Bio


My professional goal as a pediatrician specializing in immunology, has been to challenge the limits of "inexplicable" and "untreatable" diseases, and apply current scientific knowledge to understand the mechanisms of impaired cellular immune function underlying the clinical manifestations in order to develop curative treatments.

Following the completion of my pediatrics residency, I received training in molecular and cellular immunology in France (UNICET, Lyon) and the United States (DNAX Research Institute of Molecular and Cellular Biology, Palo Alto) under scientists, who critically influenced my scientific development. There, I was first exposed to the importance of integrating in depth laboratory research with clinical observations to develop a translational research approach to science. I then worked for fifteen years at the San Raffaele Scientific Institute in the Telethon Institute for Gene Therapy (HSR-TIGET), where I focused on dissecting the genetic and immunological basis of primary immunodeficiencies with autoimmune manifestations that might be treated by gene therapy.

Academic Appointments


Honors & Awards


  • Associate Professor in Pediatrics, Italian Ministry of University (01/2014)

Boards, Advisory Committees, Professional Organizations


  • Member, European Society of Immunodeficiency (ESID) (2014 - Present)
  • Member, Federal of Clinical Immunology Societies (FOCIS and CIS) (2014 - Present)
  • Member, Italian Society of Pediatric Oncology and Hematology (AIEOP) (2014 - Present)
  • Associate Editor, Frontiers in Primary Immunodeficiencies (2014 - Present)
  • Reviewer, J Medical Genetics (2014 - Present)
  • Reviewer, J Autoimmunity (2014 - Present)
  • Reviewer, J Endocrinology (2014 - Present)
  • Reviewer, European Journal of Immunology (2014 - Present)
  • Reviewer, Transplantation (2014 - Present)
  • Grants revisions, European Research Council (2014 - Present)
  • Grants revisions, INSERM (2014 - Present)
  • Grants revision, LSBR Foundation (2014 - Present)
  • Grants revision, Wellcome Trust (2014 - Present)
  • Grants revision, ANR-France (2014 - Present)
  • Teaching activities ad Hoc lessons, Vita-Salute University Medical School and Biotechnology, Milan (2014 - Present)
  • Teaching activities ad hoc lessons, Tor Vergata University, Rome (2014 - Present)
  • Teaching activities ad hoc lessons, Undergraduate Course at Stanford University, Stanford, Palo Alto, CA (2014 - Present)

Professional Education


  • Fellowship, University of Turin, Italy, General Pediatrics Immunology (1991)
  • MD, University of Turin, Italy, Medicine (1987)

Patents


  • Rosa Bacchetta. "United States Patent WO2007/131575 Tr1 dendritic cells, method to generate regulatory type 1 T (Tr1) cells and uses thereof", Rosa Bacchetta, Apr 1, 2007
  • Rosa Bacchetta. "United States Patent 6884410 Methods for modulating antigen-specific immune responses", Rosa Bacchetta, Apr 26, 2005
  • Rosa Bacchetta. "United States Patent 6277635 Use of Interleukin-10 produce a population of suppressor cells", Rosa Bacchetta, Aug 21, 2001

Current Research and Scholarly Interests


In the coming years, I plan to further determine the genetic and immunological basis of diseases with autoimmunity or immune dysregulation in children. I believe that much can still be learned from the in depth mechanistic studies of pediatric autoimmune diseases. Genomic analysis of the patients' samples has become possible which may provide a rapid indication of altered target molecules. I plan to implement robust functional studies to define the consequences of these genetic abnormalities and bridge them to the patient's clinical phenotype.

Understanding functional consequences of gene mutations in single case/family first and then validating the molecular and cellular defects in other patients with similar phenotypes, will anticipate and complement cellular and gene therapy strategies.

For further information please visit the Bacchetta Lab website:
http://med.stanford.edu/bacchettalab.html

2018-19 Courses


Stanford Advisees


Graduate and Fellowship Programs


All Publications


  • Epigenetic immune cell counting in human blood samples for immunodiagnostics SCIENCE TRANSLATIONAL MEDICINE Baron, U., Werner, J., Schildknecht, K., Schulze, J. J., Mulu, A., Liebert, U., Sack, U., Speckmann, C., Gossen, M., Wong, R. J., Stevenson, D. K., Babel, N., Schuermann, D., Baldinger, T., Bacchetta, R., Gruetzkau, A., Borte, S., Olek, S. 2018; 10 (452)

    Abstract

    Immune cell profiles provide valuable diagnostic information for hematologic and immunologic diseases. Although it is the most widely applied analytical approach, flow cytometry is limited to liquid blood. Moreover, either analysis must be performed with fresh samples or cell integrity needs to be guaranteed during storage and transport. We developed epigenetic real-time quantitative polymerase chain reaction (qPCR) assays for analysis of human leukocyte subpopulations. After method establishment, whole blood from 25 healthy donors and 97 HIV+ patients as well as dried spots from 250 healthy newborns and 24 newborns with primary immunodeficiencies were analyzed. Concordance between flow cytometric and epigenetic data for neutrophils and B, natural killer, CD3+ T, CD8+ T, CD4+ T, and FOXP3+ regulatory T cells was evaluated, demonstrating substantial equivalence between epigenetic qPCR analysis and flow cytometry. Epigenetic qPCR achieves both relative and absolute quantifications. Applied to dried blood spots, epigenetic immune cell quantification was shown to identify newborns suffering from various primary immunodeficiencies. Using epigenetic qPCR not only provides a precise means for immune cell counting in fresh-frozen blood but also extends applicability to dried blood spots. This method could expand the ability for screening immune defects and facilitates diagnostics of unobservantly collected samples, for example, in underdeveloped areas, where logistics are major barriers to screening.

    View details for DOI 10.1126/scitranslmed.aan3508

    View details for Web of Science ID 000440494900001

    View details for PubMedID 30068569

  • Reprogramming human T cell function and specificity with non-viral genome targeting NATURE Roth, T. L., Puig-Saus, C., Yu, R., Shifrut, E., Carnevale, J., Li, P., Hiatt, J., Saco, J., Krystofinski, P., Li, H., Tobin, V., Nguyen, D. N., Lee, M. R., Putnam, A. L., Ferris, A. L., Chen, J. W., Schickel, J., Pellerin, L., Carmody, D., Alkorta-Aranburu, G., del Gaudio, D., Matsumoto, H., Morell, M., Mao, Y., Cho, M., Quadros, R. M., Gurumurthy, C. B., Smith, B., Haugwitz, M., Hughes, S. H., Weissman, J. S., Schumann, K., Esensten, J. H., May, A. P., Ashworth, A., Kupfer, G. M., Greeley, S. W., Bacchetta, R., Meffre, E., Roncarolo, M., Romberg, N., Herold, K. C., Ribas, A., Leonetti, M. D., Marson, A. 2018; 559 (7714): 405-+

    Abstract

    Decades of work have aimed to genetically reprogram T cells for therapeutic purposes1,2 using recombinant viral vectors, which do not target transgenes to specific genomic sites3,4. The need for viral vectors has slowed down research and clinical use as their manufacturing and testing is lengthy and expensive. Genome editing brought the promise of specific and efficient insertion of large transgenes into target cells using homology-directed repair5,6. Here we developed a CRISPR-Cas9 genome-targeting system that does not require viral vectors, allowing rapid and efficient insertion of large DNA sequences (greater than one kilobase) at specific sites in the genomes of primary human T cells, while preserving cell viability and function. This permits individual or multiplexed modification of endogenous genes. First, we applied this strategy to correct a pathogenic IL2RA mutation in cells from patients with monogenic autoimmune disease, and demonstrate improved signalling function. Second, we replaced the endogenous T cell receptor (TCR) locus with a new TCR that redirected T cells to a cancer antigen. The resulting TCR-engineered T cells specifically recognized tumour antigens and mounted productive anti-tumour cell responses in vitro and in vivo. Together, these studies provide preclinical evidence that non-viral genome targeting can enable rapid and flexible experimental manipulation and therapeutic engineering of primary human immune cells.

    View details for DOI 10.1038/s41586-018-0326-5

    View details for Web of Science ID 000439059800057

    View details for PubMedID 29995861

  • Long-term follow-up of IPEX syndrome patients after different therapeutic strategies: An international multicenter retrospective study JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Barzaghi, F., Hernandez, L., Neven, B., Ricci, S., Kucuk, Z., Bleesing, J. J., Nademi, Z., Slatter, M., Ulloa, E., Shcherbina, A., Roppelt, A., Worth, A., Silva, J., Aiuti, A., Murguia-Favela, L., Speckmann, C., Carneiro-Sampaio, M., Fernandes, J., Baris, S., Ozen, A., Karakoc-Aydiner, E., Kiykim, A., Schulz, A., Steinmann, S., Notarangelo, L., Gambineri, E., Lionetti, P., Shearer, W., Forbes, L. R., Martinez, C., Moshous, D., Blanche, S., Fisher, A., Ruemmele, F. M., Tissandier, C., Ouachee-Chardin, M., Rieux-Laucat, F., Cavazzana, M., Qasim, W., Lucarelli, B., Albert, M. H., Kobayashi, I., Alonso, L., De Heredia, C., Kanegane, H., Lawitschka, A., Seo, J., Gonzalez-Vicent, M., Diaz, M., Goyal, R., Sauer, M. G., Yesilipek, A., Kim, M., Yilmaz-Demirdag, Y., Bhatia, M., Khlevner, J., Padilla, E., Martino, S., Montin, D., Neth, O., Molinos-Quintana, A., Valverde-Fernandez, J., Broides, A., Pinsk, V., Ballauf, A., Haerynck, F., Bordon, V., Dhooge, C., Garcia-Lloret, M., Bredius, R. G., Kawak, K., Haddad, E., Seidel, M., Duckers, G., Pai, S., Dvorak, C. C., Ehl, S., Locatelli, F., Goldman, F., Gennery, A., Cowan, M. J., Roncarolo, M., Bacchetta, R., PIDTC, IEWP, European Soc Blood Marrow 2018; 141 (3): 1036-+

    Abstract

    Immunodysregulation polyendocrinopathy enteropathy x-linked (IPEX) syndrome is a monogenic autoimmune disease caused by FOXP3 mutations. Because it is a rare disease, the natural history and response to treatments, including allogeneic hematopoietic stem cell transplantation (HSCT) and immunosuppression (IS), have not been thoroughly examined.This analysis sought to evaluate disease onset, progression, and long-term outcome of the 2 main treatments in long-term IPEX survivors.Clinical histories of 96 patients with a genetically proven IPEX syndrome were collected from 38 institutions worldwide and retrospectively analyzed. To investigate possible factors suitable to predict the outcome, an organ involvement (OI) scoring system was developed.We confirm neonatal onset with enteropathy, type 1 diabetes, and eczema. In addition, we found less common manifestations in delayed onset patients or during disease evolution. There is no correlation between the site of mutation and the disease course or outcome, and the same genotype can present with variable phenotypes. HSCT patients (n = 58) had a median follow-up of 2.7 years (range, 1 week-15 years). Patients receiving chronic IS (n = 34) had a median follow-up of 4 years (range, 2 months-25 years). The overall survival after HSCT was 73.2% (95% CI, 59.4-83.0) and after IS was 65.1% (95% CI, 62.8-95.8). The pretreatment OI score was the only significant predictor of overall survival after transplant (P = .035) but not under IS.Patients receiving chronic IS were hampered by disease recurrence or complications, impacting long-term disease-free survival. When performed in patients with a low OI score, HSCT resulted in disease resolution with better quality of life, independent of age, donor source, or conditioning regimen.

    View details for DOI 10.1016/j.jaci.2017.10.041

    View details for Web of Science ID 000426974800024

    View details for PubMedID 29241729

  • Forkhead-Box-P3 Gene Transfer in Human CD4(+) T Conventional Cells for the Generation of Stable and Efficient Regulatory T Cells, Suitable for Immune Modulatory Therapy FRONTIERS IN IMMUNOLOGY Passerini, L., Bacchetta, R. 2017; 8: 1282

    Abstract

    The development of novel approaches to control immune responses to self- and allogenic tissues/organs represents an ambitious goal for the management of autoimmune diseases and in transplantation. Regulatory T cells (Tregs) are recognized as key players in the maintenance of peripheral tolerance in physiological and pathological conditions, and Treg-based cell therapies to restore tolerance in T cell-mediated disorders have been designed. However, several hurdles, including insufficient number of Tregs, their stability, and their antigen specificity, have challenged Tregs clinical applicability. In the past decade, the ability to engineer T cells has proven a powerful tool to redirect specificity and function of different cell types for specific therapeutic purposes. By using lentivirus-mediated gene transfer of the thymic-derived Treg transcription factor forkhead-box-P3 (FOXP3) in conventional CD4+ T cells, we converted effector T cells into Treg-like cells, endowed with potent in vitro and in vivo suppressive activity. The resulting CD4FOXP3 T-cell population displays stable phenotype and suppressive function. We showed that this strategy restores Treg function in T lymphocytes from patients carrying mutations in FOXP3 [immune-dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX)], in whom CD4FOXP3 T cell could be used as therapeutics to control autoimmunity. Here, we will discuss the potential advantages of using CD4FOXP3 T cells for in vivo application in inflammatory diseases, where tissue inflammation may undermine the function of natural Tregs. These findings pave the way for the use of engineered Tregs not only in IPEX syndrome but also in autoimmune disorders of different origin and in the context of stem cell and organ transplantation.

    View details for DOI 10.3389/fimmu.2017.01282

    View details for Web of Science ID 000412734100001

    View details for PubMedID 29075264

    View details for PubMedCentralID PMC5643480

  • From IPEX syndrome to FOXP3 mutation: a lesson on immune dysregulation. Annals of the New York Academy of Sciences Bacchetta, R., Barzaghi, F., Roncarolo, M. 2016

    Abstract

    Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a rare disorder that increasingly has gained attention as a model of genetic autoimmunity. Numerous papers documenting the key clinical and molecular characteristics of IPEX have provided a detailed understanding of this devastating disease. IPEX is a primary immunodeficiency caused by mutations in the gene FOXP3, which encodes an essential transcription factor required for maintenance of thymus-derived regulatory T (tTreg ) cells. tTreg  cell dysfunction is the main pathogenic event leading to multiorgan autoimmunity in IPEX. In addition to the traditional clinical presentation (i.e., severe enteropathy, type 1 diabetes, and eczema), IPEX may encompass other variable and distinct clinical manifestations. As IPEX awareness and characterization have increased, so has identification of FOXP3 mutations, with at least 70 to date. Thus, while FOXP3 is the unifying gene, IPEX is a complex and diverse clinical continuum of disorders. Despite understanding IPEX pathogenesis, new treatment options have remained elusive, although early diagnosis led to hematopoietic stem cell transplantation (HSCT) and immunosuppression treatment and improved patient outcomes. Here, we review current knowledge about IPEX syndrome and highlight findings that could lead to novel targeted treatments.

    View details for DOI 10.1111/nyas.13011

    View details for PubMedID 26918796

  • Congenital diarrhoeal disorders: advances in this evolving web of inherited enteropathies NATURE REVIEWS GASTROENTEROLOGY & HEPATOLOGY Canani, R. B., Castaldo, G., Bacchetta, R., Martin, M. G., Goulet, O. 2015; 12 (5): 293-302

    Abstract

    Congenital diarrhoeal disorders (CDDs) represent an evolving web of rare chronic enteropathies, with a typical onset early in life. In many of these conditions, severe chronic diarrhoea represents the primary clinical manifestation, whereas in others diarrhoea is only a component of a more complex multi-organ or systemic disorder. Typically, within the first days of life, diarrhoea leads to a life-threatening condition highlighted by severe dehydration and serum electrolyte abnormalities. Thus, in the vast majority of cases appropriate therapy must be started immediately to prevent dehydration and long-term, sometimes severe, complications. The number of well-characterized disorders attributed to CDDs has gradually increased over the past several years, and many new genes have been identified and functionally related to CDDs, opening new diagnostic and therapeutic perspectives. Molecular analysis has changed the diagnostic scenario in CDDs, and led to a reduction in invasive and expensive procedures. Major advances have been made in terms of pathogenesis, enabling a better understanding not only of these rare conditions but also of more common diseases mechanisms.

    View details for DOI 10.1038/nrgastro.2015.44

    View details for Web of Science ID 000354070800007

    View details for PubMedID 25782092

  • Forkhead box P3: The Peacekeeper of the Immune System INTERNATIONAL REVIEWS OF IMMUNOLOGY Passerini, L., de Sio, F. R., Roncarolo, M. G., Bacchetta, R. 2014; 33 (2): 129-145

    Abstract

    Ten years ago Forkhead box P3 (FOXP3) was discovered as master gene driving CD4(+)CD25(+) T cell regulatory (Treg) function. Since then, several layers of complexity have emerged in the regulation of its expression and function, which is not only exerted in Treg cells. While the mechanisms leading to the highly selective expression of FOXP3 in thymus-derived Treg cells still remain to be elucidated, we review here the current knowledge on the role of FOXP3 in the development of Treg cells and the direct and indirect consequences of FOXP3 mutations on multiple arms of the immune response. Finally, we summarize the newly acquired knowledge on the epigenetic regulation of FOXP3, still largely undefined in human cells.

    View details for DOI 10.3109/08830185.2013.863303

    View details for Web of Science ID 000332870100005

    View details for PubMedID 24354325

  • Immunological Outcome in Haploidentical-HSC Transplanted Patients Treated with IL-10-Anergized Donor T Cells. Frontiers in immunology Bacchetta, R., Lucarelli, B., Sartirana, C., Gregori, S., Lupo Stanghellini, M. T., Miqueu, P., Tomiuk, S., Hernandez-Fuentes, M., Gianolini, M. E., Greco, R., Bernardi, M., Zappone, E., Rossini, S., Janssen, U., Ambrosi, A., Salomoni, M., Peccatori, J., Ciceri, F., Roncarolo, M. 2014; 5: 16-?

    Abstract

    T-cell therapy after hematopoietic stem cell transplantation (HSCT) has been used alone or in combination with immunosuppression to cure hematologic malignancies and to prevent disease recurrence. Here, we describe the outcome of patients with high-risk/advanced stage hematologic malignancies, who received T-cell depleted (TCD) haploidentical-HSCT (haplo-HSCT) combined with donor T lymphocytes pretreated with IL-10 (ALT-TEN trial). IL-10-anergized donor T cells (IL-10-DLI) contained T regulatory type 1 (Tr1) cells specific for the host alloantigens, limiting donor-vs.-host-reactivity, and memory T cells able to respond to pathogens. IL-10-DLI were infused in 12 patients with the goal of improving immune reconstitution after haplo-HSCT without increasing the risk of graft-versus-host-disease (GvHD). IL-10-DLI led to fast immune reconstitution in five patients. In four out of the five patients, total T-cell counts, TCR-Vβ repertoire and T-cell functions progressively normalized after IL-10-DLI. These four patients are alive, in complete disease remission and immunosuppression-free at 7.2 years (median follow-up) after haplo-HSCT. Transient GvHD was observed in the immune reconstituted (IR) patients, despite persistent host-specific hypo-responsiveness of donor T cells in vitro and enrichment of cells with Tr1-specific biomarkers in vivo. Gene-expression profiles of IR patients showed a common signature of tolerance. This study provides the first indication of the feasibility of Tr1 cell-based therapy and paves way for the use of these Tr1 cells as adjuvant treatment for malignancies and immune-mediated disorders.

    View details for DOI 10.3389/fimmu.2014.00016

    View details for PubMedID 24550909

    View details for PubMedCentralID PMC3907718

  • Gene/Cell Therapy Approaches for Immune Dysregulation Polyendocrinopathy Enteropathy X-Linked Syndrome CURRENT GENE THERAPY Passerini, L., de Sio, F. R., Porteus, M. H., Bacchetta, R. 2014; 14 (6): 422-428
  • CD4(+) T Cells from IPEX Patients Convert into Functional and Stable Regulatory T Cells by FOXP3 Gene Transfer SCIENCE TRANSLATIONAL MEDICINE Passerini, L., Mel, E. R., Sartirana, C., Fousteri, G., Bondanza, A., Naldini, L., Roncarolo, M. G., Bacchetta, R. 2013; 5 (215)

    Abstract

    In humans, mutations in the gene encoding for forkhead box P3 (FOXP3), a critically important transcription factor for CD4⁺CD25⁺ regulatory T (T(reg)) cell function, lead to a life-threatening systemic poly-autoimmune disease, known as immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome. Severe autoimmunity results from the inborn dysfunction and instability of FOXP3-mutated T(reg) cells. Hematopoietic stem cell transplantation is the only current curative option for affected patients. We show here that when CD4⁺ T cells are converted into T(reg) cells after lentivirus-mediated FOXP3 gene transfer, the resulting CD4(FOXP3) T cell population displays stable phenotype and suppressive function, especially when naïve T cells are converted. We further demonstrate that CD4(FOXP3) T cells are stable in inflammatory conditions not only in vitro but also in vivo in a model of xenogeneic graft-versus-host disease. We therefore applied this FOXP3 gene transfer strategy for the development of a T(reg) cell-based therapeutic approach to restore tolerance in IPEX syndrome. IPEX-derived CD4(FOXP3) T cells mirrored T(reg) cells from healthy donors in terms of cellular markers, anergic phenotype, cytokine production, and suppressive function. These findings pave the way for the treatment of IPEX patients by adoptive cell therapy with genetically engineered T(reg) cells and are seminal for future potential application in patients with autoimmune disorders of different origin.

    View details for DOI 10.1126/scitranslmed.3007320

    View details for Web of Science ID 000328685500005

    View details for PubMedID 24337481

  • Autoantibodies to Harmonin and Villin Are Diagnostic Markers in Children with IPEX Syndrome PLOS ONE Lampasona, V., Passerini, L., Barzaghi, F., Lombardoni, C., Bazzigaluppi, E., Brigatti, C., Bacchetta, R., Bosi, E. 2013; 8 (11)

    Abstract

    Autoantibodies to enterocyte antigens harmonin (75 kDa USH1C protein) and villin (actin-binding 95 kDa protein) are associated with the Immune dysregulation, Polyendocrinopathy, Enteropathy, X-linked (IPEX) syndrome. In this study we evaluated the diagnostic value of harmonin and villin autoantibodies in IPEX and IPEX-like syndromes. Harmonin and villin autoantibodies were measured by a novel Luminescent-Immuno-Precipitation-System (LIPS) quantitative assay, in patients with IPEX, IPEX-like syndrome, Primary Immunodeficiencies (PID) with enteropathy, all diagnosed by sequencing of the FOXP3 gene, and in type 1 diabetes (T1D), celiac disease and healthy blood donors as control groups. Harmonin and villin autoantibodies were detected in 12 (92%) and 6 (46%) of 13 IPEX patients, and in none of the IPEX-like, PID, T1D, celiac patients, respectively. All IPEX patients, including one case with late and atypical clinical presentation, had either harmonin and/or villin autoantibodies and tested positive for enterocyte antibodies by indirect immunofluorescence. When measured in IPEX patients in remission after immunosuppressive therapy or hematopoietic stem cell transplantation, harmonin and villin autoantibodies became undetectable or persisted at low titers in all cases but one in whom harmonin autoantibodies remained constantly high. In one patient, a peak of harmonin antibodies paralleled a relapse phase of enteropathy. Our study demonstrates that harmonin and villin autoantibodies, measured by LIPS, are sensitive and specific markers of IPEX, differentiate IPEX, including atypical cases, from other early childhood disorders associated with enteropathy, and are useful for screening and clinical monitoring of affected children.

    View details for DOI 10.1371/journal.pone.0078664

    View details for Web of Science ID 000327216200039

    View details for PubMedID 24250806

  • Coexpression of CD49b and LAG-3 identifies human and mouse T regulatory type 1 cells NATURE MEDICINE Gagliani, N., Magnani, C. F., Huber, S., Gianolini, M. E., Pala, M., Licona-Limon, P., Guo, B., Herbert, D. R., Bulfone, A., Trentini, F., Di Serio, C., Bacchetta, R., Andreani, M., Brockmann, L., Gregori, S., Flavell, R. A., Roncarolo, M. 2013; 19 (6): 739-?

    Abstract

    CD4(+) type 1 T regulatory (Tr1) cells are induced in the periphery and have a pivotal role in promoting and maintaining tolerance. The absence of surface markers that uniquely identify Tr1 cells has limited their study and clinical applications. By gene expression profiling of human Tr1 cell clones, we identified the surface markers CD49b and lymphocyte activation gene 3 (LAG-3) as being stably and selectively coexpressed on mouse and human Tr1 cells. We showed the specificity of these markers in mouse models of intestinal inflammation and helminth infection and in the peripheral blood of healthy volunteers. The coexpression of CD49b and LAG-3 enables the isolation of highly suppressive human Tr1 cells from in vitro anergized cultures and allows the tracking of Tr1 cells in the peripheral blood of subjects who developed tolerance after allogeneic hematopoietic stem cell transplantation. The use of these markers makes it feasible to track Tr1 cells in vivo and purify Tr1 cells for cell therapy to induce or restore tolerance in subjects with immune-mediated diseases.

    View details for DOI 10.1038/nm.3179

    View details for Web of Science ID 000319981600023

    View details for PubMedID 23624599

  • Human IL2RA null mutation mediates immunodeficiency with lymphoproliferation and autoimmunity CLINICAL IMMUNOLOGY Goudy, K., Aydin, D., Barzaghi, F., Gambineri, E., Vignoli, M., Mannurita, S. C., Doglioni, C., Ponzoni, M., Cicalese, M. P., Assanelli, A., Tommasini, A., Brigida, I., Dellepiane, R. M., Martino, S., Olek, S., Aiuti, A., Ciceri, F., Roncarolo, M. G., Bacchetta, R. 2013; 146 (3): 248-261

    Abstract

    Cell-surface CD25 expression is critical for maintaining immune function and homeostasis. As in few reported cases, CD25 deficiency manifests with severe autoimmune enteritis and viral infections. To dissect the underlying immunological mechanisms driving these symptoms, we analyzed the regulatory and effector T cell functions in a CD25 deficient patient harboring a novel IL2RA mutation. Pronounced lymphoproliferation, mainly of the CD8(+) T cells, was detected together with an increase in T cell activation markers and elevated serum cytokines. However, Ag-specific responses were impaired in vivo and in vitro. Activated CD8(+)STAT5(+) T cells with lytic potential infiltrated the skin, even though FOXP3(+) Tregs were present and maintained a higher capacity to respond to IL-2 compared to other T-cell subsets. Thus, the complex pathogenesis of CD25 deficiency provides invaluable insight into the role of IL2/IL-2RA-dependent regulation in autoimmunity and inflammatory diseases.

    View details for DOI 10.1016/j.clim.2013.01.004

    View details for Web of Science ID 000316241700010

    View details for PubMedID 23416241

  • Accumulation of peripheral autoreactive B cells in the absence of functional human regulatory T cells BLOOD Kinnunen, T., Chamberlain, N., Morbach, H., Choi, J., Kim, S., Craft, J., Mayer, L., Cancrini, C., Passerini, L., Bacchetta, R., Ochs, H. D., Torgerson, T. R., Meffre, E. 2013; 121 (9): 1595-1603

    Abstract

    Regulatory T cells (Tregs) play an essential role in preventing autoimmunity. Mutations in the forkhead box protein 3 (FOXP3) gene, which encodes a transcription factor critical for Treg function, result in a severe autoimmune disorder and the production of various autoantibodies in mice and in IPEX (immune dysregulation, polyendocrinopathy, enteropathy, X-linked) patients. However, it is unknown whether Tregs normally suppress autoreactive B cells. To investigate a role for Tregs in maintaining human B-cell tolerance, we tested the reactivity of recombinant antibodies isolated from single B cells isolated from IPEX patients. Characteristics and reactivity of antibodies expressed by new emigrant/transitional B cells from IPEX patients were similar to those from healthy donors, demonstrating that defective Treg function does not impact central B-cell tolerance. In contrast, mature naive B cells from IPEX patients often expressed autoreactive antibodies, suggesting an important role for Tregs in maintaining peripheral B-cell tolerance. T cells displayed an activated phenotype in IPEX patients, including their Treg-like cells, and showed up-regulation of CD40L, PD-1, and inducibl T-cell costimulator (ICOS), which may favor the accumulation of autoreactive mature naive B cells in these patients. Hence, our data demonstrate an essential role for Tregs in the establishment and the maintenance of peripheral B-cell tolerance in humans.

    View details for DOI 10.1182/blood-2012-09-457465

    View details for Web of Science ID 000321750300021

    View details for PubMedID 23223361

  • APVO210: A Bispecific Anti-CD86-IL-10 Fusion Protein (ADAPTIR (TM)) to Induce Antigen-Specific T Regulatory Type 1 Cells FRONTIERS IN IMMUNOLOGY Pellerin, L., Chen, P., Gregori, S., Hernandez-Hoyos, G., Bacchetta, R., Roncarolo, M. 2018; 9
  • CRISPR-Based Therapy for IPEX Syndrome as a Model of Genetic Autoimmunity Goodwin, M., Lee, E., Lakshmanan, U., Shipp, S., Roncarolo, M., Porteus, M., Bacchetta, R. CELL PRESS. 2018: 95–96
  • Minimum Information about T Regulatory Cells: A Step toward Reproducibility and Standardization FRONTIERS IN IMMUNOLOGY Fuchs, A., Gliwinski, M., Grageda, N., Spiering, R., Abbas, A. K., Appel, S., Bacchetta, R., Battaglia, M., Berglund, D., Blazar, B., Bluestone, J. A., Bornhaeuser, M., ten Brinke, A., Brusko, T. M., Cools, N., Cuturi, M., Geissler, E., Giannoukakis, N., Golab, K., Hafler, D. A., van Ham, S., Hester, J., Hippen, K., Di Ianni, M., Ilic, N., Isaacs, J., Issa, F., Iwaszkiewicz-Grzes, D., Jaeckel, E., Joosten, I., Klatzmann, D., Koenen, H., van Kooten, C., Korsgren, O., Kretschmer, K., Levings, M., Marek-Trzonkowska, N., Martinez-Llordella, M., Miljkovic, D., Mills, K. G., Miranda, J. P., Piccirillo, C. A., Putnam, A. L., Ritter, T., Roncarolo, M., Sakaguchi, S., Sanchez-Ramon, S., Sawitzki, B., Sofronic-Milosavljevic, L., Sykes, M., Tang, Q., Vives-Pi, M., Waldmann, H., Witkowski, P., Wood, K. J., Gregori, S., Hilkens, C. U., Lombardi, G., Lord, P., Martinez-Caceres, E. M., Trzonkowski, P. 2018; 8: 1844

    Abstract

    Cellular therapies with CD4+ T regulatory cells (Tregs) hold promise of efficacious treatment for the variety of autoimmune and allergic diseases as well as posttransplant complications. Nevertheless, current manufacturing of Tregs as a cellular medicinal product varies between different laboratories, which in turn hampers precise comparisons of the results between the studies performed. While the number of clinical trials testing Tregs is already substantial, it seems to be crucial to provide some standardized characteristics of Treg products in order to minimize the problem. We have previously developed reporting guidelines called minimum information about tolerogenic antigen-presenting cells, which allows the comparison between different preparations of tolerance-inducing antigen-presenting cells. Having this experience, here we describe another minimum information about Tregs (MITREG). It is important to note that MITREG does not dictate how investigators should generate or characterize Tregs, but it does require investigators to report their Treg data in a consistent and transparent manner. We hope this will, therefore, be a useful tool facilitating standardized reporting on the manufacturing of Tregs, either for research purposes or for clinical application. This way MITREG might also be an important step toward more standardized and reproducible testing of the Tregs preparations in clinical applications.

    View details for DOI 10.3389/fimmu.2017.01844

    View details for Web of Science ID 000419897500001

    View details for PubMedID 29379498

    View details for PubMedCentralID PMC5775516

  • Peanut-specific type 1 regulatory T cells induced in vitro from allergic subjects are functionally impaired JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Pellerin, L., Jenks, J., Chinthrajah, S., Dominguez, T., Block, W., Zhou, X., Noshirvan, A., Gregori, S., Roncarolo, M., Nadeau, K., Bacchetta, R. 2018; 141 (1): 202-+

    Abstract

    Peanut allergy (PA) is a life-threatening condition that lacks regulator-approved treatment. Regulatory T type 1 (TR1) cells are potent suppressors of immune responses and can be induced in vivo upon repeated antigen exposure or in vitro by using tolerogenic dendritic cells. Whether oral immunotherapy (OIT) leads to antigen-specific TR1 cell induction has not been established.We sought to determine whether peanut-specific TR1 cells can be generated in vitro from peripheral blood of patients with PA at baseline or during OIT and whether they are functional compared with peanut-specific TR1 cells induced from healthy control (HC) subjects.Tolerogenic dendritic cells were differentiated in the presence of IL-10 from PBMCs of patients with PA and HC subjects pulsed with the main peanut allergens of Arachis hypogaea, Ara h 1 and 2, and used as antigen-presenting cells for autologous CD4+ T cells (CD4+ T cells coincubated with tolerogenic dendritic cells pulsed with the main peanut allergens [pea-T10 cells]). Pea-T10 cells were characterized by the presence of CD49b+ lymphocyte-activation gene 3 (LAG3)+ TR1 cells, antigen-specific proliferative responses, and cytokine production.CD49b+LAG3+ TR1 cells were induced in pea-T10 cells at comparable percentages from HC subjects and patients with PA. Despite their antigen specificity, pea-T10 cells of patients with PA with or without OIT, as compared with those of HC subjects, were not anergic and had high TH2 cytokine production upon peanut-specific restimulation.Peanut-specific TR1 cells can be induced from HC subjects and patients with PA, but those from patients with PA are functionally defective independent of OIT. The unfavorable TR1/TH2 ratio is discussed as a possible cause of PA TR1 cell impairment.

    View details for DOI 10.1016/j.jaci.2017.05.045

    View details for Web of Science ID 000419312200026

    View details for PubMedID 28689791

  • Identity and Diversity of Human Peripheral Th and T Regulatory Cells Defined by Single-Cell Mass Cytometry JOURNAL OF IMMUNOLOGY Kunicki, M. A., Hernandez, L., Davis, K. L., Bacchetta, R., Roncarolo, M. 2018; 200 (1): 336–46

    Abstract

    Human CD3+CD4+ Th cells, FOXP3+ T regulatory (Treg) cells, and T regulatory type 1 (Tr1) cells are essential for ensuring peripheral immune response and tolerance, but the diversity of Th, Treg, and Tr1 cell subsets has not been fully characterized. Independent functional characterization of human Th1, Th2, Th17, T follicular helper (Tfh), Treg, and Tr1 cells has helped to define unique surface molecules, transcription factors, and signaling profiles for each subset. However, the adequacy of these markers to recapitulate the whole CD3+CD4+ T cell compartment remains questionable. In this study, we examined CD3+CD4+ T cell populations by single-cell mass cytometry. We characterize the CD3+CD4+ Th, Treg, and Tr1 cell populations simultaneously across 23 memory T cell-associated surface and intracellular molecules. High-dimensional analysis identified several new subsets, in addition to the already defined CD3+CD4+ Th, Treg, and Tr1 cell populations, for a total of 11 Th cell, 4 Treg, and 1 Tr1 cell subsets. Some of these subsets share markers previously thought to be selective for Treg, Th1, Th2, Th17, and Tfh cells, including CD194 (CCR4)+FOXP3+ Treg and CD183 (CXCR3)+T-bet+ Th17 cell subsets. Unsupervised clustering displayed a phenotypic organization of CD3+CD4+ T cells that confirmed their diversity but showed interrelation between the different subsets, including similarity between Th1-Th2-Tfh cell populations and Th17 cells, as well as similarity of Th2 cells with Treg cells. In conclusion, the use of single-cell mass cytometry provides a systems-level characterization of CD3+CD4+ T cells in healthy human blood, which represents an important baseline reference to investigate abnormalities of different subsets in immune-mediated pathologies.

    View details for DOI 10.4049/jimmunol.1701025

    View details for Web of Science ID 000418271200032

    View details for PubMedID 29180490

  • Hurdles in therapy with regulatory T cells. Science translational medicine Trzonkowski, P., Bacchetta, R., Battaglia, M., Berglund, D., Bohnenkamp, H. R., Ten brinke, A., Bushell, A., Cools, N., Geissler, E. K., Gregori, S., Marieke van Ham, S., Hilkens, C., Hutchinson, J. A., Lombardi, G., Madrigal, J. A., Marek-Trzonkowska, N., Martinez-Caceres, E. M., Roncarolo, M. G., Sanchez-Ramon, S., Saudemont, A., Sawitzki, B. 2015; 7 (304): 304ps18-?

    Abstract

    Improper activation of the immune system contributes to a variety of clinical conditions, including autoimmune and allergic diseases as well as solid organ and bone marrow transplantation. One approach to counteract this activation is through adoptive therapy with regulatory T cells (Tregs). Efforts to manufacture these cells have led to good maunfacturing practice-compliant protocols, and Treg products are entering early clinical trials. Here, we report the stance of the European Union Cooperation in Science and Technology Action BM1305, "Action to Focus and Accelerate Cell-based Tolerance-inducing Therapies-A FACTT," which identifies hurdles hindering Treg clinical applications in Europe and provides possible solutions.

    View details for DOI 10.1126/scitranslmed.aaa7721

    View details for PubMedID 26355029

  • Hurdles in therapy with regulatory T cells. Science translational medicine Trzonkowski, P., Bacchetta, R., Battaglia, M., Berglund, D., Bohnenkamp, H. R., Ten brinke, A., Bushell, A., Cools, N., Geissler, E. K., Gregori, S., Marieke van Ham, S., Hilkens, C., Hutchinson, J. A., Lombardi, G., Madrigal, J. A., Marek-Trzonkowska, N., Martinez-Caceres, E. M., Roncarolo, M. G., Sanchez-Ramon, S., Saudemont, A., Sawitzki, B. 2015; 7 (304): 304ps18-?

    View details for DOI 10.1126/scitranslmed.aaa7721

    View details for PubMedID 26355029

  • Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nature biotechnology Hendel, A., Bak, R. O., Clark, J. T., Kennedy, A. B., Ryan, D. E., Roy, S., Steinfeld, I., Lunstad, B. D., Kaiser, R. J., Wilkens, A. B., Bacchetta, R., Tsalenko, A., Dellinger, D., Bruhn, L., Porteus, M. H. 2015; 33 (9): 985-989

    Abstract

    CRISPR-Cas-mediated genome editing relies on guide RNAs that direct site-specific DNA cleavage facilitated by the Cas endonuclease. Here we report that chemical alterations to synthesized single guide RNAs (sgRNAs) enhance genome editing efficiency in human primary T cells and CD34(+) hematopoietic stem and progenitor cells. Co-delivering chemically modified sgRNAs with Cas9 mRNA or protein is an efficient RNA- or ribonucleoprotein (RNP)-based delivery method for the CRISPR-Cas system, without the toxicity associated with DNA delivery. This approach is a simple and effective way to streamline the development of genome editing with the potential to accelerate a wide array of biotechnological and therapeutic applications of the CRISPR-Cas technology.

    View details for DOI 10.1038/nbt.3290

    View details for PubMedID 26121415

  • Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nature biotechnology Hendel, A., Bak, R. O., Clark, J. T., Kennedy, A. B., Ryan, D. E., Roy, S., Steinfeld, I., Lunstad, B. D., Kaiser, R. J., Wilkens, A. B., Bacchetta, R., Tsalenko, A., Dellinger, D., Bruhn, L., Porteus, M. H. 2015; 33 (9): 985-989

    View details for DOI 10.1038/nbt.3290

    View details for PubMedID 26121415

  • Clinical Features and Follow-Up in Patients with 22q11.2 Deletion Syndrome JOURNAL OF PEDIATRICS Cancrini, C., Puliafito, P., Digilio, M. C., Soresina, A., Martino, S., Rondelli, R., Consolini, R., Ruga, E. M., Cardinale, F., Finocchi, A., Romiti, M. L., Martire, B., Bacchetta, R., Albano, V., Carotti, A., Specchia, F., Montin, D., Cirillo, E., Cocchi, G., Trizzino, A., Bossi, G., Milanesi, O., Azzari, C., Corsello, G., Pignata, C., Aiuti, A., Pietrogrande, M. C., Marino, B., Ugazio, A. G., Plebani, A., Rossi, P. 2014; 164 (6): 1475-?

    Abstract

    To investigate the clinical manifestations at diagnosis and during follow-up in patients with 22q11.2 deletion syndrome to better define the natural history of the disease.A retrospective and prospective multicenter study was conducted with 228 patients in the context of the Italian Network for Primary Immunodeficiencies. Clinical diagnosis was confirmed by cytogenetic or molecular analysis.The cohort consisted of 112 males and 116 females; median age at diagnosis was 4 months (range 0 to 36 years 10 months). The diagnosis was made before 2 years of age in 71% of patients, predominantly related to the presence of heart anomalies and neonatal hypocalcemia. In patients diagnosed after 2 years of age, clinical features such as speech and language impairment, developmental delay, minor cardiac defects, recurrent infections, and facial features were the main elements leading to diagnosis. During follow-up (available for 172 patients), the frequency of autoimmune manifestations (P = .015) and speech disorders (P = .002) increased. After a median follow-up of 43 months, the survival probability was 0.92 at 15 years from diagnosis.Our data show a delay in the diagnosis of 22q11.2 deletion syndrome with noncardiac symptoms. This study provides guidelines for pediatricians and specialists for early identification of cases that can be confirmed by genetic testing, which would permit the provision of appropriate clinical management.

    View details for DOI 10.1016/j.jpeds.2014.01.056

    View details for Web of Science ID 000336503200046

    View details for PubMedID 24657119

  • Identification of STAT5A and STAT5B Target Genes in Human T Cells. PloS one Kanai, T., Seki, S., Jenks, J. A., Kohli, A., Kawli, T., Martin, D. P., Snyder, M., Bacchetta, R., Nadeau, K. C. 2014; 9 (1)

    View details for DOI 10.1371/journal.pone.0086790

    View details for PubMedID 24497979

  • Identification of STAT5A and STAT5B target genes in human T cells. PloS one Kanai, T., Seki, S., Jenks, J. A., Kohli, A., Kawli, T., Martin, D. P., Snyder, M., Bacchetta, R., Nadeau, K. C. 2014; 9 (1)

    Abstract

    Signal transducer and activator of transcription (STAT) comprises a family of universal transcription factors that help cells sense and respond to environmental signals. STAT5 refers to two highly related proteins, STAT5A and STAT5B, with critical function: their complete deficiency is lethal in mice; in humans, STAT5B deficiency alone leads to endocrine and immunological problems, while STAT5A deficiency has not been reported. STAT5A and STAT5B show peptide sequence similarities greater than 90%, but subtle structural differences suggest possible non-redundant roles in gene regulation. However, these roles remain unclear in humans. We applied chromatin immunoprecipitation followed by DNA sequencing using human CD4(+) T cells to detect candidate genes regulated by STAT5A and/or STAT5B, and quantitative-PCR in STAT5A or STAT5B knock-down (KD) human CD4(+) T cells to validate the findings. Our data show STAT5A and STAT5B play redundant roles in cell proliferation and apoptosis via SGK1 interaction. Interestingly, we found a novel, unique role for STAT5A in binding to genes involved in neural development and function (NDRG1, DNAJC6, and SSH2), while STAT5B appears to play a distinct role in T cell development and function via DOCK8, SNX9, FOXP3 and IL2RA binding. Our results also suggest that one or more co-activators for STAT5A and/or STAT5B may play important roles in establishing different binding abilities and gene regulation behaviors. The new identification of these genes regulated by STAT5A and/or STAT5B has major implications for understanding the pathophysiology of cancer progression, neural disorders, and immune abnormalities.

    View details for DOI 10.1371/journal.pone.0086790

    View details for PubMedID 24497979

    View details for PubMedCentralID PMC3907443

  • Tr1 cells and the counter-regulation of immunity: natural mechanisms and therapeutic applications. Current topics in microbiology and immunology Roncarolo, M. G., Gregori, S., Bacchetta, R., Battaglia, M. 2014; 380: 39-68

    Abstract

    T regulatory Type 1 (Tr1) cells are adaptive T regulatory cells characterized by the ability to secrete high levels of IL-10 and minimal amounts of IL-4 and IL-17. Recently, CD49b and LAG-3 have been identified as Tr1-cell-specific biomarkers in mice and humans. Tr1 cells suppress T-cell- and antigen-presenting cell- (APC) responses primarily via the secretion of IL-10 and TGF-β. In addition, Tr1 cells release granzyme B and perforin and kill myeloid cells. Tr1 cells inhibit T cell responses also via cell-contact dependent mechanisms mediated by CTLA-4 or PD-1, and by disrupting the metabolic state of T effector cells via the production of the ectoenzymes CD39 and CD73. Tr1 cells were first described in peripheral blood of patients who developed tolerance after HLA-mismatched fetal liver hematopoietic stem cell transplant. Since their discovery, Tr1 cells have been proven to be important in maintaining immunological homeostasis and preventing T-cell-mediated diseases. Furthermore, the possibility to generate and expand Tr1 cells in vitro has led to their utilization as cellular therapy in humans. In this chapter we summarize the unique and distinctive biological properties of Tr1 cells, the well-known and newly discovered Tr1-cell biomarkers, and the different methods to induce Tr1 cells in vitro and in vivo. We also address the role of Tr1 cells in infectious diseases, autoimmunity, and transplant rejection in different pre-clinical disease models and in patients. Finally, we highlight the pathological settings in which Tr1 cells can be beneficial to prevent or to cure the disease.

    View details for DOI 10.1007/978-3-662-43492-5_3

    View details for PubMedID 25004813

  • IL-21 signalling via STAT3 primes human naive B cells to respond to IL-2 to enhance their differentiation into plasmablasts BLOOD Berglund, L. J., Avery, D. T., Ma, C. S., Moens, L., Deenick, E. K., Bustamante, J., Boisson-Dupuis, S., Wong, M., Adelstein, S., Arkwright, P. D., Bacchetta, R., Bezrodnik, L., Dadi, H., Roifman, C. M., Fulcher, D. A., Ziegler, J. B., Smart, J. M., Kobayashi, M., Picard, C., Durandy, A., Cook, M. C., Casanova, J., Uzel, G., Tangye, S. G. 2013; 122 (24): 3940-3950

    Abstract

    B-cell responses are guided by the integration of signals through the B-cell receptor (BCR), CD40, and cytokine receptors. The common γ chain (γc)-binding cytokine interleukin (IL)-21 drives humoral immune responses via STAT3-dependent induction of transcription factors required for plasma cell generation. We investigated additional mechanisms by which IL-21/STAT3 signaling modulates human B-cell responses by studying patients with STAT3 mutations. IL-21 strongly induced CD25 (IL-2Rα) in normal, but not STAT3-deficient, CD40L-stimulated naïve B cells. Chromatin immunoprecipitation confirmed IL2RA as a direct target of STAT3. IL-21-induced CD25 expression was also impaired on B cells from patients with IL2RG or IL21R mutations, confirming a requirement for intact IL-21R signaling in this process. IL-2 increased plasmablast generation and immunoglobulin secretion from normal, but not CD25-deficient, naïve B cells stimulated with CD40L/IL-21. IL-2 and IL-21 were produced by T follicular helper cells, and neutralizing both cytokines abolished the B-cell helper capacity of these cells. Our results demonstrate that IL-21, via STAT3, sensitizes B cells to the stimulatory effects of IL-2. Thus, IL-2 may play an adjunctive role in IL-21-induced B-cell differentiation. Lack of this secondary effect of IL-21 may amplify the humoral immunodeficiency in patients with mutations in STAT3, IL2RG, or IL21R due to impaired responsiveness to IL-21.

    View details for DOI 10.1182/blood-2013-06-506865

    View details for Web of Science ID 000329737600018

    View details for PubMedID 24159173

  • Combined DOCK8 and CLEC7A mutations causing immunodeficiency in 3 brothers with diarrhea, eczema, and infections JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY Dinwiddie, D. L., Kingsmore, S. F., Caracciolo, S., Rossi, G., Moratto, D., Mazza, C., Sabelli, C., Bacchetta, R., Passerini, L., Magri, C., Bell, C. J., Miller, N. A., Hateley, S. L., Saunders, C. J., Zhang, L., Schroth, G. P., Barlati, S., Badolato, R. 2013; 131 (2): 594-597

    View details for DOI 10.1016/j.jaci.2012.10.062

    View details for Web of Science ID 000314661500045

    View details for PubMedID 23374272

  • Immunodeficiency with autoimmunity: beyond the paradox. Frontiers in immunology Bacchetta, R., Notarangelo, L. D. 2013; 4: 77-?

    View details for DOI 10.3389/fimmu.2013.00077

    View details for PubMedID 23630524