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Exploration of Pharmacogenomic Biomarkers in Chronic Immune Diseases Using Single-Cell RNA Sequencing
dc.contributor | Morić, Ivana | |
dc.contributor | Đorđević, Valentina | |
dc.creator | Gorenjak, Mario | |
dc.creator | Goričan, Larisa | |
dc.creator | Gole, Boris | |
dc.creator | Prosenc, Uršula | |
dc.creator | Melén, Erik | |
dc.creator | Kabesch, Michael | |
dc.creator | Maitland-van der Zee, Anke H. | |
dc.creator | Reinartz, Susanne | |
dc.creator | J.H. Vijverberg, Susanne | |
dc.creator | Potočnik, Uroš | |
dc.creator | PERMEABLE consortium | |
dc.date.accessioned | 2023-08-02T12:23:47Z | |
dc.date.available | 2023-08-02T12:23:47Z | |
dc.date.issued | 2023 | |
dc.identifier.isbn | 978-86-82679-14-1 | |
dc.identifier.uri | https://belbi.bg.ac.rs/ | |
dc.identifier.uri | https://imagine.imgge.bg.ac.rs/handle/123456789/1996 | |
dc.description.abstract | Biological therapies have revolutionized management of the severe cases of Chronic Immune Diseases refractory to the standard therapies. However, many patients do not respond to the selected biological therapy, loose response over time, or develop adverse effects. A personalized approach to treatment of these patients, based on reliable biomarkers is thus clearly needed. Non-invasive approaches, such as use of the peripheral blood immune cells, are favored for novel biomarker discovery. However, the attention has shifted away from the bulk immune cells and towards specific immune cell sub-populations. Thus, the single-cell RNA sequencing (scRNA-seq) can prove highly valuable. By simultaneously capturing and profiling all the cells in a sample, scRNA-seq allows the analysis of cellular heterogeneity and gene expression in all immune cell sub-populations, targeted or adversely affected by the biological treatment. In our ongoing research, scRNA-seq was utilized to analyze samples from Inflammatory Bowel Disease and Childhood Asthma patients with varied response to the biological therapy. Confounding effects of disease conditions and (biological) therapies on marker genes were eliminated using computational integration in order to identify conserved marker genes across all states. It turned out, that a reliable identification of the different immune cell sub-populations in this setting is quite challenging due to subjective cell-landscape clustering resolution. Several resolutions and automated annotation approaches were subsequently tested and validated.A reference-based approach (Seurat-Azimuth) combined with manual cluster validation proved superior. Alas, manual cluster validation is time consuming. Annotation validation is important, especially to provide additional insights into unidentified clusters, which are essential for the identification of predictive biomarkers for personalized therapies in the vast heterogeneity of immune cell landscapes residing behind pathophysiology of chronic immune diseases. | sr |
dc.language.iso | en | sr |
dc.publisher | Belgrade : Institute of molecular genetics and genetic engineering | sr |
dc.relation | This research was funded by the Slovenian Research Agency- Research core funding P3-0427; Research grant J3-9258; the Labena company with Grant challenge program and the PERMEABLE consortium. | sr |
dc.relation | The PERMEABLE consortium is supported by the ZonMW (project number: 456008004), the Swedish Research Council (proj.nr. 2018-05619), the Ministry of Education, Science and Sport of the Republic of Slovenia (proj.nr. C3330-19-252012), and the German Ministry of Education and Research (BMBF) (proj.nr. FKZ01KU1909A), under the frame of the ERA PerMed JTC 2018 Call. | sr |
dc.rights | openAccess | sr |
dc.source | 4th Belgrade Bioinformatics Conference | sr |
dc.subject | precision medicine | sr |
dc.subject | chronic immune diseases | sr |
dc.subject | biological therapy | sr |
dc.subject | Single-Cell RNA Sequencing | sr |
dc.subject | dentification of cell sub-populations | sr |
dc.title | Exploration of Pharmacogenomic Biomarkers in Chronic Immune Diseases Using Single-Cell RNA Sequencing | sr |
dc.type | conferenceObject | sr |
dc.rights.license | ARR | sr |
dc.rights.holder | © 2023 Institute of Molecular Genetics and Genetic Engineering, University of Belgrade | sr |
dc.citation.epage | 56 | |
dc.citation.spage | 55 | |
dc.citation.volume | 4 | |
dc.description.other | Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 2023 | sr |
dc.identifier.fulltext | https://imagine.imgge.bg.ac.rs/bitstream/id/305690/BELBI-Abstracts-final-07072023_1-15,71-72,129.pdf | |
dc.identifier.rcub | https://hdl.handle.net/21.15107/rcub_imagine_1996 | |
dc.type.version | publishedVersion | sr |
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