Evidence map›Paper›PMID 41274870›Full record

ArticleNature communications2025

Single-cell and spatially resolved omics reveal transcriptional and metabolic signatures of ovarian endometriomas.

Yujuan Qi, Xia Chen, Sen Zheng, Tiantian Wu, Zhenbei Li, Jie Cheng, Xinhui Yang, Wei Tao, Qiuru Huang, Juan Gu and 22 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.

0numbers the graph read from it
0cells of the map it votes in
9citing 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

9 citing papers in PubMed.

  1. Review
  2. Review
  3. Review
  4. Review
  5. Review
  6. Article
  7. Review
  8. Review
  9. Review
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

32 authors.

Yujuan Qi *Clinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Xia Chen *Institute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Sen Zheng *Clinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Tiantian Wu *State Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School of Nanjing Medical University, Suzhou, China.
Zhenbei Li *Clinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Jie ChengDepartment of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Xinhui YangDepartment of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Wei TaoDepartment of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Qiuru HuangInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Juan GuClinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Qingqing SunClinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Ning ChenClinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Xiangnan CaoClinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China.
Jiaxin LiInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Lei HeInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Chenyu WangInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Xinda WangInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Qingqing HuInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Qiushi XiaInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Yi ZhangInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Jiangming RengInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Weiyi QianInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Lingyi KongInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Yuqi HuangInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Yanting WangInstitute of Reproductive Medicine, Medical School of Nantong University, Nantong University, Nantong, China.
Chen QiaoDepartment of Clinical Pharmacy, Affiliated Hospital of Jiangsu University, Jiangsu University, Zhenjiang, China.
Xinyuan ZhaoDepartment of Occupational Medicine and Environmental Toxicology, Nantong Key Laboratory of Environmental Toxicology, School of Public Health, Nantong University, Nantong, China.
Ying ZhengDepartment of Histology and Embryology, School of Medicine, Yangzhou University, Yangzhou, China.ORCID http://orcid.org/0000-0002-8852-5738
Mei XuDepartment of Obstetrics and Gynecology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China. xzxumei@163.com.ORCID http://orcid.org/0009-0005-2372-7530
Bo ZhengState Key Laboratory of Reproductive Medicine and Offspring Health, Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School of Nanjing Medical University, Suzhou, China. bozheng@njmu.edu.cn.ORCID http://orcid.org/0000-0002-1496-0753
Yijuan CaoClinical Center of Reproductive Medicine, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Southeast University Affiliated Xuzhou Central Hospital, Xuzhou, China. xzjj2002@126.com.ORCID http://orcid.org/0000-0001-5364-9442
Jun YuInstitute of Reproductive Medicine, Jiangsu Province Key Laboratory in University for Inflammation and Molecular Drug Target, Medical School of Nantong University, Nantong University, Nantong, China. yujun9117@ntu.edu.cn.ORCID http://orcid.org/0009-0003-8165-7345

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Endometriosis involves ectopic growth of endometrial-like tissue, yet the spatial transcriptomic and metabolic landscape of ovarian endometriomas remains poorly understood. This investigation presents a comprehensive multi-omics analysis of ovarian endometriomas incorporating single-cell RNA sequencing in conjunction with Digital Spatial Profiler-Whole Transcriptome Atlas for spatial transcriptomics, and non-targeted Matrix-Assisted Laser Desorption/Ionization-Mass Spectrometry Imaging for spatially resolved metabolomics. Our integrated analysis confirms the importance of cell adhesion, ECM-receptor interaction, and focal adhesion pathways in disease context. We identify XBP1, VCAN, and CLDN7 as key markers in epithelial cells, and THBS1 in perivascular cells. Spatially resolved metabolomics further reveals altered activity of cytochrome P450 enzymes, lipoprotein particles, and cholesterol metabolism in mesenchymal regions, along with several undefined metabolites enriched in epithelial areas of endometriomas compared to ovarian cortex controls. These findings reveal potential markers and metabolic pathways linked to ovarian endometriomas, offering a foundation for future diagnostic and therapeutic strategies.

Indexed as

EndometriosisOvarian DiseasesTranscriptomeAdultEndometriumEpithelial CellsFemaleGene Expression ProfilingHumansMetabolomicsOvarySingle-Cell Analysis

Identifiers

PMID41274870
PMCPMC12749035

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.