Evidence map›Paper›PMID 39118103›Full record

ArticleBMC cancer2024

Identification and experimental verification of a biomarker by combining the unfolded protein response with the immune cells in colon cancer.

Yichao Ma, Jingqiu Zhang, Chen Wei, Fei Wang, Hao Ji, Jiahao Zhao, Daorong Wang, Xinyue Zhang, Dong Tang

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC cancer, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

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

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Yichao Ma *Department of General Surgery, Institute of General Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China.
Jingqiu Zhang *Department of General Surgery, Institute of General Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China.
Chen Wei *Department of General Surgery, Institute of General Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China.
Fei WangThe Yangzhou School of Clinical Medicine of Dalian Medical University, Northern Jiangsu People's Hospital, Yangzhou, 116044, Liaoning, P.R. China.
Hao JiDepartment of General Surgery, Institute of General Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China.
Jiahao ZhaoDepartment of General Surgery, Institute of General Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China.
Daorong WangDepartment of General Surgery, Institute of General Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China.
Xinyue ZhangCollege of Bioscience and Biotechnology, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
Dong TangDepartment of General Surgery, Institute of General Surgery, Northern Jiangsu People's Hospital Affiliated to Yangzhou University, Northern Jiangsu People's Hospital, Yangzhou, Jiangsu Province, China. 18952783556@yzu.edu.cn.

Funding

Academic Science and Technology Innovation Fund for College Students 202011117056YGraduate Research- Innovation Project in Jiangsu province SJCX21_1644High-level talent "six one projects" top talent scientific research project of Jiangsu Province LGY2019034Social development project of key R & D plan of Jiangsu Provincial Department of science and technology BE2022773the Graduate Research- Innovation Project in Jiangsu province SJCX22_1816the Social Development-Health Care Project of Yangzhou, Jiangsu Province YZ2021075
6 · The paper itself

Abstract

backgroundThe unfolded protein response (UPR) is associated with immune cells that regulate the biological behavior of tumors. This article aims to combine UPR-associated genes with immune cells to find a prognostic marker and to verify its connection to the UPR.

methodsUnivariate cox analysis was used to screen prognostically relevant UPRs and further screened for key UPRs among them by machine learning. ssGSEA was used to calculate immune cell abundance. Univariate cox analysis was used to screen for prognostically relevant immune cells. Multivariate cox analysis was used to calculate UPR_score and Tumor Immune Microenvironment score (TIME_score). WGCNA was used to screen UPR-Immune-related (UI-related) genes. Consensus clustering analysis was used to classify patients into molecular subtype. Based on the UI-related genes, we classified colon adenocarcinoma (COAD) samples by cluster analysis. Single-cell analysis was used to analyze the role of UI-related genes. We detected the function of TIMP1 by cell counting and transwell. Immunoblotting was used to detect whether TIMP1 was regulated by key UPR genes.

resultsCombined UPR-related genes and immune cells can determine the prognosis of COAD patients. Cluster analysis showed that UI-related genes were associated with clinical features of COAD. Single-cell analysis revealed that UI-related genes may act through stromal cells. We defined three key UI-related genes by machine learning algorithms. Finally, we found that TIMP1, regulated by key genes of UPR, promoted colon cancer proliferation and metastasis.

conclusionsWe found that TIMP1 was a prognostic marker and experimentally confirmed that TIMP1 was regulated by key genes of UPR.

Indexed as

Biomarkers, TumorColonic NeoplasmsTissue Inhibitor of Metalloproteinase-1Tumor MicroenvironmentUnfolded Protein ResponseAdenocarcinomaCell Line, TumorCluster AnalysisFemaleGene Expression Regulation, NeoplasticHumansMachine LearningMalePrognosisSingle-Cell AnalysisBiomarkers, TumorTIMP1 protein, humanTissue Inhibitor of Metalloproteinase-1Colon cancerImmune cellsPrognostic markerUnfolded protein response

Identifiers

PMID39118103
PMCPMC11311949

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.