Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-02-25DOI: 10.1016/j.ymthe.2025.02.020
Steven M Jay
{"title":"Addressing barriers to clinical translation of extracellular vesicle therapeutics.","authors":"Steven M Jay","doi":"10.1016/j.ymthe.2025.02.020","DOIUrl":"10.1016/j.ymthe.2025.02.020","url":null,"abstract":"","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"1879-1880"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143516153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-04-02DOI: 10.1016/j.ymthe.2025.03.053
John J Rossi, Saumya Das
{"title":"Small RNAs as therapeutic agents: From catalytic motifs to regulatory pathways.","authors":"John J Rossi, Saumya Das","doi":"10.1016/j.ymthe.2025.03.053","DOIUrl":"10.1016/j.ymthe.2025.03.053","url":null,"abstract":"<p><p>RNA molecules have long been recognized for their central role in protein synthesis, primarily as messengers (mRNAs), ribosomal components, and adaptors (transfer RNAs). Over the past few decades, however, the discovery of small RNAs with regulatory or catalytic functions has dramatically expanded our understanding of RNA biology. These small RNAs can target specific transcripts for cleavage, alter mRNA translation, direct epigenetic changes at gene promoters, or even guide enzyme complexes to their substrates. In this review, we highlight and discuss the therapeutic potential of key classes of small RNAs, including ribozymes, RNA interference elements, antisense oligonucleotides, small nuclear-targeting RNAs, and transfer RNA-derived small RNAs.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"2238-2242"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143780549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-04-03DOI: 10.1016/j.ymthe.2025.04.002
Allancer Nunes, Tianpeng Zhang, Xiaodong Mu, Paul D Robbins
{"title":"Therapeutic application of extracellular vesicles in human diseases.","authors":"Allancer Nunes, Tianpeng Zhang, Xiaodong Mu, Paul D Robbins","doi":"10.1016/j.ymthe.2025.04.002","DOIUrl":"10.1016/j.ymthe.2025.04.002","url":null,"abstract":"<p><p>Extracellular vesicles (EVs) are membrane vesicles released or secreted from almost all cell types. EVs are derived from multivesicular bodies or from the plasma membrane and contain a subset of proteins, lipids, and nucleic acids (e.g., DNA, RNA, and microRNA [miRNA]) derived from the parent cell. EVs play important roles in intercellular communication by efficiently transferring the content between cells both locally and systemically. Given their natural ability to transfer cargo to cells, sometimes in a targeted manner, and their apparent lack of immunogenicity, EVs are being engineered for delivery of therapeutic RNAs, DNAs, miRNAs, viral particles, drugs, and even proteins. In addition, many of the therapeutic effects of stem cell treatments are mediated by stem cell-derived EVs, which are safer and potentially more effective than the parental stem cells. Here we provide an overview of the use of EVs for delivery of different therapeutic nucleic acids, viruses, and drugs, as well as the use of therapeutic stem cell-derived EVs.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"2243-2251"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143788692","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Spatial Multi-Omics Reveals the Potential Involvement of SPP1+ Fibroblasts in Determining Metabolic Heterogeneity and Promoting Metastatic Growth of Colorectal Cancer Liver Metastasis.","authors":"Yuzhen Gao,Xiuping Zhang,Shenglong Xia,Qing Chen,Qinchao Tong,Shaobo Yu,Rui An,Cheng Cheng,Wenbo Zou,Leilei Liang,Xinyou Xie,Zhangfa Song,Rong Liu,Jun Zhang","doi":"10.1016/j.ymthe.2025.05.004","DOIUrl":"https://doi.org/10.1016/j.ymthe.2025.05.004","url":null,"abstract":"This study aims to investigate key microscopic regions involved in colorectal cancer liver metastasis (CRLM), focusing on the crucial role of cancer-associated fibroblasts (CAFs) in promoting tumor progression and providing molecular and metabolism-level insights for its diagnosis and treatment using multi-omics. We followed 12 fresh surgical samples from 2 untreated CRLM patients. Among these, 4 samples were used for spatial transcriptomics (ST), 4 for spatial metabolomics, and 4 for single-cell RNA sequencing (scRNA-seq). Additionally, 92 frozen tissue samples from 40 patients were collected. 7 patients were used for immunofluorescence and RT-qPCR, while 33 patients were used for untargeted metabolomics. ST revealed that the spatial regions of CRLM consists of 7 major components, with fibroblast-dominated regions being the most prominent. These regions are characterized by diverse cell-cell interactions and immunosuppressive, and tumor growth-promoting environments. scRNA-seq identified that SPP1+ fibroblasts interact with CD44+ tumor cells, as confirmed through immunofluorescence. Spatial metabolomics revealed suberic acid and tetraethylene glycol as specific metabolic components of this structure, which was further validated by untargeted metabolomics. In conclusion, a SPP1+fibroblast-rich spatial region with metabolic reprogramming capabilities and immunosuppressive properties was identified in CRLM, which potentially facilitates metastatic outgrowth through interactions with tumor cells.","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":"12 1","pages":""},"PeriodicalIF":12.4,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143926387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-02-28DOI: 10.1016/j.ymthe.2025.02.040
Dan Wang, Gregg Stevens, Terence R Flotte
{"title":"Gene therapy then and now: A look back at changes in the field over the past 25 years.","authors":"Dan Wang, Gregg Stevens, Terence R Flotte","doi":"10.1016/j.ymthe.2025.02.040","DOIUrl":"10.1016/j.ymthe.2025.02.040","url":null,"abstract":"<p><p>Since the inception of Molecular Therapy in 2000, the field of gene therapy has made remarkable progress, evolving from no approved clinical products to 23 clinical gene therapy products today. In this review, we aim to capture the transformative changes in the field by surveying the literature over this period, with a particular focus on advancements in gene delivery vector technology, disease and tissue targeting, and the revolutionary molecular tools that have become central to the field. We also discuss the current challenges facing gene therapy and the need for greater collaboration to ensure its accessibility worldwide.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"1889-1902"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143531626","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-04-01DOI: 10.1016/j.ymthe.2025.03.058
David A Williams, Donald B Kohn, Adrian J Thrasher
{"title":"Ex vivo modification of hematopoietic stem and progenitor cells for gene therapy.","authors":"David A Williams, Donald B Kohn, Adrian J Thrasher","doi":"10.1016/j.ymthe.2025.03.058","DOIUrl":"10.1016/j.ymthe.2025.03.058","url":null,"abstract":"<p><p>The development of viral vectors has been particularly critical for genetic therapies of hematological diseases. Before the development of retrovirus vectors (RVVs), gene transfer into mammalian cells was accomplished by transduction of DNA plasmids by chemical means and later by electroporation. The main limitation of these methods is the inefficiency of transfer of intact sequences, and particularly with electroporation significant cell death of the manipulated cells. The earliest successful human gene therapy trials utilized γ-RVVs and many of the techniques developed in the 1980s. A breakthrough for the field was the exploitation and development of HIV for transfer vectors, termed lentivirus vectors. In this review, we highlight uses of retro- and lentivirus vectors in monogenic diseases in which hematopoietic stem cells are used in the autologous setting to treat immunodeficiencies, hemoglobinopathies and metabolic diseases. The three authors' perspective represent experiences in the field over four decades that encompasses both basic translational research and development and oversight of early and ongoing gene therapy trials utilizing viral vectors.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"2141-2153"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143772765","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-04-06DOI: 10.1016/j.ymthe.2025.04.003
Rongqing Yuan, Jing Zhang, Jian Zhou, Qian Cong
{"title":"Recent progress and future challenges in structure-based protein-protein interaction prediction.","authors":"Rongqing Yuan, Jing Zhang, Jian Zhou, Qian Cong","doi":"10.1016/j.ymthe.2025.04.003","DOIUrl":"10.1016/j.ymthe.2025.04.003","url":null,"abstract":"<p><p>Protein-protein interactions (PPIs) play a fundamental role in cellular processes, and understanding these interactions is crucial for advances in both basic biological science and biomedical applications. This review presents an overview of recent progress in computational methods for modeling protein complexes and predicting PPIs based on 3D structures, focusing on the transformative role of artificial intelligence-based approaches. We further discuss the expanding biomedical applications of PPI research, including the elucidation of disease mechanisms, drug discovery, and therapeutic design. Despite these advances, significant challenges remain in predicting host-pathogen interactions, interactions between intrinsically disordered regions, and interactions related to immune responses. These challenges are worthwhile for future explorations and represent the frontier of research in this field.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"2252-2268"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Redefining quality in cell and gene therapies: Lessons from implementing electronic QMS in academic cGMP facility.","authors":"Xia Wu, Amaia Cadinanos-Garai, Vivian Quach, Eric Jurado, Alix Vaissié, Mohamed Abou-El-Enein","doi":"10.1016/j.ymthe.2025.03.050","DOIUrl":"10.1016/j.ymthe.2025.03.050","url":null,"abstract":"<p><p>Manufacturing cell and gene therapies (CGTs) involves complex processes that require robust quality management, especially within academic current Good Manufacturing Practice (cGMP) facilities, where resources are often limited. Traditional paper-based quality management systems (QMSs), while initially convenient, often become burdensome, leading to errors, poor traceability, and compliance risks. Electronic QMSs (eQMSs) are gaining recognition for their ability to centralize and automate key quality processes, significantly enhancing operational efficiency and regulatory readiness. Through an in-depth case study of the University of Southern California and Children's Hospital of Los Angeles academic cGMP facility, this review demonstrates tangible improvements achieved by adopting an eQMS. Practical insights gained from this experience are shared, including careful selection of eQMS platforms, phased rollout strategies, and comprehensive staff training. The review also addresses common implementation challenges and suggests practical solutions to overcome them. Lessons learned and strategies discussed here can serve as valuable guidance for other academic institutions considering eQMS adoption. Ultimately, embracing an eQMS enables academic CGT manufacturers to operate more efficiently and stay ahead in a fast-moving field.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"2091-2103"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-04-06DOI: 10.1016/j.ymthe.2025.04.004
Gabriel L Butterfield, Samuel J Reisman, Nahid Iglesias, Charles A Gersbach
{"title":"Gene regulation technologies for gene and cell therapy.","authors":"Gabriel L Butterfield, Samuel J Reisman, Nahid Iglesias, Charles A Gersbach","doi":"10.1016/j.ymthe.2025.04.004","DOIUrl":"10.1016/j.ymthe.2025.04.004","url":null,"abstract":"<p><p>Gene therapy stands at the forefront of medical innovation, offering unique potential to treat the underlying causes of genetic disorders and broadly enable regenerative medicine. However, unregulated production of therapeutic genes can lead to decreased clinical utility due to various complications. Thus, many technologies for controlled gene expression are under development, including regulated transgenes, modulation of endogenous genes to leverage native biological regulation, mapping and repurposing of transcriptional regulatory networks, and engineered systems that dynamically react to cell state changes. Transformative therapies enabled by advances in tissue-specific promoters, inducible systems, and targeted delivery have already entered clinical testing and demonstrated significantly improved specificity and efficacy. This review highlights next-generation technologies under development to expand the reach of gene therapies by enabling precise modulation of gene expression. These technologies, including epigenome editing, antisense oligonucleotides, RNA editing, transcription factor-mediated reprogramming, and synthetic genetic circuits, have the potential to provide powerful control over cellular functions. Despite these remarkable achievements, challenges remain in optimizing delivery, minimizing off-target effects, and addressing regulatory hurdles. However, the ongoing integration of biological insights with engineering innovations promises to expand the potential for gene therapy, offering hope for treating not only rare genetic disorders but also complex multifactorial diseases.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"2104-2122"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143803844","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular TherapyPub Date : 2025-05-07Epub Date: 2025-03-27DOI: 10.1016/j.ymthe.2025.03.037
Allison M Keeler, Wei Zhan, Sanjay Ram, Katherine A Fitzgerald, Guangping Gao
{"title":"The curious case of AAV immunology.","authors":"Allison M Keeler, Wei Zhan, Sanjay Ram, Katherine A Fitzgerald, Guangping Gao","doi":"10.1016/j.ymthe.2025.03.037","DOIUrl":"10.1016/j.ymthe.2025.03.037","url":null,"abstract":"<p><p>Immune responses to adeno-associated virus (AAV) have long been perplexing, from its first discovery to the latest clinical trials of recombinant AAV (rAAV) therapy. Wild-type AAV (wtAAV) does not cause any known disease, making it an ideal vector for gene therapy, as viral vectors retain virus-like properties. Although AAV stimulates only a mild immune response compared with other viruses, it is still recognized by the innate immune system and induces adaptive immune responses. B cell responses against both wtAAV and rAAV are robust and can hinder gene therapy applications and prevent redosing. T cell responses can clear transduced cells or establish tolerance against gene therapy. Immune responses to AAV gene therapy are influenced by many factors. Most clinical immunotoxicities that develop in response to gene therapies have emerged as higher doses of AAV vectors have been utilized and were not properly modeled in preclinical animal studies. Thus, several strategies have been undertaken to reduce or mitigate immune responses to AAV. While we have learned a considerable amount about how the immune system responds to AAV gene therapy since the discovery of AAV virus, it still remains a curious case that requires more investigation to fully understand.</p>","PeriodicalId":19020,"journal":{"name":"Molecular Therapy","volume":" ","pages":"1946-1965"},"PeriodicalIF":12.1,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143743178","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}