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Wu S, Fan Z, Kim P, Huang L, Zhou X. The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:619-631. [PMID: 36708807 PMCID: PMC10787018 DOI: 10.1016/j.gpb.2022.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 11/04/2022] [Accepted: 12/28/2022] [Indexed: 01/26/2023]
Abstract
Adenosine-to-inosine (A-to-I) RNA editing, constituting nearly 90% of all RNA editing events in humans, has been reported to contribute to the tumorigenesis in diverse cancers. However, the comprehensive map for functional A-to-I RNA editing events in cancers is still insufficient. To fill this gap, we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome Atlas. For individual candidate among ∼ 1,500,000 quantified RNA editing events, we performed diverse types of downstream functional annotations. Finally, we identified 24,236 potentially functional A-to-I RNA editing events, including the cases in APOL1, IGFBP3, GRIA2, BLCAP, and miR-589-3p. These events might play crucial roles in the scenarios of tumorigenesis, due to their tumor-related editing frequencies or probable effects on altered expression profiles, protein functions, splicing patterns, and microRNA regulations of tumor genes. Our functional A-to-I RNA editing events (https://ccsm.uth.edu/CAeditome/) will help better understand the cancer pathology from the A-to-I RNA editing aspect.
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Affiliation(s)
- Sijia Wu
- School of Life Science and Technology, Xidian University, Xi'an 710071, China
| | - Zhiwei Fan
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu 610040, China; Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
| | - Liyu Huang
- School of Life Science and Technology, Xidian University, Xi'an 710071, China.
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
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2
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Israr M, Lam F, DeVoti J, Mace EM, Papayannakos C, Abramson A, Steinberg BM, Bonagura VR. PGE 2 expression by HPV6/11-induced respiratory papillomas blocks NK cell activation in patients with recurrent respiratory papillomatosis. Eur J Immunol 2023; 53:e2250036. [PMID: 36608264 DOI: 10.1002/eji.202250036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 12/12/2022] [Accepted: 01/05/2023] [Indexed: 01/07/2023]
Abstract
Recurrent respiratory papillomatosis (RRP), a rare chronic disease caused primarily by human papillomavirus types 6 and 11, consists of repeated growth of premalignant papillomas in the airway. RRP is characterized by multiple abnormalities in innate and adaptive immunity. Natural killer (NK) cells play important roles in immune surveillance and are part of the innate immune responses that help prevent tumor growth. We identified that papillomas lack classical class I MHC and retain nonclassical class I MHC expression. Moreover, in this study, we have identified and characterized the mechanism that blocks NK cell targeting of papilloma cells. Here, we show for the first time that the PGE2 secreted by papilloma cells directly inhibits NK cells activation/degranulation principally through the PGE2 receptor EP2, and to a lesser extent through EP4 signaling. Thus, papilloma cells have a potent mechanism to block NK cell function that likely supports papilloma cell growth.
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Affiliation(s)
- Mohd Israr
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Fung Lam
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - James DeVoti
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Emily M Mace
- Department of Pediatrics, Vagelos College of Physicians and Surgeons, Columbia Medical Center, NY, USA
| | | | - Allan Abramson
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Bettie M Steinberg
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Vincent R Bonagura
- The Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
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3
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Insight into the potential candidate genes and signaling pathways involved in lymphoma disease in dogs using a comprehensive whole blood transcriptome analysis. Gene 2022; 838:146735. [PMID: 35835403 DOI: 10.1016/j.gene.2022.146735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/20/2022] [Accepted: 07/08/2022] [Indexed: 11/04/2022]
Abstract
Lymphoma is one of the most prevalent hematological cancers, accounting for 15-20 % of new cancer diagnoses in dogs. Therefore, this study aims to explore the important genes and pathways involved in canine lymphoma progression and understand the underlying molecular mechanisms using RNA sequencing. In this study, RNAs acquired from seven pairs of lymphoma and non-lymphoma blood samples were sequenced from different breeds of dogs. Sequencing reads were preprocessed, aligned with the reference genome, assembled and expressions were estimated through bioinformatics approaches. At a false discovery rate (FDR) < 0.05 and fold change (FC) ≥ 1.5, a total of 625 differentially expressed genes (DEGs) were identified between lymphoma and non-lymphoma samples, including 347 up-regulated DEGs such as SLC38A11, SCN3A, ZIC5 etc. and 278 down-regulated DEGs such as LOC475937, CSMD1, KRT14 etc. GO enrichment analysis showed that these DEGs were highly enriched for molecular function of ATP binding and calcium ion binding, cellular process of focal adhesion, and biological process of immune response, and defense response to virus. Similarly, KEGG pathways analysis revealed 11 significantly enriched pathways such as ECM-receptor interaction, cell cycle, PI3K-Akt signaling pathway, ABC transporters etc. In the protein-protein interaction (PPI) network, CDK1 was found to be a top hub gene with highest degree of connectivity. Three modules selected from the PPI network showed that canine lymphoma was highly associated with cell cycle, ECM-receptor interaction, hypertrophic cardiomyopathy, dilated cardiomyopathy and RIG-I-like receptor signaling pathway. Overall, our findings highlighted new candidate therapeutic targets for further testing in canine lymphoma and facilitate the understanding of molecular mechanism of lymphoma's progression in dogs.
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4
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Alizadeh-Ghodsi M, Owen KL, Townley SL, Zanker D, Rollin SP, Hanson AR, Shrestha R, Toubia J, Gargett T, Chernukhin I, Luu J, Cowley KJ, Clark A, Carroll JS, Simpson KJ, Winter JM, Lawrence MG, Butler LM, Risbridger GP, Thierry B, Taylor RA, Hickey TE, Parker BS, Tilley WD, Selth LA. Potent Stimulation of the Androgen Receptor Instigates a Viral Mimicry Response in Prostate Cancer. CANCER RESEARCH COMMUNICATIONS 2022; 2:706-724. [PMID: 36923279 PMCID: PMC10010308 DOI: 10.1158/2767-9764.crc-21-0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 05/18/2022] [Accepted: 07/01/2022] [Indexed: 11/16/2022]
Abstract
Inhibiting the androgen receptor (AR), a ligand-activated transcription factor, with androgen deprivation therapy is a standard-of-care treatment for metastatic prostate cancer. Paradoxically, activation of AR can also inhibit the growth of prostate cancer in some patients and experimental systems, but the mechanisms underlying this phenomenon are poorly understood. This study exploited a potent synthetic androgen, methyltestosterone (MeT), to investigate AR agonist-induced growth inhibition. MeT strongly inhibited growth of prostate cancer cells expressing AR, but not AR-negative models. Genes and pathways regulated by MeT were highly analogous to those regulated by DHT, although MeT induced a quantitatively greater androgenic response in prostate cancer cells. MeT potently downregulated DNA methyltransferases, leading to global DNA hypomethylation. These epigenomic changes were associated with dysregulation of transposable element expression, including upregulation of endogenous retrovirus (ERV) transcripts after sustained MeT treatment. Increased ERV expression led to accumulation of double-stranded RNA and a "viral mimicry" response characterized by activation of IFN signaling, upregulation of MHC class I molecules, and enhanced recognition of murine prostate cancer cells by CD8+ T cells. Positive associations between AR activity and ERVs/antiviral pathways were evident in patient transcriptomic data, supporting the clinical relevance of our findings. Collectively, our study reveals that the potent androgen MeT can increase the immunogenicity of prostate cancer cells via a viral mimicry response, a finding that has potential implications for the development of strategies to sensitize this cancer type to immunotherapies. Significance Our study demonstrates that potent androgen stimulation of prostate cancer cells can elicit a viral mimicry response, resulting in enhanced IFN signaling. This finding may have implications for the development of strategies to sensitize prostate cancer to immunotherapies.
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Affiliation(s)
- Mohammadreza Alizadeh-Ghodsi
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, SA, Australia
| | - Katie L. Owen
- Cancer Evolution and Metastasis Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Scott L. Townley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, SA, Australia
| | - Damien Zanker
- Cancer Evolution and Metastasis Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Samuel P.G. Rollin
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, SA, Australia
| | - Adrienne R. Hanson
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, SA, Australia
| | - Raj Shrestha
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
| | - John Toubia
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology and University of South Australia, Frome Road, Adelaide, SA, Australia
| | - Tessa Gargett
- Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, SA, Australia
| | - Igor Chernukhin
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Jennii Luu
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Karla J. Cowley
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Ashlee Clark
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Jason S. Carroll
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Kaylene J. Simpson
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jean M. Winter
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Mitchell G. Lawrence
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Cabrini Institute, Malvern, Victoria, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Lisa M. Butler
- South Australian Health and Medical Research Institute, Adelaide, SA, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA, Australia
| | - Gail P. Risbridger
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Cabrini Institute, Malvern, Victoria, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Benjamin Thierry
- ARC Centre of Excellence in Convergent Bio and Nano Science and Technology, University of South Australia, Frome Road, Adelaide, SA, Australia
- Future Industries Institute, University of South Australia, Mawson Lakes, SA, Australia
| | - Renea A. Taylor
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
- Cabrini Institute, Malvern, Victoria, Australia
- Melbourne Urological Research Alliance (MURAL), Monash Biomedicine Discovery Institute Cancer Program, Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
- Monash Partners Comprehensive Cancer Consortium, Monash Biomedicine Discovery Institute Cancer Program, Prostate Cancer Research Group, Department of Physiology, Monash University, Clayton, Victoria, Australia
| | - Theresa E. Hickey
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
| | - Belinda S. Parker
- Cancer Evolution and Metastasis Program, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Wayne D. Tilley
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, SA, Australia
| | - Luke A. Selth
- Dame Roma Mitchell Cancer Research Laboratories, Adelaide Medical School, The University of Adelaide, Adelaide, SA, Australia
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA, Australia
- Freemasons Centre for Male Health and Wellbeing, Flinders University, Bedford Park, SA, Australia
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5
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Renaude E, Kroemer M, Borg C, Peixoto P, Hervouet E, Loyon R, Adotévi O. Epigenetic Reprogramming of CD4 + Helper T Cells as a Strategy to Improve Anticancer Immunotherapy. Front Immunol 2021; 12:669992. [PMID: 34262562 PMCID: PMC8273698 DOI: 10.3389/fimmu.2021.669992] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/15/2021] [Indexed: 01/22/2023] Open
Abstract
Evidences highlight the role of various CD4+ helper T cells (CD4+ Th) subpopulations in orchestrating the immune responses against cancers. Epigenetics takes an important part in the regulation of CD4+ Th polarization and plasticity. In this review, we described the epigenetic factors that govern CD4+ T cells differentiation and recruitment in the tumor microenvironment and their subsequent involvement in the antitumor immunity. Finally, we discussed how to manipulate tumor reactive CD4+ Th responses by epigenetic drugs to improve anticancer immunotherapy.
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Affiliation(s)
- Elodie Renaude
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Centre Hospitalier Universitaire de Besançon, Centre d'Investigation Clinique, INSERM CIC 1431, Besançon, France
| | - Marie Kroemer
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Department of Pharmacy, University Hospital of Besançon, Besançon, France
| | - Christophe Borg
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Centre Hospitalier Universitaire de Besançon, Centre d'Investigation Clinique, INSERM CIC 1431, Besançon, France.,Department of Medical Oncology, University Hospital of Besançon, Besançon, France
| | - Paul Peixoto
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,EPIGENEXP Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Eric Hervouet
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,EPIGENEXP Platform, University of Bourgogne Franche-Comté, Besançon, France.,DImaCell Platform, University of Bourgogne Franche-Comté, Besançon, France
| | - Romain Loyon
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France
| | - Olivier Adotévi
- University of Bourgogne Franche-Comté, INSERM, EFS BFC, UMR1098, Interactions Hôte-Greffon-Tumeur/Ingénierie Cellulaire et Génique, Besançon, France.,Centre Hospitalier Universitaire de Besançon, Centre d'Investigation Clinique, INSERM CIC 1431, Besançon, France.,Department of Medical Oncology, University Hospital of Besançon, Besançon, France
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6
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Chianese A, Santella B, Ambrosino A, Stelitano D, Rinaldi L, Galdiero M, Zannella C, Franci G. Oncolytic Viruses in Combination Therapeutic Approaches with Epigenetic Modulators: Past, Present, and Future Perspectives. Cancers (Basel) 2021; 13:cancers13112761. [PMID: 34199429 PMCID: PMC8199618 DOI: 10.3390/cancers13112761] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/28/2021] [Accepted: 05/29/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Cancer rates have been accelerating significantly in recent years. Despite notable advances having been made in cancer therapy, and numerous studies being currently conducted in clinical trials, research is always looking for new treatment. Novel and promising anticancer therapies comprise combinations of oncolytic viruses and epigenetic modulators, including chromatin modifiers, such as DNA methyltransferase and histone deacetylases, and microRNA. Combinatorial treatments have several advantages: they enhance viral entry, replication, and spread between proximal cells and, moreover, they strengthen the immune response. In this review we summarize the main combination of therapeutic approaches, giving an insight into past, present, and future perspectives. Abstract According to the World Cancer Report, cancer rates have been increased by 50% with 15 million new cases in the year 2020. Hepatocellular carcinoma (HCC) is the only one of the most common tumors to cause a huge increase in mortality with a survival rate between 40% and 70% at 5 years, due to the high relapse and limitations associated with current therapies. Despite great progress in medicine, oncological research is always looking for new therapies: different technologies have been evaluated in clinical trials and others have been already used in clinics. Among them, oncolytic virotherapy represents a therapeutic option with a widespread possibility of approaches and applications. Oncolytic viruses are naturally occurring, or are engineered, viruses characterized by the unique features of preferentially infecting, replicating, and lysing malignant tumor cells, as well as activating the immune response. The combination of oncolytic virotherapy and chemical drugs are arousing great interest in the tumor treatment. In this scenario, novel and promising anticancer therapies comprise combinations of oncolytic viruses and epigenetic modulators or inhibitors of the signalling pathways. Combination treatments are required to improve the immune response and allow viral entry, replication, and diffusion between proximal cells. In this review, we summarize all combination therapies associated with virotherapy, including co-administered inhibitors of chromatin modifiers (combination strategies) and inserted target sites for miRNAs (recombination or arming strategies).
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Affiliation(s)
- Annalisa Chianese
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (A.A.); (D.S.); (M.G.)
| | - Biagio Santella
- Section of Microbiology and Virology, University Hospital “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Annalisa Ambrosino
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (A.A.); (D.S.); (M.G.)
| | - Debora Stelitano
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (A.A.); (D.S.); (M.G.)
| | - Luca Rinaldi
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (A.A.); (D.S.); (M.G.)
- Section of Microbiology and Virology, University Hospital “Luigi Vanvitelli”, 80138 Naples, Italy;
| | - Carla Zannella
- Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, 80138 Naples, Italy; (A.C.); (A.A.); (D.S.); (M.G.)
- Correspondence: (C.Z.); (G.F.)
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry “Scuola Medica Salernitana”, University of Salerno, 84081 Baronissi, Italy
- Correspondence: (C.Z.); (G.F.)
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7
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Human Endogenous Retrovirus Reactivation: Implications for Cancer Immunotherapy. Cancers (Basel) 2021; 13:cancers13091999. [PMID: 33919186 PMCID: PMC8122352 DOI: 10.3390/cancers13091999] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/08/2021] [Accepted: 04/18/2021] [Indexed: 12/16/2022] Open
Abstract
Human endogenous retroviruses (HERVs) derive from ancestral exogenous retroviruses whose genetic material has been integrated in our germline DNA. Several lines of evidence indicate that cancer immunotherapy may benefit from HERV reactivation, which can be induced either by drugs or by cellular changes occurring in tumor cells. Indeed, several studies indicate that HERV proviral DNA can be transcribed either to double-stranded RNA (dsRNA) that is sensed as a "danger signal" by pattern recognition receptors (PRRs), leading to a viral mimicry state, or to mRNA that is translated into proteins that may contribute to the landscape of tumor-specific antigens (TSAs). Alternatively, HERV reactivation is associated with the expression of long noncoding RNAs (lncRNAs). In this review, we will highlight recent findings on HERV reactivation in cancer and its implications for cancer immunotherapy.
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8
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Cunha Pereira T, Rodrigues-Santos P, Almeida JS, Rêgo Salgueiro F, Monteiro AR, Macedo F, Soares RF, Domingues I, Jacinto P, Sousa G. Immunotherapy and predictive immunologic profile: the tip of the iceberg. Med Oncol 2021; 38:51. [PMID: 33788049 DOI: 10.1007/s12032-021-01497-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 03/14/2021] [Indexed: 12/14/2022]
Abstract
The interplay between cancer and the immune system has been under investigation for more than a century. Immune checkpoint inhibitors have changed the outcome of several tumors; however, there is a significant percentage of patients presenting resistance to immunotherapy. Besides the action mechanism, it is essential to unravel this complex interplay between host immune system and tumorigenesis to determine an immune profile as a predictive factor to immune checkpoint blockade agents. Tumor expression of programmed death-ligand 1 (PD-L1), tumor mutational burden, or mismatch repair deficiency are recognized predictive biomarkers to immunotherapy but are insufficient to explain the response rates and heterogeneity across tumor sites. Therefore, it is crucial to explore the role of the tumor microenvironment in the diversity and clonality of tumor-infiltrating immune cells since different checkpoint molecules play an influential role in cytotoxic T cell activation. Moreover, cytokines, chemokines, and growth factors regulated by epigenetic factors play a complex part. Peripheral immune cells expressing PD-1/PD-L1 and the biologic roles of soluble immune checkpoint molecules are the subject of new lines of investigation. This article addresses some of the new molecules and mechanisms studied as possible predictive biomarkers to immunotherapy, linked with the concept of immune dynamics monitoring.
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Affiliation(s)
- Tatiana Cunha Pereira
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal.
| | - Paulo Rodrigues-Santos
- Immunology Institute, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Laboratory of Immunology and Oncology, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Jani Sofia Almeida
- Immunology Institute, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Laboratory of Immunology and Oncology, Center for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal
- Center of Investigation in Environment, Genetics and Oncobiology (CIMAGO), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Coimbra Institute for Clinical and Biomedical Research (iCBR), Faculty of Medicine, University of Coimbra, Coimbra, Portugal
- Center for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Fábio Rêgo Salgueiro
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal
| | - Ana Raquel Monteiro
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal
| | - Filipa Macedo
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal
| | - Rita Félix Soares
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal
| | - Isabel Domingues
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal
| | - Paula Jacinto
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal
| | - Gabriela Sousa
- Medical Oncology Department, Portuguese Oncolology Institute of Coimbra Francisco Gentil, Avenida Bissaya Barreto, 98, 3000-075, Coimbra, Portugal
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9
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Chen F, Zhang Y, Sucgang R, Ramani S, Corry D, Kheradmand F, Creighton CJ. Meta-analysis of host transcriptional responses to SARS-CoV-2 infection reveals their manifestation in human tumors. Sci Rep 2021; 11:2459. [PMID: 33510359 PMCID: PMC7844278 DOI: 10.1038/s41598-021-82221-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 01/18/2021] [Indexed: 12/15/2022] Open
Abstract
A deeper understanding of the molecular biology of SARS-CoV-2 infection, including the host response to the virus, is urgently needed. Commonalities exist between the host immune response to viral infections and cancer. Here, we defined transcriptional signatures of SARS-CoV-2 infection involving hundreds of genes common across lung adenocarcinoma cell lines (A549, Calu-3) and normal human bronchial epithelial cells (NHBE), with additional signatures being specific to one or both adenocarcinoma lines. Cross-examining eight transcriptomic databases, we found that host transcriptional responses of lung adenocarcinoma cells to SARS-CoV-2 infection shared broad similarities with host responses to multiple viruses across different model systems and patient samples. Furthermore, these SARS-CoV-2 transcriptional signatures were manifested within specific subsets of human cancer, involving ~ 20% of cases across a wide range of histopathological types. These cancer subsets show immune cell infiltration and inflammation and involve pathways linked to the SARS-CoV-2 response, such as immune checkpoint, IL-6, type II interferon signaling, and NF-κB. The cell line data represented immune responses activated specifically within the cancer cells of the tumor. Common genes and pathways implicated as part of the viral host response point to therapeutic strategies that may apply to both SARS-CoV-2 and cancer.
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Affiliation(s)
- Fengju Chen
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yiqun Zhang
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Richard Sucgang
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Sasirekha Ramani
- Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - David Corry
- Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey VA, Houston, TX, 77030, USA
- Departments of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Farrah Kheradmand
- Center for Translational Research in Inflammatory Diseases, Michael E. DeBakey VA, Houston, TX, 77030, USA
- Departments of Pathology and Immunology, Baylor College of Medicine, Houston, TX, 77030, USA
- Biology of Inflammation Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Chad J Creighton
- Dan L. Duncan Comprehensive Cancer Center Division of Biostatistics, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Medicine, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
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10
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Domankevich V, Efrati M, Schmidt M, Glikson E, Mansour F, Shai A, Cohen A, Zilberstein Y, Flaisher E, Galalae R, Kelson I, Keisari Y. RIG-1-Like Receptor Activation Synergizes With Intratumoral Alpha Radiation to Induce Pancreatic Tumor Rejection, Triple-Negative Breast Metastases Clearance, and Antitumor Immune Memory in Mice. Front Oncol 2020; 10:990. [PMID: 32766128 PMCID: PMC7379859 DOI: 10.3389/fonc.2020.00990] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/19/2020] [Indexed: 12/19/2022] Open
Abstract
Diffusing alpha-emitting radiation therapy (DaRT) employs intratumoral Ra-224-coated seeds that efficiently destroy solid tumors by slowly releasing alpha-emitting atoms inside the tumor. In immunogenic tumor models, DaRT was shown to activate systemic antitumor immunity. Agonists of the membrane-bound toll-like receptors (TLRs) enhanced these effects and led to tumor rejection. Here, we examined the combination of DaRT with agents that activate a different type of pattern recognition receptors, the cytoplasmatic RIG1-like receptors (RLRs). In response to cytoplasmatic viral dsRNA, RLRs activate an antiviral immune response that includes the elevation of antigen presentation. Thus, it was postulated that in low-immunogenic tumor models, RLR activation in tumor cells prior to the induction of their death by DaRT will be superior compared to TLR activation. Intratumoral cytoplasmatic delivery of the dsRNA mimic polyIC by polyethylenimine (PEI), was used to activate RLR, while polyIC without PEI was used to activate TLR. PolyIC(PEI) prior to DaRT synergistically retarded 4T1 triple-negative breast tumors and metastasis development more efficiently than polyIC and rejected panc02 pancreatic tumors in some of the treated mice. Splenocytes from treated mice, adoptively transferred to naive mice in combination with 4T1 tumor cells, delayed tumor development compared to naïve splenocytes. Low-dose cyclophosphamide, known to reduce T regulatory cell number, enhanced the effect of DaRT and polyIC(PEI) and led to high long-term survival rates under neoadjuvant settings, which confirmed metastasis clearance. The epigenetic drug decitabine, known to activate RLR in low doses, was given intraperitoneally prior to DaRT and caused tumor growth retardation, similar to local polyIC(PEI). The systemic and/or local administration of RLR activators was also tested in the squamous cell carcinoma (SCC) tumor model SQ2, in which a delay in tumor re-challenge development was demonstrated. We conclude that RIG-I-like activation prior to intratumoral alpha radiation may serve as a potent combination technique to reduce both tumor growth and the spread of distant metastases in low-immunogenic and metastatic tumor models.
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Affiliation(s)
- Vered Domankevich
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Alpha Tau Medical, Tel Aviv-Yafo, Israel
| | - Margalit Efrati
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Alpha Tau Medical, Tel Aviv-Yafo, Israel
| | - Michael Schmidt
- Alpha Tau Medical, Tel Aviv-Yafo, Israel.,Sackler Faculty of Exact Sciences, School of Physics and Astronomy, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Eran Glikson
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel.,Department of Otolaryngology, Head and Neck Surgery, Sheba Medical Center, Tel HaShomer, Israel
| | - Fairuz Mansour
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Amit Shai
- Alpha Tau Medical, Tel Aviv-Yafo, Israel
| | - Adi Cohen
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Yael Zilberstein
- Sackler Cellular and Molecular Imaging Center, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
| | | | - Razvan Galalae
- MedAustron, Wiener Neustadt, Austria.,Medical Faculty, Christian-Albrechts University, Kiel, Germany
| | - Itzhak Kelson
- Sackler Faculty of Exact Sciences, School of Physics and Astronomy, Tel Aviv University, Tel Aviv-Yafo, Israel
| | - Yona Keisari
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv-Yafo, Israel
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11
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Bolis M, Paroni G, Fratelli M, Vallerga A, Guarrera L, Zanetti A, Kurosaki M, Garattini SK, Gianni’ M, Lupi M, Pattini L, Barzago MM, Terao M, Garattini E. All-Trans Retinoic Acid Stimulates Viral Mimicry, Interferon Responses and Antigen Presentation in Breast-Cancer Cells. Cancers (Basel) 2020; 12:cancers12051169. [PMID: 32384653 PMCID: PMC7281473 DOI: 10.3390/cancers12051169] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/27/2020] [Accepted: 05/02/2020] [Indexed: 12/16/2022] Open
Abstract
All-trans retinoic acid (ATRA), a recognized differentiating agent, has significant potential in the personalized/stratified treatment of breast cancer. The present study reports on the molecular mechanisms underlying the anti-tumor activity of ATRA in breast cancer. The work is based on transcriptomic experiments performed on ATRA-treated breast cancer cell-lines, short-term tissue cultures of patient-derived mammary-tumors and a xenograft model. ATRA upregulates gene networks involved in interferon-responses, immune-modulation and antigen-presentation in retinoid-sensitive cells and tumors characterized by poor immunogenicity. ATRA-dependent upregulation of these gene networks is caused by a viral mimicry process, involving the activation of endogenous retroviruses. ATRA induces a non-canonical type of viral mimicry, which results in increased expression of the IRF1 (Interferon Responsive Factor 1) transcription factor and the DTX3L (Deltex-E3-Ubiquitin-Ligase-3L) downstream effector. Functional knockdown studies indicate that IRF1 and DTX3L are part of a negative feedback loop controlling ATRA-dependent growth inhibition of breast cancer cells. The study is of relevance from a clinical/therapeutic perspective. In fact, ATRA stimulates processes controlling the sensitivity to immuno-modulatory drugs, such as immune-checkpoint-inhibitors. This suggests that ATRA and immunotherapeutic agents represent rational combinations for the personalized treatment of breast cancer. Remarkably, ATRA-sensitivity seems to be relatively high in immune-cold mammary tumors, which are generally resistant to immunotherapy.
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Affiliation(s)
- Marco Bolis
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
- Functional Cancer Genomics Laboratory, Institute of Oncology Research, USI, University of Southern Switzerland, 6500 Bellinzona, Switzerland
- Bioinformatics Core Unit Institute of Oncology Research, Swiss Institute of Bioinformatics, 1000 Lausanne, Switzerland
| | - Gabriela Paroni
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Maddalena Fratelli
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Arianna Vallerga
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Luca Guarrera
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Adriana Zanetti
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Mami Kurosaki
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Silvio Ken Garattini
- Department of Oncology, Azienda Ospedaliera di Udine, DAME, Dipartimento di Area Medica Università degli Studi di Udine, 33100 Udine, Italy;
| | - Maurizio Gianni’
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Monica Lupi
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via La Masa 19, 20156 Milano, Italy;
| | - Linda Pattini
- Department of Electronics, Information and Bioengineering, Politecnico di Milano, 20156 Milano, Italy;
| | - Maria Monica Barzago
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Mineko Terao
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
| | - Enrico Garattini
- Laboratory of Molecular Biology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, via Mario Negri 2, 20156 Milano, Italy; (M.B.); (G.P.); (M.F.); (A.V.); (L.G.); (A.Z.); (M.K.); (M.G.); (M.M.B.); (M.T.)
- Correspondence: ; Tel.: +39-02-3901-4533
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