Fibroblast and myofibroblast activation in normal tissue repair and fibrosis

FS Younesi, AE Miller, TH Barker, FMV Rossi… - … Reviews Molecular Cell …, 2024 - nature.com
The term 'fibroblast'often serves as a catch-all for a diverse array of mesenchymal cells,
including perivascular cells, stromal progenitor cells and bona fide fibroblasts. Although …

Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Spatially resolved multiomics of human cardiac niches

K Kanemaru, J Cranley, D Muraro, AMA Miranda… - Nature, 2023 - nature.com
The function of a cell is defined by its intrinsic characteristics and its niche: the tissue
microenvironment in which it dwells. Here we combine single-cell and spatial …

The emerging landscape of spatial profiling technologies

JR Moffitt, E Lundberg, H Heyn - Nature Reviews Genetics, 2022 - nature.com
Improved scale, multiplexing and resolution are establishing spatial nucleic acid and protein
profiling methods as a major pillar for cellular atlas building of complex samples, from …

Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities

S Müller-Dott, E Tsirvouli, M Vazquez… - Nucleic Acids …, 2023 - academic.oup.com
Gene regulation plays a critical role in the cellular processes that underlie human health and
disease. The regulatory relationship between transcription factors (TFs), key regulators of …

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 …

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

Macrophages in cardiovascular diseases: molecular mechanisms and therapeutic targets

R Chen, H Zhang, B Tang, Y Luo, Y Yang… - Signal transduction and …, 2024 - nature.com
The immune response holds a pivotal role in cardiovascular disease development. As
multifunctional cells of the innate immune system, macrophages play an essential role in …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Immunology of human fibrosis

M Bhattacharya, P Ramachandran - Nature Immunology, 2023 - nature.com
Fibrosis, defined by the excess deposition of structural and matricellular proteins in the
extracellular space, underlies tissue dysfunction in multiple chronic diseases. Approved …