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Kailankangas V, Katayama S, Gröndahl-Yli-Hannuksela K, Vilhonen J, Tervaniemi MH, Rantakokko-Jalava K, Seiskari T, Lönnqvist E, Kere J, Oksi J, Syrjänen J, Vuopio J. Low expression of the CCL5 gene and low serum concentrations of CCL5 in severe invasive group a streptococcal disease. Infection 2024:10.1007/s15010-024-02318-6. [PMID: 38865072 DOI: 10.1007/s15010-024-02318-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/05/2024] [Indexed: 06/13/2024]
Abstract
PURPOSE Our objective was to elucidate host dependent factors of disease severity in invasive group A Streptococcal disease (iGAS) using transcriptome profiling of iGAS cases of varying degrees of severity at different timepoints. To our knowledge there are no previous transcriptome studies in iGAS patients. METHODS We recruited iGAS cases from June 2018 to July 2020. Whole blood samples for transcriptome analysis and serum for biomarker analysis were collected at three timepoints representing the acute (A), the convalescent (B) and the post-infection phase (C). Gene expression was compared against clinical traits and disease course. Serum chemokine ligand 5 (CCL5, an inflammatory cytokine) concentration was also measured. RESULTS Forty-five patients were enrolled. After disqualifying degraded or impure RNAs we had 34, 31 and 21 subjects at timepoints A, B, and C, respectively. Low expression of the CCL5 gene correlated strongly with severity (death or need for intensive care) at timepoint A (AUC = 0.92), supported by low concentrations of CCL5 in sera. CONCLUSIONS Low gene expression levels and low serum concentration of CCL5 in the early stages of an iGAS infection were associated with a more severe disease course. CCL5 might have potential as a predictor of disease severity. Low expression of genes of cytotoxic immunity, especially CCL5, and corresponding low serum concentrations of CCL5 associated with a severe disease course, i.e. death, or need for intensive care, in early phase of invasive group A Streptococcal disease.
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Affiliation(s)
- V Kailankangas
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland.
| | - S Katayama
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Solna, Sweden
| | | | - J Vilhonen
- Department of Infectious Diseases, Turku University Hospital, Turku, Finland
| | - M H Tervaniemi
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - K Rantakokko-Jalava
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Clinical Microbiology, Laboratory Division, Turku University Hospital, Turku, Finland
| | - T Seiskari
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland
| | - E Lönnqvist
- Department of Clinical Microbiology, Fimlab Laboratories, Tampere, Finland
| | - J Kere
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Solna, Sweden
| | - J Oksi
- Department of Infectious Diseases, Turku University Hospital, Turku, Finland
- Faculty of Medicine, University of Turku, Turku, Finland
| | - J Syrjänen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
| | - J Vuopio
- Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Clinical Microbiology, Laboratory Division, Turku University Hospital, Turku, Finland
- Finnish Institute for Health and Welfare (THL), Helsinki, Finland
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Hao J, Li T, Heinzelmann M, Moussaud-Lamodière E, Lebre F, Krjutškov K, Damdimopoulos A, Arnelo C, Pettersson K, Alfaro-Moreno E, Lindskog C, van Duursen M, Damdimopoulou P. Effects of chemical in vitro activation versus fragmentation on human ovarian tissue and follicle growth in culture. Hum Reprod Open 2024; 2024:hoae028. [PMID: 38803550 PMCID: PMC11128059 DOI: 10.1093/hropen/hoae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 04/15/2024] [Indexed: 05/29/2024] Open
Abstract
STUDY QUESTION What is the effect of the chemical in vitro activation (cIVA) protocol compared with fragmentation only (Frag, also known as mechanical IVA) on gene expression, follicle activation and growth in human ovarian tissue in vitro? SUMMARY ANSWER Although histological assessment shows that cIVA significantly increases follicle survival and growth compared to Frag, both protocols stimulate extensive and nearly identical transcriptomic changes in cultured tissue compared to freshly collected ovarian tissue, including marked changes in energy metabolism and inflammatory responses. WHAT IS KNOWN ALREADY Treatments based on cIVA of the phosphatase and tensin homolog (PTEN)-phosphatidylinositol 3-kinase (PI3K) pathway in ovarian tissue followed by auto-transplantation have been administered to patients with refractory premature ovarian insufficiency (POI) and resulted in live births. However, comparable effects with mere tissue fragmentation have been shown, questioning the added value of chemical stimulation that could potentially activate oncogenic responses. STUDY DESIGN SIZE DURATION Fifty-nine ovarian cortical biopsies were obtained from consenting women undergoing elective caesarean section (C-section). The samples were fragmented for culture studies. Half of the fragments were exposed to bpV (HOpic)+740Y-P (Frag+cIVA group) during the first 24 h of culture, while the other half were cultured with medium only (Frag group). Subsequently, both groups were cultured with medium only for an additional 6 days. Tissue and media samples were collected for histological, transcriptomic, steroid hormone, and cytokine/chemokine analyses at various time points. PARTICIPANTS/MATERIALS SETTING METHODS Effects on follicles were evaluated by counting and scoring serial sections stained with hematoxylin and eosin before and after the 7-day culture. Follicle function was assessed by quantification of steroids by ultra-performance liquid chromatography tandem-mass spectrometry at different time points. Cytokines and chemokines were measured by multiplex assay. Transcriptomic effects were measured by RNA-sequencing (RNA-seq) of the tissue after the initial 24-h culture. Selected differentially expressed genes (DEGs) were validated by quantitative PCR and immunofluorescence in cultured ovarian tissue as well as in KGN cell (human ovarian granulosa-like tumor cell line) culture experiments. MAIN RESULTS AND THE ROLE OF CHANCE Compared to the Frag group, the Frag+cIVA group exhibited a significantly higher follicle survival rate, increased numbers of secondary follicles, and larger follicle sizes. Additionally, the tissue in the Frag+cIVA group produced less dehydroepiandrosterone compared to Frag. Cytokine measurement showed a strong inflammatory response at the start of the culture in both groups. The RNA-seq data revealed modest differences between the Frag+cIVA and Frag groups, with only 164 DEGs identified using a relaxed cut-off of false discovery rate (FDR) <0.1. Apart from the expected PI3K-protein kinase B (Akt) pathway, cIVA also regulated pathways related to hypoxia, cytokines, and inflammation. In comparison to freshly collected ovarian tissue, gene expression in general was markedly affected in both the Frag+cIVA and Frag groups, with a total of 3119 and 2900 DEGs identified (FDR < 0.001), respectively. The top enriched gene sets in both groups included several pathways known to modulate follicle growth such as mammalian target of rapamycin (mTOR)C1 signaling. Significant changes compared to fresh tissue were also observed in the expression of genes encoding for steroidogenesis enzymes and classical granulosa cell markers in both groups. Intriguingly, we discovered a profound upregulation of genes related to glycolysis and its upstream regulator in both Frag and Frag+cIVA groups, and these changes were further boosted by the cIVA treatment. Cell culture experiments confirmed glycolysis-related genes as direct targets of the cIVA drugs. In conclusion, cIVA enhances follicle growth, as expected, but the mechanisms may be more complex than PI3K-Akt-mTOR alone, and the impact on function and quality of the follicles after the culture period remains an open question. LARGE SCALE DATA Data were deposited in the GEO data base, accession number GSE234765. The code for sequencing analysis can be found in https://github.com/tialiv/IVA_project. LIMITATIONS REASONS FOR CAUTION Similar to the published IVA protocols, the first steps in our study were performed in an in vitro culture model where the ovarian tissue was isolated from the regulation of hypothalamic-pituitary-ovarian axis. Further in vivo experiments will be needed, for example in xeno-transplantation models, to explore the long-term impacts of the discovered effects. The tissue collected from patients undergoing C-section may not be comparable to tissue of patients with POI. WIDER IMPLICATIONS OF THE FINDINGS The general impact of fragmentation and short (24 h) in vitro culture on gene expression in ovarian tissue far exceeded the effects of cIVA. Yet, follicle growth was stimulated by cIVA, which may suggest effects on specific cell populations that may be diluted in bulk RNA-seq. Nevertheless, we confirmed the impact of cIVA on glycolysis using a cell culture model, suggesting impacts on cellular signaling beyond the PI3K pathway. The profound changes in inflammation and glycolysis following fragmentation and culture could contribute to follicle activation and loss in ovarian tissue culture, as well as in clinical applications, such as fertility preservation by ovarian tissue auto-transplantation. STUDY FUNDING/COMPETING INTERESTS This study was funded by research grants from European Union's Horizon 2020 Research and Innovation Programme (Project ERIN No. 952516, FREIA No. 825100), Swedish Research Council VR (2020-02132), StratRegen funding from Karolinska Institutet, KI-China Scholarship Council (CSC) Programme and the Natural Science Foundation of Hunan (2022JJ40782). International Iberian Nanotechnology Laboratory Research was funded by the European Union's H2020 Project Sinfonia (857253) and SbDToolBox (NORTE-01-0145-FEDER-000047), supported by Norte Portugal Regional Operational Programme (NORTE 2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund. No competing interests are declared.
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Affiliation(s)
- Jie Hao
- Department of Reproductive Medicine, Xiangya Hospital, Central South University, Changsha, P.R. China
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Tianyi Li
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Manuel Heinzelmann
- Department of Environment and Health, Amsterdam Institute for Life and Environment, Amsterdam, The Netherlands
| | - Elisabeth Moussaud-Lamodière
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Filipa Lebre
- Nanosafety Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Kaarel Krjutškov
- Faculty of Medicine, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | | | - Catarina Arnelo
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Pettersson
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | | | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Cancer Precision Medicine Research Program, Uppsala University, Uppsala, Sweden
| | - Majorie van Duursen
- Department of Environment and Health, Amsterdam Institute for Life and Environment, Amsterdam, The Netherlands
| | - Pauliina Damdimopoulou
- Department of Gynecology and Reproductive Medicine, Karolinska University Hospital, Stockholm, Sweden
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
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Wei D, Su Y, Leung PCK, Li Y, Chen ZJ. Roles of bone morphogenetic proteins in endometrial remodeling during the human menstrual cycle and pregnancy. Hum Reprod Update 2024; 30:215-237. [PMID: 38037193 DOI: 10.1093/humupd/dmad031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/17/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND During the human menstrual cycle and pregnancy, the endometrium undergoes a series of dynamic remodeling processes to adapt to physiological changes. Insufficient endometrial remodeling, characterized by inadequate endometrial proliferation, decidualization and spiral artery remodeling, is associated with infertility, endometriosis, dysfunctional uterine bleeding, and pregnancy-related complications such as preeclampsia and miscarriage. Bone morphogenetic proteins (BMPs), a subset of the transforming growth factor-β (TGF-β) superfamily, are multifunctional cytokines that regulate diverse cellular activities, such as differentiation, proliferation, apoptosis, and extracellular matrix synthesis, are now understood as integral to multiple reproductive processes in women. Investigations using human biological samples have shown that BMPs are essential for regulating human endometrial remodeling processes, including endometrial proliferation and decidualization. OBJECTIVE AND RATIONALE This review summarizes our current knowledge on the known pathophysiological roles of BMPs and their underlying molecular mechanisms in regulating human endometrial proliferation and decidualization, with the goal of promoting the development of innovative strategies for diagnosing, treating and preventing infertility and adverse pregnancy complications associated with dysregulated human endometrial remodeling. SEARCH METHODS A literature search for original articles published up to June 2023 was conducted in the PubMed, MEDLINE, and Google Scholar databases, identifying studies on the roles of BMPs in endometrial remodeling during the human menstrual cycle and pregnancy. Articles identified were restricted to English language full-text papers. OUTCOMES BMP ligands and receptors and their transduction molecules are expressed in the endometrium and at the maternal-fetal interface. Along with emerging technologies such as tissue microarrays, 3D organoid cultures and advanced single-cell transcriptomics, and given the clinical availability of recombinant human proteins and ongoing pharmaceutical development, it is now clear that BMPs exert multiple roles in regulating human endometrial remodeling and that these biomolecules (and their receptors) can be targeted for diagnostic and therapeutic purposes. Moreover, dysregulation of these ligands, their receptors, or signaling determinants can impact endometrial remodeling, contributing to infertility or pregnancy-related complications (e.g. preeclampsia and miscarriage). WIDER IMPLICATIONS Although further clinical trials are needed, recent advancements in the development of recombinant BMP ligands, synthetic BMP inhibitors, receptor antagonists, BMP ligand sequestration tools, and gene therapies have underscored the BMPs as candidate diagnostic biomarkers and positioned the BMP signaling pathway as a promising therapeutic target for addressing infertility and pregnancy complications related to dysregulated human endometrial remodeling.
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Affiliation(s)
- Daimin Wei
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Medical Integration and Practice Center, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
| | - Yaxin Su
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
| | - Peter C K Leung
- Department of Obstetrics and Gynaecology, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Yan Li
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- Medical Integration and Practice Center, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, Shandong, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, China
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, Shandong, China
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Coschiera A, Yoshihara M, Lauter G, Ezer S, Pucci M, Li H, Kavšek A, Riedel CG, Kere J, Swoboda P. Primary cilia promote the differentiation of human neurons through the WNT signaling pathway. BMC Biol 2024; 22:48. [PMID: 38413974 PMCID: PMC10900739 DOI: 10.1186/s12915-024-01845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Primary cilia emanate from most human cell types, including neurons. Cilia are important for communicating with the cell's immediate environment: signal reception and transduction to/from the ciliated cell. Deregulation of ciliary signaling can lead to ciliopathies and certain neurodevelopmental disorders. In the developing brain cilia play well-documented roles for the expansion of the neural progenitor cell pool, while information about the roles of cilia during post-mitotic neuron differentiation and maturation is scarce. RESULTS We employed ciliated Lund Human Mesencephalic (LUHMES) cells in time course experiments to assess the impact of ciliary signaling on neuron differentiation. By comparing ciliated and non-ciliated neuronal precursor cells and neurons in wild type and in RFX2 -/- mutant neurons with altered cilia, we discovered an early-differentiation "ciliary time window" during which transient cilia promote axon outgrowth, branching and arborization. Experiments in neurons with IFT88 and IFT172 ciliary gene knockdowns, leading to shorter cilia, confirm these results. Cilia promote neuron differentiation by tipping WNT signaling toward the non-canonical pathway, in turn activating WNT pathway output genes implicated in cyto-architectural changes. CONCLUSIONS We provide a mechanistic entry point into when and how ciliary signaling coordinates, promotes and translates into anatomical changes. We hypothesize that ciliary alterations causing neuron differentiation defects may result in "mild" impairments of brain development, possibly underpinning certain aspects of neurodevelopmental disorders.
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Affiliation(s)
- Andrea Coschiera
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba, Japan
- Chiba University, Chiba, Japan
| | - Gilbert Lauter
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala, Sweden
- Uppsala University, Uppsala, Sweden
| | - Sini Ezer
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Mariangela Pucci
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- Department of Bioscience and Technology for Food, Agriculture and Environment, Teramo, Italy
- University of Teramo, Teramo, Italy
| | - Haonan Li
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Alan Kavšek
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Christian G Riedel
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
- University of Helsinki, Stem Cells and Metabolism Research Program, and Folkhälsan Research Center, Helsinki, Finland
| | - Peter Swoboda
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden.
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Altmäe S, Plaza-Florido A, Esteban FJ, Anguita-Ruiz A, Krjutškov K, Katayama S, Einarsdottir E, Kere J, Radom-Aizik S, Ortega FB. Effects of exercise on whole-blood transcriptome profile in children with overweight/obesity. Am J Hum Biol 2024; 36:e23983. [PMID: 37715654 DOI: 10.1002/ajhb.23983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND The current knowledge about the molecular mechanisms underlying the health benefits of exercise is still limited, especially in childhood. We set out to investigate the effects of a 20-week exercise intervention on whole-blood transcriptome profile (RNA-seq) in children with overweight/obesity. METHODS Twenty-four children (10.21 ± 1.33 years, 46% girls) with overweight/obesity, were randomized to either a 20-week exercise program (intervention group; n = 10), or to a no-exercise control group (n = 14). Whole-blood transcriptome profile was analyzed using RNA-seq by STRT technique with GlobinLock technology. RESULTS Following the 20-week exercise intervention program, 161 genes were differentially expressed between the exercise and the control groups among boys, and 121 genes among girls (p-value <0.05), while after multiple correction, no significant difference between exercise and control groups persisted in gene expression profiles (FDR >0.05). Genes enriched in GO processes and molecular pathways showed different immune response in boys (antigen processing and presentation, infections, and T cell receptor complex) and in girls (Fc epsilon RI signaling pathway) (FDR <0.05). CONCLUSION These results suggest that 20-week exercise intervention program alters the molecular pathways involved in immune processes in children with overweight/obesity.
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Affiliation(s)
- Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Abel Plaza-Florido
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada Granada, Granada, Spain
- Pediatric Exercise and Genomics Research Center, Department of Pediatrics, School of Medicine, University of California at Irvine, Irvine, California, USA
| | - Francisco J Esteban
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen, Spain
| | - Augusto Anguita-Ruiz
- Barcelona Institute for Global Health, ISGlobal Barcelona, Barcelona, Spain
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada Granada, Granada, Spain
- Center of Biomedical Research, Institute of Nutrition and Food Technology "José Mataix", University of Granada, Granada, Spain
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, Madrid, Spain
| | - Kaarel Krjutškov
- Competence Centre for Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Shintaro Katayama
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Shlomit Radom-Aizik
- Pediatric Exercise and Genomics Research Center, Department of Pediatrics, School of Medicine, University of California at Irvine, Irvine, California, USA
| | - Francisco B Ortega
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada Granada, Granada, Spain
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
- CIBERobn Physiopathology of Obesity and Nutrition, Granada, Spain
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Roberson EC, Tran NK, Godambe AN, Mark H, Nguimtsop M, Rust T, Ung E, Barker LJ, Fitch RD, Wallingford JB. Hedgehog signaling is required for endometrial remodeling and myometrial homeostasis in the cycling mouse uterus. iScience 2023; 26:107993. [PMID: 37810243 PMCID: PMC10551904 DOI: 10.1016/j.isci.2023.107993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 08/24/2023] [Accepted: 09/16/2023] [Indexed: 10/10/2023] Open
Abstract
Decades of work demonstrate that the mammalian estrous cycle is controlled by cycling steroid hormones. However, the signaling mechanisms that act downstream, linking hormonal action to the physical remodeling of the cycling uterus, remain unclear. To address this issue, we analyzed gene expression at all stages of the mouse estrous cycle. Strikingly, we found that several genetic programs well-known to control tissue morphogenesis in developing embryos displayed cyclical patterns of expression. We find that most of the genetic architectures of Hedgehog signaling (ligands, receptors, effectors, and transcription factors) are transcribed cyclically in the uterus, and that conditional disruption of the Hedgehog receptor smoothened not only elicits a failure of normal cyclical thickening of the endometrial lining but also induces aberrant deformation of the uterine smooth muscle. Together, our data shed light on the mechanisms underlying normal uterine remodeling specifically and cyclical gene expression generally.
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Affiliation(s)
- Elle C Roberson
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Ngan Kim Tran
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Anushka N Godambe
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Harrison Mark
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Michelle Nguimtsop
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Trinity Rust
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - Elizabeth Ung
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - LeCaine J Barker
- Department of Pediatrics, Section of Developmental Biology, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Rebecca D Fitch
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
| | - John B Wallingford
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA
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Pirttiniemi A, Adeshara K, Happonen N, Einarsdottir E, Katayama S, Salmenkari H, Hörkkö S, Kere J, Groop PH, Lehto M. Long-chain polyphosphates inhibit type I interferon signaling and augment LPS-induced cytokine secretion in human leukocytes. J Leukoc Biol 2023; 114:250-265. [PMID: 37224571 DOI: 10.1093/jleuko/qiad058] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 04/20/2023] [Accepted: 05/12/2023] [Indexed: 05/26/2023] Open
Abstract
Inorganic polyphosphates are evolutionarily conserved bioactive phosphate polymers found as various chain lengths in all living organisms. In mammals, polyphosphates play a vital role in the regulation of cellular metabolism, coagulation, and inflammation. Long-chain polyphosphates are found along with endotoxins in pathogenic gram-negative bacteria and can participate in bacterial virulence. We aimed to investigate whether exogenously administered polyphosphates modulate human leukocyte function in vitro by treating the cells with 3 different chain lengths of polyphosphates (P14, P100, and P700). The long-chain polyphosphates, P700, had a remarkable capacity to downregulate type I interferon signaling dose dependently in THP1-Dual cells while only a slight elevation could be observed in the NF-κB pathway with the highest dose of P700. P700 treatment decreased lipopolysaccharide-induced IFNβ transcription and secretion, reduced STAT1 phosphorylation, and downregulated subsequent interferon-stimulated gene expression in primary human peripheral blood mononuclear cells. P700 also augmented lipopolysaccharide-induced secretion of IL-1α, IL-1β, IL-4, IL-5, IL-10, and IFNγ. Furthermore, P700 has previously been reported to increase the phosphorylation of several intracellular signaling mediators, such as AKT, mTOR, ERK, p38, GSK3α/β, HSP27, and JNK pathway components, which was supported by our findings. Taken together, these observations demonstrate the extensive modulatory effects P700 has on cytokine signaling and the inhibitory effects specifically targeted to type I interferon signaling in human leukocytes.
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Affiliation(s)
- Anniina Pirttiniemi
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
- Clinical and Molecular Metabolism, Faculty of Medicine Research Programs, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Krishna Adeshara
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
- Clinical and Molecular Metabolism, Faculty of Medicine Research Programs, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Natalie Happonen
- Medical Microbiology and Immunology, Research Unit of Biomedicine, University of Oulu, Aapistie 5A, 90220 Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Aapistie 5A, 90220 Oulu, Finland
- Nordlab, Oulu University Hospital, Kajaanintie 50, 90220 Oulu, Finland
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Shintaro Katayama
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Blickagången 16, Flemingsberg, SE-14183 Huddinge, Sweden
| | - Hanne Salmenkari
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
- Clinical and Molecular Metabolism, Faculty of Medicine Research Programs, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
| | - Sohvi Hörkkö
- Medical Microbiology and Immunology, Research Unit of Biomedicine, University of Oulu, Aapistie 5A, 90220 Oulu, Finland
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Aapistie 5A, 90220 Oulu, Finland
| | - Juha Kere
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Stem Cells and Metabolism Research Program, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Neo, Blickagången 16, Flemingsberg, SE-14183 Huddinge, Sweden
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
- Clinical and Molecular Metabolism, Faculty of Medicine Research Programs, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Alfred Centre, 99 Commercial Road, Melbourne 3004, VIC, Australia
| | - Markku Lehto
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 4, 00290 Helsinki, Finland
- Clinical and Molecular Metabolism, Faculty of Medicine Research Programs, University of Helsinki, Biomedicum, Haartmaninkatu 8, 00290 Helsinki, Finland
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8
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Sudoma I, Goncharova Y, Dons'koy B, Mykytenko D. Immune phenotype of the endometrium in patients with recurrent implantation failures after the transfer of genetically tested embryos in assisted reproductive technology programs. J Reprod Immunol 2023; 157:103943. [PMID: 36966647 DOI: 10.1016/j.jri.2023.103943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 03/08/2023] [Accepted: 03/20/2023] [Indexed: 05/25/2023]
Abstract
Recurrent implantation failures (RIF) in assisted reproduction programs are one of the most challenging problems. Among the factors that can adversely affect implantation, endometrial immune structural disorders may be one of the leading causes. The aim of our work was to study the immune features of the endometrium in women with RIF after genetically tested embryo transfer in comparison with fertile gestational carriers. Immune cells in endometrial samples were studied by flow cytometry and RNA expression of IL (interleukin)15, IL18, fibroblast growth factor-inducible 14 receptor (Fn14), and tumor necrosis factor-like weak inducer of apoptosis (TWEAK) by reverse polymerase chain reaction. In one-third of the cases, a unique immune profile of the endometrium, which we called the not transformed endometrial immune phenotype, was found. It is characterized by a combination of features, such as high expression of HLA-DR on natural killers (NK), increased fraction of CD16 + , and a decreased fraction of CD56bright endometrial NK. In addition, when compared to gestational carriers, patients with RIF had a greater discrepancy between IL18 mRNA expression data, reduced mean TWEAK and Fn14 levels, and increased IL18/TWEAK and IL15/Fn14 ratios. Immune abnormalities that were found in more than half of the patients (66.7 %) may be the cause of implantation failures in genetically tested embryo transfer programs.
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Affiliation(s)
- Iryna Sudoma
- Shupyk National Healthcare University of Ukraine, Ukraine; Clinic of Reproductive Medicine NADIYA, Ukraine
| | | | - Borys Dons'koy
- State Institution "Institute of Pediatrics, Obstetrics and Gynecology of NAMS of Ukraine", Ukraine
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9
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Kirschen GW, Hessami K, AlAshqar A, Afrin S, Lulseged B, Borahay M. Uterine Transcriptome: Understanding Physiology and Disease Processes. BIOLOGY 2023; 12:634. [PMID: 37106834 PMCID: PMC10136129 DOI: 10.3390/biology12040634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/16/2023] [Accepted: 04/20/2023] [Indexed: 04/29/2023]
Abstract
In recent years, transcriptomics has enabled us to gain a deeper understanding of fundamental reproductive physiology, including the menstrual cycle, through a more precise molecular analysis. The endometrial mRNA transcript levels fluctuate during the normal menstrual cycle, indicating changes in the relative recruitment and abundance of inflammatory cells, as well as changes in the receptivity and remodeling of the endometrium. In addition to providing a more comprehensive understanding of the molecular underpinnings of pathological gynecological conditions such as endometriosis, leiomyomas, and adenomyosis through RNA sequencing, this has allowed researchers to create transcriptome profiles during both normal menstrual cycles and pathological gynecological conditions. Such insights could potentially lead to more targeted and personalized therapies for benign gynecological conditions. Here, we provide an overview of recent advances in transcriptome analysis of normal and pathological endometrium.
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Affiliation(s)
- Gregory W. Kirschen
- Department of Gynecology & Obstetrics, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Kamran Hessami
- Maternal Fetal Care Center, Boston Children’s Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Abdelrahman AlAshqar
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sadia Afrin
- Department of Gynecology & Obstetrics, Johns Hopkins University, Baltimore, MD 21287, USA
| | | | - Mostafa Borahay
- Department of Gynecology & Obstetrics, Johns Hopkins University, Baltimore, MD 21287, USA
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10
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Pohl ST, Prada ML, Espinet E, Jurkowska R. Practical Considerations for Complex Tissue Dissociation for Single-Cell Transcriptomics. Methods Mol Biol 2022; 2584:371-387. [PMID: 36495461 DOI: 10.1007/978-1-0716-2756-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-cell and single-nucleus RNA sequencing have revolutionized biomedical research, allowing analysis of complex tissues, identification of novel cell types, and mapping of development as well as disease states. Successful application of this technology critically relies on the dissociation of solid organs and tissues into high-quality single-cell (or nuclei) suspensions.In this chapter, we examine several key aspects of the tissue handling workflow that need to be considered when establishing an efficient tissue processing protocol for single-cell RNA sequencing (scRNA-seq). These include tissue collection, transport, and storage, as well as the choice of the dissociation conditions. We emphasize the importance of the tissue quality check and discuss the advantages (and potential limitations) of tissue cryopreservation. We provide practical tips and considerations on each of the steps of the processing workflow, and comment on how to maximize cell viability and integrity, which are critical for obtaining high-quality single-cell transcriptomic data.
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Affiliation(s)
- Stephanie T Pohl
- Division of Biomedicine, School of Biosciences, Cardiff University, Cardiff, UK
| | - Maria Llamazares Prada
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ) and Translational Lung Research Center, Heidelberg, Germany
| | - Elisa Espinet
- Anatomy Unit, Department of Pathology and Experimental Therapy, School of Medicine, University of Barcelona (UB), L'Hospitalet de Llobregat, Barcelona, Spain
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11
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Ding L, Li X, Zhu H, Luo H. Single-Cell Sequencing in Rheumatic Diseases: New Insights from the Perspective of the Cell Type. Aging Dis 2022; 13:1633-1651. [PMID: 36465169 PMCID: PMC9662270 DOI: 10.14336/ad.2022.0323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 03/23/2022] [Indexed: 11/02/2023] Open
Abstract
Rheumatic diseases are a group of highly heterogeneous autoimmune and inflammatory disorders involving multiple systems. Dysfunction of immune and non-immune cells participates in the complex pathogenesis of rheumatic diseases. Therefore, studies on the abnormal activation of cell subtypes provided a specific basis for understanding the pathogenesis of rheumatic diseases, which promoted the accuracy of disease diagnosis and the effectiveness of various treatments. However, there was still a far way to achieve individualized precision medicine as the result of heterogeneity among cell subtypes. To obtain the biological information of cell subtypes, single-cell sequencing, a cutting-edge technology, is used for analyzing their genomes, transcriptomes, epigenetics, and proteomics. Novel results identified multiple cell subtypes in tissues of patients with rheumatic diseases by single-cell sequencing. Consequently, we provide an overview of recent applications of single-cell sequencing in rheumatic disease and cross-tissue to understand the cell subtypes and functions.
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Affiliation(s)
- Liqing Ding
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Xiaojing Li
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
| | - Honglin Zhu
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
| | - Hui Luo
- The Department of Rheumatology and Immunology, Xiangya Hospital of Central South University, Changsha, Hunan, China.
- Provincial Clinical Research Center for Rheumatic and Immunologic Diseases, Xiangya Hospital, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China.
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12
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Live slow-frozen human tumor tissues viable for 2D, 3D, ex vivo cultures and single-cell RNAseq. Commun Biol 2022; 5:1144. [PMID: 36307545 PMCID: PMC9616892 DOI: 10.1038/s42003-022-04025-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022] Open
Abstract
Biobanking of surplus human healthy and disease-derived tissues is essential for diagnostics and translational research. An enormous amount of formalin-fixed and paraffin-embedded (FFPE), Tissue-Tek OCT embedded or snap-frozen tissues are preserved in many biobanks worldwide and have been the basis of translational studies. However, their usage is limited to assays that do not require viable cells. The access to intact and viable human material is a prerequisite for translational validation of basic research, for novel therapeutic target discovery, and functional testing. Here we show that surplus tissues from multiple solid human cancers directly slow-frozen after resection can subsequently be used for different types of methods including the establishment of 2D, 3D, and ex vivo cultures as well as single-cell RNA sequencing with similar results when compared to freshly analyzed material. Fresh vs. slow-frozen tissues from various malignancies are compared for the establishment of 2D, 3D and ex vivo cultures, as well as for scRNAseq analysis, and found to be comparable and suitable for cancer research.
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13
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Miller D, Garcia-Flores V, Romero R, Galaz J, Pique-Regi R, Gomez-Lopez N. Single-Cell Immunobiology of the Maternal-Fetal Interface. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1450-1464. [PMID: 36192116 PMCID: PMC9536179 DOI: 10.4049/jimmunol.2200433] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/31/2022] [Indexed: 11/06/2022]
Abstract
Pregnancy success requires constant dialogue between the mother and developing conceptus. Such crosstalk is facilitated through complex interactions between maternal and fetal cells at distinct tissue sites, collectively termed the "maternal-fetal interface." The emergence of single-cell technologies has enabled a deeper understanding of the unique processes taking place at the maternal-fetal interface as well as the discovery of novel pathways and immune and nonimmune cell types. Single-cell approaches have also been applied to decipher the cellular dynamics throughout pregnancy, in parturition, and in obstetrical syndromes such as recurrent spontaneous abortion, preeclampsia, and preterm labor. Furthermore, single-cell technologies have been used during the recent COVID-19 pandemic to evaluate placental viral cell entry and the impact of SARS-CoV-2 infection on maternal and fetal immunity. In this brief review, we summarize the current knowledge of cellular immunobiology in pregnancy and its complications that has been generated through single-cell investigations of the maternal-fetal interface.
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Affiliation(s)
- Derek Miller
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Valeria Garcia-Flores
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
| | - Roberto Romero
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI
- Department of Obstetrics and Gynecology, University of Michigan, Ann Arbor, MI
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI
- Detroit Medical Center, Detroit, MI
| | - Jose Galaz
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
- Division of Obstetrics and Gynecology, School of Medicine, Faculty of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile; and
| | - Roger Pique-Regi
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI
| | - Nardhy Gomez-Lopez
- Perinatology Research Branch, Division of Obstetrics and Maternal-Fetal Medicine, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, U.S. Department of Health and Human Services, Detroit, MI;
- Department of Obstetrics and Gynecology, Wayne State University School of Medicine, Detroit, MI
- Department of Biochemistry, Microbiology and Immunology, Wayne State University School of Medicine, Detroit, MI
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14
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Koel M, Krjutškov K, Saare M, Samuel K, Lubenets D, Katayama S, Einarsdottir E, Vargas E, Sola-Leyva A, Lalitkumar PG, Gemzell-Danielsson K, Blesa D, Simon C, Lanner F, Kere J, Salumets A, Altmäe S. Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo-endometrium interplay. Hum Reprod Open 2022; 2022:hoac043. [PMID: 36339249 PMCID: PMC9632455 DOI: 10.1093/hropen/hoac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 09/21/2022] [Indexed: 08/17/2023] Open
Abstract
STUDY QUESTION Which genes regulate receptivity in the epithelial and stromal cellular compartments of the human endometrium, and which molecules are interacting in the implantation process between the blastocyst and the endometrial cells? SUMMARY ANSWER A set of receptivity-specific genes in the endometrial epithelial and stromal cells was identified, and the role of galectins (LGALS1 and LGALS3), integrin β1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in embryo-endometrium dialogue among many other protein-protein interactions were highlighted. WHAT IS KNOWN ALREADY The molecular dialogue taking place between the human embryo and the endometrium is poorly understood due to ethical and technical reasons, leaving human embryo implantation mostly uncharted. STUDY DESIGN SIZE DURATION Paired pre-receptive and receptive phase endometrial tissue samples from 16 healthy women were used for RNA sequencing. Trophectoderm RNA sequences were from blastocysts. PARTICIPANTS/MATERIALS SETTING METHODS Cell-type-specific RNA-seq analysis of freshly isolated endometrial epithelial and stromal cells using fluorescence-activated cell sorting (FACS) from 16 paired pre-receptive and receptive tissue samples was performed. Endometrial transcriptome data were further combined in silico with trophectodermal gene expression data from 466 single cells originating from 17 blastocysts to characterize the first steps of embryo implantation. We constructed a protein-protein interaction network between endometrial epithelial and embryonal trophectodermal cells, and between endometrial stromal and trophectodermal cells, thereby focusing on the very first phases of embryo implantation, and highlighting the molecules likely to be involved in the embryo apposition, attachment and invasion. MAIN RESULTS AND THE ROLE OF CHANCE In total, 499 epithelial and 581 stromal genes were up-regulated in the receptive phase endometria when compared to pre-receptive samples. The constructed protein-protein interactions identified a complex network of 558 prioritized protein-protein interactions between trophectodermal, epithelial and stromal cells, which were grouped into clusters based on the function of the involved molecules. The role of galectins (LGALS1 and LGALS3), integrin β1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in the embryo implantation process were highlighted. LARGE SCALE DATA RNA-seq data are available at www.ncbi.nlm.nih.gov/geo under accession number GSE97929. LIMITATIONS REASONS FOR CAUTION Providing a static snap-shot of a dynamic process and the nature of prediction analysis is limited to the known interactions available in databases. Furthermore, the cell sorting technique used separated enriched epithelial cells and stromal cells but did not separate luminal from glandular epithelium. Also, the use of biopsies taken from non-pregnant women and using spare IVF embryos (due to ethical considerations) might miss some of the critical interactions characteristic of natural conception only. WIDER IMPLICATIONS OF THE FINDINGS The findings of our study provide new insights into the molecular embryo-endometrium interplay in the first steps of implantation process in humans. Knowledge about the endometrial cell-type-specific molecules that coordinate successful implantation is vital for understanding human reproduction and the underlying causes of implantation failure and infertility. Our study results provide a useful resource for future reproductive research, allowing the exploration of unknown mechanisms of implantation. We envision that those studies will help to improve the understanding of the complex embryo implantation process, and hopefully generate new prognostic and diagnostic biomarkers and therapeutic approaches to target both infertility and fertility, in the form of new contraceptives. STUDY FUNDING/COMPETING INTERESTS This research was funded by the Estonian Research Council (grant PRG1076); Horizon 2020 innovation grant (ERIN, grant no. EU952516); Enterprise Estonia (grant EU48695); the EU-FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP, grant SARM, EU324509); Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER) (grants RYC-2016-21199, ENDORE SAF2017-87526-R, and Endo-Map PID2021-127280OB-100); Programa Operativo FEDER Andalucía (B-CTS-500-UGR18; A-CTS-614-UGR20), Junta de Andalucía (PAIDI P20_00158); Margarita Salas program for the Requalification of the Spanish University system (UJAR01MS); the Knut and Alice Wallenberg Foundation (KAW 2015.0096); Swedish Research Council (2012-2844); and Sigrid Jusélius Foundation; Academy of Finland. A.S.-L. is funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-085440). K.G.-D. has received consulting fees and/or honoraria from RemovAid AS, Norway Bayer, MSD, Gedeon Richter, Mithra, Exeltis, MedinCell, Natural cycles, Exelgyn, Vifor, Organon, Campus Pharma and HRA-Pharma and NIH support to the institution; D.B. is an employee of IGENOMIX. The rest of the authors declare no conflict of interest.
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Affiliation(s)
- Mariann Koel
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Merli Saare
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Külli Samuel
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Dmitri Lubenets
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Shintaro Katayama
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Eva Vargas
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Jaén, Spain
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Parameswaran Grace Lalitkumar
- Department of Women’s and Children’s Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska Univeristy Hospital, Stockholm,Sweden
| | - Kristina Gemzell-Danielsson
- Department of Women’s and Children’s Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska Univeristy Hospital, Stockholm,Sweden
| | - David Blesa
- Department of Product Development, IGENOMIX, Valencia, Spain
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University and INCLIVA in Valencia, Valencia, Spain
- Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm,Sweden
- Ming Wai Lau Center for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm,Sweden
| | - Signe Altmäe
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm,Sweden
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15
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SFRP4 + stromal cell subpopulation with IGF1 signaling in human endometrial regeneration. Cell Discov 2022; 8:95. [PMID: 36163341 PMCID: PMC9512788 DOI: 10.1038/s41421-022-00438-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 06/17/2022] [Indexed: 11/08/2022] Open
Abstract
Our understanding of full-thickness endometrial regeneration after injury is limited by an incomplete molecular characterization of the cell populations responsible for the organ functions. To help fill this knowledge gap, we characterized 10,551 cells of full-thickness normal human uterine from two menstrual phases (proliferative and secretory phase) using unbiased single cell RNA-sequencing. We dissected cell heterogeneity of main cell types (epithelial, stromal, endothelial, and immune cells) of the full thickness uterine tissues, cell population architectures of human uterus cells across the menstrual cycle. We identified an SFRP4+ stromal cell subpopulation that was highly enriched in the regenerative stage of the human endometria during the menstrual cycle, and the SFRP4+ stromal cells could significantly enhance the proliferation of human endometrial epithelial organoid in vitro, and promote the regeneration of endometrial epithelial glands and full-thickness endometrial injury through IGF1 signaling pathway in vivo. Our cell atlas of full-thickness uterine tissues revealed the cellular heterogeneities, cell population architectures, and their cell-cell communications during the monthly regeneration of the human endometria, which provide insight into the biology of human endometrial regeneration and the development of regenerative medicine treatments against endometrial damage and intrauterine adhesion.
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16
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Valta M, Yoshihara M, Einarsdottir E, Pahkuri S, Ezer S, Katayama S, Knip M, Veijola R, Toppari J, Ilonen J, Kere J, Lempainen J. Viral infection-related gene upregulation in monocytes in children with signs of β-cell autoimmunity. Pediatr Diabetes 2022; 23:703-713. [PMID: 35419920 PMCID: PMC9545759 DOI: 10.1111/pedi.13346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/24/2022] [Accepted: 04/08/2022] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVE The pathogenesis of type 1 diabetes (T1D) is associated with genetic predisposition and immunological changes during presymptomatic disease. Differences in immune cell subset numbers and phenotypes between T1D patients and healthy controls have been described; however, the role and function of these changes in the pathogenesis is still unclear. Here we aimed to analyze the transcriptomic landscapes of peripheral blood mononuclear cells (PBMCs) during presymptomatic disease. METHODS Transcriptomic differences in PBMCs were compared between cases positive for islet autoantibodies and autoantibody negative controls (9 case-control pairs) and further in monocytes and lymphocytes separately in autoantibody positive subjects and control subjects (25 case-control pairs). RESULTS No significant differential expression was found in either data set. However, when gene set enrichment analysis was performed, the gene sets "defence response to virus" (FDR <0.001, ranking 2), "response to virus" (FDR <0.001, ranking 3) and "response to type I interferon" (FDR = 0.002, ranking 12) were enriched in the upregulated genes among PBMCs in cases. Upon further analysis, this was also seen in monocytes in cases (FDR = 0.01, ranking 2; FDR = 0.04, ranking 3 and FDR = 0.02, ranking 1, respectively) but not in lymphocytes. CONCLUSION Gene set enrichment analysis of children with T1D-associated autoimmunity revealed changes in pathways relevant for virus infection in PBMCs, particularly in monocytes. Virus infections have been repeatedly implicated in the pathogenesis of T1D. These results support the viral hypothesis by suggesting altered immune activation of viral immune pathways in monocytes during diabetes.
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Affiliation(s)
- Milla Valta
- Immunogenetics Laboratory, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Masahito Yoshihara
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene TechnologyKTH‐Royal Institute of TechnologySolnaSweden
| | - Sirpa Pahkuri
- Immunogenetics Laboratory, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Sini Ezer
- Stem Cells and Metabolism Research ProgramUniversity of Helsinki, and Folkhälsan Research CenterHelsinkiFinland
| | - Shintaro Katayama
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden,Stem Cells and Metabolism Research ProgramUniversity of Helsinki, and Folkhälsan Research CenterHelsinkiFinland
| | - Mikael Knip
- Pediatric Research Center, Children's HospitalUniversity of Helsinki and Helsinki University HospitalHelsinkiFinland,Research Program for Clinical and Molecular MetabolismFaculty of Medicine, University of HelsinkiHelsinkiFinland,Folkhälsan Research CenterHelsinkiFinland,Department of PediatricsTampere University HospitalTampereFinland
| | - Riitta Veijola
- Department of Pediatrics, PEDEGO Research Unit, MRC OuluOulu University Hospital and University of OuluOuluFinland
| | - Jorma Toppari
- Institute of Biomedicine, Research Centre for Integrative Physiology and PharmacologyUniversity of TurkuTurkuFinland,Department of PediatricsUniversity of Turku and Turku University HospitalTurkuFinland
| | - Jorma Ilonen
- Immunogenetics Laboratory, Institute of BiomedicineUniversity of TurkuTurkuFinland
| | - Juha Kere
- Department of Biosciences and NutritionKarolinska InstitutetHuddingeSweden,Stem Cells and Metabolism Research ProgramUniversity of Helsinki, and Folkhälsan Research CenterHelsinkiFinland
| | - Johanna Lempainen
- Immunogenetics Laboratory, Institute of BiomedicineUniversity of TurkuTurkuFinland,Department of PediatricsUniversity of Turku and Turku University HospitalTurkuFinland,Clinical MicrobiologyTurku University HospitalTurkuFinland
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17
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Lavogina D, Visser N, Samuel K, Davey E, Björvang RD, Hassan J, Koponen J, Rantakokko P, Kiviranta H, Rinken A, Olovsson M, Salumets A, Damdimopoulou P. Endocrine disrupting chemicals interfere with decidualization of human primary endometrial stromal cells in vitro. Front Endocrinol (Lausanne) 2022; 13:903505. [PMID: 36060944 PMCID: PMC9437351 DOI: 10.3389/fendo.2022.903505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/03/2022] [Indexed: 11/22/2022] Open
Abstract
Multiple studies have shown associations between exposure to endocrine disrupting chemicals (EDCs) and reduced fertility in women. However, little is known about the target organs of chemical disruption of female fertility. Here, we focus on the hormone-sensitive uterine lining, the endometrium, as a potential target. Decidualization is the morphological and functional change that endometrial stromal cells undergo to support endometrial receptivity, which is crucial for successful implantation, placentation, and pregnancy. We investigated the effect of nine selected EDCs on primary human endometrial stromal cell decidualization in vitro. The cells were exposed to a decidualization-inducing mixture in the presence or absence of 1 μM of nine different EDCs for nine days. Extent of decidualization was assessed by measuring the activity of cAMP dependent protein kinase, Rho-associated coiled-coil containing protein kinase, and protein kinase B in lysates using photoluminescent probes, and secretion of prolactin into the media by using ELISA. Decidualization-inducing mixture upregulated activity of protein kinases and prolactin secretion in cells derived from all women. Of the tested chemicals, dichlorodiphenyldichloroethylene (p,p'-DDE), hexachlorobenzene (HCB) and perfluorooctanesulfonic acid (PFOS) significantly reduced decidualization as judged by the kinase markers and prolactin secretion. In addition, bisphenol A (BPA) reduced prolactin secretion but did not significantly affect activity of the kinases. None of the EDCs was cytotoxic, based on the assessment of total protein content or activity of the viability marker casein kinase 2 in lysates. These results indicate that EDCs commonly present in the blood circulation of reproductive-aged women can reduce decidualization of human endometrial stromal cells in vitro. Future studies should focus on detailed hazard assessment to define possible risks of EDC exposure to endometrial dysfunction and implantation failure in women.
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Affiliation(s)
- Darja Lavogina
- Institute of Chemistry, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Nadja Visser
- Department of Women´s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Külli Samuel
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Eva Davey
- Department of Women´s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Richelle D. Björvang
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jasmin Hassan
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jani Koponen
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Panu Rantakokko
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Hannu Kiviranta
- Department of Health Security, Finnish Institute for Health and Welfare, Kuopio, Finland
| | - Ago Rinken
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Matts Olovsson
- Department of Women´s and Children’s Health, Uppsala University, Uppsala, Sweden
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Pauliina Damdimopoulou
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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18
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George AF, McGregor M, Gingrich D, Neidleman J, Marquez RS, Young KC, Thanigaivelan KL, Greene WC, Tien PC, Deitchman AN, Spitzer TL, Roan NR. Female Genital Fibroblasts Diminish the In Vitro Efficacy of PrEP against HIV. Viruses 2022; 14:v14081723. [PMID: 36016345 PMCID: PMC9413545 DOI: 10.3390/v14081723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 01/09/2023] Open
Abstract
The efficacy of HIV pre-exposure prophylaxis (PrEP) is high in men who have sex with men, but much more variable in women, in a manner largely attributed to low adherence. This reduced efficacy, however, could also reflect biological factors. Transmission to women is typically via the female reproductive tract (FRT), and vaginal dysbiosis, genital inflammation, and other factors specific to the FRT mucosa can all increase transmission risk. We have demonstrated that mucosal fibroblasts from the lower and upper FRT can markedly enhance HIV infection of CD4+ T cells. Given the current testing of tenofovir disoproxil fumarate, cabotegravir, and dapivirine regimens as candidate PrEP agents for women, we set out to determine using in vitro assays whether endometrial stromal fibroblasts (eSF) isolated from the FRT can affect the anti-HIV activity of these PrEP drugs. We found that PrEP drugs exhibit significantly reduced antiviral efficacy in the presence of eSFs, not because of decreased PrEP drug availability, but rather of eSF-mediated enhancement of HIV infection. These findings suggest that drug combinations that target both the virus and infection-promoting factors in the FRT-such as mucosal fibroblasts-may be more effective than PrEP alone at preventing sexual transmission of HIV to women.
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Affiliation(s)
- Ashley F. George
- Gladstone Institute of Virology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Matthew McGregor
- Gladstone Institute of Virology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - David Gingrich
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Jason Neidleman
- Gladstone Institute of Virology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA
| | | | - Kyrlia C. Young
- Gladstone Institute of Virology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Kaavya L. Thanigaivelan
- Gladstone Institute of Virology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Warner C. Greene
- Gladstone Institute of Virology, University of California at San Francisco, San Francisco, CA 94158, USA
- Departments of Medicine and Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Phyllis C. Tien
- Departments of Medicine and Veterans Affairs, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Amelia N. Deitchman
- Drug Research Unit, Department of Clinical Pharmacy, School of Pharmacy, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Trimble L. Spitzer
- Lieutenant Colonel, United States Air Force, Medical Center, Women’s Health Clinic, Naval Medical Center, Portsmouth, VA 23708, USA
| | - Nadia R. Roan
- Gladstone Institute of Virology, University of California at San Francisco, San Francisco, CA 94158, USA
- Department of Urology, University of California at San Francisco, San Francisco, CA 94143, USA
- Correspondence:
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19
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Yoshihara M, Kirjanov I, Nykänen S, Sokka J, Weltner J, Lundin K, Gawriyski L, Jouhilahti EM, Varjosalo M, Tervaniemi MH, Otonkoski T, Trokovic R, Katayama S, Vuoristo S, Kere J. Transient DUX4 expression in human embryonic stem cells induces blastomere-like expression program that is marked by SLC34A2. Stem Cell Reports 2022; 17:1743-1756. [PMID: 35777358 PMCID: PMC9287684 DOI: 10.1016/j.stemcr.2022.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/02/2022] [Accepted: 06/02/2022] [Indexed: 10/25/2022] Open
Abstract
Embryonic genome activation (EGA) is critical for embryonic development. However, our understanding of the regulatory mechanisms of human EGA is still incomplete. Human embryonic stem cells (hESCs) are an established model for studying developmental processes, but they resemble epiblast and are sub-optimal for modeling EGA. DUX4 regulates human EGA by inducing cleavage-stage-specific genes, while it also induces cell death. We report here that a short-pulsed expression of DUX4 in primed hESCs activates an EGA-like gene expression program in up to 17% of the cells, retaining cell viability. These DUX4-induced cells resembled eight-cell stage blastomeres and were named induced blastomere-like (iBM) cells. The iBM cells showed marked reduction of POU5F1 protein, as previously observed in mouse two-cell-like cells. Finally, the iBM cells were successfully enriched using an antibody against NaPi2b (SLC34A2), which is expressed in human blastomeres. The iBM cells provide an improved model system to study human EGA transcriptome.
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Affiliation(s)
- Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Institute for Advanced Academic Research, Chiba University, Chiba, Japan; Department of Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan.
| | - Ida Kirjanov
- Department of Obstetrics and Gynecology, University of Helsinki, Helsinki, Finland
| | - Sonja Nykänen
- Department of Obstetrics and Gynecology, University of Helsinki, Helsinki, Finland
| | - Joonas Sokka
- Research Programs Unit, Stem Cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jere Weltner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden; Division of Obstetrics and Gynecology, Karolinska University Hospital, Stockholm, Sweden
| | - Karolina Lundin
- Department of Obstetrics and Gynecology, University of Helsinki, Helsinki, Finland
| | - Lisa Gawriyski
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Research Programs Unit, Stem Cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mari H Tervaniemi
- Research Programs Unit, Stem Cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland
| | - Timo Otonkoski
- Research Programs Unit, Stem Cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Children's Hospital, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Ras Trokovic
- Research Programs Unit, Stem Cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Research Programs Unit, Stem Cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland
| | - Sanna Vuoristo
- Department of Obstetrics and Gynecology, University of Helsinki, Helsinki, Finland.
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Research Programs Unit, Stem Cells and Metabolism and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Folkhälsan Research Center, Helsinki, Finland.
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20
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Altered differentiation of endometrial mesenchymal stromal fibroblasts is associated with endometriosis susceptibility. Commun Biol 2022; 5:600. [PMID: 35725766 PMCID: PMC9209414 DOI: 10.1038/s42003-022-03541-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 05/31/2022] [Indexed: 01/10/2023] Open
Abstract
Cellular development is tightly regulated as mature cells with aberrant functions may initiate pathogenic processes. The endometrium is a highly regenerative tissue, shedding and regenerating each month. Endometrial stromal fibroblasts are regenerated each cycle from mesenchymal stem cells and play a pivotal role in endometriosis, a disease characterised by endometrial cells that grow outside the uterus. Why the cells of some women are more capable of developing into endometriosis lesions is not clear. Using isolated, purified and cultured endometrial cells of mesenchymal origin from 19 women with (n = 10) and without (n = 9) endometriosis we analysed the transcriptome of 33,758 individual cells and compared these to clinical characteristics and in vitro growth profiles. We show purified mesenchymal cell cultures include a mix of mesenchymal stem cells and two endometrial stromal fibroblast subtypes with distinct transcriptomic signatures indicative of varied progression through the differentiation processes. The fibroblast subgroup characterised by incomplete differentiation was predominantly (81%) derived from women with endometriosis and exhibited an altered in vitro growth profile. These results uncover an inherent difference in endometrial cells of women with endometriosis and highlight the relevance of cellular differentiation and its potential to contribute to disease susceptibility. Comparing single cell transcriptome data to clinical characteristics and in vitro growth profiles uncovers a potential role for divergent mesenchymal-derived stromal fibroblast maturation in endometriosis susceptibility.
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21
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Zhang L, Long W, Xu W, Chen X, Zhao X, Wu B. Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage. Front Genet 2022; 13:847646. [PMID: 35669188 PMCID: PMC9163836 DOI: 10.3389/fgene.2022.847646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 05/03/2022] [Indexed: 11/23/2022] Open
Abstract
Endometrium undergoes repeated repair and regeneration during the menstrual cycle. Previous attempts using gene expression data to define the menstrual cycle failed to come to an agreement. Here we used single-cell RNA sequencing data of C57BL/6J mice uteri to construct a novel integrated cell atlas of mice uteri from the regenerative endometrium to the maturational endometrium at the single-cell level, providing a more accurate cytological-based elucidation for the changes that occurred in the endometrium during the estrus cycle. Based on the expression levels of proliferating cell nuclear antigen, differentially expressed genes, and gene ontology terms, we delineated in detail the transitions of epithelial cells, stromal cells, and immune cells that happened during the estrus cycle. The transcription factors that shaped the differentiation of the mononuclear phagocyte system had been proposed, being Mafb, Irf7, and Nr4a1. The amounts and functions of immune cells varied sharply in two stages, especially NK cells and macrophages. We also found putative uterus tissue-resident macrophages and identified potential endometrial mesenchymal stem cells (high expression of Cd34, Pdgfrb, Aldh1a2) in vivo. The cell atlas of mice uteri presented here would improve our understanding of the transitions that occurred in the endometrium from the regenerative endometrium to the maturational endometrium. With the assistance of a normal cell atlas as a reference, we may identify morphologically unaffected abnormalities in future clinical practice. Cautions would be needed when adopting our conclusions, for the limited number of mice that participated in this study may affect the strength of our conclusions.
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Affiliation(s)
- Leyi Zhang
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- Key Laboratory of Tumor Microenvironment and Immune Therapy of Zhejiang Province, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute (Key Laboratory of Cancer Prevention & Intervention, National Ministry of Education), Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Wenying Long
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Wanwan Xu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Xiuying Chen
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Xiaofeng Zhao
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
| | - Bingbing Wu
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, China
- *Correspondence: Bingbing Wu,
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22
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Vuoristo S, Bhagat S, Hydén-Granskog C, Yoshihara M, Gawriyski L, Jouhilahti EM, Ranga V, Tamirat M, Huhtala M, Kirjanov I, Nykänen S, Krjutškov K, Damdimopoulos A, Weltner J, Hashimoto K, Recher G, Ezer S, Paluoja P, Paloviita P, Takegami Y, Kanemaru A, Lundin K, Airenne TT, Otonkoski T, Tapanainen JS, Kawaji H, Murakawa Y, Bürglin TR, Varjosalo M, Johnson MS, Tuuri T, Katayama S, Kere J. DUX4 is a multifunctional factor priming human embryonic genome activation. iScience 2022; 25:104137. [PMID: 35402882 PMCID: PMC8990217 DOI: 10.1016/j.isci.2022.104137] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/04/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Double homeobox 4 (DUX4) is expressed at the early pre-implantation stage in human embryos. Here we show that induced human DUX4 expression substantially alters the chromatin accessibility of non-coding DNA and activates thousands of newly identified transcribed enhancer-like regions, preferentially located within ERVL-MaLR repeat elements. CRISPR activation of transcribed enhancers by C-terminal DUX4 motifs results in the increased expression of target embryonic genome activation (EGA) genes ZSCAN4 and KHDC1P1. We show that DUX4 is markedly enriched in human zygotes, followed by intense nuclear DUX4 localization preceding and coinciding with minor EGA. DUX4 knockdown in human zygotes led to changes in the EGA transcriptome but did not terminate the embryos. We also show that the DUX4 protein interacts with the Mediator complex via the C-terminal KIX binding motif. Our findings contribute to the understanding of DUX4 as a regulator of the non-coding genome.
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Affiliation(s)
- Sanna Vuoristo
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
| | | | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden
| | - Lisa Gawriyski
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Vipin Ranga
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mahlet Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mikko Huhtala
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Ida Kirjanov
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Sonja Nykänen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Competence Centre for Health Technologies, 51010 Tartu, Estonia.,University of Tartu, Department of Obstetrics and Gynecology, Institute of Clinical Medicine, 50406 Tartu, Estonia
| | | | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Gaëlle Recher
- Laboratoire Photonique Numérique et Nanosciences, CNRS, Institut d'Optique Graduate School, University of Bordeaux, UMR 5298, 33400 Bordeaux, France
| | - Sini Ezer
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Priit Paluoja
- Competence Centre for Health Technologies, 51010 Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50090 Tartu, Estonia.,University of Helsinki, Doctoral Program in Population Health, 00014 Helsinki, Finland
| | - Pauliina Paloviita
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | | | | | - Karolina Lundin
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Tomi T Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Children's Hospital, Helsinki University Central Hospital, 00290
| | - Juha S Tapanainen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland.,Oulu University Hospital, 90220 Oulu, Finland
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan.,IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Thomas R Bürglin
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
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23
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Cousins FL, Filby CE, Gargett CE. Endometrial Stem/Progenitor Cells–Their Role in Endometrial Repair and Regeneration. FRONTIERS IN REPRODUCTIVE HEALTH 2022; 3:811537. [PMID: 36304009 PMCID: PMC9580754 DOI: 10.3389/frph.2021.811537] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022] Open
Abstract
The human endometrium is a remarkable tissue, undergoing ~450 cycles of proliferation, differentiation, shedding (menstruation), repair, and regeneration over a woman's reproductive lifespan. Post-menstrual repair is an extremely rapid and scar-free process, with re-epithelialization of the luminal epithelium completed within 48 h of initiation of shedding. Following menstruation, the functionalis grows from the residual basalis layer during the proliferative phase under the influence of rising circulating estrogen levels. The regenerative capacity of the endometrium is attributed to stem/progenitor cells which reside in both the epithelial and stromal cell compartments of the basalis layer. Finding a definitive marker for endometrial epithelial progenitors (eEPCs) has proven difficult. A number of different markers have been suggested as putative progenitor markers including, N-cadherin, SSEA-1, AXIN2, SOX-9 and ALDH1A1, some of which show functional stem cell activity in in vitro assays. Each marker has a unique location(s) in the glandular epithelium, which has led to the suggestion that a differentiation hierarchy exists, from the base of epithelial glands in the basalis to the luminal epithelium lining the functionalis, where epithelial cells express different combinations of markers as they differentiate and move up the gland into the functionalis away from the basalis niche. Perivascular endometrial mesenchymal stem cells (eMSCs) can be identified by co-expression of PDGFRβ and CD146 or by a single marker, SUSD2. This review will detail the known endometrial stem/progenitor markers; their identity, location and known interactions and hierarchy across the menstrual cycle, in particular post-menstrual repair and estrogen-driven regeneration, as well as their possible contributions to menstruation-related disorders such as endometriosis and regeneration-related disorder Asherman's syndrome. We will also highlight new techniques that allow for a greater understanding of stem/progenitor cells' role in repair and regeneration, including 3D organoids, 3D slice cultures and gene sequencing at the single cell level. Since mouse models are commonly used to study menstruation, repair and regeneration we will also detail the mouse stem/progenitor markers that have been investigated in vivo.
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Affiliation(s)
- Fiona L. Cousins
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
- *Correspondence: Fiona L. Cousins
| | - Caitlin E. Filby
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
| | - Caroline E. Gargett
- The Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Obstetrics and Gynecology, Monash University, Clayton, VIC, Australia
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24
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Emerging in vitro platforms and omics technologies for studying the endometrium and early embryo-maternal interface in humans. Placenta 2022; 125:36-46. [DOI: 10.1016/j.placenta.2022.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/09/2021] [Accepted: 01/09/2022] [Indexed: 12/11/2022]
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25
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Plaza-Florido A, Altmäe S, Esteban FJ, Löf M, Radom-Aizik S, Ortega FB. Cardiorespiratory fitness in children with overweight/obesity: Insights into the molecular mechanisms. Scand J Med Sci Sports 2021; 31:2083-2091. [PMID: 34333829 DOI: 10.1111/sms.14028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 07/29/2021] [Indexed: 01/06/2023]
Abstract
OBJECTIVES High cardiorespiratory fitness (CRF) levels reduce the risk of developing cardiovascular disease (CVD) during adulthood. However, little is known about the molecular mechanisms underlying the health benefits of high CRF levels at the early stage of life. This study aimed to analyze the whole-blood transcriptome profile of fit children with overweight/obesity (OW/OB) compared to unfit children with OW/OB. DESIGN 27 children with OW/OB (10.14 ± 1.3 years, 59% boys) from the ActiveBrains project were evaluated. VO2 peak was assessed using a gas analyzer, and participants were categorized into fit or unfit according to the CVD risk-related cut-points. Whole-blood transcriptome profile (RNA sequencing) was analyzed. Differential gene expression analysis was performed using the limma R/Bioconductor software package (analyses adjusted by sex and maturational status), and pathways' enrichment analysis was performed with DAVID. In addition, in silico validation data mining was performed using the PHENOPEDIA database. RESULTS 256 genes were differentially expressed in fit children with OW/OB compared to unfit children with OW/OB after adjusting by sex and maturational status (FDR < 0.05). Enriched pathway analysis identified gene pathways related to inflammation (eg, dopaminergic and GABAergic synapse pathways). Interestingly, in silico validation data mining detected a set of the differentially expressed genes to be related to CVD, metabolic syndrome, hypertension, inflammation, and asthma. CONCLUSION The distinct pattern of whole-blood gene expression in fit children with OW/OB reveals genes and gene pathways that might play a role in reducing CVD risk factors later in life.
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Affiliation(s)
- Abel Plaza-Florido
- Department of Physical and Sports Education, Faculty of Sport Sciences, PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS, University of Granada, Granada, Spain
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Francisco J Esteban
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen, Spain
| | - Marie Löf
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Department of Health, Medicine and Caring Sciences, Linköping University, Linköping, Sweden
| | - Shlomit Radom-Aizik
- Pediatric Exercise and Genomics Research Center, UC Irvine School of Medicine, Irvine, CA, USA
| | - Francisco B Ortega
- Department of Physical and Sports Education, Faculty of Sport Sciences, PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS, University of Granada, Granada, Spain.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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26
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He JP, Tian Q, Zhu QY, Liu JL. Identification of Intercellular Crosstalk between Decidual Cells and Niche Cells in Mice. Int J Mol Sci 2021; 22:ijms22147696. [PMID: 34299317 PMCID: PMC8306874 DOI: 10.3390/ijms22147696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/15/2021] [Accepted: 07/16/2021] [Indexed: 12/23/2022] Open
Abstract
Decidualization is a crucial step for human reproduction, which is a prerequisite for embryo implantation, placentation and pregnancy maintenance. Despite rapid advances over recent years, the molecular mechanism underlying decidualization remains poorly understood. Here, we used the mouse as an animal model and generated a single-cell transcriptomic atlas of a mouse uterus during decidualization. By analyzing the undecidualized inter-implantation site of the uterus as a control, we were able to identify global gene expression changes associated with decidualization in each cell type. Additionally, we identified intercellular crosstalk between decidual cells and niche cells, including immune cells, endothelial cells and trophoblast cells. Our data provide a valuable resource for deciphering the molecular mechanism underlying decidualization.
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27
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Plaza-Florido A, Altmäe S, Esteban FJ, Cadenas-Sanchez C, Aguilera CM, Einarsdottir E, Katayama S, Krjutškov K, Kere J, Zaldivar F, Radom-Aizik S, Ortega FB. Distinct whole-blood transcriptome profile of children with metabolic healthy overweight/obesity compared to metabolic unhealthy overweight/obesity. Pediatr Res 2021; 89:1687-1694. [PMID: 33230195 DOI: 10.1038/s41390-020-01276-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/18/2020] [Accepted: 10/27/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Youth populations with overweight/obesity (OW/OB) exhibit heterogeneity in cardiometabolic health phenotypes. The underlying mechanisms for those differences are still unclear. This study aimed to analyze the whole-blood transcriptome profile (RNA-seq) of children with metabolic healthy overweight/obesity (MHO) and metabolic unhealthy overweight/obesity (MUO) phenotypes. METHODS Twenty-seven children with OW/OB (10.1 ± 1.3 years, 59% boys) from the ActiveBrains project were included. MHO was defined as having none of the following criteria for metabolic syndrome: elevated fasting glucose, high serum triglycerides, low high-density lipoprotein-cholesterol, and high systolic or diastolic blood pressure, while MUO was defined as presenting one or more of these criteria. Inflammatory markers were additionally determined. Total blood RNA was analyzed by 5'-end RNA-sequencing. RESULTS Whole-blood transcriptome analysis revealed a distinct pattern of gene expression in children with MHO compared to MUO children. Thirty-two genes differentially expressed were linked to metabolism, mitochondrial, and immune functions. CONCLUSIONS The identified gene expression patterns related to metabolism, mitochondrial, and immune functions contribute to a better understanding of why a subset of the population remains metabolically healthy despite having overweight/obesity. IMPACT A distinct pattern of whole-blood transcriptome profile (RNA-seq) was identified in children with metabolic healthy overweight/obesity (MHO) compared to metabolic unhealthy overweight/obesity (MUO) phenotype. The most relevant genes in understanding the molecular basis underlying the MHO/MUO phenotypes in children could be: RREB1, FAM83E, SLC44A1, NRG1, TMC5, CYP3A5, TRIM11, and ADAMTSL2. The identified whole-blood transcriptome profile related to metabolism, mitochondrial, and immune functions contribute to a better understanding of why a subset of the population remains metabolically healthy despite having overweight/obesity.
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Affiliation(s)
- Abel Plaza-Florido
- PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18011, Granada, Spain.
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain.,Competence Centre on Health Technologies, Tartu, Estonia.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Francisco J Esteban
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen, Spain
| | - Cristina Cadenas-Sanchez
- PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18011, Granada, Spain.,Institute for Innovation & Sustainable Development in Food Chain (IS-FOOD), Public University of Navarra, Pamplona, Spain
| | - Concepción M Aguilera
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.,Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Centre for Biomedical Research, University of Granada, Granada, Spain.,CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Madrid, Spain
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, SE-171 21, Solna, Sweden
| | - Shintaro Katayama
- Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
| | - Juha Kere
- Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Frank Zaldivar
- Pediatric Exercise and Genomics Research Center, UC Irvine School of Medicine, Irvine, CA, USA
| | - Shlomit Radom-Aizik
- Pediatric Exercise and Genomics Research Center, UC Irvine School of Medicine, Irvine, CA, USA
| | - Francisco B Ortega
- PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18011, Granada, Spain.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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28
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Käck U, Einarsdottir E, van Hage M, Asarnoj A, James A, Nopp A, Krjutškov K, Katayama S, Kere J, Lilja G, Söderhäll C, Konradsen JR. Nasal upregulation of CST1 in dog-sensitised children with severe allergic airway disease. ERJ Open Res 2021; 7:00917-2020. [PMID: 33898616 DOI: 10.1183/23120541.00917-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/27/2021] [Indexed: 12/27/2022] Open
Abstract
Background The clinical presentation of children sensitised to dog dander varies from asymptomatic to severe allergic airway disease, but the genetic mechanisms underlying these differences are not clear. The objective of the present study was to investigate nasal transcriptomic profiles associated with dog dander sensitisation in school children and to reveal clinical symptoms related with these profiles. Methods RNA was extracted from nasal epithelial cell brushings of children sensitised to dog dander and healthy controls. Blood sample analyses included IgE against dog dander, dog allergen molecules, other airborne and food allergens, basophil activation and white blood cell counts. Clinical history of asthma and rhinitis was recorded, and lung function was assessed (spirometry, methacholine provocation and exhaled nitric oxide fraction). Results The most overexpressed gene in children sensitised to dog dander compared to healthy controls was CST1, coding for Cystatin 1. A cluster of these children with enhanced CST1 expression showed lower forced expiratory volume in 1 s, increased bronchial hyperreactivity, pronounced eosinophilia and higher basophil allergen threshold sensitivity compared with other children sensitised to dog dander. In addition, multi-sensitisation to lipocalins was more common in this group. Conclusions Overexpression of CST1 is associated with more severe allergic airway disease in children sensitised to dog dander. CST1 is thus a possible biomarker of the severity of allergic airway disease and a possible therapeutic target for the future treatment of airborne allergy.
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Affiliation(s)
- Ulrika Käck
- Dept of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sach's Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden.,Folkhälsan Research Center, Helsinki, Finland
| | - Marianne van Hage
- Dept of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Anna Asarnoj
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Anna James
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Nopp
- Dept of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sach's Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Kaarel Krjutškov
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Shintaro Katayama
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Folkhälsan Research Center, Helsinki, Finland.,University of Helsinki, Stem Cells and Metabolism Research Program, Helsinki, Finland
| | - Juha Kere
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Folkhälsan Research Institute, and Stem Cell and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Gunnar Lilja
- Dept of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sach's Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Cilla Söderhäll
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,These authors contributed equally
| | - Jon R Konradsen
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,These authors contributed equally
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29
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Llamazares-Prada M, Espinet E, Mijošek V, Schwartz U, Lutsik P, Tamas R, Richter M, Behrendt A, Pohl ST, Benz NP, Muley T, Warth A, Heußel CP, Winter H, Landry JJM, Herth FJ, Mertens TC, Karmouty-Quintana H, Koch I, Benes V, Korbel JO, Waszak SM, Trumpp A, Wyatt DM, Stahl HF, Plass C, Jurkowska RZ. Versatile workflow for cell type-resolved transcriptional and epigenetic profiles from cryopreserved human lung. JCI Insight 2021; 6:140443. [PMID: 33630765 PMCID: PMC8026197 DOI: 10.1172/jci.insight.140443] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 02/10/2021] [Indexed: 12/12/2022] Open
Abstract
Complexity of lung microenvironment and changes in cellular composition during disease make it exceptionally hard to understand molecular mechanisms driving development of chronic lung diseases. Although recent advances in cell type-resolved approaches hold great promise for studying complex diseases, their implementation relies on local access to fresh tissue, as traditional tissue storage methods do not allow viable cell isolation. To overcome these hurdles, we developed a versatile workflow that allows storage of lung tissue with high viability, permits thorough sample quality check before cell isolation, and befits sequencing-based profiling. We demonstrate that cryopreservation enables isolation of multiple cell types from both healthy and diseased lungs. Basal cells from cryopreserved airways retain their differentiation ability, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing and EPIC Array, we show that gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for omics profiling of lung cells. Moreover, we obtained high-quality single-cell RNA-sequencing data of cells from cryopreserved human lungs, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our workflow is well suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to viable human tissue.
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Affiliation(s)
| | - Elisa Espinet
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | | | | | - Pavlo Lutsik
- Division of Cancer Epigenomics, DKFZ, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | | | | | | | | | | | - Thomas Muley
- Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
- Translational Lung Research Center, Member of the DZL, Heidelberg, Germany
| | - Arne Warth
- Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Claus Peter Heußel
- Translational Lung Research Center, Member of the DZL, Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology with Nuclear Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
- Department of Diagnostic and Interventional Radiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Hauke Winter
- Translational Lung Research Center, Member of the DZL, Heidelberg, Germany
- Department of Surgery, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Felix J.F. Herth
- Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine and Translational Research Unit, Thoraxklinik, University Hospital Heidelberg, Heidelberg, Germany
| | - Tinne C.J. Mertens
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Harry Karmouty-Quintana
- Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, USA
| | - Ina Koch
- Asklepios Biobank for Lung Diseases, Department of Thoracic Surgery, Asklepios Fachkliniken München-Gauting, DZL, Gauting, Germany
| | | | | | | | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM), Heidelberg, Germany
| | | | - Heiko F. Stahl
- Immunology and Respiratory Disease Research, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, DKFZ, Member of the German Center for Lung Research (DZL), Heidelberg, Germany
| | - Renata Z. Jurkowska
- BioMed X Institute, Heidelberg, Germany
- School of Biosciences, Cardiff University, Cardiff, United Kingdom
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30
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Kirkwood PM, Gibson DA, Smith JR, Wilson-Kanamori JR, Kelepouri O, Esnal-Zufiaurre A, Dobie R, Henderson NC, Saunders PTK. Single-cell RNA sequencing redefines the mesenchymal cell landscape of mouse endometrium. FASEB J 2021; 35:e21285. [PMID: 33710643 PMCID: PMC9328940 DOI: 10.1096/fj.202002123r] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/26/2020] [Accepted: 12/01/2020] [Indexed: 12/11/2022]
Abstract
The endometrium is a dynamic tissue that exhibits remarkable resilience to repeated episodes of differentiation, breakdown, regeneration, and remodeling. Endometrial physiology relies on a complex interplay between the stromal and epithelial compartments with the former containing a mixture of fibroblasts, vascular, and immune cells. There is evidence for rare populations of putative mesenchymal progenitor cells located in the perivascular niche of human endometrium, but the existence of an equivalent cell population in mouse is unclear. We used the Pdgfrb‐BAC‐eGFP transgenic reporter mouse in combination with bulk and single‐cell RNA sequencing to redefine the endometrial mesenchyme. In contrast to previous reports we show that CD146 is expressed in both PDGFRβ + perivascular cells and CD31 + endothelial cells. Bulk RNAseq revealed cells in the perivascular niche which express the high levels of Pdgfrb as well as genes previously identified in pericytes and/or vascular smooth muscle cells (Acta2, Myh11, Olfr78, Cspg4, Rgs4, Rgs5, Kcnj8, and Abcc9). scRNA‐seq identified five subpopulations of cells including closely related pericytes/vascular smooth muscle cells and three subpopulations of fibroblasts. All three fibroblast populations were PDGFRα+/CD34 + but were distinct in their expression of Ngfr/Spon2/Angptl7 (F1), Cxcl14/Smoc2/Rgs2 (F2), and Clec3b/Col14a1/Mmp3 (F3), with potential functions in the regulation of immune responses, response to wounding, and organization of extracellular matrix, respectively. Immunohistochemistry was used to investigate the spatial distribution of these populations revealing F1/NGFR + cells in most abundance beside epithelial cells. We provide the first definitive analysis of mesenchymal cells in the adult mouse endometrium identifying five subpopulations providing a platform for comparisons between mesenchymal cells in endometrium and other adult tissues which are prone to fibrosis.
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Affiliation(s)
- Phoebe M Kirkwood
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Douglas A Gibson
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - James R Smith
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Olympia Kelepouri
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ross Dobie
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
| | - Neil C Henderson
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Philippa T K Saunders
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom
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31
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Varshney MK, Yu NYL, Katayama S, Li X, Liu T, Wu WF, Töhönen V, Krjutškov K, Kere J, Fan X, Inzunza J, Gustafsson JÅ, Nalvarte I. Motor Function Deficits in the Estrogen Receptor Beta Knockout Mouse: Role on Excitatory Neurotransmission and Myelination in the Motor Cortex. Neuroendocrinology 2021; 111:27-44. [PMID: 31991411 DOI: 10.1159/000506162] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/25/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Male estrogen receptor beta (ERβ) knockout (BERKO) mice display anxiety and aggression linked to, among others, altered serotonergic signaling in the basolateral amygdala and dorsal raphe, impaired cortical radial glia migration, and reduced GABAergic signaling. The effects on primary motor cortex (M1 cortex) and locomotor activity as a consequence of ERβ loss have not been investigated. OBJECTIVE The aim of this study was to determine whether locomotor activity is altered as a consequence of the changes in the M1 cortex. METHODS The locomotor activity of male wild-type (WT) and BERKO mice was evaluated using the open-field and rotarod tests. Molecular changes in the M1 cortex were analyzed by RNA sequencing, electron microscopy, electrophysiology, and immunohistological techniques. In addition, we established oligodendrocyte (OL) cultures from WT and BERKO mouse embryonic stem cells to evaluate OL function. RESULTS Locomotor profiling revealed that BERKO mice were more active than WT mice but had impaired motor coordination. Analysis of the M1 cortex pointed out differences in synapse function and myelination. There was a reduction in GABAergic signaling resulting in imbalanced excitatory and inhibitory neurotransmission as well as a defective OL differentiation accompanied by myelin defects. The effects of ERβ loss on OL differentiation were confirmed in vitro. CONCLUSION ERβ is an important regulator of GABAergic interneurons and OL differentiation, which impacts on adult M1 cortex function and may be linked to increased locomotor activity and decreased motor coordination in BERKO mice.
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Affiliation(s)
| | - Nancy Yiu-Lin Yu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Xin Li
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Tianyao Liu
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Wan-Fu Wu
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, USA
| | - Virpi Töhönen
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Competence Center on Health Technologies, Tartu, Estonia
- Folkhälsan Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsan Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Xiaotang Fan
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - José Inzunza
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jan-Åke Gustafsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, USA
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ivan Nalvarte
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden,
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32
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Reproductive medicine, as seen through single-cell glasses. Fertil Steril 2020; 115:296-297. [PMID: 33386110 DOI: 10.1016/j.fertnstert.2020.11.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 11/23/2020] [Indexed: 11/23/2022]
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33
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Lauter G, Coschiera A, Yoshihara M, Sugiaman-Trapman D, Ezer S, Sethurathinam S, Katayama S, Kere J, Swoboda P. Differentiation of ciliated human midbrain-derived LUHMES neurons. J Cell Sci 2020; 133:jcs249789. [PMID: 33115758 DOI: 10.1242/jcs.249789] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/05/2020] [Indexed: 12/15/2022] Open
Abstract
Many human cell types are ciliated, including neural progenitors and differentiated neurons. Ciliopathies are characterized by defective cilia and comprise various disease states, including brain phenotypes, where the underlying biological pathways are largely unknown. Our understanding of neuronal cilia is rudimentary, and an easy-to-maintain, ciliated human neuronal cell model is absent. The Lund human mesencephalic (LUHMES) cell line is a ciliated neuronal cell line derived from human fetal mesencephalon. LUHMES cells can easily be maintained and differentiated into mature, functional neurons within one week. They have a single primary cilium as proliferating progenitor cells and as postmitotic, differentiating neurons. These developmental stages are completely separable within one day of culture condition change. The sonic hedgehog (SHH) signaling pathway is active in differentiating LUHMES neurons. RNA-sequencing timecourse analyses reveal molecular pathways and gene-regulatory networks critical for ciliogenesis and axon outgrowth at the interface between progenitor cell proliferation, polarization and neuronal differentiation. Gene expression dynamics of cultured LUHMES neurons faithfully mimic the corresponding in vivo dynamics of human fetal midbrain. In LUHMES cells, neuronal cilia biology can be investigated from proliferation through differentiation to mature neurons.
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Affiliation(s)
- Gilbert Lauter
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | - Andrea Coschiera
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | - Masahito Yoshihara
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | | | - Sini Ezer
- University of Helsinki, Research Program of Molecular Neurology and Folkhälsan Institute of Genetics, FI-00290 Helsinki, Finland
| | - Shalini Sethurathinam
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
| | - Shintaro Katayama
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
- University of Helsinki, Stem Cells and Metabolism Research Program and Folkhälsan Research Center, FI-00290 Helsinki, Finland
| | - Juha Kere
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
- University of Helsinki, Research Program of Molecular Neurology and Folkhälsan Institute of Genetics, FI-00290 Helsinki, Finland
| | - Peter Swoboda
- Karolinska Institute, Department of Biosciences and Nutrition, SE-141 83 Huddinge, Sweden
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Single-cell transcriptomic atlas of the human endometrium during the menstrual cycle. Nat Med 2020; 26:1644-1653. [PMID: 32929266 DOI: 10.1038/s41591-020-1040-z] [Citation(s) in RCA: 252] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 07/29/2020] [Indexed: 12/20/2022]
Abstract
In a human menstrual cycle the endometrium undergoes remodeling, shedding and regeneration, all of which are driven by substantial gene expression changes in the underlying cellular hierarchy. Despite its importance in human fertility and regenerative biology, our understanding of this unique type of tissue homeostasis remains rudimentary. We characterized the transcriptomic transformation of human endometrium at single-cell resolution across the menstrual cycle, resolving cellular heterogeneity in multiple dimensions. We profiled the behavior of seven endometrial cell types, including a previously uncharacterized ciliated cell type, during four major phases of endometrial transformation, and found characteristic signatures for each cell type and phase. We discovered that the human window of implantation opens with an abrupt and discontinuous transcriptomic activation in the epithelia, accompanied with a widespread decidualization feature in the stromal fibroblasts. Our study provides a high-resolution molecular and cellular characterization of human endometrial transformation across the menstrual cycle, providing insights into this essential physiological process.
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Fetal HLA-G mediated immune tolerance and interferon response in preeclampsia. EBioMedicine 2020; 59:102872. [PMID: 32680723 PMCID: PMC7502669 DOI: 10.1016/j.ebiom.2020.102872] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Fetal immune tolerance is crucial for pregnancy success. We studied the link between preeclampsia, a severe pregnancy disorder with uncertain pathogenesis, and fetal human leukocyte antigen G (HLA-G) and other genes regulating maternal immune responses. METHODS We assessed sex ratios and regulatory HLA-G haplotypes in population cohorts and series of preeclampsia and stillbirth. We studied placental mRNA expression of 136 genes by sequencing and HLA-G and interferon alpha (IFNα) protein expression by immunohistochemistry. FINDINGS We found underrepresentation of males in preeclamptic births, especially those delivered preterm or small for gestational age. Balancing selection at HLA-G associated with the sex ratio, stillbirth, and preeclampsia. We observed downregulation of HLA-G, its receptors, and many other tolerogenic genes, and marked upregulation of IFNA1 in preeclamptic placentas. INTERPRETATION These findings indicate that an evolutionary trade-off between immune tolerance and protection against infections at the maternal-fetal interface promotes genetic diversity in fetal HLA-G, thereby affecting survival, preeclampsia, and sex ratio. We highlight IFNA1 as a potential mediator of preeclampsia and a target for therapeutic trials. FUNDING Finnish Medical Foundation, Päivikki and Sakari Sohlberg Foundation, Karolinska Institutet Research Foundation, Scandinavia-Japan Sasakawa Foundation, Japan Eye Bank Association, Astellas Foundation for Research on Metabolic Disorders, Japan Society for the Promotion of Science, Knut and Alice Wallenberg Foundation, Swedish Research Council, Medical Society Liv och Hälsa, Sigrid Jusélius Foundation, Helsinki University Hospital and University of Helsinki, Jane and Aatos Erkko Foundation, Academy of Finland, Finska Läkaresällskapet, Novo Nordisk Foundation, Finnish Foundation for Pediatric Research, and Emil Aaltonen Foundation.
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Bieder A, Yoshihara M, Katayama S, Krjutškov K, Falk A, Kere J, Tapia-Páez I. Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation. Mol Neurobiol 2020; 57:2944-2958. [PMID: 32445086 PMCID: PMC7320047 DOI: 10.1007/s12035-020-01905-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 11/30/2022]
Abstract
Developmental dyslexia (DD) is a neurodevelopmental condition with complex genetic mechanisms. A number of candidate genes have been identified, some of which are linked to neuronal development and migration and to ciliary functions. However, expression and regulation of these genes in human brain development and neuronal differentiation remain uncharted. Here, we used human long-term self-renewing neuroepithelial stem (lt-NES, here termed NES) cells derived from human induced pluripotent stem cells to study neuronal differentiation in vitro. We characterized gene expression changes during differentiation by using RNA sequencing and validated dynamics for selected genes by qRT-PCR. Interestingly, we found that genes related to cilia were significantly enriched among upregulated genes during differentiation, including genes linked to ciliopathies with neurodevelopmental phenotypes. We confirmed the presence of primary cilia throughout neuronal differentiation. Focusing on dyslexia candidate genes, 33 out of 50 DD candidate genes were detected in NES cells by RNA sequencing, and seven candidate genes were upregulated during differentiation to neurons, including DYX1C1 (DNAAF4), a highly replicated DD candidate gene. Our results suggest a role of ciliary genes in differentiating neuronal cells and show that NES cells provide a relevant human neuronal model to study ciliary and DD candidate genes.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden. .,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland. .,School of Basic and Medical Biosciences, King's College London, London, UK.
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Katayama S, Stenberg Hammar K, Krjutškov K, Einarsdottir E, Hedlin G, Kere J, Söderhäll C. Acute wheeze-specific gene module shows correlation with vitamin D and asthma medication. Eur Respir J 2020; 55:13993003.01330-2019. [PMID: 31619476 DOI: 10.1183/13993003.01330-2019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Airway obstruction and wheezing in preschool children with recurrent viral infections are a major clinical problem, and are recognised as a risk factor for the development of chronic asthma. We aimed to analyse whether gene expression profiling provides evidence for pathways that delineate distinct groups of children with wheeze, and in combination with clinical information could contribute to diagnosis and prognosis of disease development. METHODS We analysed leukocyte transcriptomes from preschool children (6 months-3 years) at acute wheeze (n=107), and at a revisit 2-3 months later, comparing them to age-matched healthy controls (n=66). RNA-sequencing applying GlobinLock was used. The cases were followed clinically until age 7 years. Differential expression tests, weighted correlation network analysis and logistic regression were applied and correlations to 76 clinical traits evaluated. FINDINGS Significant enrichment of genes involved in the innate immune responses was observed in children with wheeze. We identified a unique acute wheeze-specific gene-module, which was associated with vitamin D levels (p<0.005) in infancy, and asthma medication and FEV1%/FVC (forced expiratory volume in 1 s/forced vital capacity) ratio several years later, at age 7 years (p<0.005). A model that predicts leukotriene receptor antagonist medication at 7 years of age with high accuracy was developed (area under the curve 0.815, 95% CI 0.668-0.962). INTERPRETATION Gene expression profiles in blood from preschool wheezers predict asthma symptoms at school age, and therefore serve as biomarkers. The acute wheeze-specific gene module suggests that molecular phenotyping in combination with clinical information already at an early episode of wheeze may help to distinguish children who will outgrow their wheeze from those who will develop chronic asthma.
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Affiliation(s)
- Shintaro Katayama
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Both authors contributed equally
| | - Katarina Stenberg Hammar
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Both authors contributed equally
| | - Kaarel Krjutškov
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Elisabet Einarsdottir
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.,SciLifeLab, Dept of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Gunilla Hedlin
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Cilla Söderhäll
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden .,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
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38
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Transcriptome meta-analysis reveals differences of immune profile between eutopic endometrium from stage I-II and III-IV endometriosis independently of hormonal milieu. Sci Rep 2020; 10:313. [PMID: 31941945 PMCID: PMC6962450 DOI: 10.1038/s41598-019-57207-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 12/19/2019] [Indexed: 02/06/2023] Open
Abstract
Eutopic endometrium appears to be crucial for endometriosis development. Despite of the evident importance, data regarding the cellular microenvironment remain unclear. Our objective was to explore the tissue microenvironment heterogeneity, transcripts, and pathways that are enriched in all phases of the menstrual cycle by analysing publicly deposited data derived from whole transcriptome microarrays of eutopic endometria of women with and without endometriosis. A meta-analysis of the transcriptome microarrays was performed using raw data available from a public database. Eligibility criteria included eutopic endometrium samples from women with endometriosis and healthy controls without any pathological condition reported the presence of an adequately reported normal menstrual phase, and samples containing both glandular and stromal components. Raw data were processed using a robust multiarray average method to provide background correction, normalisation, and summarisation. The batch effect was estimated by principal variant component analysis and removed using an empirical Bayes method. Cellular tissue heterogeneity was inferred using the xCell package. Differentially expressed genes were identified based on a 5% adjusted p value and a 2.0-fold change. Pathways were identified by functional enrichment based on the Molecular Signatures Database, a p value of < 5%, and an FDR q value of ≤ 25%. Genes that were more frequently found in pathways were identified using leading edge analysis. In a manner independent of cycle phase, the subpopulations of activated dendritic cells, CD4 T effector memory phenotype cells, eosinophils, macrophages M1, and natural killer T cells (NKT) were all higher in stage I-II endometriosis compared to those in healthy controls. The subpopulations of M2 macrophages and natural killer T cells were elevated in eutopic endometriums from women with stage III-IV endometriosis, and smooth muscle cells were always more prevalent in healthy eutopic endometriums. Among the differently expressed genes, FOS, FOSB, JUNB, and EGR1 were the most frequently mapped within the interaction networks, and this was independent of stage and cycle phase. The enriched pathways were directly related to immune surveillance, stem cell self-renewal, and epithelial mesenchymal transition. PI3K AKT mTOR, TGF signalling, and interferon alpha/gamma responses were enriched exclusively in stage III-IV endometriosis. The cellular microenvironments and immune cell profiles were different between eutopic endometriums from women with stage I-II and stage III-IV endometriosis, and these differences were independent of the hormonal milieu. Specifically, a pro-inflammatory profile was predominant in stage I-II endometriosis, and M1-M2 polarization into eutopic endometrium may be crucial for the progression of the disease. The higher prevalence of NKT cells in eutopic endometriums from women with endometriosis that was independent of cycle phase or staging suggested a sustained stress and/or damage to these eutopic endometriums. Based on this, the results of this meta-analysis are important for identifying challenges and opportunities for future research.
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39
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Madissoon E, Wilbrey-Clark A, Miragaia RJ, Saeb-Parsy K, Mahbubani KT, Georgakopoulos N, Harding P, Polanski K, Huang N, Nowicki-Osuch K, Fitzgerald RC, Loudon KW, Ferdinand JR, Clatworthy MR, Tsingene A, van Dongen S, Dabrowska M, Patel M, Stubbington MJT, Teichmann SA, Stegle O, Meyer KB. scRNA-seq assessment of the human lung, spleen, and esophagus tissue stability after cold preservation. Genome Biol 2019; 21:1. [PMID: 31892341 PMCID: PMC6937944 DOI: 10.1186/s13059-019-1906-x] [Citation(s) in RCA: 261] [Impact Index Per Article: 52.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/28/2019] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND The Human Cell Atlas is a large international collaborative effort to map all cell types of the human body. Single-cell RNA sequencing can generate high-quality data for the delivery of such an atlas. However, delays between fresh sample collection and processing may lead to poor data and difficulties in experimental design. RESULTS This study assesses the effect of cold storage on fresh healthy spleen, esophagus, and lung from ≥ 5 donors over 72 h. We collect 240,000 high-quality single-cell transcriptomes with detailed cell type annotations and whole genome sequences of donors, enabling future eQTL studies. Our data provide a valuable resource for the study of these 3 organs and will allow cross-organ comparison of cell types. We see little effect of cold ischemic time on cell yield, total number of reads per cell, and other quality control metrics in any of the tissues within the first 24 h. However, we observe a decrease in the proportions of lung T cells at 72 h, higher percentage of mitochondrial reads, and increased contamination by background ambient RNA reads in the 72-h samples in the spleen, which is cell type specific. CONCLUSIONS In conclusion, we present robust protocols for tissue preservation for up to 24 h prior to scRNA-seq analysis. This greatly facilitates the logistics of sample collection for Human Cell Atlas or clinical studies since it increases the time frames for sample processing.
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Affiliation(s)
- E. Madissoon
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD UK
| | - A. Wilbrey-Clark
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - R. J. Miragaia
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - K. Saeb-Parsy
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ UK
| | - K. T. Mahbubani
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ UK
| | - N. Georgakopoulos
- Department of Surgery, University of Cambridge and NIHR Cambridge Biomedical Research Centre, Cambridge, CB2 0QQ UK
| | - P. Harding
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - K. Polanski
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - N. Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - K. Nowicki-Osuch
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ UK
| | - R. C. Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, CB2 0XZ UK
| | - K. W. Loudon
- Molecular Immunology Unit, Department of Medicine, Cambridge, CB2 0QQ UK
| | - J. R. Ferdinand
- Molecular Immunology Unit, Department of Medicine, Cambridge, CB2 0QQ UK
| | - M. R. Clatworthy
- Molecular Immunology Unit, Department of Medicine, Cambridge, CB2 0QQ UK
| | - A. Tsingene
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - S. van Dongen
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - M. Dabrowska
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - M. Patel
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - M. J. T. Stubbington
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
- 10x Genomics Inc., 6230 Stoneridge Mall Road, Pleasanton, CA 94588 USA
| | - S. A. Teichmann
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
| | - O. Stegle
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD UK
| | - K. B. Meyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA UK
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Saare M, Krigul KL, Laisk-Podar T, Ponandai-Srinivasan S, Rahmioglu N, Lalit Kumar PG, Zondervan K, Salumets A, Peters M. DNA methylation alterations-potential cause of endometriosis pathogenesis or a reflection of tissue heterogeneity? Biol Reprod 2019; 99:273-282. [PMID: 29796617 DOI: 10.1093/biolre/ioy067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/20/2018] [Indexed: 01/10/2023] Open
Abstract
Alterations in the DNA methylation pattern of endometriotic lesions and endometrium of endometriosis patients have been proposed as one potential factor accompanying the endometriosis development. Although many differentially methylated genes have been associated with the pathogenesis of this disease, the overlap between the results of different studies has remained small. Among other potential confounders, the impact of tissue heterogeneity on the outcome of DNA methylation studies should be considered, as tissues are mixtures of different cell types with their own specific DNA methylation signatures. This review focuses on the results of DNA methylation studies in endometriosis from the cellular heterogeneity perspective. We consider both the studies using highly heterogeneous whole-lesion biopsies and endometrial tissue, as well as pure cell fractions isolated from lesions and endometrium to understand the potential impact of the cellular composition to the results of endometriosis DNA methylation studies. Also, future perspectives on how to diminish the impact of tissue heterogeneity in similar studies are provided.
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Affiliation(s)
- Merli Saare
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
| | - Kertu Liis Krigul
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Triin Laisk-Podar
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
| | | | - Nilufer Rahmioglu
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Parameswaran Grace Lalit Kumar
- Division of Obstetrics and Gynecology, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Krina Zondervan
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Endometriosis CaRe Centre, Nuffield Department of Obstetrics & Gynaecology, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Insitute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
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Vakkilainen S, Skoog T, Einarsdottir E, Middleton A, Pekkinen M, Öhman T, Katayama S, Krjutškov K, Kovanen PE, Varjosalo M, Lindqvist A, Kere J, Mäkitie O. The human long non-coding RNA gene RMRP has pleiotropic effects and regulates cell-cycle progression at G2. Sci Rep 2019; 9:13758. [PMID: 31551465 PMCID: PMC6760211 DOI: 10.1038/s41598-019-50334-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
RMRP was the first non-coding nuclear RNA gene implicated in a disease. Its mutations cause cartilage-hair hypoplasia (CHH), an autosomal recessive skeletal dysplasia with growth failure, immunodeficiency, and a high risk for malignancies. This study aimed to gain further insight into the role of RNA Component of Mitochondrial RNA Processing Endoribonuclease (RMRP) in cellular physiology and disease pathogenesis. We combined transcriptome analysis with single-cell analysis using fibroblasts from CHH patients and healthy controls. To directly assess cell cycle progression, we followed CHH fibroblasts by pulse-labeling and time-lapse microscopy. Transcriptome analysis identified 35 significantly upregulated and 130 downregulated genes in CHH fibroblasts. The downregulated genes were significantly connected to the cell cycle. Multiple other pathways, involving regulation of apoptosis, bone and cartilage formation, and lymphocyte function, were also affected, as well as PI3K-Akt signaling. Cell-cycle studies indicated that the CHH cells were delayed specifically in the passage from G2 phase to mitosis. Our findings expand the mechanistic understanding of CHH, indicate possible pathways for therapeutic intervention and add to the limited understanding of the functions of RMRP.
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Affiliation(s)
- Svetlana Vakkilainen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. .,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Anna Middleton
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Minna Pekkinen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland
| | - Tiina Öhman
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Panu E Kovanen
- Department of Pathology, University of Helsinki, and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Medical and Molecular Genetics, King's College, London, UK
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Molecular Medicine and Surgery, Karolinska Institutet and Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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42
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Stepanjuk A, Koel M, Pook M, Saare M, Jääger K, Peters M, Krjutškov K, Ingerpuu S, Salumets A. MUC20 expression marks the receptive phase of the human endometrium. Reprod Biomed Online 2019; 39:725-736. [PMID: 31519421 DOI: 10.1016/j.rbmo.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 04/20/2019] [Accepted: 05/08/2019] [Indexed: 11/19/2022]
Abstract
RESEARCH QUESTION How does mucin MUC20 expression change during the menstrual cycle in different cell types of human endometrium? DESIGN Study involved examination of MUC20 expression in two previously published RNA-seq datasets in whole endometrial tissue (n = 10), sorted endometrial epithelial (n = 44) or stromal (n = 42) cell samples. RNA-Seq results were validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) in whole tissue (n = 10), sorted epithelial (n = 17) and stromal (n = 17) cell samples. MUC20 protein localization and expression were analysed in human endometrium by immunohistochemical analysis of intact endometrial tissue (n = 6) and also Western blot of cultured stromal and epithelial cells (n = 2). RESULTS MUC20 is differentially expressed in the endometrium between the pre-receptive and receptive phases. We show that MUC20 is predominantly expressed by epithelial cells of the receptive endometrium, both at the mRNA (RNA-Seq, P = 0.005; qRT-PCR, P = 0.039) and protein levels (Western blot; immunohistochemistry, P = 0.029). CONCLUSION Our results indicate MUC20 as a novel marker of mid-secretory endometrial biology. We propose a model of MUC20 function in the hepatocyte growth factor (HGF)-activated mesenchymal-epithelial transition (MET) receptor signalling specifically in the receptive phase. Further investigations should reveal the precise function of MUC20 in human endometrium and the possible connection between MUC20 and HGF-activated MET receptor signalling. MUC20 could potentially be included in the list of endometrial receptivity markers after further clinical validation.
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Affiliation(s)
- Artjom Stepanjuk
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
| | - Mariann Koel
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia; Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - Martin Pook
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
| | - Merli Saare
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, Tartu 50406, Estonia
| | - Kersti Jääger
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, Tartu 50406, Estonia
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, and Folkhälsan Institute of Genetics, Haartmaninkatu 8, Helsinki 00290, Finland
| | - Sulev Ingerpuu
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, Tartu 50406, Estonia; Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia; Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 2, Helsinki 00014, Finland.
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43
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Katayama S, Panelius J, Koskenmies S, Skoog T, Mähönen K, Kisand K, Bondet V, Duffy D, Krjutškov K, Kere J, Ranki A. Delineating the Healthy Human Skin UV Response and Early Induction of Interferon Pathway in Cutaneous Lupus Erythematosus. J Invest Dermatol 2019; 139:2058-2061.e4. [DOI: 10.1016/j.jid.2019.02.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/05/2019] [Accepted: 02/28/2019] [Indexed: 12/21/2022]
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Katayama S, Skoog T, Söderhäll C, Einarsdottir E, Krjutškov K, Kere J. Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods. BMC Bioinformatics 2019; 20:418. [PMID: 31409293 PMCID: PMC6693229 DOI: 10.1186/s12859-019-3017-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling. Preparation of hundreds or more samples for a large study often requires multiple library pools. However, sometimes correlation between expression profiles among the libraries is low and batch effect biases make integration of data between library pools difficult. RESULTS We investigated 166 technical replicates in 14 RNAseq libraries made using the STRT method. The patterns of the library biases differed by genes, and uneven library yields were associated with library biases. The former bias was corrected using the NBGLM-LBC algorithm, which we present in the current study. The latter bias could not be corrected directly, but could be solved by omitting libraries with particularly low yields. A simulation experiment suggested that the library bias correction using NBGLM-LBC requires a consistent sample layout. The NBGLM-LBC correction method was applied to an expression profile for a cohort study of childhood acute respiratory illness, and the library biases were resolved. CONCLUSIONS The R source code for the library bias correction named NBGLM-LBC is available at https://shka.github.io/NBGLM-LBC and https://shka.bitbucket.io/NBGLM-LBC . This method is applicable to correct the library biases in various studies that use highly multiplexed sequencing-based profiling methods with a consistent sample layout with samples to be compared (e.g., "cases" and "controls") equally distributed in each library.
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Affiliation(s)
- Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
- Department of Women’s and Children’s Health, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
- Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
- Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014 Helsinki, Finland
- Competence Centre on Health Technologies, 50410 Tartu, Estonia
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
- Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014 Helsinki, Finland
- School of Basic and Medical Biosciences, King’s College London, Guy’s Hospital, London, SE1 9RT UK
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45
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Neradugomma NK, Drafton K, Mor GG, Mao Q. Marijuana-derived cannabinoids inhibit uterine endometrial stromal cell decidualization and compromise trophoblast-endometrium cross-talk. Reprod Toxicol 2019; 87:100-107. [PMID: 31154070 PMCID: PMC6613995 DOI: 10.1016/j.reprotox.2019.05.064] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 12/31/2022]
Abstract
Marijuana (cannabis) use by pregnant women in the United States is increasing and there is a dire need to understand the beneficial or harmful effects of cannabis during pregnancy. Uterine endometrial stromal cells are fibroblast-like cells that differentiate into secretory cells, a process called decidualization, to create a microenvironment conducive for placenta formation and early embryonic growth. In this study, using model human cell lines, we for the first time demonstrate that Δ9-tetrahydrocannabinol (THC), cannabidiol (CBD) and cannabinol (CBN) inhibit endometrial stromal cell decidualization and have adverse effects on trophoblast-endometrium cross-talk.
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Affiliation(s)
- Naveen K Neradugomma
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA 98195, USA.
| | - Kaitlyn Drafton
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Gil G Mor
- Division of Reproductive Sciences, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Qingcheng Mao
- Department of Pharmaceutics, School of Pharmacy, University of Washington, Seattle, WA 98195, USA.
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Madissoon E, Damdimopoulos A, Katayama S, Krjutškov K, Einarsdottir E, Mamia K, De Groef B, Hovatta O, Kere J, Damdimopoulou P. Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development. Sci Rep 2019; 9:8411. [PMID: 31182756 PMCID: PMC6557853 DOI: 10.1038/s41598-019-44882-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/22/2019] [Indexed: 01/09/2023] Open
Abstract
Pleomorphic adenoma gene 1 (PLAG1) is a transcription factor involved in cancer and growth. We discovered a de novo DNA motif containing a PLAG1 binding site in the promoters of genes activated during zygotic genome activation (ZGA) in human embryos. This motif was located within an Alu element in a region that was conserved in the murine B1 element. We show that maternally provided Plag1 is needed for timely mouse preimplantation embryo development. Heterozygous mouse embryos lacking maternal Plag1 showed disrupted regulation of 1,089 genes, spent significantly longer time in the 2-cell stage, and started expressing Plag1 ectopically from the paternal allele. The de novo PLAG1 motif was enriched in the promoters of the genes whose activation was delayed in the absence of Plag1. Further, these mouse genes showed a significant overlap with genes upregulated during human ZGA that also contain the motif. By gene ontology, the mouse and human ZGA genes with de novo PLAG1 motifs were involved in ribosome biogenesis and protein synthesis. Collectively, our data suggest that PLAG1 affects embryo development in mice and humans through a conserved DNA motif within Alu/B1 elements located in the promoters of a subset of ZGA genes.
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Affiliation(s)
- Elo Madissoon
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden.
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Analysis core facility, Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, 50410, Tartu, Estonia.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland
| | - Katariina Mamia
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Bert De Groef
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden. .,Research Programs Unit, Molecular Neurology, University of Helsinki, and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland. .,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, WC2R 2LS, UK.
| | - Pauliina Damdimopoulou
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden. .,Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden.
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47
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Einarsdottir E, Pekkinen M, Krjutškov K, Katayama S, Kere J, Mäkitie O, Viljakainen H. A preliminary transcriptome analysis suggests a transitory effect of vitamin D on mitochondrial function in obese young Finnish subjects. Endocr Connect 2019; 8:559-570. [PMID: 30965285 PMCID: PMC6499919 DOI: 10.1530/ec-18-0537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The effect of vitamin D at the transcriptome level is poorly understood, and furthermore, it is unclear if it differs between obese and normal-weight subjects. The objective of the study was to explore the transcriptome effects of vitamin D supplementation. DESIGN AND METHODS We analysed peripheral blood gene expression using GlobinLock oligonucleotides followed by RNA sequencing in individuals participating in a 12-week randomised double-blinded placebo-controlled vitamin D intervention study. The study involved 18 obese and 18 normal-weight subjects (of which 20 males) with mean (±s.d.) age 20.4 (±2.5) years and BMIs 36 (±10) and 23 (±4) kg/m2, respectively. The supplemental daily vitamin D dose was 50 µg (2000 IU). Data were available at baseline, 6- and 12-week time points and comparisons were performed between the vitamin D and placebo groups separately in obese and normal-weight subjects. RESULTS Significant transcriptomic changes were observed at 6 weeks, and only in the obese subjects: 1724 genes were significantly upregulated and 186 genes were downregulated in the vitamin D group compared with placebo. Further analyses showed several enriched gene categories connected to mitochondrial function and metabolism, and the most significantly enriched pathway was related to oxidative phosphorylation (adjusted P value 3.08 × 10-14). Taken together, our data suggest an effect of vitamin D supplementation on mitochondrial function in obese subjects. CONCLUSIONS Vitamin D supplementation affects gene expression in obese, but not in normal-weight subjects. The altered genes are enriched in pathways related to mitochondrial function. The present study increases the understanding of the effects of vitamin D at the transcriptome level.
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Affiliation(s)
- Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Minna Pekkinen
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kaarel Krjutškov
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Heli Viljakainen
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Correspondence should be addressed to H Viljakainen:
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Yang X, Gilman-Sachs A, Kwak-Kim J. Ovarian and endometrial immunity during the ovarian cycle. J Reprod Immunol 2019; 133:7-14. [PMID: 31055226 DOI: 10.1016/j.jri.2019.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 03/29/2019] [Accepted: 04/03/2019] [Indexed: 10/27/2022]
Abstract
Immune tolerance is crucial for the successful pregnancy, while immune effectors and their products are required to safeguard a fetus from the infectious pathogens. The key immune effectors, such as T, B, and natural killer (NK) cells, monocytes, macrophages, and dendritic cells take part in regulating the immune responses at the maternal-fetal interface. The immune effectors become involved in intraovarian reproductive processes as well, such as ovulation, production of corpus luteum (CL) and its degeneration and determine the quality and evolution of the oocyte during the folliculogenesis. In the cycling endometrium, NK cells are rapidly infiltrated into the endometrium after ovulation and participate in angiogenesis and spiral artery remodeling process. In this study, we reviewed the characteristics and action mechanisms of immune effectors and their products in the peripheral blood, ovary, and endometrium during the ovarian cycle, since a comprehensive understanding of immune responses during the ovarian cycle and the time of implantation can help us to predict the pregnancy outcome and take effective measures for the prevention of potential obstetrical complications.
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Affiliation(s)
- Xiuhua Yang
- Reproductive Medicine and Immunology, Department of Obstetrics and Gynecology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, Vernon Hills, IL, 60061, USA; Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, Vernon Hills, IL, 60061, USA; Department of Obstetrics, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Alice Gilman-Sachs
- Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, Vernon Hills, IL, 60061, USA
| | - Joanne Kwak-Kim
- Reproductive Medicine and Immunology, Department of Obstetrics and Gynecology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, Vernon Hills, IL, 60061, USA; Department of Microbiology and Immunology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, Vernon Hills, IL, 60061, USA.
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49
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Transcriptomic analysis of the interaction of choriocarcinoma spheroids with receptive vs. non-receptive endometrial epithelium cell lines: an in vitro model for human implantation. J Assist Reprod Genet 2019; 36:857-873. [PMID: 30972518 DOI: 10.1007/s10815-019-01442-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/19/2019] [Indexed: 10/27/2022] Open
Abstract
PURPOSE Several in vitro systems have been reported to model human implantation; however, the molecular dynamics of the trophoblast vs. the epithelial substrate during attachment have not been described. We have established an in vitro model which allowed us to dissect the transcriptional responses of the trophoblast and the receptive vs. non-receptive epithelium after co-culture. METHODS We established an in vitro system based on co-culture of (a) immortalized cells representing receptive (Ishikawa) or non-receptive (HEC-1-A) endometrial epithelium with (b) spheroids of a trophoblastic cell line (JEG-3) modified to express green fluorescent protein (GFP). After 48 h of co-culture, GFP+ (trophoblast cells) and GFP- cell fractions (receptive or non-receptive epithelial cells) were isolated by fluorescence-activated flow cytometry (FACS) and subjected to RNA-seq profiling and gene set enrichment analysis (GSEA). RESULTS Compared to HEC-1-A, the trophoblast challenge to Ishikawa cells differentially regulated the expression of 495 genes, which mainly involved cell adhesion and extracellular matrix (ECM) molecules. GSEA revealed enrichment of pathways related to cell division, cell cycle regulation, and metabolism in the Ishikawa substrate. Comparing the gene expression profile of trophoblast spheroids revealed that 1877 and 323 genes were upregulated or downregulated when co-cultured on Ishikawa substrates (compared to HEC-1-A), respectively. Pathways favorable to development, including tissue remodeling, organogenesis, and angiogenesis, were enhanced in the trophoblast compartment after co-culture of spheroids with receptive epithelium. By contrast, the co-culture with less receptive epithelium enriched pathways mainly related to trophoblast cell proliferation and cell cycle regulation. CONCLUSIONS Endometrial receptivity requires a transcriptional signature that determines the trophoblast response and drives attachment.
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50
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He JP, Zhao M, Zhang WQ, Huang MY, Zhu C, Cheng HZ, Liu JL. Identification of Gene Expression Changes Associated With Uterine Receptivity in Mice. Front Physiol 2019; 10:125. [PMID: 30890945 PMCID: PMC6413723 DOI: 10.3389/fphys.2019.00125] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 01/31/2019] [Indexed: 01/22/2023] Open
Abstract
The mouse is a widely used animal model for studying human reproduction. Although global gene expression changes associated with human uterine receptivity have been determined by independent groups, the same studies in the mouse are scarce. The extent of similarities/differences between mice and humans on uterine receptivity at the molecular level remains to be determined. In the present study, we analyzed global gene expression changes in receptive uterus on day 4 of pregnancy compared to non-receptive uterus on day 3 of pregnancy in mice. A total of 541 differentially expressed genes were identified, of which 316 genes were up-regulated and 225 genes were down-regulated in receptive uterus compared to non-receptive uterus. Gene ontology and gene network analysis highlighted the activation of inflammatory response in the receptive uterus. By analyzing the promoter sequences of differentially expressed genes, we identified 12 causal transcription factors. Through connectivity map (CMap) analysis, we revealed several compounds with potential anti-receptivity activity. Finally, we performed a cross-species comparison against human uterine receptivity from a published dataset. Our study provides a valuable resource for understanding the molecular mechanism underlying uterine receptivity in mice.
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Affiliation(s)
- Jia-Peng He
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Miao Zhao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wen-Qian Zhang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ming-Yu Huang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Can Zhu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Hao-Zhuang Cheng
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ji-Long Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
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