Current Issues in Molecular Biology

22 pages, 2123 KB

Open AccessArticle

Exogenous Salicylic Acid Improves Fruit Yield and Quality of Lycium barbarum Under Summer High Temperature

by Xiaoya Qin, Qi Li, Yue Yin, Yunfang Fan, Xiaojie Liang and Ken Qin

Curr. Issues Mol. Biol. 2026, 48(8), 836; https://doi.org/10.3390/cimb48080836 - 17 Aug 2026

Global warming poses an escalating threat to crop yield and quality, particularly for thermosensitive medicinal-edible plants such as goji berry (Lycium barbarum). Although salicylic acid (SA) is recognized for enhancing plant thermotolerance, its effects on fruit productivity and quality under summer [...] Read more.

Global warming poses an escalating threat to crop yield and quality, particularly for thermosensitive medicinal-edible plants such as goji berry (Lycium barbarum). Although salicylic acid (SA) is recognized for enhancing plant thermotolerance, its effects on fruit productivity and quality under summer high temperatures remain inadequately quantified. This study investigated the physiological, metabolic, and transcriptomic responses of field-grown Ningqi No. 7 (N7) goji berry to exogenous SA application under summer heat stress. SA treatment significantly increased fruit yield by 22%, while reducing leaf defoliation rate by 32%. Metabolite profiling revealed that SA elevated total soluble sugar content by 30% and flavonoid concentration by 14% but decreased total organic acid content by 16%. Transcriptomic analysis identified SA-induced differential expression of genes involved in sugar metabolism (phosphofructokinase), secondary biosynthesis (flavonoid and alkaloid related pathways), and stress responses (HSPs, E3 ubiquitin ligases, SRK2). These results demonstrate that exogenous SA enhances goji berry productivity and improves fruit taste (via increased sugar/organic acid ratio) and functional quality under summer high temperatures. Consequently, SA application thus represents a promising and cost-effective strategy for climate-resilient goji berry cultivation. Full article

(This article belongs to the Special Issue Abiotic Stress in Plants)

27 pages, 6779 KB

Open AccessReview

New Immunological Insights into Bisphosphonate-Related Osteonecrosis of the Jaw: A Multidimensional Reappraisal from Molecular Switches to Clinical Phenotypes

by Yao Li, Shengao Qin, Jiaqi Wang, Zhaochen Shan, Jiaxin Song, Haitong Zhang, Wen Pan and Zhao Zhu

Curr. Issues Mol. Biol. 2026, 48(8), 835; https://doi.org/10.3390/cimb48080835 - 17 Aug 2026

Abstract

Bisphosphonates (BPs) are cornerstone therapeutic agents for the management of metabolic bone disorders and skeletal complications associated with malignant tumors. However, their long-term administration is accompanied by the risk of developing bisphosphonate-related osteonecrosis of the jaw (BRONJ). In recent years, the pathogenesis of [...] Read more.

Bisphosphonates (BPs) are cornerstone therapeutic agents for the management of metabolic bone disorders and skeletal complications associated with malignant tumors. However, their long-term administration is accompanied by the risk of developing bisphosphonate-related osteonecrosis of the jaw (BRONJ). In recent years, the pathogenesis of BRONJ has remained a major focus at the intersection of osteoimmunology and oral medicine. This review systematically summarizes the latest advances in the understanding of BRONJ pathogenesis, including the direct disruption of osteoclast differentiation and bone remodeling coupling by bisphosphonates, the systemic reprogramming of immune cell subsets and inflammatory signaling pathways, the multifaceted suppression of angiogenesis and the endothelial–stromal–immune axis, and the toxic impairment of oral soft tissue repair capacity. Building upon these mechanistic insights, we further discuss the modifying and synergistic effects of local oral risk factors, microbial dysbiosis, systemic comorbidities, and genetic susceptibility on the initiation and progression of BRONJ. Furthermore, emerging therapeutic strategies targeting these pathogenic mechanisms are highlighted, including restoration of small GTPase prenylation through modulation of metabolic pathways, reconstruction of T-cell subset homeostasis via immunomodulatory approaches, enhancement of local vascularization through pro-angiogenic interventions, and preservation of soft tissue barrier integrity. Collectively, this review provides a comprehensive and multidimensional overview of the pathological landscape of BRONJ and offers a theoretical framework for clinical risk stratification and the development of personalized prevention and treatment strategies. Full article

(This article belongs to the Section Molecular Medicine)

► Show Figures

Figure 1

18 pages, 11272 KB

Open AccessArticle

Ginkgo biloba Extract Inhibits Cisplatin-Induced Acute Kidney Injury-to-Chronic Kidney Disease Through Downregulating Apoptosis Mediated by the HIF-1α/Phosphatidylinositol Pathway

by Weimin Xu, Ju Huang, Shasha Chen, Yufang Yang, Peiyuan Wan, Xingqing Chen, Xiang Ye and Songqing Huang

Curr. Issues Mol. Biol. 2026, 48(8), 834; https://doi.org/10.3390/cimb48080834 - 17 Aug 2026

Abstract

Ginkgo biloba extract (GBe) attenuates the transition of cisplatin (CDDP)-induced acute kidney injury to chronic kidney disease (AKI-to-CKD). Purpose: This study aimed to reveal the mechanism by which GBe inhibits CDDP-induced AKI-to-CKD. The potential targets of GBe in alleviating CDDP-induced renal interstitial fibrosis [...] Read more.

Ginkgo biloba extract (GBe) attenuates the transition of cisplatin (CDDP)-induced acute kidney injury to chronic kidney disease (AKI-to-CKD). Purpose: This study aimed to reveal the mechanism by which GBe inhibits CDDP-induced AKI-to-CKD. The potential targets of GBe in alleviating CDDP-induced renal interstitial fibrosis (Cis-RIF) were predicted through network pharmacology. Transcriptomics and metabolomics were used to detect differentially expressed genes (DEGs) and metabolites (DEMs) in renal tissues from Cis-RIF rats. Integrated multi-omics analysis was performed to determine the potential mechanism underlying GBe inhibiting AKI-to-CKD, and experimental verification was conducted in vivo, in vitro, and using siRNA. We identified 100 targets of GBe that could inhibit Cis-RIF using network pharmacology, and these targets were enriched in 194 signaling pathways. Transcriptomics and metabolomics revealed 8907 DEGs (enriched in 51 pathways) and 424 DEMs (enriched in 16 pathways), respectively. Collectively, the phosphatidylinositol signaling pathway was a co-enriched pathway, which may be the key pathway through which GBe inhibits AKI-to-CKD. This was verified experimentally. The related apoptosis and fibrosis indicators, and the key targets of the phosphatidylinositol signaling pathway (PLC, PKC, PIP2, IP3, DAG, Ca²⁺), in rat renal tissues and renal tubular epithelial cells (RTECs) with CDDP-induced AKI-to-CKD were significantly increased. Inhibition of HIF-1α and knockdown of HIF-1α in RTECs reversed the changes the phosphatidylinositol pathway targets. Moreover, both GBe and the HIF-1α inhibitor could inhibit HIF-1α and the phosphatidylinositol pathway targets, as well as the apoptosis and EMT of RTECs. Conclusion: This study reveals for the first time that GBe may inhibit AKI-to-CKD by downregulating apoptosis and EMT in RTECs through the HIF-1α/phosphatidylinositol signaling axis. Full article

(This article belongs to the Section Molecular Pharmacology)

► Show Figures

Figure 1

21 pages, 5479 KB

Open AccessArticle

Pinoresinol as a Potential c-Myc Complex Modulator: An In Silico Study

by Arnulfo Villanueva-Castillo, Claudia Mancilla-Simbro, Fernando Villa-Diaz, Alberto Ramírez-Mata, Cesar F. Pastelín-Rojas, Ruby S. Moreno-Mejía, Hermilo Lucio-Castillo, Briseida L. Castro-Bautista, Carlos G. Castillo-Sosa, Fátima Matamoros-González, Alexis Cruz-Espinosa, Angélica Abascal-Grajales, Mónica A. Olea-Amezcua, Evili Báez Castillo, Laura G. Hernández-Aragón, Alejandra Escobar Noriega, Sandra R. Reyes Carmona, Fernando Utrera Quintana and Sagrario Lobato Huerta

Curr. Issues Mol. Biol. 2026, 48(8), 833; https://doi.org/10.3390/cimb48080833 - 17 Aug 2026

Abstract

The c-Myc oncoprotein is a central regulator of oncogenic transcriptional programs that remains challenging to inhibit directly, necessitating strategies that target c-Myc–associated protein complexes rather than the protein alone. This study conducted an in silico evaluation of the natural biphenolic lignan pinoresinol as [...] Read more.

The c-Myc oncoprotein is a central regulator of oncogenic transcriptional programs that remains challenging to inhibit directly, necessitating strategies that target c-Myc–associated protein complexes rather than the protein alone. This study conducted an in silico evaluation of the natural biphenolic lignan pinoresinol as a potential modulator of the c-Myc–TBP–TAF1 (TATA-binding protein (TBP)- Multiple direct interactions of TBP with the MYC oncoprotein) transcriptional complex (PDB ID: 6E16). Prior to molecular docking, the protein structure was subjected to energy minimization using the AMBER ff14SB force field to optimize conformational stability and structural reliability; ligand preparation and docking were performed with standard, widely used tools (e.g., AutoDock Vina v1.1.2; visualization and interface analyses in UCSF Chimera/ChimeraX and SeamDock). Molecular docking and binding-interface analyses identified reproducible interactions within defined pockets P₀, P₁, and P₂, with pocket P₀ exhibiting the highest Drug Score of 0.82. Binding affinities ranged from −5.0 to −7.1 kcal/mol, which are consistent with moderate docking scores typical for small natural ligands. Across multiple ligand poses, LYS327, LYS310, and ASP209 emerged as consistent interaction hotspots, with LYS327 showing the most frequent contacts. Furthermore, in silico ADMET analysis predicted a high probability of cytotoxic inactivity (0.98), suggesting a favorable safety profile compared to traditional agents like vincristine. These results support a protein–protein interface-oriented approach and position pinoresinol as a promising lead scaffold for disrupting c-Myc–associated transcriptional regulation. Full article

(This article belongs to the Special Issue Targeted Therapeutic Approaches in Cancer: Combining Natural Compounds and Conventional Drugs)

► Show Figures

Graphical abstract

24 pages, 2083 KB

Open AccessReview

The Role of Macrophages in Endometrial Cyclical Changes and Female Reproductive System Diseases: A Review

by Shuyuan Zhang, Luyang Zha, Chenyuan Liu, Aijia Wang, Yaxin Guo and Kun Qian

Curr. Issues Mol. Biol. 2026, 48(8), 832; https://doi.org/10.3390/cimb48080832 - 17 Aug 2026

Abstract

Background: This review aims to systematically summarize the lineage origins, subtype classification, and functional dynamics of endometrial macrophages, clarify their mechanisms of action in normal reproductive physiology (menstrual cycle, pregnancy) and common reproductive diseases, integrate cognitive breakthroughs brought by cutting-edge research technologies, [...] Read more.

Background: This review aims to systematically summarize the lineage origins, subtype classification, and functional dynamics of endometrial macrophages, clarify their mechanisms of action in normal reproductive physiology (menstrual cycle, pregnancy) and common reproductive diseases, integrate cognitive breakthroughs brought by cutting-edge research technologies, and provide theoretical support for basic research and clinical translation in reproductive medicine. Methods: Recent basic and clinical research studies related to endometrial macrophages were retrieved, with a focus on incorporating findings from technologies such as single-cell sequencing and multi-omics. The reviewed content covers core aspects including macrophage origins (embryonic-derived, bone marrow-derived), subtype classification (M1/M2 and novel metabolism-related subtypes), cycle- and pregnancy-specific functions, and disease-associated mechanisms. A comprehensive analysis of the regulatory networks of endometrial macrophages under physiological and pathological conditions was conducted. Results: Endometrial macrophages, by virtue of their phenotypic plasticity and functional heterogeneity, play a central role in cyclical endometrial remodeling, pregnancy establishment, and the regulation of reproductive immune homeostasis. Dysregulation of their function is closely associated with various reproductive disorders such as recurrent spontaneous abortion and endometriosis. In-depth exploration of their biological characteristics and regulatory mechanisms holds great significance for filling knowledge gaps in the field of reproductive immunology and advancing precise prevention and treatment of related diseases. Conclusions: Endometrial macrophages are core regulators of the reproductive immune microenvironment, and their spatiotemporal dynamic functions are closely linked to reproductive health. The revelation of novel classification systems and regulatory mechanisms provides new perspectives for in-depth understanding of reproductive physiological and pathological processes, as well as important targets for immune-targeted therapy of reproductive-related diseases. This holds great clinical translational significance for promoting the precision development of reproductive medicine. Full article

(This article belongs to the Special Issue Molecular Pathways and Therapeutic Targets in Endometriosis)

► Show Figures

Figure 1

17 pages, 4867 KB

Open AccessReview

Host-Microbiome Integration as a Biomarker Framework in Esophageal Cancer: Current Evidence and Translational Challenges

by Shamimeh Pourbahrighesmat, Alireza Tojjari, George Laliotis and Anwaar Saeed

Curr. Issues Mol. Biol. 2026, 48(8), 831; https://doi.org/10.3390/cimb48080831 - 16 Aug 2026

Abstract

Immune checkpoint inhibitors have improved outcomes in esophageal cancer across settings, yet clinical benefit remains heterogeneous, with current host-derived biomarkers incompletely predicting response. This mini review evaluates recent studies that integrate gut or intratumoral microbial features with host immune, molecular, or metabolic assessment [...] Read more.

Immune checkpoint inhibitors have improved outcomes in esophageal cancer across settings, yet clinical benefit remains heterogeneous, with current host-derived biomarkers incompletely predicting response. This mini review evaluates recent studies that integrate gut or intratumoral microbial features with host immune, molecular, or metabolic assessment in esophageal cancer. We classify the evidence using a four-level hierarchy of host-microbiome integration: ecological association, functional association, mechanistic integration, and clinical predictive integration. Tissue studies reveal compartment-specific relationships between microbial diversity or individual taxa and immune architecture, whereas treatment cohorts identify bacterial and fungal signatures associated with pathological or immunotherapy response. Mechanistic studies offer the strongest biological evidence, most notably the Lactobacillus salivarius-indole-3-lactic acid-AhR/NF-κB axis, which drives CD8-positive T-cell exhaustion and resistance to anti-PD-1 therapy. However, biological integration is substantially more advanced than clinical response prediction. Small cohorts, heterogeneous regimens, contamination of low-biomass samples, coarse taxonomic (rather than functional) resolution, confounding by histology, multi-omic layers measured in different patients, and lack of external validation currently jeopardize integration of microbiome to guide treatment. Future studies should use longitudinal, multicenter, compartment-matched sampling and test whether microbial genes or metabolites improve patient selection and predict clinical response beyond established clinical and host biomarkers. Full article

(This article belongs to the Special Issue Omics Analysis for Personalized Medicine)

► Show Figures

Figure 1

34 pages, 3981 KB

Open AccessReview

Antiseizure Medications in Development: Novel Mechanisms, Precision Therapy, and the Move Towards Disease Modification

by William Alves Martins

Curr. Issues Mol. Biol. 2026, 48(8), 830; https://doi.org/10.3390/cimb48080830 - 16 Aug 2026

Abstract

Background: Despite more than 30 licenced antiseizure medications (ASMs), approximately one third of people with epilepsy remain drug-resistant, and developmental and epileptic encephalopathies represent one of the greatest unmet needs in epilepsy therapeutics. The past decade has produced a substantial reorientation of [...] Read more.

Background: Despite more than 30 licenced antiseizure medications (ASMs), approximately one third of people with epilepsy remain drug-resistant, and developmental and epileptic encephalopathies represent one of the greatest unmet needs in epilepsy therapeutics. The past decade has produced a substantial reorientation of ASM discovery, driven by epilepsy genetics, new disease models, advances in drug screening, and innovative therapeutic modalities. Objective: The objective of this study was to review the contemporary clinical-stage pipeline of ASMs with novel or differentiated mechanisms of action, organized by molecular target, while placing recent regulatory successes and instructive failures within the broader transition toward mechanism-based, precision, and potentially disease-modifying therapies. Findings: A 2024 pipeline analysis identified more than 200 epilepsy therapies in preclinical or clinical development; at the cutoff of the present literature search (30 June 2026), over 40 compounds had reached phase II or III, with the majority directed at DEEs. Functional-state-selective sodium channel modulation has emerged as a leading conceptual advance supported by converging mechanistic and early clinical evidence, exemplified by relutrigine (PRAX-562), a preferential persistent-current inhibitor for which a regulatory decision is pending in SCN2A/SCN8A-DEEs, and vormatrigine (PRAX-628), whose large open-label effect was not reproduced in a controlled (blinded) trial. Several of the efficacy figures summarized here derive from congress presentations, interim analyses, or open-label extensions and await full peer-reviewed publication. Parallel advances include the selective Kv7 opener azetukalner; the dual-mechanism benchmark cenobamate; cholesterol-24-hydroxylase inhibition (soticlestat); selective serotonergic agonism (bexicaserin); glutamatergic precision agents (radiprodil); subtype-selective GABA_A modulators (darigabat, ganaxolone); and gene-directed therapies (zorevunersen, elsunersen). Pre-symptomatic intervention in tuberous sclerosis complex provides an early, single-trial clinical proof of principle for delaying and reducing the incidence of epilepsy in a genetically defined population; this should not yet be equated with established disease prevention. Conclusions: The pipeline reflects an ongoing shift from broad symptomatic agents toward mechanism-led, genotype-matched, and potentially disease-modifying treatments. This shift is tempered by a persistent translational gap between early signals and randomized-trial confirmation, and by the preliminary status of much of the supporting evidence. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Therapeutic Targets in Epilepsy)

► Show Figures

Figure 1

18 pages, 2075 KB

Open AccessArticle

Cross-Cohort, Renal Compartment-Aware Transcriptomic Assessment of Lycii Fructus-Annotated Targets in Diabetic Kidney Disease

by Jinhao Zou, Xiaowei Tian, Ye Sun and Siyi Wang

Curr. Issues Mol. Biol. 2026, 48(8), 829; https://doi.org/10.3390/cimb48080829 - 14 Aug 2026

Abstract

Diabetic kidney disease (DKD) differs transcriptionally across renal compartments. We assessed whether Lycii Fructus-annotated targets showed reproducible DKD-associated changes and enrichment beyond matched expectations. Linked glomerular (GSE30528) and tubulointerstitial (GSE30529) cohorts were used for discovery; GSE96804 and platform-specific GSE104954 subsets provided external assessment. [...] Read more.

Diabetic kidney disease (DKD) differs transcriptionally across renal compartments. We assessed whether Lycii Fructus-annotated targets showed reproducible DKD-associated changes and enrichment beyond matched expectations. Linked glomerular (GSE30528) and tubulointerstitial (GSE30529) cohorts were used for discovery; GSE96804 and platform-specific GSE104954 subsets provided external assessment. Phenotype-independent probe aggregation preceded limma analysis. Of 106 standardized HERB targets, 91 were measurable. Specificity was tested by hypergeometric analysis and 10,000 expression- and publication-matched permutations; external evidence was graded symmetrically. Thirty-six targets met the primary criterion in at least one compartment, but the target set was not enriched. CASP8 and VEGFA met Tier A external criteria, whereas ADRB2 and SLC6A2 met Tier B criteria. At the stricter |log₂FC| ≥ 0.585 threshold, ADRB2 passed in both discovery compartments, VEGFA only in glomeruli, and CASP8/SLC6A2 in neither. STRING analysis used the measured-gene background. Reference redocking reproduced carazolol in ADRB2 and atomoxetine in SLC6A2 (RMSD, 1.08 and 1.09 Å). Thus, the four genes are reproducible DKD-perturbed candidates carrying Lycii Fructus annotations, not evidence of a Lycii Fructus-specific mechanism; they warrant targeted pharmacological testing. Full article

(This article belongs to the Section Bioinformatics and Systems Biology)

► Show Figures

Figure 1

18 pages, 29310 KB

Open AccessArticle

Integrative Transcriptomics and Mendelian Randomization Identify RGS1 as a Causal Immune Regulator in Alzheimer’s Disease

by Zhiyun Cheng, Ruyu Bai and Yong Diao

Curr. Issues Mol. Biol. 2026, 48(8), 828; https://doi.org/10.3390/cimb48080828 - 14 Aug 2026

Abstract

Alzheimer’s disease (AD) has a complex pathogenesis, involving molecular and neuroimmune dysregulation, but the causal drivers linking transcriptomic changes to immune remodeling are not yet clear. In a discovery cohort, differential expression analysis was performed, and it was independently validated in two external [...] Read more.

Alzheimer’s disease (AD) has a complex pathogenesis, involving molecular and neuroimmune dysregulation, but the causal drivers linking transcriptomic changes to immune remodeling are not yet clear. In a discovery cohort, differential expression analysis was performed, and it was independently validated in two external cohorts. Key genes were prioritized via LASSO/logistic regression, functionally annotated, and causally linked to AD using two-sample MR. The neuroimmune landscape was mapped by ssGSEA, and top candidates were validated in vitro. RGS1 is a key node in neuroinflammation and cytoskeletal dynamics, which is prioritized by the algorithmic intersection. MR analysis suggested a potential causal association between genetically predicted RGS1 expression and AD risk. RGS1 was consistently upregulated in both discovery and validation cohorts (AUC: 0.61–0.67) and was confirmed in vitro. Immune deconvolution showed that AD-specific enrichment profiles occur, and RGS1 is strongly correlated with activated CD4+ T cells and pro-inflammatory chemokines. RGS1 is identified as a robust key gene that may contribute to immune microenvironment dysregulation in AD, and combining discovery-validation transcriptomics, causal inference, and experimental validation, we find that RGS1 is a potential immunomodulatory target. Full article

(This article belongs to the Special Issue Genetics, Epigenetics, and Molecular Mechanisms of Neurodegenerative Diseases)

► Show Figures

Figure 1

14 pages, 3167 KB

Open AccessArticle

Evaluation of Oral Toxicity of Palatinose/Fructooligosaccharide and Palatinose/Invert Sugar in Sprague–Dawley Rats

by Seung-U Son, Hye-Ryung Park, Sue Jung Lee and Kwang-Soon Shin

Curr. Issues Mol. Biol. 2026, 48(8), 827; https://doi.org/10.3390/cimb48080827 - 14 Aug 2026

Abstract

An evaluation of the safety profile of palatinose/fructooligosaccharide (P/FOS) and palatinose/invert sugar (P/IS), as novel low-glycemic and functional sweetener combinations, is essential for their application. This study aimed to evaluate the safety of 1000 mg/kg/day of P/FOS and 1000 mg/kg/day of P/IS through [...] Read more.

An evaluation of the safety profile of palatinose/fructooligosaccharide (P/FOS) and palatinose/invert sugar (P/IS), as novel low-glycemic and functional sweetener combinations, is essential for their application. This study aimed to evaluate the safety of 1000 mg/kg/day of P/FOS and 1000 mg/kg/day of P/IS through a 14-day repeated-dose oral toxicity study using male and female Sprague–Dawley (SD) rats. Clinical signs, such as body weight and organ weights, food/water consumption, hematology results, blood biochemical analysis results, urinalysis results, and histological changes in the liver and kidneys, were recorded in all SD rats. Barely any significant changes in food/water consumption, body weight, and organ weight were observed during the experimental period. Although there were some alterations in the results of hematological analysis, serum biochemical analysis, and urinalysis, these changes were not considered toxicologically significant within the normal ranges in both male and female SD rats administered with P/FOS and P/IS at 1000 mg/kg/day. Additionally, a histopathological analysis of the liver and kidneys showed no toxicological changes in P/FOS- and P/IS-treated SD rats of both sexes at the tested dose. Collectively, the above results confirmed that no overt treatment-related adverse effects of P/FOS and P/IS were observed under the tested conditions. Full article

(This article belongs to the Collection Molecular Advances in Veterinary Pharmacology and Toxicology)

► Show Figures

Figure 1

18 pages, 1306 KB

Open AccessArticle

A Comprehensive Pipeline for the Use of Short Read Next-Generation Sequencing (SR-NGS) in CYP21A2 Diagnostic Genotyping

by Irene Fylaktou, Faidon-Nikolaos Tilemis, Anny Mertzanian, Chrysi Kontse, Periklis Makrythanasis, Christina Kanaka-Gantenbein and Amalia Sertedaki

Curr. Issues Mol. Biol. 2026, 48(8), 826; https://doi.org/10.3390/cimb48080826 - 13 Aug 2026

Abstract

Background: Although Short Read Next-Generation Sequencing (SR-NGS) is widely employed in diagnosis, its application in CYP21A2 genotyping remains limited due to its high sequence homology with its pseudogene, CYP21A1P. Herein, we present (a) a complete pipeline for the diagnostic use of SR-NGS in [...] Read more.

Background: Although Short Read Next-Generation Sequencing (SR-NGS) is widely employed in diagnosis, its application in CYP21A2 genotyping remains limited due to its high sequence homology with its pseudogene, CYP21A1P. Herein, we present (a) a complete pipeline for the diagnostic use of SR-NGS in CYP21A2 genotyping following its assessment; (b) two distinct in-house bioinformatics pipelines for variant calling; and (c) the results by implementing this pipeline in diagnosis. Methods: A total of 221 subjects were studied, comprising a pilot group (n = 21), recruited for assessment of the assay, and a study group (n = 200) categorized in three subgroups, referred for CYP21A2 genotyping. Both groups underwent SR-NGS. Two different bioinformatics algorithms for variant calling were applied and variant filtration was performed using VarAFT (v2.17). In the study group, MLPA was additionally employed. Results: The SR-NGS assay, employing GATK HaplotypeCaller, demonstrated 100% sensitivity and specificity when compared to Sanger Sequencing; however, complex CYP21A2 rearrangements cannot be detected. In the study group, pathogenic variants were identified in 52.7%, 100% and 25% of cases in subgroups (a), (b) and (c) respectively, whereas gene duplications accounted for 12.3% (7/57) of subjects tested. Conclusions: This study provides a comprehensive protocol for the use of SR-NGS in a CYP21A2 diagnostic genotyping, integrating complementary bioinformatics pipelines and MLPA for copy number analysis. Full article

(This article belongs to the Special Issue Technological Advances Around Next-Generation Sequencing Application, 2nd Edition)

► Show Figures

Figure 1

23 pages, 13256 KB

Open AccessArticle

Coordinated Expression of ADC Targets ERBB2, TACSTD2, and NECTIN4 in Bladder Cancer: A Multi-Scale Transcriptomic and Proteomic Landscape Analysis

by Sanhe Liu, Liqun Duan and Shaozhong Wei

Curr. Issues Mol. Biol. 2026, 48(8), 825; https://doi.org/10.3390/cimb48080825 - 13 Aug 2026

Abstract

Antibody–drug conjugates (ADCs) targeting HER2 (encoded by ERBB2), Trop2 (TACSTD2), and Nectin-4 (NECTIN4) have demonstrated clinical activity in bladder cancer. However, the co-expression relationships among these three targets at both the transcriptomic and protein levels, and their spatial [...] Read more.

Antibody–drug conjugates (ADCs) targeting HER2 (encoded by ERBB2), Trop2 (TACSTD2), and Nectin-4 (NECTIN4) have demonstrated clinical activity in bladder cancer. However, the co-expression relationships among these three targets at both the transcriptomic and protein levels, and their spatial organization within the tumor microenvironment, remain incompletely characterized. To address this, we performed a multi-platform, multi-resolution analysis integrating ten bulk RNA-seq datasets (n = 1628 samples), six spatial transcriptomics datasets (10x Visium and Visium HD, n = 31 specimens), and multiplex immunofluorescence (mIF) staining on three paired tumor–adjacent normal bladder specimens. Pairwise Pearson correlation analyses were conducted for ERBB2, TACSTD2, and NECTIN4 across bulk transcriptomes and spatial compartments (tumor core, interface, and stroma). High-resolution co-expression hotspot mapping was performed using Visium HD data. Preliminary protein-level evidence was obtained using mIF, with quantitative three-dimensional surface plot reconstructions illustrating the spatial distribution of marker co-expression. Given the limited number of specimens (three paired tumor–normal samples), these findings should be regarded as exploratory and illustrative rather than definitive validation. Moderate-to-strong positive correlations among the three genes were consistently observed across all ten bulk datasets, with the strongest association between TACSTD2 and NECTIN4 (Pearson r up to 0.969). Spatial transcriptomic analyses recapitulated these positive correlations across all histopathological compartments, with the tumor core generally exhibiting the highest coefficients. No consistent spatial gradient was observed, indicating preservation of co-expression across tissue niches. Visium HD analysis confirmed positive pairwise correlations and identified discrete co-expression hotspots. mIF revealed extensive Trop2–Nectin-4 protein colocalization across all tumors, whereas HER2 showed more restricted and heterogeneous expression. Triple-positive subpopulations were identified but were limited. Strikingly, all three markers exhibited pronounced tumor-specific upregulation relative to paired adjacent normal tissues, with surface plot analysis showing markedly elevated cumulative fluorescence intensities in tumors (Z-values approaching 240 arbitrary units) compared with a flattened landscape in normal tissues (Z-values < 100–120 arbitrary units). These findings provide a multi-scale description of ADC-target co-expression in bladder cancer and generate hypotheses for biomarker-driven patient stratification, which require validation in larger, independent cohorts. Full article

(This article belongs to the Special Issue Molecular Mechanisms in Cancer Treatment and Anticancer Drugs)

► Show Figures

Figure 1

13 pages, 6740 KB

Open AccessArticle

Detection of TDP-43 Proteinopathies in Brain and Cerebrospinal Fluid Using Seed Amplification Assay

by Katsuya Satoh, Mika Inada Shimamura, Takeshi Fujimoto, Michio Kitayama, Akio Akagi, Yasushi Iwasaki, Yuu Satoh, Katsuhiro Ichinose, Akira Satoh, Ikuko Takahashi Iwata and Ichiro Yabe

Curr. Issues Mol. Biol. 2026, 48(8), 824; https://doi.org/10.3390/cimb48080824 - 13 Aug 2026

Abstract

Misfolded TAR DNA-binding protein 43 (TDP-43) is the primary pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). While seed amplification assays (SAAs), such as real-time quaking-induced conversion (RT-QuIC), have shown promise in detecting misfolded TDP-43 in cerebrospinal fluid (CSF) [...] Read more.

Misfolded TAR DNA-binding protein 43 (TDP-43) is the primary pathological hallmark of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). While seed amplification assays (SAAs), such as real-time quaking-induced conversion (RT-QuIC), have shown promise in detecting misfolded TDP-43 in cerebrospinal fluid (CSF) and olfactory mucosa, technically accessible methodologies are urgently required for widespread clinical application. We developed a streamlined, non-immunoprecipitation-based TDP-43 RT-QuIC assay to assess seeding activity in brain tissue and CSF. We evaluated its diagnostic performance using CSF from patients with TDP-43 proteinopathies and control subjects, and further examined its association with neurofilament light chain (NfL) and tau-related biomarkers. In CSF analysis, the assay demonstrated positive seeding activity in 70% (21/30) of patients with ALS and dementia, 50% (5/10) of patients with FTLD, and 40% (8/20) of patients with ALS alone. The assay exhibited excellent specificity, yielding negative results in >99% (199/200) of control samples, including those with autoimmune or electrophysiological abnormalities. Furthermore, CSF analysis demonstrated significantly higher NfL levels in TDP-43 SAA-positive cases compared to SAA-negative cases (p < 0.0008). The highest NfL concentrations were observed in the SAA-positive ALS with dementia and ALS cohorts, contrasting with lower levels in FTLD. Tau-related biomarkers exhibited no significant differences between the groups. Our streamlined, non-immunoprecipitation TDP-43 RT-QuIC assay provides highly specific detection of pathological TDP-43 seeding activity. While the assay detects the underlying TDP-43 proteinopathy rather than distinguishing between ALS and FTLD clinical phenotypes, its technical simplicity and combined utility with NfL measurements offer a robust, scalable framework for biomarker development. This approach provides a practical foundation for future multi-center validation and international standardization efforts. Full article

(This article belongs to the Special Issue Genetics, Epigenetics, and Molecular Mechanisms of Neurodegenerative Diseases)

► Show Figures

Graphical abstract

20 pages, 3603 KB

Open AccessArticle

Neuro-Mechanical Regulation of Vascular Smooth Muscle Cell Behaviour Under Ageing-Associated Substrate Stiffness

by Yumin Hou, Sejal Singal, Pamela Swiatlowska and Jose L. Sanchez-Alonso

Curr. Issues Mol. Biol. 2026, 48(8), 823; https://doi.org/10.3390/cimb48080823 - 12 Aug 2026

Abstract

Cardiovascular diseases (CVDs) remain a leading cause of mortality worldwide, and ageing is strongly associated with progressive arterial stiffening. Age-related alterations in extracellular matrix (ECM) mechanics influence vascular smooth muscle cell (VSMC) behaviour, while sympathetic innervation represents an additional regulator of vascular homeostasis. [...] Read more.

Cardiovascular diseases (CVDs) remain a leading cause of mortality worldwide, and ageing is strongly associated with progressive arterial stiffening. Age-related alterations in extracellular matrix (ECM) mechanics influence vascular smooth muscle cell (VSMC) behaviour, while sympathetic innervation represents an additional regulator of vascular homeostasis. However, how neural signalling interacts with ageing-associated mechanical conditions to regulate VSMC behaviour remains unclear. In this study, an in vitro sympathetic neuron–VSMC co-culture model was established to investigate neuro-mechanical regulation. Primary rat sympathetic neurons and A7r5 VSMCs were cultured on glass or polydimethylsiloxane (PDMS) substrates with defined stiffness (20 and 130 kPa), representing healthy and ageing-associated stiffened arterial environments, respectively. VSMC behaviour was assessed through analysis of cell area, proliferation, migration, cellular Young’s modulus (YM), and DNA damage marker γH2AX. Sympathetic neuronal co-culture was associated with reduced VSMC spreading and decreased γH2AX levels. Under the conditions tested, neural signalling exerted limited effects on cell proliferation and migration. In contrast, increased substrate stiffness promoted cell proliferation and elevated YM. Both neuronal input and substrate stiffness were associated with increased cellular YM. Together, these findings indicate that neural and mechanical cues may jointly influence VSMC behaviour within ageing-associated mechanical environments. This co-culture system provides a controllable platform for studying neuro-mechanical interactions in vascular biology. Full article

(This article belongs to the Special Issue Molecular and Cellular Mechanisms of Cardiac Repair and Regeneration)

► Show Figures

Figure 1

21 pages, 3213 KB

Open AccessArticle

Comparative Chloroplast Genomics, Codon Usage Bias, and Phylogenetic Placement of Euonymus alatus

by Yuemei Zhao, Weiwang Kong, Yushan Huang, Rongxiang Zhang and Changjiang Qian

Curr. Issues Mol. Biol. 2026, 48(8), 822; https://doi.org/10.3390/cimb48080822 - 12 Aug 2026

Abstract

Euonymus alatus is a species of medicinal and ornamental value, yet high-quality chloroplast genome resources for this taxon remain scarce. The complete chloroplast genome of E. alatus was assembled and compared with 15 congeneric species to investigate genomic structure and evolutionary dynamics. The [...] Read more.

Euonymus alatus is a species of medicinal and ornamental value, yet high-quality chloroplast genome resources for this taxon remain scarce. The complete chloroplast genome of E. alatus was assembled and compared with 15 congeneric species to investigate genomic structure and evolutionary dynamics. The genome is 157,416 bp with a GC content of 37.3%, containing 131 genes and 156 repeats (67 tandem repeats, 49 dispersed repeats, and 40 SSRs). Divergence was concentrated in non-coding regions, with 14 hypervariable regions identified as potential markers. IR expansion occurred independently in E. fortunei and E. japonicus, while no genome-wide inversions were detected. 11 protein-coding genes were identified under positive selection, among which clpP exhibited the strongest signal, suggesting a possible role in adaptive evolution. Codon usage bias analysis revealed that both mutation pressure and natural selection shape codon usage patterns, with the latter playing a relatively prominent role; 17 optimal codons were identified. Phylogenetic analysis strongly supported E. alatus as sister to E. phellomanus. This study provides a valuable genomic resource for species authentication, phylogenetic revision, and breeding in this genus. Full article

(This article belongs to the Special Issue Molecular Breeding and Genetics Research in Plants—3rd Edition)

► Show Figures

Figure 1

18 pages, 1802 KB

Open AccessReview

Proteinase-Activated Receptor 2 (PAR2) Deficiency and Cardiovascular Regulation: Context-Dependent Effects on Inflammation and Fibrosis

by Stephanie A. Viola, Shahnaz Siddiqua, Jesutofunmi Adesuyi, Yebin Jang, Maryia Ryskina and John J. McGuire

Curr. Issues Mol. Biol. 2026, 48(8), 821; https://doi.org/10.3390/cimb48080821 - 12 Aug 2026

Abstract

Proteinase-activated receptor 2 is a G protein-coupled receptor that regulates vascular tone and inflammatory signalling in the circulatory system. The roles of PAR2 appear complex and sometimes opposing. Studies using PAR2-deficient mice provide a framework to define these effects at the system level. [...] Read more.

Proteinase-activated receptor 2 is a G protein-coupled receptor that regulates vascular tone and inflammatory signalling in the circulatory system. The roles of PAR2 appear complex and sometimes opposing. Studies using PAR2-deficient mice provide a framework to define these effects at the system level. This review examines cardiovascular phenotypes associated with PAR2 deficiency in basal conditions and in disease. PAR2 deficiency produces modest increases in arterial blood pressure and vascular stiffness while preserving endothelial vasodilator function. Cardiac function remains largely normal in young PAR2-deficient animals but changes with age. Older PAR2-deficient mice develop diastolic dysfunction and cardiac fibrosis. In disease models, PAR2 deficiency has been associated with increased fibrosis in cardiac and vascular tissues and reduced vascular inflammation in atherosclerosis. PAR2 deficiency is also associated with reduced plaque progression and features of plaque stabilisation. In myocardial ischaemia models, PAR2 deficiency has been associated with reduced cardiac injury and adverse remodelling. The effects of PAR2 deficiency on inflammatory signalling vary according to tissue and disease context. Together, these findings suggest that the cardiovascular consequences of PAR2 deficiency depend on physiological and pathological context. Future studies should define cell-specific mechanisms to guide therapeutic targeting of PAR2. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Therapeutic Approaches in Fibrosis and Tissue Remodeling)

► Show Figures

Graphical abstract

22 pages, 1956 KB

Open AccessArticle

The Metabolic Rheostat Index Uncovers Pathway-Level Coordination, Immunosuppressive Microenvironment Remodeling, and Therapeutic Co-Vulnerabilities in Pancreatic Ductal Adenocarcinoma

by Funda Demirtas Korkmaz, Yasemin Sevim, Zekeriya Duzgun and Asuman Deveci Ozkan

Curr. Issues Mol. Biol. 2026, 48(8), 820; https://doi.org/10.3390/cimb48080820 - 12 Aug 2026

Abstract

Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive metabolic reprogramming, yet how major metabolic pathways are organized at single-cell resolution, and how this relates to the tumor microenvironment and therapeutic vulnerabilities, remains incompletely understood. We analyzed 32,227 cells from the GSE155698 discovery cohort [...] Read more.

Pancreatic ductal adenocarcinoma (PDAC) is characterized by extensive metabolic reprogramming, yet how major metabolic pathways are organized at single-cell resolution, and how this relates to the tumor microenvironment and therapeutic vulnerabilities, remains incompletely understood. We analyzed 32,227 cells from the GSE155698 discovery cohort and 32,627 cells from an independent healthy-pancreas reference (GSE229413; n = 5 donors) and introduce the Metabolic Rheostat Index (MRI), the standard deviation across per-cell glycolysis, OXPHOS, and hypoxia pathway scores. A pseudobulk analysis, hallmark gene-set validation, unified-threshold classification, a GDSC2 drug-sensitivity analysis with robust regression, EPIC tumor-purity-adjusted deconvolution, and a survival analysis of 183 TCGA-PAAD samples were performed. The pseudobulk analysis revealed a monotonic MRI gradient from healthy pancreata (mean = 0.259) to adjacent-normal tissue (0.322) to PDAC tumor tissue (0.352; p = 0.0039, Cohen’s d = 1.437), indicating progressive metabolic polarization during malignant transformation driven predominantly by cancer-associated fibroblasts rather than malignant epithelial cells. The glycolysis–hypoxia correlation was stronger in tumor cells (r = 0.121 vs. 0.019), and ERK/MAPK inhibitors showed the greatest drug sensitivity (r = 0.597, p = 0.0008). The Warburg Index correlated with fibroblast infiltration (partial r = 0.312, p = 1.76 × 10⁻⁵) but was not an independent prognostic marker (HR = 0.78, p = 0.321). These findings indicate that PDAC tissue undergoes progressive, stroma-driven metabolic polarization associated with an immunosuppressive microenvironment, providing a multi-dimensional single-cell framework for future metabolic-targeted therapeutic strategies. Full article

(This article belongs to the Section Molecular Medicine)

► Show Figures

Figure 1

22 pages, 10000 KB

Open AccessArticle

Genome-Wide and GWAS Dissection of Maize Fibrillin Genes Reveals Plastid Regulators of Drought and Salt Stress Tolerance

by Suwen Han, Renjie Zhao, Jingpei Piao, Xingzheng Zhang, Miaomiao Liu, Liangxuan Jia, Jianfeng Liu, Yuejia Yin and Hanchao Xia

Curr. Issues Mol. Biol. 2026, 48(8), 819; https://doi.org/10.3390/cimb48080819 - 12 Aug 2026

Abstract

Fibrillins (FBNs) are conserved plastid-associated proteins implicated in plant development and abiotic stress responses; however, their roles in maize remain unclear. In this study, through a genome-wide bioinformatic analysis, we identified 14 ZmFBN genes in the maize genome and characterized their phylogeny, chromosomal [...] Read more.

Fibrillins (FBNs) are conserved plastid-associated proteins implicated in plant development and abiotic stress responses; however, their roles in maize remain unclear. In this study, through a genome-wide bioinformatic analysis, we identified 14 ZmFBN genes in the maize genome and characterized their phylogeny, chromosomal distribution, gene structure, conserved motifs, and promoter cis-elements. ZmFBN members were grouped into several subfamilies that all retain a conserved PAP_fibrillin domain, whereas the variation in exon–intron organization, motif composition, and regulatory elements suggests functional diversification. Expression profiling revealed pronounced tissue-preferential patterns, with many genes highly expressed in leaves and reproductive tissues, and distinct responses to drought, salt, heat, and cold stresses. qRT-PCR assays showed that ZmFBN8 and ZmFBN9 are strongly induced by both salt and PEG-simulated drought, ZmFBN2 and ZmFBN5 are predominantly drought-responsive, and ZmFBN11 is mainly activated by salt. Genome-wide association analysis further detected significant loci near ZmFBN1 and ZmFBN4, whose allelic variants are associated with the survival rate under drought and with key agronomic traits, including the tassel branch number, flowering time, ear diameter, and kernel length. These results demonstrate that ZmFBN genes make diversified contributions to maize growth, development, and stress adaptation and highlight several members as promising targets for functional studies and the molecular breeding of stress-tolerant maize. Moreover, selection pressure analysis indicated ZmFBN7 experienced relaxed purifying selection, and ZmFBN12 underwent positive selection, which drives the functional diversification of the ZmFBN family during maize evolution. Full article

(This article belongs to the Section Molecular Plant Sciences)

► Show Figures

Figure 1

22 pages, 3462 KB

Open AccessArticle

Comprehensive Proteomic Profiling of Alternaria gansuense Provides Insights into Candidate Virulence-Associated Proteins and Core Physiological Features

by Huaqi Liu, Lili Zhang, Tongtong Wang and Yanzhong Li

Curr. Issues Mol. Biol. 2026, 48(8), 818; https://doi.org/10.3390/cimb48080818 - 12 Aug 2026

Abstract

Although Alternaria gansuense causes yellow stunt and root rot (YSRR)—a destructive disease of the leguminous forage Astragalus adsurgens in northern China—systematic investigations of this pathogen at the protein level remain scarce. In this study, we establish an optimized proteomic workflow for A. gansuense [...] Read more.

Although Alternaria gansuense causes yellow stunt and root rot (YSRR)—a destructive disease of the leguminous forage Astragalus adsurgens in northern China—systematic investigations of this pathogen at the protein level remain scarce. In this study, we establish an optimized proteomic workflow for A. gansuense by comparing two protein extraction methods. Using data-independent acquisition (DIA) mass spectrometry with a DIA-NN search against the Alternaria protein database, we construct the first comprehensive proteome reference map of A. gansuense, then perform functional annotation via Gene Ontology, KOG, KEGG, InterPro domain, and subcellular localization analyses. A total of 5052 proteins were identified from vegetative mycelia, and the proteome was found to be predominantly composed of proteins involved in primary metabolism, signal transduction, secondary metabolism, and stress responses. Notably, a set of putative pathogenicity-associated proteins, including two-component regulators (SSK1p), protein kinases, cytochrome P450 enzymes, and ABC transporters, was identified. These proteins are homologs of well-characterized virulence factors in other pathogenic fungi, suggesting a potential coordinated signaling—metabolism—defense network that may contribute to fungal virulence. Subcellular localization further shows that cytoplasmic and nuclear proteins together account for over 50% of the annotated proteome. This study presents the first comprehensive proteomic reference map for A. gansuense, providing a valuable resource for functional genomics. Subsequent experimental validation of the bioinformatically predicted candidate molecular targets presented here may help to dissect the pathogenic mechanisms of YSRR and enable the development of novel disease management strategies. Full article

(This article belongs to the Section Molecular Microbiology)

► Show Figures

Figure 1

Journal Description

Current Issues in Molecular Biology

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI