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Stem cell activation in organ culture reveals novel transcriptional programs underlying metabolic, fibrotic, vascular, and immune dysregulation in uterine leiomyomas

ABSTRACT: Background and objective: Uterine leiomyomas may arise from somatic stem or progenitor cells, leading to abnormal activation, proliferation, and clonal expansion. In organ cultures of myometrium and leiomyoma, differentiated cells decline after 7 days, whereas resident stem cells may persist within their niches and subsequently become activated, proliferate, and repopulate tissue slices. This study investigated gene expression programs that regulate the proliferation and differentiation of myometrial and MED12-mutant leiomyoma stem cells during long-term organ culture. Results: Comparison of normal and tumor tissues at baseline and after culture revealed several fibroid transcriptional signatures that were preserved during prolonged ex vivo culture. The MED12 mutation persisted in the repopulated fibroid slices, supporting the hypothesis that fibroids originate from stem or progenitor cells harboring MED12 mutation. Both tissues activated hypoxia and stemness-associated programs, including robust induction of HMGA1, HMGA2, and PLAG1. Myometrium induced KITLG/KIT expression, a limited number of CD49b (ITGA2)-stem-positive and Ki67-positive proliferating cells, indicating restrained proliferation, likely mediated by upregulation of ITGA2-AS1. Additionally, myometrial slice cultures were enriched for immune and endothelial/vascular programs, including several SOX family members. In contrast, leiomyoma cultures exhibited widespread CD24/CD73 expression, focal CD49b clusters, high Ki67 positivity, metabolic reprogramming toward complex carbohydrate degradation, SLC-mediated transport, and a low-PLIN2/high-ACLY signature. Uterine leiomyoma cultures repressed genes involved in vascular homeostasis (e.g., PLPP3) and preferentially activated pathways related to smooth muscle excitability and vesicle secretion. Extracellular matrix (ECM) remodeling was strongly pro-fibrotic in leiomyomas, with significant upregulation of several TGFB-regulated and related genes, a disrupted balance of KLF regulators, including loss of the anti-fibrotic repressor KLF10 and induction of the pro-fibrotic KLF5 factor, and broad upregulation of integrins. Differential expression of multiple HOX genes further distinguished ECM regulation between tissues. From niche survival to pro-fibrotic expansion, the study delineates checkpoints primed for intervention, highlighting potential therapeutic opportunities targeting profibrotic signaling, metabolic dependencies, and integrin-mediated ECM interactions. Conclusion: Long-term organ culture recapitulates key molecular features of fibroids and reveals tissue-specific mechanisms governing stem cell activation and differentiation. These findings identify potential therapeutic opportunities and establish long-term organ culture as a robust, physiologically relevant platform for investigating normal and tumor biology.

ORGANISM(S): Homo sapiens

PROVIDER: GSE309174 | GEO | 2026/05/11

REPOSITORIES: GEO

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Project description:Purpose:Our goal was to identify and characterize a new molecular target of Bisphenol A（BPA）in uterine leiomyoma cells to better understand how this compound may affect uterine leiomyomas growth and development. Methods: Primary cultured cell lines of uterine leiomyoma were treated with 0.1% DMSO or 10.0 μmol/L BPA for 48 h before RNA-seq and histone 3 lysine 27 acetylation (H3K27ac) ChIP-seq were performed. Integrative analysis of ChIP-seq and RNA-seq data identifies the key transcription factor (TF)，target gene and signaling pathway. To confirm the expression level of TF and target gene in uterine leiomyomas tissues, we analyzed 10 human uterine leiomyoma tissues and the matched adjacent uterine smooth muscle tissues using western blotting, and 96 paired paraffin-embedded human uterine samples by immunohistochemistry(IHC). The ChIP assay used to confirm the combination between the TF and target gene. In order to verify the functions of key TF, lentivirus was used to knock down the expression level and detect the effects on cell proliferation, cell cycle, and cell tumorigenicity. We further conducted Western blot analysis to confirm the whether the downstream signaling pathway is activated. RESULTS: Integrative Analysis of ChIP-seq and RNA-seq data identifies the key transcription factor XBP1and target gene ITGA2. The qPCR and ChIP- qPCR initially verified the sequencing results. XBP1 and ITGA2 were overexpressed in human uterine leiomyoma tissues. The IHC results confirmed that ITGA2 was significantly correlated with XBP1 expression (R = 0.6708, P < 0.001)， and the ChIP assay showed that XBP1 binds to the the ITGA2 predicted promoter region. BPA promoted uterine leiomyoma cells proliferation both in vitro and in vivo and that XBP1 expression levels modulated the cellular response to this endocrine disruptor. BPA upregulated ITGA2 through XBP1 and activated the downstream PI3K-AKT signaling pathway to promote the proliferation of human uterine leiomyoma cells. CONCLUSION: In conclusion, our current work reveals a novel mechanism by which BPA promotes the proliferation in uterine leiomyoma cells. The XBP1 transcription factor regulates and activates the downstream ITGA2/PI3K/AKT pathway. By defining XBP1 as an important regulatory role of BPA in uterine leiomyoma cell proliferation, they provide new insights into the pathogenesis related to the exposure to BPA and other endocrine disruptors acting similarly, and XBP1 may serve as a candidate molecular target for intervention and treatment of uterine leiomyomas.

Project description:Uterine fibroids are benign tumours affecting up to 80% of women of reproductive age, with 30% of patients suffering severe symptoms including abnormal uterine bleeding, pain and infertility. Several studies have identified mutations in MED12 or HMGA2 that account for the vast majority of genomic abnormalities in uterine fibroids, however, the processes by which these lead to UFs and HMB remain poorly understood. To systematically correlate genetic, transcriptional and proteomic phenotypes we collected fibroid, myometrium and endometrium tissues from 137 donors undergoing hysterectomy, myomectomy, or transcervical resection. Donors were profiled by genome-wide SNP arrays and their fibroids were genotyped for known mutations using a targeted sequencing approach. Tissues were analysed by RNA-sequencing and proteomics followed by a systems level approach using multiomics factor analysis. Whilst genotyping revealed 39.7% of common MED12 UF mutations, we observe multiple novel exonic and intronic variants of previously known mutated genes like COL4A5 and COL4A6. Systems level analysis of genotype, transcriptomic, and proteomic data between myometrium and fibroid donors identified multiple interrelated gene sets involved in UF pathophysiology, including extracellular matrix deposition and remodelling, protein glycosylation and sulphate biology. Equivalent analysis of endometrium stratified by donor HMB status revealed gene sets implicated in the condition, in particular RNA splicing in MED12 mutant fibroids. A paradigm is proposed, supported by a mouse model of HMB, whereby aberrant production of signalling molecules by MED12 mutant fibroids influences RNA transcript isoform expression in the endometrium, associated with abnormal bleeding. By merging clinical, genetic, transcriptomic, and proteomic information, we highlight multiple pathways which may underlie the pathomechanisms of UF biology and may facilitate the development of novel therapeutic strategies to treat heavy menstrual bleeding

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Stem cell activation in organ culture reveals novel transcriptional programs underlying metabolic, fibrotic, vascular, and immune dysregulation in uterine leiomyomas

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