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Stunnenberg HG,…, Spicuglia S et al. The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery. Cell. 2016 Nov...

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Salvatore Spicuglia

Functional genomics of normal and leukemic T cells




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  • Salvatore Spicuglia (CR1 Inserm)
  • Eve-Lyne Mathieu (Post-doc, AMIDEX)
  • Ariel Galindo (Post-doc, Conacyt)
  • Aurélien Griffon (PhD student; co-direction with Benoit Ballester, TAGC)
  • Mohamed Belhocine (PhD student; co-direction with Vahid Asnafi, Necker's Hospital, Paris)
  • Dao Mai  Lan (PhD student)

Old Members

  • Laurent Vanhille (Post-doc, Blueprint Project)
  • Charbel Souaid (Master Student)
  • Marc Antoine Garibal (Master Student)
  • Zhonglin Li (Master Student)


The Spicuglia’s group is focused on the characterization of the mouse and human epigenomes during the differentiation of T cells and in leukemia. We aim to address how the epigenetic marks are governing the way in which genomic information is organized within the cell and how these phenomena play a role in regulating gene expression and in controlling specific cellular functions during cell differentiation and cancer.


Our team has a long-standing interest in the fields of epigenetics and transcriptional regulation during lymphoid cell differentiation. We have set up and developed up-to-date genome-wide investigating approaches (MeDIP, ChIP-seq, FAIRE-seq, MNase-seq and RNA-seq), along with state-of-the-art bioinformatics, in order to study epigenetics together with transcriptional regulation in normal developing and transformed T lymphocytes. In the past years, we have explored the dynamics of selected histone modifications and transcription factors during early T cell development in vivo, using ChIP assays coupled to either microarrays or HTS technologies. Our data evidenced a previously unappreciated combinatorial of histone methylations associated to the activity of developmentally regulated enhancers. and highlighted an epigenetic signature linked to the regulation of tissue specific gene expression, suggesting a direct connection between chromatin landscapes and distinct modes of transcriptional regulation. In parallel, we have made significant effort in implementing collaborative projects with clinicians, aiming to apply these techniques to the definition of epigenetic signatures (both DNA methylation and histone modifications) in large collections of human lymphoma and leukemia primary cell samples.


Research interests:

1. Chromatin dynamics in developing T-cells using genome-wide approaches

2. Control of tissue-specific gene expression in normal and leukemic T cells

3. Epigenetic characterization of cancer cells using genome-wide approaches




Ongoing Projects


"A BLUEPRINT of Haematopoietic Epigenomes".

FP7-HEALTH-2011: High impact initiative on the human epigenome (2011-2015). Coordinator: H. Stunnenberg, NCMLS, The Netherlands. This project aims to characterize the full epigenome of normal and neoplastic hematopoietic cells (including RNA, histone modifications and key transcription factors). S. Spicuglia is responsible of the Work Package “Epigenome of Normal and neoplastic T cells”.

The BLUEPRINT Consortium has been formed with the aim of generating at least 100 reference epigenomes and studying them to advance and exploit knowledge of the underlying biological processes and mechanisms in health and disease. BLUEPRINT will focus on distinct types of haematopoietic cells from healthy individuals and on their malignant leukaemic counterparts. Reference epigenomes will be generated by state-of-the-art technologies from highly purified cells for a comprehensive set of epigenetic marks in accordance with quality standards set by the International Human Epigeneome Consortium (IHEC). This resource-generating activity will be conducted at dedicated centres to be complemented by confederated hypothesis-driven research into blood-based diseases, including common leukaemias and autoimmune disease (T1D), by epigenetic targets and compound identification, and by discovery and validation of epigenetic markers for diagnostic use. Key to the success of BLUEPRINT will be the integration with other data sources (i.e. ICGC, 1000 genomes and ENCODE), comprehensive bioinformatic analysis, and user-friendly dissemination to the wider scientific community. The involvement of innovative companies will energize epigenomic research in the private sector by creating new targets for compounds and the development of smart technologies for better diagnostic tests.


ChIp-seq experiments performed at two stages of T cell differentiation


Identification and functional characterization of LincRNA expressed during T-cell differentiation and leukemia

Transcription of essentially the entire eukayotic genome generates a myriad of non-coding RNA species that show complex overlapping patterns of expression and regulation. Of those, the so-called Long Intergenic NonCoding RNAs (lincRNAs) are among the least well-understood transcript species. Although, only few LincRNAs has been fully characterized to date, they are suggested to play important roles in transcriptional and epigenetic regulation of gene expression, and diseases. Here, we propose to characterize LincRNAs important for T-cell differentiation and potentially relevant in T-cell acute lymphoblastic leukemia (T-ALL). First, we will identify and define the complete set of LincRNAs expressed at key stages of mouse and human T cell differentiation. This will be achieved by performing RNA-Seq and ChIP-Seq experiments. Secondly, a set of differentially expressed LincRNAs will be selected for thorough functional characterization, including (1) Analyses of LincRNAs expression in other tissues; (2) knock-down and/or overexpression in primary thymocytes; and (3) Analyses of their expression in large collections of T-ALLs and correlation with their clinical outcome.



Selected publications

1.    Vanhille L., A. Griffon, M.A. Maqbool, J. Zacarias, L.T.M. Dao, N. Fernandez, B. Ballester, J.C. Andrau, S. Spicuglia. CapStarr-seq: a high-throughput method for quantitative assessment of enhancer activity in mammals. Nat. Comm. 6:6905

2.    J. Zacarías-Cabeza, M. Belhocine, L. Vanhille, P. Cauchy, F. Koch, A. Pekowska, R. Fenouil,A. Bergon, M. Gut, I. Gut, D. Eick, J. Imbert, P. Ferrier, J.C. Andrau and S. Spicuglia. Transcription dependent generation of a specialized chromatin structure at the TCRb locus. J. Immunol. 194(7):3432-43

3.    Lepoivre C, Belhocine M, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal M.A., Koch F, Maqbool M, Fenouil R, Loriod B, Holota H, Gut M, Gut I, Imbert J, Andrau J.C., Puthier D, Spicuglia S (2013). Divergent transcription is associated with promoters of transcriptional regulators. BMC Genomics. Dec 23;14(1):914. PMID: 24365181. Highly Accessed

4.    Spicuglia S*, Maqbool AM, Puthier D, Andrau JC* (2013). An update on recent methods applied for deciphering the diversity of the noncoding RNA genome structure and function. Methods. Sep 1;63(1):3-17. *corresponding authors

5.    Pekowska A, Benoukraf T, Zacarias-Cabeza J, Belhocine M, Koch F, Holota H, Imbert J, Andrau J.C, Ferrier P and Spicuglia S (2011). H3K4 tri-methylation provides an epigenetic signature of active enhancers. EMBO J., 30, 4198–10.

6.    Pekowska A, Benoukraf T, Ferrier P and Spicuglia S (2010A unique H3K4me2 profile marks tissue-specific gene regulation. Genome Research. 20(11):1493-502.

7.    Jia J, Pekowska A, Jaeger S, Benoukraf T, Ferrier P and Spicuglia S (2010). Assessing the efficiency and significance of Methylated DNA Immunoprecipitation (MeDIP) assays in using in vitro methylated genomic DNA. BMC Research Notes. 3:240.

8.    Bonnet, M., Huang, F., Benoukraf, T., Cabaud, O., Verthuy, C., Boucher, A., Jaeger, S., Ferrier, P., and Spicuglia, S(2009)Duality of enhancer functioning mode revealed in a reduced TCRbeta gene enhancer knockin mouse model. J Immunol 183, 7939-7948.

9.    Benoukraf T, Cauchy P, Fenouil R, Jeanniard A, Koch F, Jaeger S, Thieffry D, Imbert J, Andrau JC*, Spicuglia S*, Ferrier P.* (2009) CoCAS: a ChIP-on-chip analysis suite. Bioinformatics. 2009 1;25(7):954-5. *Corresponding authors

10.Bonnet M, Ferrier P and Spicuglia SMolecular Genetics at the T-Cell Receptor βLocus: Insights into the Regulation of V(D)J Recombination. In: Ferrier P, ed. V(D)J recombination. Austin: RG Landes Co., 2009.

11.Spicuglia S, Kumar S, Yeh J, Vachez E, Chasson L, Gorbatch S, Cautres J, and Ferrier P. (2002). Promoter activation by enhancer-dependent and -independent combination of activator/co-activator complexes. Mol.Cell 10,1479-1487.

12.Spicuglia S, Payet D, Tripathi R.K, Rameil P, Verthuy C, Imbert J, Ferrier P and Hempel,W.M. (2000). TCRa enhancer activation occurs via a conformational change of a pre-assembled nucleo-protein complex. EMBOJ. 19(9) 2034-2045.


Full Pubmed publications


Last update: 17 February 2012