The SARM project exchanges researchers and transfers knowledge between 2 industrial (Igenomix, Paterna, Spain and Competence Centre on Health Technologies, Tartu, Estonia) and 3 academic (Karolinska Institutet, Stockholm, Sweden; Katholieke Universiteit Leuven, Belgium; and University of Tartu, Estonia) cooperation partners. The members of the consortium have acquired excellent and unique expertise in diverse fields of biomedical research that, when combined, will form a strong, stimulating and coherent research environment ensuring the pooling of complementary scientific skills in reproductive genetics and medicine. Besides outstanding contribution to the current scientific understanding of human reproduction, the framework of the SARM programme also provides the possibility for more profound integration of European research at both academia and industry levels leading to more efficient and systematic transfer of knowledge and skills between the two sectors, thus increasing the overall European sustainable economic competitiveness in the area of life sciences.

The primary motivation for the current SARM project stems from the perceived need to contribute to future ART developments and benefit from the recent breakthroughs in technological innovations. SARM brings together research intensive but still commercial IVF clinics and leading research institutions in Europe to make this transfer from industry and academia reachable.

The scientific structure of the project is divided into four (4) research-oriented work packages (WP1-WP4) targeting the specific objectives and additional two (2) work packages (WP5 Broad skills development and WP6 outreach and dissemination activities). WP7 is dedicated to project management.


OBJECTIVES OF RESEARCH

1. To unravel the molecular nature of human preimplantation embryo development and endometrial maturation. This goal will be achieved by exploiting highly sophisticated single-cell genomics tools, such as fine-resolution mapping of DNA copy-number changes by using SNP-array platform and DNA-sequencing, and characterizing single-cell transcriptional status by RNA-seq technology.

2. To combine, for the first time, the chromosomal and transcriptional status at the single embryo level, which helps to understand the genome regulation dynamics in embryo development and to link the occurrence of specific chromosomal mutations with the changes in gene expression profiles.

3. Our studies are likely to propose novel embryonal and endometrial biomarkers useful for selecting the most competent embryos for transfer or identifying the causes for endometrium-related female infertility. These markers are eagerly sought for and therefore hold great promise for commercial applications.

The specific objectives on the way to achieve the primary research objective are as follows:

1. To analyse single cells of IVF embryos at different preimplantation stages by using DNA microarrays and sequencing, uncovering full and partial aneuploidies and structural defects of chromosomes.

2. To conduct gene expression profiling of human preimplantation embryos by single-cell RNA-seq, outlining the genome-scale transcriptional activity during the normal course of human preimplantation embryo development.

3. To reveal the changes in genome function pertinent to genomic mutations in oocytes and embryos.

4. To examine individual endometrial cells (apical and glandular epithelium, as well as stromal cells) from the same tissue biopsy by using RNA-seq to understand the overall genome activity regulation within the receptive endometrium.

5. To perform a bioinformatic analysis in order to update the model of human embryo implantation, revealing the putative candidate genes participating in embryo-maternal dialogue.


SARM WORK PACKAGES AND GOALS

WP1. Transcriptomic profiling of human pre-implantation embryos

Outcome: The full-genome transcriptomic scans from oocytes to blastocyst-stage embryos.

WP leader: Prof. Juha Kere, Karolinska Institutet, Stockholm, Sweden.

  • To carry out in-depth transcriptome analyses of the microarray results obtained from human immature and mature oocytes and pre-implantation embryos up to the blastocyst stage
  • To continue with single-cell RNA sequencing of individual oocytes, zygotes and blastomeres in order to reveal more details on the degradation of maternal transcripts, the start of zygotic/embryonal transcription as well as embryo polarization and blastomere fate
WP2. Genomic mutations in preimplantation embryos: prevalence, influential factors and molecular mechanisms

Outcomes: Novel knowledge on chromosomal pathologies in human early embryos and improved methodologies for embryo selection in IVF.

WP leader: Prof. Joris Vermeesch, Katholieke Universiteit Leuven, Belgium.
  • To develop, optimize and combine single cell SNP-, CNV- and haplotyping proof-of-concepts into a novel diagnostics method for preimplantation genetic diagnosis (PGD)
  • To develop massively parallel paired-end sequencing technologies for single-cell DNA analysis
  • To apply those new technologies to oocytes, polar bodies, blastomeres and cells from the blastocyst stages and to analyse the correlations between cell division kinetics and chromosomal rearrangements

WP3. Endometrial receptivity: cell specific gene expression signatures and testing for implantation failure patients

Outcomes: Gene activity analysed in different tissue components of receptive endometrium and to improved molecular testing of endometrial receptivity.

WP leader: Prof. Carlos Simón Vallés / Dr. David Blesa, Igenomix S.L., Paterna, Spain.

  • To provide detailed and validated laser capture microdissection and cell-sorting protocols for different endometrial cell populations
  • To optimize single-cell RNA sequencing technology for application on single cells derived from endometrial cellular subpopulations
  • To apply these technologies on cells originating from endometrial biopsies and reveal, for the very first time, the global transcriptome of different endometrial cell populations, both at single cell and cell population level
  • To combine our results with pre-existing knowledge and expertise to develop a diagnostic approach also applicable to whole endometrial biopsies in the clinical setting
WP4. Interactome of human embryo implantation: identification of gene expression pathways, regulation and integrated regulatory networks

Outcomes: (i) To improve the understanding on the molecular mechanisms of human embryo implantation based on critical analysis of transcriptomic networks of blastocyst-stage embryos and receptive-phase endometrium, and evaluation of curated protein-protein interaction data sets. (ii) Functional validation of key proteins in implantation by using RNA interference (RNAi) and an in vitro implantation model.

WP leader: Prof. Andres Salumets / Dr. Signe Altmäe, Competence Centre on Health Technologies, Tartu, Estonia.
  • To develop a novel bioinformatic model of human embryo implantation
  • Functional validation of key proteins important in implantation process by using RNAi technology
WP5. Broad skills development: providing for the transfer of knowledge between partnering organisations

Objective: Collecting and sharing results generated during the project to better exploit the complementary competences of partners.

Tasks: (i) Regular common workshops and joint activities. (ii) SARM annual research workshops and the Final Research Conference. (iii) Establishment of Online Repository and Database for SARM.

WP6. Outreach and dissemination activities

Objective: Building a sustainable network within Europe to support research contribution to knowledge based economy and society and disseminate project results, also to the general public, by using the competence and resources of the seconded and recruited personnel.

Tasks: (i) Participation in international research and technological development conferences to disseminate the outcome of SARM’s research among the scientific community. (ii) Outreach activities targeting the general public. (iii) Development of a Market Development and Outreach Plan.

WP7. Management

Objective: To provide the co-ordination of the project in both administrative and technical terms aiming towards achieving effective operation of the project as well as timely delivery of quality results.

Tasks: (i) Establishment of Project Management Structure and organisation of Project Management Board meetings. (ii) Preparation of management reports (including the final report) and cost statements.