Tiziana Bonaldi
e-mail: tiziana.bonaldi AT ieo.eu
affiliation: IEO - Istituto Europeo di Oncologia
research area(s): Chemical Biology, Cancer Biology
Courses:
- Molecular Medicine: Molecular Oncology and Computational Biology
- Medical Nanotechnology
Since February 2008
Group Leader at the Department of Experimental Oncology of the European Institute of Oncology, Milano
2006-2008
Post Doc at the Max Plank Institute of Biochemistry in Martinsried, Germany (Head of the group: Prof. M. Mann)
2003-2005
Embo-long Term Fellow as Post Doc at the Molecular Biology Department (Head: Prof. P. B. Becker), n the Ludwig Maximilians University (LUM), in Munich, Germany
2002-2003
Visiting Scientist in the Mass Spectrometry Group, (Head: Dr. M. Wilm) at the EMBL in Heidelberg, Germany
23/2/2003
PhD Award at Dibit- HSR Institute, Milan (Italy)
1999- 2003
PhD student in the PhD program of the Open University (London- UK) at HSR, Milan. Supervisors: Prof. M.E. Bianchi, Prof. B. Turner (University of Birmingham)
1998-1999
Graduated fellow at the Department of Genetics and Microbiology, University of Milano
1992-1997
Degree in Biological Science (Laurea) at the University of Milan, Italy 110/110 cum laudae
Present Rsearch Activity
The group focuses on investigating the multiple levels of gene expression regulation, by proteomics and functional genomics approaches. Fields of expertise are: quantitative proteomics based on Mass Spectrometry, gene expression regulation, epigenetics, post-transcriptional regulation miRNA-mediated, integration of gene expression -"omics" data.
Group Leader at the Department of Experimental Oncology of the European Institute of Oncology, Milano
2006-2008
Post Doc at the Max Plank Institute of Biochemistry in Martinsried, Germany (Head of the group: Prof. M. Mann)
2003-2005
Embo-long Term Fellow as Post Doc at the Molecular Biology Department (Head: Prof. P. B. Becker), n the Ludwig Maximilians University (LUM), in Munich, Germany
2002-2003
Visiting Scientist in the Mass Spectrometry Group, (Head: Dr. M. Wilm) at the EMBL in Heidelberg, Germany
23/2/2003
PhD Award at Dibit- HSR Institute, Milan (Italy)
1999- 2003
PhD student in the PhD program of the Open University (London- UK) at HSR, Milan. Supervisors: Prof. M.E. Bianchi, Prof. B. Turner (University of Birmingham)
1998-1999
Graduated fellow at the Department of Genetics and Microbiology, University of Milano
1992-1997
Degree in Biological Science (Laurea) at the University of Milan, Italy 110/110 cum laudae
Present Rsearch Activity
The group focuses on investigating the multiple levels of gene expression regulation, by proteomics and functional genomics approaches. Fields of expertise are: quantitative proteomics based on Mass Spectrometry, gene expression regulation, epigenetics, post-transcriptional regulation miRNA-mediated, integration of gene expression -"omics" data.
The long-standing goal of my research is to investigate gene expression regulation, at different levels. Historically my research has focused on the epigenetic regulation of gene expression mediated by histone post-translational modifications (hPTMs) and variants. By using mass-spectrometry (MS) technology of choice, we study: the combinatorial aspects of hPTMs at the level of single histone, mono- or poly-nucleosomes, up to small chromatin regions; the in vivo action of histone-modifying enzymes and the quantitative aspects related to modification dynamics. In addition we are extending the analysis of methylations of non-histonic proteins, to explore the regulatory networks mediated by this modification in the cell.
More recently, with the advent of quantitative proteomics that allows accurate and large-scale protein expression profiling, we appreciated the potential of this technology to examine the post-transcriptional events regulating gene expression, with a focus on micro-RNA mediated translational inhibition. My research elaborates on this observation developing novel strategies to study these processes globally.
One quality of my team is the ambition to design and apply innovative and unconventional approaches to investigate various aspects of gene expression, in order to gain original perspectives and contribute new concepts to the field. Hopefully this will contribute to building up a tri-dimensional picture, not achievable only with conventional strategies.
Two lines of research are carried out in the group: one focuses on the role, regulation and dynamics of post-translational modifications on chromatin and is structured in three sub-projects; another usees qProteomics to study the molecular role of mir17-92 in B-cells lymphoma.
More recently, with the advent of quantitative proteomics that allows accurate and large-scale protein expression profiling, we appreciated the potential of this technology to examine the post-transcriptional events regulating gene expression, with a focus on micro-RNA mediated translational inhibition. My research elaborates on this observation developing novel strategies to study these processes globally.
One quality of my team is the ambition to design and apply innovative and unconventional approaches to investigate various aspects of gene expression, in order to gain original perspectives and contribute new concepts to the field. Hopefully this will contribute to building up a tri-dimensional picture, not achievable only with conventional strategies.
Two lines of research are carried out in the group: one focuses on the role, regulation and dynamics of post-translational modifications on chromatin and is structured in three sub-projects; another usees qProteomics to study the molecular role of mir17-92 in B-cells lymphoma.
Since 2005
1. Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Paganii M, Bonaldi T., Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A. "Genomewide Reduction in Nucleosomal Occupancy Increases DNA Transcription and Sensitivity to DNA Damage", accepted in PloS Biology
2. Cuomo A, Moretti S, Minucci S, Bonaldi T. "SILAC-based proteomic analysis to dissect the "histone modification signature" of Human Breast Cancer Cells". Amino Acids. 2010 Jul 9, PubMed PMID: 20617350.
3. Loyola A, Tagami H, Bonaldi T, Roche D, Quivy JP, Imhof A, Nakatani Y, Dent SY, Almouzni G. "The HP1alpha-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin". EMBO Rep. 2009 Jul;10(7):769-75. PubMed PMID: 19498464.
4. Hilger M, Bonaldi T, Gnad F, Mann M. "Systems-wide analysis of a phosphatase knock down by quantitative proteomics and phosphoproteomics". Mol Cell Proteomics. 2009 May 9. PubMed PMID: 19429919.
5. Bonaldi T, Straub T, Cox T, Kumar C, Becker PB, Mann M "Combined use of RNAi and quantitative proteomics to study gene function in Drosophila". Mol Cell, 2008 Sep 5;31(5):762-72.
6. Bachi A., Bonaldi T. "Quantitative proteomics as a new piece of the systems biology puzzle". J Proteomics, 2008 Aug 21;71(3):357-67.
7. Lund Nielsen M, Vermeulen M, Bonaldi T, Mann M "Chemical artifact can lead to misidentification of ubiquitination-substrates by mass-spectrometry", Nat. Methods., 2008.
8. Lu A, Waanders LF, Almeida R, Li G, Allen M, Cox J, Olsen JV, Bonaldi T, Mann M. ""Nanoelectrospray peptide mapping revisited: Composite survey spectra allow high dynamic range protein characterization without LCMS on an orbitrap mass spectrometer". Int. Journal of Mass Spectrometry, 2007
9. Ferreira R, Eberharter A, Bonaldi T, Chioda M, Imhof A, Becker PB. "Site-specific acetylation of ISWI by GCN5". BMC Mol Biol., 2007
10. Loyola A*, Bonaldi T*, Roche D, Imhof A, Almouzni G. "PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state". Mol Cell, * 2006 equal contribution
11. Imhof A, Bonaldi T. ""Chromatomics" the analysis of the chromatome". Mol Biosyst., 2005
12. Greiner D, Bonaldi T, Eskeland R, Roemer E, Imhof A. "Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9". Nat Chem Biol., 2005
13. Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M. "Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer". Nat Genet., 2005
Chapters in Textbooks
1 A. Cuomo and T. Bonaldi "Systems biology on-the-fly: Quantitative Proteomics of Functional States in D. melanogaster cell lines". System Biology in Drug Discovery and Development: methods and protocol. Chapter 3. Springer Protocols; Humana Press (2010).
2 T. Bonaldi, J. Regula, A. Imhof (2004) "The use of mass spectrometry for the analysis of histone modifications'. Methods in Enzymology 377: 111-30
1. Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Paganii M, Bonaldi T., Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A. "Genomewide Reduction in Nucleosomal Occupancy Increases DNA Transcription and Sensitivity to DNA Damage", accepted in PloS Biology
2. Cuomo A, Moretti S, Minucci S, Bonaldi T. "SILAC-based proteomic analysis to dissect the "histone modification signature" of Human Breast Cancer Cells". Amino Acids. 2010 Jul 9, PubMed PMID: 20617350.
3. Loyola A, Tagami H, Bonaldi T, Roche D, Quivy JP, Imhof A, Nakatani Y, Dent SY, Almouzni G. "The HP1alpha-CAF1-SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin". EMBO Rep. 2009 Jul;10(7):769-75. PubMed PMID: 19498464.
4. Hilger M, Bonaldi T, Gnad F, Mann M. "Systems-wide analysis of a phosphatase knock down by quantitative proteomics and phosphoproteomics". Mol Cell Proteomics. 2009 May 9. PubMed PMID: 19429919.
5. Bonaldi T, Straub T, Cox T, Kumar C, Becker PB, Mann M "Combined use of RNAi and quantitative proteomics to study gene function in Drosophila". Mol Cell, 2008 Sep 5;31(5):762-72.
6. Bachi A., Bonaldi T. "Quantitative proteomics as a new piece of the systems biology puzzle". J Proteomics, 2008 Aug 21;71(3):357-67.
7. Lund Nielsen M, Vermeulen M, Bonaldi T, Mann M "Chemical artifact can lead to misidentification of ubiquitination-substrates by mass-spectrometry", Nat. Methods., 2008.
8. Lu A, Waanders LF, Almeida R, Li G, Allen M, Cox J, Olsen JV, Bonaldi T, Mann M. ""Nanoelectrospray peptide mapping revisited: Composite survey spectra allow high dynamic range protein characterization without LCMS on an orbitrap mass spectrometer". Int. Journal of Mass Spectrometry, 2007
9. Ferreira R, Eberharter A, Bonaldi T, Chioda M, Imhof A, Becker PB. "Site-specific acetylation of ISWI by GCN5". BMC Mol Biol., 2007
10. Loyola A*, Bonaldi T*, Roche D, Imhof A, Almouzni G. "PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state". Mol Cell, * 2006 equal contribution
11. Imhof A, Bonaldi T. ""Chromatomics" the analysis of the chromatome". Mol Biosyst., 2005
12. Greiner D, Bonaldi T, Eskeland R, Roemer E, Imhof A. "Identification of a specific inhibitor of the histone methyltransferase SU(VAR)3-9". Nat Chem Biol., 2005
13. Fraga MF, Ballestar E, Villar-Garea A, Boix-Chornet M, Espada J, Schotta G, Bonaldi T, Haydon C, Ropero S, Petrie K, Iyer NG, Pérez-Rosado A, Calvo E, Lopez JA, Cano A, Calasanz MJ, Colomer D, Piris MA, Ahn N, Imhof A, Caldas C, Jenuwein T, Esteller M. "Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer". Nat Genet., 2005
Chapters in Textbooks
1 A. Cuomo and T. Bonaldi "Systems biology on-the-fly: Quantitative Proteomics of Functional States in D. melanogaster cell lines". System Biology in Drug Discovery and Development: methods and protocol. Chapter 3. Springer Protocols; Humana Press (2010).
2 T. Bonaldi, J. Regula, A. Imhof (2004) "The use of mass spectrometry for the analysis of histone modifications'. Methods in Enzymology 377: 111-30
No projects are available to students for the current accademic year.