CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics

S **, MV Plikus, Q Nie - Nature Protocols, 2025 - nature.com
Recent advances in single-cell sequencing technologies offer an opportunity to explore cell–
cell communication in tissues systematically and with reduced bias. A key challenge is …

Cell–cell communication: new insights and clinical implications

J Su, Y Song, Z Zhu, X Huang, J Fan, J Qiao… - Signal Transduction and …, 2024 - nature.com
Multicellular organisms are composed of diverse cell types that must coordinate their
behaviors through communication. Cell–cell communication (CCC) is essential for growth …

The diversification of methods for studying cell–cell interactions and communication

E Armingol, HM Baghdassarian, NE Lewis - Nature Reviews Genetics, 2024 - nature.com
No cell lives in a vacuum, and the molecular interactions between cells define most
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …

An organotypic atlas of human vascular cells

SN Barnett, AM Cujba, L Yang, AR Maceiras, S Li… - Nature Medicine, 2024 - nature.com
The human vascular system, comprising endothelial (EC) and mural cells, covers a vast
surface area in the body, providing a critical interface between blood and tissue …

Inflammatory crosstalk impairs phagocytic receptors and aggravates atherosclerosis in clonal hematopoiesis in mice

W Liu, BD Hardaway, E Kim, J Pauli, JL Wettich… - The Journal of Clinical …, 2025 - jci.org
Clonal hematopoiesis (CH) increases inflammasome-linked atherosclerosis, but the
mechanisms by which CH mutant cells transmit inflammatory signals to nonmutant cells are …

Synovial tissue myeloid dendritic cell subsets exhibit distinct tissue-niche localization and function in health and rheumatoid arthritis

L MacDonald, A Elmesmari, D Somma, J Frew… - Immunity, 2024 - cell.com
Current rheumatoid arthritis (RA) treatments do not restore immune tolerance. Investigating
dendritic cell (DC) populations in human synovial tissue (ST) may reveal pathways to …

MetalinksDB: a flexible and contextualizable resource of metabolite-protein interactions

E Farr, D Dimitrov, C Schmidt, D Turei… - Briefings in …, 2024 - academic.oup.com
From the catalytic breakdown of nutrients to signaling, interactions between metabolites and
proteins play an essential role in cellular function. An important case is cell–cell …

[HTML][HTML] Mucosal single-cell profiling of Crohn's-like disease of the pouch reveals unique pathogenesis and therapeutic targets

S Cao, KM Nguyen, K Ma, X Du, X Liu, AU Antonova… - Gastroenterology, 2024 - Elsevier
Background & Aims The pathophysiology of Crohn's-like disease of the pouch (CDP) in
patients with a history of ulcerative colitis (UC) is unknown. We examined mucosal cells from …

Epstein-barr virus orchestrates spatial reorganization and immunomodulation within the classic hodgkin lymphoma tumor microenvironment

YY Yeo, H Qiu, Y Bai, B Zhu, Y Chang, J Yeung… - bioRxiv, 2024 - biorxiv.org
Classic Hodgkin Lymphoma (cHL) is a tumor composed of rare malignant Hodgkin and
Reed-Sternberg (HRS) cells nested within a T-cell rich inflammatory immune infiltrate. cHL is …

[HTML][HTML] Comprehensive analysis of heterogeneity and cell-cell interactions in Crohn's disease reveals novel location-specific insights

J Feng, LN He, R Yao, Y Qiao, T Yang, Z Cui… - Journal of Advanced …, 2024 - Elsevier
Abstract Introduction In Crohn's disease (CD), lesions are mainly distributed in a segmental
manner, with the primary sites of involvement being the ileum and colon. Heterogeneity in …