Carpi Donatella, Post Doc
Martinovic Martina, PhD Student
Torri Anna, Laboratory Technician

Scientific Background

Communication between immune cells involves not only secretion of cytokines and chemokines, but also the release of membrane vesicles of very small size (20-100 nanometers) called exosomes (or also nanovesicles), that enclose soluble cellular components derived from donor cells. It has been demonstrated that this second mechanism has functional consequences including the induction, amplification and/or modulation of immune responses. In addition, a novel mechanism of nucleic acid exchange between cells has been recently described, characterized by exosome-mediated transfer of mRNAs but also regulatory RNA, such as microRNA (miRNA).

Our working hypothesis is that there exists not only a paracrine but also a systemic exchange involving miRNAs containing vesicles released by activated immune cells.

Interestingly, several published results report that blood circulating miRNAs can be used as powerful biomarkers showing that their profiles have the ability to discriminate healthy subjects from patients within a largely diversified range of human diseases.

In line with these studies, our laboratory is strongly interested in developing serum circulating miRNAs (and in particular, exosome-associated miRNAs) as potential biomarkers of immune response.

Ongoing Projects

  1. The complete characterization of signatures of exosome-associated microRNAs present in the extra-cellular environment of ex vivo purified primary human CD4+ T lymphocyte subsets (Th1, Th2, Th17 and Treg) upon activation in vitro.
  2. The analysis of human serum miRNome in order to assess whether the extracellular microRNA signatures associated with in vitro activation in vitro of CD4+ T lymphocyte subsets are indeed able to discriminate the different in vivo elicitation of these effector populations that occurs upon vaccination with different vaccines/adjuvants; or in conditions of aberrant immune activation as in the case of autoimmunity.
  3. The dissection of the potential functional role of exosome-associated microRNAs released by T regulatory cells in the maintenance/loss of immune tolerance in health and disease.

Recent Publications

Lack of evidence for post-vaccine onset of autoimmune/lymphoproliferative disorders, during a nine-month follow-up in multiply vaccinated Italian military.
Ferlito C, Barnaba V, Abrignani S, Bombaci M, Sette A, Sidney J, Biselli R, Tomao E, Cattaruzza MS, Germano V, Biondo MI, Salerno G, Lulli P, Caporuscio S, Diamanti AP, Falco M, Biselli V, Cardelli P, Autore A, Lucertini E, De Cesare DP, Peragallo MS, Lista F, Martire C, Salemi S, Nisini R, D’Amelio R.
Clin Immunol. 2017 Jun 15. pii: S1521-6616(17)30357-1. doi: 10.1016/j.clim.2017.06.001. [Epub ahead of print]

The Enigmatic Role of Viruses in Multiple Sclerosis: Molecular Mimicry or Disturbed Immune Surveillance?
Geginat J, Paroni M, Pagani M, Galimberti D, De Francesco R, Scarpini E, Abrignani S.
Trends Immunol. 2017 May 23. pii: S1471-4906(17)30077-7. doi: 10.1016/ [Epub ahead of print] Review.

Next-Generation Sequencing Analysis of Long Noncoding RNAs in CD4+ T Cell Differentiation.
Ranzani V, Arrigoni A, Rossetti G, Panzeri I, Abrignani S, Bonnal RJ, Pagani M.
Methods Mol Biol. 2017;1514:173-185.

Differences in serum and synovial CD4+ T cells and cytokine profiles to stratify patients with inflammatory osteoarthritis and rheumatoid arthritis.
Penatti A, Facciotti F, De Matteis R, Larghi P, Paroni M, Murgo A, De Lucia O, Pagani M, Pierannunzii L, Truzzi M, Ioan-Facsinay A, Abrignani S, Geginat J, Meroni PL.
Arthritis Res Ther. 2017 May 19;19(1):103. doi: 10.1186/s13075-017-1305-1.

CombiROC: an interactive web tool for selecting accurate marker combinations of omics data.
Mazzara S, Rossi RL, Grifantini R, Donizetti S, Abrignani S, Bombaci M.
Sci Rep. 2017 Mar 30;7:45477. doi: 10.1038/srep45477.

Recognition of viral and self-antigens by TH1 and TH1/TH17 central memory cells in patients with multiple sclerosis reveals distinct roles in immune surveillance and relapses.
Paroni M, Maltese V, De Simone M, Ranzani V, Larghi P, Fenoglio C, Pietroboni AM, De Riz MA, Crosti MC, Maglie S, Moro M, Caprioli F, Rossi R, Rossetti G, Galimberti D, Pagani M, Scarpini E, Abrignani S, Geginat J.
J Allergy Clin Immunol. 2017 Feb 16. pii: S0091-6749(17)30043-X. doi: 10.1016/j.jaci.2016.11.045. [Epub ahead of print]

Extracellular MicroRNA Signature of Human Helper T Cell Subsets in Health and Autoimmunity.
Torri A, Carpi D, Bulgheroni E, Crosti MC, Moro M, Gruarin P, Rossi RL, Rossetti G, Di Vizio D, Hoxha M, Bollati V, Gagliani C, Tacchetti C, Paroni M, Geginat J, Corti L, Venegoni L, Berti E, Pagani M, Matarese G, Abrignani S, de Candia P.
J Biol Chem. 2017 Feb 17;292(7):2903-2915. doi: 10.1074/jbc.M116.769893. Epub 2017 Jan 11.

Endovascular Mechanical Thromboaspiration of Right Hepatic Arterial Thrombosis After Liver Transplantation.
Gandini R, Konda D, Toti L, Abrignani S, Merolla S, Tisone G, Floris R.
Cardiovasc Intervent Radiol. 2017 Apr;40(4):621-624. doi: 10.1007/s00270-016-1538-4. Epub 2016 Dec 28.

miR-17∼92 family clusters control iNKT cell ontogenesis via modulation of TGF-β signaling.
Fedeli M, Riba M, Garcia Manteiga JM, Tian L, Viganò V, Rossetti G, Pagani M, Xiao C, Liston A, Stupka E, Cittaro D, Abrignani S, Provero P, Dellabona P, Casorati G.
Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):E8286-E8295. doi: 10.1073/pnas.1612024114. Epub 2016 Dec 5.

Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells.
De Simone M, Arrigoni A, Rossetti G, Gruarin P, Ranzani V, Politano C, Bonnal RJ, Provasi E, Sarnicola ML, Panzeri I, Moro M, Crosti M, Mazzara S, Vaira V, Bosari S, Palleschi A, Santambrogio L, Bovo G, Zucchini N, Totis M, Gianotti L, Cesana G, Perego RA, Maroni N, Pisani Ceretti A, Opocher E, De Francesco R, Geginat J, Stunnenberg HG, Abrignani S, Pagani M.
Immunity. 2016 Nov 15;45(5):1135-1147. doi: 10.1016/j.immuni.2016.10.021.

Reverse plasticity: TGF-β and IL-6 induce Th1-to-Th17-cell transdifferentiation in the gut.
Geginat J, Paroni M, Kastirr I, Larghi P, Pagani M, Abrignani S.
Eur J Immunol. 2016 Oct;46(10):2306-2310. doi: 10.1002/eji.201646618.

Analysis RNA-seq and Noncoding RNA.
Arrigoni A, Ranzani V, Rossetti G, Panzeri I, Abrignani S, Bonnal RJ, Pagani M.
Methods Mol Biol. 2016;1480:125-35. doi: 10.1007/978-1-4939-6380-5_11.

Uncontrolled IL-17 Production by Intraepithelial Lymphocytes in a Case of non-IPEX Autoimmune Enteropathy.
Paroni M, Magarotto A, Tartari S, Nizzoli G, Larghi P, Ercoli G, Gianelli U, Pagani M, Elli L, Abrignani S, Conte D, Geginat J, Caprioli F.
Clin Transl Gastroenterol. 2016 Jul 14;7(7):e182. doi: 10.1038/ctg.2016.41.

IL-10 promotes homeostatic proliferation of human CD8(+) memory T cells and, when produced by CD1c(+) DCs, shapes naive CD8(+) T-cell priming.
Nizzoli G, Larghi P, Paroni M, Crosti MC, Moro M, Neddermann P, Caprioli F, Pagani M, De Francesco R, Abrignani S, Geginat J.
Eur J Immunol. 2016 Jul;46(7):1622-32. doi: 10.1002/eji.201546136. Epub 2016 May 17.

Intraprocedural Foot Embolization during In-Stent Restenosis Superficial Femoral Artery Recanalization: Plantar to Pedal Loop Aspiration Thrombectomy Technique Using the Penumbra MAX Catheter.
Gandini R, Merolla S, Chegai F, Pratesi G, Abrignani S, Loreni G, Pistolese CA, Pampana E.
J Vasc Interv Radiol. 2016 Apr;27(4):606-8. doi: 10.1016/j.jvir.2015.12.020. No abstract available.

The light and the dark sides of Interleukin-10 in immune-mediated diseases and cancer
Geginat J, Larghi P, Paroni M, Nizzoli G, Penatti A, Pagani M, Gagliani N, Meroni P, Abrignani S, Flavell RA.
Cytokine Growth Factor Rev. 2016 Mar 8. pii: S1359-6101(16)30019-3. doi: 10.1016/j.cytogfr.2016.02.003. [Epub ahead of print]

De novo transcriptome profiling of highly purified human lymphocytes primary cells.
Bonnal RJ, Ranzani V, Arrigoni A, Curti S, Panzeri I, Gruarin P, Abrignani S, Rossetti G, Pagani M.
Sci Data. 2015 Sep 29;2:150051.

Normalization of circulating microRNA expression data obtained by quantitative real-time RT-PCR.
Marabita F, de Candia P, Torri A, Tegnér J, Abrignani S, Rossi RL.
Brief Bioinform. 2015 Aug 3. pii: bbv056. [Epub ahead of print]

Serum microRNAs as Biomarkers of Human Lymphocyte Activation in Health and Disease.
de Candia P, Torri A, Pagani M, Abrignani S.
Front Immunol. 2014 Feb 10;5:43. eCollection 2014. Review.

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):e75348. doi: 10.1371/journal.pone.0075348. eCollection 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. 2013 May;253(1):82-96. doi: 10.1111/imr.12055. Review.

Large oncosomes mediate intercellular transfer of functional microRNA.
Morello M, Minciacchi VR, de Candia P, Yang J, Posadas E, Kim H, Griffiths D, Bhowmick N, Chung LW, Gandellini P, Freeman MR, Demichelis F, Di Vizio D.
Cell Cycle. 2013 Nov 15;12(22):3526-36. doi: 10.4161/cc.26539.




Bombaci Mauro, Group Leader
Mazzara Saveria, Bioinformatician
Pesce Elisa, Post Doc

Scientific Background

Nowadays there is an urgent need for new molecular markers that allow for better identification and stratification of autoimmune or cancer patients into different classes.

The use of antibodies and/or their antigen targets as biomarkers can greatly facilitate the development of new therapeutics and diagnostics in this direction. Protein microarrays technology is becoming a widely used proteomic tool to detect proteins and investigate their interactions (such as protein-antibody, protein-protein, protein-ligand interactions or enzyme-substrate screenings).

The INGM Protein MicroArray Laboratory aims at identifying new biomarkers in autoimmune diseases and tumors.

We developed a protein microarray containing about 2000 poorly-characterized recombinant human proteins, that were predicted to be surface-exposed or secreted proteins, in order to identify signature profiles with high specificity and sensitivity, able to monitor disease susceptibility and to predict disease severity. We are interested in the developing in diagnostic and therapeutic tools.

The identification of specific signatures would be useful for the development of predictive tests and trying to figure out the phatogenic mechanism. We would like to identify in silico patient cohort at risk of developing autoimmune diseases, and monitoring the effects of therapies. Optimization patients’ therapy will be easier and focused on specific case.

The interaction between our Institute and most of the important italian Hospitals (Fondazione IRCCS Ospedale Maggiore Policlinico Milano, Policlinico Sant’Orsola, Azienda Ospedaliera Universitaria Pisana, Pisa, Fondazione IRCCS Istituto Clinico Humanitas, Milano) is crucial for the access to suitable high-quality samples in their biobanks, allowing identification and validation of the new identified biomarkers.

Ongoing Projects

  1. Development of a Protein array which include specific biomarkers in order to determine certain quality and survivability parameters in Red Blood Cells (RBC).
  2. Discovery and identification of new autoantigens in autoimmune diseases, including autoimmune hepatitis (AIH), primary sclerosing cholangitis (PSC), primary biliary cirrhosis (PBC).
  3. Biochemical characterization of new biomarker, protein-protein interaction profiling.
  4. Application of multivariate analyses for classification diseases profiles in protein microarrays.

Clinical relevance

Identification of new autoantigens help us to understand the mechanisms underpinning the initiation, natural remission, and progression of autoimmune diseases, and to develop targeted therapeutics that treat these diseases without incurring serious adverse side effects. Moreover, functional characterization of these new autoantigens might be important to unveil the pathogenic mechanisms underlying autoimmune diseases and tumors.

Recent Publications

Two of Them Do It Better: Novel Serum Biomarkers Improve Autoimmune Hepatitis Diagnosis.
Mazzara S, Sinisi A, Cardaci A, Rossi RL, Muratori L, Abrignani S, Bombaci M.
PLoS One. 2015 Sep 16;10(9):e0137927

Identification of new autoantigens by protein array indicates a role for IL4 neutralization in Autoimmune Hepatitis
Zingaretti C, Arigò M, Cardaci A, Moro M, Crosti M, Sinisi A, Sugliano E, Cheroni C, Marabita F, Nogarotto R, Bonnal RJP, Marcatili P, Marconi M, Zignego A, Muratori P, Invernizzi P, Colombatto P, Brunetto M, Bonino B, De Francesco R, Geginat J, Pagani M, Muratori L, Abrignani S, Bombaci M.
Mol Cell Proteomics. 2012; 11 (12), pp. 1885-1897

Development of an Influenza virus Protein Array Using Sortagging Technology
Sinisi A, Popp MW, Antos JM, Pansegrau W, Savino S, Nissum M, Rappuoli R, Ploegh HL, Buti L.
Bioconjug Chem. 2012 May 25.

Multi high-throughput approach for highly selective identification of vaccine candidates: the group a streptococcus case
Bensi G, Mora M, Tuscano G, Biagini M, Chiarot E, Bombaci M, Capo S, Falugi F, Manetti AG, Donato P, Swennen E, Gallotta M, Garibaldi M, Pinto V, Chiappini N, Musser JM, Janulczyk R, Mariani M, Scarselli M, Telford JL, Grifantini R, Norais N, Margarit I, Grandi G.
Mol Cell Proteomics. 2012 Jun;11(6):M111.015693. Epub 2012 Jan 27.

Surface interactome in Streptococcus pyogenes
Galeotti CL, Bove E, Pezzicoli A, Nogarotto R, Norais N, Pileri S, Lelli B, Falugi F, Balloni S, Tedde V, Chiarot E, Bombaci M, Soriani M, Bracci L, Grandi G, Grifantini R.
Mol Cell Proteomics. 2012 Apr;11(4):M111.015206. Epub 2011 Dec 22.

Protein microarrays applications in biological and medical research
Bombaci M, Grifantini R.
New Research Trends in Protein Chip Technology, Transworld Research Network. 2010; Chapter book 1: pg, 1-24.

Protein array profiling of tic patient sera reveals a broad range and enhanced immune response against Group A Streptococcus antigens
Bombaci M, Grifantini R, Mora M, Reguzzi V, Petracca R, Meoni E, Balloni S, Zingaretti C, Falugi F, Manetti AG, Margarit I, Musser JM, Cardona F, Orefici G, Grandi G, Bensi G.
PLoS One. 2009 Jul 22;4(7):e6332.

Capturing host-pathogen interactions by protein microarrays: identification of novel streptococcal proteins binding to human fibronectin, fibrinogen, and C4BP
Margarit I, Bonacci S, Pietrocola G, Rindi S, Ghezzo C, Bombaci M, Nardi-Dei V, Grifantini R, Speziale P, Grandi G.
FASEB J. 2009 Sep;23(9):3100-12. Epub 2009 May 5.

INGM researches are supported by