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 …

Targeting transcription factors in cancer—from undruggable to reality

JH Bushweller - Nature Reviews Cancer, 2019 - nature.com
Mutated or dysregulated transcription factors represent a unique class of drug targets that
mediate aberrant gene expression, including blockade of differentiation and cell death gene …

cGAS–STING drives the IL-6-dependent survival of chromosomally instable cancers

C Hong, M Schubert, AE Tijhuis, M Requesens… - Nature, 2022 - nature.com
Chromosomal instability (CIN) drives cancer cell evolution, metastasis and therapy
resistance, and is associated with poor prognosis. CIN leads to micronuclei that release …

[HTML][HTML] Effective drug combinations in breast, colon and pancreatic cancer cells

P Jaaks, EA Coker, DJ Vis, O Edwards, EF Carpenter… - Nature, 2022 - nature.com
Combinations of anti-cancer drugs can overcome resistance and provide new treatments,.
The number of possible drug combinations vastly exceeds what could be tested clinically …

[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 …

[HTML][HTML] Pan-cancer proteomic map of 949 human cell lines

E Gonçalves, RC Poulos, Z Cai, S Barthorpe… - Cancer Cell, 2022 - cell.com
The proteome provides unique insights into disease biology beyond the genome and
transcriptome. A lack of large proteomic datasets has restricted the identification of new …

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

FM Behan, F Iorio, G Picco, E Gonçalves, CM Beaver… - Nature, 2019 - nature.com
Functional genomics approaches can overcome limitations—such as the lack of
identification of robust targets and poor clinical efficacy—that hamper cancer drug …

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

AB Keenan, D Torre, A Lachmann… - Nucleic acids …, 2019 - academic.oup.com
Identifying the transcription factors (TFs) responsible for observed changes in gene
expression is an important step in understanding gene regulatory networks. ChIP-X …

Benchmark and integration of resources for the estimation of human transcription factor activities

L Garcia-Alonso, CH Holland, MM Ibrahim… - Genome …, 2019 - genome.cshlp.org
The prediction of transcription factor (TF) activities from the gene expression of their targets
(ie, TF regulon) is becoming a widely used approach to characterize the functional status of …

Analysis of single-cell RNA-seq identifies cell-cell communication associated with tumor characteristics

MP Kumar, J Du, G Lagoudas, Y Jiao, A Sawyer… - Cell reports, 2018 - cell.com
Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor
interactions. Targeting ligand-receptor interactions (for instance, with immune checkpoint …