Pagani Massimiliano

Principal Investigator



Massimiliano Pagani has experience in molecular biology and biochemistry, specialist in the development of high throughput systems of gene cloning/expression and protein purification and in the study of regulatory non-coding RNAs in human immune system.
He received his degree “cum laude” in Biological Sciences at the University of Milan (1995) and the PhD in Molecular and Cellular Biology from the San Raffaele Hospital in Milan Italy, in 2000.  He then worked as group leader in the biotech company Primm (Milan) specialized in R&D and custom biotechnology products and services for academic and industrial laboratories. In 2006 he became the Primm R&D manager and was involved in the supervision of different research projects in close collaboration with several international companies and research centers.
Since July 2008 he joined INGM (National Institute of Molecular Genetics) and founded the Integrative Biology program (IBP). IBP is devoted to deciphering the molecular mechanisms and the regulatory networks underlying T cell differentiation and plasticity in the human immune system, employing several techniques and multiple know-how in fields like, molecular and cellular biology, biochemistry, genomics, transcriptomics and bioinformatics. IBP is mainly focused on the identification of microRNAs involved in differentiation of human T lymphocytes, identification of microRNA targets and Studies on Epigenetic regulation of human lymphocytes by long non-coding RNAs.
Massimiliano Pagani has been awarded a European Research Council (ERC) Consolidator Grant of €2 million for five years. He was selected from 3,673 applicants (8.7 % success rate). ERC Starting Grants aim to support researchers at the stage at which they are consolidating their own independent research team or programme. The scheme will strengthen independent and excellent new individual research teams that have been recently created. Established in 2007 by the EU, the ERC in Strasbourg is the first pan-European funding organisation to support investigator-driven cutting-edge research on the basis of scientific excellence. More information on ERC funding and statistics here.
Altogether 3 INGM researchers have been awarded one of the highly endowed ERC grants. Besides Massimiliano Pagani, these are Sergio Abrignani, and Stefano Biffo.
Massimiliano’s group will investigate the role of Long non-coding RNAs of tumor infiltrating lymphocytes as novel anti-cancer therapeutic targets.
Although tumor tissues can be infiltrated by T cells specific for tumor antigens, the effector functions of these lymphocytes are generally suppressed by CD4+ regulatory T cells (Tregs). However, tumor infiltrating Tregs can display function heterogeneity, depending on both the tumor type and the inflammatory milieu. Thus, only inhibition of the right Treg activity should result in the unleash of an effective anti-tumor T cell responses. With the aim of identifying the Tregs that truly inhibit anti-tumor T cells, we will profile by RNA-Seq the transcriptome of Tregs infiltrating both tumor and healthy tissues. In particular, we will focus on lncRNAs and the gene networks they modulate, since they have recently emerged as relevant epigenetic regulators of cell differentiation and identity. We will exploit this new knowledge to determine the association of specific transcripts with different Treg cell populations, including those specific for truly inhibitory Tregs. Since downregulation of specific lncRNAs might be an efficient way to inhibit the “unwanted” Tregs at tumor sites, we aim at targeting lncRNAs uniquely expressed in these Tregs and propose to develop AsiCs, chimeric molecules composed by an aptamer, single stranded oligonucleotides that bind to cell surface markers, and a siRNA, short RNAs downregulating specific lncRNAs.

Altogether 3 INGM researchers have been awarded one of the highly endowed ERC grants. Besides Massimiliano Pagani, these are Sergio Abrignani, and Stefano Biffo.

Massimiliano Pagani has been appointed as Professor of Molecular Biology in the “Dipartimento di Biotecnologie Mediche e Medicina Traslazionale” Università degli Studi di Milano, from 1st January 2015.



Integrative Biology is a multidisciplinary research approach that emphasizes the amalgamation of expertises from different sub-disciplines. The INGM Integrative Biology Program is devoted to deciphering the molecular mechanisms and the regulatory networks underlying T cell differentiation and plasticity in the human immune system. We will be employing several techniques and multiple know-how in fields like, molecular and cellular biology, biochemistry, genomics, transcriptomics and bioinformatics.
We are mainly focused on the following research topics:

  • Identification of microRNAs involved in differentiation of human T lymphocyte
    In recent years it has become clear that microRNAs play a pivotal role in regulation of gene expression. MicroRNAs are small non-coding RNAs ~22 nucleotides long that bind mostly to the 3′ UTR of target mRNAs, thereby affecting transcript stability and/or translation. Several human microRNAs identified so far show tissue or development stage-specific expression profiles, suggesting that they are integrated in the regulatory networks defining cellular identity.
    Our group firstly has focused on the identification of those microRNAs defining the different human T-lymphocytes subsets. Integration of these data with gene expression profiling allowed us to identify microRNA specifically involved in lymphocyte differentiation, in particular of CD4+ T cells subsets. The functional relevance on CD4+ T cell differentiation of some of the identified microRNAs is being further investigated. Aberrant expression of microRNAs has been implicated in numerous disease states, and microRNA-based diagnostics and/or therapy will be under investigation in certain diseases.


  • Identification of microRNA targets
    A detailed understanding of microRNAs biological function requires concomitant identification of their direct mRNA targets. Several computational methods have been developed to predict the most probable target sequences. However, many microRNA targets that were identified by prediction algorithms could not be validated in vivo, suggesting that factors other than sequence matching may play an important role in microRNA regulation and targeting. As each microRNA may have potentially hundreds of matching target mRNAs, a great effort must be put in target identification, this is becoming a major challenge. In order to achieve this goal, we are developing biochemistry methods pursuing target identification in primary cells deriving from the human immune system, based on RNA-Induced-Silencing Compex (RISC) immunoprecipitations followed by direct identification of the associated microRNA and target mRNA through a deep-sequencing approach.


  • Studies on Epigenetic regulation of human lymphocytes by long non-coding RNAs
    Non-coding RNA genes include highly abundant and functionally important RNAs such as transfer RNA (tRNA) or ribosomal RNA (rRNA), as well as microRNAs, siRNA and the class of long non-coding RNAs which plays a key role in gene regulation, genome stability and chromatin modification. Long non-codingRNAs epigenetically regulate several physio-pathological processes, including development, cell differentiation, cancer, inflammation and chronic viral infection. Thus, regulation of long non-codingRNAs has the potential of being an important mechanism in preserving and altering lymphocyte cell phenotypes. Thus, we need to deeply understand, when and how expression of key long non-codingRNAs changes during T cell differentiation and how they can influence epigenetic regulation. To address these questions, we are performing a whole transcriptome analysis of highly purified human lymphocyte subsets by deep-sequencing, in order to identify the differentially expressed long non-codingRNAs in human lymphocyte subsets. Long non-codingRNAs emerging from our combined experimental and bioinformatics analysis will be further investigated to define their precise functional role(s) through gain and loss of function experiments.


IL-10-producing forkhead box protein 3-negative regulatory T cells inhibit B-cell responses and are involved in systemic lupus erythematosus.
Facciotti F, Gagliani N, Häringer B, Alfen JS, Penatti A, Maglie S, Paroni M, Iseppon A, Moro M, Crosti MC, Stölzel K, Romagnani C, Moroni G,Ingegnoli F, Torretta S, Pignataro L, Annoni A, Russo F, Pagani M, Abrignani S, Meroni P, Flavell R, Geginat J.
J Allergy Clin Immunol. 2015 Aug 25. pii: S0091-6749(15)00999-9. doi: 10.1016/j.jaci.2015.06.044. [Epub ahead of print]

The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4
Ranzani V, Rossetti G, Panzeri I, Arrigoni A, Bonnal RJP, Curti S, Gruarin P, Provasi E, Sugliano E, Marconi M, De Francesco R, Geginat J, Bodega B, Abrignani S, Pagani M.
Nature Immunol. 2015 Jan 26. DOI:10.1038/ni.3093

Plasticity of human CD4 T cell subsets
Geginat J, Paroni M, Maglie S, Alfen JA, Kastirr I, Gruarin P, De Simone M, Pagani M, Abrignani S.
Frontiers in Immunology, 2014

NS5A inhibitors impair NS5A- PI4KIIIα complex formation and cause a decrease of PI4P and cholesterol levels in HCV-associated membranes
Reghellin V, Donnici L, Fenu S, Berno V, Calabrese V, Pagani M, Abrignani S, Peri F, De Francesco R, Neddermann P.
Antimicrob Agents Chemother. 2014 Dec;58(12):7128-40.

IL-21 Is a Central Memory T Cell-Associated Cytokine That Inhibits the Generation of Pathogenic Th1/17 Effector Cells
Kastirr I, Maglie S, Paroni M, Alfen JS, Nizzoli G, Sugliano E, Crosti MC, Moro M, Steckel B, Steinfelder S, Stölzel K, Romagnani C, Botti F, Caprioli F, Pagani M, Abrignani S, Geginat J.
J Immunol. 2014 Oct 1;193(7):3322-31.

Serum microRNAs as biomarkers of human lymphocyte activation in health and disease
De Candia P. Torri A, Pagani M, Abrignani S
Frontiers in Immunology, 2014

Intracellular Modulation, Extracellular Disposal and Serum Increase of MiR-150 Mark Lymphocyte Activation
De Candia P, Torri A, Gorletta T, Fedeli M, Bulgheroni E, Cheroni C, Marabita F, Crosti M, Moro M, Pariani E, Romanò L, Esposito S, Mosca F, Rossetti G, Rossi RL, Geginat J, Casorati G, Dellabona P, Pagani M, Abrignani S
PLoS One. 2013 Sep 26;8(9).

The CD4-centered universe of human T cell subsets
Geginat J, Paroni M, Facciotti F, Gruarin P, Kastirr I, Caprioli F, Pagani M, Abrignani S
Semin Immunol. 2013

Role of microRNAs and long-non-coding RNAs in CD4(+) T-cell differentiation
Pagani M, Rossetti G, Panzeri I, de Candia P, Bonnal RJ, Rossi RL, Geginat J, Abrignani S.
Immunol Rev. 253(1):82-96, 2013.

Reduction of CD68+ Macrophages and Decreased IL-17 Expression in Intestinal Mucosa of Patients with Inflammatory Bowel Disease Strongly Correlate With Endoscopic Response and Mucosal Healing following Infliximab Therapy
Caprioli F, Bosè F, Rossi RL, Petti L, Viganò C, Ciafardini C, Raeli L, Basilisco G, Ferrero S, Pagani M, Conte D, Altomare G, Monteleone G, Abrignani S, Reali E.
Inflamm Bowel Dis. 19(4):729-739, 2013.

Identification of new autoantigens by protein array indicates a role for IL4 neutralization in Autoimmune Hepatitis
Zingaretti C, Arigo’ M, Cardaci A, Moro M, Crosti M, Sinisi A, Sugliano E, Cheroni C, Marabita F, Nogarotto R, Bonnal RJ, Marcatili P, Marconi M, Zignego A, Muratori P, Invernizzi P, Colombatto P, Brunetto M, Bonino F, De Francesco R, Geginat J, Pagani M, Muratori L, Abrignani S, Bombaci M.
Mol Cell Proteomics. 11(12):1885-97, 2012.

Identification of new hematopoietic cell subsets with a polyclonal antibody library specific for neglected proteins
Moro M, Crosti M, Creo P, Gallina P, Curti S, Sugliano E, Scavelli R, Cattaneo D, Canidio E, Marconi M, Rebulla P, Sarmientos P, Viale G, Pagani M, Abrignani S.
PLoS One. 7(4):e34395, 2012.

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.
Bonnal RJ, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P.
Bioinformatics. 2012 28: 1035-7

Circulating hepatitis B surface antigen particles carry hepatocellular microRNAs
Novellino L, Rossi RL, Bonino F, Cavallone D, Abrignani S, Pagani M, Brunetto MR.
PLoS One. 7(3), e31952. 2012.

Metabolism of Phosphatidylinositol 4-Kinase IIIα-Dependent PI4P Is Subverted by HCV and Is Targeted by a 4-Anilino Quinazoline with Antiviral Activity
Bianco A, Reghellin V, Donnici L, Fenu S, Alvarez R, Baruffa C, Peri F, Pagani M, Abrignani S, Neddermann P, De Francesco R.
PLoS Pathog. 8(3):e1002576, 2012.

Substantial histone reduction modulates genomewide nucleosomal occupancy and global transcriptional output
Celona B, Weiner A, Di Felice F, Mancuso FM, Cesarini E, Rossi RL, Gregory L, Baban D, Rossetti G, Grianti P, Pagani M, Bonaldi T, Ragoussis J, Friedman N, Camilloni G, Bianchi ME, Agresti A.
PLoS Biol. 2011, 9: e1001086

A high-resolution anatomical atlas of the transcriptome in the mouse embryo
Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I, Lin-Marq N, Koch M, Bilio M, Cantiello I, Verde R, De Masi C, Bianchi SA, Cicchini J, Perroud E, Mehmeti S, Dagand E, Schrinner S, Nurnberger A, Schmidt K, Metz K, Zwingmann C, Brieske N, Springer C, Hernandez AM, Herzog S, Grabbe F, Sieverding C, Fischer B, Schrader K, Brockmeyer M, Dettmer S, Helbig C, Alunni V, Battaini MA, Mura C, Henrichsen CN, Garcia-Lopez R, Echevarria D, Puelles E, Garcia-Calero E, Kruse S, Uhr M, Kauck C, Feng G, Milyaev N, Ong CK, Kumar L, Lam M, Semple CA, Gyenesei A, Mundlos S, Radelof U, Lehrach H, Sarmientos P, Reymond A, Davidson DR, Dolle P, Antonarakis SE, Yaspo ML, Martinez S, Baldock RA, Eichele G, Ballabio A.
PLoS Biol. 2011, 9: e1000582

A novel polyclonal antibody library for expression profiling of poorly characterized, membrane and secreted human proteins
Grifantini R, Pagani M, Pierleoni A, Grandi A, Parri M, Campagnoli S, Pileri P, Cattaneo D, Canidio E, Pontillo A, De Camilli E, Bresciani A, Marinoni F, Pedrazzoli E, Nogarotto R, Abrignani S, Viale G, Sarmientos P, Grandi G.
J. Proteomics. 75(2): 532-47, 2011.

Distinct microRNA signatures in human lymphocyte subsets and enforcement of T cell naïve state by miR-125b
Rossi RL., Rossetti G., Wenandy L., Curti S., Ripamonti A., Bonnal RJP., Sciarretta BR., Moro M., Crosti MC., Gruarin P., Maglie S., Marabita F., Mascheroni D., Parente V., Comelli M., Trabucchi E., De Francesco R., Geginat J., Abrignani S., Pagani M.
Nature Immunol. 12, 796-803, 2011.

Preventing bacterial infections with pilus-based vaccines: the group B streptococcus paradigm
Margarit I, Rinaudo CD, Galeotti CL, Maione D, Ghezzo C, Buttazzoni E, Rosini R, Runci Y, Mora M, Buccato S, Pagani M, Tresoldi E, Berardi A, Creti R, Baker CJ, Telford JL, Grandi G.
J Infect Dis 2009, 199: 108-15

The C-terminal domain of yeast Ero1p mediates membrane localization and is essential for function
Pagani M, Pilati S, Bertoli G, Valsasina B, Sitia R.
FEBS Lett 2001 508: 117-20

Endoplasmic reticulum oxidoreductin 1-lbeta (ERO1-Lbeta), a human gene induced in the course of the unfolded protein response
Pagani M, Fabbri M, Benedetti C, Fassio A, Pilati S, Bulleid NJ, Cabibbo A, Sitia R.
J Biol Chem 2000, 275: 23685-92

ERO1-L, a human protein that favors disulfide bond formation in the endoplasmic reticulum
Cabibbo A, Pagani M, Fabbri M, Rocchi M, Farmery MR, Bulleid NJ, Sitia R.
J Biol Chem 2000, 275: 4827-33

The association of HIV-1 Tat with nuclei is regulated by Ca2+ ions and cytosolic factors
Morgavi P, Bonifaci N, Pagani M, Costigliolo S, Sitia R, Rubartelli A.
J Biol Chem 1997, 272: 11256-60

INGM researches are supported by