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Hoch M, Rauthe J, Cesnulevicius K, Schultz M, Lescheid D, Wolkenhauer O, Chiurchiù V, Gupta S. Cell-Type-Specific Gene Regulatory Networks of Pro-Inflammatory and Pro-Resolving Lipid Mediator Biosynthesis in the Immune System. Int J Mol Sci 2023; 24:ijms24054342. [PMID: 36901771 PMCID: PMC10001763 DOI: 10.3390/ijms24054342] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/19/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Lipid mediators are important regulators in inflammatory responses, and their biosynthetic pathways are targeted by commonly used anti-inflammatory drugs. Switching from pro-inflammatory lipid mediators (PIMs) to specialized pro-resolving (SPMs) is a critical step toward acute inflammation resolution and preventing chronic inflammation. Although the biosynthetic pathways and enzymes for PIMs and SPMs have now been largely identified, the actual transcriptional profiles underlying the immune cell type-specific transcriptional profiles of these mediators are still unknown. Using the Atlas of Inflammation Resolution, we created a large network of gene regulatory interactions linked to the biosynthesis of SPMs and PIMs. By mapping single-cell sequencing data, we identified cell type-specific gene regulatory networks of the lipid mediator biosynthesis. Using machine learning approaches combined with network features, we identified cell clusters of similar transcriptional regulation and demonstrated how specific immune cell activation affects PIM and SPM profiles. We found substantial differences in regulatory networks in related cells, accounting for network-based preprocessing in functional single-cell analyses. Our results not only provide further insight into the gene regulation of lipid mediators in the immune response but also shed light on the contribution of selected cell types in their biosynthesis.
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Affiliation(s)
- Matti Hoch
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
| | - Jannik Rauthe
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
| | | | | | | | - Olaf Wolkenhauer
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
- Leibniz-Institute for Food Systems Biology, Technical University of Munich, 85354 Freising, Germany
- Stellenbosch Institute of Advanced Study, Wallenberg Research Centre, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Valerio Chiurchiù
- Institute of Translational Pharmacology, National Research Council, 00133 Rome, Italy
- Laboratory of Resolution of Neuroinflammation, IRCCS Santa Lucia Foundation, 00179 Rome, Italy
| | - Shailendra Gupta
- Department of Systems Biology and Bioinformatics, University of Rostock, 18055 Rostock, Germany
- Correspondence:
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Li W, Gu P, Gao B, Zou L, Zhang A, Huang H, Zhao X, Xu D, Cheng C. Characteristics and transcriptomic analysis of scar tissues on the inner uterine cavity wall in patients with intrauterine adhesions. Front Physiol 2022; 13:990009. [PMID: 36620214 PMCID: PMC9815801 DOI: 10.3389/fphys.2022.990009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022] Open
Abstract
Introduction: It has been previously reported that intrauterine adhesions (IUAs) are the main cause of uterine infertility. However, the histological origin of scar tissue present on the inner wall of the uterine cavity with IUAs has not been previously studied, which is particularly necessary for follow-up research and prevention and treatment. Methods: In this study, myometrium with normal uterus were assigned to the control group and scar tissues with IUAs were assigned to the experimental group. And pathological characteristics and transcriptomic were analyzed between the two groups. Results: We founded no difference was noted in the histological morphology and the α-SMA expression between the experimental and control groups. A total of 698 differentially expressed genes were identified between the two groups. Gene Ontology (GO) analyses revealed that the DEGs were significantly enriched in cell proliferation, AP-1 complex formation, and angiogenesis. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses revealed that the target genes were significantly enriched in the AGE-RAGE, FOXO and TNF signaling pathway. Discussion: As far as we know, this is the first study to propose that the scar tissues are mainly derived from the myometrium and the first one to report differentially expressed genes in the scar tissues of IUAs.
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Affiliation(s)
- Waixing Li
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China
| | - Pan Gu
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China,The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Bingsi Gao
- The Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Lingxiao Zou
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China
| | - Aiqian Zhang
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China
| | - Huan Huang
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China
| | - Xingping Zhao
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China,*Correspondence: Xingping Zhao, ; Dabao Xu,
| | - Dabao Xu
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China,*Correspondence: Xingping Zhao, ; Dabao Xu,
| | - Chunxia Cheng
- Department of Obstetrics and Gynecology, The Third Xiangya Hospital of the Central South University, Changsha, Hunan, China
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Establishment of Adenomyosis Organoids as a Preclinical Model to Study Infertility. J Pers Med 2022; 12:jpm12020219. [PMID: 35207707 PMCID: PMC8876865 DOI: 10.3390/jpm12020219] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/16/2022] Open
Abstract
Adenomyosis is related to infertility and miscarriages, but so far there are no robust in vitro models that reproduce its pathological features to study the molecular mechanisms involved in this disease. Endometrial organoids are in vitro 3D models that recapitulate the native microenvironment and reproduce tissue characteristics that would allow the study of adenomyosis pathogenesis and related infertility disorders. In our study, human endometrial biopsies from adenomyosis (n = 6) and healthy women (n = 6) were recruited. Organoids were established and hormonally differentiated to recapitulate midsecretory and gestational endometrial phases. Physiological and pathological characteristics were evaluated by immunohistochemistry, immunofluorescence, qRT-PCR, and ELISA. Secretory and gestational organoids recapitulated in vivo glandular epithelial phenotype (pan-cytokeratin, Muc-1, PAS, Laminin, and Ki67) and secretory and gestational features (α-tubulin, SOX9, SPP1, PAEP, LIF, and 17βHSD2 expression and SPP1 secretion). Adenomyosis organoids showed higher expression of TGF-β2 and SMAD3 and increased gene expression of SPP1, PAEP, LIF, and 17βHSD2 compared with control organoids. Our results demonstrate that organoids derived from endometria of adenomyosis patients and differentiated to secretory and gestational phases recapitulate native endometrial-tissue-specific features and disease-specific traits. Adenomyosis-derived organoids are a promising in vitro preclinical model to study impaired implantation and pregnancy disorders in adenomyosis and enable personalized drug screening.
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Khader N, Shchuka VM, Shynlova O, Mitchell JA. Transcriptional control of parturition: insights from gene regulation studies in the myometrium. Mol Hum Reprod 2021; 27:gaab024. [PMID: 33823545 PMCID: PMC8126590 DOI: 10.1093/molehr/gaab024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/09/2021] [Indexed: 12/19/2022] Open
Abstract
The onset of labour is a culmination of a series of highly coordinated and preparatory physiological events that take place throughout the gestational period. In order to produce the associated contractions needed for foetal delivery, smooth muscle cells in the muscular layer of the uterus (i.e. myometrium) undergo a transition from quiescent to contractile phenotypes. Here, we present the current understanding of the roles transcription factors play in critical labour-associated gene expression changes as part of the molecular mechanistic basis for this transition. Consideration is given to both transcription factors that have been well-studied in a myometrial context, i.e. activator protein 1, progesterone receptors, oestrogen receptors, and nuclear factor kappa B, as well as additional transcription factors whose gestational event-driving contributions have been demonstrated more recently. These transcription factors may form pregnancy- and labour-associated transcriptional regulatory networks in the myometrium to modulate the timing of labour onset. A more thorough understanding of the transcription factor-mediated, labour-promoting regulatory pathways holds promise for the development of new therapeutic treatments that can be used for the prevention of preterm labour in at-risk women.
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Affiliation(s)
- Nawrah Khader
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Virlana M Shchuka
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Oksana Shynlova
- Lunenfeld Tanenbaum Research Institute, Sinai Health System, Toronto, ON, Canada
- Department of Obstetrics & Gynaecology, University of Toronto, ON, Canada
| | - Jennifer A Mitchell
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
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