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17 pages, 1890 KB  
Article
Genetic Determinants of T-Cell Homeostasis in Critical Illness: An Exploratory Analysis of Immune Gene Variants and TREC Dynamics
by Alesya S. Gracheva, Darya A. Kashatnikova, Maryam B. Khadzhieva, Vladislav E. Zakharchenko, Tatyana N. Krylova, Artem N. Kuzovlev and Lyubov E. Salnikova
J. Pers. Med. 2026, 16(6), 278; https://doi.org/10.3390/jpm16060278 (registering DOI) - 23 May 2026
Abstract
Background: Chronic critical illness (CCI) following acute brain injury involves persistent immune dysfunction, yet its genetic determinants remain unclear. We investigated whether the rate of T-cell receptor excision circle (TREC) depletion—a proposed marker of adaptive homeostatic resilience—is associated with the burden of rare [...] Read more.
Background: Chronic critical illness (CCI) following acute brain injury involves persistent immune dysfunction, yet its genetic determinants remain unclear. We investigated whether the rate of T-cell receptor excision circle (TREC) depletion—a proposed marker of adaptive homeostatic resilience—is associated with the burden of rare damaging genetic variants. Methods: Whole-exome sequencing (WES) was performed on a cohort of 84 patients (64 with traumatic brain injury, 20 with stroke). In a longitudinal sub-cohort (n = 27), patients were stratified into quartiles (Q1–Q4) based on the slope of their TREC trajectories. ‘Qualifying variants’ (QVs) were defined using strict rarity (gnomAD allele frequency ≤ 0.001) and pathogenicity criteria. Gene-level burden (collapsing) analysis and permutation-based statistical testing (10,000 iterations) were employed to evaluate genetic enrichment in the extreme quartiles. Results: While baseline TREC levels were strictly age dependent (p < 0.0001), the rate of change (TREC slope) was age independent. Rapid TREC decline (Q1) correlated with significantly higher final SOFA scores (p = 0.001) and neutrophil-to-lymphocyte ratios (p = 0.020). Rare variant burden analysis revealed that Q1 patients were significantly more likely to harbor QVs in immune-related genes compared to the Q4 recovery group (odds ratio = 8.25; permutation p = 0.016). Patients with rapid decline were enriched for QVs in putative core “housekeeping” pathways essential for T-cell maintenance and DNA repair (e.g., ERCC3, FANCM), whereas variants in recovering patients were restricted to peripheral effector or structural pathways. Conclusions: Our findings suggest, as a conceptual framework, that an individual’s ability to maintain T-cell homeostasis during critical illness is influenced by their underlying genetic buffering capacity. We propose a hypothetical “two-hit” framework where physiological stress unmasks pre-existing fragilities in core homeostatic pathways—potentially reflecting a state of functional haploinsufficiency under extreme proliferative demand—leading to accelerated immune exhaustion. These results position the TREC slope as a dynamic, age-independent biomarker of genomic resilience in the ICU. All findings are exploratory and hypothesis generating. Full article
(This article belongs to the Special Issue Personalized Medicine in the ICU—2nd Edition)
34 pages, 3994 KB  
Review
Immunotherapy Landscape of Advanced Clear Cell Renal Cell Carcinoma: Targeting the Cancer-Immunity Cycle and Future Perspectives
by Xuanyu Jin, Junkai Yang, Daojia Miao, Wei Xiong and Zhiyong Xiong
Biomedicines 2026, 14(6), 1181; https://doi.org/10.3390/biomedicines14061181 - 22 May 2026
Abstract
Renal cell carcinoma (RCC) is a predominant malignancy of the urinary system, with clear cell renal cell carcinoma (ccRCC) representing 75–85% of clinical cases. Since the early stages are often asymptomatic, nearly 30% of patients present with metastases at diagnosis, which significantly complicates [...] Read more.
Renal cell carcinoma (RCC) is a predominant malignancy of the urinary system, with clear cell renal cell carcinoma (ccRCC) representing 75–85% of clinical cases. Since the early stages are often asymptomatic, nearly 30% of patients present with metastases at diagnosis, which significantly complicates the prognosis. The diverse mechanisms and clinical indications of current strategies, despite recent breakthroughs in immunotherapy, pose a major challenge for systematic application. This review employs the cancer-immunity cycle as a framework to evaluate four critical steps: antigen presentation, T-cell activation, reversal of exhaustion, and immune evasion in the tumor microenvironment. We introduce the major immunotherapy strategies in RCC in this cycle and summarize their clinical position. Combining immune checkpoint inhibitors (ICIs) with tyrosine kinase inhibitors (TKI) has redefined the first-line standard for advanced RCC by addressing both T-cell infiltration barriers and functional suppression. Standalone approaches such as tumor vaccines and cytokines in contrast have shown limited efficacy in advanced settings. In this context, we further propose emerging research directions, such as individualized immunotherapy and multi-target blockade, and point out the relevant biomarkers, offering an integrated perspective of the RCC immune landscape and providing insights for both clinical practice and future research. Full article
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24 pages, 1275 KB  
Review
Two Faces of NFAT Transcription Factors in Lymphocytes—A Personal Account
by Edgar Serfling
Biomolecules 2026, 16(6), 757; https://doi.org/10.3390/biom16060757 - 22 May 2026
Viewed by 48
Abstract
The two NFAT transcription factors NFATc1 and NFATc2 are the most prominent Ca++-dependent TFs in the nuclei of activated peripheral lymphocytes. They control the activity of thousands of genes during immune responses. Although their structure and function show numerous things in [...] Read more.
The two NFAT transcription factors NFATc1 and NFATc2 are the most prominent Ca++-dependent TFs in the nuclei of activated peripheral lymphocytes. They control the activity of thousands of genes during immune responses. Although their structure and function show numerous things in common, their expression and activity differ markedly in most types of lymphocytes. Over the last 40 years, the work of our laboratory revealed a strong inducible transcription of the Nfatc1 gene upon lymphocyte (co-)activation, compared to the ‘tonic’ transcription of Nfatc2. This leads to the inducible expression of a short NFATc1 isoform that we designated as NFATc1/αA, which differs from longer NFATc1 proteins and NFATc2 by an individual N-terminal ‘α’ peptide and the absence of a C-terminal peptide of approximately 250 amino acid residues. While comprehensive experimental studies led to the conclusion that NFATc2 supports (i) apoptosis, (ii) the induction of anergy, and (iii) the ‘exhaustion’ of peripheral T cells, opposite conclusions can be derived from our studies of NFATc1/αA. This view on the ‘two faces’ of NFAT transcription factors will be presented in this review and discussed in the role of NFATs in cancerogenesis. Full article
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32 pages, 1125 KB  
Review
Immune Checkpoint-Based Therapies in Colorectal Cancer—Current Approaches and Future Perspectives
by Katarzyna Nakielska, Jacek Plewka and Marzena Lenart
Int. J. Mol. Sci. 2026, 27(10), 4628; https://doi.org/10.3390/ijms27104628 - 21 May 2026
Viewed by 64
Abstract
Colorectal cancer (CRC) is the third most frequently diagnosed malignancy and the second leading cause of cancer-related mortality worldwide, underscoring the need for the development of more effective and durable therapeutic strategies. A key mechanism of tumor immune evasion involves activation of immune [...] Read more.
Colorectal cancer (CRC) is the third most frequently diagnosed malignancy and the second leading cause of cancer-related mortality worldwide, underscoring the need for the development of more effective and durable therapeutic strategies. A key mechanism of tumor immune evasion involves activation of immune checkpoint pathways through the upregulation of inhibitory ligand expression within the tumor microenvironment, leading to lymphocyte exhaustion and impaired antitumor immunity. Consequently, immune checkpoints have emerged as important targets for immunotherapeutic intervention, with significant advances over the past decade. Nevertheless, despite demonstrated clinical benefits in selected patient subpopulations, the overall therapeutic efficacy of immune checkpoint inhibitors remains limited, particularly in the context of CRC. In this review, we provide a comprehensive overview of currently approved immune checkpoint-based immunotherapies for cancer treatment, with a specific focus on CRC, as well as ongoing clinical trials and evolving trends in this area. Furthermore, we discuss emerging targets and novel therapeutic strategies, with particular emphasis on innovative small-molecule inhibitors as potential alternatives to monoclonal antibody-based approaches. Finally, we outline future perspectives and potential directions for advancing immune checkpoint-targeted therapies in CRC. Full article
(This article belongs to the Special Issue Molecular Mechanisms and Therapies of Colorectal Cancer: 4th Edition)
24 pages, 616 KB  
Review
Regulatory T Cells in Hepatocellular Carcinoma: Spatial Niches, Biomarkers, and Clinical Implications
by Dimitris Liapopoulos, Panagiotis Sarantis, Georgios Zogas, Eleni-Myrto Trifylli, Thaleia-Eleftheria Bousou, Konstantina Kamitaki, Ioanna A. Anastasiou, Stefania Kokkali, Sotiris Mavromatis, Evangelos Koustas, Ioannis Elefsiniotis, Theodora Biniari and Michalis V. Karamouzis
Int. J. Mol. Sci. 2026, 27(10), 4630; https://doi.org/10.3390/ijms27104630 - 21 May 2026
Viewed by 58
Abstract
Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality worldwide, increasingly driven by metabolic dysfunction-associated steatotic liver disease alongside viral and alcohol-related cirrhosis. The tolerogenic immune environment of the liver enables tumor immune escape, with regulatory T cells (Tregs) playing a central [...] Read more.
Hepatocellular carcinoma (HCC) is a leading cause of cancer mortality worldwide, increasingly driven by metabolic dysfunction-associated steatotic liver disease alongside viral and alcohol-related cirrhosis. The tolerogenic immune environment of the liver enables tumor immune escape, with regulatory T cells (Tregs) playing a central role. This review synthesizes human-focused evidence (tissues, blood, clinical cohorts, and single-cell/spatial studies) through September 2025 to define how Tregs are recruited, maintained, and functionally deployed in HCC. Across datasets, intratumoral effector-like Tregs (eTregs) expressing ICOS, CTLA-4, CCR8, and CD39/CD73 accumulate within tumors and co-localize with exhausted cytotoxic PD-1hi CD8⁺ T cells and suppressive myeloid cells. Recruitment is driven mainly by CCL20–CCR6 and CCL22/CCL17–CCR4 signaling, while CCR8 marks highly suppressive tumor-resident Tregs. Their persistence is supported by TGF-β, IL-10, IL-35, adenosine signaling, IL-2 sequestration, and metabolic adaptation. Spatial biomarkers, including ICOS⁺/CCR8⁺ eTreg density and CD8:Treg ratios, associate with prognosis and emerging immunotherapy responses. Etiology further shapes immune architecture: HBV-related HCC often forms Treg-exhausted T-cell niches around viral antigens, whereas MASLD/MASH promotes stromal and metabolic barriers that may reduce PD-(L)1 efficacy. Current treatments (PD-(L)1 blockade with anti-VEGF or CTLA-4, and some TKIs) intersect with Treg biology, while emerging strategies targeting CCR8, CCR4, ICOS, or the adenosine pathway aim to selectively disrupt intratumoral eTreg networks. This review underscores that an etiology-aware, spatial-biomarker framework may guide the integration of selective Treg targeting with PD-(L)1-based therapies in HCC. Full article
(This article belongs to the Special Issue Next-Gen Biomarkers for Cancer Immunotherapy)
33 pages, 3811 KB  
Article
High Regnase-1 Expression Is Associated with an Immunosuppressive Tumor Microenvironment and Aggressive Features in Glioma Patients
by Kenza Miyara, Hamza Benthami, Hayat Miftah, Saadia Ait Ssi, Chaimae Boulhen, Abdelhakim Lakhdar and Abdallah Badou
Cancers 2026, 18(10), 1658; https://doi.org/10.3390/cancers18101658 - 20 May 2026
Viewed by 139
Abstract
Background/Objectives: Gliomas are among the most aggressive primary brain tumors in adults, characterized by profound molecular heterogeneity and poor response to conventional therapies. Immunotherapy has transformed outcomes in several cancers, yet glioma remains largely refractory, due in part to an immunosuppressive tumor [...] Read more.
Background/Objectives: Gliomas are among the most aggressive primary brain tumors in adults, characterized by profound molecular heterogeneity and poor response to conventional therapies. Immunotherapy has transformed outcomes in several cancers, yet glioma remains largely refractory, due in part to an immunosuppressive tumor microenvironment. Post-transcriptional regulation of gene expression is increasingly recognized as a key mechanism controlling immune cell function in tumors. Regnase-1, an endoribonuclease regulating the stability of inflammation- and immunity-related mRNAs, is a central modulator of immune responses; however, its role in glioma progression and immune modulation remains poorly understood. This study aimed to evaluate Regnase-1 expression in glioma and investigate its association with tumor grade, prognosis, and immune microenvironment characteristics. Methods: Regnase-1 transcript levels were evaluated by RT-PCR in tumor samples from 40 Moroccan glioma patients and validated using transcriptomic data from The Cancer Genome Atlas (TCGA, n = 672) and the Chinese Glioma Genome Atlas (CGGA, n = 959). Bioinformatic analyses and statistical assessments were performed using established pipelines. Results: Regnase-1 expression was significantly elevated in glioblastoma, IDH-wildtype tumors, and higher tumor grades, correlating with poorer overall survival, and emerging as an independent prognostic factor in the CGGA cohort. High Regnase-1 expression was associated with enrichment of pathways related to angiogenesis, hypoxia, invasion, and immune evasion. Tumors with elevated Regnase-1 showed reduced infiltration of effector immune cells (CD8+ T cells, Th1 cells) and increased presence of immunosuppressive populations, including regulatory T cells, myeloid-derived suppressor cells, and M2 macrophages. Single-cell analyses further highlighted exhausted CD8+ T cells and regulatory T cells as major populations linked to Regnase-1 expression. Notably, Regnase-1 expression also exhibited strong positive correlations with multiple inhibitory immune checkpoint pathways. Conclusions: Elevated Regnase-1 expression defines an aggressive, immunosuppressive glioma phenotype and is associated with poor prognosis, supporting its potential as a prognostic biomarker and a target for immunomodulatory strategies. Full article
(This article belongs to the Special Issue Immune Microenvironment and Immunotherapy in Malignant Brain Tumors)
25 pages, 3246 KB  
Article
Comprehensive Immunophenotyping of Monocytes and Dendritic Cells Suggests Distinct Pathophysiology in Chronic Fatigue Syndrome and Long COVID
by Steliyan Petrov, Martina Bozhkova, Mariya Ivanovska, Teodora Kalfova, Dobrina Dudova, Yana Todorova, Radostina Dimitrova, Marianna Murdjeva, Hristo Taskov, Maria Nikolova and Michael Maes
Int. J. Mol. Sci. 2026, 27(10), 4488; https://doi.org/10.3390/ijms27104488 - 17 May 2026
Viewed by 1296
Abstract
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long Coronavirus Disease 2019 (long COVID) are complex chronic conditions that often follow infectious triggers with overlapping clinical features but poorly defined pathophysiological relationships. This study aimed to identify disease-specific immune signatures through multiparameter immunophenotyping of monocytes, [...] Read more.
Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) and long Coronavirus Disease 2019 (long COVID) are complex chronic conditions that often follow infectious triggers with overlapping clinical features but poorly defined pathophysiological relationships. This study aimed to identify disease-specific immune signatures through multiparameter immunophenotyping of monocytes, dendritic cells, and T cell subsets. A total of 207 participants were included (ME/CFS: n = 103; long COVID: n = 63; healthy controls: n = 41). Peripheral blood mononuclear cells were analyzed using multiparameter flow cytometry. Statistical analyses included non-parametric testing, age-adjusted Analysis of covariance (ANCOVA), correlation network analysis, and principal component analysis (PCA). Long COVID was characterized by increased M2-like monocyte polarization, elevated CD80 expression across monocyte subsets, expansion of dendritic cells, and reduced expression of activation markers, indicating persistent immune activation with features of immune exhaustion. In contrast, ME/CFS exhibited reduced costimulatory molecule expression, impaired C-C chemokine receptor type 7 (CCR7)-mediated immune cell trafficking, and less coordinated activation patterns, consistent with a state of immune suppression. Correlation network analysis revealed more extensive and integrated immune interactions in long COVID, while PCA identified distinct immunophenotypic components and enabled moderate discrimination between the two conditions. These findings demonstrate that ME/CFS and long COVID are characterized by distinct immune profiles, supporting the concept of divergent immunopathological mechanisms. The identified signatures may contribute to biomarker development and guide targeted therapeutic approaches. Full article
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20 pages, 3611 KB  
Review
Dynamic Time-Resolved Remodeling of the Immune Microenvironment After Resistance to BRAF/MEK Inhibitors in Melanoma: Mechanisms, Biomarkers, and Emerging Therapeutic Strategies
by Wenjun Meng, Yan Liu, Haoran Zhang, Manting Wang, Xiaoli Mu, Ziqi Zhang and Yan Tie
Int. J. Mol. Sci. 2026, 27(10), 4484; https://doi.org/10.3390/ijms27104484 - 16 May 2026
Viewed by 199
Abstract
Targeted inhibition of the MAPK pathway with BRAF and MEK inhibitors (BRAFi/MEKi) produces rapid tumor regressions in BRAF V600-mutant melanoma, yet most patients ultimately develop acquired resistance. Resistance is not solely a tumor-cell-intrinsic phenomenon; it is accompanied by time-dependent remodeling of the tumor [...] Read more.
Targeted inhibition of the MAPK pathway with BRAF and MEK inhibitors (BRAFi/MEKi) produces rapid tumor regressions in BRAF V600-mutant melanoma, yet most patients ultimately develop acquired resistance. Resistance is not solely a tumor-cell-intrinsic phenomenon; it is accompanied by time-dependent remodeling of the tumor immune microenvironment (TIME) that can shape sensitivity to immune checkpoint inhibitors (ICIs) and inform rational combination or sequencing strategies. Early during MAPK inhibition, melanomas often display increased melanoma antigen expression and enhanced CD8+ T-cell infiltration, along with reduced immunosuppressive cytokines, suggesting a transient “immune-permissive” window. However, the same period can show induction of PD-L1 and T-cell exhaustion markers, foreshadowing adaptive immune resistance. At progression, immune-favorable features may diminish and immune evasion mechanisms, such as impaired antigen presentation and MHC-I downregulation, can become prominent and associate with resistance to immunotherapy. Here we review the temporal dynamics of TIME under MAPK inhibition, mechanistic links between resistance programs and immune remodeling, including signaling adaptation, focal adhesion/FAK signaling, dendritic cell dysfunction, antigen-presentation defects, and lymphatic/perilymphatic adipose remodeling, and practical biomarker opportunities across baseline, on-treatment, and progression timepoints. We also summarize emerging therapeutic strategies for post-resistance disease, including optimized ICI combinations, triple therapy concepts, and novel approaches such as combining FAK inhibition with RAF-MEK “clamp” therapy. Finally, we highlight key gaps and propose a framework for longitudinal sampling, standardized multi-omics integration, and TIME-informed trial design. The key distinguishing feature of this review is its time-resolved perspective on TIME remodeling, which links baseline immune contexture, early treatment-induced immune permissiveness, and the immune-evasive state that emerges during acquired resistance. Full article
(This article belongs to the Special Issue Advances in Melanoma and Skin Cancers: 2nd Edition)
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17 pages, 323 KB  
Review
Toward a Molecular Reclassification of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: Integrating Multi-Omics, Machine Learning, and Precision Medicine
by Joshua Frank, Nicole Nesterovitch, Chetana Movva, Nancy G. Klimas and Lubov Nathanson
Int. J. Mol. Sci. 2026, 27(10), 4436; https://doi.org/10.3390/ijms27104436 - 15 May 2026
Viewed by 331
Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system disease characterized by a multitude of symptoms across various organ systems. Diagnosis has relied heavily on heterogeneous clinical symptom presentation and evolving case definitions, with treatment focused on addressing presenting symptoms due to the [...] Read more.
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) is a complex, multi-system disease characterized by a multitude of symptoms across various organ systems. Diagnosis has relied heavily on heterogeneous clinical symptom presentation and evolving case definitions, with treatment focused on addressing presenting symptoms due to the paucity of validated biomarkers. Meanwhile, advances have been made in understanding the underlying pathophysiology through strong epidemiologic, clinical, and basic science studies. This narrative review synthesizes recent advances that are likely to drive a shift in understanding from symptom-based classification toward a molecularly defined understanding of the disease. This shift in understanding will likely provide the foundation for future research efforts focused on targeting diagnosis and treatment more effectively. Specifically, we reference the identification of rare genetic risk variants through the HEAL2 deep learning framework, the large-scale DecodeME genome-wide association study, and dynamic epigenetic markers of disease state. In addition, the findings revealed the downstream consequences of this genetic and epigenetic priming: chronic innate immune activation, CD8+ T cell exhaustion characterized by upregulation of the exhaustion-driving transcription factors Thymocyte Selection-Associated HMG Box (TOX) and Eomesodermin (EOMES), and a cellular energy crisis centered on mitochondrial dysfunction. Furthermore, results of recent studies have revealed sex-specific transcriptomic and proteomic signatures of maladaptive recovery. We also highlight the role of machine learning and artificial intelligence integrations in translating high-dimensional multi-omics data into actionable biological insights, including the identification of monocyte subsets via Positive Unlabeled Learning, circulating cell-free RNA diagnostic signatures, and integrated multi-modal disease models such as BioMapAI. The combination of these findings, which highlight multiple identifiable mechanisms of molecular activity, support the feasibility of molecular subtyping, precision diagnostics, and targeted therapeutic strategies for ME/CFS. Full article
27 pages, 13817 KB  
Article
Deciphering the Transcription Factor-Dominated Ecosystem During Esophageal Squamous Cell Carcinoma Progression at the Single-Cell Level
by Congxue Hu, Xinyu Li, Weixin Liang, Shujuan Li, Xiaozhi Huang, Jing Chen, Kaiyue Yang, Xia Li, Yunpeng Zhang and Jing Bai
Int. J. Mol. Sci. 2026, 27(10), 4433; https://doi.org/10.3390/ijms27104433 - 15 May 2026
Viewed by 136
Abstract
Esophageal squamous cell carcinoma (ESCC) progression involves dynamic cellular state transitions and tumor microenvironment remodeling, accompanied by extensive transcriptional regulation reprogramming. Here, we systematically mapped the TF-mediated regulatory landscape underlying ESCC progression at single-cell resolution by integrating stage-specific ESCC single-cell transcriptomic datasets comprising [...] Read more.
Esophageal squamous cell carcinoma (ESCC) progression involves dynamic cellular state transitions and tumor microenvironment remodeling, accompanied by extensive transcriptional regulation reprogramming. Here, we systematically mapped the TF-mediated regulatory landscape underlying ESCC progression at single-cell resolution by integrating stage-specific ESCC single-cell transcriptomic datasets comprising over 200,000 cells with TF–target interaction networks. Using a random walk algorithm combined with hypergeometric testing, we identified malignant progression-associated TFs (mpTFs) across multiple cell types and disease stages. Our analysis revealed extensive stage-dependent regulatory remodeling during ESCC progression. TCF4 was identified as an early-stage regulator associated with epithelial–mesenchymal transition activation and malignant invasive phenotypes. In immune lineages, BATF and IRF4 exhibited trajectory-associated activation during CD4+ T-cell differentiation and CD8+ T-cell exhaustion, suggesting critical roles in immunosuppressive T-cell state transitions. Additionally, mpTF-mediated remodeling of M2 macrophage subpopulations contributed to immunosuppressive tumor microenvironment formation during advanced ESCC progression. We further identified prognosis-associated cell-type-specific and shared mpTFs, including TFAP2C, which was associated with stabilized fibroblast and monocyte functional states and a less aggressive tumor microenvironment phenotype. Collectively, this study provides a comprehensive single-cell atlas of TF-mediated regulatory programs during ESCC progression and offers potential therapeutic targets for precision oncology. Full article
(This article belongs to the Special Issue Advanced Research on Esophageal Cancer)
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22 pages, 2428 KB  
Article
Computational Analysis of SPI1 Missense Mutations and ADMET-Guided Molecular Docking of Cinnamic Acid Targeting the PU.1 ETS Domain: Implications for Hematopoietic Dysregulation and Leukemogenesis
by Mariam M. Jaddah, Samer N. Khalaf, Mohammed Mukhles Ahmed and Aisha Abdullah Alshanqiti
Int. J. Mol. Sci. 2026, 27(10), 4278; https://doi.org/10.3390/ijms27104278 - 11 May 2026
Viewed by 309
Abstract
Spi-1 Proto-Oncogene (SPI1) encodes Purine-rich box 1 Transcription Factor (PU.1), a transcription factor of the ETS family that regulates hematopoietic lineage commitment and immune cell differentiation. Alteration of PU.1 dose or ETS domain integrity may interfere with transcriptional programs, which adds [...] Read more.
Spi-1 Proto-Oncogene (SPI1) encodes Purine-rich box 1 Transcription Factor (PU.1), a transcription factor of the ETS family that regulates hematopoietic lineage commitment and immune cell differentiation. Alteration of PU.1 dose or ETS domain integrity may interfere with transcriptional programs, which adds to hematopoietic dysregulation and leukemogenesis. Even though changes in SPI1 expression have been associated with acute myeloid leukemia (AML), the structural and regulatory effects of missense mutations at the PU.1 ETS domain have not been entirely studied, and targeting the PU.1 ETS domain by ligands is an area of computational analysis that should be further pursued. To computationally describe deleterious missense variants of SPI1 in terms of structural stability, evolutionary conservation, post-translational modification (PTM) context and interaction networks, and to measure ADMET-mediated molecular docking of cinnamic acid with the PU.1 ETS domain (8EQG) as a potential modulator. Missense nsSNPs were obtained through Ensembl and narrowed down by consensus prediction of pathogenicity (PredictSNP, combining SIFT, PolyPhen, SNAP and PhD-SNP and other tools). InterPro/UniProt was used for domain mapping. SWISS-MODEL was used to produce wild-type and mutant PU.1 versions, which were analyzed on the structural alignment and Cα–Cα displacement parameters in UCSF Chimera (v1.19). The estimation of stability change was carried out with I-Mutant and MUpro. Prediction of PTM sites was done using MusiteDeep and exploration of functional partners was done using STRING. Human, mouse and zebrafish orthologue conservation was measured by means of MAFFT alignment. GEPIA2 was used to compare the expression of SPI1 in AML (TCGA-LAML) and normal tissues (GTEx). AutoDock Vina (grid center 6, −2, −9 A; 20 × 20 × 20 A; 16 exhaustiveness) was used to prepare cinnamic acid and dock it into the PU.1 ETS domain (8EQG), with SwissDock being used for consistency checks. SwissADME and ADMETlab 2.0 were used to predict drug-likeness, pharmacokinetics, and toxicity. Nine missense mutations were routinely considered as deleterious with the majority of them being located in or near the ETS DNA-binding domain. Structural comparisons showed local perturbations of the structure and I189F and H211P yielded the greatest conformational changes between prioritized variants whereas other forms had minimal movements. A predominantly destabilizing trend was supported by stability prediction whereby V241G had the strongest destabilization signal with further destabilizations being predicted in I189F and R259C. PTM mapping revealed several potential regulatory residues (phosphorylation, acetylation, ubiquitination, and methylation), which indicated that there could be crosstalk between the sequence variation and the transcriptional regulation. The SPI1 was placed in a central hematopoietic transcriptional module (containing RUNX1, CEBP members, GATA1 and IRF factors) by the STRING network. The cross-species alignment showed that there was high conservation of a number of the mutation sites, which would support functional constraint at the ETS region. The expression analysis revealed that the level of SPI1 mRNA in AML was significantly elevated compared to normal tissues. Docking also indicated a slight and reproducible interaction of cinnamic acid with the ETS domain (top affinity −4.27 kcal/mol), with a solitary leading polar anchor and supportive hydrophobic interactions, which is akin to interaction between fragments. The ADMET profiling revealed the likelihood of success in the oral drug-likeness and low CYP inhibition liability, as well as signifying the presence of a possible hepatotoxicity signal that needs further confirmation through experiments. Comprehensive computational studies suggest that certain pathogenic variants of SPI1 missense defects, especially in the ETS domain, can result in loss of PU.1 structural stability and regulatory environment, which are in line with the disturbed hematopoietic regulation and AML-related dysregulation. Cinnamic acid demonstrates moderate yet reproducible binding to the PU.1 ETS domain and has an overall favorable developability profile, which indicates that it is better considered as a starting scaffold, as opposed to an active inhibitor. The results give a logical basis of focused biochemical validation and structure-directed optimization of ETS domain modulators in hematologic disease settings. Full article
(This article belongs to the Special Issue Computational Studies of Natural Products)
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22 pages, 7864 KB  
Article
Identification and Characterization of Cancer-Related Risk Metabolic Subpathways Reveal Their Functional Significance in Cancer
by Hongying Zhao, Jinxing Yan, Ming Wu, Shiyi Li, Weiming He, Xiangzhe Yin, Wangyang Liu, Ying Liu, Meiting Fei, Wan Li, Junjie Lv, Lina Chen and Li Wang
Int. J. Mol. Sci. 2026, 27(10), 4246; https://doi.org/10.3390/ijms27104246 - 10 May 2026
Viewed by 184
Abstract
Cancer progression is accompanied by significant metabolic alterations. We developed a novel computational approach to identify cancer-related risk metabolic subpathways (CMSubpathway). By leveraging the topology of large-scale metabolic pathway gene networks, we initially identified metabolic subpathways and then refined them by taking into [...] Read more.
Cancer progression is accompanied by significant metabolic alterations. We developed a novel computational approach to identify cancer-related risk metabolic subpathways (CMSubpathway). By leveraging the topology of large-scale metabolic pathway gene networks, we initially identified metabolic subpathways and then refined them by taking into account pathway activity dysregulation, prognostic efficacy, and classification performance. We employed the CMSubpathway to extensively identify cancer-related metabolic subpathways across 21 cancer types. Ultimately, 12 risk metabolic subpathways were identified in six cancer types. Subsequently, the 12 overlapping genes of risk metabolic subpathways were identified as the core metabolic module genes. Utilizing the public CRISPR knockout screening datasets sourced from DepMap, we further supported our hypothesis that the essential roles of ADH5, ALDH1B1, and ALDH7A1 in breast cancer cell growth and development. The core metabolic module and its associated genes exhibited significant down-regulation at both the transcriptome and proteome levels based on data from tissues, blood, and single cells. The activity of this core metabolic module was associated with the immune infiltration levels of multiple immune cells, especially T cells. Notably, an abnormal core metabolic module was observed in CD8 T cell subtypes, with the stem-like CD8 T cell subtype showing high metabolic activity and exhaustion markers. Thus, we established a method for identifying risk metabolic subpathways in cancers, which helps to identify more precise biomarkers for cancer patients. Full article
(This article belongs to the Section Molecular Oncology)
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20 pages, 999 KB  
Review
NLR Inflammasomes in Viral Infections: From Molecular Mechanisms to Therapeutic Interventions
by Shiyuan Hou, Xing Shen, Danni Sun, Yulin An, Yuxuan Zhou, Xing Sun, Shuhan Wang, Xinyue Liu, Mengting Zhu, Shuai Zhao, Ziyu Liu, Xingan Wu and Rongrong Liu
Viruses 2026, 18(5), 546; https://doi.org/10.3390/v18050546 - 8 May 2026
Viewed by 1116
Abstract
The innate immune system serves as the primary barrier against viral invasion, utilizing pattern recognition receptors (PRRs) to orchestrate a rapid defense. Among these, the nucleotide-binding domain and leucine-rich repeat (NLR) containing proteins function as central signaling scaffolds, assembling into multiprotein complexes known [...] Read more.
The innate immune system serves as the primary barrier against viral invasion, utilizing pattern recognition receptors (PRRs) to orchestrate a rapid defense. Among these, the nucleotide-binding domain and leucine-rich repeat (NLR) containing proteins function as central signaling scaffolds, assembling into multiprotein complexes known as inflammasomes. These complexes drive the maturation of pro-inflammatory cytokines IL-1β and IL-18, and initiate gasdermin D (GSDMD)-mediated pyroptosis, a lytic cell death pathway that eliminates intracellular replication niches. This comprehensive review synthesizes the diversified landscape of inflammasome activation during viral infections, extending beyond the canonical NLRP3 inflammasome to include specialized sensors such as NLRP6, NLRP9, NLRP1, NLRP12, and NLRC4. We critically evaluate the evolutionary “arms race” between host defenses and viral pathogens, detailing the sophisticated immune evasion strategies employed by viruses—ranging from the expression of decoy proteins and direct proteolytic cleavage of immune sensors to the manipulation of post-translational modifications (PTMs). Furthermore, we discuss the dual nature of inflammasome activation, which balances protective viral clearance against pathological hyperinflammation, and provide an exhaustive analysis of novel therapeutic strategies, including direct NLR inhibitors and downstream cytokine blockers, currently navigating clinical transition. Full article
(This article belongs to the Special Issue Viral Mechanisms of Immune Evasion)
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16 pages, 909 KB  
Review
The Aging Skin–Psoriasis Interface: Could Cellular Senescence and Immunosenescence Slow Therapeutic Response?
by Umberto Santaniello, François Rosset, Luca Mastorino, Orsola Crespi, Pietro Quaglino and Simone Ribero
Dermato 2026, 6(2), 18; https://doi.org/10.3390/dermato6020018 - 8 May 2026
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Abstract
Elderly psoriasis patients (≥65 years) demonstrate mainly preserved but substantially delayed therapeutic responses to IL-17 and IL-23 inhibitors, achieving lower PASI90 rates at early time-points with eventual “catch-up” by week 52, alongside increased adverse-event-driven discontinuation. This review synthesizes clinical efficacy data from real-world [...] Read more.
Elderly psoriasis patients (≥65 years) demonstrate mainly preserved but substantially delayed therapeutic responses to IL-17 and IL-23 inhibitors, achieving lower PASI90 rates at early time-points with eventual “catch-up” by week 52, alongside increased adverse-event-driven discontinuation. This review synthesizes clinical efficacy data from real-world studies with emerging mechanistic evidence on immunosenescence and cellular senescence to propose the “Inflammatory Noise Floor” hypothesis. We postulate that senescent keratinocytes and fibroblasts constitutively secrete SASP cytokines (IL-6, IL-8, TNF-α) through pathways partially independent of IL-23/IL-17, potentially establishing a persistent baseline inflammation that IL-23/IL-17 blockade might not suppress. Concurrently, immunosenescence, characterized by CD8+CD28 T-cell accumulation, exhaustion marker upregulation, and Treg dysfunction, is hypothesized to impair adaptive immune re-equilibration. This dual mechanism represents one plausible, albeit theoretical, explanatory framework for the temporal lag, PASI plateau effects, and infection risk observed in elderly patients. Optimizing outcomes in the elderly may require a pragmatic approach: accepting stable PASI 75-90 as a successful endpoint and prospectively validating extended assessment timelines. While a direct correlation remains to be proven, this framework identifies cellular and immunosenescence as potential targets for future senotherapeutic interventions. Full article
(This article belongs to the Special Issue Reviews in Dermatology: Current Advances and Future Directions)
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24 pages, 4682 KB  
Article
Transcriptomic Evidence of Immune–Tumor Uncoupling Defines a High-Risk State in Uterine Corpus Endometrial Carcinoma
by Chia-Hung Chen, Hui-Ju Kao, Chen-Lin Yu, Tzu-Hsiang Weng, Tsung-Tao Huang, Kai-Yao Huang and Shun-Long Weng
Int. J. Mol. Sci. 2026, 27(10), 4170; https://doi.org/10.3390/ijms27104170 - 7 May 2026
Viewed by 327
Abstract
This study aimed to develop and validate a transcriptomic risk signature for uterine corpus endometrial carcinoma (UCEC) and to investigate whether the identified prognostic program reflects immune–tumor uncoupling within the tumor microenvironment. Using transcriptomic data from The Cancer Genome Atlas (TCGA) UCEC cohort, [...] Read more.
This study aimed to develop and validate a transcriptomic risk signature for uterine corpus endometrial carcinoma (UCEC) and to investigate whether the identified prognostic program reflects immune–tumor uncoupling within the tumor microenvironment. Using transcriptomic data from The Cancer Genome Atlas (TCGA) UCEC cohort, we identified a 28-gene transcriptomic signature defining a high-risk state. The derived risk score robustly stratified patients into distinct survival groups and remained an independent predictor of overall survival after adjustment for clinical covariates. Functional analyses revealed that high-risk tumors are characterized by a distinct immune–tumor uncoupling phenotype, in which interferon-gamma (IFNG)-associated inflammatory signaling is preserved but fails to translate into effective antitumor immune activity. Specifically, effector immune programs, including CD8 T cell-related signatures and cytotoxic activity, were consistently reduced despite elevated IFNG-associated signaling, indicating a functional discordance between immune activation and immune execution rather than classical T cell exhaustion. In parallel, high-risk tumors exhibited consistently elevated cell cycle and DNA repair-associated transcriptional programs, suggesting that proliferative and stress-adaptive mechanisms represent dominant drivers of poor prognosis. External assessment in an independent GEO cohort (GSE17025) demonstrated consistent associations between signature activity, tumor status, and histological grade, supporting the reproducibility of the underlying transcriptional program at the biological and clinicopathological level. Collectively, this study provides transcriptomic evidence for a previously underappreciated immune–tumor uncoupling state in UCEC and highlights the importance of integrating immune signaling and tumor-intrinsic programs to understand disease progression. Full article
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