Browsing by Subject "gene set enrichment analysis"

Now showing 1 - 2 of 2
  • No Thumbnail Available
    Item
    Shared Biological Pathways and Processes in Patients with Intellectual Disability: A Multicenter Study
    (Georg Thieme Verlag, 2022) Günay Ç.; Aykol D.; Özsoy Ö.; Sönmezler E.; Hanci Y.S.; Kara B.; Akkoyunlu Sünnetçi D.; Cine N.; Deniz A.; Özer T.; Ölçülü C.B.; Yilmaz Ö.; Kanmaz S.; Yilmaz S.; Tekgül H.; Yildiz N.; Acar Arslan E.; Cansu A.; Olgaç Dündar N.; Kusgoz F.; Didinmez E.; Gençpinar P.; Aksu Uzunhan T.; Ertürk B.; Gezdirici A.; Ayaz A.; Ölmez A.; Ayanoǧlu M.; Tosun A.; Topçu Y.; Kiliç B.; Aydin K.; Çaǧlar E.; Ersoy Kosvali Ö.; Okuyaz Ç.; Besen Ş.; Tekin Orgun L.; Erol İ.; Yüksel D.; Sezer A.; Atasoy E.; Toprak Ü.; Güngör S.; Ozgor B.; Karadaǧ M.; Dilber C.; Şahinoǧlu B.; Uyur Yalçin E.; Eldes Hacifazlioglu N.; Yaramiś A.; Edem P.; Gezici Tekin H.; Yilmaz Ü.; Ünalp A.; Turay S.; Biçer D.; Gül Mert G.; Dokurel Çetin İ.; Kirik S.; Öztürk G.; Karal Y.; Sanri A.; Aksoy A.; Polat M.; Özgün N.; Soydemir D.; Sarikaya Uzan G.; Ülker Üstebay D.; Gök A.; Yeśilmen M.C.; Yiś U.; Karakülah G.; Bursali A.; Oktay Y.; Hiz Kurul S.
    Background  Although the underlying genetic causes of intellectual disability (ID) continue to be rapidly identified, the biological pathways and processes that could be targets for a potential molecular therapy are not yet known. This study aimed to identify ID-related shared pathways and processes utilizing enrichment analyses. Methods  In this multicenter study, causative genes of patients with ID were used as input for Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes enrichment analysis. Results  Genetic test results of 720 patients from 27 centers were obtained. Patients with chromosomal deletion/duplication, non-ID genes, novel genes, and results with changes in more than one gene were excluded. A total of 558 patients with 341 different causative genes were included in the study. Pathway-based enrichment analysis of the ID-related genes via ClusterProfiler revealed 18 shared pathways, with lysine degradation and nicotine addiction being the most common. The most common of the 25 overrepresented DO terms was ID. The most frequently overrepresented GO biological process, cellular component, and molecular function terms were regulation of membrane potential, ion channel complex, and voltage-gated ion channel activity/voltage-gated channel activity, respectively. Conclusion  Lysine degradation, nicotine addiction, and thyroid hormone signaling pathways are well-suited to be research areas for the discovery of new targeted therapies in ID patients. © 2022 Hippokrates Verlag GmbH. All rights reserved.
  • No Thumbnail Available
    Item
    Transcriptomic analysis of plasma exosomes provides molecular information of response to cabazitaxel treatment in men with metastatic castration-resistant prostate cancer
    (John Wiley and Sons Inc, 2023) Vardaki I.; Özcan S.S.; Fonseca P.; Lin S.-H.; Logothetis C.J.; Yachnin J.; Ullen A.; Panaretakis T.
    Background: Prostate cancer is the second most common cancer type and the second most common cancer-related cause of death in men. Cabazitaxel, a next-generation taxane, shows favorable toxicity profile and is effective in docetaxel-resistant tumors. Despite initial responses, in most cases, prostate cancer patients acquire resistance to cabazitaxel. There is a need to identify molecular markers that can monitor and predict treatment response. Methods: We performed transcriptional exosome profiling (Human Transcriptome Array-HTA 2.0) from the plasma of 19 patients with castration-resistant prostate cancer at baseline and in patients after one cycle of cabazitaxel (C1). The patients were stratified in two groups (responders and nonresponders) according to their clinical response to cabazitaxel. Gene set enrichment analysis and ingenuity pathway analysis platforms were used for gene and pathway analysis. Results: We detected molecular differences in the exosomes from two groups of patients (nonresponders vs. responders) at baseline in pathways related to prostate cancer, oncogenic signaling, cytoskeleton, and immune system. In nonresponders, we found enrichment of cytoskeleton related gene (Stathmin-1 and ITSN1) that have been associated with resistance to cabazitaxel. Monitoring of exosomal transcripts after the first cycle of treatment revealed changes in pathways associated with response to treatment. Conclusions: Sequential transcriptional profiling of plasma-derived exosomes reveals differential expression of genes that may reflect resistance to cabazitaxel treatment and therapy response. © 2023 Wiley Periodicals LLC.