| Abstract | CILJ. Ispitati utjecaj demografskih, agonalnih i procesnih osobitosti uzoraka na
transkripcijsku varijabilnost i kontrolu kvalitete u cjelogenomskoj RNASeq analizi tkiva
štitnjače (bioinformatička analiza).
USTROJ STUDIJE. Istraživanje je ustrojeno kao eksploracijska studija (in silico analiza).
METODE. Analizirana je transkripcijska varijabilnost tkiva štitnjače korištenjem knjižnica
RNK sekvenciranja iz GTEx projekta (v8 izdanje). Ukupno je analizirano 228 profila
cjelogenomske ekspresije u ovisnosti o demografskim podacima donora i atributima uzoraka.
Provedena je analiza particije varijance, hijerarhijsko grupiranje i faktorizacija matrica, nakon
čega je uslijedilo profiliranje bioloških puteva unutar visoko izraženih metagena (Gene
Ontology, Hallmark, Kyoto Encyclopedia of Genes and Genomes, Cell Signatures, Broad
Molecular Signatures Database v7.4).
REZULTATI. U potpunosti razvijen Hashimotov tiroiditis, kada je bio prisutan, dominantan
je izvor transkripcijske varijabilnosti. Za zdravo tkivo štitnjače doprinos tehničkih kovarijata
nadmašuje utjecaj demografskih podataka (starost, spol i etnička pripadnost). Mlađa dob, smrt
na respiratoru, bolje očuvana RNK, kratka ishemija i ograničena autoliza povezani su s
izražajem detoksikacijskih i antioksidativnih, obrambenih gena iz NRF2 puta. Nasuprot tome,
starija dob, spora smrt, lošije očuvana RNK, produljena ishemija i viši stupanj autolize
povezani su s transkripcijskim biljezima hipoksijskog odgovora, ishemijske ozljede
vaskulature, NFκB signaliziranja i aktivacije perivaskularnih fibroblasta.
ZAKLJUČAK. Identificirani su različiti obrasci transkripcijske varijabilnosti koji proizlaze
iz širokog raspona demografskih i tehničkih kovarijata. Brojni geni koordinirano mijenjaju
izražaj, odražavajući rezidualnu transkripciju dugo nakon prestanka života. |
| Abstract (english) | TITLE. Biological and technical sources of variations in transcriptome sequencing of thyroid
tissue
AIM. To assess the effect of demographic, agonal and technical factors on whole-genome
transcriptional variability of thyroid tissue using bulk RNASeq analysis (bioinformatics
analysis).
STUDY DESIGN. This research is designed as an exploratory research (in silica analysis).
METHODS. The transcriptional variability of thyroid tissue was dissected by using RNAsequencing libraries from the Genotype-Tissue Expression project (v8 release). In total, 228
whole-genome expression profiles were analyzed in relation to their host demographics and
sample attributes. Variance partition analysis, hierarchical clustering and matrix factorization
were performed, followed by pathway enrichment profiling of highly expressed metagenes
(Gene Ontology, Hallmark, Kyoto Encyclopedia of Genes and Genomes, Cell Signatures,
Broad Molecular Signatures Database v7.4).
RESULTS. Full blown Hashimoto’s thyroiditis, when present, was the dominant source of
transcriptional variability. For healthy thyroid tissue, technical covariates outweighed the
contribution from demographic data (age, sex, and ethnicity). Younger age, death on the
ventilator, higher RNA integrity, short ischemia, and low autolysis were associated with an
array of detoxifying and antioxidant defence genes from the NFR2 pathway. In contrast, older
age, slow death, poor RNA integrity, long ischemia, and higher autolysis score were
associated with transcriptional markers of vascular injury, hypoxic response, NFκB
signalling, and fibroblast activation.
CONCLUSIONS. Different patterns of transcriptional variability stemming from a broad
range of demographic and technical covariates were identified. Many genes co-ordinately
changed their expression, reflecting an ongoing transcription long after cessation of life. |
