Characterisation of molecular pathways of differentiation in normal human lympho-myeloid differentiation using a systems biology approach

Supervisor:  Profs Paresh Vyas and Claus Nerlov

The human hemopoietic progenitor hierarchy producing lymphoid and granulocytic-monocytic (myeloid) lineages is unclear. Multiple progenitor populations produce lymphoid and myeloid cells, but remain incompletely characterized. Vyas lab has recently shown that the three human progenitor populations with lympho-myeloid potential - the lymphoid-primed multi-potential progenitor (LMPP), granulocyte-macrophage progenitor (GMP) and multi-lymphoid progenitor (MLP) are functionally and transcriptionally distinct and heterogeneous at the clonal level,[1]. Most combined lympho-myeloid and myeloid potential was captured within the LMPP and GMP. In terms of functional potential, uni-lineage myeloid or lymphoid potential, bi- and rarer multi-lineage progenitors occurred in LMPP, GMP and MLP This, coupled with single cell expression analyses, suggested a continuum of progenitors execute lymphoid and myeloid differentiation rather than only uni-lineage progenitors being present downstream of stem cells.

The focus of this project is to build on this work[1] and define the detailed molecular mechanisms that permit a lympho-myeloid LMPP to differentiate into a myeloid restricted progenitor, and for that myeloid progenitor to then complete differentiation. This is a critical set of questions not only for our understanding of normal progenitor cell biology, but has direct and important implications for Acute Myeloid Leukaemia (AML). We have previously shown that AML-propagating stem cells (AML LSCs) are partially arrested at the LMPP/GMP stage of differentiation([2] and unpublished data).

The project will combine state-of-the-art technologies in single cell RNA-Seq, single cell analysis of DNA methylation (in collaboration with the Ludwig Institute Oxford) and REAP-SEQ[3] and/or CITE-Seq[4] (WIMM collaboration). These complex datasets will be orthogonally interrogated and the student will require computational skills (ability to code) to achieve this. Training will be provided but prior background will be most helpful. Functional validation of transcriptional and signalling pathways required to execute this differentiation programme will require perturbation experiments based on Cas9-CRISPR modification of primary human haemopoietic cells, technology that is established in the laboratory.

Training Opportunities
The project: This project will provide a comprehensive training in state of the art single cell biology, human haemopoiesis (including flow sorting and functional assays), molecular biology and biochemistry including gene editing and computational biology.

The environment: The Vyas laboratory is based in the MRC Molecular Haematology Unit (MHU), Weatherall Institute of Molecular Medicine (WIMM) (www.imm.ox.ac.uk). There is a world-class single cell facility, a large computational biology core with a dedicated training core (CGAT), largest FACS facility in Europe, expertise in in vitro and in vivo functional analysis of blood cells at a single cell level.

Formal Training:
2-day WIMM Induction course.
Weekly 2 hour, a year-long small group technique teaching sessions.

Informal Training

  • Weekly meeting with Professor Vyas.

  • Day-to-day supervision by senior post-doctoral fellows.


Presentation


  • Formal data presentation to the weekly laboratory meeting.

  • Presentation of published papers at the weekly journal club.
  • The applicant will present at locally and at national/international meetings.

Academic activities

MHU and WIMM have separate weekly international/national speaker seminar series.

Scientific Themes: Developmental Biology & Stem Cells, Cancer

Publications

  1. Karamitros, D., et al., Human lympho-myeloid progenitors are heterogeneous at the single cell level. Nature Immunology, 2017. In press.
  2. Goardon, N., et al., Coexistence of LMPP-like and GMP-like leukemia stem cells in acute myeloid leukemia. Cancer Cell, 2011. 19(1): p. 138-52.
  3. Peterson, V.M., et al., Multiplexed quantification of proteins and transcripts in single cells. Nat Biotechnol, 2017. 35(10): p. 936-939.
  4. Stoeckius, M., et al., Simultaneous epitope and transcriptome measurement in single cells. Nat Methods, 2017. 14(9): p. 865-868. 
For further information, please contact Prof Paresh Vyas