Current Gene Therapy - Online First
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Precision Medicine: Design of Immune Inert Exosomes for Targeted Gene Delivery
Available online: 30 September 2025More LessExosomes represent the smallest size among extracellular vesicles, which also include apoptotic bodies and microvesicles. Exosomes are natural nanocarriers that play a key role in intracellular communication, consisting of a hydrophobic lipid bilayer membrane and a hydrophilic core. The membrane compositions of exosomes are similar to those of the parent cells from which they are generated. Normally, the exosome membrane contains diacylglycerol, ceramide, cholesterol, and various surface proteins, including tetraspanins and Lamb2. Almost all cell types secrete exosomes into body fluids through exocytosis, including stem cells, epithelial cells, endothelial cells, immune cells, tumor cells, neurons, mast cells, oligodendrocytes, reticulocytes, macrophages, platelets, and astrocytes. Every cell type expresses a distinct type of exosomes carrying various bioactive molecules. Exosomes are major transporters of bioactive cargo, including enzymes, receptors, growth and transcription factors, nucleic acids, lipids, and other metabolites, which strongly affect the physiology of recipient cells. Exosomes are not only potent drug and gene delivery nanocarriers, but also have potential for disease diagnosis, tissue regeneration, and immunomodulation. Exosomes are present in various body fluids, including plasma, serum, saliva, milk, nasal secretions, urine, amniotic fluid, semen, and cerebrospinal fluid, among others. Stem cell-made exosomes are potential natural therapeutics, which is due to their rejuvenating cargo and ability to cross biological barriers. However, natural exosomes' inefficient cargo transfer and short lifespan in the bloodstream have hindered their progress in therapeutic interventions. Genetic engineering of the parent cell allows for loading specific therapeutic cargo into the lumen of newly generated exosomes and/or displaying certain homing peptides or ligands at their surface, leading to extension of their lifespan and precise delivery to specific organs or tissues. This minireview explores the creation of designer exosomes through parent cell engineering and their utilization for guiding the delivery of tailored therapeutic cargo to specific organs while evading the host innate immune response.
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Advances in Gene Therapy Clinical Trials for Hemophilia Care
Authors: Amita Joshi Rana, Md Sadique Hussain, Vikas Jakhmola and Gaurav GuptaAvailable online: 05 September 2025More LessGene therapy has revolutionized the therapeutic landscape for hemophilia A and B, offering the potential for sustained endogenous production of coagulation factors VIII and IX. Recent advances in adeno-associated virus (AAV)-mediated gene transfer, particularly the approvals of valoctocogene roxaparvovec (Roctavian) and etranacogene dezaparvovec (Hemgenix), represent significant milestones in hemophilia care. This mini-review synthesizes emerging clinical data from phase I–III trials published between 2022 and 2025, emphasizing efficacy, durability, and immunogenicity profiles of leading AAV-based therapies. Innovations in vector design, such as liver-specific promoters, codon-optimized constructs, and novel capsids (e.g., AAVhu37, AAVrh10, AAV-Spark100), have improved transgene expression and expanded eligibility. Despite notable success, challenges persist, including immune-mediated transaminitis, declining factor activity over time, particularly in hemophilia A, and limitations posed by preexisting neutralizing antibodies. Additionally, CRISPR-Cas9 and non-viral delivery systems are emerging as complementary strategies, potentially enhancing therapeutic precision and overcoming AAV-related barriers. The minireview also addresses the critical need for equitable access and scalable production models to ensure global availability of gene therapies. With ongoing innovation and multidisciplinary collaboration, gene therapy is poised to transition from experimental intervention to mainstream curative care in hemophilia and other hematologic diseases.
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Tailored Therapies for Hereditary Diabetes: Unraveling the Genetic Underpinnings of MODY and Neonatal Diabetes
Available online: 29 August 2025More LessIntroductionHereditary forms of diabetes, including Maturity-Onset Diabetes of the Young (MODY) and Neonatal Diabetes Mellitus (NDM), are rare monogenic disorders caused by mutations in genes involved in pancreatic development, beta-cell function, and insulin secretion. Unlike the polygenic nature of type 1 and type 2 diabetes, these forms provide a unique model for precision medicine.
MethodsA comprehensive literature review was conducted to explore the molecular genetics, clinical features, diagnostic advancements, and therapeutic strategies related to MODY and NDM. Particular focus was placed on genotype-phenotype correlations and responsiveness to targeted treatments.
ResultsDistinct gene mutations such as GCK, HNF1A, and HNF4A in MODY, and KCNJ11, ABCC8, and INS in NDM are associated with specific clinical characteristics and treatment responses. Genetic testing plays a crucial role in early diagnosis and management. For instance, sulfonylurea therapy has effectively replaced insulin in some cases of NDMre with KATP channel mutations. In MODY, accurate genetic classification helps guide the use of oral hypoglycemics or dietary interventions instead of unnecessary insulin therapy.
DiscussionUnderstanding the genetic basis of MODY and NDM has enabled clinicians to personalize treatment plans, improving disease outcomes. Genetic diagnosis not only facilitates better classification but also informs prognosis and guides family screening. Despite these advances, challenges remain in access to testing and awareness among healthcare providers.
ConclusionMolecular insights into MODY and NDM have revolutionized their diagnosis and treatment. Gene-based therapeutic approaches enhance glycemic control and quality of life, marking a significant step toward precision medicine in diabetes care. Ongoing research will be key to further optimizing individualized treatment strategies.
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Targeted Therapies and Computational Approaches in the Management of Crohn’s Disease
Authors: Ajay Kumar Pandey and Sayali MukherjeeAvailable online: 27 August 2025More LessCrohn's disease (CD), a chronic inflammatory disorder of the gastrointestinal tract, presents significant challenges in clinical medicine due to its multifactorial etiology and varied therapeutic responses. This review examines the diverse causes of CD, including genetic predispositions identified through genome-wide association studies (GWAS), which involve scanning the genome for single-nucleotide polymorphisms associated with CD risk, as well as environmental triggers, such as diet and alterations in the microbiome. Biomarkers, such as fecal calprotectin and C-reactive protein (CRP), as well as genetic markers like NOD2 mutations, provide critical tools for diagnosis and treatment stratification. Advances in computational methodologies, including multi-omics analyses and machine learning, have enhanced our understanding of CD pathophysiology and therapeutic outcomes. Traditional treatments, including immunomodulators and biologics, such as anti-TNF agents, have laid the groundwork for novel cytokine-targeted therapies, such as IL-12/23 inhibitors (e.g., ustekinumab) and integrin inhibitors (e.g., vedolizumab), which aim to improve mucosal healing and reduce relapse rates. However, integrating personalized medicine into clinical practice remains challenging due to the heterogeneity of CD and limitations in biomarker validation. The integration of predictive biomarkers with computational tools enables clinicians to tailor therapy at the individual level, improving remission rates, minimizing adverse effects, and enhancing long-term disease control. These personalized strategies show promise in shifting CD management toward a more effective, patient-specific model of care. This review underscores the potential of personalized therapeutic strategies, leveraging molecular and computational insights, to optimize disease management and improve patient outcomes in CD.
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Role of Exosomal miRNAs and Epigenetic Modifications in Diabetic Nephropathy: Insights into Novel Diagnostic and Therapeutic Strategies
Available online: 25 August 2025More LessIntroductionDiabetic Nephropathy (DN) is a leading cause of chronic kidney disease and end-stage renal failure, highlighting the need for improved diagnostic and therapeutic strategies. This review examines the emerging roles of exosomal microRNAs (miRNAs) and epigenetic modifications in disease, with a focus on their diagnostic and therapeutic potential.
MethodsA comprehensive analysis of the current literature was conducted, focusing on exosomal miRNAs—particularly miR-21, miR-192, and miR-29—and their impact on inflammatory pathways, such as IL-6 and NF-κB. The role of epigenetic alterations, including DNA methylation, histone modification, and noncoding RNAs, in DN progression is also discussed. Techniques for miRNA detection and exosome isolation are briefly reviewed.
ResultsExosomal miRNAs contribute to DN pathophysiology by promoting oxidative stress, inflammation, and fibrosis. Their stability and noninvasive detectability make them promising early biomarkers. Epigenetic modifications further modulate gene expression relevant to disease progression.
DiscussionThese molecular changes offer novel targets for early diagnosis and therapeutic intervention in DN. The interplay between miRNAs and epigenetic regulation may provide insights into disease heterogeneity and progression. However, limitations exist regarding the standardization of detection techniques and clinical translation, necessitating further research.
ConclusionExosomal miRNAs and epigenetic markers present valuable tools for advancing the diagnosis and personalized treatment of DN. Enhancing detection techniques and understanding their molecular roles could pave the way for more effective clinical applications.
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Unraveling Etiological Indications and Therapeutic Implications of Familial Cerebral Cavernous Malformations in the Dawn of Gene Therapy for Monogenic Conditions
Authors: Ke Ma, Moksada Regmi, Shikun Liu, Ying Xiong, Yingjie Wang, Weihai Liu, Yuwei Dai, Guozhong Lin, Jun Yang and Chenlong YangAvailable online: 19 August 2025More LessCerebral Cavernous Malformations (CCMs) are vascular anomalies in the central nervous system that arise from both genetic and non-genetic factors, and can cause hemorrhage, seizures, and neurological deficits. Approximately 80% of CCMs are sporadic, while 20% are Familial (FCCMs), an autosomal dominant, monogenic disorder characterized by multiple lesions and severe clinical manifestations. Over the past three decades, linkage analyses have identified KRIT1/CCM1, MGC4607/CCM2, and PDCD10/CCM3 as major pathogenic genes in FCCMs. However, existing surgical and pharmacological treatments have not adequately prevented disease progression, underscoring the need for more effective strategies. Recent advancements in gene editing tools and delivery systems have transformed gene therapy from a laboratory concept to a clinical reality, offering renewed hope for FCCM patients. Given the multifactorial nature, complexity, and neurological comorbidities of FCCMs, exploring non-surgical gene therapies provides a promising approach for addressing these cerebrovascular lesions. This review summarizes the latest progress in gene editing for FCCMs and examines its therapeutic potential, while acknowledging both the promising benefits and the remaining uncertainties in this evolving field.
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Transcriptomic Signatures in TP53 Positive and Negative Tumor Samples in NSCLC
Authors: Miao Xie, Baoguang Liu, Ziyi Chen, Tongtong Cao and Xiaoyan ZhangAvailable online: 08 August 2025More LessIntroductionLung cancer, specifically non-small cell lung cancer (NSCLC), is a leading cause of cancer-related mortality worldwide. TP53, a crucial tumor suppressor gene, is often mutated in various cancers, including lung cancer. This study focuses on the differences in transcriptomic profiles between TP53-mutated (TP53+) and TP53-wildtype (TP53-) NSCLC tumor samples, aiming to develop a gene signature that can predict overall survival and immune response, particularly in the context of immunotherapy. It aims to identify differentially expressed genes (DEGs) associated with TP53 status in non-small cell lung cancer and develop a gene signature that can predict overall survival and immune response.
MethodsGene expression profiles from TP53-positive and TP53-negative NSCLC tumor samples were analyzed. Data were sourced from the GEO database (GSE8569, n = 69) and the TCGA database (n = 1026). Differential expression analysis was conducted to identify DEGs, which were further analyzed using LASSO regression to develop a prognostic gene signature. Quantitative PCR (qPCR) was performed to validate the expression of selected genes.
ResultsA total of 535 DEGs (168 up-regulated, 367 down-regulated) were identified in TP53+ samples. Further analysis with TCGA data narrowed this down to 29 genes, from which 12 were identified as prognostic features using LASSO analysis. This 12-gene signature effectively stratified patients into low- and high-risk groups for overall survival. Differences in immune cell infiltration and immune pathway activity were significant between these groups, indicating the potential of the gene signature to predict immune response. Among the genes analyzed, BMP2, LPXN, IER3, ANLN, TNNT1, OGT, KRT8, BARX2, PRC1, and SNX30 showed statistically significant differences in qPCR results.
DiscussionThe 12-gene signature demonstrates robust predictive capability for survival outcomes and immune response patterns in NSCLC patients, suggesting its potential clinical utility in precision oncology. The observed correlation between TP53 mutation status and immune microenvironment alterations provides valuable insights into the mechanistic basis of immunotherapy resistance and response.
ConclusionThis study identifies a TP53-associated transcriptomic signature that is significantly associated with overall survival in lung cancer patients. The gene signature also correlates with differences in immune cell infiltration patterns between risk groups, offering potential insights into the tumor immune microenvironment. These findings may contribute to future efforts to stratify patients and guide immunotherapy decisions, pending further experimental validation.
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A Paradigm Shift in Hemophilia Care: The Promise of Gene Therapy
Available online: 07 August 2025More LessIntroductionThe discovery of the gene as the primary unit of inheritance marked the beginning of intensive research into targeted genome modifications for treating rare genetic diseases. Despite conventional approaches such as continuous factor replacement or novel non-factor therapies, the need for a one-time infusion and long-term sustenance of clotting factors is evident. This review focuses on gene therapies discovered to treat patients with hemophilia. This narrative review seeks to highlight the current potential of gene therapies for hemophilia, elucidate their mode of action, and assess their long-term effectiveness and clinical significance.
MethodsA literature search in PubMed, Embase, Google Scholar, and Scopus databases was done using search terms like gene therapy, viral vectors, Roctavian, hemophilia, etranacogene dezaparvovec, AAV, and FIX-Padua variant.
ResultsFollowing intensive clinical trials and successful outcomes, the currently available FDA-approved gene therapies include valoctocogene roxaparvovec (Roctavian) for hemophilia A and etranacogene dezaparvovec (Hemgenix), and fidanacogene elaparvovec (Beqvez) for hemophilia B, and an antibody-based therapy, Marstacimab (Hympavzi) for both hemophilia A and B.
DiscussionDecades of clinical research on introducing gene therapy as a potential therapy for hemophilia A and B have paved the way for successful discovery to overcome the long-term burden of factor replacement and other adjunct therapies. Gene therapy has shown persistent success in hemophilia, with clinical trials demonstrating long-term expression of functional clotting factors (Factor VIII or IX). This has reduced bleeding episodes remarkably and the need for regular factor replacement therapy. Yet the drugs need to be studied further to assess long term safety and efficacy following administration.
ConclusionsGene therapy has shown new possibilities in hemophilia, with many patients achieving near-normal levels of clotting factors and experiencing a significant reduction in bleeding episodes. However, challenges remain, including potential declines in Factor VIII levels over time, immune responses to viral vectors, and high treatment costs. Ongoing research is focused on improving durability, expanding eligibility, and exploring alternative delivery methods.
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Harnessing Nanotechnology and Gene Editing for Cancer Therapy: A Synergistic Approach to Precision Medicine
Authors: Anjana Goel, Istuti Saraswat, Sahaj Sharma and Rijul JoshiAvailable online: 01 August 2025More LessThe fusion of nanotechnology with gene editing promises a revolutionary strategy in combating cancer, providing the possibility of precise and focused treatments. This review examines the synergistic integration of these two potent technologies, specifically emphasising their combined effectiveness in oncological therapies. Nanotechnology offers a flexible framework for administering gene-editing tools, improving their accuracy, and reducing unintended side effects, all of which are significant obstacles in existing cancer treatments. Nanoparticles can improve the effectiveness of therapies, lower the risk of systemic toxicity, and allow the simultaneous manipulation of many genetic pathways involved in cancer growth by delivering CRISPR-Cas9 and other gene-editing systems directly to tumour sites. We conduct a thorough analysis of recent progress in this burgeoning field, emphasising significant advancements in the design of nanoparticles and gene-editing techniques that propel the development of next-generation cancer medicines. In addition, we address the present obstacles and constraints, such as the effectiveness of delivery, apprehensions over safety, and regulatory obstacles, while suggesting potential areas of future research to surmount these barriers. This study thoroughly examines the promise of nano-precision gene editing as a transformative approach to cancer treatment by incorporating findings from recent clinical trials and case studies. By highlighting recent clinical advancements and emerging innovations, this review underscores the potential of nano-precision gene editing as a groundbreaking approach in next-generation cancer therapy.
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Pathogens Association with Alzheimer Disease: Emerging Concepts and New Perspectives
Authors: Uma Agarwal, Rajiv Kumar Tonk and Saroj VermaAvailable online: 28 July 2025More LessAlzheimer’s Disease (AD) represents a significant global health challenge, distinguished by a complex pathology that involves the accumulation of abnormal proteins in the brain, leading to neuronal loss and brain atrophy. Recent research has indicated a potential association between various pathogens and the development of AD, suggesting that infectious pathogens may play a role in its pathology. The study focuses on the exploration of pathogens linked to AD. It aims to enhance the understanding of the disease's etiopathogenesis, which refers to the causes and development of the condition. The findings from this analysis have the potential to contribute to improved diagnostic methods and treatment strategies for AD. Overall, the manuscript highlights the importance of exploring infectious pathogens relating to neurodegenerative disorders. This comprehensive literature review was conducted using databases such as PubMed and Scopus, focusing on research published up to March 2025. Articles were searched based on keywords related to reviews and research exploring the association/link between different pathogens and AD, emerging interventions, preventive strategies, and limitations in study design. This study indicates that various viruses, bacteria, and fungi are significant contributors to the condition, while parasites and prions play a lesser role. Notably, the variability in pathogen species among patients could provide insights into the evolution and severity of clinical symptoms associated with the disease. Additionally, some studies propose that after modification, certain fungi may actually reduce the amyloid burden in Alzheimer's patients. However, it is crucial to emphasize that there is currently no definitive evidence supporting the notion that treating infections alone can prevent or cure AD. The prevention and treatment of pathogens, including viruses, bacteria, and fungi, as well as infectious prions, may play a significant role in reducing the risk of AD. Effective management of these pathogens can help to control and prevent further damage in individuals who have already been diagnosed with AD. There is a pressing need for additional pre-clinical and clinical research to deepen the understanding of the pathophysiological connections between pathogens and AD.
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Association of KIM-1 (HAVCR1) Expression with the Tumor Immune Microenvironment in Clear Cell Renal Cell Carcinoma
Available online: 28 July 2025More LessIntroductionKidney injury molecule 1 (KIM-1) is a cell-surface glycoprotein expressed in the proximal tubules and encoded by the hepatitis A virus cellular receptor 1 (HAVCR1) gene. It is also expressed in renal cell carcinoma (RCC).
ObjectiveThis study examined the immune landscape of clear cell RCC in association with HAVCR1 expression.
MethodsNext-generation sequencing (NGS) data from ccRCC tumor samples of patients from The Cancer Genome Atlas (TCGA) were interrogated for enrichment of immune infiltrates and checkpoints in tumors harboring high HAVCR1 mRNA expression or/and amplification.
ResultsHAVCR1 mRNA expression was positively associated with presence of CD8+ (r = 0.254, p = 3.03 x 10-8) and CD4 T-cells (r = 0.329, p = 3.98 x 10-13), while it was negatively associated with T-regulatory (T-regs) (r = ̶ 0.2, p = 1.47 x 10-5) and myeloid-derived suppressor cells (MDSCs) (r = ̶.0.285, p = 4.92 x 10-10). HAVCR1 amplification was also associated with CD8+ (p = 0.0019), CD4+ T cells (p = 0.0002) while expression of HAVCR1 gene was positively associated with immune checkpoints PD-L1 (CD274) (r = 0.331, p = 4.64 x 10-15) and CTLA4 mRNA expression (r = 0.085, p = 0.05). HAVCR1 transcript levels were directly correlated with those of Polybromo-1 (PBRM1) (r = 0.276, p = 9.36 x 10-11) while inversely related with BRCA-associated protein 1 (BAP1) gene expression (r = ̶ 0.134, p = 1.94 x 10-3).
DiscussionThe study reveals that high HAVCR1 (KIM-1) expression in clear cell RCC is associated with a distinct immune profile characterized by increased CD8+/CD4+ T-cell infiltration and immune checkpoint expression, suggesting a potential role in predicting immunotherapy response, though the observational nature and reliance on TCGA data limit causal inference.
ConclusionsCollectively, a potential immune-regulatory role of KIM-1 in clear cell RCC is implicated. This could be exploited for predicting benefit from adjuvant immunotherapy.
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DrugSurvPlot: A Novel Web-Based Platform Harnessing Drug Sensitivity Scores as Molecular Biomarkers for Pan-Cancer Survival Prognosis
Authors: Ying Shi, Qirui Shen, Aimin Jiang, Hong Yang, Kexin Li, Jian Zhang, Anqi Lin and Peng LuoAvailable online: 24 July 2025More LessBackgroundUsing predicted drug sensitivity scores as survival biomarkers may improve precision medicine and overcome the limitations of genomically guided approaches in clinical trials.
MethodsPan-Cancer Drug Sensitivity Score Survival Analysis (DrugSurvPlot) is an interactive, login-free web analyzer built with R (v4.3.1), leveraging the Shiny package for interface/server logic, the DT package for data table queries/downloads, and the survival package for survival analysis. Data preprocessing was performed using OncoPredict, enabling users to export processed tables and results.
ResultsDrugSurvPlot integrates 189 GEO datasets (including 10 immune checkpoint inhibitor treatment datasets) and 33 TCGA datasets, totaling 85,531 records across 52 cancer types and 13 survival status data types, while incorporating 198 anticancer drugs from GDSC2. This tool supports two cutoff strategies for drug sensitivity scores, offers advanced survival analysis methods, and enables customizable high-definition visualization of results.
DiscussionDrugSurvPlot represents a significant advancement in computational oncology by establishing predicted drug sensitivity scores as novel prognostic biomarkers for tumor survival analysis. This interactive platform integrates comprehensive datasets spanning 198 anticancer drugs and 52 cancer types, while providing researchers with intuitive tools for generating publication-ready Kaplan-Meier analyses. Current limitations in drug repertoire coverage and dataset diversity will be addressed through ongoing expansion of pharmacological databases and incorporation of emerging data modalities, including single-cell transcriptomics.
ConclusionsIn summary, DrugSurvPlot offers a no-code platform with comprehensive datasets, diverse cancer coverage, and customizable survival analysis, addressing critical research gaps. Continuous enhancements will improve predictive accuracy and clinical utility, establishing it as an evolving powerhouse in drug-survival investigations.
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Genomic Medicine: A Critical Review of its Impact on Diagnosing and Treating Genetic Disorders
Available online: 22 July 2025More LessGenomic medicine is revolutionizing genetic disease diagnosis and therapy; has a major impact on clinical practice, particularly in diagnosis and treatment. In addition, next-generation sequencing (NGS) has transformed diagnostics. These advances have made genome profiling cost-effective and fast, helping us find pathogenic variations that cause a variety of genetic illnesses. Given its influence on diagnostic methods, NGS mutation detection accuracy and reliability must be assessed. In therapeutics, genomic medicine has introduced precision methods. CRISPR-Cas9 gene editing, and new RNA-based therapies are being evaluated for the treatment of genetic mutations Pharmacogenomics' capacity to customize medication regimens to genetic profiles, optimizing therapeutic results while minimizing side effects, is also evaluated. Although genetic medicine has transformational promise, its widespread acceptance is difficult. Obtaining widespread acceptance of genetic medicine is difficult because of worries around ethical implications, privacy problems, and the possibility for genetic information to be misused. Ethics and privacy issues surrounding genetic information usage require considerable thought. Genomic data integration into clinical practice requires robust regulatory frameworks. The influence of NGS technology and precision treatments on genetic disease diagnosis and therapy is significant. This review emphasizes the importance of assessing diagnostic tools, comprehending novel therapy modalities, and addressing ethical and regulatory issues to enable responsible and successful clinical integration.
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The Mitochondrial Deoxyribonucleic Acid Puzzle: Controversies, Challenges, and Critical Perspectives – A Narrative Review
Authors: Naina Kumar and Mishu ManglaAvailable online: 21 July 2025More LessHuman mitochondrial DNA (mtDNA) stands at the nexus of scientific intrigue and controversy, owing to its distinctive genetic features and indispensable role in cellular energy dynamics. This narrative review explores the complexities, controversies, and key issues in current research on human mtDNA. A comprehensive search on literature spanning from January 2000 to January 2025 was conducted across electronic databases including PubMed, Scopus, Web of Science, and Google Scholar. Keywords such as “mitochondrial DNA,” “mtDNA mutations,” “mtDNA inheritance,” “mitochondrial genetics,” “mitochondrial diseases,” and “future perspectives of mtDNA” were used to identify relevant studies published in peer-reviewed journals, books, and reputable conference proceedings. Articles selected for inclusion were limited to those written in English and focused on human mtDNA research. Review articles, original research papers, meta-analyses, and authoritative texts were prioritized. Information extracted from selected studies was synthesized to provide a comprehensive overview. The synthesized data were critically analyzed to highlight emerging trends, unresolved controversies, and future research directions in the field of mtDNA research. Decoding the complexities of human mtDNA offers profound insights into fundamental biological processes and evolutionary history. This review emphasizes the ongoing significance of mtDNA research in shaping the future of biomedical sciences and highlights the importance of continued exploration into its intricate molecular code.
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Identification of Key Features Pivotal to the Characteristics and Functions of Gut Bacteria Taxa through Machine Learning Methods
Authors: ZhanDong Li, QingLan Ma, Hao Li, Lin Lu, Lei Chen, Wei Guo, KaiYan Feng, Tao Huang and Yu-Dong CaiAvailable online: 15 July 2025More LessBackgroundGut bacteria critically influence digestion, facilitate the breakdown of complex food substances, aid in essential nutrient synthesis, and contribute to immune system balance. However, current knowledge regarding intestinal bacteria remains insufficient.
ObjectiveThis study aims to discover essential differences for different intestinal bacteria.
MethodsThis study was conducted by investigating a total of 1478 gut bacterial samples comprising 235 Actinobacteria, 447 Bacteroidetes, and 796 Firmicutes, by utilizing sophisticated machine learning algorithms. By building on the dataset provided by Chen et al., we engaged sophisticated machine learning techniques to further investigate and analyze the gut bacterial samples. Each sample in the dataset was described by 993 unique features associated with gut bacteria, including 342 features annotated by the Antibiotic Resistance Genes Database, Comprehensive Antibiotic Research Database, Kyoto Encyclopedia of Genes and Genomes, and Virulence Factors of Pathogenic Bacteria. We employed incremental feature selection methods within a computational framework to identify the optimal features for classification.
ResultsEleven feature ranking algorithms selected several key features as pivotal to the characteristics and functions of gut bacteria. These features appear to facilitate the identification of specific gut bacterial species. Additionally, we established quantitative rules for identifying Actinobacteria, Bacteroidetes, and Firmicutes.
ConclusionThis research underscores the significant potential of machine learning in studying gut microbes and enhances our understanding of the multifaceted roles of gut bacteria.
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Immunoinformatic Based Designing of Immune Boosting and Non-allergenic Multi-epitope Subunit Vaccine Against the Enterovirus D68
Available online: 11 July 2025More LessIntroductionEnterovirus D68 (EV-D68) is a non-enveloped, positive-sense, single-stranded RNA virus known for causing severe respiratory illnesses and its association with acute flaccid myelitis (AFM) in children. Despite its increasing public health significance, no vaccines or antiviral drugs are currently available for EV-D68. This study aimed to design an immune-boosting multi-epitope subunit vaccine against EV-D68 using advanced immunoinformatic and machine learning approaches.
MethodsCapsid proteins VP1, VP2, and VP3 of EV-D68 were screened for immunogenic HTL, CTL, and B-cell epitopes to develop a non-allergenic, highly immunogenic multi-epitope vaccine. Predicted epitopes were subjected to 3D structural modeling and molecular dynamics simulations to validate folding and structural stability. Molecular docking and immune simulation techniques were employed to evaluate vaccine-TLR3 interactions and predict immune responses, respectively.
ResultsMolecular docking analysis revealed strong binding affinities between the vaccine constructs and the TLR3 receptor, with scores of -299 kcal/mol, -361 kcal/mol, -258 kcal/mol, and -312 kcal/mol for VP1, VP2, VP3, and combined vaccine-TLR3 complexes. Molecular dynamic simulation and dissociation constant analyses confirmed the strength of these interactions, with binding free energies ranging from -57.75 kcal/mol to -101.35 kcal/mol. Codon adaptation index (CAI) values of 0.96 and GC content of ~69% supported the high expression potential of the vaccine constructs. Immune simulations demonstrated robust immune responses characterized by elevated IgG, IgM, cytokines, and interleukins, along with effective antigen clearance.
DiscussionThe strong molecular interactions with TLR3 and simulated immune responses suggest that the designed vaccines can activate both innate and adaptive immunity. The high CAI and GC values support their expression feasibility in E. coli, enhancing prospects for production.
ConclusionThis study provides a strong foundation for the development of a safe and effective EV-D68 vaccine, showcasing the potential of computational vaccine design.
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Review Deciphering the Anticancer Efficacy of Oroxylin A Targeting Dysregulated Oncogenes
Available online: 09 July 2025More LessFlavonoids exhibit anti-tumor properties against many human cancer cells, indicating their potential as effective anticancer medicines. Oroxylin A (OrA) is a monoflavonoid molecule that shows significant promise against several types of cancer and possesses a substantial anticancer impact while causing minimal harm to normal tissue. Limited studies have provided a systematic review deciphering the role of oroxylin A in combating breast carcinoma. Hence, we thoroughly analyzed existing research to report various mechanism by which OrA impedes tumor advancement in breast carcinoma, including autophagy, cell cycle arrest, angiogenesis suppression, apoptosis, and glycolysis inhibition. We collected several significant research related to the anticancer potential of oroxylin A and demonstrated anticancerous potential of OrA and its specific mode of action in several human carcinomas. Additionally, we have also incorporated several studies to decipher the structure, bioavailability, and anti-breast cancer potential of Oroxylin A in breast cancer. Overall, this review supports the potential of oroxylin A for developing better anti breast cancer therapeutic approach.
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Machine Learning-Driven PCDI Classifier for Invasive PitNETs
Authors: Guanyu Wang, Song Yan, Luyang Zhang, Lu Lin, Rentong Liu, Yiling Han and Yan ZhaoAvailable online: 04 July 2025More LessIntroductionAggressive Pituitary Neuroendocrine Tumors (PitNETs) pose significant therapeutic challenges due to their invasive behavior and resistance to conventional therapies. Current prognostic markers lack the ability to capture molecular heterogeneity, necessitating novel biomarkers. Dysregulated Programmed Cell Death (PCD) pathways are implicated in tumorigenesis, but their prognostic relevance in invasive PitNETs remains unexplored.
MethodGEO datasets (GSE51618, GSE169498, GSE260487) were analyzed to identify differential gene expression between noninvasive and invasive PitNETs. A curated panel of 1,548 PCD-related genes was integrated. Machine learning (LASSO regression and SVM-RFE) was employed to construct a PCD-associated Index (PCDI). For validation, ROC analysis, immune infiltration assessment (CIBERSORT, TIMER, ssGSEA), and experimental validation via RT-qPCR were performed.
ResultsThe PCDI, comprising 11 genes (e.g., FGFR3, MAPK11, SLC7A11), distinguished invasive from noninvasive PitNETs with high accuracy. High-PCDI tumors exhibited enriched metabolic pathways and immune activation. Consensus clustering stratified PitNETs into two molecular subtypes (C1/C2), with C2 (high-PCDI) showing elevated immune scores and pathway activity. Experimental validation confirmed the differential expression of key genes in invasive tumors (*p<0.05).
DiscussionThe PCDI outperforms traditional prognostic models by capturing PCD-immune-metabolic crosstalk. High-PCDI tumors demonstrate adaptive immune evasion despite an elevated checkpoint molecule expression, suggesting therapeutic potential for combined MAPK inhibitors and immunotherapy. Limitations include retrospective data and small validation cohorts.
ConclusionThe PCDI provides a robust molecular framework for risk stratification and personalized therapy in invasive PitNETs. Future studies should validate its clinical utility and explore pan-cancer relevance.
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Bridging Mind and Gut: The Molecular Mechanisms of microRNA, Microbiota, and Cytokine Interactions in Depression
Available online: 27 June 2025More LessDepression is a complex psychiatric disorder that arises from various underlying biological mechanisms. In this review, the role of microRNAs (miRNAs) in modulating gut microbiota-cytokine communication and their potential to unravel the pathophysiology of depression and develop novel therapeutic strategies are discussed. MiRNAs are small non-coding RNA molecules that have emerged as key regulators in the bidirectional signaling of the gut-brain axis by modulating gene expression and fine-tuning an intricate dialogue between the microbiota, immune system, and central nervous system. Results show how gut microbiota can shape miRNA expression in brain regions involved in mood regulation; conversely, evidence is accumulating, elucidating how miRNA perturbations can shape microbial ecology. Gut bacteria-derived short-chain fatty acids (SCFAs) fuel this nexus by exerting effects on neurogenesis, neurotransmitter synthesis, neuroinflammation, affective behavior alterations, and depressive-like phenotypes. Pro-inflammatory cytokines such as IL-6, TNF-α, and IL-1β are also known to be associated with depressive symptoms related to altered expression patterns of specific miRNAs across these disorders. This review exposes the novel potential biomarkers and therapeutic targets/strategies to develop innovative methods in the diagnosis and treatment of depression by exploring bidirectional relations among miRNAs, gut microbiota, and cytokines. The knowledge of these molecular networks and pathways has provided the opportunity for designing new-generation therapeutics such as phytobiotics, probiotics, psychobiotics, diet therapies, and nanomedicine based on miRNAs from a future perspective, which will revolutionize the management of mental disorders.
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Advancements in Targeted Therapies and Pharmacogenomics for Personalized Breast Cancer Treatment: The Role of Gene SNPs in Treatment Resistance
Available online: 27 June 2025More LessBreast cancer remains a prevalent and diverse disease, significantly contributing to cancer-related deaths among women worldwide. Recent advancements in molecular biology have paved the way for targeted therapies and pharmacogenomics, which are crucial for developing personalized treatment strategies. This literature review synthesizes findings from recent studies on these approaches, emphasizing clinical trials, genomic profiling, and personalized medicine. It aims to focus on studies examining targeted treatments, such as human epidermal growth factor receptor-2 (HER2) inhibitors and CDK4/6 inhibitors, alongside pharmacogenomic data that influence drug metabolism, efficacy, and toxicity. Additionally, it examines the role of gene SNPs (Single Nucleotide Polymorphisms) correlated with treatment resistance, which have emerged as key biomarkers affecting therapeutic outcomes in breast cancer. These SNPs, found in genes involved in drug metabolism and tumor progression, contribute to variability in treatment responses and resistance in specific subtypes. They encompass various breast cancer subtypes, including hormone receptor-positive (HR+), HER2-positive, and triple-negative breast cancer (TNBC). The targeted therapies, particularly HER2 inhibitors, have markedly improved outcomes for specific subtypes. Furthermore, pharmacogenomics personalizes treatment by identifying genetic variations that affect drug response, optimizing therapy selection, and minimizing adverse effects. Despite these advancements, drug resistance remains a significant challenge, highlighting the necessity for ongoing research in molecular diagnostics and innovative therapeutic combinations. The literature suggests that precision medicine, driven by genomic profiling, pharmacogenomic data, and single nucleotide polymorphisms (SNPs) analysis, is enhancing treatment efficacy for breast cancer patients. HER2-positive and HR+ patients have especially benefitted from these targeted therapies while emerging treatments are addressing the complexities of TNBC. Additionally, genetic testing, such as BRCA1/2 mutation screening, is vital for guiding treatment decisions. Targeted therapies and pharmacogenomics have revolutionized breast cancer treatment, providing more personalized and effective care. Nevertheless, overcoming drug resistance and expanding access to genomic testing are essential for future advancements in this field.
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