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Singh S, Pandey AK, Malemnganba T, Prajapati VK. Technological advancements in viral vector designing and optimization for therapeutic applications. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 139:57-87. [PMID: 38448144 DOI: 10.1016/bs.apcsb.2023.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Viral vector engineering is critical to the advancement of several sectors of biotechnology, gene therapy, and vaccine development. These vectors were produced from viruses, were employed to deliver therapeutic genes or to alter biological processes. The potential for viral vectors to improve the precision, safety, and efficiency of therapeutic interventions has boosted their demand. The dynamic interplay between technological advancements and computational tools in establishing the landscape of viral vector engineering and vector optimization for therapeutic reasons is discussed in this chapter. It also emphasizes the importance of in silico techniques in maximizing vector potential for therapeutics and many phases of viral vector engineering, from genomic analysis to computer modelling and advancements to improve precise gene delivery. High-throughput screening propels the expedited process of vector selection, and computational techniques to analyze complex omics data to further enhance vector capabilities have been discussed. As in silico models reveal insights into off-target effects and integration sites, vector safety (biodistribution and toxicity) remains a crucial part and bridges the gap between preclinical and clinical investigations. Despite the limitations, this chapter depicts a future in which technology and computing merge to catapult viral vector therapy into an era of boundless possibilities.
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Affiliation(s)
- Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Kishangarh, Ajmer, Rajasthan, India
| | - Anurag Kumar Pandey
- College of Biotechnology, Sardar Vallabhbhai Patel University of Agriculture and Technology, Meerut, Uttar Pradesh, India
| | | | - Vijay Kumar Prajapati
- Department of Biochemistry, University of Delhi South Campus, Dhaula Kuan, New Delhi, India.
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Merelli I, Beretta S, Cesana D, Gennari A, Benedicenti F, Spinozzi G, Cesini D, Montini E, D’Agostino D, Calabria A. InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration. Database (Oxford) 2023; 2023:baad069. [PMID: 37935583 PMCID: PMC10630073 DOI: 10.1093/database/baad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/15/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
High-throughput clonal tracking in patients under hematopoietic stem cell gene therapy with integrating vector is instrumental in assessing bio-safety and efficacy. Monitoring the fate of millions of transplanted clones and their progeny across differentiation and proliferation over time leverages the identification of the vector integration sites, used as surrogates of clonal identity. Although γ-tracking retroviral insertion sites (γ-TRIS) is the state-of-the-art algorithm for clonal identification, the computational drawbacks in the tracking algorithm, based on a combinatorial all-versus-all strategy, limit its use in clinical studies with several thousands of samples per patient. We developed the first clonal tracking graph database, InCliniGene (https://github.com/calabrialab/InCliniGene), that imports the output files of γ-TRIS and generates the graph of clones (nodes) connected by arches if two nodes share common genomic features as defined by the γ-TRIS rules. Embedding both clonal data and their connections in the graph, InCliniGene can track all clones longitudinally over samples through data queries that fully explore the graph. This approach resulted in being highly accurate and scalable. We validated InCliniGene using an in vitro dataset, specifically designed to mimic clinical cases, and tested the accuracy and precision. InCliniGene allows extensive use of γ-TRIS in large gene therapy clinical applications and naturally realizes the full data integration of molecular and genomics data, clinical and treatment measurements and genomic annotations. Further extensions of InCliniGene with data federation and with application programming interface will support data mining toward precision, personalized and predictive medicine in gene therapy. Database URL: https://github.com/calabrialab/InCliniGene.
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Affiliation(s)
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniela Cesana
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Alessandro Gennari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniele Cesini
- Centro Nazionale Analisi Fotogrammi (CNAF), Istituto Nazionale di Fisica Nucleare, Viale Carlo Berti Pichat 6/2, Bologna 40127, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniele D’Agostino
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi (DIBRIS), Università degli Studi di Genova, Viale Causa 13, Genoa 16145, Italy
- Institute of Biomedical Technologies, Italian National Research Council, Via Fratelli Cervi 93, Segrate (MI) 20054, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
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Yan A, Baricordi C, Nguyen Q, Barbarossa L, Loperfido M, Biasco L. IS-Seq: a bioinformatics pipeline for integration sites analysis with comprehensive abundance quantification methods. BMC Bioinformatics 2023; 24:286. [PMID: 37464281 DOI: 10.1186/s12859-023-05390-1] [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: 02/14/2023] [Accepted: 06/16/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Integration site (IS) analysis is a fundamental analytical platform for evaluating the safety and efficacy of viral vector based preclinical and clinical Gene Therapy (GT). A handful of groups have developed standardized bioinformatics pipelines to process IS sequencing data, to generate reports, and/or to perform comparative studies across different GT trials. Keeping up with the technological advances in the field of IS analysis, different computational pipelines have been published over the past decade. These pipelines focus on identifying IS from single-read sequencing or paired-end sequencing data either using read-based or using sonication fragment-based methods, but there is a lack of a bioinformatics tool that automatically includes unique molecular identifiers (UMI) for IS abundance estimations and allows comparing multiple quantification methods in one integrated pipeline. RESULTS Here we present IS-Seq a bioinformatics pipeline that can process data from paired-end sequencing of both old restriction sites-based IS collection methods and new sonication-based IS retrieval systems while allowing the selection of different abundance estimation methods, including read-based, Fragment-based and UMI-based systems. CONCLUSIONS We validated the performance of IS-Seq by testing it against the most popular analytical workflow available in the literature (INSPIIRED) and using different scenarios. Lastly, by performing extensive simulation studies and a comprehensive wet-lab assessment of our IS-Seq pipeline we could show that in clinically relevant scenarios, UMI quantification provides better accuracy than the currently most widely used sonication fragment counts as a method for IS abundance estimation.
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Affiliation(s)
| | | | | | | | | | - Luca Biasco
- AVROBIO, Inc., Cambridge, MA, USA.
- Infection, Immunity and Inflammation Department, Great Ormond Street Institute of Child Health, University College London, London, UK.
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Cornetta K, Lin TY, Pellin D, Kohn DB. Meeting FDA Guidance recommendations for replication-competent virus and insertional oncogenesis testing. Mol Ther Methods Clin Dev 2023; 28:28-39. [PMID: 36588821 PMCID: PMC9791246 DOI: 10.1016/j.omtm.2022.11.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Integrating vectors are associated with alterations in cellular function related to disruption of normal gene function. This has been associated with clonal expansion of cells and, in some instances, cancer. These events have been associated with replication-defective vectors and suggest that the inadvertent exposure to a replication-competent virus arising during vector manufacture would significantly increase the risk of treatment-related adverse events. These risks have led regulatory agencies to require specific monitoring for replication-competent viruses, both prior to and after treatment of patients with gene therapy products. Monitoring the risk of cell expansion and malignancy is also required. In this review, we discuss the rational potential approaches and challenges to meeting the US FDA expectations listed in current guidance documents.
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Affiliation(s)
- Kenneth Cornetta
- Gene Therapy Testing Laboratory, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- National Gene Vector Biorepository, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Tsai-Yu Lin
- Gene Therapy Testing Laboratory, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
- National Gene Vector Biorepository, Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Danilo Pellin
- Gene Therapy Program, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Donald B. Kohn
- Departments of Microbiology, Immunology and Molecular Genetics, and Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
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Kukkar D, Sharma PK, Kim KH. Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass. ENVIRONMENTAL RESEARCH 2022; 215:114369. [PMID: 36165858 DOI: 10.1016/j.envres.2022.114369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/06/2022] [Accepted: 09/15/2022] [Indexed: 06/16/2023]
Abstract
Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.
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Affiliation(s)
- Deepak Kukkar
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India; University Centre for Research and Development, Chandigarh University, Gharuan, Mohali - 140413, Punjab, India.
| | | | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, Seongdong-gu, Wangsimni-ro, Seoul - 04763, South Korea.
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Dalwadi DA, Calabria A, Tiyaboonchai A, Posey J, Naugler WE, Montini E, Grompe M. AAV integration in human hepatocytes. Mol Ther 2021; 29:2898-2909. [PMID: 34461297 DOI: 10.1016/j.ymthe.2021.08.031] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 08/01/2021] [Accepted: 08/24/2021] [Indexed: 12/17/2022] Open
Abstract
Recombinant adeno-associated viral (rAAV) vectors are considered promising tools for gene therapy directed at the liver. Whereas rAAV is thought to be an episomal vector, its single-stranded DNA genome is prone to intra- and inter-molecular recombination leading to rearrangements and integration into the host cell genome. Here, we ascertained the integration frequency of rAAV in human hepatocytes transduced either ex vivo or in vivo and subsequently expanded in a mouse model of xenogeneic liver regeneration. Chromosomal rAAV integration events and vector integrity were determined using the capture-PacBio sequencing approach, a long-read next-generation sequencing method that has not previously been used for this purpose. Chromosomal integrations were found at a surprisingly high frequency of 1%-3% both in vitro and in vivo. Importantly, most of the inserted rAAV sequences were heavily rearranged and were accompanied by deletions of the host genomic sequence at the integration site.
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Affiliation(s)
- Dhwanil A Dalwadi
- Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Amita Tiyaboonchai
- Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Jeffrey Posey
- Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA
| | - Willscott E Naugler
- Department of Medicine, Division of Gastroenterology and Hepatology, Oregon Health and Science University, Portland, OR 97239, USA
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
| | - Markus Grompe
- Papé Family Pediatric Research Institute, Department of Pediatrics, Oregon Health and Science University, Portland, OR 97239, USA.
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Ricca A, Cascino F, Morena F, Martino S, Gritti A. In vitro Validation of Chimeric β-Galactosylceramidase Enzymes With Improved Enzymatic Activity and Increased Secretion. Front Mol Biosci 2020; 7:167. [PMID: 32850960 PMCID: PMC7396597 DOI: 10.3389/fmolb.2020.00167] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 07/01/2020] [Indexed: 12/27/2022] Open
Abstract
Globoid Cell Leukodystrophy (GLD) is a lysosomal storage disease (LSD) caused by inherited defects of the β-galactosylceramidase (GALC) gene. The infantile forms display a rapid and aggressive central and peripheral nervous system (CNS and PNS) dysfunction. No treatments are available for GLD patients. Effective gene therapy (GT) strategies for GLD require a safe and widespread delivery of the functional GALC enzyme to all affected tissues/organs, and particularly to the CNS. The use of chimeric lysosomal enzymes with increased secretion and enhanced transport across the blood-brain barrier (BBB) that boost the efficacy of GT approaches in pre-clinical models of similar neurodegenerative LSDs may benefit GLD as well. Here, we tested the safety and biological efficacy of chimeric GALC enzymes engineered to express an alternative signal peptide (iduronate-2-sulfatase - IDSsp) and the low-density lipoprotein receptor (LDLr)-binding domain from the Apolipoprotein E II (ApoE II) in GLD murine neural and hematopoietic stem/progenitor cells and progeny, which are relevant cells types in the context of in vivo and ex vivo GT platforms. We show that the lentiviral vector-mediated expression of the chimeric GALC enzymes is safe and leads to supranormal enzymatic activity in both neural and hematopoietic cells. The IDSsp.GALC shows enhanced expression and secretion in comparison to the unmodified GALC. The chimeric GALC enzymes produced by LV-transduced cells reduce intracellular galactosylceramide (GalCer) storage and effectively cross-correct GLD murine neurons and glial cells, indicating that the transgenic enzymes are delivered to lysosomes, efficiently secreted, and functional. Of note, the expression of LDLr and LDLr-related proteins in GLD neurons and glial cells supports the exploitation of this system to enhance the GALC supply in affected CNS cells and tissues. These in vitro studies support the use of chimeric GALC enzymes to develop novel and more effective GT approaches for GLD.
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Affiliation(s)
- Alessandra Ricca
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Federica Cascino
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University, Milan, Italy
| | - Francesco Morena
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Sabata Martino
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Angela Gritti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy
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Calabria A, Beretta S, Merelli I, Spinozzi G, Brasca S, Pirola Y, Benedicenti F, Tenderini E, Bonizzoni P, Milanesi L, Montini E. γ-TRIS: a graph-algorithm for comprehensive identification of vector genomic insertion sites. Bioinformatics 2020; 36:1622-1624. [PMID: 31589304 PMCID: PMC7703754 DOI: 10.1093/bioinformatics/btz747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 09/18/2019] [Accepted: 10/01/2019] [Indexed: 01/01/2023] Open
Abstract
Summary Retroviruses and their vector derivatives integrate semi-randomly in the genome of host cells and are inherited by their progeny as stable genetic marks. The retrieval and mapping of the sequences flanking the virus-host DNA junctions allows the identification of insertion sites in gene therapy or virally infected patients, essential for monitoring the evolution of genetically modified cells in vivo. However, since ∼30% of insertions land in low complexity or repetitive regions of the host cell genome, they cannot be correctly assigned and are currently discarded, limiting the accuracy and predictive power of clonal tracking studies. Here, we present γ-TRIS, a new graph-based genome-free alignment tool for identifying insertion sites even if embedded in low complexity regions. By using γ-TRIS to reanalyze clinical studies, we observed improvements in clonal quantification and tracking. Availability and implementation Source code at https://bitbucket.org/bereste/g-tris. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy
| | - Stefano Beretta
- Università degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO), Viale Sarca, 336, 20126, Milano, Italy.,National Research Council, Institute for Biomedical Technologies, Via Fratelli Cervi, 93, 20090, Segrate, Italy
| | - Ivan Merelli
- National Research Council, Institute for Biomedical Technologies, Via Fratelli Cervi, 93, 20090, Segrate, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy.,Università degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO), Viale Sarca, 336, 20126, Milano, Italy
| | - Stefano Brasca
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy
| | - Yuri Pirola
- Università degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO), Viale Sarca, 336, 20126, Milano, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy
| | - Erika Tenderini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy
| | - Paola Bonizzoni
- Università degli Studi di Milano Bicocca, Dipartimento di Informatica Sistemistica e Comunicazione (DiSCO), Viale Sarca, 336, 20126, Milano, Italy
| | - Luciano Milanesi
- National Research Council, Institute for Biomedical Technologies, Via Fratelli Cervi, 93, 20090, Segrate, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, via Olgettina 60, 20132, Milan, Italy
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Visigalli I, Delai S, Ferro F, Cecere F, Vezzoli M, Sanvito F, Chanut F, Benedicenti F, Spinozzi G, Wynn R, Calabria A, Naldini L, Montini E, Cristofori P, Biffi A. Preclinical Testing of the Safety and Tolerability of Lentiviral Vector-Mediated Above-Normal Alpha-L-Iduronidase Expression in Murine and Human Hematopoietic Cells Using Toxicology and Biodistribution Good Laboratory Practice Studies. Hum Gene Ther 2018; 27:813-829. [PMID: 27431943 DOI: 10.1089/hum.2016.068] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
In order to support the clinical application of hematopoietic stem cell (HSC) gene therapy for mucopolysaccharidosis I (MPS I), biosafety studies were conducted to assess the toxicity and tumorigenic potential, as well as the biodistribution of HSCs and progenitor cells (HSPCs) transduced with lentiviral vectors (LV) encoding the cDNA of the alpha-iduronidase (IDUA) gene, which is mutated in MPS I patients. To this goal, toxicology and biodistribution studies were conducted, employing Good Laboratory Practice principles. Vector integration site (IS) studies were applied in order to predict adverse consequences of vector gene transfer and to obtain HSC-related information. Overall, the results obtained in these studies provided robust evidence to support the safety and tolerability of high-efficiency LV-mediated gene transfer and above-normal IDUA enzyme expression in both murine and human HSPCs and their in vivo progeny. Taken together, these investigations provide essential safety data to support clinical testing of HSC gene therapy in MPS I patients. These studies also underline criticisms associated with the use of currently available models, and highlight the value of surrogate markers of tumorigenicity that may be further explored in the future. Notably, biological evidence supporting the efficacy of gene therapy on MPS I disease and its feasibility on patients' HSCs were also generated, employing clinical-grade LVs. Finally, the clonal contribution of LV-transduced HSPCs to hematopoiesis along serial transplantation was quantified in a minimum of 200-300 clones, with the different level of repopulating cells in primary recipients being reflected in the secondary.
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Affiliation(s)
- Ilaria Visigalli
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Stefania Delai
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Francesca Ferro
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Francesca Cecere
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Michela Vezzoli
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Francesca Sanvito
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy.,2 Department of Pathology, IRCCS San Raffaele Scientific Institute , Milan, Italy
| | - Franck Chanut
- 3 Glaxo Smith Kline R&D UK Safety Assessment , Stevenage, United Kingdom.,5 Sanofi , Montpellier, France
| | - Fabrizio Benedicenti
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Giulio Spinozzi
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Rob Wynn
- 6 Royal Manchester Children's Hospital , Manchester, United Kingdom
| | - Andrea Calabria
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Luigi Naldini
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy.,4 Vita Salute San Raffaele University , Milan, Italy
| | - Eugenio Montini
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
| | - Patrizia Cristofori
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy.,3 Glaxo Smith Kline R&D UK Safety Assessment , Stevenage, United Kingdom
| | - Alessandra Biffi
- 1 San Raffaele Telethon Institute for Gene Therapy (SR-TIGET) , Division of Regenerative Medicine, Stem Cells and Gene Therapy, Milan, Italy
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VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites. BMC Bioinformatics 2017; 18:520. [PMID: 29178837 PMCID: PMC5702242 DOI: 10.1186/s12859-017-1937-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/14/2017] [Indexed: 01/09/2023] Open
Abstract
Background Bioinformatics tools designed to identify lentiviral or retroviral vector insertion sites in the genome of host cells are used to address the safety and long-term efficacy of hematopoietic stem cell gene therapy applications and to study the clonal dynamics of hematopoietic reconstitution. The increasing number of gene therapy clinical trials combined with the increasing amount of Next Generation Sequencing data, aimed at identifying integration sites, require both highly accurate and efficient computational software able to correctly process “big data” in a reasonable computational time. Results Here we present VISPA2 (Vector Integration Site Parallel Analysis, version 2), the latest optimized computational pipeline for integration site identification and analysis with the following features: (1) the sequence analysis for the integration site processing is fully compliant with paired-end reads and includes a sequence quality filter before and after the alignment on the target genome; (2) an heuristic algorithm to reduce false positive integration sites at nucleotide level to reduce the impact of Polymerase Chain Reaction or trimming/alignment artifacts; (3) a classification and annotation module for integration sites; (4) a user friendly web interface as researcher front-end to perform integration site analyses without computational skills; (5) the time speedup of all steps through parallelization (Hadoop free). Conclusions We tested VISPA2 performances using simulated and real datasets of lentiviral vector integration sites, previously obtained from patients enrolled in a hematopoietic stem cell gene therapy clinical trial and compared the results with other preexisting tools for integration site analysis. On the computational side, VISPA2 showed a > 6-fold speedup and improved precision and recall metrics (1 and 0.97 respectively) compared to previously developed computational pipelines. These performances indicate that VISPA2 is a fast, reliable and user-friendly tool for integration site analysis, which allows gene therapy integration data to be handled in a cost and time effective fashion. Moreover, the web access of VISPA2 (http://openserver.itb.cnr.it/vispa/) ensures accessibility and ease of usage to researches of a complex analytical tool. We released the source code of VISPA2 in a public repository (https://bitbucket.org/andreacalabria/vispa2). Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1937-9) contains supplementary material, which is available to authorized users.
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Cesana D, Santoni de Sio FR, Rudilosso L, Gallina P, Calabria A, Beretta S, Merelli I, Bruzzesi E, Passerini L, Nozza S, Vicenzi E, Poli G, Gregori S, Tambussi G, Montini E. HIV-1-mediated insertional activation of STAT5B and BACH2 trigger viral reservoir in T regulatory cells. Nat Commun 2017; 8:498. [PMID: 28887441 PMCID: PMC5591266 DOI: 10.1038/s41467-017-00609-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 07/12/2017] [Indexed: 12/13/2022] Open
Abstract
HIV-1 insertions targeting BACH2 or MLK2 are enriched and persist for decades in hematopoietic cells from patients under combination antiretroviral therapy. However, it is unclear how these insertions provide such selective advantage to infected cell clones. Here, we show that in 30/87 (34%) patients under combination antiretroviral therapy, BACH2, and STAT5B are activated by insertions triggering the formation of mRNAs that contain viral sequences fused by splicing to their first protein-coding exon. These chimeric mRNAs, predicted to express full-length proteins, are enriched in T regulatory and T central memory cells, but not in other T lymphocyte subsets or monocytes. Overexpression of BACH2 or STAT5B in primary T regulatory cells increases their proliferation and survival without compromising their function. Hence, we provide evidence that HIV-1-mediated insertional activation of BACH2 and STAT5B favor the persistence of a viral reservoir in T regulatory cells in patients under combination antiretroviral therapy. HIV insertions in hematopoietic cells are enriched in BACH2 or MLK2 genes, but the selective advantages conferred are unknown. Here, the authors show that BACH2 and additionally STAT5B are activated by viral insertions, generating chimeric mRNAs specifically enriched in T regulatory cells favoring their persistence.
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Affiliation(s)
- Daniela Cesana
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy.
| | - Francesca R Santoni de Sio
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Laura Rudilosso
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Pierangela Gallina
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Stefano Beretta
- Department of Informatics, Systems and Communication, University of Milano-Bicocca, Viale Sarca 336, Milan, 20126, Italy.,National Research Council, Institute for Biomedical Technologies, Via Fratelli Cervi 93, Segrate, 20090, Italy
| | - Ivan Merelli
- National Research Council, Institute for Biomedical Technologies, Via Fratelli Cervi 93, Segrate, 20090, Italy
| | - Elena Bruzzesi
- Department of Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Laura Passerini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Silvia Nozza
- Department of Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Elisa Vicenzi
- Viral Pathogens and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Guido Poli
- AIDS Immunopathogenesis Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy.,Vita-Salute San Raffaele University School of Medicine, Milan, 20132, Italy
| | - Silvia Gregori
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Giuseppe Tambussi
- Department of Infectious Diseases, IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS, San Raffaele Scientific Institute, Milan, 20132, Italy.
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12
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Kamboj A, Hallwirth CV, Alexander IE, McCowage GB, Kramer B. Ub-ISAP: a streamlined UNIX pipeline for mining unique viral vector integration sites from next generation sequencing data. BMC Bioinformatics 2017. [PMID: 28623888 PMCID: PMC5474025 DOI: 10.1186/s12859-017-1719-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The analysis of viral vector genomic integration sites is an important component in assessing the safety and efficiency of patient treatment using gene therapy. Alongside this clinical application, integration site identification is a key step in the genetic mapping of viral elements in mutagenesis screens that aim to elucidate gene function. RESULTS We have developed a UNIX-based vector integration site analysis pipeline (Ub-ISAP) that utilises a UNIX-based workflow for automated integration site identification and annotation of both single and paired-end sequencing reads. Reads that contain viral sequences of interest are selected and aligned to the host genome, and unique integration sites are then classified as transcription start site-proximal, intragenic or intergenic. CONCLUSION Ub-ISAP provides a reliable and efficient pipeline to generate large datasets for assessing the safety and efficiency of integrating vectors in clinical settings, with broader applications in cancer research. Ub-ISAP is available as an open source software package at https://sourceforge.net/projects/ub-isap/ .
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Affiliation(s)
- Atul Kamboj
- Children's Cancer Research Unit, Kids' Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia.
| | - Claus V Hallwirth
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Ian E Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute and The Children's Hospital at Westmead, Westmead, NSW, Australia.,The University of Sydney, Discipline of Paediatrics and Child Health, Westmead, NSW, Australia
| | - Geoffrey B McCowage
- Cancer Centre for Children, The Children's Hospital, Westmead, NSW, Australia
| | - Belinda Kramer
- Children's Cancer Research Unit, Kids' Research Institute, The Children's Hospital at Westmead, Locked Bag 4001, Westmead, NSW, 2145, Australia
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13
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Berry CC, Nobles C, Six E, Wu Y, Malani N, Sherman E, Dryga A, Everett JK, Male F, Bailey A, Bittinger K, Drake MJ, Caccavelli L, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD. INSPIIRED: Quantification and Visualization Tools for Analyzing Integration Site Distributions. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 4:17-26. [PMID: 28344988 PMCID: PMC5363318 DOI: 10.1016/j.omtm.2016.11.003] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2016] [Accepted: 11/15/2016] [Indexed: 01/08/2023]
Abstract
Analysis of sites of newly integrated DNA in cellular genomes is important to several fields, but methods for analyzing and visualizing these datasets are still under development. Here, we describe tools for data analysis and visualization that take as input integration site data from our INSPIIRED pipeline. Paired-end sequencing allows inference of the numbers of transduced cells as well as the distributions of integration sites in target genomes. We present interactive heatmaps that allow comparison of distributions of integration sites to genomic features and that support numerous user-defined statistical tests. To summarize integration site data from human gene therapy samples, we developed a reproducible report format that catalogs sample population structure, longitudinal dynamics, and integration frequency near cancer-associated genes. We also introduce a novel summary statistic, the UC50 (unique cell progenitors contributing the most expanded 50% of progeny cell clones), which provides a single number summarizing possible clonal expansion. Using these tools, we characterize ongoing longitudinal characterization of a patient from the first trial to treat severe combined immunodeficiency-X1 (SCID-X1), showing successful reconstitution for 15 years accompanied by persistence of a cell clone with an integration site near the cancer-associated gene CCND2. Software is available at https://github.com/BushmanLab/INSPIIRED.
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Affiliation(s)
- Charles C Berry
- Department of Family Medicine and Public Health, UC San Diego, La Jolla, CA 92093, USA
| | - Christopher Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Emmanuelle Six
- Paris Descartes-Sorbonne Paris Cité University, Imagine Institute, 75015 Paris, France; INSERM 24, Laboratory of Human Lymphohematopoiesis, 75015 Paris, France
| | - Yinghua Wu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Nirav Malani
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Eric Sherman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Anatoly Dryga
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Frances Male
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Aubrey Bailey
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Kyle Bittinger
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Mary J Drake
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Laure Caccavelli
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Salima Hacein-Bey-Abina
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Marina Cavazzana
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
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14
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Sherman E, Nobles C, Berry CC, Six E, Wu Y, Dryga A, Malani N, Male F, Reddy S, Bailey A, Bittinger K, Everett JK, Caccavelli L, Drake MJ, Bates P, Hacein-Bey-Abina S, Cavazzana M, Bushman FD. INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2016; 4:39-49. [PMID: 28344990 PMCID: PMC5363316 DOI: 10.1016/j.omtm.2016.11.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 11/15/2016] [Indexed: 01/24/2023]
Abstract
Integration of new DNA into cellular genomes mediates replication of retroviruses and transposons; integration reactions have also been adapted for use in human gene therapy. Tracking the distributions of integration sites is important to characterize populations of transduced cells and to monitor potential outgrow of pathogenic cell clones. Here, we describe a pipeline for quantitative analysis of integration site distributions named INSPIIRED (integration site pipeline for paired-end reads). We describe optimized biochemical steps for site isolation using Illumina paired-end sequencing, including new technology for suppressing recovery of unwanted contaminants, then software for alignment, quality control, and management of integration site sequences. During library preparation, DNAs are broken by sonication, so that after ligation-mediated PCR the number of ligation junction sites can be used to infer abundance of gene-modified cells. We generated integration sites of known positions in silico, and we describe optimization of sample processing parameters refined by comparison to truth. We also present a novel graph-theory-based method for quantifying integration sites in repeated sequences, and we characterize the consequences using synthetic and experimental data. In an accompanying paper, we describe an additional set of statistical tools for data analysis and visualization. Software is available at https://github.com/BushmanLab/INSPIIRED.
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Affiliation(s)
- Eric Sherman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Christopher Nobles
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Charles C Berry
- Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA 92093, USA
| | - Emmanuelle Six
- Imagine Institute, Paris Descartes-Sorbonne Paris Cité University, 75014 Paris, France; Laboratory of Human Lymphohematopoiesis, INSERM 24, 75014 Paris, France
| | - Yinghua Wu
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Anatoly Dryga
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Nirav Malani
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Frances Male
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Shantan Reddy
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Aubrey Bailey
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Kyle Bittinger
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - John K Everett
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Laure Caccavelli
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Mary J Drake
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Paul Bates
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
| | - Salima Hacein-Bey-Abina
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Marina Cavazzana
- Biotherapy Department, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris, 75014 Paris, France; Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest, Assistance Publique-Hôpitaux de Paris, INSERM, 75014 Paris, France
| | - Frederic D Bushman
- Department of Microbiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6076, USA
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15
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Afzal S, Wilkening S, von Kalle C, Schmidt M, Fronza R. GENE-IS: Time-Efficient and Accurate Analysis of Viral Integration Events in Large-Scale Gene Therapy Data. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 6:133-139. [PMID: 28325279 PMCID: PMC5363413 DOI: 10.1016/j.omtn.2016.12.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 11/24/2016] [Accepted: 12/01/2016] [Indexed: 12/22/2022]
Abstract
Integration site profiling and clonality analysis of viral vector distribution in gene therapy is a key factor to monitor the fate of gene-corrected cells, assess the risk of malignant transformation, and establish vector biosafety. We developed the Genome Integration Site Analysis Pipeline (GENE-IS) for highly time-efficient and accurate detection of next-generation sequencing (NGS)-based viral vector integration sites (ISs) in gene therapy data. It is the first available tool with dual analysis mode that allows IS analysis both in data generated by PCR-based methods, such as linear amplification method PCR (LAM-PCR), and by rapidly evolving targeted sequencing (e.g., Agilent SureSelect) technologies. GENE-IS makes use of trimming strategies, customized reference genome, and soft-clipped information with sequential filtering steps to provide annotated IS with clonality information. It is a scalable, robust, precise, and reliable tool for large-scale pre-clinical and clinical data analysis that provides users complete flexibility and control over analysis with a broad range of configurable parameters. GENE-IS is available at https://github.com/G100DKFZ/gene-is.
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Affiliation(s)
- Saira Afzal
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Stefan Wilkening
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Raffaele Fronza
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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16
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Cavazzana M, Six E, Lagresle-Peyrou C, André-Schmutz I, Hacein-Bey-Abina S. Gene Therapy for X-Linked Severe Combined Immunodeficiency: Where Do We Stand? Hum Gene Ther 2016; 27:108-16. [PMID: 26790362 DOI: 10.1089/hum.2015.137] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
More than 20 years ago, X-linked severe combined immunodeficiency (SCID-X1) appeared to be the best condition to test the feasibility of hematopoietic stem cell gene therapy. The seminal SCID-X1 clinical studies, based on first-generation gammaretroviral vectors, demonstrated good long-term immune reconstitution in most treated patients despite the occurrence of vector-related leukemia in a few of them. This gene therapy has successfully enabled correction of the T cell defect. Natural killer and B cell defects were only partially restored, most likely due to the absence of a conditioning regimen. The success of these pioneering trials paved the way for the extension of gene-based treatment to many other diseases of the hematopoietic system, but the unfortunate serious adverse events led to extensive investigations to define the retrovirus integration profiles. This review puts into perspective the clinical experience of gene therapy for SCID-X1, with the development and implementation of new generations of safer vectors such as self-inactivating gammaretroviral or lentiviral vectors as well as major advances in integrome knowledge.
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Affiliation(s)
- Marina Cavazzana
- 1 Biotherapy Department, Necker Children's Hospital , Assistance Publique-Hôpitaux de Paris, Paris.,2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Emmanuelle Six
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Chantal Lagresle-Peyrou
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Isabelle André-Schmutz
- 2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,3 Paris Descartes-Sorbonne Paris Cité University, Imagine Institute , Paris.,4 INSERM UMR 1163, Laboratory of Human Lymphohematopoiesis , Paris
| | - Salima Hacein-Bey-Abina
- 1 Biotherapy Department, Necker Children's Hospital , Assistance Publique-Hôpitaux de Paris, Paris.,2 Biotherapy Clinical Investigation Center, Groupe Hospitalier Universitaire Ouest , Assistance Publique-Hôpitaux de Paris, INSERM, Paris.,5 UTCBS CNRS 8258-INSERM U1022, Faculté des Sciences Pharmaceutiques et Biologiques, Université Paris Descartes , Paris.,6 Immunology Laboratory, Groupe Hospitalier Universitaire Paris-Sud , AP-HP, Le-Kremlin-Bicêtre, France
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17
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Oliveira G, Ruggiero E, Stanghellini MTL, Cieri N, D'Agostino M, D'Agostino M, Fronza R, Lulay C, Dionisio F, Mastaglio S, Greco R, Peccatori J, Aiuti A, Ambrosi A, Biasco L, Bondanza A, Lambiase A, Traversari C, Vago L, von Kalle C, Schmidt M, Bordignon C, Ciceri F, Bonini C. Tracking genetically engineered lymphocytes long-term reveals the dynamics of T cell immunological memory. Sci Transl Med 2016; 7:317ra198. [PMID: 26659572 DOI: 10.1126/scitranslmed.aac8265] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Long-lasting immune protection from pathogens and cancer requires the generation of memory T cells able to survive long-term. To unravel the immunological requirements for long-term persistence of human memory T cells, we characterized and traced, over several years, T lymphocytes genetically modified to express the thymidine kinase (TK) suicide gene that were infused in 10 patients after haploidentical hematopoietic stem cell transplantation (HSCT). At 2 to 14 years after infusion and in the presence of a broad and resting immune system, we could still detect effectors/effector memory (TEM/EFF), central memory (TCM), and stem memory (TSCM) TK(+) cells, circulating at low but stable levels in all patients. Longitudinal analysis of cytomegalovirus (CMV)- and Flu-specific TK(+) cells indicated that antigen recognition was dominant in driving in vivo expansion and persistence at detectable levels. The amount of infused TSCM cells positively correlated with early expansion and with the absolute counts of long-term persisting gene-marked cells. By combining T cell sorting with sequencing of integration (IS), TCRα and TCRβ clonal markers, we showed that T cells retrieved long-term were enriched in clones originally shared in different memory T cell subsets, whereas dominant long-term clonotypes appeared to preferentially originate from infused TSCM and TCM clones. Together, these results indicate that long-term persistence of gene-modified memory T cells after haploidentical HSCT is influenced by antigen exposure and by the original phenotype of infused cells. Cancer adoptive immunotherapy might thus benefit from cellular products enriched in lymphocytes with an early-differentiated phenotype.
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Affiliation(s)
- Giacomo Oliveira
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Program in Immunology and Bio-Immunotherapy of Cancer (PIBIC), San Raffaele Scientific Institute, Milan 20132, Italy. Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Eliana Ruggiero
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Program in Immunology and Bio-Immunotherapy of Cancer (PIBIC), San Raffaele Scientific Institute, Milan 20132, Italy. Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg 69120, Germany
| | | | - Nicoletta Cieri
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Program in Immunology and Bio-Immunotherapy of Cancer (PIBIC), San Raffaele Scientific Institute, Milan 20132, Italy
| | - Mattia D'Agostino
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Program in Immunology and Bio-Immunotherapy of Cancer (PIBIC), San Raffaele Scientific Institute, Milan 20132, Italy. Vita-Salute San Raffaele University, Milan 20132, Italy
| | | | - Raffaele Fronza
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg 69120, Germany
| | - Christina Lulay
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg 69120, Germany
| | - Francesca Dionisio
- Telethon Institute for Gene Therapy (HSR-TIGET), San Raffaele Scientific Institute, Milan 20132, Italy
| | - Sara Mastaglio
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Program in Immunology and Bio-Immunotherapy of Cancer (PIBIC), San Raffaele Scientific Institute, Milan 20132, Italy. Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Raffaella Greco
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Jacopo Peccatori
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Alessandro Aiuti
- Telethon Institute for Gene Therapy (HSR-TIGET), San Raffaele Scientific Institute, Milan 20132, Italy
| | | | - Luca Biasco
- Telethon Institute for Gene Therapy (HSR-TIGET), San Raffaele Scientific Institute, Milan 20132, Italy
| | - Attilio Bondanza
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan 20132, Italy. Innovative Immunotherapies Unit, Division of Immunology, Transplantation and Infectious Diseases, PIBIC, San Raffaele Scientific Institute, Milan 20132, Italy
| | | | | | - Luca Vago
- Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan 20132, Italy. Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Christof von Kalle
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg 69120, Germany
| | - Manfred Schmidt
- Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center, Heidelberg 69120, Germany
| | - Claudio Bordignon
- Vita-Salute San Raffaele University, Milan 20132, Italy. MolMed S.p.A, Milan 20132, Italy
| | - Fabio Ciceri
- Vita-Salute San Raffaele University, Milan 20132, Italy. Hematology and Bone Marrow Transplantation Unit, San Raffaele Scientific Institute, Milan 20132, Italy. Unit of Immunogenetics, Leukemia Genomics and Immunobiology, Division of Regenerative Medicine, Stem Cells and Gene Therapy, San Raffaele Scientific Institute, Milan 20132, Italy
| | - Chiara Bonini
- Experimental Hematology Unit, Division of Immunology, Transplantation and Infectious Diseases, Program in Immunology and Bio-Immunotherapy of Cancer (PIBIC), San Raffaele Scientific Institute, Milan 20132, Italy. Vita-Salute San Raffaele University, Milan 20132, Italy.
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18
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Meneghini V, Lattanzi A, Tiradani L, Bravo G, Morena F, Sanvito F, Calabria A, Bringas J, Fisher-Perkins JM, Dufour JP, Baker KC, Doglioni C, Montini E, Bunnell BA, Bankiewicz K, Martino S, Naldini L, Gritti A. Pervasive supply of therapeutic lysosomal enzymes in the CNS of normal and Krabbe-affected non-human primates by intracerebral lentiviral gene therapy. EMBO Mol Med 2016; 8:489-510. [PMID: 27025653 PMCID: PMC5128736 DOI: 10.15252/emmm.201505850] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Metachromatic leukodystrophy (MLD) and globoid cell leukodystrophy (GLD or Krabbe disease) are severe neurodegenerative lysosomal storage diseases (LSD) caused by arylsulfatase A (ARSA) and galactosylceramidase (GALC) deficiency, respectively. Our previous studies established lentiviral gene therapy (GT) as a rapid and effective intervention to provide pervasive supply of therapeutic lysosomal enzymes in CNS tissues of MLD and GLD mice. Here, we investigated whether this strategy is similarly effective in juvenile non-human primates (NHP). To provide proof of principle for tolerability and biological efficacy of the strategy, we established a comprehensive study in normal NHP delivering a clinically relevant lentiviral vector encoding for the human ARSA transgene. Then, we injected a lentiviral vector coding for the human GALC transgene in Krabbe-affected rhesus macaques, evaluating for the first time the therapeutic potential of lentiviral GT in this unique LSD model. We showed favorable safety profile and consistent pattern of LV transduction and enzyme biodistribution in the two models, supporting the robustness of the proposed GT platform. We documented moderate inflammation at the injection sites, mild immune response to vector particles in few treated animals, no indication of immune response against transgenic products, and no molecular evidence of insertional genotoxicity. Efficient gene transfer in neurons, astrocytes, and oligodendrocytes close to the injection sites resulted in robust production and extensive spreading of transgenic enzymes in the whole CNS and in CSF, leading to supraphysiological ARSA activity in normal NHP and close to physiological GALC activity in the Krabbe NHP, in which biological efficacy was associated with preliminary indication of therapeutic benefit. These results support the rationale for the clinical translation of intracerebral lentiviral GT to address CNS pathology in MLD, GLD, and other neurodegenerative LSD.
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Affiliation(s)
- Vasco Meneghini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Annalisa Lattanzi
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Luigi Tiradani
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Gabriele Bravo
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Francesco Morena
- Department of Chemistry, Biology and Biotechnologies, Biochemistry and Molecular Biology Unit, University of Perugia, Perugia, Italy
| | - Francesca Sanvito
- Anatomy and Histopathology Department, San Raffaele Scientific Institute, Milano, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - John Bringas
- University of California San Francisco (UCSF), San Francisco, CA, USA
| | - Jeanne M Fisher-Perkins
- Division of Regenerative Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Jason P Dufour
- Division of Regenerative Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Kate C Baker
- Division of Regenerative Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | - Claudio Doglioni
- Anatomy and Histopathology Department, San Raffaele Scientific Institute, Milano, Italy Vita-Salute San Raffaele University, Milan, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bruce A Bunnell
- Division of Regenerative Medicine, Tulane National Primate Research Center, Covington, LA, USA
| | | | - Sabata Martino
- Department of Chemistry, Biology and Biotechnologies, Biochemistry and Molecular Biology Unit, University of Perugia, Perugia, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy Vita-Salute San Raffaele University, Milan, Italy
| | - Angela Gritti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET), Division of Regenerative Medicine, Stem Cells and Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
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Hocum JD, Battrell LR, Maynard R, Adair JE, Beard BC, Rawlings DJ, Kiem HP, Miller DG, Trobridge GD. VISA--Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing. BMC Bioinformatics 2015; 16:212. [PMID: 26150117 PMCID: PMC4493804 DOI: 10.1186/s12859-015-0653-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 06/29/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens. RESULTS We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads. CONCLUSIONS VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.
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Affiliation(s)
- Jonah D Hocum
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA.
| | - Logan R Battrell
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA.
| | - Ryan Maynard
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA.
| | - Jennifer E Adair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Brian C Beard
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - David J Rawlings
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
| | - Daniel G Miller
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
| | - Grant D Trobridge
- Department of Pharmaceutical Sciences, Washington State University, Spokane, WA, 99210, USA. .,School of Molecular Biosciences, Washington State University, Pullman, WA, 99164, USA.
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Calabria A, Spinozzi G, Benedicenti F, Tenderini E, Montini E. adLIMS: a customized open source software that allows bridging clinical and basic molecular research studies. BMC Bioinformatics 2015; 16 Suppl 9:S5. [PMID: 26051409 PMCID: PMC4464029 DOI: 10.1186/1471-2105-16-s9-s5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background Many biological laboratories that deal with genomic samples are facing the problem of sample tracking, both for pure laboratory management and for efficiency. Our laboratory exploits PCR techniques and Next Generation Sequencing (NGS) methods to perform high-throughput integration site monitoring in different clinical trials and scientific projects. Because of the huge amount of samples that we process every year, which result in hundreds of millions of sequencing reads, we need to standardize data management and tracking systems, building up a scalable and flexible structure with web-based interfaces, which are usually called Laboratory Information Management System (LIMS). Methods We started collecting end-users' requirements, composed of desired functionalities of the system and Graphical User Interfaces (GUI), and then we evaluated available tools that could address our requirements, spanning from pure LIMS to Content Management Systems (CMS) up to enterprise information systems. Our analysis identified ADempiere ERP, an open source Enterprise Resource Planning written in Java J2EE, as the best software that also natively implements some highly desirable technological advances, such as the high usability and modularity that grants high use-case flexibility and software scalability for custom solutions. Results We extended and customized ADempiere ERP to fulfil LIMS requirements and we developed adLIMS. It has been validated by our end-users verifying functionalities and GUIs through test cases for PCRs samples and pre-sequencing data and it is currently in use in our laboratories. adLIMS implements authorization and authentication policies, allowing multiple users management and roles definition that enables specific permissions, operations and data views to each user. For example, adLIMS allows creating sample sheets from stored data using available exporting operations. This simplicity and process standardization may avoid manual errors and information backtracking, features that are not granted using track recording on files or spreadsheets. Conclusions adLIMS aims to combine sample tracking and data reporting features with higher accessibility and usability of GUIs, thus allowing time to be saved on doing repetitive laboratory tasks, and reducing errors with respect to manual data collection methods. Moreover, adLIMS implements automated data entry, exploiting sample data multiplexing and parallel/transactional processing. adLIMS is natively extensible to cope with laboratory automation through platform-dependent API interfaces, and could be extended to genomic facilities due to the ERP functionalities.
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