Evidence map›Paper›PMID 42098407›Full record

ArticleCommunications biology2026

Spatial transcriptomics defines IM-crypt as a premalignant niche with bidirectional divergence in early gastric carcinogenesis.

Jing Wen, Yuehua Gong, Liping Sun, Ziqi Lin, Qian Xu, Jingjing Jing, Lingling Hu, Hanmin Duan, Honghao Yin, Huanyu Zhang and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Communications biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

15 authors.

Jing WenTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.ORCID http://orcid.org/0000-0002-0629-4631
Yuehua GongTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.ORCID http://orcid.org/0000-0002-0146-2165
Liping SunTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.
Ziqi LinDepartment of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.
Qian XuTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.
Jingjing JingTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.
Lingling HuCenter of Clinical Big Data and Analytics of The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China.
Hanmin DuanCenter of Clinical Big Data and Analytics of The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China.
Honghao YinTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.
Huanyu ZhangTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.
Shixuan ShenTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.
Nannan DongTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China.
Yiling LiDepartment of Gastroenterology and Endoscopy, The First Hospital of China Medical University, Shenyang, China.
Huakang TuCenter of Clinical Big Data and Analytics of The Second Affiliated Hospital and School of Public Health, Zhejiang University School of Medicine, Hangzhou, China. huakangtu@zju.edu.cn.
Yuan YuanTumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Hospital of China Medical University, Shenyang, China. yuanyuan@cmu.edu.cn.ORCID http://orcid.org/0000-0002-7394-9036

Funding

National Natural Science Foundation of China (National Science Foundation of China) 82574197
6 · The paper itself

Abstract

Early gastric carcinogenesis progresses from gastritis through intestinal metaplasia to early gastric cancer, yet the spatial origin of malignant transformation and subtype divergence remains unclear. Here we show, using spatial transcriptomics across human gastric tissues spanning disease progression, that an OLFM4-positive transitional subset emerges at the interface between gastric isthmus/glands and proliferative intestinal metaplasia crypts, consistent with an early step in intestinalization. From these crypts, transcriptional trajectories diverge toward distinct intestinal differentiation programs. Notably, proliferative crypt regions display the closest transcriptional similarity to early gastric cancer and are enriched for proliferation and DNA-repair pathways, supporting their role as a premalignant niche. We further identify increased activity of USF2-associated regulatory networks shared between crypt and cancer regions. Further stratification by Lauren subtype reveals that intestinal-type gastric cancer is characterized by a CDX2-dominated program, whereas diffuse-type gastric cancer exhibits developmental and stemness-related networks with SPP1 and CD44 co-occurring. Together, these findings highlight the intestinal metaplasia crypt as a premalignant niche and provide spatially resolved candidate markers for early detection and mechanistic investigation.

Indexed as

CarcinogenesisPrecancerous ConditionsStomach NeoplasmsTranscriptomeCell Transformation, NeoplasticGastric MucosaGene Expression Regulation, NeoplasticHumansMetaplasiaSpatial Transcriptomics

Identifiers

PMID42098407
PMCPMC13369935

What OpenQuestion holds

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LicenceCC BY-NC-ND
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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.