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29 pages, 5088 KB  
Hypothesis
Molecular Mechanism for the Selective Presentation of Antigenic Peptides by Major Histocompatibility Complex Class I and Class II Molecules: A Hypothesis
by Bao Ting Zhu
Curr. Issues Mol. Biol. 2025, 47(11), 945; https://doi.org/10.3390/cimb47110945 (registering DOI) - 13 Nov 2025
Abstract
The major histocompatibility complex (MHC) class I and class II molecules (abbreviated as MHC-I and MHC-II, respectively) are specialized in antigen presentation. Unlike the T cell receptors (TCRs), which have great variability, the MHC-I and MHC-II molecules essentially have no variability at all. [...] Read more.
The major histocompatibility complex (MHC) class I and class II molecules (abbreviated as MHC-I and MHC-II, respectively) are specialized in antigen presentation. Unlike the T cell receptors (TCRs), which have great variability, the MHC-I and MHC-II molecules essentially have no variability at all. It is apparent that the MHC-I and MHC-II molecules per se do not have the built-in ability to distinguish the huge populations of self-peptides from antigenic non-self-peptides. At present, the precise mechanism underlying the selective presentation of antigenic peptides by both MHC-I and MHC-II molecules is unclear. For an MHC-II molecule to gain the ability to selectively present antigenic (mostly foreign) peptides, it is hypothesized herein that all naïve CD4+ T cells in the body will release extracellular vesicles (EVs), which are specially designed for antigen-presenting cells (APCs); these EVs contain mRNAs that will be delivered to APCs and translated into an intracellular version of the TCR proteins (iTCRII), which will help select antigenic peptides for presentation by the MHC-II molecules. Similarly, it is hypothesized that the fully activated CD4+ T cells will also release EVs, and these EVs contain different mRNAs for another intracellular version of the TCR proteins (iTCRI), which will help pathogen-infected somatic cells to select the antigenic peptides (mostly from invading pathogens) for presentation by the MHC-I molecules. Understandably, while the iTCRII proteins will work closely with the MHC-II molecules in the exogenous endocytic pathway, the iTCRI proteins will work closely with the MHC-I molecules in the endogenous pathway. In this paper, a few other related hypotheses are also proposed, which jointly offer a plausible mechanistic explanation for the selective presentation of antigenic peptides by both MHC-I and MHC-II molecules. While the proposed hypotheses are partly supported by some experimental observations, it is hoped that these hypotheses will promote discussion and experimental testing of the mechanisms underlying the complex process of selective antigen presentation. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
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17 pages, 1025 KB  
Article
Phytochemicals Prime RIG-I Signaling and Th1-Leaning Responses in Human Monocyte-Derived Dendritic Cells
by Kaho Ohki, Takumi Iwasawa and Kazunori Kato
Nutrients 2025, 17(22), 3539; https://doi.org/10.3390/nu17223539 (registering DOI) - 12 Nov 2025
Abstract
Background/Objective: Dendritic cells (DCs) act as sentinels bridging innate and adaptive immunity, and their functions are strongly influenced by dietary and environmental factors. Phytochemicals such as α-Mangostin (A phytochemical, a xanthone derivative from Garcinia mangostina, known for its anti-inflammatory and antioxidant properties) [...] Read more.
Background/Objective: Dendritic cells (DCs) act as sentinels bridging innate and adaptive immunity, and their functions are strongly influenced by dietary and environmental factors. Phytochemicals such as α-Mangostin (A phytochemical, a xanthone derivative from Garcinia mangostina, known for its anti-inflammatory and antioxidant properties) are widely recognized for their antioxidant and anti-inflammatory effects, but their potential to modulate antiviral pattern recognition pathways remains unclear. This study investigated whether phytochemicals activate retinoic acid–inducible gene I (RIG-I: DDX58, a cytosolic receptor recognizing viral RNA and inducing antiviral responses)–dependent signaling in human monocyte-derived dendritic cells (MoDCs) and affect downstream T cell responses. Methods: MoDCs were generated from peripheral blood and stimulated with selected phytochemicals. RIG-I pathway–related transcripts were quantified by qPCR, and protein expression was assessed by Western blotting, intracellular flow cytometry, and immunofluorescence staining. Functional outcomes were evaluated by co-culturing MoDCs with T cells, followed by phenotypic analysis via flow cytometry and measurement of IFN-γ production by ELISA. Results: α-Mangostin stimulation increased RIG-I (DDX58) mRNA levels in MoDCs and induced time-dependent changes in intracellular protein expression. In co-culture, α-Mangostin–treated MoDCs tended to increase the proportion of OX40+ 4-1BB+ CD4+ T cells, accompanied by a significant elevation of IFN-γ levels in supernatants. Experiments with CpG-ODN (synthetic oligodeoxynucleotides mimicking bacterial DNA that activate TLR9) suggested context-dependent crosstalk between the TLR9 and RIG-I signaling axes. Conclusions: Phytochemicals, exemplified by α-Mangostin, prime antiviral responses in human DCs through upregulation of RIG-I and promote Th1-dependent immune responses. These findings suggest that phytochemicals may represent promising nutritional strategies to enhance antiviral immunity while mitigating excessive inflammation under infectious conditions. Full article
15 pages, 5979 KB  
Article
Assessment and Characterization of Induced Alloantigen-Specific Regulatory T Cells Obtained by the Inhibition of CDK8/19 with the AS2863619 Compound
by Aleksey Bulygin, Marina Fisher, Vasily Kurilin, Saleh Alrhmoun, Roman Perik-Zavodskii, Olga Perik-Zavodskaia, Marina Volynets, Nadezhda Shkaruba, Irina Obleukhova, Julia Khantakova, Elena Golikova, Alexandr Silkov and Sergey Sennikov
Int. J. Mol. Sci. 2025, 26(22), 10957; https://doi.org/10.3390/ijms262210957 (registering DOI) - 12 Nov 2025
Abstract
Foxp3+ regulatory T (Treg) cells play a pivotal role in inducing immune tolerance. The expression of Foxp3 in Treg cells depends on the stability of transcription factors that are directly linked to the molecular interplay between Stat5a and cyclin-dependent kinase CDK8/19. In this [...] Read more.
Foxp3+ regulatory T (Treg) cells play a pivotal role in inducing immune tolerance. The expression of Foxp3 in Treg cells depends on the stability of transcription factors that are directly linked to the molecular interplay between Stat5a and cyclin-dependent kinase CDK8/19. In this study, dendritic cells obtained from C57BL/6 male mice were co-cultured with CD4+ splenocytes obtained from Balb/c male mice to obtain alloantigen-specific CD4+ T cells. Next, these alloantigen-specific CD4+ T cells were cultured with the addition of the CDK8/19 inhibitor AS2863619 compound, TGF-β1, and IL-2 to induce their transdifferentiation into alloantigen-specific CD4+ Foxp3+ Treg cells. The efficacy of this cocktail in promoting the transdifferentiation of activated CD4+ lymphocytes into alloantigen-specific Treg cells (ag-Tregs) was further evaluated using Nanostring gene expression profiling, flow cytometry, ELISA, and in vivo migration assays. The results showed that the addition of the AS2863619 compound along with IL-2 generated effector memory ag-Tregs exhibiting tolerogenic activity, migration properties, and mechanisms for regulating immune homeostasis in the spleen. In conclusion, these findings suggest that the AS2863619-derived effector memory Tregs possess functional properties that support immune tolerance and regulate homeostasis in the spleen, thereby regulating the affinity of naïve T cells to alloantigens, highlighting their potential relevance in transplantology. Full article
(This article belongs to the Section Molecular Biology)
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16 pages, 1667 KB  
Article
3-Gene-TB-SCORE Accuracy for Tuberculosis Disease Diagnosis Is Not Affected by Immune-Mediated Inflammatory Disease Comorbidity
by Elisa Petruccioli, Tonino Alonzi, Assunta Navarra, Anna Maria Gerarda Altera, Gilda Cuzzi, Chiara Farroni, Federica Repele, Gina Gualano, Cecilia S. Lindestam Arlehamn, Fabrizio Palmieri, Andrea Salmi, Valentina Vanini and Delia Goletti
Int. J. Mol. Sci. 2025, 26(22), 10931; https://doi.org/10.3390/ijms262210931 - 12 Nov 2025
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a major global health threat. Approximately one-quarter of the world’s population has an Mtb-specific immune response and are classified as having tuberculosis infection (TBI), with a lifelong 5–10% risk of developing TB disease. This risk [...] Read more.
Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a major global health threat. Approximately one-quarter of the world’s population has an Mtb-specific immune response and are classified as having tuberculosis infection (TBI), with a lifelong 5–10% risk of developing TB disease. This risk is elevated in individuals with immune-mediated inflammatory diseases (IMID) undergoing immunosuppressive therapies. To evaluate the diagnostic accuracy of the 3-gene TB-SCORE for TB disease in individuals within the TB spectrum, including those with TBI-IMID in a low TB endemic country, we prospectively enrolled 104 individuals with TB, TBI, TBI-IMID, and healthy donors. The 3-gene TB-SCORE and Mtb-specific response were evaluated and correlated with the participant’s clinical status. Patients with TB disease showed a significantly lower TB-SCORE compared to other cohorts. ROC analysis showed moderate diagnostic accuracy for TB disease (AUC 0.70–0.71). TB-SCORE was unaffected by IMID status or timing of Mtb exposure. Mtb-specific CD4+ T cells had no correlation to TB-SCORE. This is the first evaluation of TB-SCORE as a diagnostic tool for TB disease in a low-endemic setting. While further validation is needed, our findings support its potential as a biomarker for TB disease, even in complex clinical settings involving IMID. Full article
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22 pages, 2750 KB  
Article
T Cell Exhaustion in the Cervical Cancer Tumor Microenvironment: PD-1 Overexpression and Co-Expression with TIGIT, Tim-3, LAG-3, and NKG2A
by Nadia Tatiana García-Barrientos, Fabiola Solorzano-Ibarra, Ksenia Klimov-Kravtchenko, Jose Manuel Rojas-Diaz, Marcela Sofia Guitron-Aviña, Francisco Javier Ceja-Flores, Jose Alfonso Cruz-Ramos, Pablo Cesar Ortiz-Lazareno, Felipe de Jesús Bustos-Rodriguez, Juan Carlos Vazquez-Limon, Miriam Ruth Bueno-Topete, Martha Cecilia Tellez-Bañuelos, Jesse Haramati and Susana del Toro-Arreola
Cancers 2025, 17(22), 3627; https://doi.org/10.3390/cancers17223627 - 11 Nov 2025
Abstract
Objective: T cell exhaustion is a major mechanism of immune evasion in cancer, characterized by the sustained expression of multiple inhibitory receptors. This study aimed to evaluate the expression of immune checkpoints in peripheral and tumor-infiltrating CD8+ T cells from cervical [...] Read more.
Objective: T cell exhaustion is a major mechanism of immune evasion in cancer, characterized by the sustained expression of multiple inhibitory receptors. This study aimed to evaluate the expression of immune checkpoints in peripheral and tumor-infiltrating CD8+ T cells from cervical cancer patients. Methods: We enrolled 104 participants: 37 treatment-naïve patients, 36 treated patients, and 31 age-matched healthy donors. Peripheral blood mononuclear cells (PBMCs) were isolated from all participants. Ten cervical biopsies were collected for tumor-infiltrating lymphocyte (TIL) isolation and paraffin fixation. Immune checkpoint expression was analyzed by multiparametric flow cytometry and immunohistochemistry. Results: In peripheral CD8+ T cells, we found a significant upregulation of exhaustion-associated markers PD-1, TIGIT, Tim-3, and LAG-3. In the tumor infiltrating lymphocytes, these same molecules, with the addition of NKG2A, were notably upregulated further. While BTLA and NKG2A showed no systemic changes, NKG2A increased in TILs and BTLA decreased in TILs. The co-expression of PD-1 with TIGIT, Tim-3, LAG-3, and NKG2A was notably enriched between 2- and 6-fold in TILs compared with patient PBMCs. The tumor microenvironment was highly immunosuppressive, characterized by enrichment with PD-1, PD-L1, and TIGIT; TIGIT was notably upregulated in locally advanced versus early-stage tumors. Conclusions: Our findings highlight the strongly immunosuppressive environment of cervical tumors in treatment-naïve patients and the presence of elevated inhibitory checkpoint expression in peripheral blood of both pre- and post-treatment patients. These results underscore the importance of investigating immune regulation within the tumor site itself and suggest that immune checkpoint co-expression may serve as a biomarker of T cell exhaustion and therapeutic resistance. Understanding how treatment alters these pathways could guide rational combination immunotherapies to restore CD8+ T cell function in cervical cancer. Full article
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21 pages, 5883 KB  
Article
Phase Separation Competent TIA1 Couples Glycolytic Shutdown to CD8+ T-Cell Activation and Shapes the Efficacy of Intravesical BCG in Bladder Cancer
by Wenwen Zhang, Kailiang Zhou, Pinru Chen, Xuanshuang Du and Min Liu
Biology 2025, 14(11), 1576; https://doi.org/10.3390/biology14111576 - 11 Nov 2025
Abstract
Metabolic immune evasion is a major factor limiting the long-term efficacy of intravesical Bacillus Calmette–Guérin (BCG) therapy in non-muscle-invasive bladder cancer (NMIBC). TIA1 is a stress granule RNA-binding protein with liquid–liquid phase separation (LLPS) capacity. Its role in tumor metabolism and immunotherapy response [...] Read more.
Metabolic immune evasion is a major factor limiting the long-term efficacy of intravesical Bacillus Calmette–Guérin (BCG) therapy in non-muscle-invasive bladder cancer (NMIBC). TIA1 is a stress granule RNA-binding protein with liquid–liquid phase separation (LLPS) capacity. Its role in tumor metabolism and immunotherapy response has been unclear. Here, we demonstrated that high TIA1 expression was independently associated with favorable survival across multiple cohorts. Full-length TIA1 formed cytoplasmic condensates, repressed LDHA/PKM2/HK2, reduced lactate, and lowered extracellular acidification. A condensate-defective ΔLCD (deletion of the low-complexity domain) mutant was inactive. TIA1 showed physical association with these glycolytic mRNAs in human cells, consistent with mRNA-linked control. Condensate-competent TIA1 promoted CD8+ T-cell proliferation, increased CD69 and Granzyme-B, and reduced PD-1 in co-culture. TIMER (Tumor Immune Estimation Resource) and spatial-omics supported co-localization with tumoral CD8A. BCG induced this metabolic–immune signature in cell lines, murine models, and patient explants, but the effects were abolished by TIA1 knock-down. Conversely, TIA1 over-expression alone limited tumor growth and recapitulated BCG-mediated glycolytic restraint and T-cell activation. Together, these results support an LLPS-linked, mRNA-associated regulation of tumor glycolysis. BCG-driven glycolytic suppression and CD8+ T cell activation track with the condensate-forming capacity of TIA1. TIA1 emerges as a prognostic biomarker and a potential therapeutic axis to improve intravesical immunotherapy in NMIBC. Full article
(This article belongs to the Section Cancer Biology)
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33 pages, 29073 KB  
Article
Anti-Tumoral Treatment with Thioredoxin Reductase 1 Inhibitor Auranofin Fosters Regulatory T Cell and B16F10 Expansion in Mice
by Michael Y. Bonner, Tamas Vancsik, Ana Oliveira-Coelho, Pierre Sabatier, Christian M. Beusch, Kejsi Zeqiraj, Carolin Svensson, Roman A. Zubarev, Elias S. J. Arnér and Rikard Holmdahl
Antioxidants 2025, 14(11), 1351; https://doi.org/10.3390/antiox14111351 - 11 Nov 2025
Abstract
Auranofin, an FDA-approved antirheumatic drug and thioredoxin reductase 1 (TXNRD1) inhibitor, has demonstrated anti-tumoral properties, but its immunological effects are not well characterized. Here, we report that auranofin unexpectedly promotes regulatory T cell (Treg) expansion. In a B16F10 melanoma model, auranofin treatment increased [...] Read more.
Auranofin, an FDA-approved antirheumatic drug and thioredoxin reductase 1 (TXNRD1) inhibitor, has demonstrated anti-tumoral properties, but its immunological effects are not well characterized. Here, we report that auranofin unexpectedly promotes regulatory T cell (Treg) expansion. In a B16F10 melanoma model, auranofin treatment increased lung tumor coverage, IL-10 serum levels, and FOXP3+CD44+CD4+ T cell frequencies. It also altered the proportion of antigen-presenting cells (APCs), increasing B cells and reducing dendritic cells. To test whether Treg expansion occurs independently of tumor antigens, we stimulated T cells ex vivo in lymph node cultures from naïve mice using anti-CD3/CD28, with or without auranofin. Auranofin increased Treg frequency in these cultures, as well as in treated human PBMCs. Similar effects were observed with the TXNRD1 inhibitor TRi-1, suggesting a ROS-dependent mechanism. Using mice with conditional expression of neutrophil cytosolic factor 1 (NCF1), we found that both TXNRD1 inhibition and APC-specific NCF1-NOX2-ROS expression enhanced tumor burden and Treg expansion. Alternatively, sorted T cells from mice harboring conditional TXNRD1 knockouts showed reduced FOXP3 and GITR expression in the naïve state and reduced tumor burden when challenged with B16F10. These data suggest TXNRD1 inhibitors likely drive Treg expansion by elevating ROS levels in APCs during T cell priming and less by intrinsic Treg TXNRD1 blockade. Our findings reveal a paradoxical immunosuppressive effect of TXNRD1 inhibitors that may contribute to their limited efficacy in immunocompetent cancer models. This work provides mechanistic insight and underscores the need to consider Treg-mediated immune suppression when designing TXNRD1-targeted therapies. Full article
(This article belongs to the Section Health Outcomes of Antioxidants and Oxidative Stress)
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18 pages, 5244 KB  
Article
Injectable Matrix Metalloproteinase-Responsive Polypeptide Hydrogels as Drug Depots for Antitumor Chemo-Immunotherapy
by Shuang Liang, Tianran Wang, Junfeng Ding, Jiaxuan Yang, Chaoliang He and Yan Rong
Pharmaceutics 2025, 17(11), 1453; https://doi.org/10.3390/pharmaceutics17111453 - 11 Nov 2025
Abstract
Background: The potential of injectable hydrogels as drug depots lies in their ability to achieve local and sustained co-delivery of chemotherapeutic drugs and immunostimulants for combined tumor therapy. Method: In this study, we devised a localized chemo-immunotherapeutic strategy by co-loading the chemotherapeutic drug, [...] Read more.
Background: The potential of injectable hydrogels as drug depots lies in their ability to achieve local and sustained co-delivery of chemotherapeutic drugs and immunostimulants for combined tumor therapy. Method: In this study, we devised a localized chemo-immunotherapeutic strategy by co-loading the chemotherapeutic drug, oxaliplatin (OXA), and the immune-checkpoint blockade (ICB) antibody, anti-programmed cell death protein ligand 1 (anti-PD-L1), into a matrix metalloproteinase (MMP)-responsive injectable poly(L-glutamic acid) hydrogel (MMP-gel). Results: The in situ gelation of hydrogels enables local retention of OXA and model antibody IgG, as well as MMP-triggered sustained release. Meanwhile, the OXA-loaded MMP-gel caused the immunogenic cell death (ICD) of tumor cells. When administered intratumorally in mice carrying B16F10 melanoma, the MMP-gel co-loaded with OXA and anti-PD-L1 (OXA&anti-PD-L1@MMP-gel) demonstrated superior tumor suppression efficacy and prolonged the survival time of the animals with low systemic toxicity. Meanwhile, the OXA&anti-PD-L1@MMP-gel induced an increase in CD8+ T cells and M1 macrophages within tumors, and a decrease in Treg cells and M2 macrophages, demonstrating that the drug-loaded system enhanced the antitumor immune response. Moreover, the OXA&anti-PD-L1@MMP-gel effectively inhibited the growth of distal tumors in a bilateral-tumor experiment. Conclusions: Consequently, the responsive hydrogel-based chemo-immunotherapy holds potential in tumor treatment. Full article
(This article belongs to the Section Drug Targeting and Design)
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17 pages, 1913 KB  
Article
A Machine Learning Framework for Cancer Prognostics: Integrating Temporal and Immune Gene Dynamics via ARIMA-CNN
by Rui-Bin Lin, Linlin Zhou, Yu-Chun Lin, Yu Yu, Hung-Chih Yang and Chen-Wei Yu
Biomedicines 2025, 13(11), 2751; https://doi.org/10.3390/biomedicines13112751 - 11 Nov 2025
Abstract
Background: Hepatocellular carcinoma remains a global health challenge with high mortality rates. The tumor immune microenvironment significantly impacts disease progression and survival. However, traditional analyses predominantly focus on single immune genes, overlooking the critical interplay among multiple immune gene signatures. Our study explores [...] Read more.
Background: Hepatocellular carcinoma remains a global health challenge with high mortality rates. The tumor immune microenvironment significantly impacts disease progression and survival. However, traditional analyses predominantly focus on single immune genes, overlooking the critical interplay among multiple immune gene signatures. Our study explores the prognostic significance of chemokine (C-C motif) ligand 5 (CCL5) expression and associated immune genes through an innovative combination of Autoregressive Integrated Moving Average (ARIMA) and Convolutional Neural Network (CNN) models. Methods: A time series dataset of CCL5 expression, comprising 230 liver cancer patients, was analyzed using an ARIMA model to capture its temporal dynamics. The residuals from the ARIMA model, combined with immune gene expression data, were utilized as input features for a CNN to predict survival outcomes. Survival analyses were conducted using the Cox proportional hazards model and Kaplan–Meier curves. Furthermore, the ARIMA-CNN framework’s results were systematically compared with traditional median-based stratification methods, establishing a benchmark for evaluating model efficacy and highlighting the enhanced predictive power of the proposed integrative approach. Results: CNN-extracted features demonstrated superior prognostic capability compared to traditional median-split analyses of single-gene datasets. Features derived from CD8+ T cells and effector T cells achieved a hazard ratio (HR) of 0.7324 (p = 0.0008) with a statistically significant log-rank p-value (0.0131), highlighting their critical role in anti-tumor immunity. Hierarchical clustering of immune genes further identified distinct survival associations. Notably, a cluster comprising B cells, Th2 cells, T cells, and NK cells demonstrated a moderate protective effect (HR: 0.8714, p = 0.1093) with a significant log-rank p-value (0.0233). Conversely, granulocytes, Tregs, macrophages, and myeloid-derived suppressor cells showed no significant survival association, emphasizing the complex regulatory landscape within the tumor immune microenvironment. Conclusions: Our study provides the first ARIMA-CNN framework for modeling gene expression and survival analysis, marking a significant innovation in integrating temporal dynamics and machine learning for biological data interpretation. This model offers deeper insights into the tumor immune microenvironment and underscores the potential for advancing precision immunotherapy strategies and identifying novel biomarkers, contributing significantly to innovative cancer management solutions. Full article
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16 pages, 9263 KB  
Article
Immunohistochemical Characterization and CT-Derived Volume of Epicardial Adipose Tissue in Patients with Coronary Artery Disease
by Matija Furtula, Igor Zivkovic, Slobodan Micovic, Zoran Tabakovic, Gorica Vidovic, Zelimir Antonic, Jelica Vukmirovic, David Savic, Milovan Bojic, Branko Beleslin, Milan Dobric and Jelena Rakocevic
Cells 2025, 14(22), 1760; https://doi.org/10.3390/cells14221760 - 11 Nov 2025
Abstract
Background: Epicardial adipose tissue (EAT) is a visceral fat depot surrounding the myocardium. It contributes to coronary artery disease (CAD) through local inflammation, while its metabolic activity, including the expression of uncoupling protein-1 (UCP-1) and incretin receptors (GLP-1R, GIPR), may exert protective effects. [...] Read more.
Background: Epicardial adipose tissue (EAT) is a visceral fat depot surrounding the myocardium. It contributes to coronary artery disease (CAD) through local inflammation, while its metabolic activity, including the expression of uncoupling protein-1 (UCP-1) and incretin receptors (GLP-1R, GIPR), may exert protective effects. The relationship between EAT immunohistochemical features and imaging-derived volume remains unclear. Methods: We prospectively studied 50 patients undergoing cardiac surgery: 25 with CAD undergoing coronary artery bypass grafting and 25 without CAD undergoing valve replacement. EAT samples were immunohistochemically stained for CD3, CD68, MPO, UCP-1, GLP-1R, and GIPR. Preoperative CT was used to quantify EAT volume. Results: Patients with CAD more frequently had higher CD3 immunopositivity compared to the control group (84.0 vs. 58.3%, p = 0.047), with no difference in MPO and CD68 immunoexpression. UCP-1 expression was elevated in CAD patients (p = 0.004), whereas GLP-1R and GIPR immunopositivity were similar. EAT volume did not differ between CAD and non-CAD patients (102.87 cm3 vs. 99.38 cm3, p = 0.964) but correlated modestly with BMI (rs = 0.325, p = 0.021). UCP-1 and GLP-1R immunopositivity, as well as larger LVEDD (left ventricular end-diastolic diameter), were positively associated with greater EAT volume. Conclusions: EAT in CAD exhibits increased T-cell infiltration and elevated UCP-1 expression, indicating an inflammatory yet metabolically active profile. Larger EAT volume was associated with UCP-1 and GLP-1R expression, underscoring the immunometabolic role of EAT in CAD. Full article
(This article belongs to the Special Issue Ischemic Heart Disease: From Cellular Level to Clinical Approaches)
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13 pages, 2829 KB  
Article
Gene Expression Profiling Provides an Improved Characterization of CD79B-Mutated Diffuse Large B-Cell Lymphomas
by Luis Grossmann, Wolfgang Jagla, Marcus Bettstetter, Simone Bertz, Stephan Schwarz-Furlan, Thomas Richter, Tobias Dechow, Thomas Decker, Martin Dreyling, Karl Sotlar, Harald Bartsch, Arndt Hartmann, Julius Honecker and Andreas Gaumann
J. Pers. Med. 2025, 15(11), 548; https://doi.org/10.3390/jpm15110548 - 10 Nov 2025
Abstract
Background and Objectives: Diffuse large B-cell lymphomas (DLBCLs) are heterogeneous neoplasms. CD79B and MYD88 mutations are associated with the activated B-cell-like (ABC) subtype of DLBCL and often co-occur and lead to constitutive activation of the NF-κB pathway. Several different genetic classifications to [...] Read more.
Background and Objectives: Diffuse large B-cell lymphomas (DLBCLs) are heterogeneous neoplasms. CD79B and MYD88 mutations are associated with the activated B-cell-like (ABC) subtype of DLBCL and often co-occur and lead to constitutive activation of the NF-κB pathway. Several different genetic classifications to date have recognized CD79B- and MYD88-mutated DLBCLs as a unique subtype with poor response to therapy and unfavorable survival. However, little is known about gene expression in DLBCLs with mutated CD79B (and MYD88) in comparison to their wild type counterparts. The objective of this study was to compare the gene expression in DLBCLs according to their CD79B mutational status. Methods: A total of 48 primary, treatment-naïve DLBCLs (CD79B-mutated: 35%/n = 17, CD79B-wild type: 65%/n = 31) were investigated using RNA expression profiling (770 genes), followed by immunohistochemical analysis of the up-regulated genes and survival analysis. Results: The gene expression analysis revealed that downstream of CD79B CARD11 and the NF-κB targets NFKBIZ, IL10, IL12A, PIM1 and BCL2A1 were up-regulated in CD79B-mutated DLBCLs. The strongest up-regulation was detected for ARNT2 and WNT11. Other up-regulated genes included the apoptosis-related BID and granzyme B, as well as genes of cell cycle regulation such as RUNX1, RUNX1T1 and RASGRF1. Up-regulation was also found for IL7, STAT3, MLLT4, CD14 and the HSP90B1 subunit. TP53 mutation showed an association with poorer overall survival in a secondary analysis, consistent with prior reports, while survival by CD79B/MYD88 mutation status and the differentially expressed genes showed no significant differences in this cohort. Conclusions: In conclusion, the current study identified novel up-regulated genes in CD79B-mutated DLBCLs beyond NF-κB pathway signaling, which may contribute to a better definition of potential therapeutic targets and further improves the characterization of this distinct and aggressive DLBCL subgroup. Full article
(This article belongs to the Special Issue Molecular Pathology in Cancer Research)
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18 pages, 25745 KB  
Article
Clinicopathological Implications of Maspin, CD8, and PD-L1 Expression in Liposarcomas
by Andrei-Ionuț Patrichi, Ioan Jung and Simona Gurzu
Curr. Issues Mol. Biol. 2025, 47(11), 935; https://doi.org/10.3390/cimb47110935 - 10 Nov 2025
Abstract
Liposarcomas, the most common subtype of soft tissue sarcomas, show variable biological behavior and therapeutic response. Programmed death-ligand 1 (PD-L1) and cytotoxic T lymphocyte marker CD8 have been implicated in tumor immune evasion and prognosis in various malignancies, while Maspin, a tumor suppressor, [...] Read more.
Liposarcomas, the most common subtype of soft tissue sarcomas, show variable biological behavior and therapeutic response. Programmed death-ligand 1 (PD-L1) and cytotoxic T lymphocyte marker CD8 have been implicated in tumor immune evasion and prognosis in various malignancies, while Maspin, a tumor suppressor, has shown a negative prognostic impact in sarcomas. This study aimed to investigate the clinicopathological significance of PD-L1, CD8, and Maspin expression in liposarcomas. A retrospective analysis of 42 liposarcoma cases diagnosed between 2016 and 2023 was conducted. Immunohistochemical staining for PD-L1 (using DAKO 22C3 and 28-8 clones), CD8, and Maspin was performed. PD-L1 expression was assessed using the tumor proportion score (TPS) and tumor cell score (TC). CD8 expression was evaluated using an H-score, and Maspin positivity was assessed based on subcellular localization. Correlations with clinicopathological parameters were statistically analyzed using chi-squared and Fisher’s exact tests. Most liposarcomas exhibited low PD-L1 expression (<10%), but increased PD-L1 levels correlated with poor differentiation (G3), higher CD8 infiltration (H-score > 10%), and cytoplasmic Maspin positivity. Statistically significant associations were found between high PD-L1 expression and high CD8 infiltration (p = 0.007 for 22C3; p = 0.0331 for 28-8) and between PD-L1 positivity and Maspin expression (p = 0.003 for 22C3; p = 0.0113 for 28-8). CD8 infiltration was generally low across cases, and PD-L1 expression in inflammatory cells was noted predominantly in tumors with higher PD-L1 TPS/TC scores. High PD-L1 expression in liposarcomas is associated with poor tumor differentiation, increased CD8 infiltration, and Maspin positivity, suggesting an immune-evasive phenotype. Despite low overall expression rates, PD-L1 could serve as a prognostic biomarker and a potential target for immunotherapeutic strategies in liposarcomas. Further studies are necessary to standardize PD-L1 assessment and explore effective immunotherapy approaches for these tumors. Full article
(This article belongs to the Special Issue Future Challenges of Targeted Therapy of Cancers: 2nd Edition)
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20 pages, 4334 KB  
Article
Impact of Wuchereria bancrofti Infection on Cervical Mucosal Immunity and Human Papillomavirus Prevalence in Women from Lindi and Mbeya Regions, Tanzania
by Maureen Mosoba, Thomas F. Marandu, Lucas Maganga, Jacklina Mhidze, Anifrid Mahenge, Jonathan Mnkai, Agatha Urio, Nhamo Chiwarengo, Liset Torres, Winfrida John, Abdallah Ngenya, Akili Kalinga, Upendo J. Mwingira, Manuel Ritter, Achim Hoerauf, Sacha Horn, Christof Geldmacher, Michael Hoelscher, Mkunde Chachage and Inge Kroidl
Trop. Med. Infect. Dis. 2025, 10(11), 317; https://doi.org/10.3390/tropicalmed10110317 - 10 Nov 2025
Abstract
We previously described an increased incidence of HIV among individuals infected with Wuchereria bancrofti (WB). However, no host, parasite, or viral factors were reported as directly associated with the increase in HIV incidence in this group. To investigate this, we compared T cell [...] Read more.
We previously described an increased incidence of HIV among individuals infected with Wuchereria bancrofti (WB). However, no host, parasite, or viral factors were reported as directly associated with the increase in HIV incidence in this group. To investigate this, we compared T cell phenotypes between WB+ and WB− women. Flow cytometry analysis of activation and differentiation markers on CD4 T cells, as well as HIV entry receptor CCR5 was performed on cervical and peripheral blood samples from 54 women living without HIV (WLWoH). Additionally, HPV testing was performed on their specimens and for 13 WLWH. WB infection was associated with a significantly increased frequency of CD3+γδ2+ T cells in the cervical mucosa (median 4.0% vs. 1.4%, p = 0.012). Contrary to our expectations, we found lower frequencies of CCR5 on total, memory and activated memory CD4 T cells in the WB+ group. However, differences diminished after accounting for age and site of recruitment. WB and HIV infections were associated with an increased likelihood of high-risk human papillomavirus (HR HPV) positivity. (WB status: odds ratio (OR) 4.1, p = 0.066; HIV status: OR 5.5, p = 0.068). Our findings suggest immunological mechanisms by which WB increases the risk for other infections, e.g., HIV and HR HPV, albeit independent of the CCR5 receptor. Full article
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23 pages, 4080 KB  
Article
Contrasting Impacts of Targeted Disruption of the Cancer Stem Cell Marker CD133 and Its Epigenetic Regulator TRIM28 in Colorectal Cancer Cells
by Irina V. Kholodenko, Aleena A. Saidova, Daria M. Potashnikova, Viktoriia A. Arzumanian, Daniil D. Romashin, Anna V. Tvorogova, Ekaterina V. Poverennaya, Konstantin N. Yarygin and Yan S. Kim
Int. J. Mol. Sci. 2025, 26(22), 10862; https://doi.org/10.3390/ijms262210862 - 9 Nov 2025
Viewed by 172
Abstract
Cancer stem cells (CSCs) play a crucial role in colorectal cancer by sustaining intratumoral heterogeneity, therapeutic resistance, and metastatic potential. CD133 (PROM1) is among the most frequently used surface markers for CSC identification, whereas TRIM28, a versatile epigenetic regulator, has been implicated in [...] Read more.
Cancer stem cells (CSCs) play a crucial role in colorectal cancer by sustaining intratumoral heterogeneity, therapeutic resistance, and metastatic potential. CD133 (PROM1) is among the most frequently used surface markers for CSC identification, whereas TRIM28, a versatile epigenetic regulator, has been implicated in controlling CD133 expression and stem-like features. In this study, we performed a detailed molecular and functional analysis of Caco2 colorectal cancer cell clones with individual knockouts of CD133 or TRIM28. Elimination of CD133 neither altered global gene expression, as confirmed by transcriptome profiling, nor affected key cellular properties. In contrast, loss of TRIM28 led to a marked reduction in CD133 protein abundance and induced extensive molecular and phenotypic remodeling. TRIM28 knockout was associated with broad transcriptomic changes involving more than 500 differentially expressed genes, decreased proliferative activity monitored by time-lapse imaging, and reduced sensitivity to paclitaxel, cisplatin, and curcumin. Furthermore, immune evasion molecules CD24 and CD47 (“don’t eat me” signals) were strongly upregulated in TRIM28-deficient cells, consistently confirmed by both RNA-Seq and flow cytometry analyses. At the same time, imaging flow cytometry and mitochondrial activity assays indicated that these effects were not due to major shifts in mitotic index or bioenergetic status. Altogether, our results demonstrate that TRIM28, rather than CD133, functions as a central regulator of CSC-associated phenotypes in colorectal cancer. These findings highlight the importance of epigenetic context in CSC biology and may inform the development of more effective therapeutic strategies. Full article
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21 pages, 2897 KB  
Article
IgG Idiotype Diversity Shapes Cytokine Profiles and Autoantibody Targets in HTLV-1 Clinical Outcomes
by Isabela Siuffi Bergamasco, Nicolle Rakanidis Machado, Lais Alves do Nascimento, Beatriz Oliveira Fagundes, Fabio da Ressureição Sgnotto, Jorge Casseb, Sabri Saeed Sanabani, Luiz Henrique Da Silva Nali, Denis Miyashiro, José Antonio Sanches and Jefferson Russo Victor
Int. J. Mol. Sci. 2025, 26(22), 10858; https://doi.org/10.3390/ijms262210858 - 8 Nov 2025
Viewed by 121
Abstract
Human T-lymphotropic virus type 1 (HTLV-1) infection is associated with a spectrum of clinical outcomes, ranging from lifelong asymptomatic carriage to severe conditions such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and adult T-cell leukemia/lymphoma (ATLL). Although antibody responses are known to shape immune [...] Read more.
Human T-lymphotropic virus type 1 (HTLV-1) infection is associated with a spectrum of clinical outcomes, ranging from lifelong asymptomatic carriage to severe conditions such as HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP) and adult T-cell leukemia/lymphoma (ATLL). Although antibody responses are known to shape immune regulation, the functional relevance of IgG idiotype repertoires in HTLV-1 pathogenesis remains poorly understood. This study investigated the immunomodulatory effects of IgG from individuals with distinct HTLV-1 clinical outcomes. IgG was purified from pooled serum samples of asymptomatic carriers (ACs), HAM/TSP, and ATLL patients and used to stimulate peripheral blood mononuclear cells (PBMCs) from healthy donors. Cytokine production in CD4+, CD8+, and γδ T cells was assessed by flow cytometry. Additionally, proteome-wide IgG reactivity was evaluated using a human protein microarray encompassing over 21,000 proteins, and bioinformatic analyses were conducted to identify protein–protein interaction networks and tissue-specific autoreactivity. HAM/TSP-derived IgG selectively enhanced IFN-γ production in all T-cell subsets and suppressed IL-4 in CD4+ T cells. ATLL-derived IgG induced IL-9 and IL-13 production in CD4+ T cells, and both HAM/TSP and ATLL IgG elevated IL-13 levels in CD8+ T cells. Microarray data revealed distinct autoreactive IgG profiles across clinical groups, targeting immune-related proteins, apoptotic regulators, and proteins expressed in T cells, monocytes, and non-immune tissues such as brain and testis. Notably, no functional or structural clustering was observed in protein–protein interaction networks, suggesting these reactivities reflect complex, idiotype-specific immune alterations rather than compensatory responses. The present findings suggest that HTLV-1 infection may be associated with the development of distinct IgG repertoires that potentially modulate cytokine responses and exhibit broad reactivity toward human proteins. Such patterns could contribute to immune dysregulation and may partially explain the divergent clinical trajectories observed in HAM/TSP and ATLL. Further investigations are warranted to validate these observations at the individual level and to clarify their mechanistic relevance in disease progression. Full article
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