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Keywords = DNA transfection

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29 pages, 3654 KB  
Article
Direct Cytoplasmic Transcription and Trimeric RBD Design Synergize to Enhance DNA Vaccine Potency Against SARS-CoV-2
by Yunju Nam, Sang Chul Shin, Sang Won Cho and Hyung Jun Ahn
Pharmaceutics 2026, 18(2), 164; https://doi.org/10.3390/pharmaceutics18020164 - 26 Jan 2026
Abstract
Background/Objectives: The emergence of immune-evasive SARS-CoV-2 variants highlights the need for adaptable vaccine strategies. Trimeric receptor-binding domain (tRBD) antigens offer structural and immunological advantages over monomeric RBDs, but DNA vaccine efficacy has been limited by inefficient antigen expression, particularly in non-dividing antigen-presenting cells. [...] Read more.
Background/Objectives: The emergence of immune-evasive SARS-CoV-2 variants highlights the need for adaptable vaccine strategies. Trimeric receptor-binding domain (tRBD) antigens offer structural and immunological advantages over monomeric RBDs, but DNA vaccine efficacy has been limited by inefficient antigen expression, particularly in non-dividing antigen-presenting cells. Although cytoplasmic transcription–based DNA platforms have been developed to overcome nuclear entry barriers, their utility for antigen structure–function optimization remains underexplored. This study evaluated whether integrating a rationally designed trimeric RBD with a T7-driven cytoplasmic transcription system could enhance immunogenic performance. Methods: A DNA vaccine encoding a tandem trimeric SARS-CoV-2 RBD was delivered using a T7 RNA polymerase-driven cytoplasmic transcription system. In vitro antigen expression was assessed following Lipofectamine 3000-mediated transfection. In vivo, mice were immunized with the SM-102-based Rpol/tRBD/LNP formulation, and immunogenicity was assessed by antigen-specific antibody titers, serum neutralizing activity, and T-cell response profiling, together with basic safety/tolerability evaluations. Results: The T7-driven cytoplasmic transcription system markedly increased antigen mRNA and protein expression compared with conventional plasmid delivery. Rpol/tRBD vaccination induced higher anti-RBD IgG titers, enhanced neutralizing antibody activity, and robust CD8⁺ T cell responses relative to monomeric RBD and plasmid-based trimeric RBD vaccines. Immune responses were Th1-skewed and accompanied by germinal center activation without excessive inflammatory cytokine induction, body-weight loss, or hepatic and renal toxicity. Conclusions: This study demonstrates that integrating rational trimeric antigen engineering with direct cytoplasmic transcription enables balanced and well-tolerated immune activation in a DNA vaccine context. The T7 autogene-based platform provides a flexible framework for antigen structure–function optimization and supports the development of next-generation DNA vaccines targeting rapidly evolving viral pathogens. Full article
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13 pages, 2132 KB  
Article
Vaccination with Lipid Nanoparticle-Delivered VP2-DNA Elicits Immune Protection in Chickens Against Novel Variant Infectious Bursal Disease Virus (nVarIBDV)
by Yulong Zhang, Ziwen Wu, Hangbo Yu, Guodong Wang, Runhang Liu, Dan Ling, Erjing Ke, Xianyun Liu, Tengfei Xu, Suyan Wang, Yuntong Chen, Yongzhen Liu, Hongyu Cui, Yanping Zhang, Yulu Duan, Yulong Gao and Xiaole Qi
Vaccines 2026, 14(2), 113; https://doi.org/10.3390/vaccines14020113 - 24 Jan 2026
Viewed by 110
Abstract
Background/Objective: Infectious bursal disease (IBD) is an acute and highly contagious immunosuppressive disease in chickens caused by infectious bursal disease virus (IBDV). In recent years, a novel variant IBDV (nVarIBDV) has emerged and spread widely, inducing severe immunosuppression and posing a substantial threat [...] Read more.
Background/Objective: Infectious bursal disease (IBD) is an acute and highly contagious immunosuppressive disease in chickens caused by infectious bursal disease virus (IBDV). In recent years, a novel variant IBDV (nVarIBDV) has emerged and spread widely, inducing severe immunosuppression and posing a substantial threat to the poultry industry. More importantly, owing to antigenic variations, nVarIBDV can escape the immune protection of the existing vaccines. Therefore, it is imperative to develop a new vaccine that is antigenically matched to nVarIBDV. Methods: The major protective antigen gene VP2 of the representative nVarIBDV strain SHG19 was inserted into the eukaryotic expression plasmid pCAGGS to construct the recombinant plasmid pCASHGVP2. Subsequently, pCASHGVP2 was encapsulated in lipid nanoparticles (LNPs) to form pCASHGVP2-LNP nanoparticles. Finally, using the SPF chicken model, the immune efficacy of pCASHGVP2-LNP was preliminarily assessed by administering two vaccine doses (10 and 20 μg) and two immunization regimens (single or double immunization). Results: Efficient VP2 protein expression from pCASHGVP2 was confirmed by in vitro transfection experiments. The prepared pCASHGVP2-LNP nanoparticles exhibited an optimal particle size distribution and acceptable polydispersity index, indicating a homogeneous formulation. Furthermore, animal experiments showed that the candidate DNA vaccine elicited specific neutralizing antibodies after double immunization and protected immunized chickens from disease induced by nVarIBDV challenge. Conclusions: This study reports the first development of an LNP-encapsulated VP2 DNA vaccine (pCASHGVP2-LNP) against nVarIBDV, highlighting its potential application for the prevention of nVarIBDV. Full article
(This article belongs to the Special Issue Advances in DNA Vaccine Research)
21 pages, 3000 KB  
Article
Intracellular Oxidant Levels Are Crucial for Cell Survival and JAK/STAT Signaling in Classical Hodgkin’s Lymphoma
by Julia Wildfeuer, Rashmi P. Dheenadayalan, Svenja Hartung, Malena Zahn, Timo P. Albrecht, Zhouli Cao, Alexey Ushmorov, Peter Möller, Nadine T. Gaisa and Ralf Marienfeld
Antioxidants 2026, 15(1), 90; https://doi.org/10.3390/antiox15010090 - 9 Jan 2026
Viewed by 395
Abstract
Although oxidants are known to be deleterious for cellular homeostasis by oxidizing macromolecules like DNA or proteins, they are also involved in signaling processes essential for cellular proliferation and survival. Here, we investigated the role of superoxide anion (O2) and [...] Read more.
Although oxidants are known to be deleterious for cellular homeostasis by oxidizing macromolecules like DNA or proteins, they are also involved in signaling processes essential for cellular proliferation and survival. Here, we investigated the role of superoxide anion (O2) and hydrogen peroxide (H2O2) homeostasis for the proliferation and survival of classical Hodgkin’s lymphoma (cHL) cell lines. Inhibition of NADPH oxidases (NOX) using apocynin (Apo) and diphenylene iodonium (DPI), or treatment with the antioxidant butylated hydroxyanisole (BHA), significantly reduced proliferation and induced apoptosis in HL cell lines. These effects correlated with transcriptomic alterations involving redox regulation, immune signaling, and cell cycle control. Interestingly, treatment with DPI or antioxidants attenuated constitutive Signal Transducer and Activator of Transcription (STAT) activity, as seen by decreased phospho-STAT6 levels and reduced STAT6 DNA binding. This suggests a sensitivity of the Janus kinase (JAK)/STAT pathway in cHL cell lines to O2 and H2O2 depletion. Functional assays confirmed this by demonstrating partial restoration of proliferation or apoptosis in L428 cells that expressed constitutively active STAT6 or were transfected with small interfering RNAs (siRNAs) that targeted STAT regulators. These findings highlight that oxidants, particularly H2O2, act as both general oxidative stressors and essential modulators of oncogenic signaling pathways. Specifically, maintenance of oxidant homeostasis is critical for sustaining JAK/STAT-mediated growth and survival programs in cHL cells. Targeting redox homeostasis might offer a promising therapeutic strategy to impair JAK/STAT-driven proliferation and survival in cHL. Full article
(This article belongs to the Section Health Outcomes of Antioxidants and Oxidative Stress)
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12 pages, 5349 KB  
Communication
Mammary Intraductal Gene Electroporation (MIGE): A Novel Non-Viral Gene Delivery Method Targeting Murine Mammary Epithelial Cells
by Kazunori Morohoshi, Miho Ohba, Masahiro Sato and Shingo Nakamura
Appl. Sci. 2026, 16(1), 557; https://doi.org/10.3390/app16010557 - 5 Jan 2026
Viewed by 204
Abstract
The mammary gland is a valuable model in cancer research and developmental biology. Gene delivery techniques are crucial for mammary tissue research to understand how genes function and study on diseases such as cancer. Viral vector-based approaches provide a high degree of transduction [...] Read more.
The mammary gland is a valuable model in cancer research and developmental biology. Gene delivery techniques are crucial for mammary tissue research to understand how genes function and study on diseases such as cancer. Viral vector-based approaches provide a high degree of transduction efficiency, but they raise safety and immunogenicity concerns, whereas non-viral vector-based approaches are considered safer and have lower immunogenicity than viral methods. Unfortunately, non-viral gene delivery has rarely been applied to the mammary glands because it is technically challenging. Here, we developed a novel method for in vivo transfection of epithelial cells lining murine mammary glands via intraductal injection of plasmid DNA using a breath-controlled glass capillary and subsequent electroporation (EP) of the injected area. Female mice were transfected with plasmids harboring the enhanced green fluorescent protein (EGFP) gene. Widespread EGFP fluorescence was observed in the mammary epithelial cells of the ducts and adipocytes adjacent to the ducts. As this in vivo gene delivery method is simple, safe, and efficient for gene transfer to the mammary glands, we named this technique “Mammary Intraductal Gene Electroporation” (MIGE). The MIGE method is a useful experimental tool for studies on mammary gland development and differentiation as well as breast cancer research. Full article
(This article belongs to the Section Biomedical Engineering)
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24 pages, 3196 KB  
Article
Development of RALA-Based Mannosylated Nanocarriers for Targeted Delivery of Minicircle DNA Vaccines Encoding HPV-16 Oncogenes
by Andressa Giusti, Dalinda Eusébio, Matilde Costa, Inês Silveira, Swati Biswas, Diana Costa and Ângela Sousa
Vaccines 2026, 14(1), 18; https://doi.org/10.3390/vaccines14010018 - 23 Dec 2025
Viewed by 434
Abstract
Background/Objectives: Cervical cancer is a leading cause of cancer-related mortality among women, primarily driven by persistent infections with high-risk human papillomavirus (HPV), particularly HPV-16. Vaccines based on plasmid DNA encoding the viral oncogenes E6 and E7 represent a promising immunotherapeutic strategy, but their [...] Read more.
Background/Objectives: Cervical cancer is a leading cause of cancer-related mortality among women, primarily driven by persistent infections with high-risk human papillomavirus (HPV), particularly HPV-16. Vaccines based on plasmid DNA encoding the viral oncogenes E6 and E7 represent a promising immunotherapeutic strategy, but their efficacy remains limited due to poor cellular uptake. Cell-penetrating peptides such as RALA improve intracellular delivery, and functionalization with octa-arginine peptide conjugated to mannose (R8M) further enhances targeting of antigen-presenting cells (APCs). This study aimed to obtain the minicircle DNA (mcDNA) encoding mutant HPV-16 E6 and/or E7 antigens, and optimize its complexation with mannosylated RALA-based nanoparticles to improve vector delivery and consequently antigen presentation. Methods: Nanoparticles were formulated at different concentrations of RALA, with and without R8M functionalization. Their characterization included hydrodynamic diameter, polydispersity index, zeta potential, complexation efficiency (CE), stability, morphology, and Fourier-Transform Infrared Spectroscopy. In vitro assays in JAWS II dendritic cells (DCs) assessed biocompatibility, transfection efficiency and target gene expression. Results: Optimal conditions were obtained at 72.5 µg/mL of RALA, producing nanoparticles smaller than 150 nm with high CE (>97%) and uniform size distribution. Functionalization with R8M at 58 µg/mL preserved these characteristics when complexed with all mcDNA vectors. The formulations were biocompatible and effectively transfected DCs. Mannosylated formulations enhanced antigenic expression compared to non-mannosylated counterparts, evidencing a mannose-receptor-mediated uptake, while increasing the production of pro-inflammatory cytokines. Conclusions: Nanoparticles based on the RALA peptide and functionalized with R8M significantly improved mcDNA transfection and gene expression in APCs. These findings support further investigation of this system as a targeted DNA vector delivery platform against HPV-16. Full article
(This article belongs to the Special Issue New Approaches to Vaccine Development and Delivery)
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19 pages, 4836 KB  
Article
Robust Functionality and Regulation of Selectively Expressed RNA as AAV Vectors and In Vitro Transcribed Molecules
by Frederik Rastfeld, Nils Hersch, Georg Dreissen, Hajaani Manoharan, Laura Wagner, Lukas Lövenich, Elke Barczak, Hildegard Büning, Rudolf Merkel and Bernd Hoffmann
Pharmaceutics 2025, 17(12), 1595; https://doi.org/10.3390/pharmaceutics17121595 - 10 Dec 2025
Viewed by 600
Abstract
Background/Objectives: Selectively expressible RNA (seRNA) molecules represent a promising new platform for the induction of cell type-specific protein expression. Based on the sense–antisense interaction of the seRNA antisense domain with target cell-specific RNA molecules, the partial degradation of the seRNA molecule induces the [...] Read more.
Background/Objectives: Selectively expressible RNA (seRNA) molecules represent a promising new platform for the induction of cell type-specific protein expression. Based on the sense–antisense interaction of the seRNA antisense domain with target cell-specific RNA molecules, the partial degradation of the seRNA molecule induces the activation of an internal ribosomal entry site to initiate translation. The selective expression of seRNA encoded proteins exclusively in target cells works both in vitro and in vivo but is associated with a lower expression intensity compared with classical mRNAs. Furthermore, seRNAs have so far been transfected into cells by plasmid-encoded seRNA expression systems, which is limiting their broad medical applicability. Here, we focus on the characterization of plasmid-based seRNA uptake and activation as well as on options to transfer the seRNA technology to additional vector systems to increase target cell-specific effector expression. Methods: seRNA constructs were generated as expression plasmids, AAV, DNA minicircles and IVT-RNA and delivered into different eukaryotic cell lines by transfection/transduction. Analyses were performed using fluorescence microscopy and, for quantitative analyses, flow cytometry. RNA stability and expression analyses were performed using qRT-PCR. Results: We show that seRNA-based plasmid systems are efficiently transfected into cells but that reduced RNA steady-state levels are present compared with control expression plasmids. This effect is most likely based on reduced transcription efficiency rather than seRNA stability. Furthermore, seRNA transcription from viral vectors or circular DNA significantly increased the effector expression of seRNAs and enabled linear expression regulation while maintaining target cell-specific activation and inactivation in non-target cells. Optimal results were achieved by adapting the technology to in vitro transcribed seRNA. Conclusions: Our data show that seRNA technology develops its full functionality regardless of the type of transfer vector used. Furthermore, expression strength can be regulated within a wide range while maintaining consistent functionality which will enable broad applicability in medicine in the future. Full article
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19 pages, 2375 KB  
Article
The Intrinsic Innate Immunity of Hepatocytes Suppresses HBV Replication and Is Antagonized by HBx
by Chui Zeng, Fayed Attia Koutb Megahed, Yiqiong Guo, Dongmei Sun, Yaru Wang, Qin Liu, Yanwei Bi, Jinghang Li, Qi Zhou, Qingdong Xie, Pingnan Sun and Xiaoling Zhou
Viruses 2025, 17(12), 1599; https://doi.org/10.3390/v17121599 - 10 Dec 2025
Viewed by 677
Abstract
(1) Background: Hepatitis B virus (HBV) belongs to the Hepadnaviridae family of viruses that interact with hepatocytes. HBV infection is a major global health problem. Most adults clear the infection quickly after being infected with HBV, while a few people develop chronic HBV [...] Read more.
(1) Background: Hepatitis B virus (HBV) belongs to the Hepadnaviridae family of viruses that interact with hepatocytes. HBV infection is a major global health problem. Most adults clear the infection quickly after being infected with HBV, while a few people develop chronic HBV infection. It is well-known that the early innate immune response of host cells plays an important role in the fight against virus infection. However, the interactions between HBV and the intrinsic innate immune system of hepatocytes are still not fully understood. The aim of this study was to confirm the interaction between HBV and hepatocytes, and to identify the interferon-stimulated genes (ISGs) regulated by HBx and their expression in association with HBV-associated HCC (HBV-HCC), so that we can refine our understanding of the interaction between HBV and ISGs and its potential influence on HBV-HCC. (2) Methods: We analyzed data concerning the stimulation of IFN-dependent genes in primary human hepatocytes (PHHs) transfected with pathogen DNA mimetics or infected with HBV in the GSE69590 database. Bioinformatic methods, such as GSEA, GO, and KEGG, were used to analyze the differentially expressed innate immunity genes and their related pathways to identify candidate intrinsic innate immune factors. qPCR on HepG2 and Huh7 cells, which highly express HBx, was used to detect relevant intrinsic innate immune factors. qPCR, RNAi, and Elisa methods were used to identify intrinsic innate immune factors in HBV-integrated HepG2.2.15 cells, and bioinformatics analysis was conducted on the HBV-infected tissues and cells in the GEO database. (3) Results: Inhibition of the JAK-STAT pathway enhanced HBV replication in HepG2 cells transfected with HBV plasmid and HepG2-NTCP cells infected with HBV. GSEA analysis of the GSE69590 data revealed significant changes in intrinsic innate immune pathways during HBV infection with PHH for 40 h. A total of 84 differentially expressed, candidate innate immunity genes were identified in GSE69590. Validation showed that TRIM22 and TRIM56 were down-regulated when HBx was expressed. Consistently, TRIM22 and TRIM56 were up-regulated following inhibition of HBx by transfection of HBx siRNA into HepG2.2.15 cells, and HBV pgRNA was up-regulated following down-regulated expression of TRIM22 and TRIM56 in HEK293 cells. Receiver operating characteristics (ROC) and overall survival (OS) analysis of 204 HBV-HCC patients showed that expression of TRIM22 was closely associated with HBV-HCC, and high expression of TRIM22 was associated with longer survival. (4) Conclusions: Innate immunity genes TRIM22 and TRIM56 are regulated by HBx, and higher expression of TRIM22 is closely related to longer survival of HBV-HCC patients. Full article
(This article belongs to the Special Issue Interferon-Stimulated Genes in Antiviral Immunity)
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39 pages, 9235 KB  
Article
Biological Performance and Molecular Mechanisms of Mesyl MicroRNA-Targeted Oligonucleotides in Colorectal Cancer Cells
by Svetlana K. Miroshnichenko, Olga A. Patutina, Andrey V. Markov, Maxim S. Kupryushkin, Valentin V. Vlassov and Marina A. Zenkova
Int. J. Mol. Sci. 2025, 26(23), 11747; https://doi.org/10.3390/ijms262311747 - 4 Dec 2025
Cited by 2 | Viewed by 663
Abstract
Colorectal cancer (CRC) remains one of the most aggressive and therapeutically resistant malignancies worldwide. This study examined the molecular mechanisms underlying the anti-oncogenic activity of methanesulfonyl phosphoramidate-modified antisense oligonucleotides (µ-ASOs) targeting miR-21, miR-17, and miR-155, which represent critical oncogenic drivers in CRC. Using [...] Read more.
Colorectal cancer (CRC) remains one of the most aggressive and therapeutically resistant malignancies worldwide. This study examined the molecular mechanisms underlying the anti-oncogenic activity of methanesulfonyl phosphoramidate-modified antisense oligonucleotides (µ-ASOs) targeting miR-21, miR-17, and miR-155, which represent critical oncogenic drivers in CRC. Using human colorectal adenocarcinoma Caco-2 cells transfected with either individual µ-ASOs or their triple combination, we assessed target miRNA downregulation, antiproliferative and anti-migratory activities, and performed extensive proteomic profiling. Protein–protein interaction network analysis of differentially expressed proteins (DEPs) revealed that, beyond modulation of core metabolic processes, each µ-ASO exhibited distinct effects: µ-21 predominantly affected apoptosis, cell cycle, and DNA repair; µ-17 influenced proliferation and chaperone responses; and µ-155 modulated intracellular transport and immune regulation. Combination treatment elicited a unique proteomic signature partially overlapping with monotherapies. The proteomic analysis revealed several validated and putative miRNA-targeted DEPs, including both established and novel candidates in the CRC context: RPL31, CCT2, and CDC37 (miR-21); DNM2, SNRPN, NUP98, and NUP85 (miR-17); as well as RPL17 (miR-155). Expression of these targets correlated with favorable clinical outcomes in CRC patients. This work provides the first comprehensive mechanistic insight into antisense oligonucleotide-mediated miRNA suppression in Caco-2 colorectal adenocarcinoma cells and expands the miRNA target landscape. Full article
(This article belongs to the Special Issue New Molecular Aspects of Colorectal Cancer)
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19 pages, 2271 KB  
Article
Plasmonic Nanopore Sensing to Probe the DNA Loading Status of Adeno-Associated Viruses
by Scott Renkes, Steven J. Gray, Minjun Kim and George Alexandrakis
Chemosensors 2025, 13(12), 418; https://doi.org/10.3390/chemosensors13120418 - 4 Dec 2025
Cited by 1 | Viewed by 1016
Abstract
Adeno-associated viruses (AAVs) are a leading vector for gene therapy, yet their clinical utility is limited by the lack of robust quality control methods to distinguish between empty (AAVempty), partially loaded (AAVpartial), and fully DNA loaded (AAVfull) [...] Read more.
Adeno-associated viruses (AAVs) are a leading vector for gene therapy, yet their clinical utility is limited by the lack of robust quality control methods to distinguish between empty (AAVempty), partially loaded (AAVpartial), and fully DNA loaded (AAVfull) capsids. Current analytical techniques provide partial insights but remain limited in sensitivity, throughput, or resolution. Here we present a multimodal plasmonic nanopore sensor that integrates optical trapping with electrical resistive-pulse sensing to characterize AAV9 capsids at the single-particle level in tens of μL sample volumes and fM range concentrations. As a model system, we employed AAV9 capsids not loaded with DNA, capsids loaded with a self-complementary 4.7 kbp DNA (AAVscDNA), and ones loaded with single-stranded 4.7 kbp DNA (AAVssDNA). Ground-truth validation was performed with analytical ultracentrifugation (AUC). Nanosensor data were acquired concurrently for optical step changes (occurring at AAV trapping and un-trapping) both in transmittance and reflectance geometries, and electrical nanopore resistive pulse signatures, making for a total of five data dimensions. The acquired data was then filtered and clustered by Gaussian mixture models (GMMs), accompanied by spectral clustering stability analysis, to successfully separate between AAV species based on their DNA load status (AAVempty, AAVpartial, AAVfull) and DNA load type (AAVscDNA versus AAVssDNA). The motivation for quantifying the AAVempty and AAVpartial population fractions is that they reduce treatment efficacy and increase immunogenicity. Likewise, the motivation to identify AAVscDNA population fractions is that these have much higher transfection rates. Importantly, the results showed that the nanosensor could differentiate between AAVscDNA and AAVssDNA despite their identical masses. In contrast, AUC could not differentiate between AAVscDNA and AAVssDNA. An equimolar mixture of AAVscDNA, AAVssDNA and AAVempty was also measured with the sensor, and the results showed the expected population fractions, supporting the capacity of the method to differentiate AAV load status in heterogeneous solutions. In addition, less common optical and electrical signal signatures were identified in the acquired data, which were attributed to debris, rapid entry re-entry to the optical trap, or weak optical trap exits, representing critical artifacts to recognize for correct interpretation of the data. Together, these findings establish plasmonic nanopore sensing as a promising platform for quantifying AAV DNA loading status and genome type with the potential to extend ultra-sensitive single-particle characterization beyond the capabilities of existing methods. Full article
(This article belongs to the Special Issue Electrochemical Sensors Based on Various Materials)
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39 pages, 1712 KB  
Review
KRAS-Wild Pancreatic Cancer—More Targets than Treatment Possibilities?
by Kamila Krupa, Marta Fudalej, Hanna Miski, Emilia Włoszek, Marta Szymczak, Anna Badowska-Kozakiewicz, Aleksandra Czerw and Andrzej Deptała
Cancers 2025, 17(23), 3769; https://doi.org/10.3390/cancers17233769 - 26 Nov 2025
Viewed by 1538
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with a five-year survival rate of 3–15% and limited effective treatment options for most patients. Approximately 5–10% of cases are wild-type KRAS and are more likely to harbor rare alterations, including gene fusions involving [...] Read more.
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy with a five-year survival rate of 3–15% and limited effective treatment options for most patients. Approximately 5–10% of cases are wild-type KRAS and are more likely to harbor rare alterations, including gene fusions involving anaplastic lymphoma kinase (ALK), ROS Proto-Oncogene 1 (ROS1), neurotrophic tyrosine receptor kinase (NTRK), Rearranged During Transfection (RET), Fibroblast Growth Factor Receptor (FGFR), or Neuregulin 1 (NRG1) genes, as well as germline mutations in DNA repair genes. This review integrates current evidence on the prevalence, molecular profile, and clinical significance of gene fusions, amplification, and somatic/germline mutations in PDAC, with a particular focus on the wild-type KRAS subgroup. Clinical trial data and case reports indicate that these alterations can enhance patient susceptibility to targeted therapies. Currently, selpercatinib, larotrectinib, and repotrectinib are approved by the FDA for the treatment of certain solid tumors harboring specific gene fusions. Recent studies on zenocutuzumab resulted in the FDA-accelerated approval for NGR1 fusion-positive NSCLC and PDAC. Germline mutations may specifically increase responsiveness to poly(ADP-ribose) polymerase (PARP) inhibitors or platinum-based treatments. Comprehensive genomic profiling, incorporating fusion detection and germline testing, is essential to identify patients who may benefit from precision-based approaches. Full article
(This article belongs to the Section Cancer Therapy)
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20 pages, 3047 KB  
Article
Protective Efficacy of Two Novel DNA Vaccine Candidates Encoding TgGRA28 and TgGRA83 with an IL-28B Molecular Adjuvant Against Acute and Chronic Toxoplasmosis in Mice
by Jun Fang, Jingqi Mu, Rui Li and Jia Chen
Vaccines 2025, 13(12), 1180; https://doi.org/10.3390/vaccines13121180 - 21 Nov 2025
Viewed by 660
Abstract
Background: Toxoplasma gondii is a globally distributed apicomplexan parasite capable of causing congenital infections and spontaneous abortions in humans. While the parasite-secreted effector proteins TgGRA28 and TgGRA83 are known to mediate virulence or immune modulation, their potential as vaccine targets remains unexplored. Despite [...] Read more.
Background: Toxoplasma gondii is a globally distributed apicomplexan parasite capable of causing congenital infections and spontaneous abortions in humans. While the parasite-secreted effector proteins TgGRA28 and TgGRA83 are known to mediate virulence or immune modulation, their potential as vaccine targets remains unexplored. Despite its immunomodulatory properties, the role of IL-28B (a type III interferon) in enhancing DNA vaccine efficacy against T. gondii infection remains unclear. Methods: In this study, we constructed eukaryotic expression plasmids pVAX-GRA28, pVAX- GRA83 and pVAX-IL-28B. After transfection into -293-T cell, protein expression encoding TgGRA28 and TgGRA83 was confirmed via indirect immunofluorescence assay (IFA), while IL-28B expression was analyzed by ELISA. Subsequently, C57BL/6J or IFNαR1 knockout mice were immunized with single or dual-antigen DNA vaccines, with or without the molecular adjuvant pVAX-IL-28B. Immune responses were assessed through Toxoplasma-specific antibody levels, cytotoxic T lymphocyte (CTL) activity, cytokine profiling (IFN-γ, IL-2, IL-12p40, IL-12p70), and flow cytometric analysis of lymphocyte subsets and dendritic cells (DCs). Protective efficacy was determined by survival rates and brain cyst burden following challenge with 100 or 10 ME49 T. gondii cysts, respectively. Results: Vaccination with pVAX-GRA28 and pVAX-GRA83 elicited robust humoral immune responses with increased T. gondii-specific IgG levels and also Th1-polarized immunity, characterized by elevated IgG2a/IgG1 ratio, IFN-γ-dominant cytokine responses, and enhanced DCs, CD4+ and CD8+ T-cell activation. The cocktail vaccine conferred superior protection compared to single-antigen formulations, significantly improving survival and reducing cyst formation. Co-administration of pVAX-IL-28B further augmented vaccine-induced immunity, enhancing both cellular and humoral responses. Moreover, these DNA immunization with pVAX-GRA28 and pVAX-GRA83 plus pVAX-IL-28B induced robust protective immunity that was largely independent of type I IFN signaling, consistent with type III IFN biology. Conclusions: Our findings demonstrate that TgGRA28 and TgGRA83 are promising vaccine candidates against toxoplasmosis, capable of inducing protective immunity against acute and chronic infection. Moreover, IL-28B serves as a potent genetic adjuvant, warranting further investigation for its broader application in vaccines targeting apicomplexan parasites. Full article
(This article belongs to the Section Vaccines Against Tropical and Other Infectious Diseases)
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15 pages, 7674 KB  
Article
MiR-10a as a Potential Biomarker and Therapeutic Target in Localized and Metastatic Prostate Cancer
by Tiago José Borelli Bovo, Juliana Alves de Camargo, Ruan Pimenta, Vanessa Ribeiro Guimarães, Patrícia Candido, Katia Ramos Moreira Leite, Carlo Camargo Passerotti, William Carlos Nahas and Sabrina T. Reis
Curr. Issues Mol. Biol. 2025, 47(11), 913; https://doi.org/10.3390/cimb47110913 - 3 Nov 2025
Cited by 2 | Viewed by 579
Abstract
Introduction: Prostate cancer (PC) accounts for around 10% of all cancers worldwide and is the fourth most common neoplasm. Localized PC has high cure rates when diagnosed early, but 35% of patients progress to the metastatic form. The search for new molecular markers, [...] Read more.
Introduction: Prostate cancer (PC) accounts for around 10% of all cancers worldwide and is the fourth most common neoplasm. Localized PC has high cure rates when diagnosed early, but 35% of patients progress to the metastatic form. The search for new molecular markers, such as microRNAs, is fundamental to improving diagnosis and treatment. The role of miR-10a is controversial between tumor tissues, opening a niche for studies on their role in PC. Objectives: To evaluate the role of miR-10a in metastatic PC cell lines, focusing on the mechanisms of proliferation, migration, and invasion, and to analyze the expression in surgical specimens of localized PC. Methods: Three commercial metastatic PC cell lines were used: LNCaP, DU145 and PC-3. Expression of mimic miR-10a was induced by cell transfection, followed by extraction of miRNA and total RNA. The synthesis of complementary DNA (cDNA) and analysis by real-time PCR enabled the expression of miR-10a and the VEGF, MYC, and HAS3 genes to be assessed. Matrigel, colony formation, invasion, and migration assays were evaluated for the transfected cells. The surgical specimens were used to evaluate the miR-10a expression. Results: Transfected cells with mimic significantly increased the expression of miR-10a in the LNCaP (p = 0.0179), PC-3 (p ≤ 0.001), and DU145 (p ≤ 0.001) cell lines. Transfected cells reduced cell invasion in the PC-3 (p = 0.001) and DU-145 (p = 0.0004) cell lines and decreased cell migration and proliferation. In surgical specimens, miR-10a expression was higher in PC compared to Benign Prostatic Hyperplasia (p = 0.0010). Conclusions: Increased expression of miR-10a affects cell migration, invasion, and proliferation, showing potential as a therapeutic target in treating PC. Full article
(This article belongs to the Section Molecular Medicine)
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23 pages, 33673 KB  
Article
Efficient Delivery of CRISPR-Cas9 RNP Complexes with Cyclodextrin-Based Nanosponges for Enhanced Genome Editing: TILD-CRISPR Integration
by Shahin Amiri, Setare Adibzadeh, Yousef Khazaei Monfared, Saeed Kaboli, Arash Arashkia, Farzaneh Barkhordari, Mohammad Mahmoudian, Mohammad Hassan Kheirandish, Francesco Trotta and Fatemeh Davami
Int. J. Mol. Sci. 2025, 26(21), 10682; https://doi.org/10.3390/ijms262110682 - 2 Nov 2025
Viewed by 1522
Abstract
The CRISPR-Cas9 system has transformed biomedical research by enabling precise genetic modifications. However, efficient delivery of CRISPR components remains a major hurdle for therapeutic applications. To address this, we employed a new modified cationic hyper-branched cyclodextrin-based polymer (Ppoly) system to deliver an integrating [...] Read more.
The CRISPR-Cas9 system has transformed biomedical research by enabling precise genetic modifications. However, efficient delivery of CRISPR components remains a major hurdle for therapeutic applications. To address this, we employed a new modified cationic hyper-branched cyclodextrin-based polymer (Ppoly) system to deliver an integrating GFP gene using the TILD-CRISPR method, which couples donor DNA linearization with RNP complexes. The physicochemical properties, loading efficiency, and cellular uptake of RNP with Ppoly were studied. After transfection, antibiotic selection and single-cell cloning were performed. Junction PCR was then performed on the isolated clones, and we compared the knock-in efficiency of Ppoly with that of the commercial CRISPRMAX™ reagent (Thermo Fisher, Invitrogen™, Waltham, MA, USA). The results demonstrate the encapsulation efficiency of over 90% for RNP and Ppoly, and cell viability remaining above 80%, reflecting the minimal toxicity of this approach. These attributes facilitated successful GFP gene integration using the TILD-CRISPR with RNP delivered via cyclodextrin-based nanosponges. The present method achieved a remarkable 50% integration efficiency in CHO-K1 cells, significantly outperforming the 14% observed with CRISPRMAX™ while maintaining lower cytotoxicity. This study highlights a promising platform for precise and efficient genome editing, with strong potential for therapeutic and regenerative medicine applications. Full article
(This article belongs to the Special Issue Nanoparticles in Molecular Pharmaceutics)
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24 pages, 4341 KB  
Article
EGFR mRNA-Engineered Mesenchymal Stem Cells (MSCs) Demonstrate Radioresistance to Moderate Dose of Simulated Cosmic Radiation
by Fay Ghani, Peng Huang, Cuiping Zhang and Abba C. Zubair
Cells 2025, 14(21), 1719; https://doi.org/10.3390/cells14211719 - 1 Nov 2025
Viewed by 893
Abstract
Galactic cosmic ray (GCR) radiation is a major barrier to human space exploration beyond Earth’s magnetic field protection. Mesenchymal stem cells (MSCs) are found in all organs and play a critical role in repair and regeneration of tissue. We engineered bone marrow-derived MSCs [...] Read more.
Galactic cosmic ray (GCR) radiation is a major barrier to human space exploration beyond Earth’s magnetic field protection. Mesenchymal stem cells (MSCs) are found in all organs and play a critical role in repair and regeneration of tissue. We engineered bone marrow-derived MSCs and evaluated their response to ionizing radiation exposure. Epidermal growth factor receptor (EGFR) expression by certain types of cancers has been shown to induce radioresistance. In this study, we tested the feasibility of transfecting MSCs to overexpress EGFR (eMSC-EGFR) and their capacity to tolerate and recover from X-ray exposure. Quantitative real-time PCR (qRT-PCR) and immunoblotting results confirmed the efficient transfection of EGFR into MSCs and EGFR protein production. eMSC-EGFR maintained characteristics of human MSCs as outlined by the International Society for Cell & Gene Therapy. Then, engineered MSCs were exposed to various dose rates of X-ray (1–20 Gy) to assess the potential radioprotective role of EGFR overexpression in MSCs. Post-irradiation analysis included evaluation of morphology, cell proliferation, viability, tumorigenic potential, and DNA damage. eMSC-EGFR showed signs of radioresistance compared to naïve MSCs when assessing relative proliferation one week following exposure to 1–8 Gy X-rays, and significantly lower DNA damage content 24 h after exposure to 4 Gy. We establish for the first time the efficient generation of EGFR overexpressing MSCs as a model for enhancing the human body to tolerate and recover from moderate dose radiation injury in long-term manned space travel. Full article
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22 pages, 4823 KB  
Article
Investigating the Cytoprotective Mechanisms of the Tardigrade Damage Suppressor (Dsup) Protein in Human Cells Under Hypoxic Stress
by Enxhi Shaba, Claudia Ricci, Lorenza Vantaggiato, Maria Francesca Paolocci, Tommaso Regoli, Kateryna Miedviedieva, Jlenia Brunetti, Valerio Ciccone, Claudia Cecchin, Sandra Donnini, Carlotta Marzocchi, Claudia Landi and Silvia Cantara
Int. J. Mol. Sci. 2025, 26(21), 10452; https://doi.org/10.3390/ijms262110452 - 28 Oct 2025
Viewed by 1059
Abstract
Ischemia/reperfusion injury (IRI) is a common damage due to the restoration of blood flow following an ischemic injury. Its pathogenesis is mainly linked to the production of reactive oxygen species (ROS), which sustain cell damage and promote cell death. The tardigrade damage suppressor [...] Read more.
Ischemia/reperfusion injury (IRI) is a common damage due to the restoration of blood flow following an ischemic injury. Its pathogenesis is mainly linked to the production of reactive oxygen species (ROS), which sustain cell damage and promote cell death. The tardigrade damage suppressor protein (Dsup) is a DNA-binding protein that enables tardigrades to tolerate stress conditions, including oxidative stress. We investigated the ability of the Dsup to protect human cells from IRI, using an in vitro model of hypoxia and reoxygenation. We exposed HEK293TT cells transfected with the Dsup to hypoxic injury and analyzed cell viability, oxidative stress, expression of antioxidant proteins using functional assays, and a proteomic approach to dissect the molecular mechanisms modulated by the Dsup. Dsup expression significantly enhanced cell survival following hypoxia-reoxygenation and markedly reduced intracellular ROS levels. Proteomic and Western blot analyses revealed a significant upregulation of antioxidant enzymes in Dsup-expressing cells. Furthermore, the Dsup modulated autophagy and key stress-related pathways, including the MAPK cascade. This study demonstrates that the Dsup protects human cells from IRI by reducing oxidative stress and modulating key cytoprotective pathways. Our results establish the Dsup as a promising candidate for future therapeutic applications against IRI, meriting further exploration in in vivo models. Full article
(This article belongs to the Special Issue Programmed Cell Death and Oxidative Stress: 3rd Edition)
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