Using clusterProfiler to characterize multiomics data

S Xu, E Hu, Y Cai, Z Xie, 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 …

EGFR-activated myofibroblasts promote metastasis of pancreatic cancer

G Mucciolo, JA Henríquez, M Jihad, SP Teles… - Cancer Cell, 2024 - cell.com
Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis. Cancer-associated
fibroblasts (CAFs) are recognized potential therapeutic targets, but poor understanding of …

Gasdermin D-mediated metabolic crosstalk promotes tissue repair

Z Chi, S Chen, D Yang, W Cui, Y Lu, Z Wang, M Li… - Nature, 2024 - nature.com
The establishment of an early pro-regenerative niche is crucial for tissue regeneration,.
Gasdermin D (GSDMD)-dependent pyroptosis accounts for the release of inflammatory …

Multiplexed, image-based pooled screens in primary cells and tissues with PerturbView

T Kudo, AM Meireles, R Moncada, Y Chen, P Wu… - Nature …, 2024 - nature.com
Optical pooled screening (OPS) is a scalable method for linking image-based phenotypes
with cellular perturbations. However, it has thus far been restricted to relatively low-plex …

Elucidating the role of tumor-associated ALOX5+ mast cells with transformative function in cervical cancer progression via single-cell RNA sequencing

F Zhao, J Hong, G Zhou, T Huang, Z Lin… - Frontiers in …, 2024 - frontiersin.org
Background Cervical cancer (CC) is the fourth most common malignancy among women
globally and serves as the main cause of cancer-related deaths among women in …

Corticosteroids impair epithelial regeneration in immune-mediated intestinal damage

V Arnhold, WY Chang, SA Jansen… - The Journal of …, 2024 - Am Soc Clin Investig
Corticosteroid treatment (CST) failure is associated with poor outcomes for patients with
gastrointestinal (GI) graft-versus-host disease (GVHD). CST is intended to target the immune …

Single-cell tumor heterogeneity landscape of hepatocellular carcinoma: unraveling the pro-metastatic subtype and its interaction loop with fibroblasts

DZ Guo, X Zhang, SQ Zhang, SY Zhang, XY Zhang… - Molecular Cancer, 2024 - Springer
Background Tumor heterogeneity presents a formidable challenge in understanding the
mechanisms driving tumor progression and metastasis. The heterogeneity of hepatocellular …

Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in heart failure with preserved ejection fraction

JD Lanzer, LM Wienecke, RO Ramirez Flores… - Basic Research in …, 2024 - Springer
Inflammation, fibrosis and metabolic stress critically promote heart failure with preserved
ejection fraction (HFpEF). Exposure to high-fat diet and nitric oxide synthase inhibitor N [w] …

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

MD Magnitov, M Maresca, NA Saiz, H Teunissen… - Molecular Cell, 2024 - cell.com
Gene expression is orchestrated by transcription factors, which function within the context of
a three-dimensional genome. Zinc-finger protein 143 (ZNF143/ZFP143) is a transcription …

Biologically interpretable multi-task deep learning pipeline predicts molecular alterations, grade, and prognosis in glioma patients

X Wu, S Zhang, Z Zhang, Z He, Z Xu, W Wang… - NPJ Precision …, 2024 - nature.com
Deep learning models have been developed for various predictions in glioma; yet, they were
constrained by manual segmentation, task-specific design, or a lack of biological …