International Journal of Molecular Sciences

32 pages, 76631 KB

Open AccessReview

TOR Signaling as a Central Integrator of Embryogenic Reprogramming During 2,4-D-Induced Somatic Embryogenesis

by José Luis Cabrera-Ponce, Alex Ricardo Bermudez-Valle, Maria del Rosario Cárdenas-Aquino, Andrea Maria Navarro-Vega, Braulio Uribe-Lopez, Aaron Barraza-Celis, Eliana Valencia-Lozano and Lisset Herrera-Isidron

Int. J. Mol. Sci. 2026, 27(14), 6191; https://doi.org/10.3390/ijms27146191 - 10 Jul 2026

Abstract

2,4-Dichlorophenoxyacetic acid (2,4-D), originally developed as a synthetic auxinic herbicide, is the most widely used chemical inducer of somatic embryogenesis (SE) in plants. Despite extensive use of 2,4-D in plant regeneration, the systems-level regulatory mechanisms connecting hormonal signaling, metabolic reprogramming, translational control, and [...] Read more.

2,4-Dichlorophenoxyacetic acid (2,4-D), originally developed as a synthetic auxinic herbicide, is the most widely used chemical inducer of somatic embryogenesis (SE) in plants. Despite extensive use of 2,4-D in plant regeneration, the systems-level regulatory mechanisms connecting hormonal signaling, metabolic reprogramming, translational control, and embryogenic competence remain poorly resolved. Here, we hypothesize that TOR signaling functions as an integrative molecular hub coordinating transcriptional, metabolic, and developmental reprogramming during somatic embryogenesis induction. To investigate the molecular regulatory landscape associated with 2,4-D-induced SE, we performed a systems-level analysis integrating publicly available transcriptomic data from Arabidopsis thaliana with high-confidence protein–protein interaction (PPI) network analyses using STRING v12.0 (confidence score ≥ 0.900). Using a previously published transcriptomic dataset, we identified 1927 upregulated genes associated with SE induction, which were organized into 34 functional modules related to transcriptional regulation, translation metabolism, hormone signaling and cellular homeostasis. Within this interactome, TARGET OF RAPAMYCIN (TOR) kinase emerged as an integrative regulatory hub associated with multiple pathways involved in embryogenic reprogramming. Network analyses revealed three major TOR-associated regulatory axes: (1) the TOR–FKBP12–RPS6A axis, associated with ribosome biogenesis and translational regulation; (2) the TOR–CBP20 axis, connected with transcriptional reprogramming; SE master regulators (LEC1, LEC2, and FUS3); and lipid, sterol, brassinosteroid (BR), and auxin-associated pathways; and (3) the TOR–TAP46 axis, linked with one-carbon metabolism, nucleotide biosynthesis, DNA replication and repair, and genome-stability pathways. Additionally, the network contained 411 embryo-lethal (EMBL) genes distributed across multiple regulatory modules, reinforcing the biological relevance of the identified interactome and highlighting the importance of coordinated developmental, metabolic, and transcriptional regulation during embryogenesis induction. These findings support a systems-level TOR-associated regulatory framework involved in the integration of transcriptional, translational, metabolic, hormonal, and genome-maintenance pathways during embryogenesis. This interactome model provides a foundation for functional studies aimed at dissecting the molecular mechanisms underlying SE and identifying candidate targets to improve regeneration and biotechnological application and crop genetic engineering. Collectively, this study proposes a mechanistic framework in which TOR signaling integrates developmental, metabolic, translational, and genome-stability pathways to orchestrate embryogenic competence, providing candidate molecular targets for improving plant regeneration and genome engineering platforms. Full article

(This article belongs to the Section Molecular Biology)

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20 pages, 1986 KB

Open AccessArticle

Anti-Alpha-Gal Antibodies Against Gangliosides: Preliminary Data on a New Autoimmune Target in Alzheimer’s Disease Patients

by Filippo Naso, Alessandro Gandaglia, Giulio Sturaro, Alessio Lepore, Alessia Arcaro, Fabrizio Gentile, Alfonso Di Costanzo and Antonella Angiolillo

Int. J. Mol. Sci. 2026, 27(14), 6190; https://doi.org/10.3390/ijms27146190 - 10 Jul 2026

Abstract

Human anti-αGal antibodies (Abs), known for their marked polyreactivity, have been detected bound to the gray matter of the brains of Alzheimer’s disease (AD) patients, although their targets were unclear. Since αGal is a strictly xenogenic antigen absent in humans, this observation raised [...] Read more.

Human anti-αGal antibodies (Abs), known for their marked polyreactivity, have been detected bound to the gray matter of the brains of Alzheimer’s disease (AD) patients, although their targets were unclear. Since αGal is a strictly xenogenic antigen absent in humans, this observation raised questions regarding the nature of the structures recognized by these antibodies. In this study, we investigated their potential interaction with gangliosides—glycan structures that are highly abundant in the central nervous system. Using a competitive inhibition ELISA, serum profiles of anti-αGal Abs isotypes and their indirect cross-reactivity with selected soluble gangliosides were analyzed in AD patients and healthy subjects (HSs). AD patients showed reduced levels of anti-αGal IgG and IgM, but increased IgA compared to HSs. Notably, pre-incubation with GM1, GM2, or GD1b did not reduce αGal–HSA binding in HS sera. In contrast, in AD sera, pre-incubation with GD1b reduced residual αGal–HSA binding for all antibody isotypes; additionally, GM1 inhibited IgM binding, and GM2 inhibited IgA binding. These results should therefore be interpreted as competitive inhibition patterns consistent with ganglioside-associated cross-reactivity rather than as direct evidence of antibody binding to immobilized gangliosides. Overall, the findings provide preliminary evidence that, in AD sera, a fraction of αGal–HSA-reactive antibodies can be competitively inhibited by selected gangliosides. This observation supports the presence of an altered humoral anti-carbohydrate signature in AD and identifies neuronal gangliosides as plausible candidate autologous targets that may help explain the previously reported binding of anti-αGal Abs to gray matter. However, given the indirect nature of the assay, these data should be considered hypothesis-generating and require confirmation by direct binding approaches. Full article

(This article belongs to the Special Issue Unraveling Neuroimmune Disorders: From Pathogenic Pathways to Biomarker-Driven Precision Medicine)

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16 pages, 1877 KB

Open AccessArticle

β-Hydroxy-β-methylbutyrate (HMB) Counteracts Atrophy and Restores Circadian Rhythms in Myotubes

by Meytal Cohen-Or, Nava Chapnik, Natalie Avital-Cohen and Oren Froy

Int. J. Mol. Sci. 2026, 27(14), 6189; https://doi.org/10.3390/ijms27146189 - 10 Jul 2026

Abstract

β-hydroxy-β-methylbutyrate (HMB), a bioactive metabolite of leucine, is widely recognized for its anabolic and anti-catabolic effects in skeletal muscle. However, the molecular mechanisms underlying these effects, particularly in relation to circadian regulation, remain incompletely understood. Here, we investigated the impact of HMB on [...] Read more.

β-hydroxy-β-methylbutyrate (HMB), a bioactive metabolite of leucine, is widely recognized for its anabolic and anti-catabolic effects in skeletal muscle. However, the molecular mechanisms underlying these effects, particularly in relation to circadian regulation, remain incompletely understood. Here, we investigated the impact of HMB on dexamethasone-induced muscle atrophy in C2C12 myotubes, with a focus on anabolic signaling and circadian clock regulation. C2C12 myotubes were treated with HMB or HMB after dexamethasone-induced atrophy. HMB treatment significantly improved cell viability, surface area and fiber diameter by reducing expression of CBL-B, MuRF1 and Atrogin1, key mediators of muscle proteolysis, and increasing myogenin expression compared with atrophic conditions. While HMB did not activate AKT or mTOR, it robustly increased phosphorylation of P70S6K and S6 through a phospholipase D (PLD)-dependent mechanism. HMB restored disrupted circadian clock gene expression induced by dexamethasone, including normalization of expression patterns. HMB also enhanced circadian rhythmic amplitude and advanced phase timing, indicating improved clock robustness. These findings identify circadian regulation as a novel target of HMB action and demonstrate that HMB preserves muscle homeostasis through coordinated modulation of anabolic signaling and intrinsic circadian machinery. This study provides mechanistic insight into how HMB protects against muscle atrophy and highlights circadian regulation as an important contributor to skeletal muscle health. Full article

(This article belongs to the Special Issue Molecular Mechanisms and Therapies in Skeletal Muscle Diseases)

36 pages, 3421 KB

Open AccessReview

Impact of Angiosperm Tree-Derived Allelochemicals on Physiological Responses of Acceptor Plants—A Systematic Review

by Maja Paterska and Konrad Osowski

Int. J. Mol. Sci. 2026, 27(14), 6188; https://doi.org/10.3390/ijms27146188 - 10 Jul 2026

Abstract

Allelopathy—the release of biologically active secondary metabolites by plants—is a key mechanism regulating plant community dynamics in forest and agro-forestry ecosystems, yet the physiological basis of allelochemical effects of angiosperm trees on acceptor plants remains insufficiently understood. This systematic review synthesises knowledge on [...] Read more.

Allelopathy—the release of biologically active secondary metabolites by plants—is a key mechanism regulating plant community dynamics in forest and agro-forestry ecosystems, yet the physiological basis of allelochemical effects of angiosperm trees on acceptor plants remains insufficiently understood. This systematic review synthesises knowledge on the physiological effects of angiosperm tree allelochemicals, focusing on photosynthesis, respiration, water relations, mineral nutrition, and growth and development. Following PRISMA 2020 guidelines, five databases (Web of Science, ScienceDirect, SpringerLink, Wiley Online Library, and Scopus) were searched between October 2025 and June 2026 for English-language peer-reviewed articles on allelopathic effects on plant physiological processes; risk of bias was assessed via methodological transparency, and, given design heterogeneity, a qualitative narrative synthesis was performed. Of 7748 records identified, 99 met the eligibility criteria. Allelochemicals, including phenolic acids, flavonoids, naphthoquinones, terpenoids, alkaloids, and coumarins, were associated with disrupted photosynthetic efficiency, impaired mitochondrial electron transport, altered stomatal functioning, reduced nutrient uptake, and suppressed cell division, with oxidative stress—often linked to reactive oxygen species accumulation—recurring as a shared mechanism; effects were concentration-dependent, with synergistic interactions noted between allelochemicals. These findings advance mechanistic understanding of angiosperm tree allelopathy and highlight its relevance for sustainable agriculture and biological weed management. Full article

(This article belongs to the Collection Latest Review Papers in Biochemistry)

21 pages, 4555 KB

Open AccessArticle

Dehydration Stress Memory Genes in Tomato (Solanum lycopersicum L.)

by Monther T. Sadder, Abdullah A. Alsadon, Bayan S. Alkharabsheh, Anas Musallam, Abdulsalam M. Alnajjar and Lana W. Al-Qadumii

Int. J. Mol. Sci. 2026, 27(14), 6187; https://doi.org/10.3390/ijms27146187 - 10 Jul 2026

Abstract

Drought is among the most serious abiotic stresses affecting tomato production worldwide, especially under climate change. Plants exposed to repeated drought events may develop stress memory, allowing them to respond more efficiently to subsequent stress exposure. In this study, physiological and transcriptomic tools [...] Read more.

Drought is among the most serious abiotic stresses affecting tomato production worldwide, especially under climate change. Plants exposed to repeated drought events may develop stress memory, allowing them to respond more efficiently to subsequent stress exposure. In this study, physiological and transcriptomic tools were combined to investigate dehydration stress memory in tomato (Solanum lycopersicum L.). Tomato plants were subjected to two consecutive drought stresses separated by a recovery stage, where control (C), first stress (S1), rehydration (H), and second stress (S2) stages were analyzed. Physiological measurements showed progressive reductions in relative water content (RWC) and PSII activity under drought stress, while proline accumulation was significantly increased during the second stress stage, indicating memory-associated adaptive responses. RNA sequencing revealed dramatic transcriptome reprogramming with thousands of differentially expressed genes (DEGs) across stress stages. Hierarchical clustering identified 30 distinct expression patterns among revealed DEGs, including clusters associated with transcriptional memory, adaptive responses, metabolic adjustment, and recovery processes. Several memory-associated clusters were enriched with transcription factors, signaling proteins, osmolyte-related genes, and reactive oxygen species detoxification enzymes. Gene Ontology analysis highlighted significant enrichment of pathways related to photosynthesis, response to water deprivation, ABA signaling, oxidative stress, carbohydrate metabolism, and chromatin organization. Recovery-associated expression of histone and chromatin remodeling genes indicates a potential involvement of epigenetic-related regulatory processes in dehydration stress memory in tomato. Tomato plants respond to repeated dehydration stress through coordinated physiological, metabolic, transcriptional, and epigenetic adjustments that improve stress adaptation. The identified candidate memory genes may provide useful targets for future breeding programs aimed at enhancing drought tolerance in tomato. Full article

(This article belongs to the Special Issue Latest Research on Plant Genomics and Genome Editing, 2nd Edition)

19 pages, 9899 KB

Open AccessArticle

First-Principles Investigation of Structural, Mechanical, Electronic and Optical Properties of Ba₂MReO₆ (M = Li, Na, K, and Rb) Double Perovskites

by Marcin Gackowski, Katarzyna Mądra-Gackowska, Muhammad Usman Khan and Łukasz Szeleszczuk

Int. J. Mol. Sci. 2026, 27(14), 6186; https://doi.org/10.3390/ijms27146186 - 10 Jul 2026

Abstract

The growing demand for efficient, stable, and environmentally friendly materials for next-generation optoelectronic and photovoltaic applications has attracted significant interest in double perovskite compounds. First-principles density functional theory (DFT) calculations were performed to systematically investigate the structural, mechanical, electronic, and optical properties of [...] Read more.

The growing demand for efficient, stable, and environmentally friendly materials for next-generation optoelectronic and photovoltaic applications has attracted significant interest in double perovskite compounds. First-principles density functional theory (DFT) calculations were performed to systematically investigate the structural, mechanical, electronic, and optical properties of Ba₂MReO₆ (M = Li, Na, K, and Rb) double perovskites. Structural optimization confirms that all compounds crystallize in the cubic Fm3̅m symmetry. The thermodynamic and geometric stability of the series is checked with negative formation energies and tolerance factor analyses (t, μ, τ). Mechanical analysis confirms that all compounds are mechanically stable; Ba₂LiReO₆ is the stiffest, while Ba₂RbReO₆ shows moderate stiffness with the highest ductility. Furthermore, ab initio molecular dynamics (AIMD) simulations at room temperature confirm the dynamical stability of all compounds, with negligible fluctuations in total energy under thermal conditions. The calculated band structures using both GGA-PBE and HSE06 hybrid functionals reveal that all compounds possess indirect band gaps, with HSE06 values of 2.236 eV for Ba₂LiReO₆, 2.133 eV for Ba₂NaReO₆, 2.116 eV for Ba₂KReO₆, and 1.395 eV for Ba₂RbReO₆. Optical measurements indicate that it is highly polarizable by dielectric polarizability, has high absorption coefficients (approximately 10⁶ cm⁻¹), and has large optical conductivity in the UV, with large inter-band interactions between 2 and 4 eV. The suitable band gap and favorable optical characteristics suggest that Ba₂RbReO₆ is the most promising candidate for photovoltaic and solar-cell applications. Full article

(This article belongs to the Special Issue Current Insights for the Development of Emerging Photovoltaics Through Molecular Research)

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19 pages, 1232 KB

Open AccessReview

Micro-Fragmented Adipose Tissue (MFAT) in Orthopedic Regenerative Medicine: A Narrative Review of the Biological Basis and Clinical Evidence

by Claire Yuan, Ashu K. Goyle, Maged Guirguis, Alan D. Kaye, Vahid Grami, Karan Dave, Ronald J. Kulich, Timothy Deer, David Rosenblum, Vwaire Orhurhu, Jamal J. Hasoon and Christopher L. Robinson

Int. J. Mol. Sci. 2026, 27(14), 6185; https://doi.org/10.3390/ijms27146185 - 10 Jul 2026

Abstract

Micro-fragmented adipose tissue (mFAT) is a promising autologous biologic in regenerative medicine because it provides a mechanically processed adipose-derived product that preserves native extracellular matrix architecture and a cellular milieu rich in mesenchymal stem cells, pericytes, growth factors, cytokines, and extracellular vesicles. Mechanistically, [...] Read more.

Micro-fragmented adipose tissue (mFAT) is a promising autologous biologic in regenerative medicine because it provides a mechanically processed adipose-derived product that preserves native extracellular matrix architecture and a cellular milieu rich in mesenchymal stem cells, pericytes, growth factors, cytokines, and extracellular vesicles. Mechanistically, mFAT is hypothesized to act largely through paracrine signaling that dampens inflammation, supports vascular stabilization, and promotes cartilage and soft-tissue repair; in vitro data suggest modulation of osteoarthritic synovial macrophage signaling, including reductions in chemokines such as CCL2 and CCL3. Preparation involves liposuction harvest followed by closed, sterile mechanical processing without enzymatic digestion or cell expansion, aligning with “minimal manipulation” concepts relevant to regulatory frameworks. Preclinical animal studies generally demonstrate favorable effects on synovial inflammation and cartilage matrix markers (e.g., glycosaminoglycan content) with limited adverse events. Clinically, the strongest body of evidence is in knee osteoarthritis, where multiple prospective and retrospective studies report improvements in pain and function from months to several years after single injections, though response rates vary and study designs are heterogeneous. Evolving data support potential benefit in hip osteoarthritis and select tendon conditions, but cohorts remain small. Overall, mFAT appears safe and potentially effective, yet larger, standardized, long-term randomized controlled trials and comparative studies versus platelet-rich plasma and bone marrow aspirate concentrates are needed to clarify indications, dosing, durability, and mechanisms in vivo. Full article

(This article belongs to the Special Issue Regenerative Medicine: Molecular Mechanisms Driving Tissue Regeneration and Repair)

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23 pages, 3612 KB

Open AccessArticle

DeepExoMir: A Reproducible RNA Language Model Framework for CLIP-Seq-Supported MicroRNA Target-Site Prioritization

by Wen-Hsien Lin, Chia-Ni Hsiung, Wen-Yu Lien and Martin Sieber

Int. J. Mol. Sci. 2026, 27(14), 6184; https://doi.org/10.3390/ijms27146184 - 10 Jul 2026

Abstract

MicroRNAs regulate gene expression post-transcriptionally, yet target prediction faces a credibility gap: published methods drop sharply against CLIP-seq-validated negatives. We present DeepExoMir, a deep learning framework integrating frozen RiNALMo RNA language model embeddings with biologically informed features. Under a dual-probe ablation protocol on [...] Read more.

MicroRNAs regulate gene expression post-transcriptionally, yet target prediction faces a credibility gap: published methods drop sharply against CLIP-seq-validated negatives. We present DeepExoMir, a deep learning framework integrating frozen RiNALMo RNA language model embeddings with biologically informed features. Under a dual-probe ablation protocol on three miRBench test sets, DeepExoMir reaches mean AU-PRC 0.855, surpassing eight retrained baselines (paired bootstrap

p < 0.001

). Evolutionary conservation and duplex structure prove largely redundant with language-model priors, motivating a structure-free Lite variant (0.863). On nine exosomal miRNAs from a companion melanogenesis study, DeepExoMir recovers literature-validated targets and ranks canonical pigmentation regulators (KITLG, MITF, TYRP1) in the top 5%. Full article

(This article belongs to the Special Issue Harnessing Bioinformatics for miRNA Research: Methods, Insights and Applications)

21 pages, 1217 KB

Open AccessArticle

Circulating miRNAs as Biomarkers of Tick-Borne Encephalitis Severity: Association with Cytokine Profile in Febrile, Meningeal, and Encephalitic Forms

by Elena V. Mikheeva, Anna S. Tolmacheva, Mark M. Melamud, Evgeny A. Ermakov, Kseniya S. Aulova, Jialin Li, Yana S. Ulyanova, Elena I. Krasnova, Georgy A. Nevinsky and Anna M. Timofeeva

Int. J. Mol. Sci. 2026, 27(14), 6183; https://doi.org/10.3390/ijms27146183 - 10 Jul 2026

Abstract

Tick-borne encephalitis (TBE) is a neuroinvasive flavivirus infection with a wide spectrum of clinical manifestations whose molecular mechanisms remain insufficiently characterized. MiRNAs regulate pro-inflammatory cytokine production; therefore, changes in their profiles across different forms of TBE may determine the nature of the cytokine [...] Read more.

Tick-borne encephalitis (TBE) is a neuroinvasive flavivirus infection with a wide spectrum of clinical manifestations whose molecular mechanisms remain insufficiently characterized. MiRNAs regulate pro-inflammatory cytokine production; therefore, changes in their profiles across different forms of TBE may determine the nature of the cytokine response. The aim of this work was to identify the specific features of the circulating miRNA and cytokine profiles in different clinical forms of TBE, as well as to analyze the correlations between them. The study included patients with febrile, meningeal, and encephalitic forms of TBE, patients with inflammatory rheumatic diseases (IRD), and healthy donors. Plasma concentrations of eight miRNAs (miR-25-3p, miR-29a-3p, miR-92a-3p, miR-146a-5p, miR-146b-5p, miR-181a-5p, miR-486-3p, and miR-766-3p) were measured by stem-loop real-time RT-PCR. Cytokine concentrations (IL-1β, IL-2, IL-8, IL-18, TNF-α) were measured by ELISA. Kendall’s rank correlation test was used for the correlation analysis. In all forms of TBE, a distinct circulating miRNA signature emerges (↑ miR-25-3p, miR-146b-5p, ↑ miR-766-3p, and ↓ miR-29a-3p), which is associated with an acute antiviral response and is not specific to chronic autoimmune inflammation. Several miRNAs (miR-29a-3p, miR-92a-3p, miR-146b-5p, and miR-486-3p) showed opposite changes in TBE and IRD, pointing to fundamentally different mechanisms of immune regulation in acute neuroinfection and systemic autoimmune pathology. Several statistical associations between circulating miRNA and pro-inflammatory cytokine levels were identified. TNF-α levels positively correlated with miR-146b-5p and negatively with miR-25-3p, while IL-2 positively correlated with miR-25-3p. In the encephalitic form of TBE, IL-1β positively correlated with miR-146b-5p and miR-92a-3p. The present study is of a pilot nature. The miRNA and cytokine patterns identified here were based on a small sample size and should therefore be regarded as preliminary. Once confirmed, these signatures may provide a basis for the differential diagnosis of TBE and the development of prognostic biomarkers of disease severity. Full article

(This article belongs to the Special Issue RNA-Based Regulation in Human Health and Disease)

17 pages, 1602 KB

Open AccessArticle

GutMGene-Guided Peripheral Blood Transcriptomics Identifies an FLNA-Associated Host-Gene Signal in Diabetic Retinopathy

by Chuanxue Ma, Yujun Wang and Yi Liu

Int. J. Mol. Sci. 2026, 27(14), 6182; https://doi.org/10.3390/ijms27146182 - 10 Jul 2026

Abstract

Diabetic retinopathy (DR) reflects retinal microvascular injury and systemic immune-metabolic stress, and most public DR transcriptomic datasets lack paired microbiome/metabolomic profiles. We used gutMGene v2.0 as a curated microbe/metabolite–host gene prior and integrated it with peripheral blood transcriptomics from GSE221521. Candidate genes were [...] Read more.

Diabetic retinopathy (DR) reflects retinal microvascular injury and systemic immune-metabolic stress, and most public DR transcriptomic datasets lack paired microbiome/metabolomic profiles. We used gutMGene v2.0 as a curated microbe/metabolite–host gene prior and integrated it with peripheral blood transcriptomics from GSE221521. Candidate genes were refined by weighted gene co-expression network analysis (WGCNA), repeated resampling, cross-dataset assessment, mechanism scoring, peripheral blood mononuclear cell (PBMC) single-cell localization and filamin A (FLNA)-centered single-cell gene regulatory network (GRN) virtual knockout. The gutMGene prior contained 238 host genes; 15 DR-associated genes overlapped this prior, and WGCNA retained ten candidate gut microbe and microbial metabolite-related genes (GMMRGs): FLNA, AKT1, IRAK1, BCL10, CDK6, CTSD, JUP, CXCL1, CXCR2 and IL4R. Resampling prioritized FLNA as the most consistent candidate. Cross-dataset assessment localized the strongest signal to type 2 diabetes (T2D) PBMCs, retinal endothelial cells and advanced proliferative diabetic retinopathy with diabetic macular edema (PDR + DME) retinal tissue, with weaker separation in whole blood, broad retinal tissue and six-donor type 1 diabetes (T1D) PBMCs. FLNA virtual knockout predicted cell-context-dependent perturbation of immune-related transcriptional programs, including IL4R in DR B cells and CTSD in DR monocytes/NK cells. This prior-guided study identifies FLNA within a ten-gene GMMRG set as a circulating host-response signal that links curated microbe/metabolite–host records to immune-vascular and cytoskeletal remodeling in DR. Full article

(This article belongs to the Section Molecular Endocrinology and Metabolism)

16 pages, 1676 KB

Open AccessArticle

Immunochemotherapy with Amphotericin B and HisAK70 Vaccine for Cutaneous Leishmaniosis

by Socorro Espuelas, Carmen Palomino-Cano, Carlos Torrado-Salmerón, Helga K. Ruiz, Paloma M. de la Torre-Iglesias, Santiago Torrado-Santiago, Juan J. Torrado, José María Alunda, Christophe Dardonville, Sergio Alberto Sánchez Guirales, Dolores R. Serrano and Javier Carrión

Int. J. Mol. Sci. 2026, 27(14), 6181; https://doi.org/10.3390/ijms27146181 - 10 Jul 2026

Abstract

Cutaneous leishmaniosis (CL) remains a major neglected tropical disease, with current therapies constrained by toxicity, high cost, and variable efficacy. Here, we evaluated an immunochemotherapy strategy combining topical amphotericin B (AmB) with the therapeutic DNA vaccine HisAK70 in a murine model of Leishmania [...] Read more.

Cutaneous leishmaniosis (CL) remains a major neglected tropical disease, with current therapies constrained by toxicity, high cost, and variable efficacy. Here, we evaluated an immunochemotherapy strategy combining topical amphotericin B (AmB) with the therapeutic DNA vaccine HisAK70 in a murine model of Leishmania major infection. BALB/c mice were subcutaneously infected and treated with topical AmB cream alone, AmB plus HisAK70, or paromomycin (PM) as a reference therapy. Therapeutic efficacy was assessed through lesion progression, parasite burden in draining lymph nodes and spleen, and immunological markers associated with parasite control. Both PM and the combined AmB + HisAK70 treatment significantly reduced lesion progression and markedly decreased parasite burden compared with infected controls, demonstrating effective control of local infection and systemic dissemination. Importantly, the combination therapy enhanced the efficacy of AmB alone, supporting the beneficial contribution of vaccine-driven immune modulation to therapeutic outcome. Therapeutic efficacy was associated with reduced arginase activity in infected tissues and an increased IFN-γ/IL-4 ratio, indicative of a protective Th1-oriented immune response. Together, these findings highlight immunochemotherapy as a promising strategy for CL treatment, integrating localized topical drug delivery with targeted immune activation to improve therapeutic efficacy while potentially reducing systemic toxicity. Full article

(This article belongs to the Special Issue Dermatology: Advances in Pathophysiology and Therapies (3rd Edition))

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34 pages, 11293 KB

Open AccessArticle

Immune Cytolytic Activity Correlates with Tumor Microenvironmental Aberrations in Colorectal Cancer

by Stephanie Agioti, George Georgoulias, Ilias Georgakopoulos-Soares, Maria-Ioanna Christodoulou and Apostolos Zaravinos

Int. J. Mol. Sci. 2026, 27(14), 6180; https://doi.org/10.3390/ijms27146180 - 10 Jul 2026

Abstract

Colorectal cancer (CRC) exhibits a highly heterogeneous tumor immune microenvironment (TME), ranging from “immune-inflamed” to “immune-desert” or “immune-excluded” phenotypes. Understanding how immune cell composition, cytolytic activity (CYT) and genomic alternations shape tumor-immune interactions is critical for improving immunotherapy outcomes. We analyzed TCGA-COAD and [...] Read more.

Colorectal cancer (CRC) exhibits a highly heterogeneous tumor immune microenvironment (TME), ranging from “immune-inflamed” to “immune-desert” or “immune-excluded” phenotypes. Understanding how immune cell composition, cytolytic activity (CYT) and genomic alternations shape tumor-immune interactions is critical for improving immunotherapy outcomes. We analyzed TCGA-COAD and TCGA-READ datasets to evaluate immune competency, CYT, immune subtypes, microsatellite instability (MSI), and genomic instability, including somatic mutations, copy number aberrations (CNAs), and chromothriptic events. Immune cell infiltration was correlated with CYT levels, immune checkpoint expression, and immune-related gene signatures. Immune-competent (IC) tumors were predominantly CYT-high, enriched in stromal and immune scores, and exhibited distinct TME characteristics compared with immune-deficient (ID) tumors. IC/CYT-high tumors expressed higher levels of immune checkpoints (PD-1, PD-L1, CTLA-4, IDO1/2, LAG-3) and cytokines/chemokines (C1QA/B/C, CXCL9/10/11, CXCL13). Differences in immune infiltration were observed across tumors with significant mutations and copy number alterations. No prognostic difference was observed between CYT-high and CYT-low patients, indicating that CYT reflects immune activation rather than clinical outcome. Functionally, stimulated CD8⁺ T cells exhibited cytotoxicity activity against MSI-high (HCT-116) and microsatellite-stable (HT-29) CRC cells, with MSI-H cells showing higher sensitivity. Dynamic 3D co-culture demonstrated tumor-guided T cell infiltration and retention of CD8 expression, and co-culture was associated with moderate upregulation of cytotoxicity-related genes GZMA and PRF1 within the system. Cytotoxic activity decreased at lower effector-to-target ratios, highlighting the importance of effector dose. Overall, these findings link CYT, immune competency, MSI status, and genomic instability to T cell cytotoxic responses, providing insights into tumor-immune interactions, and suggest potential associations relevant for immunotherapy research in CRC. Full article

(This article belongs to the Section Molecular Oncology)

14 pages, 298 KB

Open AccessArticle

Retrospective Study of Biochemical and Haematological Changes in Diabetes Mellitus

by Jovita I. Mbah, Phillip T. Bwititi, Lin K. Ong, Prajwal Gyawali and Ezekiel U. Nwose

Int. J. Mol. Sci. 2026, 27(14), 6179; https://doi.org/10.3390/ijms27146179 - 10 Jul 2026

Abstract

Routinely tested biochemical and haematological molecules in the management of diabetes control, including glycated haemoglobin (HbA1c) evaluation, are related to estimated whole blood viscosity (eWBV), which is an indicator of diabetic rheology pathology. Examination of the molecules control could establish their value for [...] Read more.

Routinely tested biochemical and haematological molecules in the management of diabetes control, including glycated haemoglobin (HbA1c) evaluation, are related to estimated whole blood viscosity (eWBV), which is an indicator of diabetic rheology pathology. Examination of the molecules control could establish their value for clinical laboratory-based cardiovascular risk assessment. The study investigated changes in full blood count (FBC) parameters and lipid profiles with eWBV and HbA1c. The predictiveness of FBC parameters for eWBV and HbA1c is explored. This was a laboratory-based observational study that used mixed-methods analyses. Cross-sectional, longitudinal, descriptive, correlation, and regression approaches were applied to archived clinical pathology data from two health facilities, including a dataset of N = 21,026. Results: Lipid profile molecules significantly change with the level of HbA1c (p < 0.001). The levels of eWBV and its determinant molecules also change with HbA1c, and with seasonal variations (p < 0.001). Considering the predictiveness of FBC parameters for HbA1c and eWBV levels, red blood cells (RBC) and their indices, i.e., haemoglobin molecules, show statistical significance. For instance, RBC most strongly predicted HbA1c (r = 0.30) and was highest for eWBV (r = 0.54), while mean cell volume (MCV) showed strongest inverse correlation with HbA1c (r = −0.47). Conclusion: This study demonstrates that routine FBC parameters, RBC and its indices, offer a practical, low-cost approach to both monitoring and prediction of HbA1c with blood flow issues. This broadens the understanding of blood rheology in diabetes. Future research should move beyond de-identified laboratory datasets and involve patients’ primary data collection to include medication and clinical information that are unavailable in pathology records. Full article

(This article belongs to the Special Issue Latest Advances in Diabetes Research and Practice)

17 pages, 24383 KB

Open AccessArticle

Integrating Proteome-Wide Association Studies and Single-Cell Transcriptomics Identifies GSTT2B as a Causal Mediator and Prioritizes COL4A1 in Diabetic Retinopathy

by Lei Wen, Yuan Liu, Ka Zhang, Aiqin Mao, Li Geng, Fan Yu, Lei Feng and Hao Kan

Int. J. Mol. Sci. 2026, 27(14), 6178; https://doi.org/10.3390/ijms27146178 - 10 Jul 2026

Abstract

Diabetic retinopathy (DR) is a leading cause of vision loss, yet its systemic proteomic mediators remain largely elusive. This study aimed to identify causal plasma proteins, map their cell-type-specific localization in the retina, and experimentally validate their expression under disease-relevant stress. We conducted [...] Read more.

Diabetic retinopathy (DR) is a leading cause of vision loss, yet its systemic proteomic mediators remain largely elusive. This study aimed to identify causal plasma proteins, map their cell-type-specific localization in the retina, and experimentally validate their expression under disease-relevant stress. We conducted a proteome-wide association study (PWAS) integrating UK Biobank plasma pQTL data (N = 53,022) with DR GWAS summary statistics. Causal relationships were inferred utilizing summary-data-based Mendelian randomization (SMR) and Bayesian colocalization. Prioritized candidates were mapped to the Human and Mouse Retina Cell Atlases via single-nucleus RNA sequencing (snRNA-seq). Finally, to substantiate the computational findings, in vitro validation of COL4A1 was performed in ARPE-19 cells cultured under hyperglycemic conditions utilizing quantitative real-time PCR (qPCR) and transcriptomic dataset re-analysis. The PWAS identified 26 proteins significantly associated with DR. Subsequent causal inference prioritized 12 high-confidence candidates, including GSTT2B, COL4A1, PAM, and GALNT3. Notably, GSTT2B emerged as a Tier-1 protective causal protein (Z = −3.609; P_SMR = 1.22 × 10⁻⁴). snRNA-seq mapping revealed that GSTT2B is robustly expressed in Müller glia and the retinal pigment epithelium (RPE), whereas COL4A1 is prominently enriched in vascular compartments. These specific expression signatures exhibited partial conservation across species with notable cell-type specific variations. Crucially, in vitro validation confirmed that COL4A1 mRNA expression is significantly upregulated under high-glucose stress. Furthermore, druggability analysis highlighted actionable targets, identifying GSTT2B as a highly probable causal mediator and COL4A1 as a prioritized candidate for structural intervention. This study provides robust genetic, single-cell, and experimental evidence implicating specific plasma proteins in DR pathogenesis. The identification of GSTT2B-mediated protective pathways and the hyperglycemia-induced upregulation of COL4A1 offer a high-resolution molecular atlas to guide drug repositioning and precision therapeutic strategies. Full article

(This article belongs to the Special Issue New Advances in Protein Analysis in Disease)

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44 pages, 2243 KB

Open AccessReview

A Network Pharmacology Review of Plant-Derived Anticancer Compounds in Lung, Breast, Colorectal and Prostate Cancer

by Anna Merecz-Sadowska, Arkadiusz Sadowski, Karolina Zajdel, Aneta Jęcek, Przemysław Sitarek and Radosław Zajdel

Int. J. Mol. Sci. 2026, 27(14), 6177; https://doi.org/10.3390/ijms27146177 - 10 Jul 2026

Abstract

Lung, breast, colorectal and prostate cancer account for over 41% of global cancer incidence and 39% of mortality, yet durable control of advanced disease remains limited. Plant secondary metabolites are promising multitarget leads, but their polypharmacological mechanisms cannot be captured by single-target approaches, [...] Read more.

Lung, breast, colorectal and prostate cancer account for over 41% of global cancer incidence and 39% of mortality, yet durable control of advanced disease remains limited. Plant secondary metabolites are promising multitarget leads, but their polypharmacological mechanisms cannot be captured by single-target approaches, and the evidence across these four cancers has not been synthesised within a unified framework. This review provides an integrated comparative analysis of network-pharmacology studies of plant-derived anticancer compounds across the four cancers, cataloguing phytochemical profiles, identifying shared and cancer-specific targets, quantifying the concordance between computational predictions and experimental validation, and appraising the translational gap. A systematic search of biomedical databases (2016–2026) identified 101 peer-reviewed studies (40 breast, 33 colorectal, 24 lung, and 14 prostate) combining network pharmacology with experimental validation. AKT1, EGFR, TP53, STAT3, MAPK1/3, CASP3, and HSP90AA1 recurred as cross-cancer hub genes, with the phosphoinositide 3-kinase/AKT and mitogen-activated protein kinase pathways most frequently implicated. Cancer-specific signatures comprised the androgen receptor in prostate, the oestrogen receptor and human epidermal growth factor receptor 2 in breast, β-catenin/Wnt in colorectal, and the epidermal growth factor receptor/RAS axis with epithelial-to-mesenchymal transition effectors in lung cancer. Flavonoids, terpenoids, alkaloids, and polyphenols predominated. The persistent validation gap remains the principal barrier to translation. Full article

(This article belongs to the Special Issue New Insights into Network Pharmacology)

21 pages, 5521 KB

Open AccessArticle

T Cell-Macrophage Interactions Influence Chemotherapeutic Response in Ovarian Cancer Patients

by Sodiq A. Hameed, Walter Kolch and Vadim Zhernovkov

Int. J. Mol. Sci. 2026, 27(14), 6176; https://doi.org/10.3390/ijms27146176 - 10 Jul 2026

Abstract

Tumour development and progression involve complex cell-cell interactions and dynamic co-evolution between cancer cells, immune cells and stromal cells in the tumour microenvironment and this may influence therapeutic resistance. A large proportion of this network relies on direct physical interactions between cells, particularly [...] Read more.

Tumour development and progression involve complex cell-cell interactions and dynamic co-evolution between cancer cells, immune cells and stromal cells in the tumour microenvironment and this may influence therapeutic resistance. A large proportion of this network relies on direct physical interactions between cells, particularly T-cell mediated interactions. Cell-cell communication inference has now become routine in downstream scRNAseq analysis but this mostly fails to capture physical cell-cell interactions due to tissue dissociation. Doublets occur naturally in scRNA-seq and are usually excluded from analysis. However, they may represent directly interacting cells that remain undissociated during library preparation. In the present study, we uncover the physical interaction landscape of the ovarian tumour microenvironment using the scRNAseq datasets from 13 treatment-naive ovarian cancer patients. Focusing on T-cell-Macrophage (T-Mac) interaction doublet, we reveal the modulatory effect of macrophages on T cells and the potential influence of this interaction on therapeutic response. Our findings show that T-Macs from resistant patients are functionally polarized to the M2 phenotype and engage T cells to induce T-cell exhaustion. Whereas, T-Macs from sensitive patients are predominantly of the M1 polarized phenotype, physically engaging T cells that lack exhaustion signatures. We also demonstrate that T cells and macrophages in T-Mac doublet are interacting primarily for the purpose of antigen presentation, with the enrichment of several ligand-receptor pairs involved in TCR-MHC interactions and immune synapse formations. We partly validated some of these findings from a spatial transcriptomics dataset of ovarian cancer patients from a separate cohort. Full article

(This article belongs to the Special Issue Molecular Dialogues in the Tumor Microenvironment: Mechanisms, Methods and Therapeutic Implications)

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12 pages, 4523 KB

Open AccessArticle

Clotrimazole Targets the c-Myc–Survivin Axis to Reduce the Viability of Ovarian Cancer Stem Cells Alone and in Combination with Chemotherapeutic Agents

by Yasufumi Ito, Kazuki Nakamura, Yurika Nakagawa-Saito, Shuhei Suzuki, Yuta Mitobe, Senri Takenouchi, Keita Togashi, Asuka Sugai, Manabu Seino, Tsuyoshi Ohta, Satoru Nagase, Chifumi Kitanaka and Masashi Okada

Int. J. Mol. Sci. 2026, 27(14), 6175; https://doi.org/10.3390/ijms27146175 - 10 Jul 2026

Abstract

Ovarian cancer stem cells (OvCSCs) are one of the main factors contributing to post-treatment recurrence and the poor prognosis of patients with ovarian cancer. Therefore, the development of therapeutic strategies targeting OvCSCs is needed to improve patient survival. We previously reported the high [...] Read more.

Ovarian cancer stem cells (OvCSCs) are one of the main factors contributing to post-treatment recurrence and the poor prognosis of patients with ovarian cancer. Therefore, the development of therapeutic strategies targeting OvCSCs is needed to improve patient survival. We previously reported the high expression of survivin/BIRC5 in OvCSCs and also that targeting pathways regulating survivin expression effectively suppressed OvCSC survival. In the present study, we tested a panel of agents consisting of FDA-approved drugs and compounds under clinical studies for their ability to suppress survivin expression in OvCSCs and identified clotrimazole (CTZ) as a potent candidate. The effects of CTZ on survivin expression were examined by RT-PCR and Western blot analyses. The effects of CTZ alone or in combination with anticancer agents on OvCSCs were evaluated using WST-8, PI uptake, and colony formation assays. CTZ preferentially impaired OvCSC survival by suppressing the c-myc–survivin axis without affecting normal fibroblasts and enhanced the efficacy of platinum- and taxane-based chemotherapeutic agents. These results suggest that CTZ suppresses survivin expression in OvCSCs and enhances the effects of conventional ovarian cancer chemotherapeutic agents, supporting further investigations of this approach as a potential strategy for ovarian cancer treatment. Full article

(This article belongs to the Special Issue Advances in Molecular Biology of Ovarian Cancer)

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1 pages, 152 KB

Open AccessCorrection

Correction: Shait Mohammed et al. Profiling the Effect of Targeting Wild Isocitrate Dehydrogenase 1 (IDH1) on the Cellular Metabolome of Leukemic Cells. Int. J. Mol. Sci. 2022, 23, 6653

by Mohammed Razeeth Shait Mohammed, Faisal Alzahrani, Salman Hosawi, Hani Choudhry and Mohammad Imran Khan

Int. J. Mol. Sci. 2026, 27(14), 6174; https://doi.org/10.3390/ijms27146174 - 10 Jul 2026

Abstract

There were some errors in the original publication [...] Full article

(This article belongs to the Special Issue Molecular Research on Acute Lymphoblastic Leukemia 2.0)

26 pages, 3418 KB

Open AccessArticle

SARS-CoV-2 mRNA Vaccination Induces Reduced T-Cell Apoptosis in Patients with Solid Tumors

by Ana Belda-Marco, Lucía Serrano-García, Andrés Moret, Carlos Fresneda-Portillo, María Victoria Domínguez-Márquez, Ana Comes-Raga, Beatriz Jávega, José-Enrique O’Connor, Juan Carlos Andreu-Ballester, Antonio Llombart-Cussac and María Leonor Fernández-Murga

Int. J. Mol. Sci. 2026, 27(14), 6173; https://doi.org/10.3390/ijms27146173 - 10 Jul 2026

Abstract

Messenger RNA (mRNA) vaccines represent a transformative platform in vaccinology, with applications extending beyond SARS-CoV-2 to other infectious diseases and cancer immunotherapy. However, patients with solid tumors receiving active anticancer treatment were largely underrepresented in pivotal vaccination trials, limiting understanding of vaccine-induced immunity [...] Read more.

Messenger RNA (mRNA) vaccines represent a transformative platform in vaccinology, with applications extending beyond SARS-CoV-2 to other infectious diseases and cancer immunotherapy. However, patients with solid tumors receiving active anticancer treatment were largely underrepresented in pivotal vaccination trials, limiting understanding of vaccine-induced immunity in this population. In this prospective exploratory study, we assessed humoral and cellular immune responses after two doses of SARS-CoV-2 mRNA vaccines in 39 patients with solid tumors undergoing active treatment. Blood samples were collected before vaccination and approximately two months after the second vaccine dose, prior to the next treatment cycle. Anti-spike IgG, neutralizing antibodies, receptor-binding domain (RBD) levels, interleukin-6 (IL-6), hematological parameters, immune cell subsets, T-cell differentiation, and early apoptosis in αβ and γδ T-cell subsets were analyzed. Vaccination induced a robust humoral response, with high post-vaccination anti-spike IgG levels (median 988.69 BAU/mL), 97.44% seropositivity, 96.88% true seroconversion among baseline IgG−/NAb− patients, and strong neutralizing antibody activity (median 85.73%). Hematological parameters and IL-6 levels remained broadly stable, suggesting no detectable increase in systemic inflammation during the study period. Cellular analyses identified a reduction in peripheral CD19+ B-cell frequencies and decreased early apoptosis, particularly in CD8+ T cells and CD3+CD56+ NKT-like cells. Although changes in T-cell frequencies and differentiation profiles were also observed, these findings were attenuated after exclusion of participants with possible prior SARS-CoV-2 exposure and should be interpreted as exploratory. Overall, these results show that patients with solid tumors receiving active treatment can mount robust humoral responses to SARS-CoV-2 mRNA vaccination and suggest measurable post-vaccination changes in lymphocyte dynamics, including reduced early T-cell apoptosis. Full article

(This article belongs to the Special Issue mRNA Vaccines Against Viral Infectious Diseases: Progress and Prospects)

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