1
|
Paroni M, Leccese G, Ranzani V, Moschetti G, Chiara M, Perillo F, Ferri S, Clemente F, Noviello D, Conforti FS, Ferrero S, Karnani B, Bosotti R, Vasco C, Curti S, Crosti MC, Gruarin P, Rossetti G, Conte MP, Vecchi M, Pagani M, Landini P, Facciotti F, Abrignani S, Caprioli F, Geginat J. An Intestinal Th17 Subset is Associated with Inflammation in Crohn's Disease and Activated by Adherent-invasive Escherichia coli. J Crohns Colitis 2023; 17:1988-2001. [PMID: 37462681 PMCID: PMC10798865 DOI: 10.1093/ecco-jcc/jjad119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/21/2024]
Abstract
IFNγ-producing ex-Th17 cells ['Th1/17'] were shown to play a key pathogenic role in experimental colitis and are abundant in the intestine. Here, we identified and characterised a novel, potentially colitogenic subset of Th17 cells in the intestine of patients with Crohn's disease [CD]. Human Th17 cells expressing CCR5 ['pTh17'] co-expressed T-bet and RORC/γt and produced very high levels of IL-17, together with IFN-γ. They had a gene signature of Th17 effector cells and were distinct from established Th1/17 cells. pTh17 cells, but not Th1/17 cells, were associated with intestinal inflammation in CD, and decreased upon successful anti-TNF therapy with infliximab. Conventional CCR5[-]Th17 cells differentiated to pTh17 cells with IL-23 in vitro. Moreover, anti-IL-23 therapy with risankizumab strongly reduced pTh17 cells in the intestine. Importantly, intestinal pTh17 cells were selectively activated by adherent-invasive Escherichia coli [AIEC], but not by a commensal/probiotic E. coli strain. AIEC induced high levels of IL-23 and RANTES from dendritic cells [DC]. Intestinal CCR5+Th1/17 cells responded instead to cytomegalovirus and were reduced in ulcerative colitis [UC], suggesting an unexpected protective role. In conclusion, we identified an IL-23-inducible subset of human intestinal Th17 cells. pTh17 cells produced high levels of pro-inflammatory cytokines, were selectively associated with intestinal inflammation in CD, and responded to CD-associated AIEC, suggesting a key colitogenic role.
Collapse
Affiliation(s)
- Moira Paroni
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Gabriella Leccese
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Valeria Ranzani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Giorgia Moschetti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Matteo Chiara
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Federica Perillo
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
| | - Sara Ferri
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Francesca Clemente
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Daniele Noviello
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Francesco Simone Conforti
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Ferrero
- Pathology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Biomedical, Surgical, and Dental Sciences, Università degli Studi di Milano, Milan, Italy
| | - Bhavna Karnani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Roberto Bosotti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Chiara Vasco
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Serena Curti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Maria Cristina Crosti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Paola Gruarin
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
| | - Grazisa Rossetti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Molecular Oncology and Immunology, FIRC Institute of Molecular Oncology [IFOM], Milan, Italy
| | - Maria Pia Conte
- Department of Public Health and Infectious Diseases, ‘Sapienza’ University of Rome, Rome, Italy
| | - Maurizio Vecchi
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Massimiliano Pagani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Molecular Oncology and Immunology, FIRC Institute of Molecular Oncology [IFOM], Milan, Italy
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Milan, Italy
| | - Paolo Landini
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Federica Facciotti
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- Department of Experimental Oncology, European Institute of Oncology, Milan, Italy
- Department of Biotechnology and Bioscience, University of Milano-Bicocca, Milan, Italy
| | - Sergio Abrignani
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- DISCCO, Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| | - Flavio Caprioli
- Gastroenterology and Endoscopy Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Jens Geginat
- INGM-National Institute of Molecular Genetics ‘Romeo ed Enrica Invernizzi’, Milan, Italy
- DISCCO, Department of Clinical Science and Community Health, University of Milan, Milan, Italy
| |
Collapse
|
2
|
Raccosta L, Marinozzi M, Costantini S, Maggioni D, Ferreira LM, Corna G, Zordan P, Sorice A, Farinello D, Bianchessi S, Riba M, Lazarevic D, Provero P, Mack M, Bondanza A, Nalvarte I, Gustafsson JA, Ranzani V, De Sanctis F, Ugel S, Baron S, Lobaccaro JMA, Pontini L, Pacciarini M, Traversari C, Pagani M, Bronte V, Sitia G, Antonson P, Brendolan A, Budillon A, Russo V. Harnessing the reverse cholesterol transport pathway to favor differentiation of monocyte-derived APCs and antitumor responses. Cell Death Dis 2023; 14:129. [PMID: 36792589 PMCID: PMC9932151 DOI: 10.1038/s41419-023-05620-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 02/17/2023]
Abstract
Lipid and cholesterol metabolism play a crucial role in tumor cell behavior and in shaping the tumor microenvironment. In particular, enzymatic and non-enzymatic cholesterol metabolism, and derived metabolites control dendritic cell (DC) functions, ultimately impacting tumor antigen presentation within and outside the tumor mass, dampening tumor immunity and immunotherapeutic attempts. The mechanisms accounting for such events remain largely to be defined. Here we perturbed (oxy)sterol metabolism genetically and pharmacologically and analyzed the tumor lipidome landscape in relation to the tumor-infiltrating immune cells. We report that perturbing the lipidome of tumor microenvironment by the expression of sulfotransferase 2B1b crucial in cholesterol and oxysterol sulfate synthesis, favored intratumoral representation of monocyte-derived antigen-presenting cells, including monocyte-DCs. We also found that treating mice with a newly developed antagonist of the oxysterol receptors Liver X Receptors (LXRs), promoted intratumoral monocyte-DC differentiation, delayed tumor growth and synergized with anti-PD-1 immunotherapy and adoptive T cell therapy. Of note, looking at LXR/cholesterol gene signature in melanoma patients treated with anti-PD-1-based immunotherapy predicted diverse clinical outcomes. Indeed, patients whose tumors were poorly infiltrated by monocytes/macrophages expressing LXR target genes showed improved survival over the course of therapy. Thus, our data support a role for (oxy)sterol metabolism in shaping monocyte-to-DC differentiation, and in tumor antigen presentation critical for responsiveness to immunotherapy. The identification of a new LXR antagonist opens new treatment avenues for cancer patients.
Collapse
Affiliation(s)
- Laura Raccosta
- grid.18887.3e0000000417581884Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Maura Marinozzi
- grid.9027.c0000 0004 1757 3630Big Ideas in Organic Synthesis (BIOS) Laboratory, Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy
| | - Susan Costantini
- grid.508451.d0000 0004 1760 8805Experimental Pharmacology Unit, Laboratori di Mercogliano, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Daniela Maggioni
- grid.18887.3e0000000417581884Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Lorena Maria Ferreira
- grid.18887.3e0000000417581884Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Gianfranca Corna
- grid.18887.3e0000000417581884Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Paola Zordan
- grid.18887.3e0000000417581884Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Angela Sorice
- grid.508451.d0000 0004 1760 8805Experimental Pharmacology Unit, Laboratori di Mercogliano, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Diego Farinello
- grid.18887.3e0000000417581884Lymphoid Organ Development Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Silvia Bianchessi
- grid.18887.3e0000000417581884Lymphoid Organ Development Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Michela Riba
- grid.18887.3e0000000417581884Center for Translational Genomics and Bioinformatics IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Dejan Lazarevic
- grid.18887.3e0000000417581884Center for Translational Genomics and Bioinformatics IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Paolo Provero
- grid.18887.3e0000000417581884Center for Translational Genomics and Bioinformatics IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Matthias Mack
- grid.7727.50000 0001 2190 5763Division of Internal Medicine II-Nephrology, University of Regensburg, Regensburg, 93042 Germany
| | - Attilio Bondanza
- grid.18887.3e0000000417581884Innovative Immunotherapy Unit, IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Ivan Nalvarte
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, S-14183 Sweden
| | - J-A Gustafsson
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, S-14183 Sweden ,grid.266436.30000 0004 1569 9707Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77004 USA
| | - Valeria Ranzani
- grid.428717.f0000 0004 1802 9805Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy
| | - Francesco De Sanctis
- grid.411475.20000 0004 1756 948XDepartment of Medicine, Section of Immunology, Verona University Hospital, 37134 Verona, Italy
| | - Stefano Ugel
- grid.411475.20000 0004 1756 948XDepartment of Medicine, Section of Immunology, Verona University Hospital, 37134 Verona, Italy
| | - Silvère Baron
- grid.463855.90000 0004 0385 8889Université Clermont Auvergne, GReD, CNRS, INSERM, and Centre de Recherche en Nutrition Humaine d’Auvergne Clermont-Ferrand, Clermont-Ferrand, France
| | - Jean-Marc A. Lobaccaro
- grid.463855.90000 0004 0385 8889Université Clermont Auvergne, GReD, CNRS, INSERM, and Centre de Recherche en Nutrition Humaine d’Auvergne Clermont-Ferrand, Clermont-Ferrand, France
| | - Lorenzo Pontini
- grid.9027.c0000 0004 1757 3630Big Ideas in Organic Synthesis (BIOS) Laboratory, Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy
| | - Manuela Pacciarini
- grid.9027.c0000 0004 1757 3630Big Ideas in Organic Synthesis (BIOS) Laboratory, Department of Pharmaceutical Sciences, University of Perugia, Perugia, 06123 Italy
| | - Catia Traversari
- grid.425866.b0000 0004 1764 3096MolMed S.p.A., Milan, 20132 Italy
| | - Massimiliano Pagani
- grid.428717.f0000 0004 1802 9805Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, 20122 Milan, Italy ,grid.4708.b0000 0004 1757 2822Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, 20133 Milan, Italy
| | - Vincenzo Bronte
- grid.419546.b0000 0004 1808 1697Veneto Institute of Oncology - Istituto di Ricovero e Cura a Carattere Scientifico (IOV-IRCCS), 35128 Padova, Italy
| | - Giovanni Sitia
- grid.18887.3e0000000417581884Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Per Antonson
- grid.4714.60000 0004 1937 0626Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, S-14183 Sweden
| | - Andrea Brendolan
- grid.18887.3e0000000417581884Lymphoid Organ Development Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, 20132 Italy
| | - Alfredo Budillon
- grid.508451.d0000 0004 1760 8805Experimental Pharmacology Unit, Laboratori di Mercogliano, Istituto Nazionale Tumori IRCCS Fondazione G. Pascale, Naples, Italy
| | - Vincenzo Russo
- Immuno-Biotherapy of Melanoma and Solid Tumors Unit, Division of Experimental Oncology, IRCCS Scientific Institute San Raffaele, Milan, 20132, Italy. .,Vita-Salute San Raffaele University, 20132, Milan, Italy.
| |
Collapse
|
3
|
Gasparotto E, Burattin FV, Di Gioia V, Panepuccia M, Ranzani V, Marasca F, Bodega B. Transposable Elements Co-Option in Genome Evolution and Gene Regulation. Int J Mol Sci 2023; 24:ijms24032610. [PMID: 36768929 PMCID: PMC9917352 DOI: 10.3390/ijms24032610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/26/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023] Open
Abstract
The genome is no longer deemed as a fixed and inert item but rather as a moldable matter that is continuously evolving and adapting. Within this frame, Transposable Elements (TEs), ubiquitous, mobile, repetitive elements, are considered an alive portion of the genomes to date, whose functions, although long considered "dark", are now coming to light. Here we will review that, besides the detrimental effects that TE mobilization can induce, TEs have shaped genomes in their current form, promoting genome sizing, genomic rearrangements and shuffling of DNA sequences. Although TEs are mostly represented in the genomes by evolutionarily old, short, degenerated, and sedentary fossils, they have been thoroughly co-opted by the hosts as a prolific and original source of regulatory instruments for the control of gene transcription and genome organization in the nuclear space. For these reasons, the deregulation of TE expression and/or activity is implicated in the onset and progression of several diseases. It is likely that we have just revealed the outermost layers of TE functions. Further studies on this portion of the genome are required to unlock novel regulatory functions that could also be exploited for diagnostic and therapeutic approaches.
Collapse
Affiliation(s)
- Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Filippo Vittorio Burattin
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
| | - Valeria Di Gioia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- SEMM, European School of Molecular Medicine, 20139 Milan, Italy
| | - Michele Panepuccia
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
| | - Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy
- Department of Biosciences, University of Milan, 20133 Milan, Italy
- Correspondence:
| |
Collapse
|
4
|
Forastieri C, Italia M, Toffolo E, Romito E, Bonasoni MP, Ranzani V, Bodega B, Rusconi F, Battaglioli E. Evolution Increases Primates Brain Complexity Extending RbFOX1 Splicing Activity to LSD1 Modulation. J Neurosci 2022; 42:3689-3703. [PMID: 35351830 PMCID: PMC9087731 DOI: 10.1523/jneurosci.1782-21.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/28/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022] Open
Abstract
Recent branching (100 MYA) of the mammalian evolutionary tree has enhanced brain complexity and functions at the putative cost of increased emotional circuitry vulnerability. Thus, to better understand psychopathology, a burden for the modern society, novel approaches should exploit evolutionary aspects of psychiatric-relevant molecular pathways. A handful of genes is nowadays tightly associated to psychiatric disorders. Among them, neuronal-enriched RbFOX1 modifies the activity of synaptic regulators in response to neuronal activity, keeping excitability within healthy domains. We here dissect a higher primates-restricted interaction between RbFOX1 and the transcriptional corepressor Lysine Specific Demethylase 1 (LSD1/KDM1A). A single nucleotide variation (AA to AG) in LSD1 gene appeared in higher primates and humans, endowing RbFOX1 with the ability to promote the alternative usage of a novel 3' AG splice site, which extends LSD1 exon E9 in the upstream intron (E9-long). Exon E9-long regulates LSD1 levels by Nonsense-Mediated mRNA Decay. As reintroduction of the archaic LSD1 variant (AA) abolishes E9-long splicing, the novel 3' AG splice site is necessary for RbFOX1 to control LSD1 levels. LSD1 is a homeostatic immediate early genes (IEGs) regulator playing a relevant part in environmental stress-response. In primates and humans, inclusion of LSD1 as RbFOX1 target provides RbFOX1 with the additional ability to regulate the IEGs. These data, together with extensive RbFOX1 involvement in psychiatric disorders and its stress-dependent regulation in male mice, suggest the RbFOX1-LSD1-IEGs axis as an evolutionary recent psychiatric-relevant pathway. Notably, outside the nervous system, RbFOX2-dependent LSD1 modulation could be a candidate deregulated mechanism in cancer.SIGNIFICANCE STATEMENT To be better understood, anxiety and depression need large human genetics studies aimed at further resolving the often ambiguous, aberrant neuronal pathomechanisms that impact corticolimbic circuitry physiology. Several genetic associations of the alternative splicing regulator RbFOX1 with psychiatric conditions suggest homeostatic unbalance as a neuronal signature of psychopathology. Here we move a step forward, characterizing a disease-relevant higher primates-specific pathway by which RbFOX1 acquires the ability to regulate neuronal levels of Lysine Specific Demethylase 1, an epigenetic modulator of environmental stress response. Thus, two brain-enriched enzymes, independently shown to homeostatically protect neurons with a clear readout in terms of emotional behavior in lower mammals, establish in higher primates and humans a new functional cooperation enhancing the complexity of environmental adaptation and stress vulnerability.
Collapse
Affiliation(s)
- Chiara Forastieri
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Maria Italia
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Emanuela Toffolo
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Elena Romito
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | | | - Valeria Ranzani
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milano, 20122, Italy
| | - Beatrice Bodega
- Istituto Nazionale di Genetica Molecolare "Romeo ed Enrica Invernizzi," Milano, 20122, Italy
- Department of Biosciences, Università degli Studi di Milano, Milano, 20133, Italy
| | - Francesco Rusconi
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| | - Elena Battaglioli
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Segrate, 20090, Italy
| |
Collapse
|
5
|
Marasca F, Sinha S, Vadalà R, Polimeni B, Ranzani V, Paraboschi EM, Burattin FV, Ghilotti M, Crosti M, Negri ML, Campagnoli S, Notarbartolo S, Sartore-Bianchi A, Siena S, Prati D, Montini G, Viale G, Torre O, Harari S, Grifantini R, Soldà G, Biffo S, Abrignani S, Bodega B. LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion. Nat Genet 2022; 54:180-193. [PMID: 35039641 DOI: 10.1038/s41588-021-00989-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 11/18/2021] [Indexed: 12/12/2022]
Abstract
How gene expression is controlled to preserve human T cell quiescence is poorly understood. Here we show that non-canonical splicing variants containing long interspersed nuclear element 1 (LINE1) enforce naive CD4+ T cell quiescence. LINE1-containing transcripts are derived from CD4+ T cell-specific genes upregulated during T cell activation. In naive CD4+ T cells, LINE1-containing transcripts are regulated by the transcription factor IRF4 and kept at chromatin by nucleolin; these transcripts act in cis, hampering levels of histone 3 (H3) lysine 36 trimethyl (H3K36me3) and stalling gene expression. T cell activation induces LINE1-containing transcript downregulation by the splicing suppressor PTBP1 and promotes expression of the corresponding protein-coding genes by the elongating factor GTF2F1 through mTORC1. Dysfunctional T cells, exhausted in vitro or tumor-infiltrating lymphocytes (TILs), accumulate LINE1-containing transcripts at chromatin. Remarkably, depletion of LINE1-containing transcripts restores TIL effector function. Our study identifies a role for LINE1 elements in maintaining T cell quiescence and suggests that an abundance of LINE1-containing transcripts is critical for T cell effector function and exhaustion.
Collapse
Affiliation(s)
- Federica Marasca
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Shruti Sinha
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Rebecca Vadalà
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Ph.D. Program in Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, Monza, Italy
| | - Benedetto Polimeni
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Ph.D. Program in Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, Monza, Italy
| | - Valeria Ranzani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Elvezia Maria Paraboschi
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | | | - Marco Ghilotti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Mariacristina Crosti
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Maria Luce Negri
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | | | - Samuele Notarbartolo
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
- Department of Oncology and Hematology-Oncology, University of Milan, Milan, Italy
| | - Daniele Prati
- Department of Transfusion Medicine and Hematology, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giovanni Montini
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Pediatric Nephrology and Dialysis Unit, Fondazione IRCCS Cà Granda, Ospedale Maggiore Policlinico, Milan, Italy
| | - Giuseppe Viale
- University of Milan, European Institute of Oncology IRCCS, Milan, Italy
| | - Olga Torre
- Department of Medical Sciences, San Giuseppe Hospital MultiMedica IRCCS, Milan, Italy
| | - Sergio Harari
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
- Department of Medical Sciences, San Giuseppe Hospital MultiMedica IRCCS, Milan, Italy
| | - Renata Grifantini
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- CheckmAb Srl, Milan, Italy
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- Humanitas Clinical and Research Center, IRCCS, Rozzano, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Sergio Abrignani
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy.
| | - Beatrice Bodega
- INGM, Istituto Nazionale di Genetica Molecolare 'Romeo ed Enrica Invernizzi', Milan, Italy.
- Department of Biosciences, University of Milan, Milan, Italy.
| |
Collapse
|
6
|
De Simone M, Chirichella M, Emming S, Mazzara S, Ranzani V, Gruarin P, Moschetti G, Pulvirenti N, Maglie S, Vasco C, Crosti MC, Rossetti G, Pagani M, Abrignani S, Monticelli S, Geginat J. Ex vivo microRNA and gene expression profiling of human Tr1-like cells suggests a role for miR-92a and -125a in the regulation of EOMES and IL-10R. Eur J Immunol 2021; 51:3243-3246. [PMID: 34528258 PMCID: PMC9293355 DOI: 10.1002/eji.202149315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/26/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022]
Abstract
Ex vivo gene expression and miRNA profiling of Eomes+ Tr1-like cells suggested that they represent a differentiation stage that is intermediate between Th1-cells and cytotoxic CD4+ T-cells. Several microRNAs were downregulated in Eomes+ Tr1-like cells that might inhibit Tr1-cell differentiation. In particular, miR-92a targeted Eomes, while miR-125a inhibited IFN-g and IL-10R expression.
Collapse
Affiliation(s)
- Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Michele Chirichella
- Institute for Research in Biomedicine (IRB)Università della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Stefan Emming
- Institute for Research in Biomedicine (IRB)Università della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Saveria Mazzara
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Giorgia Moschetti
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Nadia Pulvirenti
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Stefano Maglie
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | - Chiara Vasco
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
| | | | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- FIRC Institute of Molecular Oncology (IFOM)MilanItaly
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- FIRC Institute of Molecular Oncology (IFOM)MilanItaly
- Department of Medical Biotechnology and Translational MedicineUniversità degli StudiMilanoItaly
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- Department of Clinical Sciences and Community HealthUniversità degli StudiMilanoItaly
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB)Università della Svizzera italiana (USI)BellinzonaSwitzerland
| | - Jens Geginat
- Istituto Nazionale Genetica Molecolare INGM ‘Romeo ed Enrica Invernizzi’MilanItaly
- Department of Clinical Sciences and Community HealthUniversità degli StudiMilanoItaly
| |
Collapse
|
7
|
Notarbartolo S, Ranzani V, Bandera A, Gruarin P, Bevilacqua V, Putignano AR, Gobbini A, Galeota E, Manara C, Bombaci M, Pesce E, Zagato E, Favalli A, Sarnicola ML, Curti S, Crosti M, Martinovic M, Fabbris T, Marini F, Donnici L, Lorenzo M, Mancino M, Ungaro R, Lombardi A, Mangioni D, Muscatello A, Aliberti S, Blasi F, De Feo T, Prati D, Manganaro L, Granucci F, Lanzavecchia A, De Francesco R, Gori A, Grifantini R, Abrignani S. Integrated longitudinal immunophenotypic, transcriptional and repertoire analyses delineate immune responses in COVID-19 patients. Sci Immunol 2021; 6:6/62/eabg5021. [PMID: 34376481 DOI: 10.1126/sciimmunol.abg5021] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 08/04/2021] [Indexed: 12/12/2022]
Abstract
To understand how a protective immune response against SARS-CoV-2 develops over time, we integrated phenotypic, transcriptional and repertoire analyses on PBMCs from mild and severe COVID-19 patients during and after infection, and compared them to healthy donors (HD). A type I IFN-response signature marked all the immune populations from severe patients during the infection. Humoral immunity was dominated by IgG production primarily against the RBD and N proteins, with neutralizing antibody titers increasing post infection and with disease severity. Memory B cells, including an atypical FCRL5+ T-BET+ memory subset, increased during the infection, especially in patients with mild disease. A significant reduction of effector memory, CD8+ T cells frequency characterized patients with severe disease. Despite such impairment, we observed robust clonal expansion of CD8+ T lymphocytes, while CD4+ T cells were less expanded and skewed toward TCM and TH2-like phenotypes. MAIT cells were also expanded, but only in patients with mild disease. Terminally differentiated CD8+ GZMB+ effector cells were clonally expanded both during the infection and post-infection, while CD8+ GZMK+ lymphocytes were more expanded post-infection and represented bona fide memory precursor effector cells. TCR repertoire analysis revealed that only highly proliferating T cell clonotypes, which included SARS-CoV-2-specific cells, were maintained post-infection and shared between the CD8+ GZMB+ and GZMK+ subsets. Overall, this study describes the development of immunity against SARS-CoV-2 and identifies an effector CD8+ T cell population with memory precursor-like features.
Collapse
Affiliation(s)
- Samuele Notarbartolo
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy. .,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Valeria Ranzani
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Alessandra Bandera
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Paola Gruarin
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Valeria Bevilacqua
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Anna Rita Putignano
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy.,Unità Operativa Complessa (UOC) Coordinamento Trapianti, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Andrea Gobbini
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Eugenia Galeota
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Cristina Manara
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mauro Bombaci
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elisa Pesce
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Elena Zagato
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Unità Operativa Complessa (UOC) Coordinamento Trapianti, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Andrea Favalli
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Maria Lucia Sarnicola
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Serena Curti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mariacristina Crosti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Martina Martinovic
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Tanya Fabbris
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Federico Marini
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center, Mainz, Germany
| | - Lorena Donnici
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mariangela Lorenzo
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Marilena Mancino
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Riccardo Ungaro
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Andrea Lombardi
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Davide Mangioni
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center.,Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Antonio Muscatello
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano Aliberti
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center.,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Transfusion Medicine and Hematology, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center
| | - Francesco Blasi
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center
| | - Tullia De Feo
- Respiratory Unit and Cystic Fibrosis Adult Center, Respiratory Unit and Cystic Fibrosis Adult Center.,Unità Operativa Complessa (UOC) Coordinamento Trapianti, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Daniele Prati
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Department of Transfusion Medicine and Hematology, Milan, Italy
| | - Lara Manganaro
- INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Francesca Granucci
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Antonio Lanzavecchia
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Raffaele De Francesco
- Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy.,Unità Operativa Complessa (UOC) Coordinamento Trapianti, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy.,Centre for Multidisciplinary Research in Health Science (MACH), Università degli Studi di Milano, Milan, Italy
| | - Renata Grifantini
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy; .,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Sergio Abrignani
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy; .,Unità Operativa Complessa (UOC) Coordinamento Trapianti, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| |
Collapse
|
8
|
Marongiu L, Protti G, Facchini FA, Valache M, Mingozzi F, Ranzani V, Putignano AR, Salviati L, Bevilacqua V, Curti S, Crosti M, Sarnicola ML, D'Angiò M, Bettini LR, Biondi A, Nespoli L, Tamini N, Clementi N, Mancini N, Abrignani S, Spreafico R, Granucci F. Maturation signatures of conventional dendritic cell subtypes in COVID-19 suggest direct viral sensing. Eur J Immunol 2021; 52:109-122. [PMID: 34333764 PMCID: PMC8420462 DOI: 10.1002/eji.202149298] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/09/2021] [Accepted: 07/29/2021] [Indexed: 11/11/2022]
Abstract
Growing evidence suggests that conventional dendritic cells (cDCs) undergo aberrant maturation in COVID‐19, which negatively affects T‐cell activation. The presence of effector T cells in patients with mild disease and dysfunctional T cells in severely ill patients suggests that adequate T‐cell responses limit disease severity. Understanding how cDCs cope with SARS‐CoV‐2 can help elucidate how protective immune responses are generated. Here, we report that cDC2 subtypes exhibit similar infection‐induced gene signatures, with the upregulation of IFN‐stimulated genes and IL‐6 signaling pathways. Furthermore, comparison of cDCs between patients with severe and mild disease showed severely ill patients to exhibit profound downregulation of genes encoding molecules involved in antigen presentation, such as MHCII, TAP, and costimulatory proteins, whereas we observed the opposite for proinflammatory molecules, such as complement and coagulation factors. Thus, as disease severity increases, cDC2s exhibit enhanced inflammatory properties and lose antigen presentation capacity. Moreover, DC3s showed upregulation of anti‐apoptotic genes and accumulated during infection. Direct exposure of cDC2s to the virus in vitro recapitulated the activation profile observed in vivo. Our findings suggest that SARS‐CoV‐2 interacts directly with cDC2s and implements an efficient immune escape mechanism that correlates with disease severity by downregulating crucial molecules required for T‐cell activation.
Collapse
Affiliation(s)
- Laura Marongiu
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Giulia Protti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Fabio A Facchini
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Mihai Valache
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Francesca Mingozzi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy
| | - Valeria Ranzani
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Anna Rita Putignano
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Lorenzo Salviati
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Valeria Bevilacqua
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Serena Curti
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Mariacristina Crosti
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| | | | - Mariella D'Angiò
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Italy
| | - Laura Rachele Bettini
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Italy
| | - Andrea Biondi
- Pediatric Department and Centro Tettamanti-European Reference Network PaedCan, EuroBloodNet, MetabERN-University of Milano-Bicocca-Fondazione MBBM-Ospedale, San Gerardo, Italy
| | - Luca Nespoli
- ASST san Gerardo Hospital, School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Nicolò Tamini
- ASST san Gerardo Hospital, School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Nicola Clementi
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy.,IRCCS San Raffaele Hospital, Milan, Italy
| | - Nicasio Mancini
- Laboratory of Medical Microbiology and Virology, Vita-Salute San Raffaele University, Milan, Italy.,IRCCS San Raffaele Hospital, Milan, Italy
| | - Sergio Abrignani
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy.,Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
| | - Roberto Spreafico
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles
| | - Francesca Granucci
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.,National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi", Milan, Italy
| |
Collapse
|
9
|
Bocchi VD, Conforti P, Vezzoli E, Besusso D, Cappadona C, Lischetti T, Galimberti M, Ranzani V, Bonnal RJP, De Simone M, Rossetti G, He X, Kamimoto K, Espuny-Camacho I, Faedo A, Gervasoni F, Vuono R, Morris SA, Chen J, Felsenfeld D, Pavesi G, Barker RA, Pagani M, Cattaneo E. The coding and long noncoding single-cell atlas of the developing human fetal striatum. Science 2021; 372:372/6542/eabf5759. [PMID: 33958447 DOI: 10.1126/science.abf5759] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/29/2021] [Indexed: 12/12/2022]
Abstract
Deciphering how the human striatum develops is necessary for understanding the diseases that affect this region. To decode the transcriptional modules that regulate this structure during development, we compiled a catalog of 1116 long intergenic noncoding RNAs (lincRNAs) identified de novo and then profiled 96,789 single cells from the early human fetal striatum. We found that D1 and D2 medium spiny neurons (D1- and D2-MSNs) arise from a common progenitor and that lineage commitment is established during the postmitotic transition, across a pre-MSN phase that exhibits a continuous spectrum of fate determinants. We then uncovered cell type-specific gene regulatory networks that we validated through in silico perturbation. Finally, we identified human-specific lincRNAs that contribute to the phylogenetic divergence of this structure in humans. This work delineates the cellular hierarchies governing MSN lineage commitment.
Collapse
Affiliation(s)
- Vittoria Dickinson Bocchi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Paola Conforti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Elena Vezzoli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Dario Besusso
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Claudio Cappadona
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Tiziana Lischetti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Maura Galimberti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | | | | | | | | | - Xiaoling He
- WT-MRC Cambridge Stem Cell Institute and Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Kenji Kamimoto
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ira Espuny-Camacho
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Andrea Faedo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy.,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| | - Federica Gervasoni
- INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy.,Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Romina Vuono
- WT-MRC Cambridge Stem Cell Institute and Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Samantha A Morris
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO 63110, USA.,Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA.,Center of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jian Chen
- CHDI Management/CHDI Foundation, New York, NY, USA
| | | | - Giulio Pavesi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Roger A Barker
- WT-MRC Cambridge Stem Cell Institute and Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
| | - Massimiliano Pagani
- INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy. .,Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Milan, Italy
| | - Elena Cattaneo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy. .,INGM, Istituto Nazionale Genetica Molecolare, Milan, Italy
| |
Collapse
|
10
|
Della Chiara G, Gervasoni F, Fakiola M, Godano C, D'Oria C, Azzolin L, Bonnal RJP, Moreni G, Drufuca L, Rossetti G, Ranzani V, Bason R, De Simone M, Panariello F, Ferrari I, Fabbris T, Zanconato F, Forcato M, Romano O, Caroli J, Gruarin P, Sarnicola ML, Cordenonsi M, Bardelli A, Zucchini N, Ceretti AP, Mariani NM, Cassingena A, Sartore-Bianchi A, Testa G, Gianotti L, Opocher E, Pisati F, Tripodo C, Macino G, Siena S, Bicciato S, Piccolo S, Pagani M. Epigenomic landscape of human colorectal cancer unveils an aberrant core of pan-cancer enhancers orchestrated by YAP/TAZ. Nat Commun 2021; 12:2340. [PMID: 33879786 PMCID: PMC8058065 DOI: 10.1038/s41467-021-22544-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/18/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer is characterized by pervasive epigenetic alterations with enhancer dysfunction orchestrating the aberrant cancer transcriptional programs and transcriptional dependencies. Here, we epigenetically characterize human colorectal cancer (CRC) using de novo chromatin state discovery on a library of different patient-derived organoids. By exploring this resource, we unveil a tumor-specific deregulated enhancerome that is cancer cell-intrinsic and independent of interpatient heterogeneity. We show that the transcriptional coactivators YAP/TAZ act as key regulators of the conserved CRC gained enhancers. The same YAP/TAZ-bound enhancers display active chromatin profiles across diverse human tumors, highlighting a pan-cancer epigenetic rewiring which at single-cell level distinguishes malignant from normal cell populations. YAP/TAZ inhibition in established tumor organoids causes extensive cell death unveiling their essential role in tumor maintenance. This work indicates a common layer of YAP/TAZ-fueled enhancer reprogramming that is key for the cancer cell state and can be exploited for the development of improved therapeutic avenues. The role of epigenetic deregulation in colorectal cancer (CRC) is not fully understood yet. Here the authors use patient-derived organoids, epigenomics and single-cell RNA-seq to reveal that YAP/TAZ are key regulators that bind to active enhancers in CRC and promote tumour survival.
Collapse
Affiliation(s)
- Giulia Della Chiara
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Federica Gervasoni
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Michaela Fakiola
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Chiara Godano
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Claudia D'Oria
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Luca Azzolin
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Raoul Jean Pierre Bonnal
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Giulia Moreni
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Department of Medical Microbiology, Laboratory of Clinical Virology, Amsterdam University Medical Center, University of Amsterdam, AZ, Amsterdam, the Netherlands
| | - Lorenzo Drufuca
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Grazisa Rossetti
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Ramona Bason
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy.,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy.,Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Francesco Panariello
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy.,Telethon Institute of Genetics and Medicine TIGEM, Pozzuoli, Italy
| | - Ivan Ferrari
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Tanya Fabbris
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | | | - Mattia Forcato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Jimmy Caroli
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | - Maria Lucia Sarnicola
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy
| | | | - Alberto Bardelli
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo (TO), Italy.,Department of Oncology, University of Torino, Candiolo (TO), Italy
| | | | | | | | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Giuseppe Testa
- Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy.,Department of Experimental Oncology, European Institute of Oncology, IRCCS, Milan, Italy
| | - Luca Gianotti
- School of Medicine and Surgery, Milano-Bicocca University, and Department of Surgery, San Gerardo Hospital, Monza, Italy
| | - Enrico Opocher
- UO Chirurgia Epatobiliopancreatica e Digestiva Ospedale San Paolo, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | | | - Claudio Tripodo
- Tumor Immunology Unit, University of Palermo, Palermo, Italy.,Tumor and Microenvironment Histopathology Unit, IFOM, FIRC Institute of Molecular Oncology, Milan, Italy
| | - Giuseppe Macino
- Department of Cellular Biotechnologies and Hematology, La Sapienza University of Rome, Rome, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefano Piccolo
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy. .,Department of Molecular Medicine, University of Padua, Padua, Italy.
| | - Massimiliano Pagani
- IFOM, the FIRC Institute of Molecular Oncology, Milan, Italy. .,Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi', Milan, Italy. .,Human Organoid Models Integrative Center HOMIC, University of Milan, Milan, Italy. .,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy.
| |
Collapse
|
11
|
Marasca F, Gasparotto E, Polimeni B, Vadalà R, Ranzani V, Bodega B. The Sophisticated Transcriptional Response Governed by Transposable Elements in Human Health and Disease. Int J Mol Sci 2020; 21:ijms21093201. [PMID: 32366056 PMCID: PMC7247572 DOI: 10.3390/ijms21093201] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/29/2020] [Accepted: 04/29/2020] [Indexed: 01/15/2023] Open
Abstract
Transposable elements (TEs), which cover ~45% of the human genome, although firstly considered as “selfish” DNA, are nowadays recognized as driving forces in eukaryotic genome evolution. This capability resides in generating a plethora of sophisticated RNA regulatory networks that influence the cell type specific transcriptome in health and disease. Indeed, TEs are transcribed and their RNAs mediate multi-layered transcriptional regulatory functions in cellular identity establishment, but also in the regulation of cellular plasticity and adaptability to environmental cues, as occurs in the immune response. Moreover, TEs transcriptional deregulation also evolved to promote pathogenesis, as in autoimmune and inflammatory diseases and cancers. Importantly, many of these findings have been achieved through the employment of Next Generation Sequencing (NGS) technologies and bioinformatic tools that are in continuous improvement to overcome the limitations of analyzing TEs sequences. However, they are highly homologous, and their annotation is still ambiguous. Here, we will review some of the most recent findings, questions and improvements to study at high resolution this intriguing portion of the human genome in health and diseases, opening the scenario to novel therapeutic opportunities.
Collapse
Affiliation(s)
- Federica Marasca
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Erica Gasparotto
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Benedetto Polimeni
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Rebecca Vadalà
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
- Translational and Molecular Medicine, DIMET, University of Milan-Bicocca, 20900 Monza, Italy
| | - Valeria Ranzani
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
| | - Beatrice Bodega
- Fondazione INGM, Istituto Nazionale di Genetica Molecolare “Enrica e Romeo Invernizzi”, 20122 Milan, Italy; (F.M.); (E.G.); (B.P.); (R.V.); (V.R.)
- Correspondence:
| |
Collapse
|
12
|
Dongiovanni P, Meroni M, Baselli G, Mancina RM, Ruscica M, Longo M, Rametta R, Cespiati A, Pelusi S, Ferri N, Ranzani V, Nobili V, Pihlajamaki J, Fracanzani AL, Badiali S, Petta S, Fargion S, Romeo S, Kozlitina J, Valenti L. PCSK7 gene variation bridges atherogenic dyslipidemia with hepatic inflammation in NAFLD patients. J Lipid Res 2019; 60:1144-1153. [PMID: 30918065 DOI: 10.1194/jlr.p090449] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Revised: 03/22/2019] [Indexed: 12/22/2022] Open
Abstract
Dyslipidemia and altered iron metabolism are typical features of nonalcoholic fatty liver disease (NAFLD). Proprotein convertase subtilisin/kexin type 7 (PCSK7) gene variation has been associated with circulating lipids and liver damage during iron overload. The aim of this study was to examine the impact of the PCSK7 rs236918 variant on NAFLD-related traits in 1,801 individuals from the Liver Biopsy Cohort (LBC), 500,000 from the UK Biobank Cohort (UKBBC), and 4,580 from the Dallas Heart Study (DHS). The minor PCSK7 rs236918 C allele was associated with higher triglycerides, aminotransferases, and hepatic inflammation in the LBC (P < 0.05) and with hypercholesterolemia and liver disease in the UKBBC. In the DHS, PCSK7 missense variants were associated with circulating lipids. PCSK7 was expressed in hepatocytes and its hepatic expression correlated with that of lipogenic genes (P < 0.05). The rs236918 C allele was associated with upregulation of a new "intra-PCSK7" long noncoding RNA predicted to interact with the protein, higher hepatic and circulating PCSK7 protein (P < 0.01), which correlated with triglycerides (P = 0.04). In HepG2 cells, PCSK7 deletion reduced lipogenesis, fat accumulation, inflammation, transforming growth factor β pathway activation, and fibrogenesis. In conclusion, PCSK7 gene variation is associated with dyslipidemia and more severe liver disease in high risk individuals, likely by modulating PCSK7 expression/activity.
Collapse
Affiliation(s)
- Paola Dongiovanni
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Marica Meroni
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Departments of Pathophysiology and Transplantation Università degli Studi di Milano, Milan, Italy
| | - Guido Baselli
- Departments of Pathophysiology and Transplantation Università degli Studi di Milano, Milan, Italy
| | - Rosellina M Mancina
- Department of Molecular and Clinical Medicine University of Gothenburg, Gothenburg, Sweden
| | - Massimiliano Ruscica
- Pharmacological and Biomolecular Sciences Università degli Studi di Milano, Milan, Italy
| | - Miriam Longo
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Raffaela Rametta
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Annalisa Cespiati
- Departments of Pathophysiology and Transplantation Università degli Studi di Milano, Milan, Italy
| | - Serena Pelusi
- Departments of Pathophysiology and Transplantation Università degli Studi di Milano, Milan, Italy.,Translational Medicine, Department of Transfusion Medicine and Hematology Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Nicola Ferri
- Dipartimento di Scienze del Farmaco Università degli Studi di Padova, Padova, Italy
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valerio Nobili
- Department of Gastroenterology, Ospedale Bambin Gesù, Roma, Italy
| | - Jussi Pihlajamaki
- Departments of Medicine and Public Health and Clinical Nutrition University of Eastern Finland, and Clinical Nutrition and Obesity Center, Kuopio University Hospital, Kuopio, Finland
| | - Anna Ludovica Fracanzani
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Departments of Pathophysiology and Transplantation Università degli Studi di Milano, Milan, Italy
| | - Sara Badiali
- Surgery Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Salvatore Petta
- Department of Gastroenterology Universita di Palermo, Palermo, Italy
| | - Silvia Fargion
- General Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy.,Departments of Pathophysiology and Transplantation Università degli Studi di Milano, Milan, Italy
| | - Stefano Romeo
- Pharmacological and Biomolecular Sciences Università degli Studi di Milano, Milan, Italy.,Cardiology Department Sahlgrenska University Hospital, Gothenburg, Sweden and Clinical Nutrition Department of Medical and Surgical Science, University Magna Graecia, Catanzaro, Italy
| | - Julia Kozlitina
- McDermott Center for Human Growth and Development University of Texas Southwestern Medical Center, Dallas, TX
| | - Luca Valenti
- Departments of Pathophysiology and Transplantation Università degli Studi di Milano, Milan, Italy .,Translational Medicine, Department of Transfusion Medicine and Hematology Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| |
Collapse
|
13
|
Gruarin P, Maglie S, Simone M, Häringer B, Vasco C, Ranzani V, Bosotti R, Noddings JS, Larghi P, Facciotti F, Sarnicola ML, Martinovic M, Crosti M, Moro M, Rossi RL, Bernardo ME, Caprioli F, Locatelli F, Rossetti G, Abrignani S, Pagani M, Geginat J. Eomesodermin controls a unique differentiation program in human IL‐10 and IFN‐γ coproducing regulatory T cells. Eur J Immunol 2018; 49:96-111. [DOI: 10.1002/eji.201847722] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Revised: 09/28/2018] [Accepted: 11/09/2018] [Indexed: 01/13/2023]
Affiliation(s)
- Paola Gruarin
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Stefano Maglie
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Marco Simone
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Barbara Häringer
- German Rheumatology Research Center DRFZ Berlin Germany
- Charitè Research Center for Immunosciences RCIS Berlin Germany
| | - Chiara Vasco
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Valeria Ranzani
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Roberto Bosotti
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Johanna S. Noddings
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Paola Larghi
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Federica Facciotti
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Maria L. Sarnicola
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Martina Martinovic
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Mariacristina Crosti
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Monica Moro
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Riccardo L. Rossi
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Maria E. Bernardo
- Ospedale Pediatrico Bambino Gesù Dipartimento Onco–Ematologia e Medicina Trasfusionale Rome Italy
| | - Flavio Caprioli
- Unità Operativa di Gastroenterologia ed Endoscopia Fondazione Ca’ Granda Ospedale Maggiore Policlinico Milan Italy
| | - Franco Locatelli
- Ospedale Pediatrico Bambino Gesù Dipartimento Onco–Ematologia e Medicina Trasfusionale Rome Italy
| | - Grazisa Rossetti
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| | - Sergio Abrignani
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
- Department of Clinical Science and Community Health (DISCCO) University of Milan Milan Italy
| | - Massimiliano Pagani
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
- Department of Medical Biotechnology and Translational Medicine University of Milan Milan Italy
| | - Jens Geginat
- INGM‐National Institute of Molecular Genetics “Romeo ed Enrica Invernizzi” Milan Italy
| |
Collapse
|
14
|
DuPage M, Wang D, Quiros J, Mahuron K, Pai CC, Ranzani V, Young A, Silveria S, Harwin T, Abnousian A, Pagani M, Rosenblum M, Van Gool F, Fong L, Bluestone JA. Targeting EZH2 Selectively Alters Intratumoral Regulatory T Cells to Enhance Cancer Immunity. The Journal of Immunology 2018. [DOI: 10.4049/jimmunol.200.supp.57.39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Abstract
Immunosuppressive regulatory T cells (Tregs) are critical for maintaining immune homeostasis, but their presence in tumor tissues impairs anti-tumor immunity and portends poor prognoses in cancer patients. Targeting Tregs may be a powerful means to unleash more potent immune responses against cancer, but targeting these cells is challenging because their generalized inactivation may incite severe autoimmune toxicities. To selectively target Tregs in tumors, we investigated the role of the H3K27 methyltransferase EZH2 in Tregs and determined that its enhanced activity at tumor sites in mice and humans leads to more robust and stable Tregs. We demonstrate that blocking EZH2 activity, both pharmacologically and genetically, selectively reprograms the function of tumor-infiltrating Tregs without systemically altering Treg function. Genetic disruption of EZH2 in tumor-resident Tregs led to their acquisition of pro-inflammatory functions that remodeled the tumor microenvironment and enhanced the recruitment and function of effector T cells, leading to the complete elimination of tumors. Moreover, abolishing EZH2 function in Tregs was mechanistically distinct from, more potent than, and less toxic than a generalized Treg depletion approach. This study reveals a novel strategy to target Tregs in cancer that mitigates autoimmunity by reprogramming their function in tumors to enhance anti-cancer immunity.
Collapse
Affiliation(s)
- Michel DuPage
- 1Univ. of California, Berkeley
- 2Univ. of California, San Francisco
| | | | | | | | | | - Valeria Ranzani
- 3Istituto Nazionale Genetica Molecolare INGM
- 4’Romeo ed Enrica Invernizzi’, Italy, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
15
|
De Simone M, Arrigoni A, Rossetti G, Gruarin P, Ranzani V, Politano C, Bonnal RJP, 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. Transcriptional Landscape of Human Tissue Lymphocytes Unveils Uniqueness of Tumor-Infiltrating T Regulatory Cells. Immunity 2017; 45:1135-1147. [PMID: 27851914 PMCID: PMC5119953 DOI: 10.1016/j.immuni.2016.10.021] [Citation(s) in RCA: 438] [Impact Index Per Article: 62.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 09/07/2016] [Accepted: 10/04/2016] [Indexed: 02/08/2023]
Abstract
Tumor-infiltrating regulatory T lymphocytes (Treg) can suppress effector T cells specific for tumor antigens. Deeper molecular definitions of tumor-infiltrating-lymphocytes could thus offer therapeutic opportunities. Transcriptomes of T helper 1 (Th1), Th17, and Treg cells infiltrating colorectal or non-small-cell lung cancers were compared to transcriptomes of the same subsets from normal tissues and validated at the single-cell level. We found that tumor-infiltrating Treg cells were highly suppressive, upregulated several immune-checkpoints, and expressed on the cell surfaces specific signature molecules such as interleukin-1 receptor 2 (IL1R2), programmed death (PD)-1 Ligand1, PD-1 Ligand2, and CCR8 chemokine, which were not previously described on Treg cells. Remarkably, high expression in whole-tumor samples of Treg cell signature genes, such as LAYN, MAGEH1, or CCR8, correlated with poor prognosis. Our findings provide insights into the molecular identity and functions of human tumor-infiltrating Treg cells and define potential targets for tumor immunotherapy. Transcriptome analysis performed on tumor-resident CD4+ Th1, Th17, and Treg cells Tumor-infiltrating Treg cells are defined by the expression of signature genes Treg-specific signature genes correlate with patients’ survival in both CRC and NSCLC
Collapse
Affiliation(s)
- Marco De Simone
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Alberto Arrigoni
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Claudia Politano
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Raoul J P Bonnal
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Elena Provasi
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Maria Lucia Sarnicola
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Ilaria Panzeri
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Monica Moro
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Mariacristina Crosti
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Saveria Mazzara
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Valentina Vaira
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy; Division of Pathology, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy; Department of Pathophysiology and Organ Transplantation, Università degli Studi di Milano, Milano 20122, Italy
| | - Silvano Bosari
- Division of Pathology, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy; Department of Pathophysiology and Organ Transplantation, Università degli Studi di Milano, Milano 20122, Italy
| | - Alessandro Palleschi
- Division of Thoracic Surgery, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Luigi Santambrogio
- Division of Thoracic Surgery, IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan 20122, Italy; Department of Pathophysiology and Organ Transplantation, Università degli Studi di Milano, Milano 20122, Italy
| | - Giorgio Bovo
- Department of Pathology, San Gerardo Hospital, Monza 20900, Italy
| | - Nicola Zucchini
- Department of Pathology, San Gerardo Hospital, Monza 20900, Italy
| | - Mauro Totis
- Department of Surgery, San Gerardo Hospital, Monza 20900, Italy
| | - Luca Gianotti
- Department of Surgery, San Gerardo Hospital, Monza 20900, Italy; School of Medicine and Surgery, Milano-Bicocca University, Monza 20900 Italy
| | - Giancarlo Cesana
- School of Medicine and Surgery, Milano-Bicocca University, Monza 20900 Italy
| | - Roberto A Perego
- School of Medicine and Surgery, Milano-Bicocca University, Monza 20900 Italy
| | - Nirvana Maroni
- UO Chirurgia Epatobiliopancreatica e Digestiva Ospedale San Paolo, Milan 20142, Italy
| | - Andrea Pisani Ceretti
- UO Chirurgia Epatobiliopancreatica e Digestiva Ospedale San Paolo, Milan 20142, Italy
| | - Enrico Opocher
- UO Chirurgia Epatobiliopancreatica e Digestiva Ospedale San Paolo, Milan 20142, Italy; Department of Health Sciences, Università degli Studi di Milano, Milano 20122, Italy
| | - Raffaele De Francesco
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Jens Geginat
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milano 20122, Italy.
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare INGM 'Romeo ed Enrica Invernizzi,' Milan 20122, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milano 20129, Italy.
| |
Collapse
|
16
|
Ranzani V, Arrigoni A, Rossetti G, Panzeri I, Abrignani S, Bonnal RJP, Pagani M. Next-Generation Sequencing Analysis of Long Noncoding RNAs in CD4+ T Cell Differentiation. Methods Mol Biol 2017; 1514:173-185. [PMID: 27787801 DOI: 10.1007/978-1-4939-6548-9_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Next-generation sequencing approaches, in particular RNA-seq, provide a genome-wide expression profiling allowing the identification of novel and rare transcripts such as long noncoding RNAs (lncRNA). Many RNA-seq studies have now been performed aimed at the characterization of lncRNAs and their possible involvement in cell development and differentiation in different organisms, cell types, and tissues. The adaptive immune system is an extraordinary context for the study of the role of lncRNAs in differentiation. Indeed lncRNAs seem to be key drivers in governing flexibility and plasticity of both CD8+ and CD4+ T cell, together with lineage-specific transcription factors and cytokines, acting as fine-tuners of fate choices in T cell differentiation.We describe here a pipeline for the identification of lncRNAs starting from RNA-Seq raw data.
Collapse
Affiliation(s)
- Valeria Ranzani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Alberto Arrigoni
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Ilaria Panzeri
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via Festa del Perdono 7, Milan, 20122, Italy
| | - Raoul J P Bonnal
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Festa del Perdono 7, Milan, 20122, Italy.
| |
Collapse
|
17
|
Abstract
RNA-Seq is an approach to transcriptome profiling that uses deep-sequencing technologies to detect and accurately quantify RNA molecules originating from a genome at a given moment in time. In recent years, the advent of RNA-Seq has facilitated genome-wide expression profiling, including the identification of novel and rare transcripts like noncoding RNAs and novel alternative splicing isoforms.Here, we describe the analytical steps required for the identification and characterization of noncoding RNAs starting from RNA-Seq raw samples, with a particular emphasis on long noncoding RNAs (lncRNAs).
Collapse
Affiliation(s)
- Alberto Arrigoni
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122, Milan, Italy
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122, Milan, Italy
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122, Milan, Italy
| | - Ilaria Panzeri
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122, Milan, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122, Milan, Italy.,Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via Festa del Perdono 7, 20122, Milan, Italy
| | - Raoul J P Bonnal
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122, Milan, Italy.
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122, Milan, Italy. .,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Festa del Perdono 7, 20122, Milan, Italy.
| |
Collapse
|
18
|
Bonnal RJP, Rossi RL, Carpi D, Ranzani V, Abrignani S, Pagani M. miRiadne: a web tool for consistent integration of miRNA nomenclature. Nucleic Acids Res 2015; 43:W487-92. [PMID: 25897123 PMCID: PMC4489305 DOI: 10.1093/nar/gkv381] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 04/11/2015] [Indexed: 01/09/2023] Open
Abstract
The miRBase is the official miRNA repository which keeps the annotation updated on newly discovered miRNAs: it is also used as a reference for the design of miRNA profiling platforms. Nomenclature ambiguities generated by loosely updated platforms and design errors lead to incompatibilities among platforms, even from the same vendor. Published miRNA lists are thus generated with different profiling platforms that refer to diverse and not updated annotations. This greatly compromises searches, comparisons and analyses that rely on miRNA names only without taking into account the mature sequences, which is particularly critic when such analyses are carried over automatically. In this paper we introduce miRiadne, a web tool to harmonize miRNA nomenclature, which takes into account the original miRBase versions from 10 up to 21, and annotations of 40 common profiling platforms from nine brands that we manually curated. miRiadne uses the miRNA mature sequence to link miRBase versions and/or platforms to prevent nomenclature ambiguities. miRiadne was designed to simplify and support biologists and bioinformaticians in re-annotating their own miRNA lists and/or data sets. As Ariadne helped Theseus in escaping the mythological maze, miRiadne will help the miRNA researcher in escaping the nomenclature maze. miRiadne is freely accessible from the URL http://www.miriadne.org.
Collapse
Affiliation(s)
- Raoul J P Bonnal
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122 Milan, Italy
| | - Riccardo L Rossi
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122 Milan, Italy
| | - Donatella Carpi
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122 Milan, Italy
| | - Valeria Ranzani
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122 Milan, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122 Milan, Italy
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare 'Romeo ed Enrica Invernizzi', Via F. Sforza 35, 20122 Milan, Italy Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Festa del Perdono 7, 20122 Milano, Italy
| |
Collapse
|
19
|
Ranzani V, Rossetti G, Panzeri I, Arrigoni A, Bonnal RJ, Curti S, Gruarin P, Provasi E, Sugliano E, Marconi M, De Francesco R, Geginat J, Bodega B, Abrignani S, Pagani M. The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. Nat Immunol 2015; 16:318-325. [PMID: 25621826 PMCID: PMC4333215 DOI: 10.1038/ni.3093] [Citation(s) in RCA: 254] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 12/18/2014] [Indexed: 12/14/2022]
Abstract
Long non-coding-RNAs are emerging as important regulators of cellular functions but little is known on their role in human immune system. Here we investigated long intergenic non-coding-RNAs (lincRNAs) in thirteen T and B lymphocyte subsets by RNA-seq analysis and de novo transcriptome reconstruction. Over five hundred new lincRNAs were identified and lincRNAs signatures were described. Expression of linc-MAF-4, a chromatin-associated TH1-specific lincRNA, was inversely correlated with MAF, a TH2-associated transcription factor. Linc-MAF-4 down-regulation skewed T cell differentiation toward TH2. We identified a long-distance interaction between linc-MAF-4 and MAF genomic regions, where linc-MAF-4 associates with LSD1 and EZH2, suggesting linc-MAF-4 regulated MAF transcription by recruitment of chromatin modifiers. Our results demonstrate a key role of lincRNAs in T lymphocyte differentiation.
Collapse
Affiliation(s)
- Valeria Ranzani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Ilaria Panzeri
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Alberto Arrigoni
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Raoul Jp Bonnal
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Serena Curti
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Paola Gruarin
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Elena Provasi
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Elisa Sugliano
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Maurizio Marconi
- IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Raffaele De Francesco
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Jens Geginat
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Beatrice Bodega
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", 20122 Milano, Italy
| |
Collapse
|
20
|
Papaleo E, Tiberti M, Invernizzi G, Pasi M, Ranzani V. Molecular determinants of enzyme cold adaptation: comparative structural and computational studies of cold- and warm-adapted enzymes. Curr Protein Pept Sci 2012; 12:657-83. [PMID: 21827423 DOI: 10.2174/1389203711109070657] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2011] [Revised: 05/03/2011] [Accepted: 07/14/2011] [Indexed: 11/22/2022]
Abstract
The identification of molecular mechanisms underlying enzyme cold adaptation is a hot-topic both for fundamental research and industrial applications. In the present contribution, we review the last decades of structural computational investigations on cold-adapted enzymes in comparison to their warm-adapted counterparts. Comparative sequence and structural studies allow the definition of a multitude of adaptation strategies. Different enzymes carried out diverse mechanisms to adapt to low temperatures, so that a general theory for enzyme cold adaptation cannot be formulated. However, some common features can be traced in dynamic and flexibility properties of these enzymes, as well as in their intra- and inter-molecular interaction networks. Interestingly, the current data suggest that a family-centered point of view is necessary in the comparative analyses of cold- and warm-adapted enzymes. In fact, enzymes belonging to the same family or superfamily, thus sharing at least the three-dimensional fold and common features of the functional sites, have evolved similar structural and dynamic patterns to overcome the detrimental effects of low temperatures.
Collapse
Affiliation(s)
- Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.zza della Scienza 2, 20126, Milan, Italy.
| | | | | | | | | |
Collapse
|
21
|
Papaleo E, Tripodi F, Ranzani V, Vitriolo A, Valimberti I, Cirulli C. Towards a yeast cell cycle Sys-bio model. Regulation of family 3 ubiquitin-conjugating enzymes by phosphorylation: a molecular dynamics investigation. J Biotechnol 2010. [DOI: 10.1016/j.jbiotec.2010.09.840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|