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López-Arredondo A, Cruz-Cardenas JA, Cázares-Preciado JA, Timmins NE, Brunck ME. Neutrophils, an emerging new therapeutic platform. Curr Opin Biotechnol 2024; 87:103106. [PMID: 38490109 DOI: 10.1016/j.copbio.2024.103106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/30/2024] [Accepted: 02/19/2024] [Indexed: 03/17/2024]
Abstract
Neutrophils possess unique characteristics that render them indispensable to health, and patients with irregular neutrophil counts or functions suffer from increased morbidity and mortality. As neutrophils are short-lived postmitotic cells, genetic aberrations cannot be corrected directly in neutrophils and must be targeted in their progenitors. Neutrophils are increasingly being contemplated for a range of therapeutic applications, including restoration or modulation of immune function and targeting of solid tumors. This review addresses the state-of-the-art in neutrophil transfusions and their possible applications for infectious disease prevention and treatment. It offers a landscape of the most recent gene therapy approaches to address neutrophil-related genetic diseases. We also discuss how ongoing research could broaden the applicability of neutrophil-based therapies to solid cancer treatments and beyond.
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Affiliation(s)
- Alejandra López-Arredondo
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Tecnologico, 64849 Monterrey, Nuevo León, Mexico
| | - José A Cruz-Cardenas
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Tecnologico, 64849 Monterrey, Nuevo León, Mexico
| | - Jorge A Cázares-Preciado
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Tecnologico, 64849 Monterrey, Nuevo León, Mexico
| | - Nicholas E Timmins
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane QLD 4072, Australia
| | - Marion Eg Brunck
- Escuela de Ingeniería y Ciencias, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Tecnologico, 64849 Monterrey, Nuevo León, Mexico; The Institute for Obesity Research, Tecnologico de Monterrey, Av. Eugenio Garza Sada 2501 Sur, Tecnologico, 64849 Monterrey, Nuevo León, Mexico.
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2
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Ghanim HY, Porteus MH. Gene regulation in inborn errors of immunity: Implications for gene therapy design and efficacy. Immunol Rev 2024; 322:157-177. [PMID: 38233996 DOI: 10.1111/imr.13305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Inborn errors of immunity (IEI) present a unique paradigm in the realm of gene therapy, emphasizing the need for precision in therapeutic design. As gene therapy transitions from broad-spectrum gene addition to careful modification of specific genes, the enduring safety and effectiveness of these therapies in clinical settings have become crucial. This review discusses the significance of IEIs as foundational models for pioneering and refining precision medicine. We explore the capabilities of gene addition and gene correction platforms in modifying the DNA sequence of primary cells tailored for IEIs. The review uses four specific IEIs to highlight key issues in gene therapy strategies: X-linked agammaglobulinemia (XLA), X-linked chronic granulomatous disease (X-CGD), X-linked hyper IgM syndrome (XHIGM), and immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX). We detail the regulatory intricacies and therapeutic innovations for each disorder, incorporating insights from relevant clinical trials. For most IEIs, regulated expression is a vital aspect of the underlying biology, and we discuss the importance of endogenous regulation in developing gene therapy strategies.
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Affiliation(s)
- Hana Y Ghanim
- Division of Pediatrics, Division of Oncology, Hematology, Stem Cell Transplantation, Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew H Porteus
- Division of Pediatrics, Division of Oncology, Hematology, Stem Cell Transplantation, Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, California, USA
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3
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Grammatikos A, Gennery AR. Inflammatory Complications in Chronic Granulomatous Disease. J Clin Med 2024; 13:1092. [PMID: 38398405 PMCID: PMC10889279 DOI: 10.3390/jcm13041092] [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: 01/13/2024] [Revised: 02/08/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Chronic granulomatous disease (CGD) is a rare inborn error of immunity that typically manifests with infectious complications. As the name suggest though, inflammatory complications are also common, often affecting the gastrointestinal, respiratory, urinary tracts and other tissues. These can be seen in all various types of CGD, from X-linked and autosomal recessive to X-linked carriers. The pathogenetic mechanisms underlying these complications are not well understood, but are likely multi-factorial and reflect the body's attempt to control infections. The different levels of neutrophil residual oxidase activity are thought to contribute to the large phenotypic variations. Immunosuppressive agents have traditionally been used to treat these complications, but their use is hindered by the fact that CGD patients are predisposed to infection. Novel therapeutic agents, like anti-TNFa monoclonal antibodies, anakinra, ustekinumab, and vedolizumab offer promise for the future, while hematopoietic stem cell transplantation should also be considered in these patients.
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Affiliation(s)
- Alexandros Grammatikos
- The Bristol Immunology and Allergy Centre, North Bristol NHS Trust, Bristol BS10 5NB, UK
| | - Andrew R. Gennery
- Paediatric Stem Cell Transplant Unit, Great North Children’s Hospital, Newcastle upon Tyne NE1 4LP, UK;
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4
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Whittaker TE, Santilli G. Myelodysplasia and transgene inactivation in X-CGD-γ retroviral gene therapy: The usual suspects and new players. Mol Ther 2023; 31:3367-3368. [PMID: 37980903 PMCID: PMC10727967 DOI: 10.1016/j.ymthe.2023.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/21/2023] Open
Affiliation(s)
- Thomas E Whittaker
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Giorgia Santilli
- Infection, Immunity, and Inflammation Teaching and Research Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
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5
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Arnold DE, Pai SY. Progress in the field of hematopoietic stem cell-based therapies for inborn errors of immunity. Curr Opin Pediatr 2023; 35:663-670. [PMID: 37732933 PMCID: PMC10872717 DOI: 10.1097/mop.0000000000001292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
PURPOSE OF REVIEW Hematopoietic stem cell-based therapies, including allogeneic hematopoietic cell transplantation (HCT) and autologous gene therapy (GT), have been used as curative therapy for many inborn errors of immunity (IEI). As the number of genetically defined IEI and the use of HCT and GT increase, valuable data on outcomes and approaches for specific disorders are available. We review recent progress in HCT and GT for IEI in this article. RECENT FINDINGS Novel approaches to prevention of allogeneic complications and experience in adolescents and young adults have expanded the use of HCT. Universal newborn screening for severe combined immunodeficiency (SCID) has led to improved outcome after HCT. Analysis of outcomes of HCT and GT for SCID, Wiskott-Aldrich syndrome (WAS) and chronic granulomatous disease (CGD) reveal risk factors for survival, the impact of specific conditioning regimens, and vector- or disease-specific impacts on efficacy and safety. Preclinical studies of GT and gene editing show potential for translation to the clinic. SUMMARY Emerging data on outcome after HCT for specific IEI support early evaluation and treatment, before development of co-morbidities. Data in large cooperative retrospective databases continues to yield valuable insights clinicians can use in patient selection and choice of therapy.
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Affiliation(s)
- Danielle E. Arnold
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Sung-Yun Pai
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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Tsilifis C, Torppa T, Williams EJ, Albert MH, Hauck F, Soncini E, Kang E, Malech H, Schuetz C, von Bernuth H, Slatter MA, Gennery AR. Allogeneic HSCT for Symptomatic Female X-linked Chronic Granulomatous Disease Carriers. J Clin Immunol 2023; 43:1964-1973. [PMID: 37620741 PMCID: PMC10661721 DOI: 10.1007/s10875-023-01570-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 08/17/2023] [Indexed: 08/26/2023]
Abstract
X-linked chronic granulomatous disease (XL-CGD) is an inherited disorder of superoxide production, causing failure to generate the oxidative burst in phagocytes. It is characterized by invasive bacterial and fungal infections, inflammation, and chronic autoimmune disease. While XL-CGD carriers were previously assumed to be healthy, a range of clinical manifestations with significant morbidity have recently been described in a subgroup of carriers with impaired neutrophil oxidative burst due to skewed lyonization. Allogeneic hematopoietic stem cell transplantation (HSCT) is the standard curative treatment for CGD but has rarely been reported in individual symptomatic carriers to date. We undertook a retrospective international survey of outcome of HSCT for symptomatic XL-CGD carriers. Seven symptomatic female XL-CGD carriers aged 1-56 years underwent HSCT in four centers, indicated for severe and recurrent infection, colitis, and autoimmunity. Two patients died from transplant-related complications, following donor engraftment and restoration of oxidative burst. All surviving patients demonstrated resolution of their neutrophil oxidative burst defect with concordant reduction in infection and inflammatory symptoms and freedom from further immunosuppressive therapy. In conclusion, allogeneic HSCT may cure the phagocyte defect in symptomatic XL-CGD carriers and improve their recurrent and disabling infective and inflammatory symptoms but risks transplant-related complications.
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Affiliation(s)
- Christo Tsilifis
- Paediatric Haematopoietic Stem Cell Transplant Unit, Great North Children's Hospital, Ward 3, Newcastle Upon Tyne, NE1 4LP, UK.
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK.
| | - Tuulia Torppa
- School of Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Eleri J Williams
- Paediatric Haematopoietic Stem Cell Transplant Unit, Great North Children's Hospital, Ward 3, Newcastle Upon Tyne, NE1 4LP, UK
| | - Michael H Albert
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Fabian Hauck
- Department of Pediatrics, Dr. Von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Elena Soncini
- Paediatric Haematopoietic Stem Cell Transplant Unit, Children's Hospital ASST Spedali Civili, Brescia, Italy
| | - Elizabeth Kang
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Harry Malech
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Catharina Schuetz
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Horst von Bernuth
- Department of Pediatric Respiratory Medicine, Immunology, and Critical Care Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Immunology, Labor Berlin Charité-Vivantes, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health (BIH), Berlin, Germany
| | - Mary A Slatter
- Paediatric Haematopoietic Stem Cell Transplant Unit, Great North Children's Hospital, Ward 3, Newcastle Upon Tyne, NE1 4LP, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Andrew R Gennery
- Paediatric Haematopoietic Stem Cell Transplant Unit, Great North Children's Hospital, Ward 3, Newcastle Upon Tyne, NE1 4LP, UK
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
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Gosai SJ, Castro RI, Fuentes N, Butts JC, Kales S, Noche RR, Mouri K, Sabeti PC, Reilly SK, Tewhey R. Machine-guided design of synthetic cell type-specific cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.08.552077. [PMID: 37609287 PMCID: PMC10441439 DOI: 10.1101/2023.08.08.552077] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cis-regulatory elements (CREs) control gene expression, orchestrating tissue identity, developmental timing, and stimulus responses, which collectively define the thousands of unique cell types in the body. While there is great potential for strategically incorporating CREs in therapeutic or biotechnology applications that require tissue specificity, there is no guarantee that an optimal CRE for an intended purpose has arisen naturally through evolution. Here, we present a platform to engineer and validate synthetic CREs capable of driving gene expression with programmed cell type specificity. We leverage innovations in deep neural network modeling of CRE activity across three cell types, efficient in silico optimization, and massively parallel reporter assays (MPRAs) to design and empirically test thousands of CREs. Through in vitro and in vivo validation, we show that synthetic sequences outperform natural sequences from the human genome in driving cell type-specific expression. Synthetic sequences leverage unique sequence syntax to promote activity in the on-target cell type and simultaneously reduce activity in off-target cells. Together, we provide a generalizable framework to prospectively engineer CREs and demonstrate the required literacy to write regulatory code that is fit-for-purpose in vivo across vertebrates.
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Affiliation(s)
- SJ Gosai
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Graduate Program in Biological and Biomedical Science, Boston MA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - RI Castro
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - N Fuentes
- The Jackson Laboratory, Bar Harbor, ME, USA
- Harvard College, Harvard University, Cambridge, MA, USA
| | - JC Butts
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
| | - S Kales
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - RR Noche
- Department of Comparative Medicine, Yale School of Medicine, New Haven, CT, USA
- Yale Zebrafish Research Core, Yale School of Medicine, New Haven, CT, USA
| | - K Mouri
- The Jackson Laboratory, Bar Harbor, ME, USA
| | - PC Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department Of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - SK Reilly
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Wu Tsai Institute, Yale University, New Haven, CT, USA
| | - R Tewhey
- The Jackson Laboratory, Bar Harbor, ME, USA
- Graduate School of Biomedical Sciences and Engineering, University of Maine, Orono, ME, USA
- Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, MA, USA
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Tian M, Shen J, Qi Z, Feng Y, Fang P. Bioinformatics analysis and prediction of Alzheimer's disease and alcohol dependence based on Ferroptosis-related genes. Front Aging Neurosci 2023; 15:1201142. [PMID: 37520121 PMCID: PMC10373307 DOI: 10.3389/fnagi.2023.1201142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023] Open
Abstract
Background Alzheimer's disease (AD) is a neurodegenerative disease whose origins have not been universally accepted. Numerous studies have demonstrated the relationship between AD and alcohol dependence; however, few studies have combined the origins of AD, alcohol dependence, and programmed cell death (PCD) to analyze the mechanistic relationship between the development of this pair of diseases. We demonstrated in previous studies the relationship between psychiatric disorders and PCD, and in the same concerning neurodegeneration-related AD, we found an interesting link with the Ferroptosis pathway. In the present study, we explored the bioinformatic interactions between AD, alcohol dependence, and Ferroptosis and tried to elucidate and predict the development of AD from this aspect. Methods We selected the Alzheimer's disease dataset GSE118553 and alcohol dependence dataset GSE44456 from the Gene Expression Omnibus (GEO) database. Ferroptosis-related genes were gathered through Gene Set Enrichment Analysis (GSEA), Kyoto Encyclopedia of Genes and Genomes (KEGG), and relevant literature, resulting in a total of 88 related genes. For the AD and alcohol dependence datasets, we conducted Limma analysis to identify differentially expressed genes (DEGs) and performed functional enrichment analysis on the intersection set. Furthermore, we used ferroptosis-related genes and the DEGs to perform machine learning crossover analysis, employing Least Absolute Shrinkage and Selection Operator (LASSO) regression to identify candidate immune-related central genes. This analysis was also used to construct protein-protein interaction networks (PPI) and artificial neural networks (ANN), as well as to plot receiver operating characteristic (ROC) curves for diagnosing AD and alcohol dependence. We analyzed immune cell infiltration to explore the role of immune cell dysregulation in AD. Subsequently, we conducted consensus clustering analysis of AD using three relevant candidate gene models and examined the immune microenvironment and functional pathways between different subgroups. Finally, we generated a network of gene-gene interactions and miRNA-gene interactions using Networkanalyst. Results The crossover of AD and alcohol dependence DEG contains 278 genes, and functional enrichment analysis showed that both AD and alcohol dependence were strongly correlated with Ferroptosis, and then crossed them with Ferroptosis-related genes to obtain seven genes. Three candidate genes were finally identified by machine learning to build a diagnostic prediction model. After validation by ANN and PPI analysis, ROC curves were plotted to assess the diagnostic value of AD and alcohol dependence. The results showed a high diagnostic value of the predictive model. In the immune infiltration analysis, functional metabolism and immune microenvironment of AD patients were significantly associated with Ferroptosis. Finally, analysis of target genes and miRNA-gene interaction networks showed that hsa-mir-34a-5p and has-mir-106b-5p could simultaneously regulate the expression of both CYBB and ACSL4. Conclusion We obtained a diagnostic prediction model with good effect by comprehensive analysis, and validation of ROC in AD and alcohol dependence data sets showed good diagnostic, predictive value for both AD (AUC 0. 75, CI 0.91-0.60), and alcohol dependence (AUC 0.81, CI 0.95-0.68). In the consensus clustering grouping, we identified variability in the metabolic and immune microenvironment between subgroups as a likely cause of the different prognosis, which was all related to Ferroptosis function. Finally, we discovered that hsa-mir-34a-5p and has-mir-106b-5p could simultaneously regulate the expression of both CYBB and ACSL4.
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Affiliation(s)
- Mei Tian
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Nanjing, China
| | - Jing Shen
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Nanjing, China
| | - Zhiqiang Qi
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Nanjing, China
| | - Yu Feng
- Medicine and Health, The University of New South Wales, Kensington, NSW, Australia
- Melbourne Medical School, The University of Melbourne, Parkville, VIC, Australia
| | - Peidi Fang
- The Affiliated Jiangsu Shengze Hospital of Nanjing Medical University, Nanjing, China
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Kajaste-Rudnitski A, Aiuti A. Towards improved yet regulated gene therapy for X-CGD. Blood 2023; 141:966-967. [PMID: 36862435 DOI: 10.1182/blood.2022018800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023] Open
Affiliation(s)
| | - Alessandro Aiuti
- IRCCS San Raffaele Scientific Institute
- Vita-Salute San Raffaele University
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