Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z **e, X Luo, L Zhan, W Tang… - Nature protocols, 2024‏ - nature.com
With the advent of multiomics, software capable of multidimensional enrichment analysis
has become increasingly crucial for uncovering gene set variations in biological processes …

SOX17 enables immune evasion of early colorectal adenomas and cancers

N Goto, PMK Westcott, S Goto, S Imada, MS Taylor… - Nature, 2024‏ - nature.com
A hallmark of cancer is the avoidance of immune destruction. This process has been
primarily investigated in locally advanced or metastatic cancer,–; however, much less is …

Cell-type-specific CAG repeat expansions and toxicity of mutant Huntingtin in human striatum and cerebellum

K Mätlik, M Baffuto, L Kus, AL Deshmukh, DA Davis… - Nature …, 2024‏ - nature.com
Brain region-specific degeneration and somatic expansions of the mutant Huntingtin (mHTT)
CAG tract are key features of Huntington's disease (HD). However, the relationships among …

Intratumoral immune triads are required for immunotherapy-mediated elimination of solid tumors

G Espinosa-Carrasco, E Chiu, A Scrivo, P Zumbo… - Cancer Cell, 2024‏ - cell.com
Tumor-specific CD8+ T cells are frequently dysfunctional and unable to halt tumor growth.
We investigated whether tumor-specific CD4+ T cells can be enlisted to overcome CD8+ T …

Histone lactylation couples cellular metabolism with developmental gene regulatory networks

F Merkuri, M Rothstein, M Simoes-Costa - Nature communications, 2024‏ - nature.com
Embryonic cells exhibit diverse metabolic states. Recent studies have demonstrated that
metabolic reprogramming drives changes in cell identity by affecting gene expression …

Zygotic genome activation by the totipotency pioneer factor Nr5a2

J Gassler, W Kobayashi, I Gáspár, S Ruangroengkulrith… - Science, 2022‏ - science.org
Life begins with a switch in genetic control from the maternal to the embryonic genome
during zygotic genome activation (ZGA). Despite its importance, the essential regulators of …

[HTML][HTML] Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems

F Zenk, JS Fleck, SMJ Jansen, B Kashanian… - Nature …, 2024‏ - nature.com
Cell fate progression of pluripotent progenitors is strictly regulated, resulting in high human
cell diversity. Epigenetic modifications also orchestrate cell fate restriction. Unveiling the …

Selective vulnerability of layer 5a corticostriatal neurons in Huntington's disease

C Pressl, K Mätlik, L Kus, P Darnell, JD Luo, MR Paul… - Neuron, 2024‏ - cell.com
The properties of the cell types that are selectively vulnerable in Huntington's disease (HD)
cortex, the nature of somatic CAG expansions of mHTT in these cells, and their importance …

[HTML][HTML] Thirteen years of clusterProfiler

G Yu - The Innovation, 2024‏ - cell.com
When the human genome was fully sequenced in 2003, research focus shifted to functional
genomics, particularly the spatiotemporal expression of genes, which is crucial for …

Chromatin context-dependent regulation and epigenetic manipulation of prime editing

X Li, W Chen, BK Martin, D Calderon, C Lee, J Choi… - Cell, 2024‏ - cell.com
We set out to exhaustively characterize the impact of the cis-chromatin environment on
prime editing, a precise genome engineering tool. Using a highly sensitive method for …