Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
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Detail(s)
Original language | English |
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Pages (from-to) | 1329-1345 |
Journal / Publication | Molecular Systems Biology |
Volume | 20 |
Issue number | 12 |
Online published | 4 Nov 2024 |
Publication status | Published - Dec 2024 |
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DOI | DOI |
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Attachment(s) | Documents
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Link to Scopus | https://www.scopus.com/record/display.uri?eid=2-s2.0-85208199221&origin=recordpage |
Permanent Link | https://scholars.cityu.edu.hk/en/publications/publication(643816ba-586a-4808-8552-6daa25dc8841).html |
Abstract
T cell receptors (TCR) and gene expression provide two complementary and essential aspects in T cell understanding, yet their diversity presents challenges in integrative analysis. We introduce TCRclub, a novel method integrating single-cell RNA sequencing data and single-cell TCR sequencing data using local harmony to identify functionally similar T cell groups, termed ‘clubs’. We applied TCRclub to 298,106 T cells across seven datasets encompassing various diseases. First, TCRclub outperforms the state-of-the-art methods in clustering T cells on a dataset with over 400 verified peptide-major histocompatibility complex categories. Second, TCRclub reveals a transition from activated to exhausted T cells in cholangiocarcinoma patients. Third, TCRclub discovered the pathways that could intervene in response to anti-PD-1 therapy for patients with basal cell carcinoma by analyzing the pre-treatment and post-treatment samples. Furthermore, TCRclub unveiled different T-cell responses and gene patterns at different severity levels in patients with COVID-19. Hence, TCRclub aids in developing more effective immunotherapeutic strategies for cancer and infectious diseases. © The Author(s) 2024.
Research Area(s)
- Integration, Local Harmony, Single-Cell Analysis, T-Cell Clustering
Citation Format(s)
Identifying T-cell clubs by embracing the local harmony between TCR and gene expressions. / Zou, Yiping; Luo, Jiaqi; Chen, Lingxi et al.
In: Molecular Systems Biology, Vol. 20, No. 12, 12.2024, p. 1329-1345.
In: Molecular Systems Biology, Vol. 20, No. 12, 12.2024, p. 1329-1345.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review
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