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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 42038

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Dr. Anne-Catherine Prats

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UMR 1297-I2MC, Université de Toulouse, Inserm, UT3, FHU IMPACT, 31432 Toulouse, France
Interests: translation control; RNA; IRES; hypoxia; angiogenesis; cardiovascular disease; cancer; gene therapy
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The concept of gene therapy was introduced when M. Bishop and H. Varmus, laureates of the Nobel Prize in 1989, discovered that viral oncogenes are cellular genes picked up by retroviruses. Since this discovery, many efforts have been made to develop viral and non-viral vectors that bear therapeutic genes. After many years and disappointments, gene therapy is now successfully used to treat several rare monogenic pathologies, including immunological, hematological, neurodegenerative and neuromuscular diseases. Gene therapy is also an important perspective to consider for frequently occurring diseases, such as cancer and cardiovascular diseases.

Cell therapy consists of implanting cells to repair or regenerate an organ. These cells may be adult, embryonic or induced pluripotent stem cells, and are the subject of many research programs and clinical assays, in particular, in the field of cardiopathies and skin diseases. Immunotherapy treatment of cancer, using CAR-T, is also a cell therapy that is being increasingly employed.

In recent years, a technological health revolution has appeared, with the possibility of editing the genome, mainly using the CRISPR-Cas9 system. Two women, J. Doudna and E. Charpentier, received the 2020 Nobel Prize for developing this technology. Another medical revolution is the use of mRNA for transient gene transfer, as used in COVID-19 vaccines. The present Special Issue aims to update these fields, including preclinical research aspects of molecular and cell biology that design the medicine of the future.

Potential topics include, but are not limited to, the following:

Gene therapy (preclinical research and clinical assays);
Cell therapy (preclinical research and clinical assays);
RNA-based therapies or vaccines;
Immunotherapy;
Genome editing;
Development of vectors;
Oncolytic vectors.

Dr. Anne-Catherine Prats
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

gene therapy
cell therapy
immunotherapy
RNA
genome editing
vectorology

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Related Special Issue

Advances in Gene and Cell Therapy—2nd Edition in International Journal of Molecular Sciences (5 articles)

Published Papers (8 papers)

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15 pages, 3546 KiB

Open AccessArticle

Assessment of Therapeutic Potential of a Dual AAV Approach for Duchenne Muscular Dystrophy

by Sonia Albini, Laura Palmieri, Auriane Dubois, Nathalie Bourg, William Lostal and Isabelle Richard

Int. J. Mol. Sci. 2023, 24(14), 11421; https://doi.org/10.3390/ijms241411421 - 13 Jul 2023

Cited by 6 | Viewed by 3430

Abstract

Duchenne muscular dystrophy (DMD) is a yet incurable rare genetic disease that affects the skeletal and cardiac muscles, leading to progressive muscle wasting and premature death. DMD is caused by the lack of dystrophin, a muscle protein essential for the biochemical support and integrity of muscle fibers. Gene replacement strategies for Duchenne muscular dystrophy (DMD) employing the adeno-associated virus (AAV) face the challenge imposed by the limited packaging capacity of AAV, only allowing the accommodation of a short version of dystrophin (µDys) that is still far removed from correcting human disease. The need to develop strategies leading to the expression of a best performing dystrophin variant led to only few studies reporting on the use of dual vectors, but none reported on a method to assess in vivo transgene reconstitution efficiency, the degree of which directly affects the use of safe AAV dosing. We report here on the generation of a dual AAV vector approach for the expression of a larger dystrophin version (quasidystrophin) based on homologous recombination, and the development of a methodology employing a strategic droplet digital PCR design, to determine the recombination efficiency as well as the occurrence of unwanted concatemerization events or aberrant expression from the single vectors. We demonstrated that, upon systemic delivery in the dystrophic D2.B10-Dmd^mdx/J (DBA2mdx) mice, our dual AAV approach led to high transgene reconstitution efficiency and negligible Inverted Terminal Repeats (ITR)-dependent concatemerization, with consequent remarkable protein restoration in muscles and improvement of muscle pathology. This evidence supports the suitability of our system for gene therapy application and the potential of this methodology to assess and improve the feasibility for therapeutic translation of multiple vector approaches. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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17 pages, 3072 KiB

Open AccessArticle

Biochemical Correction of GM2 Ganglioside Accumulation in AB-Variant GM2 Gangliosidosis

by Natalie M. Deschenes, Camilyn Cheng, Alex E. Ryckman, Brianna M. Quinville, Prem Khanal, Melissa Mitchell, Zhilin Chen, Waheed Sangrar, Steven J. Gray and Jagdeep S. Walia

Int. J. Mol. Sci. 2023, 24(11), 9217; https://doi.org/10.3390/ijms24119217 - 24 May 2023

Cited by 3 | Viewed by 2651

Abstract

GM2 gangliosidosis is a group of genetic disorders that result in the accumulation of GM2 ganglioside (GM2) in brain cells, leading to progressive central nervous system (CNS) atrophy and premature death in patients. AB-variant GM2 gangliosidosis (ABGM2) arises from loss-of-function mutations in the GM2 activator protein (GM2AP), which is essential for the breakdown of GM2 in a key catabolic pathway required for CNS lipid homeostasis. In this study, we show that intrathecal delivery of self-complementary adeno-associated virus serotype-9 (scAAV9) harbouring a functional human GM2A transgene (scAAV9.hGM2A) can prevent GM2 accumulation in in GM2AP-deficient mice (Gm2a^−/− mice). Additionally, scAAV9.hGM2A efficiently distributes to all tested regions of the CNS within 14 weeks post-injection and remains detectable for the lifespan of these animals (up to 104 weeks). Remarkably, GM2AP expression from the transgene scales with increasing doses of scAAV9.hGM2A (0.5, 1.0 and 2.0 × 10¹¹ vector genomes (vg) per mouse), and this correlates with dose-dependent correction of GM2 accumulation in the brain. No severe adverse events were observed, and comorbidities in treated mice were comparable to those in disease-free cohorts. Lastly, all doses yielded corrective outcomes. These data indicate that scAAV9.hGM2A treatment is relatively non-toxic and tolerable, and biochemically corrects GM2 accumulation in the CNS—the main cause of morbidity and mortality in patients with ABGM2. Importantly, these results constitute proof-of-principle for treating ABGM2 with scAAV9.hGM2A by means of a single intrathecal administration and establish a foundation for future preclinical research. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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12 pages, 951 KiB

Open AccessArticle

Prevalence of Neutralizing Antibodies against Adeno-Associated Virus Serotypes 1, 2, and 9 in Non-Injected Latin American Patients with Heart Failure—ANVIAS Study

by Julieth A. Sierra-Delgado, Shibi Likhite, Paula K. Bautista, Sergio A. Gómez-Ochoa, Luis E. Echeverría, Elizabeth Guío, Clara Vargas, Norma C. Serrano, Kathrin C. Meyer and Melvin Y. Rincon

Int. J. Mol. Sci. 2023, 24(6), 5579; https://doi.org/10.3390/ijms24065579 - 14 Mar 2023

Cited by 7 | Viewed by 3037

Abstract

Neutralizing antibody (NAb) activity against the viral capsid of adeno-associated viral (AAV) vectors decreases transduction efficiency, thus limiting transgene expression. Several reports have mentioned a variation in NAb prevalence according to age, AAV serotype, and, most importantly, geographic location. There are currently no reports specifically describing the anti-AAV NAb prevalence in Latin America. Here, we describe the prevalence of NAb against different serotypes of AAV vectors (AAV1, AAV2, and AAV9) in Colombian patients with heart failure (HF) (referred to as cases) and healthy individuals (referred to as controls). The levels of NAb were evaluated in serum samples of 60 subjects from each group using an in vitro inhibitory assay. The neutralizing titer was reported as the first dilution inhibiting ≥50% of the transgene signal, and the samples with neutralizing titers at ≥1:50 dilution were considered positive. The prevalence of NAb in the case and control groups were similar (AAV2: 43% and 45%, respectively; AAV1 33.3% in each group; AAV9: 20% and 23.2%, respectively). The presence of NAb for two or more of the serotypes analyzed was observed in 25% of the studied samples, with the largest amount in the positive samples for AAV1 (55–75%) and AAV9 (93%), suggesting serial exposures, cross-reactivity, or coinfection. Moreover, patients in the HF group exhibited more common combined seropositivity for NAb against AAV1 d AAV9 than those in the control group (91.6% vs. 35.7%, respectively; p = 0.003). Finally, exposure to toxins was significantly associated with the presence of NAb in all regression models. These results constitute the first report of the prevalence of NAb against AAV in Latin America, being the first step to implementing therapeutic strategies based on AAV vectors in this population in our region. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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16 pages, 3557 KiB

Open AccessArticle

Cathepsin S Knockdown Suppresses Endothelial Inflammation, Angiogenesis, and Complement Protein Activity under Hyperglycemic Conditions In Vitro by Inhibiting NF-κB Signaling

by Shithima Sayed, Omar Faruq, Umma Hafsa Preya and Jee Taek Kim

Int. J. Mol. Sci. 2023, 24(6), 5428; https://doi.org/10.3390/ijms24065428 - 12 Mar 2023

Cited by 6 | Viewed by 2450

Abstract

Hyperglycemia plays a key role in the development of microvascular complications, endothelial dysfunction (ED), and inflammation. It has been demonstrated that cathepsin S (CTSS) is activated in hyperglycemia and is involved in inducing the release of inflammatory cytokines. We hypothesized that blocking CTSS might alleviate the inflammatory responses and reduce the microvascular complications and angiogenesis in hyperglycemic conditions. In this study, we treated human umbilical vein endothelial cells (HUVECs) with high glucose (HG; 30 mM) to induce hyperglycemia and measured the expression of inflammatory cytokines. When treated with glucose, hyperosmolarity could be linked to cathepsin S expression; however, many have mentioned the high expression of CTSS. Thus, we made an effort to concentrate on the immunomodulatory role of the CTSS knockdown in high glucose conditions. We validated that the HG treatment upregulated the expression of inflammatory cytokines and CTSS in HUVEC. Further, siRNA treatment significantly downregulated CTSS expression along with inflammatory marker levels by inhibiting the nuclear factor-kappa B (NF-κB) mediated signaling pathway. In addition, CTSS silencing led to the decreased expression of vascular endothelial markers and downregulated angiogenic activity in HUVECs, which was confirmed by a tube formation experiment. Concurrently, siRNA treatment reduced the activation of complement proteins C3a and C5a in HUVECs under hyperglycemic conditions. These findings show that CTSS silencing significantly reduces hyperglycemia-induced vascular inflammation. Hence, CTSS may be a novel target for preventing diabetes-induced microvascular complications. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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13 pages, 1476 KiB

Open AccessArticle

Counteracting the Common Shwachman–Diamond Syndrome-Causing SBDS c.258+2T>C Mutation by RNA Therapeutics and Base/Prime Editing

by Laura Peretto, Elena Tonetto, Iva Maestri, Valentino Bezzerri, Roberto Valli, Marco Cipolli, Mirko Pinotti and Dario Balestra

Int. J. Mol. Sci. 2023, 24(4), 4024; https://doi.org/10.3390/ijms24044024 - 16 Feb 2023

Cited by 3 | Viewed by 2928

Abstract

Shwachman–Diamond syndrome (SDS) represents one of the most common inherited bone marrow failure syndromes and is mainly caused by SBDS gene mutations. Only supportive treatments are available, with hematopoietic cell transplantation required when marrow failure occurs. Among all causative mutations, the SBDS c.258+2T>C variant at the 5′ splice site (ss) of exon 2 is one of the most frequent. Here, we investigated the molecular mechanisms underlying aberrant SBDS splicing and showed that SBDS exon 2 is dense in splicing regulatory elements and cryptic splice sites, complicating proper 5′ss selection. Studies ex vivo and in vitro demonstrated that the mutation alters splicing, but it is also compatible with tiny amounts of correct transcripts, which would explain the survival of SDS patients. Moreover, for the first time for SDS, we explored a panel of correction approaches at the RNA and DNA levels and provided experimental evidence that the mutation effect can be partially counteracted by engineered U1snRNA, trans-splicing, and base/prime editors, ultimately leading to correctly spliced transcripts (from barely detectable to 2.5–5.5%). Among them, we propose DNA editors that, by stably reverting the mutation and potentially conferring positive selection to bone-marrow cells, could lead to the development of an innovative SDS therapy. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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16 pages, 3185 KiB

Open AccessArticle

Transplantation of Adipose-Tissue-Engineered Constructs with CRISPR-Mediated UCP1 Activation

by Svetlana Michurina, Iurii Stafeev, Maria Boldyreva, Vu Anh Truong, Elizaveta Ratner, Mikhail Menshikov, Yu-Chen Hu and Yelena Parfyonova

Int. J. Mol. Sci. 2023, 24(4), 3844; https://doi.org/10.3390/ijms24043844 - 14 Feb 2023

Cited by 3 | Viewed by 2577

Abstract

Thermogenic adipocytes have potential utility for the development of approaches to treat type 2 diabetes and obesity-associated diseases. Although several reports have proved the positive effect of beige and brown adipocyte transplantation in obese mice, translation to human cell therapy needs improvement. Here, we describe the application of CRISPR activation (CRISPRa) technology for generating safe and efficient adipose-tissue-engineered constructs with enhanced mitochondrial uncoupling protein 1 (UCP1) expression. We designed the CRISPRa system for the activation of UCP1 gene expression. CRISPRa-UCP1 was delivered into mature adipocytes by a baculovirus vector. Modified adipocytes were transplanted in C57BL/6 mice, followed by analysis of grafts, inflammation and systemic glucose metabolism. Staining of grafts on day 8 after transplantation shows them to contain UCP1-positive adipocytes. Following transplantation, adipocytes remain in grafts and exhibit expression of PGC1α transcription factor and hormone sensitive lipase (HSL). Transplantation of CRISPRa-UCP1-modified adipocytes does not influence glucose metabolism or inflammation in recipient mice. We show the utility and safety of baculovirus vectors for CRISPRa-based thermogenic gene activation. Our findings suggest a means of improving existing cell therapy approaches using baculovirus vectors and CRISPRa for modification and transplantation of non-immunogenic adipocytes. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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15 pages, 2683 KiB

Open AccessArticle

Preclinical Evaluation of CRISPR-Edited CAR-NK-92 Cells for Off-the-Shelf Treatment of AML and B-ALL

by Guillermo Ureña-Bailén, Jérôme-Maurice Dobrowolski, Yujuan Hou, Alicia Dirlam, Alicia Roig-Merino, Sabine Schleicher, Daniel Atar, Christian Seitz, Judith Feucht, Justin S. Antony, Tahereh Mohammadian Gol, Rupert Handgretinger and Markus Mezger

Int. J. Mol. Sci. 2022, 23(21), 12828; https://doi.org/10.3390/ijms232112828 - 24 Oct 2022

Cited by 24 | Viewed by 4942

Abstract

Acute myeloid leukemia (AML) and B-cell acute lymphocytic leukemia (B-ALL) are severe blood malignancies affecting both adults and children. Chimeric antigen receptor (CAR)-based immunotherapies have proven highly efficacious in the treatment of leukemia. However, the challenge of the immune escape of cancer cells remains. The development of more affordable and ready-to-use therapies is essential in view of the costly and time-consuming preparation of primary cell-based treatments. In order to promote the antitumor function against AML and B-ALL, we transduced NK-92 cells with CD276-CAR or CD19-CAR constructs. We also attempted to enhance cytotoxicity by a gene knockout of three different inhibitory checkpoints in NK cell function (CBLB, NKG2A, TIGIT) with CRISPR-Cas9 technology. The antileukemic activity of the generated cell lines was tested with calcein and luciferase-based cytotoxicity assays in various leukemia cell lines. Both CAR-NK-92 exhibited targeted cytotoxicity and a significant boost in antileukemic function in comparison to parental NK-92. CRISPR-Cas9 knock-outs did not improve B-ALL cytotoxicity. However, triple knock-out CD276-CAR-NK-92 cells, as well as CBLB or TIGIT knock-out NK-92 cells, showed significantly enhanced cytotoxicity against U-937 or U-937 CD19/tag AML cell lines. These results indicate that the CD19-CAR and CD276-CAR-NK-92 cell lines’ cytotoxic performance is suitable for leukemia killing, making them promising off-the-shelf therapeutic candidates. The knock-out of CBLB and TIGIT in NK-92 and CD276-CAR-NK-92 should be further investigated for the treatment of AML. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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15 pages, 1936 KiB

Open AccessReview

A CRISPR-Cas Cure for HIV/AIDS

by Mouraya Hussein, Mariano A. Molina, Ben Berkhout and Elena Herrera-Carrillo

Int. J. Mol. Sci. 2023, 24(2), 1563; https://doi.org/10.3390/ijms24021563 - 13 Jan 2023

Cited by 25 | Viewed by 18312

Abstract

Human immunodeficiency virus (HIV) infections and HIV-induced acquired immunodeficiency syndrome (AIDS) continue to represent a global health burden. There is currently no effective vaccine, nor any cure, for HIV infections; existing antiretroviral therapy can suppress viral replication, but only as long as antiviral drugs are taken. HIV infects cells of the host immune system, and it can establish a long-lived viral reservoir, which can be targeted and edited through gene therapy. Gene editing platforms based on the clustered regularly interspaced palindromic repeat-Cas system (CRISPR-Cas) have been recognized as promising tools in the development of gene therapies for HIV infections. In this review, we evaluate the current landscape of CRISPR-Cas-based therapies against HIV, with an emphasis on the infection biology of the virus as well as the activity of host restriction factors. We discuss the potential of a combined CRISPR-Cas approach that targets host and viral genes to activate antiviral host factors and inhibit viral replication simultaneously. Lastly, we focus on the challenges and potential solutions of CRISPR-Cas gene editing approaches in achieving an HIV cure. Full article

(This article belongs to the Special Issue Advances in Gene and Cell Therapy)

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