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Peer-reviewedCC BYScientific data

An integrated single-cell transcriptomic and microbiome dataset of orbital adipose tissue in thyroid eye disease.

  • Xiang Xu1,2
  • Fei Wang3,4
  • Weiqi Liu1,2
  • Haowen Li3
  • Yingyu Wang1,2
  • Yuan Li1,2,5
  • Bing Wang1,2,5
  • Mingming Liu6,7,8
  • Yang Li9,10
10 affiliations
  1. 1Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China.
  2. 2International Center of Microvascular Medicine, Chinese Academy of Medical Sciences, Beijing, 100005, China.
  3. 3Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China.
  4. 4Department of Ophthalmology, Air Force Medical Center, Beijing, 100142, China.
  5. 5Diabetes Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China.
  6. 6Institute of Microcirculation, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100005, China. [email protected].
  7. 7International Center of Microvascular Medicine, Chinese Academy of Medical Sciences, Beijing, 100005, China. [email protected].
  8. 8Diabetes Research Center, Chinese Academy of Medical Sciences, Beijing, 100005, China. [email protected].
  9. 9Beijing Tongren Eye Center, Beijing Key Laboratory of Intraocular Tumor Diagnosis and Treatment, Beijing Tongren Hospital, Capital Medical University, Beijing, 100730, China. [email protected].
  10. 10Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Beijing Ophthalmology and Visual Science Key Lab, Capital Medical University, Beijing, 100730, China. [email protected].
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Abstract

Thyroid eye disease (TED), also historically referred to as thyroid-associated ophthalmopathy (TAO) or Graves' orbitopathy (GO), is an autoimmune ophthalmopathy characterized by inflammation and adipogenesis within orbital adipose (OA) tissue. While the contribution of immune cell infiltration and fibroblast activation is recognized, the cellular heterogeneity and the potential role of local microbial dysbiosis in the orbital microenvironment remain poorly defined. Here, we present a multi-omics dataset derived from OA of patients with TED and healthy controls collected at Beijing Tongren Hospital. The dataset comprises single-cell RNA sequencing (scRNA-seq) data generated from human orbital adipose tissue and subcutaneous fat. Following quality control filtering and doublet removal, a total of 61,302 high-quality singlet cells were retained for downstream analyses, capturing the transcriptomic landscape of orbital fibroblasts, immune subsets, and vascular cells. In parallel, 16S rRNA gene sequencing was performed on orbital adipose tissue samples collected from the integrated study cohort, alongside environmental samples for contamination assessment, to characterize the low-biomass orbital microbiome DNA signatures. Raw sequencing reads, quality-controlled gene-expression matrices, and contamination-corrected microbial feature tables are provided. Our dataset provides an opportunity to investigate the crosstalk between host cellular immunity and potential local microbiome signatures, facilitating hypothesis generation regarding host-microbiome crosstalk and the exploration of novel therapeutic targets for TED.

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Cite

BibTeXRIS
BibTeX
@article{xu2026integrated,
  title = {{An integrated single-cell transcriptomic and microbiome dataset of orbital adipose tissue in thyroid eye disease.}},
  author = {Xiang Xu and Fei Wang and Weiqi Liu and Haowen Li and Yingyu Wang and Yuan Li and Bing Wang and Mingming Liu and Yang Li},
  journal = {Scientific data},
  year = {2026},
  month = aug,
  doi = {10.1038/s41597-026-08064-8},
  url = {https://europepmc.org/article/MED/42897260},
  note = {CC BY},
}
RIS
TY  - JOUR
TI  - An integrated single-cell transcriptomic and microbiome dataset of orbital adipose tissue in thyroid eye disease.
AU  - Xiang Xu
AU  - Fei Wang
AU  - Weiqi Liu
AU  - Haowen Li
AU  - Yingyu Wang
AU  - Yuan Li
AU  - Bing Wang
AU  - Mingming Liu
AU  - Yang Li
PY  - 2026
DA  - 2026/08/13
JO  - Scientific data
DO  - 10.1038/s41597-026-08064-8
UR  - https://europepmc.org/article/MED/42897260
AB  - Thyroid eye disease (TED), also historically referred to as thyroid-associated ophthalmopathy (TAO) or Graves' orbitopathy (GO), is an autoimmune ophthalmopathy characterized by inflammation and adipogenesis within orbital adipose (OA) tissue. While the contribution of immune cell infiltration and fibroblast activation is recognized, the cellular heterogeneity and the potential role of local microbial dysbiosis in the orbital microenvironment remain poorly defined. Here, we present a multi-omics dataset derived from OA of patients with TED and healthy controls collected at Beijing Tongren Hospital. The dataset comprises single-cell RNA sequencing (scRNA-seq) data generated from human orbital adipose tissue and subcutaneous fat. Following quality control filtering and doublet removal, a total of 61,302 high-quality singlet cells were retained for downstream analyses, capturing the transcriptomic landscape of orbital fibroblasts, immune subsets, and vascular cells. In parallel, 16S rRNA gene sequencing was performed on orbital adipose tissue samples collected from the integrated study cohort, alongside environmental samples for contamination assessment, to characterize the low-biomass orbital microbiome DNA signatures. Raw sequencing reads, quality-controlled gene-expression matrices, and contamination-corrected microbial feature tables are provided. Our dataset provides an opportunity to investigate the crosstalk between host cellular immunity and potential local microbiome signatures, facilitating hypothesis generation regarding host-microbiome crosstalk and the exploration of novel therapeutic targets for TED.
SN  - 2052-4463
ER  -