1
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Borrego A, Colombo F, de Souza JG, Jensen JR, Dassano A, Piazza R, Rodrigues dos Santos BA, Ribeiro OG, De Franco M, Cabrera WHK, Icimoto MY, Starobinas N, Magalhães G, Monteleone LF, Eto SF, DeOcesano-Pereira C, Goldfeder MB, Pasqualoto KFM, Dragani TA, Ibañez OCM. Pycard and BC017158 Candidate Genes of Irm1 Locus Modulate Inflammasome Activation for IL-1β Production. Front Immunol 2022; 13:899569. [PMID: 35799794 PMCID: PMC9254735 DOI: 10.3389/fimmu.2022.899569] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/05/2022] [Indexed: 11/13/2022] Open
Abstract
We identified Pycard and BC017158 genes as putative effectors of the Quantitative Trait locus (QTL) that we mapped at distal chromosome 7 named Irm1 for Inflammatory response modulator 1, controlling acute inflammatory response (AIR) and the production of IL-1β, dependent on the activation of the NLRP3 inflammasome. We obtained the mapping through genome-wide linkage analysis of Single Nucleotide Polymorphisms (SNPs) in a cross between High (AIRmax) and Low (AIRmin) responder mouse lines that we produced by several generations of bidirectional selection for Acute Inflammatory Response. A highly significant linkage signal (LOD score peak of 72) for ex vivo IL-1β production limited a 4 Mbp interval to chromosome 7. Sequencing of the locus region revealed 14 SNPs between “High” and “Low” responders that narrowed the locus to a 420 Kb interval. Variants were detected in non-coding regions of Itgam, Rgs10 and BC017158 genes and at the first exon of Pycard gene, resulting in an E19K substitution in the protein ASC (apoptosis associated speck-like protein containing a CARD) an adaptor molecule in the inflammasome complex. Silencing of BC017158 inhibited IL1-β production by stimulated macrophages and the E19K ASC mutation carried by AIRmin mice impaired the ex vivo IL-1β response and the formation of ASC specks in stimulated cells. IL-1β and ASC specks play major roles in inflammatory reactions and in inflammation-related diseases. Our results delineate a novel genetic factor and a molecular mechanism affecting the acute inflammatory response.
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Affiliation(s)
- Andrea Borrego
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | - Francesca Colombo
- Department of Research, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Nazionale dei Tumori, Milan, Italy
| | - Jean Gabriel de Souza
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
- Centre of New Target Discovery (CENTD), Instituto Butantan/GlaxoSmithKline (GSK)/Sao Paulo Research Foundation (FAPESP), São Paulo, Brazil
| | | | - Alice Dassano
- Department of Research, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Nazionale dei Tumori, Milan, Italy
| | - Rocco Piazza
- Department of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | | | | | | | | | | | - Nancy Starobinas
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | - Geraldo Magalhães
- Laboratory of Immunopathology, Instituto Butantan, São Paulo, Brazil
| | | | - Silas Fernandes Eto
- Laboratory of Development and Innovation, Instituto Butantan, São Paulo, Brazil
| | - Carlos DeOcesano-Pereira
- Centre of New Target Discovery (CENTD), Instituto Butantan/GlaxoSmithKline (GSK)/Sao Paulo Research Foundation (FAPESP), São Paulo, Brazil
| | | | | | - Tommaso A. Dragani
- Department of Research, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Istituto Nazionale dei Tumori, Milan, Italy
| | - Olga Célia Martinez Ibañez
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
- *Correspondence: Olga Célia Martinez Ibañez,
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Maspero D, Dassano A, Pintarelli G, Noci S, De Cecco L, Incarbone M, Tosi D, Santambrogio L, Dragani TA, Colombo F. Read-through transcripts in lung: germline genetic regulation and correlation with the expression of other genes. Carcinogenesis 2021; 41:918-926. [PMID: 32157280 DOI: 10.1093/carcin/bgaa020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/24/2020] [Accepted: 03/06/2020] [Indexed: 11/14/2022] Open
Abstract
Transcripts originating from the transcriptional read through of two adjacent, similarly oriented genes have been identified in normal and neoplastic tissues, but their functional role and the mechanisms that regulate their expression are mostly unknown. Here, we investigated whether the expression of read-through transcripts previously identified in the non-involved lung tissue of lung adenocarcinoma patients was genetically regulated. Data on genome-wide single nucleotide variant genotypes and expression levels of 10 read-through transcripts in 201 samples of lung tissue were combined to identify expression quantitative trait loci (eQTLs). Then, to identify genes whose expression levels correlated with the 10 read-through transcripts, we used whole transcriptome profiles available for 154 patients. For 8 read-though transcripts, we identified 60 eQTLs (false discovery rate <0.05), including 17 cis-eQTLs and 43 trans-eQTLs. These eQTLs did not maintain their behavior on the 'parental' genes involved in the read-through transcriptional event. The expression levels of 7 read-through transcripts were found to correlate with the expression of other genes: CHIA-PIFO and CTSC-RAB38 correlated with CHIA and RAB38, respectively, while 5 other read-through transcripts correlated with 43 unique non-parental transcripts; thus offering indications about the molecular processes in which these chimeric transcripts may be involved. We confirmed 9 eQTLs (for 4 transcripts) in the non-involved lung tissue from an independent series of 188 lung adenocarcinoma patients. Therefore, this study indicates that the expression of four read-through transcripts in normal lung tissue is under germline genetic regulation, and that this regulation is independent of that of the genes involved in the read-through event.
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Affiliation(s)
- Davide Maspero
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.,Department of Informatics, Systems and Communication, University of Milan-Bicocca, Milan, Italy
| | - Alice Dassano
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulia Pintarelli
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Noci
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Platform of Integrated Biology, Department of Applied Research and Technology Development, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Incarbone
- Department of Surgery, IRCCS Multimedica, Sesto S. Giovanni, Milan, Italy
| | - Davide Tosi
- Department of Surgery, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Luigi Santambrogio
- Department of Surgery, Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Tommaso A Dragani
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Colombo
- Genetic Epidemiology and Pharmacogenomics Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
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Carnovale C, Dassano A, Mosini G, Mazhar F, D'Addio F, Pozzi M, Radice S, Fiorina P, Clementi E. The β-cell effect of verapamil-based treatment in patients with type 2 diabetes: a systematic review. Acta Diabetol 2020; 57:117-131. [PMID: 31172294 DOI: 10.1007/s00592-019-01370-1] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/17/2019] [Indexed: 12/22/2022]
Abstract
AIMS The possibility that verapamil has new beneficial effects in diabetic patients in terms of an improvement in glycometabolic control has been put forward recently in several studies. However, to date the issue is still under debate. We conducted the first systematic review examining the impact of verapamil-based treatment on glycometabolic outcomes, in type 2 diabetes (T2D) patients. METHODS We searched the PubMed, MEDLINE, Embase, Cochrane and ClinicalTrials.gov up to 9 October 2018, for all studies evaluating whether verapamil-based treatment is associated with changes in glycated haemoglobin (HbA1c), fasting plasma glucose levels, glucose and C-peptide areas from baseline in humans, without restrictions for study type. RESULTS Plasma glucose levels were lowered significantly by verapamil-based treatment in patients with T2D (mean change - 13 ± 5.29; P = 0.049); HbA1c values were instead not affected by the drug (mean change - 0.10 ± 0.12; P = 0.453). In five studies, groups exposed to verapamil achieved lower value of glycometabolic outcomes: comparison with values recorded in control groups showed a significant difference, in terms of both HbA1c and plasma glucose levels. CONCLUSIONS Despite the fact that plasma glucose levels were lowered significantly by verapamil-based treatment in patients with T2D (the HbA1c values were not affected by the drug), the clinical significance of the glycometabolic response induced by verapamil-based treatment remains unclear due to the high variety of sample size and type of studies presently available. Further experimental and clinical trials are needed to clarify unambiguously the role of verapamil in metabolic control.
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Affiliation(s)
- Carla Carnovale
- Unit Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy.
| | - Alice Dassano
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, Università di Milano, 20157, Milan, Italy
| | - Giulia Mosini
- Unit Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
| | - Faizan Mazhar
- Unit Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
| | - Francesca D'Addio
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, Università di Milano, 20157, Milan, Italy
| | - Marco Pozzi
- Scientific Institute IRCCS Eugenio Medea, 23842, Bosisio Parini, Lecco, Italy
| | - Sonia Radice
- Unit Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
| | - Paolo Fiorina
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, Università di Milano, 20157, Milan, Italy
- Nephrology Division, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, ASST Fatebenefratelli-Sacco, 20157, Milan, Italy
| | - Emilio Clementi
- Unit Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
- Scientific Institute IRCCS Eugenio Medea, 23842, Bosisio Parini, Lecco, Italy
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4
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Carnovale C, Pozzi M, Dassano A, D'Addio F, Gentili M, Magni C, Clementi E, Radice S, Fiorina P. The impact of a successful treatment of hepatitis C virus on glyco-metabolic control in diabetic patients: a systematic review and meta-analysis. Acta Diabetol 2019; 56:341-354. [PMID: 30478781 DOI: 10.1007/s00592-018-1257-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 11/06/2018] [Indexed: 01/06/2023]
Abstract
AIMS The effect of HCV eradication following the use of direct-acting antiviral drugs (DAAs) on the glyco-metabolic control is unknown. Through a meta-analysis of available clinical studies, we investigated whether eradication of HCV infection with interferon-free DAAs is associated with improved glyco-metabolic control in diabetic patients. METHODS We searched the PubMed, MEDLINE and Embase, up to 08th June 2018, for all studies evaluating whether eradication of HCV infection with DAAs is associated with changes in glycated haemoglobin (HbA1c) and fasting plasma glucose (FPG) levels from baseline in human subjects, without restrictions for study type and language. Data were independently extracted by two researchers using pre-specified forms. Random effects meta-analyses were conducted on HbA1c and FPG levels before/after HCV eradication. RESULTS We found a significant mean reduction in HbA1c levels of - 0.45% (95% CI - 0.60 to - 0.30%; P < 0.001) and in FPG levels of - 22.03 mg/dL (95% CI - 41.61 to - 2.44 mg/dL; P = 0.03), with high heterogeneity between studies (χ2 = 20.4, P < 0.001, I2 = 80% and χ2 = 35.8, P = 0.001, I2 = 94%, respectively). The number of available manuscripts did not allow conducting a meta-regression to elucidate the role of sustained virological response and other confounders in determining the effect of direct-acting antiviral agents on HbA1c reduction. CONCLUSIONS We found a significant improvement in glyco-metabolic control after HCV eradication (in terms of glycated haemoglobin and fasting plasma glucose levels reduction) following direct-acting antiviral treatment in patients with established diabetes, including a consequent positive impact on anti-diabetic therapies.
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Affiliation(s)
- Carla Carnovale
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
| | - Marco Pozzi
- Scientific Institute IRCCS Eugenio Medea, 23842, Bosisio Parini, Lecco, Italy
| | - Alice Dassano
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, Università di Milano, 20157, Milan, Italy
| | - Francesca D'Addio
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, Università di Milano, 20157, Milan, Italy
| | - Marta Gentili
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
| | - Carlo Magni
- 1st Division of Infectious Diseases, ASST Fatebenefratelli-Sacco, 20157, Milan, Italy
| | - Emilio Clementi
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
- Scientific Institute IRCCS Eugenio Medea, 23842, Bosisio Parini, Lecco, Italy
| | - Sonia Radice
- Unit of Clinical Pharmacology, Department of Biomedical and Clinical Sciences L. Sacco, "Luigi Sacco" University Hospital, Università di Milano, Via GB Grassi 74, 20157, Milan, Italy
| | - Paolo Fiorina
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, Università di Milano, 20157, Milan, Italy
- Nephrology Division, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Endocrinology, ASST Fatebenefratelli-Sacco, 20157, Milan, Italy
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5
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Ben Nasr M, D'Addio F, Malvandi AM, Faravelli S, Castillo-Leon E, Usuelli V, Rocchio F, Letizia T, El Essawy AB, Assi E, Mameli C, Giani E, Macedoni M, Maestroni A, Dassano A, Loretelli C, Paroni M, Cannalire G, Biasucci G, Sala M, Biffi A, Zuccotti GV, Fiorina P. Prostaglandin E2 Stimulates the Expansion of Regulatory Hematopoietic Stem and Progenitor Cells in Type 1 Diabetes. Front Immunol 2018; 9:1387. [PMID: 29971065 PMCID: PMC6018202 DOI: 10.3389/fimmu.2018.01387] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 06/04/2018] [Indexed: 12/29/2022] Open
Abstract
Hematopoietic stem and progenitor cells (HSPCs) are multipotent stem cells that have been harnessed as a curative therapy for patients with hematological malignancies. Notably, the discovery that HSPCs are endowed with immunoregulatory properties suggests that HSPC-based therapeutic approaches may be used to treat autoimmune diseases. Indeed, infusion with HSPCs has shown promising results in the treatment of type 1 diabetes (T1D) and remains the only “experimental therapy” that has achieved a satisfactory rate of remission (nearly 60%) in T1D. Patients with newly diagnosed T1D have been successfully reverted to normoglycemia by administration of autologous HSPCs in association with a non-myeloablative immunosuppressive regimen. However, this approach is hampered by a high incidence of adverse effects linked to immunosuppression. Herein, we report that while the use of autologous HSPCs is capable of improving C-peptide production in patients with T1D, ex vivo modulation of HSPCs with prostaglandins (PGs) increases their immunoregulatory properties by upregulating expression of the immune checkpoint-signaling molecule PD-L1. Surprisingly, CXCR4 was upregulated as well, which could enhance HSPC trafficking toward the inflamed pancreatic zone. When tested in murine and human in vitro autoimmune assays, PG-modulated HSPCs were shown to abrogate the autoreactive T cell response. The use of PG-modulated HSPCs may thus provide an attractive and novel treatment of autoimmune diabetes.
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Affiliation(s)
- Moufida Ben Nasr
- Nephrology Division, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.,International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Francesca D'Addio
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Amir Mohammad Malvandi
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Silvia Faravelli
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Eduardo Castillo-Leon
- Nephrology Division, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States
| | - Vera Usuelli
- Nephrology Division, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.,International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Francesca Rocchio
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Teresa Letizia
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | | | - Emma Assi
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Chiara Mameli
- Department of Pediatrics, Buzzi Children Hospital, Milan, Italy.,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy.,Department of Pediatrics, Children's Hospital Buzzi, Milan, Italy
| | - Elisa Giani
- Department of Pediatrics, Buzzi Children Hospital, Milan, Italy.,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy.,Department of Pediatrics, Children's Hospital Buzzi, Milan, Italy
| | - Maddalena Macedoni
- Department of Pediatrics, Diabetes Service Studies, University of Milan, Ospedale dei Bambini Vittore Buzzi, Milan, Italy
| | - Anna Maestroni
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Alice Dassano
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Cristian Loretelli
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy
| | - Moira Paroni
- Department of Bioscience, University of Milan, Milan, Italy
| | - Giuseppe Cannalire
- Department of Pediatrics and Neonatology, Ospedale Guglielmo da Saliceto, Piacenza, Italy
| | - Giacomo Biasucci
- Department of Pediatrics and Neonatology, Ospedale Guglielmo da Saliceto, Piacenza, Italy
| | - Marco Sala
- Department of Pediatrics, Tradate Hospital, Tradate, Italy
| | - Alessandra Biffi
- Gene Therapy Program, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA, United States.,Harvard Medical School, Boston, MA, United States
| | - Gian Vincenzo Zuccotti
- International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy.,Department of Pediatrics, Buzzi Children Hospital, Milan, Italy.,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy.,Department of Pediatrics, Children's Hospital Buzzi, Milan, Italy
| | - Paolo Fiorina
- Nephrology Division, Boston Children's Hospital, Harvard Medical School, Boston, MA, United States.,International Center for T1D, Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, Department of Biomedical and Clinical Science L. Sacco, University of Milan, Milan, Italy.,Division of Endocrinology, ASST Sacco Fatebenefratelli-Sacco, Milan, Italy
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6
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Pintarelli G, Dassano A, Cotroneo CE, Galvan A, Noci S, Piazza R, Pirola A, Spinelli R, Incarbone M, Palleschi A, Rosso L, Santambrogio L, Dragani TA, Colombo F. Read-through transcripts in normal human lung parenchyma are down-regulated in lung adenocarcinoma. Oncotarget 2017; 7:27889-98. [PMID: 27058892 PMCID: PMC5053695 DOI: 10.18632/oncotarget.8556] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 02/18/2016] [Indexed: 12/26/2022] Open
Abstract
Read-through transcripts result from the continuous transcription of adjacent, similarly oriented genes, with the splicing out of the intergenic region. They have been found in several neoplastic and normal tissues, but their pathophysiological significance is unclear. We used high-throughput sequencing of cDNA fragments (RNA-Seq) to identify read-through transcripts in the non-involved lung tissue of 64 surgically treated lung adenocarcinoma patients. A total of 52 distinct read-through species was identified, with 24 patients having at least one read-through event, up to a maximum of 17 such transcripts in one patient. Sanger sequencing validated 28 of these transcripts and identified an additional 15, for a total of 43 distinct read-through events involving 35 gene pairs. Expression levels of 10 validated read-through transcripts were measured by quantitative PCR in pairs of matched non-involved lung tissue and lung adenocarcinoma tissue from 45 patients. Higher expression levels were observed in normal lung tissue than in the tumor counterpart, with median relative quantification ratios between normal and tumor varying from 1.90 to 7.78; the difference was statistically significant (P < 0.001, Wilcoxon's signed-rank test for paired samples) for eight transcripts: ELAVL1–TIMM44, FAM162B–ZUFSP, IFNAR2–IL10RB, INMT–FAM188B, KIAA1841–C2orf74, NFATC3–PLA2G15, SIRPB1–SIRPD, and SHANK3–ACR. This report documents the presence of read-through transcripts in apparently normal lung tissue, with inter-individual differences in patterns and abundance. It also shows their down-regulation in tumors, suggesting that these chimeric transcripts may function as tumor suppressors in lung tissue.
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Affiliation(s)
- Giulia Pintarelli
- Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Alice Dassano
- Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara E Cotroneo
- Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy.,Present Address: UCD School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Antonella Galvan
- Formerly, Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Sara Noci
- Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Rocco Piazza
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy.,Hematology and Clinical Research Unit, San Gerardo Hospital, Monza, Italy
| | - Alessandra Pirola
- Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Roberta Spinelli
- Formerly, Department of Health Sciences, University of Milano-Bicocca, Monza, Italy
| | - Matteo Incarbone
- Department of Surgery, San Giuseppe Hospital, Multimedica, Milan, Italy
| | - Alessandro Palleschi
- Department of Surgery, IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Lorenzo Rosso
- Department of Surgery, IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Luigi Santambrogio
- Department of Surgery, IRCCS Fondazione Cà Granda Ospedale Maggiore Policlinico, Università degli Studi di Milano, Milan, Italy
| | - Tommaso A Dragani
- Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Colombo
- Department of Predictive and Prevention Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
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7
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Dassano A, Pintarelli G, Cotroneo CE, Pettinicchio A, Forcati E, De Cecco L, Borrego A, Colombo F, Dragani TA, Manenti G. Complex genetic control of lung tumorigenesis in resistant mice strains. Cancer Sci 2017; 108:2281-2286. [PMID: 28796413 PMCID: PMC5666032 DOI: 10.1111/cas.13349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/27/2017] [Accepted: 08/05/2017] [Indexed: 12/18/2022] Open
Abstract
The SM/J mouse strain is resistant to chemically‐induced lung tumorigenesis despite having a haplotype, in the pulmonary adenoma susceptibility locus (Pas1) locus, that confers tumor susceptibility in other strains. To clarify this inconsistent genotype‐phenotype correlation, we crossed SM/J mice with another resistant strain and conducted genome‐wide linkage analysis in the (C57BL/6J × SM/J)F2 progeny exposed to urethane to induce lung tumors. Overall, >80% of F2 mice of both sexes developed from 1 to 20 lung tumors. Genotyping of 372 F2 mice for 744 informative non‐redundant SNPs dispersed over all autosomal chromosomes revealed four quantitative trait loci (QTLs) affecting lung tumor multiplicity, on chromosomes 3 (near rs13477379), 15 (rs6285067), 17 (rs33373629) and 18 (rs3706601), all with logarithm of the odds (LOD) scores >5. Four QTLs modulated total lung tumor volume, on chromosome 3 (rs13477379), 10 (rs13480702), 15 (rs6285067) and 17 (rs3682923), all with LOD scores >4. No QTL modulating lung tumor multiplicity or total volume was detected in Pas1 on chromosome 6. The present study demonstrates that the SM/J strain carries, at the Pas1 locus, the resistance allele: a finding that will facilitate identification of the Pas1 causal element. More generally, it demonstrates that lung tumorigenesis is under complex polygenic control even in a pedigree with low susceptibility to this neoplasia, suggesting that the genetics of lung tumorigenesis is much more complex than evidenced by the pulmonary adenoma susceptibility and resistance loci that have, so far, been mapped in a small number of crosses between a few inbred strains.
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Affiliation(s)
- Alice Dassano
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Giulia Pintarelli
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Chiara E Cotroneo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Angela Pettinicchio
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Elena Forcati
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy.,Department of Experimental Oncology and Molecular medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Andrea Borrego
- Laboratory of Immunogenetics, Instituto Butantan, São Paulo, Brazil
| | - Francesca Colombo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Tommaso A Dragani
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Giacomo Manenti
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
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Cotroneo CE, Dassano A, Colombo F, Pettinicchio A, Lecis D, Dugo M, De Cecco L, Dragani TA, Manenti G. Expression quantitative trait analysis reveals fine germline transcript regulation in mouse lung tumors. Cancer Lett 2016; 375:221-230. [PMID: 26966001 DOI: 10.1016/j.canlet.2016.02.054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 12/02/2015] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 01/24/2023]
Abstract
Gene expression modulates cellular functions in both physiologic and pathologic conditions. Herein, we carried out a genetic linkage study on the transcriptome of lung tumors induced by urethane in an (A/J x C57BL/6)F4 intercross population, whose individual lung tumor multiplicity (Nlung) is linked to the genotype at the Pulmonary adenoma susceptibility 1 (Pas1) locus. We found that expression levels of 1179 and 1579 genes are modulated by an expression quantitative trait locus (eQTL) in cis and in trans, respectively (LOD score > 5). Of note, the genomic area surrounding and including the Pas1 locus regulated 14 genes in cis and 857 genes in trans. In lung tumors of the same (A/J x C57BL/6)F4 mice, we found 1124 genes whose transcript levels associated with Nlung (FDR < 0.001). The expression levels of about a third of these genes (n = 401) were regulated by the genotype at the Pas1 locus. Pathway analysis of the sets of genes associated with Nlung and regulated by Pas1 revealed a set of 14 recurrently represented genes that are components or targets of the Ras-Erk and Pi3k-Akt signaling pathways. Altogether our results illustrate the architecture of germline control of gene expression in mouse lung cancer: they highlight the importance of Pas1 as a tumor-modifier locus, attribute to it a novel role as a major regulator of transcription in lung tumor nodules and strengthen the candidacy of the Kras gene as the effector of this locus.
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Affiliation(s)
- Chiara E Cotroneo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Alice Dassano
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Francesca Colombo
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Angela Pettinicchio
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Daniele Lecis
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Matteo Dugo
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Loris De Cecco
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Tommaso A Dragani
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy.
| | - Giacomo Manenti
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
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Galvan A, Colombo F, Frullanti E, Dassano A, Noci S, Wang Y, Eisen T, Matakidou A, Tomasello L, Vezzalini M, Sorio C, Dugo M, Ambrogi F, Iacobucci I, Martinelli G, Incarbone M, Alloisio M, Nosotti M, Tosi D, Santambrogio L, Pelosi G, Pastorino U, Houlston RS, Dragani TA. Germline polymorphisms and survival of lung adenocarcinoma patients: a genome-wide study in two European patient series. Int J Cancer 2015; 136:E262-71. [PMID: 25196286 DOI: 10.1002/ijc.29195] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [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: 02/28/2014] [Revised: 08/04/2014] [Accepted: 08/05/2014] [Indexed: 11/09/2022]
Abstract
In lung cancer, the survival of patients with the same clinical stage varies widely for unknown reasons. In this two-phase study, we examined the hypothesis that germline variations influence the survival of patients with lung adenocarcinoma. First, we analyzed existing genotype and clinical data from 289 UK-resident patients with lung adenocarcinoma, identifying 86 single nucleotide polymorphisms (SNPs) that associated with survival (p < 0.01). We then genotyped these candidate SNPs in a validation series of 748 patients from Italy that resulted genetically compatible with the UK series based on principal component analysis. In a Cox proportional hazard model adjusted for age, sex and clinical stage, four SNPs were confirmed on the basis of their having a hazard ratio (HR) indicating the same direction of effect in the two series and p < 0.05. The strongest association was provided by rs2107561, an intronic SNP of PTPRG, protein tyrosine phosphatase, receptor type, G; the C allele was associated with poorer survival in both patient series (pooled analysis loge HR = 0.31; 95% CI: 0.15-0.46, p = 8.5 × 10(-5) ). PTPRG mRNA levels in 43 samples of lung adenocarcinoma were 40% of those observed in noninvolved lung tissue from the same patients. PTPRG overexpression significantly inhibited the clonogenicity of A549 lung carcinoma cells and the anchorage-independent growth of the NCI-H460 large cell lung cancer line. These four germline variants represent promising candidates that, with further study, may help predict clinical outcome. In addition, the PTPRG locus may have a role in tumor progression.
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Dassano A, Noci S, Galbiati F, Colombo F, Trincucci G, Pettinicchio A, Dragani TA, Manenti G. Multigenic nature of the mouse pulmonary adenoma progression 1 locus. BMC Genomics 2013; 14:152. [PMID: 23497166 PMCID: PMC3602191 DOI: 10.1186/1471-2164-14-152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 12/21/2012] [Accepted: 03/01/2013] [Indexed: 11/10/2022] Open
Abstract
Background In an intercross between the SWR/J and BALB/c mouse strains, the pulmonary adenoma progression 1 (Papg1) locus on chromosome 4 modulates lung tumor size, one of several measures of lung tumor progression. This locus has not been fully characterized and defined in its extent and genetic content. Fine mapping of this and other loci affecting lung tumor phenotype is possible using recombinant inbred strains. Results A population of 376 mice, obtained by crossing mice of the SWR/J strain with CXBN recombinant inbred mice, was treated with a single dose of urethane and assayed for multiplicity of large lung tumors (N2lung). A genome-wide analysis comparing N2lung with 6364 autosomal SNPs revealed multiple peaks of association. The Papg1 locus had two peaks, at rs3654162 (70.574 Mb, -logP=2.8) and rs6209043 (86.606 Mb, -logP=2.7), joined by an interval of weaker statistical association; these data confirm the presence of Papg1 on chromosome 4 and reduce the mapping region to two stretches of ~6.8 and ~4.2 Mb, in the proximal and distal peaks, respectively. The distal peak included Cdkn2a, a gene already proposed as being involved in Papg1 function. Other loci possibly modulating N2lung were detected on chromosomes 5, 8, 9, 11, 15, and 19, but analysis for linkage disequilibrium of these putative loci with Papg1 locus suggested that only those on chromosomes 11 and 15 were true positives. Conclusions These findings suggest that Papg1 consists, most likely, of two distinct, nearby loci, and point to putative additional loci on chromosomes 11 and 15 modulating lung tumor size. Within Papg1, Cdkn2a appears to be a strong candidate gene while additional Papg1 genes await to be identified. Greater knowledge of the genetic and biochemical mechanisms underlying the germ-line modulation of lung tumor size in mice is relevant to other species, including humans, in that it may help identify new therapeutic targets in the fight against tumor progression.
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Affiliation(s)
- Alice Dassano
- Department of Predictive and Preventive Medicine, Fondazione IRCCS, Istituto Nazionale dei Tumori, Via Amadeo 42, Milan, 20133, Italy
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