XYcellAtlas: a cell-type- and spatial-resolved pan-cancer atlas of sex-biased and Y chromosome loss-associated molecular signatures
8 affiliations
- 1Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Science, Central South University , Changsha 410078, Hunan ,
- 2HIM-BGI Omics Center, Hangzhou Institute of Medicine, Chinese Academy of Sciences , Hangzhou 310022 ,
- 3Medical AI Lab, The First Hospital of Hebei Medical University, Hebei Medical University , Shijiazhuang 050000 ,
- 4Institute of Medical Innovation and Research, Peking University Third Hospital , Beijing 100191 ,
- 5Department of Medical Biochemistry and Microbiology, Uppsala University , Uppsala 75123 ,
- 6Zhejiang Cancer Hospital, Hangzhou Institute of Medicine, Chinese Academy of Sciences , Hangzhou, Zhejiang 310022 ,
- 7Department of Radiation Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital & Institute , Beijing 100142 ,
- 8Institute of Zoology, Chinese Academy of Sciences , Beijing 100101 ,
Abstract
Sex is a critical determinant of cancer susceptibility, clinical prognosis, and therapeutic response. Sex chromosome aberrations, particularly somatic loss of the Y chromosome (LOY) in male malignancies, exert profound impacts on transcriptional regulation, tumor immune microenvironment remodeling, and malignant progression, highlighting an urgent demand for comprehensive integration of single–cell and spatial omics profiles dissecting sex-biased and LOY landscapes across human cancers. Here, we developed XYcellAtlas (http://www.xycellatlas.top/), an integrative database for integration and multidimensional visualization of sex disparities and LOY features across human tissues at single-cell transcriptomic, epigenomic, and spatial-transcriptomic resolutions. This resource aggregates data from 6764 patient samples covering 18 cancer types, eight precancerous lesions, and 21 tissue origins, encompassing over 25.8 million single cells and one million spatial-transcriptomic spots. Leveraging random forest classifiers trained on normal tissue datasets, XYcellAtlas quantifies cell-type-specific LOY frequencies across cell types. Furthermore, it systematically catalogs sex-biased and LOY-associated molecular alterations, including differentially expressed genes, chromatin peaks, core transcription factors, as well as their functional annotations and dysregulatory signatures within malignant cells and the tumor microenvironment. In summary, XYcellAtlas provides a unified, all-in-one analytical platform enabling researchers to query, inspect, quantify, and visualize sex-associated and LOY-derived multi-omics features underlying tumor evolutionary processes.
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BibTeX
@article{fan2026xycellatlas,
title = {{XYcellAtlas: a cell-type- and spatial-resolved pan-cancer atlas of sex-biased and Y chromosome loss-associated molecular signatures}},
author = {Tianda Fan and Xiaohui Shi and Liao Zhang and Leisheng Shi and Wei Lv and Zhongxu Zhu and Jieqiong Tan and Lian Zhang and Huajing Teng and Zhongsheng Sun},
journal = {Nucleic Acids Research},
year = {2026},
month = oct,
doi = {10.1093/nar/gkag1065},
url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1065/9005083},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - XYcellAtlas: a cell-type- and spatial-resolved pan-cancer atlas of sex-biased and Y chromosome loss-associated molecular signatures
AU - Tianda Fan
AU - Xiaohui Shi
AU - Liao Zhang
AU - Leisheng Shi
AU - Wei Lv
AU - Zhongxu Zhu
AU - Jieqiong Tan
AU - Lian Zhang
AU - Huajing Teng
AU - Zhongsheng Sun
PY - 2026
DA - 2026/10/30
JO - Nucleic Acids Research
DO - 10.1093/nar/gkag1065
UR - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1065/9005083
AB - Sex is a critical determinant of cancer susceptibility, clinical prognosis, and therapeutic response. Sex chromosome aberrations, particularly somatic loss of the Y chromosome (LOY) in male malignancies, exert profound impacts on transcriptional regulation, tumor immune microenvironment remodeling, and malignant progression, highlighting an urgent demand for comprehensive integration of single–cell and spatial omics profiles dissecting sex-biased and LOY landscapes across human cancers. Here, we developed XYcellAtlas (http://www.xycellatlas.top/), an integrative database for integration and multidimensional visualization of sex disparities and LOY features across human tissues at single-cell transcriptomic, epigenomic, and spatial-transcriptomic resolutions. This resource aggregates data from 6764 patient samples covering 18 cancer types, eight precancerous lesions, and 21 tissue origins, encompassing over 25.8 million single cells and one million spatial-transcriptomic spots. Leveraging random forest classifiers trained on normal tissue datasets, XYcellAtlas quantifies cell-type-specific LOY frequencies across cell types. Furthermore, it systematically catalogs sex-biased and LOY-associated molecular alterations, including differentially expressed genes, chromatin peaks, core transcription factors, as well as their functional annotations and dysregulatory signatures within malignant cells and the tumor microenvironment. In summary, XYcellAtlas provides a unified, all-in-one analytical platform enabling researchers to query, inspect, quantify, and visualize sex-associated and LOY-derived multi-omics features underlying tumor evolutionary processes.
SN - 0305-1048
SN - 1362-4962
ER -