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单细胞测序分析联合机器学习鉴定胃癌免疫原性细胞死亡的多组学特征。

Multi-omics features of immunogenic cell death in gastric cancer identified by combining single-cell sequencing analysis and machine learning.

机构信息

Department of General Surgery, Deqing People's Hospital, Deqing Campus, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 120 South Yingxi Road, Deqing, 313200, Zhejiang, P. R. China.

Department of Pathology, Deqing People's Hospital, Deqing Campus, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, 120 South Yingxi Road, Deqing, 313200, Zhejiang, P. R. China.

出版信息

Sci Rep. 2024 Sep 18;14(1):21751. doi: 10.1038/s41598-024-73071-x.


DOI:10.1038/s41598-024-73071-x
PMID:39294296
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11410816/
Abstract

Gastric cancer (GC) is a prevalent malignancy with high mortality rates. Immunogenic cell death (ICD) is a unique form of programmed cell death that is closely linked to antitumor immunity and plays a critical role in modulating the tumor microenvironment (TME). Nevertheless, elucidating the precise effect of ICD on GC remains a challenging endeavour. ICD-related genes were identified in single-cell sequencing datasets and bulk transcriptome sequencing datasets via the AddModuleScore function, weighted gene co-expression network (WGCNA), and differential expression analysis. A robust signature associated with ICD was constructed using a machine learning computational framework incorporating 101 algorithms. Furthermore, multiomics analysis, including single-cell sequencing analysis, bulk transcriptomic analysis, and proteomics analysis, was conducted to verify the correlation of these hub genes with the immune microenvironment features of GC and with GC invasion and metastasis. We screened 59 genes associated with ICD and developed a robust ICD-related gene signature (ICDRS) via a machine learning computational framework that integrates 101 different algorithms. Furthermore, we identified five key hub genes (SMAP2, TNFAIP8, LBH, TXNIP, and PIK3IP1) from the ICDRS. Through single-cell analysis of GC tumor s, we confirmed the strong correlations of the hub genes with immune microenvironment features. Among these five genes, LBH exhibited the most significant associations with a poor prognosis and with the invasion and metastasis of GC. Finally, our findings were validated through immunohistochemical staining of a large clinical sample set, and the results further supported that LBH promotes GC cell invasion by activating the epithelial-mesenchymal transition (EMT) pathway.

摘要

胃癌(GC)是一种死亡率较高的常见恶性肿瘤。免疫原性细胞死亡(ICD)是一种独特的程序性细胞死亡形式,与抗肿瘤免疫密切相关,在调节肿瘤微环境(TME)方面发挥着关键作用。然而,阐明 ICD 对 GC 的确切影响仍然是一项具有挑战性的工作。通过 AddModuleScore 功能、加权基因共表达网络(WGCNA)和差异表达分析,在单细胞测序数据集和批量转录组测序数据集中鉴定了与 ICD 相关的基因。使用包含 101 种算法的机器学习计算框架构建了与 ICD 相关的稳健特征。此外,进行了多组学分析,包括单细胞测序分析、批量转录组分析和蛋白质组学分析,以验证这些枢纽基因与 GC 的免疫微环境特征以及 GC 侵袭和转移的相关性。我们筛选了 59 个与 ICD 相关的基因,并通过机器学习计算框架开发了一个稳健的 ICD 相关基因特征(ICDRS),该框架集成了 101 种不同的算法。此外,我们从 ICDRS 中确定了五个关键枢纽基因(SMAP2、TNFAIP8、LBH、TXNIP 和 PIK3IP1)。通过 GC 肿瘤的单细胞分析,我们证实了枢纽基因与免疫微环境特征之间的强烈相关性。在这五个基因中,LBH 与预后不良以及 GC 的侵袭和转移的相关性最为显著。最后,我们通过对大量临床样本集的免疫组织化学染色进行了验证,结果进一步支持 LBH 通过激活上皮-间充质转化(EMT)途径促进 GC 细胞侵袭。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/ef7ae9727d1a/41598_2024_73071_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/af100fbb5921/41598_2024_73071_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/6376adcbdf44/41598_2024_73071_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/a5388910f8c2/41598_2024_73071_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/083a1f6eb9f6/41598_2024_73071_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/bc337fbb629e/41598_2024_73071_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/51a9d0527b90/41598_2024_73071_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/0159f9af75e0/41598_2024_73071_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/911ad312a73a/41598_2024_73071_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/ef7ae9727d1a/41598_2024_73071_Fig9_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/af100fbb5921/41598_2024_73071_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/6376adcbdf44/41598_2024_73071_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/a5388910f8c2/41598_2024_73071_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/083a1f6eb9f6/41598_2024_73071_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/bc337fbb629e/41598_2024_73071_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/51a9d0527b90/41598_2024_73071_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/0159f9af75e0/41598_2024_73071_Fig7_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/911ad312a73a/41598_2024_73071_Fig8_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/23dc/11410816/ef7ae9727d1a/41598_2024_73071_Fig9_HTML.jpg

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[1]
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引用本文的文献

[1]
Multi-omics perspectives for gastrointestinal malignancy: A systematic review.

World J Gastrointest Surg. 2025-7-27

[2]
Revolutionizing gastroenterology and hepatology with artificial intelligence: From precision diagnosis to equitable healthcare through interdisciplinary practice.

World J Gastroenterol. 2025-6-28

本文引用的文献

[1]
Cell death.

Cell. 2024-1-18

[2]
An immunogenic cell death-related signature predicts prognosis and immunotherapy response in stomach adenocarcinoma.

Apoptosis. 2023-12

[3]
Multi-omics identification of an immunogenic cell death-related signature for clear cell renal cell carcinoma in the context of 3P medicine and based on a 101-combination machine learning computational framework.

EPMA J. 2023-5-31

[4]
A comprehensive analysis of immunogenic cell death and its key gene HSP90AA1 in bladder cancer.

Clin Transl Oncol. 2023-8

[5]
Identification of Immunogenic Cell-Death-Related Subtypes and Development of a Prognostic Signature in Gastric Cancer.

Biomolecules. 2023-3-14

[6]
Definition of a Novel Immunogenic Cell Death-Relevant Gene Signature Associated with Immune Landscape in Gastric Cancer.

Biochem Genet. 2023-10

[7]
Immunogenic cell death in cancer: concept and therapeutic implications.

J Transl Med. 2023-3-2

[8]
Cell death, therapeutics, and the immune response in cancer.

Trends Cancer. 2023-5

[9]
Identification of Key Biomarkers Associated with Immunogenic Cell Death and Their Regulatory Mechanisms in Severe Acute Pancreatitis Based on WGCNA and Machine Learning.

Int J Mol Sci. 2023-2-3

[10]
CD4 helper T cells endow cDC1 with cancer-impeding functions in the human tumor micro-environment.

Nat Commun. 2023-1-13

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