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  • Catherine Porcher, Marella de Bruijn, Thomas Milne, Jim Hughes
Porcher group

About the Research

Understanding the molecular mechanisms underlying cell fate decisions during embryonic development is a key biological question, not only from a fundamental scientific point of view but also to inform attempts at producing tissue stem cells in vitro for regenerative medicine purposes. The Porcher lab investigates how Haematopoietic Stem Cells (HSCs, the cells with self-renewal and multilineage potentialities that give rise to the entire blood system) are specified during embryonic development.

This is achieved by studying the developmental trajectory of the blood lineage from mesoderm through to production of HSCs, and characterising the transcriptional and epigenetic control of blood cell production throughout this developmental progression. These studies rely on cutting edge technologies, such as in vivo lineage tracing approaches; single cell transcriptomics and imaging; chromatin immunoprecipitation (ChIP), chromatin accessibility (ATAC) and next generation sequencing; genome editing (CRISPR/Cas9); multi-colour flow cytometry; mouse and human ES cell differentiation cultures.

Over the past decade, numerous efforts have been deployed to reproduce the development of HSCs in vitro from pluripotent stem cells as it happens in the embryo, for mechanistic and therapeutic purposes. However, none of the differentiation cultures developed so far have been able to produce long-term repopulating HSCs without genetic manipulation. This reflects our limited understanding of the developmental pathway leading to HSC development. To address this question, we have recently developed an in vivo prospective lineage tracing approach in mice, based on a system originally established in zebrafish (McKenna et al. Science 353: aaf7907, 2016). This allows to track the development of cell lineages through progressive editing of a barcode by a spatio-temporally inducible CRISPR/Cas9 system. Single cell transcriptomics retrieves the scarred barcodes and assigns cell identity, thus allowing lineage trajectory reconstruction and branching point identification. We are currently using this approach to reconstruct the developmental trajectory of the blood lineage, with a particular interest in the mesodermal origin of the haematopoietic wave giving rise to the HSC lineage. Potential PhD projects will focus on subsequent developmental stages and use high-throughput analyses of chromatin and epigenetic landscapes as well as single cell imaging to characterise the molecular determinants of cell fate potential and the cellular niches supporting the HSC lineage at key branching points.

The above studies will help us refine protocols aiming at supporting development of the HSC lineage in vitro. Our current approach is to progressively reproduce key stages of this pathway in serum-free differentiation cultures of mouse and human pluripotent stem cells (PSCs). Cell fate replating studies combined with single cell transcriptomics, epigenetics and chromatin accessibility approaches as well as comparison with the in vivo corresponding cellular populations, inform on the cellular potential and the evolution of the molecular landscape as the cells transit through the stages leading to production of HSCs. Ultimately, our goal is to translate our findings to the clinic for patient-specific production of HSCs from iPSCs.

We have recently shown that multilineage-primed mesodermal cells acquire a blood fate at the expense of other mesodermal-derived lineages (heart, bones or muscles) through tight transcriptional and epigenetic control of gene expression (Chagraoui et al. Nature Communications, 2018). This has revealed the establishment of a global, but transient, repressive environment by the key transcription factor also driving haematopoietic specification, SCL. We are currently further investigating these repressive transcriptional activities and their link to the chromatin remodelling complex Polycomb PRC1, both in vivo and in vitro in ES cell differentiation cultures, using functional, biochemical and structural approaches. In this context, a potential PhD project is the study of the 3D organisation of the genome in cells undergoing global transcriptional repression by using HiC and Capture C technologies. Altogether, these studies will identify key principles in the control of cell fate decisions.

Prospective PhD students with interests in cell fate decisions and transcriptional/epigenetic regulation of gene expession are strongly encouraged to discuss possible PhD projects with the PI.

 

Please see the Weatherall Institute for Molecular Medicine (WIMM) for information about applications for a DPhil in Medical Sciences with groups based in the WIMM.

 

Training Opportunities

The students will learn how to design their PhD project under the guidance of the PI and collaborators. This will help them frame their project both conceptually and experimentally and will be an excellent way to learn about the field. Once a thesis plan is in place, weekly one-to-one meetings with the thesis supervisor, as well as regular lab meetings, thesis committee meetings and opportunities to present to a wider audience will further the intellectual training.

Initially, students will work closely with senior students or post-docs in the lab who will provide training at the bench on a daily basis. This will ensure that they rapidly master the molecular and cellular technologies required for their project. Training in computing science is available in the Institute as well as externally, and strongly recommended to anyone whose project requires bio-informatics analyses.

Students will be enrolled on the MRC WIMM DPhil Course, which takes place in the autumn of their first year. Running over several days, this course helps students to develop basic research and presentation skills, as well as introducing them to a wide-range of scientific techniques and principles, ensuring that students have the opportunity to build a broad-based understanding of differing research methodologies.

Generic skills training is offered through the Medical Sciences Division's Skills Training Programme. This programme offers a comprehensive range of courses covering many important areas of researcher development: knowledge and intellectual abilities, personal effectiveness, research governance and organisation, and engagement, influence and impact. Students are actively encouraged to take advantage of the training opportunities available to them.

As well as the specific training detailed above, students will have access to a wide-range of seminars and training opportunities through the many research institutes and centres based in Oxford.

All MRC WIMM graduate students are encouraged to participate in the successful mentoring scheme of the Radcliffe Department of Medicine, which is the host department of the MRC WIMM. This mentoring scheme provides an additional possible channel for personal and professional development outside the regular supervisory framework. The RDM also holds an Athena SWAN Silver Award in recognition of our efforts to build a happy and rewarding environment where all staff and students are supported to achieve their full potential.

 

Publications

Li L, Rispoli R, Patient R, Ciau-Uitz A, Porcher C. Etv6 activates vegfa expression through positive and negative transcriptional regulatory networks in Xenopus embryos. Nature Communications, 10:1083 (2019).

Chagraoui H, Kristiansen  MS, Ruiz  JP, Serra-Barros  A, Richter J, Hall-Ponselé E, Gray N, Waithe D, Clark K, Hublitz P, Repapi E, Otto G, Kerry J, Sopp P, Taylor S, Vyas P and Porcher C. SCL establishes a global repressive environment and co-operates with RYBP-PRC1 to repress alternative lineages in blood-fated cells. Nature Communications, 9:5375 (2018)

Karamitros D et al. Heterogenetiy of human lympho-myeloid progenitors at the single cell level. Nature Immunology 19:85-97 (2018)

Porcher C, Chagraoui H, Kristiansen MS. SCL/TAL1, a multifaceted regulator from blood development to disease. Blood, 129:2051- 60 (2017).

Chen II, Caprioli A, Ohnuki H, Kwak H, Porcher C, Tosato G. EphrinB2 regulates the emergence of a hemogenic endothelium from the aorta. Scientific Reports 6:27195 (2016)

El Omari K, Hoosdally SJ, Tuladhar K, Karia D, Hall-Ponsele E, Platonova O, Vyas P, Patient R, Porcher C*, Mancini EJ*. Structural Basis for LMO2-Driven Recruitment of the SCL: E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets. Cell Reports 4:135 (2013).