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Stem Cell Epigenetics

Director

Giuseppe Testa

  • +39 02.94375.105
  • +39 02.94375.990

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Our lab studies the epigenetics of cell fate programming and reprogramming, including the use of reprogramming-based modeling for cancer and neurodevelopmental disorders. 

Activities

Our lab pursues the following lines of research:

• Modeling disease through cell reprogramming. We harness the unprecedented potential of cell reprogramming to develop physiopathologically meaningful models of both neurodevelopmental disorders and cancer.
• Epigenetic regulation of neural fate. We study the role of two major pathways of chromatin regulation, methylation of histone H3 on lysine tails 4 and 27, on the acquisition of neuronal fate, with a special focus on corticogenesis.
• Aberrant genome programming in brain cancer. Consistent with the role of Polycomb-mediated H3K27 methylation in lineage choices, this line of research investigates the oncogenic counterpart of the acquisition of neural fate, focusing on malignant gliomas, combining advanced murine models with the analysis of human tumors.
• Epigenetics of cell fate reprogramming. Finally, consistent with the role of the Trithorax and Polycomb families in cell fate transitions, we study their contribution to cell fate reassignment, both for induced pluripotency and direct transdifferentiation.

  • Research projects

    1. Modeling disease through cell reprogramming
      One of the most tangible outputs of somatic cell reprogramming has been a paradigm shift in our ability to model human diseases, for which fundamental limitations have been so far: i) the scarce availability of primary diseased tissues, which is particularly salient for disorders of the nervous system; and ii) the difficulty of reconstructing disease history, which is salient also for cancer pathogenesis.
      We are thus harnessing the unprecedented potential of cell reprogramming to develop physiopathologically meaningful models of both neurodevelopmental disorders and cancer, thereby aiming at the dissection of the genomic versus epigenomic components of their pathogenesis.
      Specifically, within neurodevelopmental disorders we focus on a unique range of intellectual disability syndromes (including autism spectrum disorders) caused by mutations or dosage alterations in epigenetic regulators and transcription factors.
      As far as cancer is concerned, we focus on ovarian cancer, a critical example of unmet medical need due to the lack of relevant cellular models and the very limited understanding of the developmental aberrations that underlie its pathogenesis.
    2. Epigenetic regulation of neural fate
      The methylations of histone H3 on lysine tails 4 and 27 (H3K4me and H3K27me), respectively mediated by the Trithorax (Trx) and Polycomb (PcG) protein families, are central regulators of the establishment and maintenance of differentiated cell states. In particular, the central nervous system has become a paradigm-setting model to define the functional relevance of H3K27me for cell fate transitions, with the realization that this mark is dynamically regulated throughout neuronal differentiation by the interplay of methyltransferases and demethylases.
      Following the identification of JMJD3 as the first enzyme that antagonizes Polycomb silencing by demethylating H3K27 (De Santa et al. Cell 2007), our key contributions include the characterization of its essential role for the early neural commitment of embryonic stem cells (Burgold et al. PLoS One, 2008), and the discovery that aberrations in H3K27 methylation caused by JMJD3 loss in neural precursors impact the late maturation and function of neuronal circuits (Burgold et al. Cell Reports 2012). We are now using conditional approaches to study the role that H3K27me and H3K4me play in the expansion of neural stem cells and the sequential acquisition of neuronal fate during murine corticogenesis (Testa Bioessays 2011).
    3. Aberrant genome programming in brain cancer
      Consistent with the role of Polycomb in lineage choices, alterations in H3K27me figure prominently among the epigenetic aberrations of cancer. Furthermore, the majority of genes that are CpG hypermethylated in cancer are pre-marked by H3K27me3 in embryonic stem cells, suggesting that the Polycomb-dependent gene expression program that orchestrates development in normal cells is hijacked in cancer cells as the main template for cancer DNA methylation.
      Hence, this line of research in the lab investigates the oncogenic counterpart of the acquisition of neural fate, focusing on malignant gliomas with the aim of elucidating the epigenetic basis of the lineage aberrations that characterize this disease. Specifically, we test the proposition that loss of the physiologic regulation centered around H3K27me3 is important for the initiation and/or maintenance of gliomas, combining the conditional modulation of this epigenetic axis in advanced murine models of glioblastoma with its functional dissection in primary cells isolated from both primary and recurrent human high grade gliomas.
    4. Epigenetics of cell fate reprogramming
      Consistent with the role of the Trithorax and Polycomb families in cell fate transitions, widespread changes in H3K4 and H3K27 methylation have been shown to accompany transcription factor-induced cell fate reassignment. Our objective is to dissect functionally their relative contribution to cell fate reassignment, using both experimental paradigms of induced pluripotency - where fibroblasts are reprogrammed to induced pluripotent stem cells (iPSC) – and direct transdifferentiation, where fibroblasts are reprogrammed to induced neuronal cells (iNCs). Our recent contribution includes the discovery that in iPSC generation, Polycomb-mediated H3K27 trimethylation is required on a highly selective core of Polycomb targets, setting stage for defining the functional relevance of this core gene subset in other physiopathological paradigms of cell reprogramming, including cancer (Fragola et al. PLoS Genetics 2013).

     

  • Publications

    1. P.L. Germain, G. Testa Taming Human Genetic Variability: Transcriptomic Meta-Analysis Guides the Experimental Design and Interpretation of iPSC-Based Disease Modeling. Stem Cell Reports 2017 8(6):1784-1796. doi: 10.1016/j.stemcr.2017.05.012.
    2. M. Gabriele, A.T.Vulto-van Silfhout, P.L. Germain, A. Vitriolo, R. Kumar, E. Douglas, E. Haan, K. Kosaki, T. Takenouchi, A. Rauch, K. Steindl, E. Frengen, D. Misceo, C.R.J. Pedurupillay, P. Stromme, J.A. Rosenfeld, Y. Shao, W.J. Craigen, C.P. Schaaf, D. Rodriguez-Buritica, L. Farach, J. Friedman, P. Thulin, S.D. McLean, K.M. Nugent, J. Morton, J. Nicholl, J. Andrieux, A. Stray-Pedersen, P. Chambon, S. Patrier, S.A. Lynch, S. Kjaergaard, P.M. Tørring, C. Brasch-Andersen, A. Ronan, A. van Haeringen, P.J. Anderson, Z. Powis, H.G. Brunner, R. Pfundt, J.H.M. Schuurs-Hoeijmakers, B.W.M. van Bon, S. Lelieveld, C. Gilissen, W.M. Nillesen, L.E.L.M. Vissers, J. Gecz, D.A. Koolen, G. Testa, B.B.A. de Vries YY1 Haploinsufficiency Causes an Intellectual Disability Syndrome Featuring Transcriptional and Chromatin Dysfunction American Journal of Human Genetics 2017 100(6):907-925. doi: 10.1016/j.ajhg.2017.05.006  *corresponding author
    3. H. L. Röst, Y. Liu, G. D'Agostino, M. Zanella, P. Navarro,G. Rosenberger, B.C. Collins, L. Gillet, G. Testa, L. Malmström and R. Aebersold TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics Nature Methods 2016 DOI:10.1038/nmeth.3954
    4. P.L. Germain, A. Vitriolo, A. Adamo, P. Laise, V. Das and G. Testa RNAontheBENCH: Computational and empirical resources for benchmarking
      RNAseq quantification and differential expression methods Nucleic Acid Research 2016 44(11):5054-⁠5067 DOI: 10.1093/⁠nar/⁠gkw448
    5. E. Signaroldi, P. Laise, S. Cristofanon, A. Brancaccio, E. Reisoli, S. Atashpaz, M. R. Terreni, C. Doglioni, G. Pruneri, P. Malatesta and G. Testa Polycomb dysregulation in gliomagenesis targets a Zfp423-dependent differentiation network Nature Communications 2016 DOI:10.1038/ncomms10753
    6. A. Adamo, S. Atashpaz, P.L. Germain, M. Zanella, G. D’Agostino, V. Albertin, J. Chenoweth, L. Micale, C. Fusco, C. Unger, B. Augello, O. Palumbo, B. Hamilton, M. Carella, E. Donti, G. Pruneri, A. Selicorni, E. Biamino, P. Prontera, R. McKay, G. Merla and G. Testa  7q11.23 dosage-dependent dysregulation in human pluripotent stem cells affects transcriptional programs in disease-relevant lineages Nature Genetics 2015 Feb;47(2):132-41DOI 10.1038/ng.3169 News and Views in the same issue by Urban and Purmann
    7. D.H. Park, S.J. Hong, R.D. Salinas, S.J. Liu, S.W. Sun, J. Sgualdino, G. Testa, M.M. Matzuk, N. Iwamori and D.A. Lim Activation of Neuronal Gene Expression by the JMJD3 Demethylase Is Required for Postnatal and Adult Brain Neurogenesis Cell Reports 2014 DOI: http://dx.doi.org/10.1016/j.celrep.2014.07.060
    8. M. Meloni and G. Testa Scrutinizing the Epigenetics Revolution Biosocieties 2014 doi: 10.1057/biosoc.2014.22
    9. A. Piunti, A. Rossi, A. Cerutti, M. Albert, S. Jammula, A. Scelfo, L. Cedrone, G. Fragola, L. Olsson, H. Koseki, G. Testa, S. Casola, K. Helin, F. d'Adda di Fagagna and D. Pasini Polycomb proteins control proliferation and transformation independently of cell cycle checkpoints by regulating DNA replication Nature Communications 2014; 5:3649. DOI:10.1038/ncomms4649.
    10. P. Prontera, D. Serino, B. Caldini, L. Scarponi, G. Merla, G. Testa, M. Muti, V. Napolioni, G. Mazzotta, M. Piccirilli and E. Donti Brief Report: Functional MRI of a Patient with 7q11.23 Duplication Syndrome and Autism Spectrum Disorder Journal of Autism and Developmental Disorders 2014 DOI10.1007/s10803-014-2117-7
    11. C. Palacios, J. Harris and G. Testa Multiplex parenting: In Vitro Gametes and the generations to come Journal of Medical Ethics (2014 doi:10.1136/medethics-2013-101810)
    12. M. Caganova, C. Carrisi, F. Mainoldi, F. Zanardi, P.L. Germain, L. George, F. Alberghini, G. Varano, L. Ferrarini, A.K. Talukder, M. Ponzoni, G. Testa, T. Nojima, C. Doglioni, D. Kitamura, K.M. Toellner, I. Su and S. Casola EZH2 contributes to lymphomagenesis via regulation of the germinal center response Journal of Clinical Investigation 123(12), 2013:5009-22
    13. L. Schneider, S. Pellegatta, R. Favaro, F. Pisati, P. Roncaglia, G. Testa, S.K. Nicolis, G. Finocchiaro and F. D’Adda di Fagagna DNA damage in mammalian neural stem cells leads to astrocytic differentiation mediated by BMP2 signaling through JAK-STAT Stem Cell Reports (in press, DOI: 10.1016/j.stemcr.2013.06.004
    14. G. Fragola, P.L. Germain, P. Laise, A. Cuomo, A. Blasimme, F. Gross, E. Signaroldi, G. Bucci, C. Sommer, G. Pruneri, G. Mazzarol, T. Bonaldi, G. Mostoslavsky, S. Casola and G. Testa Cell reprogramming requires silencing of a core subset of Polycomb targets PLoS Genetics 9(2), 2013: e1003292
    15. A. Blasimme, B. Schmietow and G. Testa Reprogramming potentiality: the co-production of stem cell policy and democracy American Journal of Bioethics 13(1), 2013: 30-2
    16. T. Burgold, N. Voituron, M. Caganova, P.P. Tripathi, C Menuet, B.K. Tusi, F. Spreafico, M. Bévengut, C. Gestreau, S. Buontempo, A. Simeone, L. Kruidenier, G. Natoli, S. Casola, G. Hilaire and G. Testa The H3K27 demethylase JMJD3 is required for maintenance of the embryonic respiratory neuronal network, neonatal breathing and survival, Cell Reports 2(5), 2012: 1244-58
    17. L. Austenaa, I. Barozzi, A. Chronowska, A. Termanini, R. Ostuni, F. Stewart, G. Testa and G. Natoli The histone methyltransferase Wbp7 (Mll4) controls macrophage function through GPI anchor synthesis, Immunity 36(4), 2012: 572-85
    18. M. Curnutte and G. Testa Consuming genomes: scientific and social innovation in direct-to-consumer genetic testing (2012) New Genetics and Society, 31:2, 159-181
    19. S. Campaner, F. Spreafico, T. Burgold, M. Doni, U. Rosato, B. Amati, and G. Testa The methyltransferase Set7/9(Setd7) is dispensable for the p53-mediated DNA damage response Molecular Cell 43, 2011; 681-688
    20. G. Testa The time of timing: How Polycomb proteins regulate neurogenesis Bioessays, 2011; 33(7):519-28
    21. G. Boniolo and G. Testa The Identity of Living Beings, Epigenetics, and the Modesty of Philosophy. Erkenntnis, 2011; DOI 10.1007/s10670-011-9308-9
    22. C.E. Pasi, A. Dereli-Oz, S. Negrini, M. Friedli, G. Fragola, A. Lombardo, G. Van Houwe, L. Naldini, S. Casola, G. Testa, D. Trono, P.G. Pelicci, and T.D. Halazonetis Genomic instability in induced stem cells Cell Death and Differentiation, 2011; 18(5):745-53
    23. G. Testa Stem Cell Teathrics Nature 2010, 465: 1012
    24. G. Testa What to do with the Grail now that we have it? iPSCs, potentiality, and public policy. Cell Stem Cell, 2009 5(4):358-9
    25. F. De Santa, N. Vipin, Z. H.Yap; B. K.Tusi, T. Burgold, L. Austenaa, G. Bucci, M. Caganova, S. Notarbartolo, S. Casola, G. Testa, W. Sung, C. Wei and G. Natoli Jmjd3 contributes to the control of gene expression in LPS activated macrophages The EMBO Journal, 2009; 28(21):3341-52
    26. G. Natoli, G. Testa and F. De Santa The future therapeutic potential of histone demethylases: a critical analysis Current Opinion in Drug Discovery and Development 2009; 12(5):607-15
    27. L. Skene, G. Testa, I. Hyun, K. W. Jung, A. McNab, J. Robertson, C. T. Scott, J. H. Solbakk, P. Taylor, L. Zoloth Ethics Report on Interspecies Somatic Cell Nuclear Transfer Research Cell Stem Cell, 2009; 5(1): 27-30
    28. T. Burgold, F. Spreafico, F. De Santa, M. Totaro, E. Prosperini, G. Natoli and G. Testa The histone H3 lysine 27-specific demethylase Jmjd3 is required for neural commitment PloS One 2008 3(8): e3034
    29. J.A. Adjaye, A.G. Byskov, J.B. Cibelli, R. De Maria, S. Minger, M. Sampaolesi, G. Testa, C. Verfaillie, M. Zernicka-Goetz, H. Schöler, M. Boiani, N. Crosetto, C.A. Redi Pluripotency and differentiation in embryos and stem cells Int J Dev Biol 2008 52(7):801-9
    30. G. Testa Stem cells through stem beliefs: the co-production of biotechnological pluralism Science as Culture 2008 17(4): 435-448
    31. F. De Santa, M. Totaro, E. Prosperini, S. Notarbartolo, G. Testa, and G. Natoli The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing Cell 2007 130(6):1083-94
    32. I. Hyun*, P. Taylor*, G. Testa*, B. Dickens, K. W. Jung, A. McNab, J. Robertson, L. Skene and L. Zoloth Ethical Standards for Human-to-Animal Chimera Experiments in Stem Cell Research Cell Stem Cell 2007 1(2):159-163 *equal contribution
    33. G. Testa, L. Borghese, J. Steinbeck, and O. Brüstle Breakdown of the Potentiality Principle and Its Impact on Global Stem Cell Research Cell Stem Cell 2007 1(2):153-156
    34. J. Scholten, K. Hartmann, A. Gerbaulet, T. Krieg, W. Müller, G. Testa, and A. Roers Mast cell-specific Cre/loxP-mediated recombination in vivo Transgenic Res. Epub 2007 Oct 31 (2008 (2):307-15)
    35. G. Testa Nuclear Transfer: an Example of Responsive Epistemologies Preprint 310 of the Proceedings of the Max Planck Institute for the History of Science 2006 pp. 205-214
    36. G. Testa and J. Harris Ethics and synthetic gametes Bioethics, 2005; 19: 146-166
    37. G. Testa and J. Harris Ethical aspects of ES cell-derived gametes Science, 2004; 305:1719
    38. G. Testa and J. Harris The ethics of deriving gametes from ES cells, response to A. Lippman and S.A. Newman Science, 2005;307: 515c-517c
    39. G. Testa, J. Schaft, F.v.d. Hoeven, S. Glaser, Y. Zhang, T. Hermann, W. Stremmel and A. F. Stewart A reliable lacZ expression reporter cassette for multipurpose, knock-out-first, alleles Genesis, 2004, 38(3):151-8
    40. G. Testa, K. Vintersten, Y. Zhang, V. Benes, J.P.P. Muyrers and A. F. Stewart BAC Engineering for the generation of ES cell-targeting constructs and mouse transgenes Methods Mol Biol. 2004; 256:141-58
    41. K. Vintersten, G. Testa, A. F. Stewart. Microinjection of BAC DNA into the pronucei of fertilised mouse oocytes Methods Mol Biol. 2004; 256: 141-58
    42. J.P.P. Muyrers, Y. Zhang, V. Benes, J.M.J. Rientjes, G. Testa and A. F. Stewart ET recombination: DNA engineering using homologous recombination in E. coli Methods Mol Biol. 2004; 256: 107-22
    43. G. Testa, Y. Zhang, K. Vintersten, V. Benes, I. Chambers, W. W. M. Pim Pijnappel, A. J.H. Smith, A. A. Smith and A. F. Stewart Engineering the mouse genome with bacterial artificial chromosomes to create multipurpose alleles Nature Biotechnology, 2003; 21(4): 443-7
    44. T. Schell, G. Testa, S. Castagnetti, B. Rutz, M. Hannus and F. Frischknecht Neuroscience from different angles. Student symposium: From genes to thoughts EMBO Reports 2001 Jun; 2(6):471-5
    45. G. Testa and A. F. Stewart Creating a transloxation: engineering interchromosomal translocations in the mouse EMBO Reports, 2000 Aug; 1(2):120-1
    46. Y. Zhang, J. P. P. Muyrers, G. Testa and A. F. Stewart DNA cloning by homologous recombination in Escherichia coli. Nature Biotechnology 2000 Dec; 18(12):1314-7
    47. J. P. P. Muyrers, Y. Zhang, V. Benes, G. Testa, W. Ansorge and A. F. Stewart Point mutation of bacterial artificial chromosomes by ET recombination. EMBO Reports 2000 Sep; 1(3):239-43
    48. J. P. P. Muyrers, Y. Zhang, G. Testa and A. F. Stewart Rapid modification of bacterial artificial chromosomes by ET-recombination Nucleic Acid Research, 1999 Mar 15; 27(6): 1555-1557
    49. G. Nocentini, S. Ronchetti, A. Bartoli, G. Testa, F. D’Adamio, C. Riccardi and G. Migliorati TCRi: an alternatively sliced product of the T cell receptor zeta gene European Journal of Immunology 1995 25: 1405-1409


    Peer-reviewed books and book chapters

    1. L. Chiapperino and G. Testa ‘The Epigenomic Self in Personalised Medicine: between Responsibility and Empowerment’ in M. Meloni, S. Williams, P. Martin (Eds.) ‘Biosocial Matters: Rethinking Sociology-Biology Relations in the Twenty-First Century’, Wiley-Blackwell 2016
    2. G. Testa ‘Democracies of stemness: stem cell technologies from generation to regeneration’ in F. Calegari and C. Waskow (Eds.) ‘Stem Cells. From Basic Research to Therapy’, CRC Press, 2014
    3. G. Boniolo and G. Testa Legittimità morale, cellule staminali embrionali umane ed embrioni umani in G. Boniolo and P. Maugeri (Eds.) Etica alle frontiere della biomedicina. Per una cittadinanza consapevole. Mondadori Università, 2014
    4. G. Testa and A. Maturo ‘Medicina rigenerativa ed embrioni’, in G. remuzzi and A. Maturo (Eds.) ‘Ci curano o ci curiamo? Il malato tra crisi economica e responsabilità individuale’, Franco Angeli, Milano 2013
    5. G. Testa ‘Stem cells and the structuring of the Italian biopolity’ in H. R. Rheinberger and R. Mazzolini (Eds.) ‘Different routes to stem cell research: Germany and Italy’, Il Mulino (Bologna) and Duncker & Humblot (Berlin)(2012)
    6. G. Testa ´More Than Just a Nucleus: Cloning and the Alignment of Scientific and Political Rationalities´ in Sheila Jasanoff (Ed.) ´Reframing Rights: Bioconstitutionalism in the Genetic Age´, 2011 MIT Press, pp. 86-104
    7. H. Nowotny and G. Testa Naked Genes. Reinventing the Human in the Molecular Age, 2011 MIT Press (originally appeared as 'Die gläsernen Gene. Die Erfindung des Individuums im molekularen Zeitalter’, 2009 Suhrkamp Verlag; Italian translation ‘Geni a nudo. Ripensare l’uomo nel XXI secolo’, Codice Edizioni 2012; Russian translation forthcoming) Reviewed in Nature, The Financial Times, Die Zeit, Der Spiegel, Il Corriere della Sera, BBC Science
    8. G. Testa ´Cloning as Mirror´ in Cristoph Zollikofer (Ed.) ´Klon statt Person´, 2011 Hochschulverlag AG an der ETH Zuerich, pp. 45-50
    9. G. Testa ´Le scienze della vita. Verso nuove antropogenesi?´ in Antonio Pavan and Emanuela Magno (Eds.) ´Antropogenesi. Ricerche sull'origine e lo sviluppo del fenomeno umano´ 2010, Il Mulino
    10. G. Boniolo, G. Gatti, G. Pelicci and G. Testa Cellule staminali. La base scientifica, le future terapie. La riflessione etica al di là dello slogan ideologico. Le risposte della scienza. Quaderno 11 Libertà di sapere libertà di scegliere Fondazione Umberto Veronesi per il progresso delle scienze
    11. G. Testa and S. Giaimo ´Il concetto di gene´ in Giovanni Boniolo e Stefano Giaimo (Eds.) ´Filosofia e Scienze della Vita. Un´analisi dei fondamenti della biologia e della biomedicina´ 2008 Bruno Mondadori
    12. G. Testa and A. Minelli ´Vincoli ed epigenesi´ in Giovanni Boniolo e Stefano Giaimo (Eds.) ´Filosofia e Scienze della Vita. Un´analisi dei fondamenti delal biologia e della biomedicina´ 2008 Bruno Mondadori
    13. G. Testa ´Che cos'è un clone? Practiche e significato delle biotecnologie rosse in un mondo globale´ in Massimiano Bucchi and Federico Neresini (Eds.) ´Cellule e Cittadini´ (Cells and citizens), 2006 Sironi Editore

     

  • Funding

    • European Research Council Proof of Concept
    • European Research Council Consolidator Grant
    • European Union Horizon2020
    • Associazione Italiana Ricerca sul Cancro (AIRC – Italian Association for Cancer Research)
    • Ministero della Salute (Italian Health Ministry)
    • Worldwide Cancer Research (formerly AICR)
    • Telethon investigator grant
    • Telethon exploratory grant
    • EPIGEN Flagship Project of the Italian National Research Council (CNR)
    • Fondation Jerome Lejeune
    • ERANET-NEURON
    • Fondazione Umberto Veronesi (FUV)
    • Fondazione Italiana Ricerca sul Cancro (FIRC)(Italian Foundation for Cancer Research)
    • Federation of European Biochemical Societies (FEBS)

    •  Regione Lombardia

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Ministero della Salute Joint Commission International Breastcertification bollinirosa
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