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 …

Activated fibroblasts in cancer: Perspectives and challenges

G Caligiuri, DA Tuveson - Cancer cell, 2023 - cell.com
Activated fibroblasts in tumors, or cancer-associated fibroblasts (CAFs), have become a
popular research area over the past decade. As important players in many aspects of tumor …

Androgen receptor activity in T cells limits checkpoint blockade efficacy

X Guan, F Polesso, C Wang, A Sehrawat, RM Hawkins… - Nature, 2022 - nature.com
Immune checkpoint blockade has revolutionized the field of oncology, inducing durable anti-
tumour immunity in solid tumours. In patients with advanced prostate cancer …

[HTML][HTML] Spatial multiomics map of trophoblast development in early pregnancy

A Arutyunyan, K Roberts, K Troulé, FCK Wong… - Nature, 2023 - nature.com
The relationship between the human placenta—the extraembryonic organ made by the
fetus, and the decidua—the mucosal layer of the uterus, is essential to nurture and protect …

A molecular single-cell lung atlas of lethal COVID-19

JC Melms, J Biermann, H Huang, Y Wang, A Nair… - Nature, 2021 - nature.com
Respiratory failure is the leading cause of death in patients with severe SARS-CoV-2
infection,, but the host response at the lung tissue level is poorly understood. Here we …

Evolution of enhanced innate immune evasion by SARS-CoV-2

LG Thorne, M Bouhaddou, AK Reuschl… - Nature, 2022 - nature.com
The emergence of SARS-CoV-2 variants of concern suggests viral adaptation to enhance
human-to-human transmission,. Although much effort has focused on the characterization of …

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

D Sun, X Guan, AE Moran, LY Wu, DZ Qian… - Nature …, 2022 - nature.com
Single-cell RNA sequencing (scRNA-seq) distinguishes cell types, states and lineages
within the context of heterogeneous tissues. However, current single-cell data cannot …

Decoding myofibroblast origins in human kidney fibrosis

C Kuppe, MM Ibrahim, J Kranz, X Zhang, S Ziegler… - Nature, 2021 - nature.com
Kidney fibrosis is the hallmark of chronic kidney disease progression; however, at present
no antifibrotic therapies exist,–. The origin, functional heterogeneity and regulation of scar …

[HTML][HTML] SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

J Jansen, KC Reimer, JS Nagai, FS Varghese… - Cell stem cell, 2022 - cell.com
Kidney failure is frequently observed during and after COVID-19, but it remains elusive
whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects …

Single-cell genomics reveals a novel cell state during smooth muscle cell phenotypic switching and potential therapeutic targets for atherosclerosis in mouse and …

H Pan, C Xue, BJ Auerbach, J Fan, AC Bashore, J Cui… - Circulation, 2020 - Am Heart Assoc
Background: Smooth muscle cells (SMCs) play significant roles in atherosclerosis via
phenotypic switching, a pathological process in which SMC dedifferentiation, migration, and …