{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T05:01:44Z","timestamp":1789794104929,"version":"4.0.1"},"reference-count":38,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["Grant No. 2021YFD1200903"],"award-info":[{"award-number":["Grant No. 2021YFD1200903"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shandong Special Economic Animal Industry Technology System","award":["Grant No. SDAIT-21-02"],"award-info":[{"award-number":["Grant No. SDAIT-21-02"]}]},{"name":"Qingdao Science and Technology Benefiting People Demonstration Project","award":["Grant No. 25-1-5-xdny-26-nsh"],"award-info":[{"award-number":["Grant No. 25-1-5-xdny-26-nsh"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: The cellular composition and molecular features of the rabbit uterus remain incompletely understood. This study aimed to provide an initial single-cell characterization of the cell populations, transcriptional features, and predicted communication networks identified in one rabbit uterine-body specimen. Methods: Single-cell RNA sequencing was performed on uterine-body tissue from one 70-day-old female Kangda V-line rabbit. Following quality control, cells were clustered and annotated using canonical markers. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses, descriptive functional module scoring, CellChat, and high-dimensional weighted gene co-expression network analysis were used to characterize cell-associated expression patterns, predicted intercellular communication, and fibroblast co-expression modules. Results: A total of 9251 cells from this single specimen were retained and resolved into 16 preliminary clusters; 15 clusters were assigned to nine major cell types, whereas one small cluster remained unclassified. Fibroblasts were the predominant cell population among the analyzed cells (76.6%), followed by smooth muscle cells (10.9%). Functional analyses highlighted expression programs related to extracellular matrix organization, contractility, vascular function, epithelial barrier maintenance, and immune responses. CellChat analysis using an unadjusted empirical permutation p value &lt; 0.05 predicted prominent COLLAGEN, LAMININ, CD99, MIF, and PTN signaling. Integration with fibroblast co-expression modules identified 21 candidate genes, including COL1A1, COL1A2, COL6A2, LAMC1, PTN, BMP2, and PDGFRA, linking fibroblast-associated expression programs with predicted extracellular-matrix, adhesion, vascular, and developmental relationships. Conclusions: This single-specimen study provides a preliminary cell-level reference for rabbit uterine tissue. The relatively high proportion of fibroblasts and the predicted communication patterns generate testable hypotheses for future studies using independent animals and functional validation.<\/jats:p>","DOI":"10.3390\/genes17091131","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T13:50:27Z","timestamp":1789566627000},"page":"1131","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Single-Cell RNA Sequencing of Uterine Tissue from a 70-Day-Old Female Rabbit: Cellular Composition and Fibroblast-Associated Networks"],"prefix":"10.3390","volume":"17","author":[{"given":"Tianyou","family":"Du","sequence":"first","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5934-5025","authenticated-orcid":false,"given":"Kerui","family":"Xie","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenli","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xun","family":"Xie","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinzhong","family":"Fan","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan","family":"Wang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai\u2019an 271018, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,16]]},"reference":[{"key":"ref_1","first-page":"106","article-title":"Study on the comparative with rabbit meat quality of two breeds","volume":"34","author":"Liu","year":"2013","journal-title":"Sci. Technol. Food Ind."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.1038\/s41587-020-0547-7","article-title":"A tissue-engineered uterus supports live births in rabbits","volume":"38","author":"Magalhaes","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1644","DOI":"10.1038\/s41591-020-1040-z","article-title":"Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle","volume":"26","author":"Wang","year":"2020","journal-title":"Nat. Med."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1038\/s41588-021-00972-2","article-title":"Mapping the temporal and spatial dynamics of the human endometrium in vivo and in vitro","volume":"53","author":"Handfield","year":"2021","journal-title":"Nat. Genet."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1186\/s40246-025-00884-w","article-title":"From bulk RNA sequencing to spatial transcriptomics: A comparative review of differential gene expression analysis methods","volume":"20","year":"2025","journal-title":"Hum. Genom."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"2385","DOI":"10.1016\/j.fertnstert.2009.01.091","article-title":"Reconstruction of endometrium in vitro via rabbit uterine endometrial cells expanded by sex steroid","volume":"93","author":"Wang","year":"2010","journal-title":"Fertil. Steril."},{"key":"ref_7","first-page":"189","article-title":"Dissecting cellular heterogeneity using single-cell RNA sequencing","volume":"42","author":"Choi","year":"2019","journal-title":"Mol. Cells"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"e694","DOI":"10.1002\/ctm2.694","article-title":"Single-cell RNA sequencing technologies and applications: A brief overview","volume":"12","author":"Jovic","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e8746","DOI":"10.15252\/msb.20188746","article-title":"Current best practices in single-cell RNA-seq analysis: A tutorial","volume":"15","author":"Luecken","year":"2019","journal-title":"Mol. Syst. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"2610","DOI":"10.1016\/j.cell.2023.04.037","article-title":"Time-aligned hourglass gastrulation models in rabbit and mouse","volume":"186","author":"Mayshar","year":"2023","journal-title":"Cell"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1167\/iovs.66.6.83","article-title":"Single-cell RNA sequencing of rabbit sclera at different developmental stages: Unveiling scleral cells atlas and the heterogeneity of fibroblasts","volume":"66","author":"Li","year":"2025","journal-title":"Investig. Ophthalmol. Vis. Sci."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2546","DOI":"10.1038\/s41588-025-02329-5","article-title":"A multi-tissue single-cell expression atlas in cattle","volume":"57","author":"Han","year":"2025","journal-title":"Nat. Genet."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"e04961","DOI":"10.1002\/advs.202504961","article-title":"Construction of a multitissue cell atlas reveals cell-type-specific regulation of molecular and complex phenotypes in pigs","volume":"13","author":"Chen","year":"2026","journal-title":"Adv. Sci."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1925","DOI":"10.1038\/s41591-025-03592-z","article-title":"Single-cell profiling of the human endometrium in polycystic ovary syndrome","volume":"31","author":"Eriksson","year":"2025","journal-title":"Nat. Med."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"4557","DOI":"10.1038\/s41598-019-40923-w","article-title":"Single cell RNA-seq study of wild type and Hox9,10,11 mutant developing uterus","volume":"9","author":"Mucenski","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat. Commun."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat. Biotechnol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: Doublet detection in single-cell RNA sequencing data using artificial nearest neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1038\/s41596-024-01045-4","article-title":"CellChat for systematic analysis of cell\u2013cell communication from single-cell transcriptomics","volume":"20","author":"Jin","year":"2025","journal-title":"Nat. Protoc."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"1088","DOI":"10.1038\/s41467-021-21246-9","article-title":"Inference and analysis of cell\u2013cell communication using CellChat","volume":"12","author":"Jin","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1038\/s41576-020-00292-x","article-title":"Deciphering cell\u2013cell interactions and communication from gene expression","volume":"22","author":"Armingol","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"100498","DOI":"10.1016\/j.crmeth.2023.100498","article-title":"hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data","volume":"3","author":"Morabito","year":"2023","journal-title":"Cell Rep. Methods"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"W169","DOI":"10.1093\/nar\/gkm415","article-title":"DAVID Bioinformatics Resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists","volume":"35","author":"Huang","year":"2007","journal-title":"Nucleic Acids Res."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: Tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: Kyoto Encyclopedia of Genes and Genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1186\/s12958-025-01348-5","article-title":"Extracellular matrix and pregnancy: Functions and opportunities caught in the net","volume":"23","author":"Rossi","year":"2025","journal-title":"Reprod. Biol. Endocrinol."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.gene.2014.08.047","article-title":"Endometrial stromal cells and decidualized stromal cells: Origins, transformation and functions","volume":"551","author":"Zhu","year":"2014","journal-title":"Gene"},{"key":"ref_28","first-page":"1","article-title":"The rabbit estrous cycle: A comprehensive review","volume":"2","author":"Kumcu","year":"2024","journal-title":"Rats"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1038\/s41586-018-0698-6","article-title":"Single-cell reconstruction of the early maternal\u2013fetal interface in humans","volume":"563","author":"Efremova","year":"2018","journal-title":"Nature"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"922","DOI":"10.1016\/j.ympev.2004.07.014","article-title":"Rabbits, if anything, are likely Glires","volume":"33","author":"Douzery","year":"2004","journal-title":"Mol. Phylogenet. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1016\/S0890-6238(00)00101-5","article-title":"The rabbit as a model for reproductive and developmental toxicity studies","volume":"14","author":"Foote","year":"2000","journal-title":"Reprod. Toxicol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"77","DOI":"10.4995\/wrs.2023.18762","article-title":"Managing sexual receptivity and ovulation induction in rabbit does: Evidence from recent research","volume":"31","author":"Rebollar","year":"2023","journal-title":"World Rabbit Sci."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1006\/frne.2000.0198","article-title":"Neuroendocrine regulation of GnRH release in induced ovulators","volume":"21","author":"Bakker","year":"2000","journal-title":"Front. Neuroendocrinol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1210\/er.2014-1045","article-title":"Cyclic decidualization of the human endometrium in reproductive health and failure","volume":"35","author":"Gellersen","year":"2014","journal-title":"Endocr. Rev."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"346","DOI":"10.1002\/stem.2222","article-title":"Loss of endometrial plasticity in recurrent pregnancy loss","volume":"34","author":"Lucas","year":"2016","journal-title":"Stem Cells"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/1477-7827-2-46","article-title":"Comparative aspects of trophoblast development and placentation","volume":"2","author":"Carter","year":"2004","journal-title":"Reprod. Biol. Endocrinol."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1293\/tox.2013-0060","article-title":"A comparison of the histological structure of the placenta in experimental animals","volume":"27","author":"Furukawa","year":"2014","journal-title":"J. Toxicol. Pathol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1126\/science.aaf2403","article-title":"Visualization and analysis of gene expression in tissue sections by spatial transcriptomics","volume":"353","author":"Vickovic","year":"2016","journal-title":"Science"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1131\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,19]],"date-time":"2026-09-19T04:13:24Z","timestamp":1789791204000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/1131"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,16]]},"references-count":38,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["genes17091131"],"URL":"https:\/\/doi.org\/10.3390\/genes17091131","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,16]]}}}