Comprehensive analysis of autoimmune-related genes in amyotrophic lateral sclerosis from the perspective of 3P medicine

Li, Shifu; Zhang, Qian; Li, Jian; Weng, Ling

doi:10.1007/s13167-022-00299-w

Cited by 3 publications

(3 citation statements)

References 61 publications

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“…The Seurat package's PercentageFeatureSet function determined the expression of mitochondrial genes. Cells with mitochondrial gene expression levels above 5% were eliminated to remove those with low activity 28 . Cell cluster annotation followed previous research 29 .…”

Section: Methodsmentioning

confidence: 99%

“…Cells with mitochondrial gene expression levels above 5% were eliminated to remove those with low activity. 28 Cell cluster annotation followed previous research. 29 Subsequently, gene expression levels of key genes in each cell were quantified, and the expression differences of these genes between ITP and control groups in each cell cluster were compared.…”

Section: Scrna-seq Analysismentioning

confidence: 99%

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Comprehensive analysis and prediction model of mitophagy and ferroptosis in primary immune thrombocytopenia

Mo,

Liu,

Zhang

et al. 2024

Br J Haematol

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SummaryPrimary immune thrombocytopenia (ITP) is linked to specific pathogenic mechanisms, yet its relationship with mitophagy and ferroptosis is poorly understood. This study aimed to identify new biomarkers and explore the role of mitophagy and ferroptosis in ITP pathogenesis. Techniques such as differential analysis, Mfuzz expression pattern clustering, machine learning, gene set enrichment analysis, single‐cell RNA sequencing (scRNA‐seq) and immune infiltration analysis were employed to investigate the molecular pathways of pivotal genes. Two‐sample Mendelian randomization (TSMR) assessed the causal effects in ITP. Key genes identified in the training set included GABARAPL1, S100A8, LIN28A, and GDF9, which demonstrated diagnostic potential in validation sets. Functional analysis indicated these genes' involvement in ubiquitin phosphorylation, PPAR signalling pathway and T‐cell differentiation. Immune infiltration analysis revealed increased macrophage presence in ITP, related to the critical genes. scRNA‐seq indicated reduced GABARAPL1 expression in ITP bone marrow macrophages. TSMR linked S100A8 with ITP diagnosis, presenting an OR of 0.856 (95% CI = 0.736–0.997, p = 0.045). The study pinpointed four central genes, GABARAPL1, S100A8, LIN28A, and GDF9, tied to mitophagy and ferroptosis in ITP. It posits that diminished GABARAPL1 expression may disrupts ubiquitin phosphorylation and PPAR signalling, impairing mitophagy and inhibiting ferroptosis, leading to immune imbalance.

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Section: Methodsmentioning

confidence: 99%

Section: Scrna-seq Analysismentioning

confidence: 99%

Comprehensive analysis and prediction model of mitophagy and ferroptosis in primary immune thrombocytopenia

Mo,

Liu,

Zhang

et al. 2024

Br J Haematol

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“…For single-cell characteristics investigations, we analyzed the scRNA-seq dataset GSE193533, following the “Seurat” standard procedure [ 26 ]. Cells with less than 200 genes, more than 7000 counts in total, and more than 20% mitochondria genes were filtered out according to the previous reports [ 27 ]. The batch effect among samples was reduced using the R package “harmony” [ 28 ].…”

Section: Methodsmentioning

confidence: 99%

Comprehensive analysis of mitochondrial dysfunction and necroptosis in intracranial aneurysms from the perspective of predictive, preventative, and personalized medicine

et al. 2023

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Mitochondrial dysfunction and necroptosis are closely associated, and play vital roles in the medical strategy of multiple cardiovascular diseases. However, their implications in intracranial aneurysms (IAs) remain unclear. In this study, we aimed to explore whether mitochondrial dysfunction and necroptosis could be identified as valuable starting points for predictive, preventive, and personalized medicine for IAs. The transcriptional profiles of 75 IAs and 37 control samples were collected from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs), weighted gene co-expression network analysis, and least absolute shrinkage and selection operator (LASSO) regression were used to screen key genes. The ssGSEA algorithm was performed to establish phenotype scores. The correlation between mitochondrial dysfunction and necroptosis was evaluated using functional enrichment crossover, phenotype score correlation, immune infiltration, and interaction network construction. The IA diagnostic values of key genes were identified using machine learning. Finally, we performed the single-cell sequencing (scRNA-seq) analysis to explore mitochondrial dysfunction and necroptosis at the cellular level. In total, 42 IA-mitochondrial DEGs and 15 IA-necroptosis DEGs were identified. Screening revealed seven key genes invovled in mitochondrial dysfunction (KMO, HADH, BAX, AADAT, SDSL, PYCR1, and MAOA) and five genes involved in necroptosis (IL1B, CAMK2G, STAT1, NLRP3, and BAX). Machine learning confirmed the high diagnostic value of these key genes for IA. The IA samples showed higher expression of mitochondrial dysfunction and necroptosis. Mitochondrial dysfunction and necroptosis exhibited a close association. Furthermore, scRNA-seq indicated that mitochondrial dysfunction and necroptosis were preferentially up-regulated in monocytes/macrophages and vascular smooth muscle cells (VSMCs) within IA lesions. In conclusion, mitochondria-induced necroptosis was involved in IA formation, and was mainly up-regulated in monocytes/macrophages and VSMCs within IA lesions. Mitochondria-induced necroptosis may be a novel potential target for diagnosis, prevention, and treatment of IA.

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Machine Learning for Improving Immunotherapy Outcomes in Lung Adenocarcinoma

Chen,

Yu,

Lyu

et al. 2024

Preprint

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Comprehensive analysis of autoimmune-related genes in amyotrophic lateral sclerosis from the perspective of 3P medicine

Cited by 3 publications

References 61 publications

Comprehensive analysis and prediction model of mitophagy and ferroptosis in primary immune thrombocytopenia

Comprehensive analysis and prediction model of mitophagy and ferroptosis in primary immune thrombocytopenia

Comprehensive analysis of mitochondrial dysfunction and necroptosis in intracranial aneurysms from the perspective of predictive, preventative, and personalized medicine

Machine Learning for Improving Immunotherapy Outcomes in Lung Adenocarcinoma

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