Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

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 …

Hallmarks of transcriptional intratumour heterogeneity across a thousand tumours

A Gavish, M Tyler, AC Greenwald, R Hoefflin, D Simkin… - Nature, 2023 - nature.com
Each tumour contains diverse cellular states that underlie intratumour heterogeneity (ITH), a
central challenge of cancer therapeutics. Dozens of recent studies have begun to describe …

hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

S Morabito, F Reese, N Rahimzadeh, E Miyoshi… - Cell reports …, 2023 - cell.com
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …

A pan-cancer single-cell panorama of human natural killer cells

F Tang, J Li, L Qi, D Liu, Y Bo, S Qin, Y Miao, K Yu… - Cell, 2023 - cell.com
Natural killer (NK) cells play indispensable roles in innate immune responses against tumor
progression. To depict their phenotypic and functional diversities in the tumor …

Pan-cancer single-cell analysis reveals the heterogeneity and plasticity of cancer-associated fibroblasts in the tumor microenvironment

H Luo, X **a, LB Huang, H An, M Cao, GD Kim… - Nature …, 2022 - nature.com
Cancer-associated fibroblasts (CAFs) are the predominant components of the tumor
microenvironment (TME) and influence cancer hallmarks, but without systematic …

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 …

Targeting M2-like tumor-associated macrophages is a potential therapeutic approach to overcome antitumor drug resistance

S Wang, J Wang, Z Chen, J Luo, W Guo, L Sun… - NPJ precision …, 2024 - nature.com
Tumor drug resistance emerges from the interaction of two critical factors: tumor cellular
heterogeneity and the immunosuppressive nature of the tumor microenvironment (TME) …