENATAL DIAGNOSIS OF ANEUPLOIDIES

Abstract

Chromosome diseases, associated with developmental abnormalities, represent an important health problem and often lead to pregnancy loss. Numerical autosome abnormalities are incompatible with life, with the exception of trisomy of chromosomes 21, 18 and 13 (T21, T18 and T13). A multiomics approach allows for combined genome and transcriptome analysis and the identification of biomarkers for various pathological conditions, where chromosome syndromes with a well-defined clinical presentation can serve as a model of the pathological condition. Reported transcriptomic studies on prenatal samples with T21, T18 and T13 showed changes in gene expression, but they did not investigate the diagnostic potential for predicting high-risk pregnancies, nor did they identify the common features in gene expression among trisomies. We hypothesized that specific gene expression signature can be used as a diagnostic biomarker for certain trisomy and that there are some similarities in gene expression that are common in different trisomies and can be considered as a homeostatic genome response. We performed gene-expression experiments on prenatal samples of cultivated amniocytes with T21 and T18, and cultivated cells of chorionic villi with T13 in comparison to matched prenatal samples with normal karyotype. In the first part of the study, we carried out differential gene expression (DGE) analyses and selected gene expression signatures as biomarkers specific for T21, 18 and T13. The classification performance of the selected gene subsets were verified on independent GEO datasets and confirmed that the selected biomarkers predict the T21, 18 or T13 with high reliability. In the second part of the study, we compared the similarities in DGE for T21 and T18 and found 6 same-directionally dysregulated genes that are common in both data sets. The gene set enrichment and pathway analyses showed enrichment of genes associated with the PI3K / AKT signal pathway, the G2 / M check point in DNA defects and the predicted inhibition of the TP53 regulator and the enrichment of gene-related cell cycle, cell death and survival, the survival of the organism, and the development and function of tissues. Our study found gene expression signature specific for the individual trisomy that can be used as a biomarker. In addition, we detected some similar differences in gene expression, that are common in T21 and T18, which may reflect the genomic homeostatic response to the chromosome change. Our results provide a basis for further investigations of biomarkers in high risk pregnancies and understanding of the mechanisms of trisomic cell resisting chromosomal perturbation.

• Keywords: gene expression signature, expression microarray, prenatal diagnosis, aneuploidy, biomarker, homeostatic mechanism