Transcriptional Analysis Reveals That the FHL1/JAK-STAT Pathway is Involved in Acute Cartilage Injury in Mice DOI Creative Commons
Jian Lu, Zhenhua Shi, Lindan Geng

et al.

Cartilage, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Objective This study aimed to identify genes and signaling pathways associated with acute cartilage injury using RNA sequencing (RNA-seq). Methods Knee joint samples were collected from normal mice 2 models of (non-invasive groove models) within an 8-hour time limit. RNA-seq revealed differential gene expression between the controls, subsequent validation real-time quantitative polymerase chain reaction (RT-qPCR) for 9 representative genes. Results Compared non-invasive model showed 36 differentially expressed (DEGs) (13 up-regulated, 23 down-regulated), Gm14648 Gm35438 showing most significant upregulation downregulation, respectively. The exhibited 255 DEGs (222 33 down-regulated). Six overlapping identified models, including up-regulated ( Igfn1, Muc6, Hmox1 ) down-regulated Pthlh, Cyp1a1, Gm13490 ), validated by RT-qPCR. Gene ontology (GO) analysis highlighted involvement in environmental information processing organ system function, while Kyoto Encyclopedia Genes Genomes (KEGG) implicated JAK-STAT pathway. RT-qPCR immunohistochemistry confirmed downregulation Fhl1 model, supported Western blotting p-JAK2/t-JAK2 levels. Conclusions identifies injury, suggesting potential therapeutic targets. role protection via pathway warrants further investigation research.

Language: Английский

Application of Deep Learning for Single Cell Multi-Omics: A State-of-the-Art Review DOI
Shahid Ahmad Wani,

Sumeer Ahmad Khan,

S. M. K. Quadri

et al.

Archives of Computational Methods in Engineering, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

0
Keratin: A potential driver of tumor metastasis DOI
Yu‐Chuan Li,

Yiming Sun,

Kun Yu

et al.

International Journal of Biological Macromolecules, Journal Year: 2025, Volume and Issue: unknown, P. 141752 - 141752

Published: March 1, 2025

Language: Английский

Citations

0
scHeteroNet: A Heterophily‐Aware Graph Neural Network for Accurate Cell Type Annotation and Novel Cell Detection DOI Creative Commons
Jiacheng Liu,

Xingyu Fan,

Chunbin Gu

et al.

Advanced Science, Journal Year: 2025, Volume and Issue: unknown

Published: March 5, 2025

Single-cell RNA sequencing (scRNA-seq) has unveiled extensive cellular heterogeneity, yet precise cell type annotation and the identification of novel populations remain significant challenges. scHeteroNet, a graph neural network framework specifically designed to leverage heterophily in scRNA-seq data, is presented. Unlike traditional methods that assume homophily, scHeteroNet captures complex cell-cell interactions by integrating information from both immediate extended neighborhoods, resulting highly accurate representations. Additionally, incorporates an innovative novelty propagation mechanism robustly detects previously uncharacterized types. Comprehensive evaluations across diverse datasets demonstrate consistently outperforms state-of-the-art approaches classification detection. This heterophily-aware approach enhances ability uncover diversity, providing deeper insights into biological systems advancing field single-cell analysis.

Language: Английский

Citations

0
Investigating ferroptosis-related genes NFE2L2 in neutrophils for ankylosing spondylitis: therapeutic potential of cassia twigs DOI Creative Commons
Tianyou Chen, Jichong Zhu, Xinli Zhan

et al.

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: March 10, 2025

We determined the relationship between ferroptosis and immune cells in ankylosing spondylitis role of Chinese herbal medicine Cassia twigs treating spondylitis. analyzed clinical data on spondylitis, transcriptome data, single-cell sequencing genes related to twigs. Clinical variables AS were selected through logistic regression analysis combined with machine learning. GSEA enrichment performed ferroptosis, drug-related genes, identify key drug targets AS, as well as, cells. Then, cell subtypes analyzed. Finally, interconnections intercellular communication. Five variables, including neutrophils, screened for analysis. The AUC experimental group was 0.859 that validation 0.807. Ferroptosis gene NFE2L2 identified final target AS; it upregulated downregulated control by immunohistochemical verification, both which statistically significant (P < 0.001). Neutrophils divided into two subgroups: high expression low NFE2L2. Through molecular docking, found effectively act important AS. herb can treat acting protein structure

Language: Английский

Citations

0
Transcriptional Analysis Reveals That the FHL1/JAK-STAT Pathway is Involved in Acute Cartilage Injury in Mice DOI Creative Commons
Jian Lu, Zhenhua Shi, Lindan Geng

et al.

Cartilage, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Objective This study aimed to identify genes and signaling pathways associated with acute cartilage injury using RNA sequencing (RNA-seq). Methods Knee joint samples were collected from normal mice 2 models of (non-invasive groove models) within an 8-hour time limit. RNA-seq revealed differential gene expression between the controls, subsequent validation real-time quantitative polymerase chain reaction (RT-qPCR) for 9 representative genes. Results Compared non-invasive model showed 36 differentially expressed (DEGs) (13 up-regulated, 23 down-regulated), Gm14648 Gm35438 showing most significant upregulation downregulation, respectively. The exhibited 255 DEGs (222 33 down-regulated). Six overlapping identified models, including up-regulated ( Igfn1, Muc6, Hmox1 ) down-regulated Pthlh, Cyp1a1, Gm13490 ), validated by RT-qPCR. Gene ontology (GO) analysis highlighted involvement in environmental information processing organ system function, while Kyoto Encyclopedia Genes Genomes (KEGG) implicated JAK-STAT pathway. RT-qPCR immunohistochemistry confirmed downregulation Fhl1 model, supported Western blotting p-JAK2/t-JAK2 levels. Conclusions identifies injury, suggesting potential therapeutic targets. role protection via pathway warrants further investigation research.

Language: Английский

Citations

0