Evidence map›Paper›PMID 40205350›Full record

ArticleBMC cancer2025

Comprehensive analysis of scRNA-seq and bulk RNA-seq data via machine learning and bioinformatics reveals the role of lysine metabolism-related genes in gastric carcinogenesis.

Yongfu Shao, Chujia Chen, Xuan Yu, Jianing Yan, Junming Guo, Guoliang Ye

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Article in BMC cancer, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
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1 · What the graph read from it

What it found

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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

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3 · Its place in the literature

Who cites it

5 citing papers in PubMed.

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4 · The record

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5 · Who and what money

Authors and funding

6 authors.

Yongfu Shao *Department of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, 315020, China.
Chujia Chen *Health Science Center, Ningbo University, Ningbo, 315211, China.
Xuan Yu *Health Science Center, Ningbo University, Ningbo, 315211, China.
Jianing YanDepartment of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, 315020, China.
Junming GuoHealth Science Center, Ningbo University, Ningbo, 315211, China. guojunming@nbu.edu.cn.
Guoliang YeDepartment of Gastroenterology, the First Affiliated Hospital of Ningbo University, Ningbo, 315020, China. yeguoliang@nbu.edu.cn.

Funding

Key Scientific and Technological Projects of Ningbo 2021Z133Key Scientific and Technological Projects of Ningbo 2022Z130Ningbo Top Medical and Health Research Program 2023020612
6 · The paper itself

Abstract

backgroundGastric cancer (GC) is a highly aggressive and heterogeneous cancer with extremely complex biological characteristics. Lysine and its metabolism are closely related to human cancer, but little is known about how lysine metabolism-related genes contribute to gastric carcinogenesis.

methodsThe roles of lysine metabolism-related genes in GC were investigated by in-depth analysis of single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (RNA-seq) data via machine learning and multiple bioinformatics methods and confirmed by multiple cell and molecular biology methods.

resultsBy systematically analyzing the heterogeneity of GC cells and interactions among cell subtypes, two key genes, solute carrier family 7 member 7 (SLC7A7) and vimentin (VIM), were innovatively identified as lysine metabolism-related genes involved in gastric carcinogenesis. The potential functional mechanisms involved immune infiltration, signaling pathway regulation, drug sensitivity, molecular regulatory networks, tumor regulatory genes, and metabolic pathways. A reliable prognostic risk nomogram was established for GC prognosis prediction. Moreover, the expression of the lysine metabolism-related genes SLC7A7 and VIM and their effect on cellular phenotypes in gastric carcinogenesis were verified in clinical samples and in vitro experiments, including cell proliferation, migration, invasion and cell cycle assays.

conclusionsWe explored the role of lysine metabolism-related genes and prognostic models in GC with multiple datasets, providing novel metabolic targets.

Indexed as

CarcinogenesisLysineMachine LearningStomach NeoplasmsVimentinBiomarkers, TumorCell Line, TumorCell ProliferationComputational BiologyGene Expression Regulation, NeoplasticGene Regulatory NetworksHumansNomogramsPrognosisRNA-SeqSequence Analysis, RNABiomarkers, TumorLysineVimentinVIM protein, humanBulk RNA-seqGastric cancerImmune infiltrationLysine metabolismMachine learningPrognostic modelScRNA-seq

Identifiers

PMID40205350
PMCPMC11984278

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