Hematopoietic Stem Cells, Transdifferentiation and Reprogramming

GENE REGULATION, STEM CELLS AND CANCER

GROUP LEADER:
Thomas Graf (Senior Scientist)

POSTDOCTORAL FELLOWS:
Jose Luis Sardina (Juan de la Cierva), Tian Tian (Juan de la Cierva), Gregoire Stik (Marie Curie), Ralph Stadhouders (Marie Curie; left in February 2017)

PHD STUDENTS:
Guillem Torcal (Severo Ochoa, joined October 2017), Marcos Plana (FIB)

TECHNICIANS:
Luisa de Andres (CRG), Clara Berenguer (Plan Nacional), Carolina Segura (ERC), Johanna Goldmann (ERC; joined April 2017)

BIOINFORMATICIAN:
Antonio Gomez Moruno (ERC; left Dec 2017)

MASTER STUDENT:
Mercedes Barrero (CRG, joined October 2017)

Summary

Our laboratory studies mechanisms of mammalian cell fate decisions by over-express transcription factors in B cells to induce cell fate conversions. In particular, we are studying the rapid and efficient reprogramming of B cells into induced pluripotent stem (iPS) cells. For this, cells are first exposed to a pulse of C/EBPa, followed by the activation of the Yamanaka factors OSKM.

This unique two-step reprogramming system permitted us to ask whether changes in genome topology follow changes in gene expression. Surprisingly, by comparing the dynamics of different topological parameters (compartments, TADs, TAD borders and loops), we found that in most genomic regions with topological alterations transcription changes follow architectural changes with the reverse only occurying rarely. These findings suggest that 3D genome topology has an informational value for gene expression, shaping chromatin so as to acquire a permissive or non- permissive architecture for subsequent waves of TF binding. Strikingly, we also found the selective binding of our lineage instructive TFs to genomic regions that subsequently show 3D changes, suggesting that they have an as yet unrecognized architectural role (Stadhouders et al., Nature Genetics, 2018).

The screenshot shows a 20Mb fragment of chromosome 13 with A and B compartments (yellow and blue peaks) in B cells induced to reprogram into iPS cells by the C/EBPa-OSKM transcription factors. Ba, B cells exposed to an 18h pulse of C/EBPa. D2-D8, Ba cells exposed to 2, 4, 6 and 8 days of OSKM.

Fig. 1

The screenshot shows a 20Mb fragment of chromosome 13 with A and B compartments (yellow and blue peaks) in B cells induced to reprogram into iPS cells by the C/EBPa-OSKM transcription factors. Ba, B cells exposed to an 18h pulse of C/EBPa. D2-D8, Ba cells exposed to 2, 4, 6 and 8 days of OSKM.

Research Projects

  • How do lineage instructive transcription factors alter the 3D genome structure during reprogramming and transdifferentiation?
  • What are the single cell conversion trajectories of B cells converting into either macrophages or iPSCs?
  • How does the methylome and hydroxymethylome change during cell reprogramming?

Selected Publications

Ruetz T, Pfisterer U, Di Stefano B, Ashmore J, Beniazza M, Tian TV, Kaemena DF, Tosti L, Tan W, Manning JR, Chantzoura E, Ottosson DR, Collombet S, Johnsson A, Cohen E, Yusa K, Linnarsson S, Graf T, Parmar M, Kaji K.
“Constitutively Active SMAD2/3 Are Broad-Scope Potentiators of Transcription-Factor-Mediated Cellular Reprogramming.”
Cell Stem Cell, 21(6):791-805 (2017).

Quilez J, Vidal E, Dily FL, Serra F, Cuartero Y, Stadhouders R, Graf T, Marti-Renom MA, Beato M, Filion G.
“Parallel sequencing lives, or what makes large sequencing projects successful.”
Gigascience, 6(11) (2017).

Graf T.
“Covering the Stem Cell Explosion at the 2017 ISSCR Conference in Boston.”
Stem Cell Reports, 10;9(4):1017-1023 (2017)

Collombet S, Oevelen C, Sardina Ortega JL, Abou-Jaoude W, Di Stefano B, Thomas-Chollier M, Graf T*, Thieffry D*.
“Logical modeling of lymphoid and myeloid cell specification and trans-differentiation.”
PNAS, 114:5792-5799 (2017).

Lim AI, Li Y, Lopez-Lastra S, Stadhouders R, Paul F, Casrouge A, Serafini N, Puel A, Bustamante J, Surace L, Masse-Ranson G, David E, Strick-Marchand H, Le Bourhis L, Cocchi R, Topazio D, Graziano P, Muscarella LA, Rogge L, Norel X, Sallenave JM, Allez M, Graf T, Hendriks RW, Casanova JL, Amit I, Yssel H, Di Santo JP.
“Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation.”
Cell, 168(6):1086-1100 (2017).

Iberg-Badeaux A, Collombet S, Laurent B, van Oevelen C, Chin KK, Thieffry D, Graf T*, Shi Y*.
“A Transcription Factor Pulse Can Prime Chromatin for Heritable Transcriptional Memory.”
Mol Cell Biol, 37(4) (2017).