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Khan NLA, Muhandiram S, Dissanayake K, Godakumara K, Midekessa G, Andronowska A, Heath PR, Kodithuwakku S, Hart AR, Fazeli A. Effect of 3D and 2D cell culture systems on trophoblast extracellular vesicle physico-chemical characteristics and potency. Front Cell Dev Biol 2024; 12:1382552. [PMID: 38835509 PMCID: PMC11148233 DOI: 10.3389/fcell.2024.1382552] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
The growing understanding of the role of extracellular vesicles (EVs) in embryo-maternal communication has sparked considerable interest in their therapeutic potential within assisted reproductive technology, particularly in enhancing implantation success. However, the major obstacle remains the large-scale production of EVs, and there is still a gap in understanding how different culture systems affect the characteristics of the EVs. In the current study, trophoblast analogue human chorionic carcinoma cell line was cultivated in both conventional monolayer culture (2D) and as spheroids in suspension culture (3D) and how the cell growth environment affects the physical, biochemical and cellular signalling properties of EVs produced by them was studied. Interestingly, the 3D system was more active in secreting EVs compared to the 2D system, while no significant differences were observed in terms of morphology, size, and classical EV protein marker expression between EVs derived from the two culture systems. There were substantial differences in the proteomic cargo profile and cellular signalling potency of EVs derived from the two culture systems. Notably, 2D EVs were more potent in inducing a cellular response in endometrial epithelial cells (EECs) compared to 3D EVs. Therefore, it is essential to recognize that the biological activity of EVs depends not only on the cell of origin but also on the cellular microenvironment of the parent cell. In conclusion, caution is warranted when selecting an EV production platform, especially for assessing the functional and therapeutic potential of EVs through in vitro studies.
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Affiliation(s)
- Norhayati Liaqat Ali Khan
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
- Centre of Preclinical Science Studies, Faculty of Dentistry, University Teknologi MARA (UiTM), Sg. Buloh, Selangor, Malaysia
| | - Subhashini Muhandiram
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Keerthie Dissanayake
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Kasun Godakumara
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Getnet Midekessa
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
| | - Aneta Andronowska
- Department of Hormonal Action Mechanisms, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Paul R Heath
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Suranga Kodithuwakku
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Amber Rose Hart
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Alireza Fazeli
- Division of Clinical Medicine, School of Medicine and Population Health, The Medical School, University of Sheffield, Sheffield, United Kingdom
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, Faculty of Medicine, University of Tartu, Tartu, Estonia
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Vidal MS, Radnaa E, Vora N, Khanipov K, Antich C, Ferrer M, Urrabaz-Garza R, Jacob JE, Menon R. Establishment and comparison of human term placenta-derived trophoblast cells†. Biol Reprod 2024; 110:950-970. [PMID: 38330185 PMCID: PMC11484515 DOI: 10.1093/biolre/ioae026] [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: 08/24/2023] [Revised: 11/24/2023] [Accepted: 02/02/2024] [Indexed: 02/10/2024] Open
Abstract
Research on the biology of fetal-maternal barriers has been limited by access to physiologically relevant cells, including trophoblast cells. In this study, we describe the development of a human term placenta-derived cytotrophoblast immortalized cell line (hPTCCTB) derived from the basal plate. Human-term placenta-derived cytotrophoblast immortalized cell line cells are comparable to their primary cells of origin in terms of morphology, marker expression, and functional responses. We demonstrate that these can transform into syncytiotrophoblast and extravillous trophoblasts. We also compared the hPTCCTB cells to immortalized chorionic trophoblasts (hFM-CTC), trophoblasts of the chorionic plate, and BeWo cells, choriocarcinoma cell lines of conventional use. Human-term placenta-derived cytotrophoblast immortalized cell line and hFM-CTCs displayed more similarity to each other than to BeWos, but these differ in syncytialization ability. Overall, this study (1) demonstrates that the immortalized hPTCCTB generated are cells of higher physiological relevance and (2) provides a look into the distinction between the spatially distinct placental and fetal barrier trophoblasts cells, hPTCCTB and hFM-CTC, respectively.
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Affiliation(s)
- Manuel S Vidal
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynaecology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of the Philippines Manila, Manila, Philippines
| | - Enkhtuya Radnaa
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynaecology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Natasha Vora
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynaecology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Cristina Antich
- 3D Tissue Bioprinting Laboratory, National Center for Advancing Translational Sciences, National Institute of Sciences, Bethesda, MD, USA
| | - Marc Ferrer
- 3D Tissue Bioprinting Laboratory, National Center for Advancing Translational Sciences, National Institute of Sciences, Bethesda, MD, USA
| | - Rheanna Urrabaz-Garza
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynaecology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Jeena E Jacob
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynaecology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
| | - Ramkumar Menon
- Division of Basic Science and Translational Research, Department of Obstetrics and Gynaecology, The University of Texas Medical Branch at Galveston, Galveston, TX, USA
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3
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Chettiar V, Patel A, Chettiar SS, Jhala DD. Meta-analysis of endometrial transcriptome data reveals novel molecular targets for recurrent implantation failure. J Assist Reprod Genet 2024; 41:1417-1431. [PMID: 38456991 PMCID: PMC11143096 DOI: 10.1007/s10815-024-03077-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024] Open
Abstract
PURPOSE Gene expression analysis of the endometrium has been shown to be a useful approach for identifying the molecular signatures and pathways involved in recurrent implantation failure (RIF). Nevertheless, individual studies have limitations in terms of study design, methodology and analysis to detect minor changes in expression levels or identify novel gene signatures associated with RIF. METHOD To overcome this, we conducted an in silico meta-analysis of nine studies, the systematic collection and integration of gene expression data, utilizing rigorous selection criteria and statistical techniques to ensure the robustness of our findings. RESULTS Our meta-analysis successfully unveiled a meta-signature of 49 genes closely associated with RIF. Of these genes, 38 were upregulated and 11 downregulated in RIF patients' endometrium and believed to participate in key processes like cell differentiation, communication, and adhesion. GADD45A, IGF2, and LIF, known for their roles in implantation, were identified, along with lesser-studied genes like OPRK1, PSIP1, SMCHD1, and SOD2 related to female infertility. Many of these genes are involved in MAPK and PI3K-Akt pathways, indicating their role in inflammation. We also investigated to look for key miRNAs regulating these 49 dysregulated mRNAs as potential diagnostic biomarkers. Along with this, we went to associate protein-protein interactions of 49 genes, and we could recognize one cluster consisting of 11 genes (consisted of 22 nodes and 11 edges) with the highest score (p = 0.001). Finally, we validated some of the genes by qRT-PCR in our samples. CONCLUSION In summary, the meta-signature genes hold promise for improving RIF patient identification and facilitating the development of personalized treatment strategies, illuminating the multifaceted nature of this complex condition.
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Affiliation(s)
- Venkatlaxmi Chettiar
- Department of Life Sciences, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India
| | - Alpesh Patel
- GeneXplore Diagnostics and Research Centre PVT. LTD., Ahmedabad, Gujarat, India
| | | | - Devendrasinh D Jhala
- Department of Zoology, School of Sciences, Gujarat University, Ahmedabad, Gujarat, India.
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4
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Muhandiram S, Dissanayake K, Orro T, Godakumara K, Kodithuwakku S, Fazeli A. Secretory Proteomic Responses of Endometrial Epithelial Cells to Trophoblast-Derived Extracellular Vesicles. Int J Mol Sci 2023; 24:11924. [PMID: 37569298 PMCID: PMC10418763 DOI: 10.3390/ijms241511924] [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: 06/21/2023] [Revised: 07/14/2023] [Accepted: 07/18/2023] [Indexed: 08/13/2023] Open
Abstract
Synchronized crosstalk between the embryo and endometrium during the periconception period is integral to pregnancy establishment. Increasing evidence suggests that the exchange of extracellular vesicles (EVs) of both embryonic and endometrial origin is a critical component of embryo-maternal communication during peri-implantation. Here, we investigated whether embryonic signals in the form of EVs can modulate the endometrial epithelial cell secretome. Receptive endometrial analog RL95-2 cells were supplemented with trophoblast analog JAr cell-derived EVs, and the secretory protein changes occurring in the RL95-2 cells were analyzed using mass spectrometry. EVs of non-trophoblastic origin (HEK 293 cells) were used as the control EV source to supplement endometrial cells. Trophoblast cell-derived EVs enriched endometrial epithelial cell secretions with proteins that support embryo development, attachment, or implantation, whereas control EVs were unable to induce the same effect. The present study suggests that embryonic signals in the form of EVs may prime receptive endometrial epithelial cells to enrich their secretory proteome with critical proteomic molecules with functional importance for periconception milieu formation.
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Affiliation(s)
- Subhashini Muhandiram
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (S.M.); (K.D.); (T.O.); (K.G.); (S.K.)
| | - Keerthie Dissanayake
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (S.M.); (K.D.); (T.O.); (K.G.); (S.K.)
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14B, 50411 Tartu, Estonia
- Department of Anatomy, Faculty of Medicine, University of Peradeniya, Kandy 20400, Sri Lanka
| | - Toomos Orro
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (S.M.); (K.D.); (T.O.); (K.G.); (S.K.)
| | - Kasun Godakumara
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (S.M.); (K.D.); (T.O.); (K.G.); (S.K.)
| | - Suranga Kodithuwakku
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (S.M.); (K.D.); (T.O.); (K.G.); (S.K.)
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Kandy 20400, Sri Lanka
| | - Alireza Fazeli
- Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Kreutzwaldi 62, 51006 Tartu, Estonia; (S.M.); (K.D.); (T.O.); (K.G.); (S.K.)
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila St. 14B, 50411 Tartu, Estonia
- Academic Unit of Reproductive and Developmental Medicine, Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield S10 2TN, UK
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Maxwell SM, Lhakhang TC, Lin Z, Kramer YG, Zhang Y, Wang F, Heguy A, Tsirigos A, Grifo JA, Licciardi F. Investigation of Global Gene Expression of Human Blastocysts Diagnosed as Mosaic using Next-generation Sequencing. Reprod Sci 2022; 29:1597-1607. [PMID: 35304731 DOI: 10.1007/s43032-022-00899-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 02/20/2022] [Indexed: 10/18/2022]
Abstract
Embryos are diagnosed as mosaic if their chromosomal copy number falls between euploid and aneuploid. The purpose of this study was to investigate the impact of mosaicism on global gene expression. This study included 42 blastocysts that underwent preimplantation genetic testing for aneuploidy (PGT-A) and were donated for IRB approved research. Fourteen blastocysts were diagnosed as mosaic with Next-generation Sequencing (NGS). Three NGS diagnosed euploid embryos, and 25 aneuploid embryos (9 NGS, 14 array Comparative Genomic Hybridization, 2 Single Nucleotide Polymorphism array) were used as comparisons. RNA-sequencing was performed on all of the blastocysts. Differentially expressed genes (DEGs) were calculated using DESeq2/3.5 (R Bioconductor Package) with p < 0.05 considered significantly differentially expressed. Pathway analysis was performed on mosaic embryos using EnrichR with p < 0.05 considered significant. With euploid embryo gene expression used as a control, 12 of 14 mosaic embryos had fewer DEGs compared to aneuploid embryos involving the same chromosome. On principal component analysis (PCA), mosaic embryos mapped separately from aneuploid embryos. Pathways involving cell proliferation, differentiation, and apoptosis were the most disrupted within mosaic embryos. Mosaic embryos have decreased disruption of global gene expression compared to aneuploid embryos. This study was limited by the small sample size, lack of replicate samples for each mosaic abnormality, and use of multiple different PGT-A platforms for the diagnosis of aneuploid embryos.
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Affiliation(s)
- Susan M Maxwell
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA. .,Northwell Health Fertility of New York City, 210A East 64th St., Floor 1, New York, NY, 10065, USA.
| | - Tenzin C Lhakhang
- Applied Bioinformatics Laboratories, New York University Langone Health, 227 East 30th St., 7th Floor, New York, NY, USA
| | - Ziyan Lin
- Applied Bioinformatics Laboratories, New York University Langone Health, 227 East 30th St., 7th Floor, New York, NY, USA
| | - Yael G Kramer
- Hackensack Meridian Health, 40 Prospect Ave, Hackensack, NJ, 07601, USA
| | - Yutong Zhang
- Genome Technology Center, New York University Langone Health, 550 First Ave., MSB 308, New York, NY, 10016, USA
| | - Fang Wang
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA
| | - Adriana Heguy
- Genome Technology Center, New York University Langone Health, 550 First Ave., MSB 308, New York, NY, 10016, USA
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, New York University Langone Health, 227 East 30th St., 7th Floor, New York, NY, USA
| | - James A Grifo
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA
| | - Frederick Licciardi
- New York University Langone Fertility Center, 660 First Ave., Floor 5, New York, NY, 10016, USA
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7
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Evans J, Rai A, Nguyen HPT, Poh QH, Elglass K, Simpson RJ, Salamonsen LA, Greening DW. Human Endometrial Extracellular Vesicles Functionally Prepare Human Trophectoderm Model for Implantation: Understanding Bidirectional Maternal-Embryo Communication. Proteomics 2019; 19:e1800423. [PMID: 31531940 DOI: 10.1002/pmic.201800423] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Revised: 08/02/2019] [Indexed: 12/18/2022]
Abstract
Embryo implantation into maternal endometrium is critical for initiation and establishment of pregnancy, requiring developmental synchrony between endometrium and blastocyst. However, factors regulating human endometrial-embryo cross talk and facilitate implantation remain largely unknown. Extracellular vesicles (EVs) are emerging as important mediators of this process. Here, a trophectoderm spheroid-based in vitro model mimicking the pre-implantation human embryo is used to recapitulate important functional aspects of blastocyst implantation. Functionally, human endometrial EVs, derived from hormonally treated cells synchronous with implantation, are readily internalized by trophectoderm cells, regulating adhesive and invasive capacity of human trophectoderm spheroids. To gain molecular insights into mechanisms underpinning endometrial EV-mediated enhancement of implantation, quantitative proteomics reveal critical alterations in trophectoderm cellular adhesion networks (cell adhesion molecule binding, cell-cell adhesion mediator activity, and cell adherens junctions) and metabolic and gene expression networks, and the soluble secretome from human trophectodermal spheroids. Importantly, transfer of endometrial EV cargo proteins to trophectoderm to mediate changes in trophectoderm function is demonstrated. This is highlighted by correlation among endometrial EVs, the trophectodermal proteome following EV uptake, and EV-mediated trophectodermal cellular proteome, important for implantation. This work provides an understanding into molecular mechanisms of endometrial EV-mediated regulation of human trophectoderm functions-fundamental in understanding human endometrium-embryo signaling during implantation.
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Affiliation(s)
- Jemma Evans
- Endometrial Remodelling Laboratory, Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, 3800, Australia.,Department of Molecular and Translational Science, Monash University, Clayton, VIC, 3800, Australia
| | - Alin Rai
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Hong P T Nguyen
- Endometrial Remodelling Laboratory, Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, 3800, Australia
| | - Qi Hui Poh
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Kirstin Elglass
- Endometrial Remodelling Laboratory, Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, 3800, Australia
| | - Richard J Simpson
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Lois A Salamonsen
- Endometrial Remodelling Laboratory, Centre for Reproductive Health, Hudson Institute of Medical Research, Clayton, VIC, 3800, Australia.,Departments of Physiology and Obstetrics and Gynaecology, Monash University, Clayton, VIC, 3800, Australia
| | - David W Greening
- Molecular Proteomics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, 3086, Australia
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8
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Baranov VS, Kogan IY, Kuznetzova TV. Advances in Developmental Genetics and Achievements in Assisted Reproductive Technology. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419100028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Stafuzza NB, Silva RMDO, Fragomeni BDO, Masuda Y, Huang Y, Gray K, Lourenco DAL. A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive. BMC Genomics 2019; 20:321. [PMID: 31029102 PMCID: PMC6487013 DOI: 10.1186/s12864-019-5687-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 04/11/2019] [Indexed: 12/19/2022] Open
Abstract
Background In this study we integrated the CNV (copy number variation) and WssGWAS (weighted single-step approach for genome-wide association) analyses to increase the knowledge about number of piglets born alive, an economically important reproductive trait with significant impact on production efficiency of pigs. Results A total of 3892 samples were genotyped with the Porcine SNP80 BeadChip. After quality control, a total of 57,962 high-quality SNPs from 3520 Duroc pigs were retained. The PennCNV algorithm identified 46,118 CNVs, which were aggregated by overlapping in 425 CNV regions (CNVRs) ranging from 2.5 Kb to 9718.4 Kb and covering 197 Mb (~ 7.01%) of the pig autosomal genome. The WssGWAS identified 16 genomic regions explaining more than 1% of the additive genetic variance for number of piglets born alive. The overlap between CNVR and WssGWAS analyses identified common regions on SSC2 (4.2–5.2 Mb), SSC3 (3.9–4.9 Mb), SSC12 (56.6–57.6 Mb), and SSC17 (17.3–18.3 Mb). Those regions are known for harboring important causative variants for pig reproductive traits based on their crucial functions in fertilization, development of gametes and embryos. Functional analysis by the Panther software identified 13 gene ontology biological processes significantly represented in this study such as reproduction, developmental process, cellular component organization or biogenesis, and immune system process, which plays relevant roles in swine reproductive traits. Conclusion Our research helps to improve the understanding of the genetic architecture of number of piglets born alive, given that the combination of GWAS and CNV analyses allows for a more efficient identification of the genomic regions and biological processes associated with this trait in Duroc pigs. Pig breeding programs could potentially benefit from a more accurate discovery of important genomic regions. Electronic supplementary material The online version of this article (10.1186/s12864-019-5687-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nedenia Bonvino Stafuzza
- Department of Exact Science, School of Agricultural and Veterinarian Sciences (FCAV), Sao Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil. .,Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.
| | - Rafael Medeiros de Oliveira Silva
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA.,National Center for Cool and Cold Water Aquaculture (NCCCWA), Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, USA
| | | | - Yutaka Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Yijian Huang
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
| | - Kent Gray
- Smithfield Premium Genetics Group, Rose Hill, NC, USA
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10
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Transcriptional profiles of crossbred embryos derived from yak oocytes in vitro fertilized with cattle sperm. Sci Rep 2018; 8:11571. [PMID: 30069024 PMCID: PMC6070518 DOI: 10.1038/s41598-018-29912-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/20/2018] [Indexed: 12/24/2022] Open
Abstract
During mammalian pre-implantation embryonic development, dramatic and orchestrated changes occur in gene transcription. Pregnancy rates were low when yak females were crossbred with cattle breeds, but few studies exist to describe the unique molecular network regulation behind the pre-implantation development of these embryos. We determined the transcriptomes of crossbred embryos derived from yak oocytes in vitro fertilized with Jersey sperm using Illumina RNA-seq for the first time in this study. Embryos were sampled at the 2-, 4-, and 8-cell, morula and blastocyst stages. The results showed that in total, 291.9 million short reads were generated from the five libraries of 2-, 4-, and 8-cell, morula and blastocyst stages, with 276.2 million high-quality reads selected for further analysis. Eighty to 91% of the clean reads were aligned against the yak reference genome. A total of 19,072 transcripts were identified in five libraries, of which 7,785 transcripts were co-expressed in each stage and 2,013 transcripts were stage-specific. When a |log2 ratio| ≥1 and q-value ≤ 0.05 were set as thresholds for identifying differentially expressed genes (DEGs), we detected a total of 3,690 to 10,298 DEGs between any two consecutive stages. Based on the results of GO and KEGG enrichment, some of these DEGs potentially play an important role in regulating pre-implantation development, but they are most likely stage-specific. There were 2,960, 7,287, 6,420, 7,724 and 10,417 DEGs in 2-, 4-, 8-cell, morula and blastocyst stages between the crossbred embryos and purebred embryos of the yak, respectively, leading to a large difference in GO terms and pathways. In conclusion, we sequenced transcriptomes of in vitro-produced crossbred embryos of yak and cattle during pre-implantation and provided comprehensive examinations of gene activities. These will be helpful for development of assisted reproductive technology and better understanding the early maternal-fetal or maternal-embryonic dialog in inter-species crossbreeding.
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11
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Zi XD, Luo B, Xia W, Zheng YC, Xiong XR, Li J, Zhong JC, Zhu JJ, Zhang ZF. Characterization of transcriptional complexity during pre-implantation development of the yak (Bos grunniens) using RNA-Seq. Reprod Domest Anim 2018; 53:759-768. [PMID: 29582471 DOI: 10.1111/rda.13167] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 02/13/2018] [Indexed: 12/18/2022]
Abstract
The objective of this study was to investigate the mechanism that regulates pre-implantation development of the yak (Bos grunniens). We determined the transcriptomes of in vitro-produced yak embryos at two-cell, four-cell, eight-cell stages, and morula and blastocyst using the Illumina RNA-seq for the first time. We obtained 47.36-50.86 million clean reads for each stage, of which, 85.65%-90.02% reads were covered in the reference genome. A total of 17,368 genes were expressed during the two-cell stage to blastocyst of the yak, of which 7,236 genes were co-expressed at all stages, whereas 10,132 genes were stage-specific expression. Transcripts from 9,827 to 14,893 different genes were detected in various developmental stages. When |log2 ratio| ≥ 1 and q-value <0.05 were set as thresholds for identifying differentially expressed genes (DEGs), we detected a total of 6,922-10,555 DEGs between any two consecutive stages. The GO distributions of these DEGs were classified into three categories: biological processes (23 terms), cellular components (22 terms) and molecular functions (22 terms). Pathway analysis revealed 310 pathways of the DEGs that were operative in early pre-implantation yak development, of which 32 were the significantly enriched pathways. In conclusion, this is the first report to investigate the mechanism that regulates yak embryonic development using high-throughput sequencing, which provides a comprehensive framework of transcriptome landscapes of yak pre-implantation embryos.
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Affiliation(s)
- X-D Zi
- Key-Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest University for Nationalities, Chengdu, China
| | - B Luo
- Key-Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest University for Nationalities, Chengdu, China
| | - W Xia
- Key-Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest University for Nationalities, Chengdu, China
| | - Y-C Zheng
- Key-Laboratory for Modern Biotechnology of State Ethnic Affairs Commission, Southwest University for Nationalities, Chengdu, China
| | - X-R Xiong
- Key-Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest University for Nationalities, Chengdu, China
| | - J Li
- Key-Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest University for Nationalities, Chengdu, China
| | - J-C Zhong
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, China
| | - J-J Zhu
- Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, China
| | - Z-F Zhang
- Key-Laboratory for Animal Science of State Ethnic Affairs Commission, Southwest University for Nationalities, Chengdu, China
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van Veen M, Matas-Rico E, van de Wetering K, Leyton-Puig D, Kedziora KM, De Lorenzi V, Stijf-Bultsma Y, van den Broek B, Jalink K, Sidenius N, Perrakis A, Moolenaar WH. Negative regulation of urokinase receptor activity by a GPI-specific phospholipase C in breast cancer cells. eLife 2017; 6. [PMID: 28849762 PMCID: PMC5576486 DOI: 10.7554/elife.23649] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Accepted: 07/28/2017] [Indexed: 12/21/2022] Open
Abstract
The urokinase receptor (uPAR) is a glycosylphosphatidylinositol (GPI)-anchored protein that promotes tissue remodeling, tumor cell adhesion, migration and invasion. uPAR mediates degradation of the extracellular matrix through protease recruitment and enhances cell adhesion, migration and signaling through vitronectin binding and interactions with integrins. Full-length uPAR is released from the cell surface, but the mechanism and significance of uPAR shedding remain obscure. Here we identify transmembrane glycerophosphodiesterase GDE3 as a GPI-specific phospholipase C that cleaves and releases uPAR with consequent loss of function, whereas its homologue GDE2 fails to attack uPAR. GDE3 overexpression depletes uPAR from distinct basolateral membrane domains in breast cancer cells, resulting in a less transformed phenotype, it slows tumor growth in a xenograft model and correlates with prolonged survival in patients. Our results establish GDE3 as a negative regulator of the uPAR signaling network and, furthermore, highlight GPI-anchor hydrolysis as a cell-intrinsic mechanism to alter cell behavior. Every process in the body, from how cells divide to how they move around, is tightly regulated. For example, cells only migrate when they receive the correct signals from their environment. These signals are recognised by receptor proteins that sit on the cell surface and connect the outside signal with the cell’s response. However, in cancer cells, these processes are out of control, which is why cancer cells can grow very quickly or spread to many different parts of the body. One important receptor protein is the urokinase receptor, which helps to reorganize the tissue, for example, when wounds heal, but also enables cancer cells to grow and spread. A special feature of urokinase receptor is the way it is connected to the cell surface, namely through a molecule that acts as an anchor, called the GPI anchor. The urokinase receptor and some other GPI-anchored proteins can be released from their anchor. However, until now it was not clear why and how the urokinase receptor is released from cells, or how losing the receptor affects the cell. Now, van Veen, Matas-Rico et al. studied breast cancer cells, and discovered that an enzyme called GDE3 cuts the urokinase receptor off its GPI anchor to release the receptor from the cells. However, when breast cancer cells shed the urokinase receptor, they also lost the receptor from the cell surface in specific areas. As a result, the receptor could not work anymore. When breast cancer cells were experimentally modified to produce high levels of GDE3, the cancer cells became less mobile and aggressive. Van Veen, Matas-Rico et al. then implanted ‘normal’ breast cancer cells, and breast cancer cells with extra GDE3 into mice, and observed that the tumors of mice with additional GDE3 grew less quickly. Moreover, breast cancer patients with high levels of GDE3 tend to live longer than patients with low levels of GDE3. These results suggest that the enzyme GDE3 can suppress tumor growth. These findings uncover a new way how cells can alter their behavior, namely by cleaving GPI anchors at the cell surface. Future experiments will need to address how GDE3 itself is controlled, and if it releases other GPI-anchored proteins from cells. Once we know how to increase GDE3 activity in tumor cells, the new knowledge could one day lead to therapies to help patients with cancer.
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Affiliation(s)
- Michiel van Veen
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Elisa Matas-Rico
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Koen van de Wetering
- Division of Molecular Oncology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Daniela Leyton-Puig
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Katarzyna M Kedziora
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Yvette Stijf-Bultsma
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Bram van den Broek
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Kees Jalink
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Anastassis Perrakis
- Division of Biochemistry, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Wouter H Moolenaar
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, Netherlands
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13
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Albertini DF. On becoming accepting of the imperfectionsin mammalian embryogenesis. J Assist Reprod Genet 2017; 33:969-70. [PMID: 27448615 DOI: 10.1007/s10815-016-0777-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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