Gregoire Stik Email & Phone Number

Barcelona, Catalonia, Spain

Barcelona, Catalonia, Spain

I have been creating the ground for an independent career, developing multiple research lines focused on understanding the role of 3D genome organization in gene regulation.CTCF chromatin residence time controls 3D genome organization, gene expression and DNA methylation in pluripotent cellsWe explored the role of CTCF chromatin residence time on different nuclear processes in embryonic stem cells. Following a loss of function approach, we showed that one zing finger domain (ZF8) of CTCF was critical for its chromatin residence time, and therefore controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells. This study, for which I am co-first author, has been published in 2021 in Nature Cell Biology. Phase separation drives 3D chromatin organization and oncogenicity in B-ALL malignancyIn September 2019, I was awarded the Spanish Association Against Cancer “Investigador” grant to lead a project studying the role of chromatin organisation in the development of B-cell Acute Lymphoblastic Leukaemia (B-ALL). We found that the chromatin acquired a specific 3D organization in B-Acute Lymphoid leukaemia (B-ALL) in comparison to healthy B cells. Some of these 3D features are associated with oncogene dysregulation and can be used for early diagnosis of the disease. Role of 3D chromatin organization in immune responseWe explore the role of the genome organization in different processes of immune response.

Barcelona, Catalonia, Spain

In September 2016, I joined the team of Thomas Graf at the CRG in Barcelona and in February 2017, I have been awarded the Marie Curie Individual Fellowship.As part of the ‘4D GENOME’ project, I studied the interplay between genome topology and gene regulation during conversion of human B cells into macrophages. In mammals, CTCF and the cohesin complex create submegabase structures with elevated internal chromatin contact frequencies, called topologically associating domains (TADs). Although TADs can contribute to transcriptional regulation, ablation of TAD organization by disrupting CTCF or the cohesin complex causes modest gene expression changes in steady-state cells. To uncouple the role of CTCF in cell-state transitions and cell proliferation, we studied the effect of CTCF depletion during the conversion of human leukemic B cells into macrophages with minimal cell division. We used CRISPR/Cas9 genome editing technology to insert into the B cells the auxin-inducible degron system to deplete CTCF. We showed that CTCF depletion disrupts TAD organization but not cell transdifferentiation. We then took advantage of our immune model to study the role of CTCF during inflammatory response after transdifferentiation in macrophages. In contrast, CTCF depletion in induced macrophages impairs the full-blown upregulation of inflammatory genes after exposure to endotoxin. Importantly, our study published in 2020 uncouples the critical role of CTCF in cell proliferation from its role as genome organizer and transcriptional regulator, and provides nuanced insights into the role of 3D chromatin organization for gene regulation. In addition, our findings indicate a critical role for genome topology in providing an optimal response to external signals in particular during inflammatory response.

Paris Area, France

We studied the molecular complexity of the stromal cells surrounding the Hematopoietic Stem and Progenitor Cells (HSPCs) so-called niche. Combining co-culture of stromal cells and HSPC with microarrays analyses of stromal cells, we identified a molecular signature shared by the niche cells. This signature was defined as a gene-set composed of around 500 mRNAs and 20 miRNAs and was predictive of the ability of cells to maintain in vitro HSPC. We took advantage of our miRNAs signature to change the behaviour of a non-supportive stromal cell line into a supportive stromal cell line. Developing multiplex qPCR, HSPC extraction, co-culture assays, hematopoietic assay and FACS analyses, we observed that the stable expression of 4 miRNAs modify the gene expression signature and could increase the ability of stromal cells to maintain HSC in vitro. In the same time, I initiated a new study investigating the role of extracellular vesicles (EVs) in the hematopoietic stem cell niche. EVs are originated from the endosome and are released from the cell membrane. In multicellular organisms, they are found in most of the tissues and biological fluids. Using microscopy, FACS, biochemistry and hematopoietic assays in 2 cell lines with distinct abilities to maintain HSPC in vitro, we showed that both cell lines secreted EVs with distinct surface markers and that only EVs secretes by the supportive cell lines could be internalized by HSPC, promoting cell survival and HSPC properties in vitro. We also analysed the RNA content by high-throughput sequencing and identified a specific RNA signature carried by EV and showed that EV RNA could be functionally transferred into recipient HSPC after few hours. This study has been published in 2017 and paved the road for new “cell-free” methods regarding HSPC ex vivo manipulation.