Expertise

Equipments

Research and Development

A three-year strategic plan allows us to plan funding requests and technological developments to be implemented. Developments are driven by (i) customer demand, (ii) scientific monitoring allowing senior researchers and engineers to keep abreast of developments in the field, (iii) regular meetings with associate researchers allowing information to be shared, (iii) webinars and the France Genomics workshop which allow different approaches to be taken advantage of. The TGML is thus dedicated to the development of single-core methods that provide significant flexibility for single-cell experiments with fragile cells on the one hand, and for all multi-omics approaches on the other hand (e.g. simultaneous scRNA-seq and ATAC-seq). A further development concerns the use of fixed cells to eliminate biases due to cell stress during thawing for single cell experiments. In addition to single cell analysis, spatial transcriptomics is becoming a complementary method to resolve organ or tissue complexity. Following the acceptance of the Emergencel project call for tender (Cancéropole PACA), in which D. Puthier is a partner, the TGML is also involved in a spatial transcriptomics project: “Spatial mapping of gene expression to decipher the thymic crosstalk upon T-cell Acute Lymphoblastic Leukemia development”, using Visium technology (10X genomics), in collaboration with M. Irla (CIML, Marseille) and A. Sergé (LAI, Marseille). The objective is to better understand the development of acute T-cell leukaemias in the thymus and the existing interactions with the stromal microenvironment. Finally, a multi-omics development project (scRNA-Seq + scATAC-seq) is currently under discussion with C. Maurange (Inmed, Marseille).

Main achievments

Over the last 5 years, the platform has accepted an average of 35 projects per year for an average number of annual samples of 600. For 2021, we have doubled the number of projects and samples planned compared to the average of the last 5 years for the same period. The main services offered are transcriptome (e.g. RNA-seq, scRNA-seq, miRNA-seq), genome (e.g. DNA-seq: SNPs, small/large InDels, full exome, targeted sequencing after capture) and epigenome (e.g. ChIP-seq, Mnase-seq, FAIRE-seq) analyses. These services include bioinformatics analyses of data quality. In addition, TGML has significant expertise in bioinformatics (e.g. MetaWorkflow, based on Snakemake (mw-lib), offers a simple metadata table interface allowing the biologist to apply routine processing, while improving traceability of analyses). At the client’s request (5x/year on average), routine workflows developed in-house can be invoiced. Dedicated analyses are performed on a case-by-case basis.

Main projects
1/ Promoters with enhancement activity: a new regulatory mechanism:
– PI: Salvatore Spicuglia, TAGC, Marseille. – Funding: INCa, ANR, Ligue, Amidex.
Publications (DP: Denis Puthier, LB: Lisa Bargier, BL: Béatrice Loriod, HV: Hortense Vachon).
– Dao, L.T.M et al, 2017. Nat. Genet. 49, 1073-1081 – DP
– Alomairi, J et al., 2020. PLoS ONE 15, e0233191 – DP
– Gutiérrez-Reyna et al. 2020. Front. Immunol. 11, 1089 – BL, DP
– Medina-Rivera, A. et al, Trends Biochem. Sci. 43, 452-468 – DP (review)

2/ The H2AL2 histone variant and its role in protamine incorporation
– PI : Saadi Khochbin, IAB, Grenoble. – Funding: INCa, ARC, ANR, FRM.
Publications (DP: Denis Puthier, LB: Lisa Bargier, BL: Béatrice Loriod, HV: Hortense Vachon, FN;Nicolas Fernandez-Nunez)
– Barral, S. et al. 2017. Mol. Cell 66, 89-101.e8 – DP, FN
– Goudarzi, A et al. 2016. Mol. Cell 62, 169-180 – DP
– Shiota, H. et al. 2018. Cell Rep. 24, 3477-3487.e6 – DP
– Hoghoughi, N. et al, 2020. Cells 9 – DP

3/ Epigenomics of T cell development and the role of HOXA genes in T cell acute lymphoblastic leukemia (Vahid Asnafi, Institut Necker-Enfants Malades).
Publications (DP: Denis Puthier, LB: Lisa Bargier, BL: Béatrice Loriod, HV: Hortense Vachon, FN; Nicolas Fernandez-Nunez)
– Bond, J. et al. 2016. Haematologica 101, 732-740.
– Bond, J. et al. 2018. Mol. Cancer Res. 16, 470-475.
– Cieslak, A. et al. 2020. J. Exp. Med. 217 – DP
– Touzart, A. et al, Clin. Cancer Res. 25, 2483-2493 – DP

4/ The role of Long Non-Coding RNAs in T cell development (D. Puthier, TAGC)
– PI : Denis Puthier, TAGC, Marseille
– Funding: ANR, ARC, AMU ANR, ARC, AMU, Hubert Curien
Publications (DP: Denis Puthier, LB: Lisa Bargier, BL: Béatrice Loriod, HV: Hortense Vachon, FN: Nicolas Fernandez-Nunez).
– Kermezli, Y. et al, 2019. Leuk. Lymphoma 60, 2002-2014 – DP
– Saadi, W. et al, S., 2019. Sci. Rep. 9, 4707. BL, DP

5/ Predicting septic outcome in patients undergoing autologous stem cell transplantation.
– PI: Regis Costello (Assistance Publique des Hôpitaux de Marseille)
– Funding: INSERM, AMU, Advanced BioDesign
Publications (DP: Denis Puthier, LB: Lisa Bargier, BL: Béatrice Loriod, HV: Hortense Vachon, FN;
Nicolas Fernandez-Nunez)
– Labiad, Y. et al. 2018. Exp. Hematol. 65, 49-56 – BL, FN
– Venton, G. et al., 2016. Immunol. Res. 64, 1225-1236 – BL, FN

Last update Nov 2021