Unraveling pancreatic ductal adenocarcinoma immune prognostic signature through a naive B cell gene set

Zhang, Shichen; Ta, Na; Zhang, Shihao; Li, Senhao; Zhu, Xinyu; Kong, Lingyun; Gong, Xueqing; Guo, Meng; Liu, Yanfang

doi:10.1016/j.canlet.2024.216981

Cited by 3 publications

(1 citation statement)

References 98 publications

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“…Recently, there has been a growing body of evidence supporting the widespread use of transcriptomics and proteomics in enhancing our understanding of pathophysiological mechanisms and facilitating the development of diagnostic tools for various diseases ( Li et al, 2020 ; Mu et al, 2020 ; Yang et al, 2021 ; Yang et al, 2023 ). Moreover, the utilization of weighted gene coexpression network analysis (WGCNA) offers the ability to illustrate the interconnections between diverse genes through the creation of a co-expression network, which not only enables the identification of modules that are associated with specific phenotypes but also proves to be more efficient in the investigation of crucial pathways and genes involved in numerous human disorders ( Langfelder and Horvath, 2008 ; Zhang et al, 2024 ). In addition, the limitations of expression-based multigene signatures in clinical settings can be attributed to their lack of uniqueness and appropriateness in selected modeling methods, and the absence of strict validation in large multicenter cohorts ( Wang et al, 2022 ; Yang et al, 2024 ).…”

Section: Introductionmentioning

confidence: 99%

Integrative transcriptome-proteome approach reveals key hypoxia-related features involved in the neuroprotective effects of Yang Xue oral liquid on Alzheimer’s and Parkinson’s disease

Chen,

Cheng,

Tang

et al. 2024

Front. Pharmacol.

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Introduction: This study investigates the role of hypoxia-related genes in the neuroprotective efficacy of Yang Xue oral liquid (YXKFY) in Alzheimer’s disease (AD) and Parkinson’s disease (PD).Methods and results: Using differential expression and weighted gene co-expression network analysis (WGCNA), we identified 106 and 9 hypoxia-associated genes in AD and PD, respectively, that are implicated in the transcriptomic and proteomic profiles. An artificial intelligence-driven hypoxia signature (AIDHS), comprising 17 and 3 genes for AD and PD, was developed and validated across nine independent cohorts (n = 1713), integrating 10 machine learning algorithms and 113 algorithmic combinations. Significant associations were observed between AIDHS markers and immune cells in AD and PD, including naive CD4+ T cells, macrophages, and neutrophils. Interactions with miRNAs (hsa-miR-1, hsa-miR-124) and transcription factors (USF1) were also identified. Single-cell RNA sequencing (scRNA-seq) data highlighted distinct expression patterns of AIDHS genes in various cell types, such as high expression of TGM2 in endothelial cells, PDGFRB in endothelial and mesenchymal cells, and SYK in microglia. YXKFY treatment was shown to repair cellular damage and decrease reactive oxygen species (ROS) levels. Notably, genes with previously dysfunctional expression, including FKBPL, TGM2, PPIL1, BLVRB, and PDGFRB, exhibited significant recovery after YXKFY treatment, associated with riboflavin and lysicamine.Conclusion: The above genes are suggested to be central to hypoxia and neuroinflammation responses in AD and PD, and are potential key mediators of YXKFY’s neuroprotective action.

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Section: Introductionmentioning

confidence: 99%

Integrative transcriptome-proteome approach reveals key hypoxia-related features involved in the neuroprotective effects of Yang Xue oral liquid on Alzheimer’s and Parkinson’s disease

Chen,

Cheng,

Tang

et al. 2024

Front. Pharmacol.

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Identification of potential biomarkers for hepatocellular carcinoma based on machine learning and bioinformatics analysis

Chen,

Peng,

Jin

et al. 2024

Discov Onc

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Metastasis is the major cause of hepatocellular carcinoma (HCC) mortality. But the effective biomarkers for HCC metastasis remain underexplored. Here we integrated GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) datasets to screen candidate genes for hepatocellular carcinoma metastasis, a consensus metastasis-derived prognostic signature (MDPS) was constructed by machine learning. Based on the risk scores, HCC patients were stratified into high-risk and low-risk groups. Comprehensive analyses were conducted to investigate various aspects including survival outcomes, clinical characteristics, immune cell infiltration, as well as in vitro experiments. Together, we develop a comprehensive machine learning-based program for constructing a consensus MDPS including four genes (SPP1, TYMS, HMMR and MYCN). Our findings revealed that four genes could serve as efficient prognostic biomarkers and therapeutic targets in HCC. In addition, in vitro experiments showed that HMMR overregulation exacerbated tumor progression, including proliferation, migration and invasion. Supplementary Information The online version contains supplementary material available at 10.1007/s12672-024-01667-w.

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Predicting and Monitoring Immune Checkpoint Inhibitor Therapy Using Artificial Intelligence in Pancreatic Cancer

Yu,

Zhang,

Eresen

et al. 2024

IJMS

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Pancreatic cancer remains one of the most lethal cancers, primarily due to its late diagnosis and limited treatment options. This review examines the challenges and potential of using immunotherapy to treat pancreatic cancer, highlighting the role of artificial intelligence (AI) as a promising tool to enhance early detection and monitor the effectiveness of these therapies. By synthesizing recent advancements and identifying gaps in the current research, this review aims to provide a comprehensive overview of how AI and immunotherapy can be integrated to develop more personalized and effective treatment strategies. The insights from this review may guide future research efforts and contribute to improving patient outcomes in pancreatic cancer management.

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Unraveling pancreatic ductal adenocarcinoma immune prognostic signature through a naive B cell gene set

Cited by 3 publications

References 98 publications

Integrative transcriptome-proteome approach reveals key hypoxia-related features involved in the neuroprotective effects of Yang Xue oral liquid on Alzheimer’s and Parkinson’s disease

Integrative transcriptome-proteome approach reveals key hypoxia-related features involved in the neuroprotective effects of Yang Xue oral liquid on Alzheimer’s and Parkinson’s disease

Identification of potential biomarkers for hepatocellular carcinoma based on machine learning and bioinformatics analysis

Predicting and Monitoring Immune Checkpoint Inhibitor Therapy Using Artificial Intelligence in Pancreatic Cancer

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