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

S Jin, MV Plikus, Q Nie - Nature Protocols, 2024 - 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 …

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 …

LIANA+ provides an all-in-one framework for cell–cell communication inference

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez-Mier… - Nature Cell …, 2024 - nature.com
The growing availability of single-cell and spatially resolved transcriptomics has led to the
development of many approaches to infer cell–cell communication, each capturing only a …

Bispecific dendritic-T cell engager potentiates anti-tumor immunity

YS Itai, O Barboy, R Salomon, A Bercovich, K Xie… - Cell, 2024 - cell.com
Immune checkpoint inhibition treatment using aPD-1 monoclonal antibodies is a promising
cancer immunotherapy approach. However, its effect on tumor immunity is narrow, as most …

Inferring pattern-driving intercellular flows from single-cell and spatial transcriptomics

AA Almet, YC Tsai, M Watanabe, Q Nie - Nature Methods, 2024 - nature.com
From single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), one can
extract high-dimensional gene expression patterns that can be described by intercellular …

Adipose-tissue regulatory T cells are a consortium of subtypes that evolves with age and diet

AR Muñoz-Rojas, G Wang… - Proceedings of the …, 2024 - National Acad Sciences
Foxp3+ CD4+ regulatory T (Treg) cells found within tissues regulate local immunity,
inflammation, and homeostasis. Tregs in epididymal visceral adipose tissue (eVAT) are …

A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease

T Thomas, M Friedrich, C Rich-Griffin, M Pohin… - Nature …, 2024 - nature.com
Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular
understanding of treatment response. We describe a therapeutic atlas for Crohn's disease …

Integrating single-cell multi-omics and prior biological knowledge for a functional characterization of the immune system

PSL Schäfer, D Dimitrov, EJ Villablanca… - Nature …, 2024 - nature.com
The immune system comprises diverse specialized cell types that cooperate to defend the
host against a wide range of pathogenic threats. Recent advancements in single-cell and …

Polyclonal-to-monoclonal transition in colorectal precancerous evolution

Z Lu, S Mo, D Xie, X Zhai, S Deng, K Zhou, K Wang… - Nature, 2024 - nature.com
Unravelling the origin and evolution of precancerous lesions is crucial for effectively
preventing malignant transformation, yet our current knowledge remains limited 1, 2, 3. Here …

[HTML][HTML] CD4+ T cells re-wire granuloma cellularity and regulatory networks to promote immunomodulation following Mtb reinfection

JD Bromley, SKC Ganchua, SK Nyquist, P Maiello… - Immunity, 2024 - cell.com
Immunological priming—in the context of either prior infection or vaccination—elicits
protective responses against subsequent Mycobacterium tuberculosis (Mtb) infection …