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 …

Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease

Y Zhang, JP Thomas, T Korcsmaros, L Gul - Cell Reports Medicine, 2024 - cell.com
The gut microbiome is crucial for nutrient metabolism, immune regulation, and intestinal
homeostasis with changes in its composition linked to complex diseases like inflammatory …

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 …

Cell type map** reveals tissue niches and interactions in subcortical multiple sclerosis lesions

C Lerma-Martin, P Badia-i-Mompel… - Nature …, 2024 - nature.com
Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system.
Inflammation is gradually compartmentalized and restricted to specific tissue niches such as …

Transcriptomic signatures of human single skeletal muscle fibers in response to high-intensity interval exercise

T Van der Stede, A Van de Loock… - … of Physiology-Cell …, 2024 - journals.physiology.org
The heterogeneous fiber type composition of skeletal muscle makes it challenging to
decipher the molecular signaling events driving the health-and performance benefits of …

LIANA+: an all-in-one cell-cell communication framework

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez Mier… - BioRxiv, 2023 - biorxiv.org
The growing availability of single-cell and spatially-resolved transcriptomics has led to the
rapidly growing popularity of methods to infer cell-cell communication. Many approaches …

Comparative network-based analysis of toll-like receptor agonist, L-pampo signaling pathways in immune and cancer cells

S Park, G Kim, A Choi, S Kim, JS Yum, E Chun… - Scientific Reports, 2024 - nature.com
Toll-like receptors (TLRs) are critical components to stimulate immune responses against
various infections. Recently, TLR agonists have emerged as a promising way to activate anti …

Disease activity drives divergent epigenetic and transcriptomic reprogramming of monocyte subpopulations in systemic lupus erythematosus

AG Ferreté-Bonastre, M Martínez-Gallo… - Annals of the Rheumatic …, 2024 - Elsevier
Objectives Systemic lupus erythematosus (SLE) is characterised by systemic inflammation
involving various immune cell types. Monocytes, pivotal in promoting and regulating …

[HTML][HTML] Chemotherapy induces myeloid-driven spatially confined T cell exhaustion in ovarian cancer

IM Launonen, I Niemiec, M Hincapié-Otero, EP Erkan… - Cancer Cell, 2024 - cell.com
Anti-tumor immunity is crucial for high-grade serous ovarian cancer (HGSC) prognosis, yet
its adaptation upon standard chemotherapy remains poorly understood. Here, we conduct …

Impaired development of memory B cells and antibody responses in humans and mice deficient in PD-1 signaling

M Ogishi, K Kitaoka, KL Good-Jacobson, D Rinchai… - Immunity, 2024 - cell.com
T follicular helper (Tfh) cells abundantly express the immunoreceptor programmed cell
death protein 1 (PD-1), and the impact of PD-1 deficiency on antibody (Ab)-mediated …