Innovative Training Network in Female Reproductive Care

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Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Introduction to Unix-Command line tools for biologists working with large-scale data

Introduction to Unix Command line tools for biologists working with largescale data isfinished The ESRs will obtain the knowledge on how to operate within the Unix environment All ESRs will participate in workshop and complete the practical assignments

Tissue specific CIN-depletion for genomic ‘live-imaging' of gestation

Tissue-specific depletion of CIN has been reported as a proof-of-the principle for genomic ‘live-imaging’ of human early gestation.

Endometrial phenotype in PCOS

"Provides report on ""Endometrial phenotype in PCOS"", related to research output of ESR7."

Evaluation of tissue histology course

‘Evaluation of tissue histology from female reproductive tract – hands-on microscopy training’ is completed (for Task 2.4, M29).

Basics of statistical analysis for biologists’

Basics of statistical analysis for biologists is completed for all ESRs The ESRs will know 1 How to analyse and visualise data in the statistical software package R 2 How to correctly interpret results and 3 How to create publicationquality tables and figures ESRs will participate in workshop and complete the practical assignments

Dissemination and Communication Plan

Communication and Dissemination Plan CCHT is responsible for compiling the plan to increase the visibility of MATER among key stakeholders and the society at large All partners will contribute in defining their respective actions resulting in a dedicated document which will be periodically reviewed

Effect of environmental factors on embryo genome activity

Information about the effects of culture media, oxygen level and embryo vitrification on embryo genome activity and CIN has been obtained.

Female reproductive endocrinology and disorders

Basics of female reproductive endocrinology and most common infertilityassociated gynaecological disorders is accomplished to all ESRs

ESR recruitment

ESRs recruitment finished T63 M8

Stem cells in female reproduction'

‘Stem cells in female reproduction’ is successfully finished for all ESRs. Different techniques in enSC research are introduced and discussed with experienced researchers. The course is completed by written assignment and presentation (for Task 2.2, M23).

The roles of mi-RNAs in folliculogenesis

The roles of mi-RNAs in folliculogenesis have been characterized (for Task 1.9, M42).

Impact of prenatal genomic technologies

‘Impact of prenatal genomic technologies – Societal aspects’ is conducted. Debates will be encouraged but no grading system is implemented for this course.

Trainig: Scientists entering life science business

The course provides the background of doing business in biotech/healthcare and trains ESRs to manage, finance and market their projects. Topics are life-sciences/healthcareas business environment, R&D and value chains in biotech/healthcare; marketing and sales; company’s strategies and planning. ESRs will gain practical training on how innovations can be developed into products. Young start-ups will be invited to present their projects and the supportive actions/funding that enabled their success.

Causes of CIN-free pregnancy loss

Novel knowledge about the causes for CIN-free pregnancy loss has been obtained.

Improved molecular model for ovarian development and folliculogenesis

Improved molecular model for ovarian development and folliculogenesis. The studies have clarified the roles of EMX2, GATA4 and FSHR in folliculogenesis and etiology of POI (for Task 1.8, M42).

Start-up company training

Hands-on business development program provides knowledge and skills for start-up projects and helps teams to shape their ideas into tested business models.

Training: Trendspotting and Future Thinking

ESRs will gain practical experience in trendspotting and futurethinking as a tool in business creation and development.

Endometrial receptivity course

‘Focus on endometrial receptivity - from endometrial cell separation to RNA-seq’ is delivered to all ESRs. The course gives ESRs hands-on experience for endometrial research with the main focus on transcriptome profiling. Course requires full-time participation (for Task 2.1, M11).

Single-cell OMICS

‘Single-cell OMICS: Fundamental and translational horizons’ is delivered to all ESRs. Afterthe course, the ESRs are able to design their single-cell experiments. A short practical assignment will be handed to all ESRs.

Functionally characterized genes involved in HPO-axis and ovarian biology

Functionally characterized genes involved in HPO-axis and ovarian biology. The selected genes are functionally characterized by using hPSC-models (for Task 1.6, M54).

FACS cell sorting, endometrial cell culture

‘FACS cell sorting and primary cell culture from endometrial tissue’ is completed for all ESRs (for Task 2.3, M29).

Non-invasive prenatal diagnosis and beyond

‘Non-invasive prenatal diagnosis and beyond’ is accomplished. All ESRs participate in group exercise.

Single-cell analysis of human embryo development

‘Application of single-cell analysis in research of human early embryo development’ is successfully finished for all ESRs. The course introduces single-cell analysis applications and helps to create a link with the leading scientists at KI to promote the career of ESRs.

Report on dissemination and communication activities

Report on dissemination and communication activities.

Common understanding about the legislation governing the use of reproductive medicine in Europe

Common understanding about the legislation governing the use of reproductive medicine in Europe, their differences and the possibilities and needs of harmonizing the legislation across Europe will be defined.

Training: Health policy, innovation and management

The course reviews healthcare systems in the context of innovation management. ESRs learn how science & innovation can be integrated into healthcare policy. ESRs will learn how different technological regimes and healthcare systems impact their project. Practitioners and policy makers from Ministry of Social Affairs will discuss examplesof personal medicine and e-Health services. All MATER industry partners will participate in Innovation clinic, i.e. companies will propose workshop topics that are based on challenges facing their business.

Report on training course: Complementary transferable skills training

The skills development programme will have three parts IIntellectual Property Rights IPR training II Research Ethics and Equality training III Communication training

The incidence and origin of CIN in bovine embryos

The incidence and origin of CIN in bovine early embryos have been elucidated.

GWA-studies for ovarian aging and related phenotypes

GWAstudies for ovarian aging and related phenotypes The GWAstudies for ovarian agingrelated phenotypes are finished by using two extensive biobanks in Estonia EGCUT and Finland NFBC66 for Task 17 M24

Clinical data and sample collection

‘Clinical data/sample collection for scientific purposes: advantages and pitfalls’ is delivered to all ESRs. ESRsare competent to conduct clinical sample collections for research.

Human embryos in clinical setting

‘Human embryos in clinical setting’ is finished for all ESRs. The course gives an overview about the profession of clinical embryologist, and deals with the most important technological, clinical and ethical aspects of IVF.

GWAS crash course

GWAS crash course is provided to all ESRs The course requires that ESRs participate in workshop and complete the practical assignments

PMC and SAM meetings, at UH, KI, UO, KUL and UT

PMC meetings, Task 6.1, M1, M17, M23, M29, M35, M41.

Summer school at KUL and UT

Summer school, T5.4, M17, M49.

Doctoral Degrees awarded
Dissemination workshops

Dissemination workshops, T5.3, M23, M48.

ESRs Kick-off meeting at KUL

ESRs Kickoff meeting at KUL T63 M8

Final Meeting, at UT

Final Meeting at UT, T6.1, M48

At least three start-up companies established

At least three start-up companies established.

Project stationary and website

Development of project stationary logotemplates banners posters flyers brochures rollup and website

At least 42 research and 14 popular-science articles

At least 42 research and 14 popular-science articles.

Publications

Ultrasensitive Microhaplotype-Based Detection of Minor Alleles in Cervical Samples of Pregnant Women Identifies Sperm Rather Than Fetal DNA

Author(s): Margot van Riel, Yan Zhao, Tatjana Jatsenko, Lore Lannoo, Dirk Timmerman, Joris R Vermeesch
Published in: Clinical Chemistry, 2023, ISSN 0009-9147
Publisher: American Association for Clinical Chemistry, Inc.
DOI: 10.1093/clinchem/hvad107

Polygenic risk scoring of human embryos: a qualitative study of media coverage

Author(s): Tiny Pagnaer, Maria Siermann, Pascal Borry, Olga Tšuiko
Published in: BMC Medical Ethics, Issue 22/1, 2021, ISSN 1472-6939
Publisher: BioMed Central
DOI: 10.1186/s12910-021-00694-4

Investigating the impact of vitrification on bovine ovarian tissue morphology, follicle survival, and transcriptomic signature

Author(s): Deligiannis, S. P., Kask, K., Modhukur, V., Boskovic, N., Ivask, M., Jaakma, Ü., Damdimopoulou, P., Tuuri, T., Velthut-Meikas, A., Salumets, A.
Published in: Journal of Assisted Reproduction and Genetics, 2024, ISSN 1058-0468
Publisher: Kluwer Academic/Plenum Publishers
DOI: 10.1007/s10815-024-03038-4

HiHo-AID2: boosting homozygous knock-in efficiency enables robust generation of human auxin-inducible degron cells

Author(s): Li, S., Wang, Y., Van Der Stoel, M. M., Zhou, X., Madhusudan, S., Kanerva, K., Nguyen, V. D., Eskici, N., Olkkonen, V. M., Zhou, Y., Raivio, T., Ikonen, E.
Published in: Genome Biology, 2024, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-024-03187-w

Congenital hypogonadotropic hypogonadism in a patient with a de novo POGZ mutation

Author(s): Eskici, N., Madhusudan, S., Vaaralahti, K., Yellapragada, V., Gómez-Sánchez, C. E., Kärkinen, J., Almusa, H., Brandstack, N., Miettinen, P. J., Wang, Y., Raivio, T.
Published in: European Journal of Endocrinology, 2023, ISSN 0804-4643
Publisher: BioScientifica Ltd.
DOI: 10.1093/ejendo/lvad111

Genome-wide equine preimplantation genetic testing enabled by simultaneous haplotyping and copy number detection

Author(s): De Coster, T., Zhao, Y., Tšuiko, O., Demyda-Peyrás, S., Van Soom, A., Vermeesch, J. R., Smits, K.
Published in: Scientific Reports, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-023-48103-7

Cell type signatures in cell-free DNA fragmentation profiles reveal disease biology

Author(s): Stanley, K. E., Jatsenko, T., Tuveri, S., Sudhakaran, D., Lannoo, L., Van Calsteren, K., De Borre, M., Parijs, I., Van Coillie, L., Van Den Bogaert, K., Toledo, R. A., Lenaerts, L., Tejpar, S., Punie, K., Rengifo, L. Y., Vandenberghe, P., Thienpont, B., Vermeesch, J. R.
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-46435-0

Dynamic changes in AI-based analysis of endometrial cellular composition: Analysis of PCOS and RIF endometrium. Journal of Pathology Informatics

Author(s): Lee, S., Arffman, R. K., Komsi, E. K., Lindgren, O., Kemppainen, J., Kask, K., Saare, M., Salumets, A., Piltonen, T.
Published in: Journal of Pathology Informatics, 2024, ISSN 2153-3539
Publisher: Elsevier Inc.
DOI: 10.1016/j.jpi.2024.100364

Leveraging Northern European population history: novel low-frequency variants for polycystic ovary syndrome

Author(s): Jaakko S Tyrmi, Riikka K Arffman, Natàlia Pujol-Gualdo, Venla Kurra, Laure Morin-Papunen, Eeva Sliz, Terhi T Piltonen, Triin Laisk, Johannes Kettunen, Hannele Laivuori
Published in: Human Reproduction, 2021, ISSN 0268-1161
Publisher: Oxford University Press
DOI: 10.1093/humrep/deab250

An update on Experimental therapeutic strategies for thin endometrium

Author(s): Tang, Y., Frisendahl, C., Lalitkumar, P. G., Danielsson, K. G.
Published in: Endocrines, 2023, ISSN 2673-396X
Publisher: MDPI
DOI: 10.3390/endocrines4040048

Optimized single-cell RNA sequencing protocol to study early genome activation in mammalian preimplantation development

Author(s): Nina Boskovic, Gamze Yazgeldi, Sini Ezer, Mari H. Tervaniemi, Jose Inzunza, Spyridon Panagiotis Deligiannis, Barış Yaşar, Tiina Skoog, Kaarel Krjutškov, Shintaro Katayama, Juha Kere
Published in: STAR Protocols, 2023, ISSN 2666-1667
Publisher: Elsevier Inc.
DOI: 10.1016/j.xpro.2023.102357

Gut bacteriome and mood disorders in women with PCOS

Author(s): Lee S., Tejesvi M.V., Hurskainen E., Aasmets O., Plaza-Díaz J., Franks S., Morin-Papunen L., Tapanainen J.S., Ruuska T.S., Altmäe S., Org E., Salumets A., Arffman R.K., Piltonen T.T.
Published in: Human Reproduction, 2024, ISSN 1460-2350
Publisher: Oxford University Press
DOI: 10.1093/humrep/deae073

Bromocriptine inhibits proliferation in the endometrium from women with adenomyosis

Author(s): Yiqun Tang; Sakthivignesh Ponandai-srinivasan; Caroline Frisendahl; Johanna K. Andersson; Dora Pavone; Elizabeth A. Stewart; Parameswaran Grace Luther Lalitkumar; Eberhard Korsching; Nageswara Rao Bogavarappu; Kristina Gemzell-Danielsson
Published in: Frontiers in Endocrinology, 2023, ISSN 1664-2392
Publisher: Frontiers Media SA
DOI: 10.3389/fendo.2023.1026168

GWAS meta-analyses clarify the genetics of cervical phenotypes and inform risk stratification for cervical cancer

Author(s): Estonian Biobank Research Team; FinnGen; Koel, Mariann; Vosa, Urmo; Joeloo, Maarja; Läll, Kristi; Gualdo, Natalia P.; Laivuori, Hannele; Lemmelä, Susanna; Daly, Mark; Palta, Priit; Mägi, Reedik; Laisk, Triin
Published in: Human Molecular Genetics, 2023, ISSN 0964-6906
Publisher: Oxford University Press
DOI: 10.1093/hmg/ddad043

CRISPR/Cas9-mediated activation of NR5A1 steers female human embryonic stem cell-derived bipotential gonadal-like cells towards a steroidogenic cell fate

Author(s): Danti, L., Lundin, K., Sepponen, K., Yohannes, D. A., Kere, J., Tuuri, T., Tapanainen, J. S.
Published in: Journal of Ovarian Research, 2023, ISSN 1757-2215
Publisher: BioMed Central
DOI: 10.1186/s13048-023-01264-5

Advancing our understanding of genetic risk factors and potential personalized strategies for pelvic organ prolapse.

Author(s): Pujol-Gualdo, N., Läll, K., Lepamets, M. et al.
Published in: Nature Communication, Issue 13, article no 3584, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-31188-5

Genome-wide association study meta-analysis supports association between MUC1 and ectopic pregnancy

Author(s): Pujol-Gualdo, N., Mägi, R., Laisk, T.
Published in: Human Reproduction, 2023, ISSN 0268-1161
Publisher: Oxford University Press
DOI: 10.1093/humrep/dead217

FGF8–FGFR1 signaling regulates human GnRH neuron differentiation in a time- and dose-dependent manner

Author(s): Venkatram Yellapragada, Nazli Eskici, Yafei Wang, Shrinidhi Madhusudan, Kirsi Vaaralahti, Timo Tuuri, Taneli Raivio
Published in: Disease Models & Mechanisms, 2022, ISSN 1754-8411
Publisher: The Company of Biologists
DOI: 10.1242/dmm.049436

Ready for polygenic risk scores? An analysis of regulation of preimplantation genetic testing in European countries

Author(s): Siermann, M., Van Der Schoot, V., Bunnik, E. M., Borry, P.
Published in: Human Reproduction, 2024, ISSN 1460-2350
Publisher: Oxford University Press
DOI: 10.1093/humrep/deae049

Evidence From Men for Ovary-independent Effects of Genetic Risk Factors for Polycystic Ovary Syndrome

Author(s): Jia Zhu, Natàlia Pujol-Gualdo, Laura B L Wittemans, Cecilia M Lindgren, Triin Laisk, Joel N Hirschhorn, Yee-Ming Chan
Published in: The Journal of Clinical Endocrinology & Metabolism, 2021, ISSN 0021-972X
Publisher: The Endocrine Society
DOI: 10.1210/clinem/dgab838

AI-algorithm training and validation for identification of endometrial CD138+ cells in infertility-associated conditions; polycystic ovary syndrome (PCOS) and recurrent implantation failure (RIF)

Author(s): Seungbaek Lee, Riikka K. Arffman, Elina K. Komsi, Outi Lindgren, Janette A. Kemppainen, Hanna Metsola, Henna-Riikka Rossi, Anne Ahtikoski, Keiu Kask, Merli Saare, Andres Salumets, Terhi T. Piltonen
Published in: Journal of Pathology Informatics, 2024, ISSN 2153-3539
Publisher: Elsevier Inc.
DOI: 10.1016/j.jpi.2024.100380

A systematic review of the views of healthcare professionals on the scope of preimplantation genetic testing

Author(s): Maria Siermann; Zoë Claesen; Laurent Pasquier; Taneli Raivio; Olga Tšuiko; Joris Robert Vermeesch; Pascal Borry
Published in: J Community Genet, 2022, ISSN 1868-310X
Publisher: Springer Verlag
DOI: 10.1007/s12687-021-00573-w

Limitations, concerns and potential: attitudes of healthcare professionals toward preimplantation genetic testing using polygenic risk scores

Author(s): Maria Siermann; Ophelia Valcke; Joris Robert Vermeesch; Taneli Raivio; Olga Tšuiko; Pascal Borry
Published in: European Journal of Human Genetics, 2023, ISSN 1476-5438
Publisher: Springer Nature
DOI: 10.1038/s41431-023-01333-9

A review of normative documents on preimplantation genetic testing: Recommendations for PGT-P

Author(s): Maria Siermann, Olga Tšuiko, Joris Robert Vermeesch, Taneli Raivio, Pascal Borry
Published in: Genetics in Medicine, 2022, ISSN 1098-3600
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1016/j.gim.2022.03.001

“Are we not going too far?“: Socio-ethical considerations of preimplantation genetic testing using polygenic risk scores according to healthcare professionals

Author(s): Siermann, M., Valcke, O., Vermeesch, J. R., Raivio, T., Tšuiko, O., Borry, P.
Published in: Social Science & Medicine, 2024, ISSN 0277-9536
Publisher: Pergamon Press Ltd.
DOI: 10.1016/j.socscimed.2024.116599

Global Transcriptomic Analysis of Placentas from Women with Gestational SARS-CoV-2 Infection during the Third Trimester of Pregnancy

Author(s): Tang, Y., Boggavarapu, N. R., Aronsson, A., Danielsson, K. G., Lalitkumar, P. G.
Published in: International Journal of Molecular Sciences, 2024, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms25031608

Deciphering the Transcriptional Landscape of Human Pluripotent Stem Cell-Derived GnRH Neurons: The Role of Wnt Signaling in Patterning the Neural Fate

Author(s): Yafei Wang, Shrinidhi Madhusudan, Ludovica Cotellessa, Jouni Kvist, Nazli Eskici, Venkatram Yellapragada, Kristiina Pulli, Carina Lund, Kirsi Vaaralahti, Timo Tuuri, Paolo Giacobini, Taneli Raivio
Published in: Stem Cells, 2022, ISSN 1549-4918
Publisher: Oxford University Press
DOI: 10.1093/stmcls/sxac069

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