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13 pages, 1149 KiB  
Article
Not All Weight Loss Is Equal: Divergent Patterns and Prognostic Roles in Head and Neck Cancer Versus High-Grade B-Cell Lymphoma
by Judith Büntzel, Gina Westhofen, Wilken Harms, Markus Maulhardt, Alexander Casimir Angleitner and Jens Büntzel
Nutrients 2025, 17(15), 2530; https://doi.org/10.3390/nu17152530 (registering DOI) - 31 Jul 2025
Viewed by 77
Abstract
Background: Malnutrition and unintended weight loss are frequent in cancer patients and linked to poorer outcomes. However, data on long-term weight trajectories, particularly comparing different cancer entities, remain limited. Methods: In this retrospective, multicenter study, we analyzed 145 patients diagnosed with either head [...] Read more.
Background: Malnutrition and unintended weight loss are frequent in cancer patients and linked to poorer outcomes. However, data on long-term weight trajectories, particularly comparing different cancer entities, remain limited. Methods: In this retrospective, multicenter study, we analyzed 145 patients diagnosed with either head and neck cancer (HNC; n = 48) or high-grade B-cell lymphoma (HGBCL; n = 97). Body weight, C-reactive protein (CrP), albumin, and modified Glasgow Prognostic Score (mGPS) were assessed at diagnosis and at 3, 6, 9, and 12 months. Clinically relevant weight loss was defined as >5% from baseline. Survival analyses were performed for HGBCL patients. Results: Weight loss was common in both cohorts, affecting 32.2% at 3 months and persisting in 42.3% at 12 months. Nearly half of HNC patients had sustained >5% weight loss at one year, whereas HGBCL patients were more likely to regain weight, with significantly higher rates of weight gain at 6 and 12 months (p = 0.04 and p = 0.02). At baseline, HGBCL patients showed elevated CrP and lower albumin compared to HNC (both p < 0.001). Weight loss at 6 months was significantly associated with reduced overall survival in HGBCL (p < 0.01). Both Δweight at 6 months and mGPS emerged as useful prognostic indicators. Conclusions: This study reveals distinct patterns of weight change and systemic inflammation between HNC and HGBCL patients during the first year after diagnosis. These findings highlight the need for entity-specific nutritional monitoring and tailored supportive care strategies extending into survivorship. Prospective studies integrating body composition analyses are warranted to better guide long-term management. Full article
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20 pages, 5322 KiB  
Article
Regulation of Tetraspanin CD63 in Chronic Myeloid Leukemia (CML): Single-Cell Analysis of Asymmetric Hematopoietic Stem Cell Division Genes
by Christophe Desterke, Annelise Bennaceur-Griscelli and Ali G. Turhan
Bioengineering 2025, 12(8), 830; https://doi.org/10.3390/bioengineering12080830 (registering DOI) - 31 Jul 2025
Viewed by 170
Abstract
(1) Background: Chronic myeloid leukemia (CML) is a myeloproliferative disorder driven by the BCR::ABL oncoprotein. During the chronic phase, Philadelphia chromosome-positive hematopoietic stem cells generate proliferative myeloid cells with various stages of maturation. Despite this expansion, leukemic stem cells (LSCs) retain self-renewal capacity [...] Read more.
(1) Background: Chronic myeloid leukemia (CML) is a myeloproliferative disorder driven by the BCR::ABL oncoprotein. During the chronic phase, Philadelphia chromosome-positive hematopoietic stem cells generate proliferative myeloid cells with various stages of maturation. Despite this expansion, leukemic stem cells (LSCs) retain self-renewal capacity via asymmetric cell divisions, sustaining the stem cell pool. Quiescent LSCs are known to be resistant to tyrosine kinase inhibitors (TKIs), potentially through BCR::ABL-independent signaling pathways. We hypothesize that dysregulation of genes governing asymmetric division in LSCs contributes to disease progression, and that their expression pattern may serve as a prognostic marker during the chronic phase of CML. (2) Methods: Genes related to asymmetric cell division in the context of hematopoietic stem cells were extracted from the PubMed database with the keyword “asymmetric hematopoietic stem cell”. The collected relative gene set was tested on two independent bulk transcriptome cohorts and the results were confirmed by single-cell RNA sequencing. (3) Results: The expression of genes involved in asymmetric hematopoietic stem cell division was found to discriminate disease phases during CML progression in the two independent transcriptome cohorts. Concordance between cohorts was observed on asymmetric molecules downregulated during blast crisis (BC) as compared to the chronic phase (CP). This downregulation during the BC phase was confirmed at single-cell level for SELL, CD63, NUMB, HK2, and LAMP2 genes. Single-cell analysis during the CP found that CD63 is associated with a poor prognosis phenotype, with the opposite prediction revealed by HK2 and NUMB expression. The single-cell trajectory reconstitution analysis in CP samples showed CD63 regulation highlighting a trajectory cluster implicating HSPB1, PIM2, ANXA5, LAMTOR1, CFL1, CD52, RAD52, MEIS1, and PDIA3, known to be implicated in hematopoietic malignancies. (4) Conclusion: Regulation of CD63, a tetraspanin involved in the asymmetric division of hematopoietic stem cells, was found to be associated with poor prognosis during CML progression and could be a potential new therapeutic target. Full article
(This article belongs to the Special Issue Micro- and Nano-Technologies for Cell Analysis)
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14 pages, 1664 KiB  
Article
Depletion of IGFALS Serum Level up to 3 Months After Cardiac Surgery, with Exploration of Potential Relationships to Surrogates of Organ Failures and Clinical Outcomes
by Krzysztof Laudanski, Mohamed A. Mahmoud, Hossam Gad and Daniel A. Diedrich
Curr. Issues Mol. Biol. 2025, 47(8), 581; https://doi.org/10.3390/cimb47080581 - 23 Jul 2025
Viewed by 205
Abstract
The insulin-like growth factor binding protein, acid-labile subunit (IGFALS), plays a crucial role in glucose metabolism and immune regulation, key processes in recovery from surgery. Here, we studied the perioperative serum IGFALS dynamics and explored potential clinical implications. A total of 79 patients [...] Read more.
The insulin-like growth factor binding protein, acid-labile subunit (IGFALS), plays a crucial role in glucose metabolism and immune regulation, key processes in recovery from surgery. Here, we studied the perioperative serum IGFALS dynamics and explored potential clinical implications. A total of 79 patients undergoing elective cardiac surgery with implementation of cardiopulmonary bypass had their serum isolated at baseline, 24 h, seven days, and three months postoperatively to assess serum concentrations of IGFALS and insulin growth factor 1 (IGF-1). Markers of perioperative injury included troponin I (TnI), high-mobility group box 1 (HMGB-1), and heat shock protein 60 (Hsp-60). Inflammatory status was assessed via interleukin-6 (IL-6) and interleukin-8 (IL-8). Additionally, we measured in vitro cytokine production to viral stimulation of whole blood and monocytes. Surrogates of neuronal distress included neurofilament light chain (NF-L), total tau (τ), phosphorylated tau at threonine 181 (τp181), and amyloid β40 and β42. Renal impairment was defined by RIFLE criteria. Cardiac dysfunction was denoted by serum N-terminal pro-brain natriuretic peptide (NT-proBNP) levels. Serum IGFALS levels declined significantly after surgery and remained depressed even at 3 months. Administration of acetaminophen and acetylsalicylic acid differentiated IGFALS levels at the 24 h postoperatively. Serum IGFALS 24 h post-operatively correlated with production of cytokines by leukocytes after in vitro viral stimulation. Serum amyloid-β1-42 was significantly associated with IGFALS at baseline and 24 h post-surgery Patients discharged home had higher IGFALS levels at 28 days and 3 months than those discharged to healthcare facilities or who died. These findings suggest that IGFALS may serve as a prognostic biomarker for recovery trajectory and postoperative outcomes in cardiac surgery patients. Full article
(This article belongs to the Special Issue The Role of Neuroinflammation in Neurodegenerative Diseases)
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25 pages, 5946 KiB  
Article
Targeting Sodium Transport Reveals CHP1 Downregulation as a Novel Molecular Feature of Malignant Progression in Clear Cell Renal Cell Carcinoma: Insights from Integrated Multi-Omics Analyses
by Yun Wu, Ri-Ting Zhu, Jia-Ru Chen, Xiao-Min Liu, Guo-Liang Huang, Jin-Cheng Zeng, Hong-Bing Yu, Xin Liu and Cui-Fang Han
Biomolecules 2025, 15(7), 1019; https://doi.org/10.3390/biom15071019 - 15 Jul 2025
Viewed by 397
Abstract
Clear cell renal cell carcinoma (ccRCC), the most common RCC subtype, displays significant intratumoral heterogeneity driven by metabolic reprogramming, which complicates our understanding of disease progression and limits treatment efficacy. This study aimed to construct a comprehensive cellular and transcriptional landscape of ccRCC, [...] Read more.
Clear cell renal cell carcinoma (ccRCC), the most common RCC subtype, displays significant intratumoral heterogeneity driven by metabolic reprogramming, which complicates our understanding of disease progression and limits treatment efficacy. This study aimed to construct a comprehensive cellular and transcriptional landscape of ccRCC, with emphasis on gene expression dynamics during malignant progression. An integrated analysis of 90 scRNA-seq samples comprising 534,227 cells revealed a progressive downregulation of sodium ion transport-related genes, particularly CHP1 (calcineurin B homologous protein isoform 1), which is predominantly expressed in epithelial cells. Reduced CHP1 expression was confirmed at both mRNA and protein levels using bulk RNA-seq, CPTAC proteomics, immunohistochemistry, and ccRCC cell lines. Survival analysis showed that high CHP1 expression correlated with improved prognosis. Functional analyses, including pseudotime trajectory, Mfuzz clustering, and cell–cell communication modeling, indicated that CHP1+ epithelial cells engage in immune interaction via PPIA–BSG signaling. Transcriptomic profiling and molecular docking suggested that CHP1 modulates amino acid transport through SLC38A1. ZNF460 was identified as a potential transcription factor of CHP1. Virtual screening identified arbutin and imatinib mesylate as candidate CHP1-targeting compounds. These findings establish CHP1 downregulation as a novel molecular feature of ccRCC progression and support its utility as a prognostic biomarker. Full article
(This article belongs to the Section Bioinformatics and Systems Biology)
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25 pages, 7641 KiB  
Article
Integrated Single-Cell Analysis Dissects Regulatory Mechanisms Underlying Tumor-Associated Macrophage Plasticity in Hepatocellular Carcinoma
by Yu Gu, Wenyong Zhu, Zhihui Zhang, Huiling Shu, Hao Huang and Xiao Sun
Genes 2025, 16(7), 817; https://doi.org/10.3390/genes16070817 - 12 Jul 2025
Viewed by 516
Abstract
Background: Tumor-associated macrophages (TAMs) are critical regulators of the hepatocellular carcinoma (HCC) microenvironment, yet their epigenetic heterogeneity and regulatory programs remain poorly defined. Methods: We performed integrative analysis on single-cell RNA-seq and ATAC-seq profiling of HCC patients to dissect TAM subtypes [...] Read more.
Background: Tumor-associated macrophages (TAMs) are critical regulators of the hepatocellular carcinoma (HCC) microenvironment, yet their epigenetic heterogeneity and regulatory programs remain poorly defined. Methods: We performed integrative analysis on single-cell RNA-seq and ATAC-seq profiling of HCC patients to dissect TAM subtypes at high resolution. By correlating chromatin accessibility with gene expression, we identified cell-type-specific candidate cis-regulatory elements (CREs). TAM subsets with prognostic significance were determined through integration with HCC clinical cohorts. Pseudotime and multi-regional analyses were used to uncover regulatory trajectories underlying macrophage phenotypic transitions. The identification framework of a super-enhancer (SE) was constructed, and potential therapeutic targets were prioritized using drug–gene interaction data. Results: We delineated the regulatory landscape of TAMs in HCC, revealing cell-type-specific chromatin accessibility patterns underlying TAM heterogeneity. The 65,342 CREs linked to gene expression were identified, with distal CREs contributing most to cell-type-specific regulation. Notably, SPP1+ TAMs were found to be enriched in tumor cores and associated with poor prognosis in HCC. Liver-resident Kupffer cells showed progressive loss of the core transcription factors SPIC and MAFB, suggesting a potential transition into SPP1+ TAMs under tumor pressure. We identified 133 SPP1+ TAM-specific SEs and constructed a TF–SE–target gene regulatory network. Notably, 13 target genes showed higher drug–gene interaction effects, highlighting their therapeutic potential. Conclusions: This study provides the chromatin accessibility map of TAMs in HCC and reveals how distal CRE-driven transcriptional programs shape TAM states. Our findings lay the foundation for understanding the epigenetic regulation of TAM heterogeneity and nominate potential targets for TAM-directed immunotherapy in HCC. Full article
(This article belongs to the Special Issue Single-Cell and Spatial Multi-Omics in Human Diseases)
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16 pages, 576 KiB  
Article
The Prognostic Potential of Insulin-like Growth Factor-Binding Protein 1 for Cardiovascular Complications in Peripheral Artery Disease
by Ben Li, Farah Shaikh, Houssam Younes, Batool Abuhalimeh, Abdelrahman Zamzam, Rawand Abdin and Mohammad Qadura
J. Cardiovasc. Dev. Dis. 2025, 12(7), 253; https://doi.org/10.3390/jcdd12070253 - 1 Jul 2025
Viewed by 398
Abstract
Background/Objectives: Patients with peripheral artery disease (PAD) have a heightened risk of major adverse cardiovascular events (MACE), including myocardial infarction, stroke, and death. Despite this, limited progress has been made in identifying reliable biomarkers to prognosticate such outcomes. Circulating growth factors, known to [...] Read more.
Background/Objectives: Patients with peripheral artery disease (PAD) have a heightened risk of major adverse cardiovascular events (MACE), including myocardial infarction, stroke, and death. Despite this, limited progress has been made in identifying reliable biomarkers to prognosticate such outcomes. Circulating growth factors, known to influence endothelial function and the progression of atherosclerosis, may hold prognostic value in this context. The objective of this research was to evaluate a broad range of blood-based growth factors to investigate their potential as predictors of MACE in patients diagnosed with PAD. Methods: A total of 465 patients with PAD were enrolled in a prospective cohort study. Baseline plasma levels of five different growth factors were measured, and participants were monitored over a two-year period. The primary outcome was the occurrence of MACE within those two years. Comparative analysis of protein levels between patients who did and did not experience MACE was performed using the Mann–Whitney U test. To assess the individual prognostic significance of each protein for predicting MACE within two years, Cox proportional hazards regression was performed, adjusting for clinical and demographic factors including a history of coronary and cerebrovascular disease. Subgroup analysis was performed to assess the prognostic value of these proteins in females, who may be at higher risk of PAD-related adverse events. Net reclassification improvement (NRI), integrated discrimination improvement (IDI), and area under the receiver operating characteristic curve (AUROC) were calculated to assess the added value of significant biomarkers to model performance for predicting 2-year MACE when compared to using demographic/clinical features alone. Kaplan–Meier curves stratified by IGFBP-1 tertiles compared using log-rank tests and Cox proportional hazards analysis were used to assess 2-year MACE risk trajectory based on plasma protein levels. Results: The average participant age was 71 years (SD 10); 31.1% were female and 47.2% had diabetes. By the end of the two-year follow-up, 18.1% (n = 84) had experienced MACE. Of all proteins studied, only insulin-like growth factor-binding protein 1 (IGFBP-1) showed a significant elevation among patients who suffered MACE versus those who remained event-free (20.66 [SD 3.91] vs. 13.94 [SD 3.80] pg/mL; p = 0.012). IGFBP-1 remained a significant independent predictor of 2-year MACE occurrence in the multivariable Cox analysis (adjusted hazard ratio [HR] 1.57, 95% CI 1.21–1.97; p = 0.012). Subgroup analyses revealed that IGFBP-1 was significantly associated with 2-year MACE occurrence in both females (adjusted HR 1.52, 95% CI 1.16–1.97; p = 0.015) and males (adjusted HR 1.04, 95% CI 1.02–1.22; p = 0.045). Incorporating IGFBP-1 into the clinical risk prediction model significantly enhanced its predictive performance, with an increase in the AUROC from 0.73 (95% CI 0.71–0.75) to 0.79 (95% CI 0.77–0.81; p = 0.01), an NRI of 0.21 (95% CI 0.07–0.36; p = 0.014), and an IDI of 0.041 (95% CI 0.015–0.066; p = 0.008), highlighting the prognostic value of IGFBP-1. Kaplan–Meier analysis showed an increase in the cumulative incidence of 2-year MACE across IGFBP-1 tertiles. Patients in the highest IGFBP-1 tertile experienced a significantly higher event rate compared to those in the lowest tertile (log-rank p = 0.008). In the Cox proportional hazards analysis, the highest tertile of IGFBP-1 was associated with increased 2-year MACE risk compared to the lowest tertile (adjusted HR 1.81; 95% CI: 1.31–2.65; p = 0.001). Conclusions: Among the growth factors analyzed, IGFBP-1 emerged as the sole biomarker independently linked to the development of MACE over a two-year span in both female and male PAD patients. The addition of IGFBP-1 to clinical features significantly improved model predictive performance for 2-year MACE. Measuring IGFBP-1 levels may enhance risk stratification and guide the intensity of therapeutic interventions and referrals to cardiovascular specialists, ultimately supporting more personalized and effective management strategies for patients with PAD to reduce systemic vascular risk. Full article
(This article belongs to the Section Cardiovascular Clinical Research)
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22 pages, 6165 KiB  
Article
Single-Cell Transcriptomic Analysis Unveils Key Regulators and Signaling Pathways in Lung Adenocarcinoma Progression
by Jialu Ma, Caleb McQuay, John Talburt, Amit K. Tiwari and Mary Qu Yang
Biomedicines 2025, 13(7), 1606; https://doi.org/10.3390/biomedicines13071606 - 30 Jun 2025
Viewed by 389
Abstract
Background: Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related mortality despite advances in treatments, necessitating more effective therapeutic strategies. Single-cell RNA sequencing (scRNA-seq) technology has revolutionized our ability to dissect the cellular complexity of cancers, which is often obscured in conventional bulk [...] Read more.
Background: Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related mortality despite advances in treatments, necessitating more effective therapeutic strategies. Single-cell RNA sequencing (scRNA-seq) technology has revolutionized our ability to dissect the cellular complexity of cancers, which is often obscured in conventional bulk transcriptomic experiments. Methods: In this study, we performed an integrative analysis of scRNA-seq data from multiple LUAD patient cohorts to investigate cell-type-specific transcriptomic changes across disease stages. Clustering, lineage trajectory analysis, and transcriptional regulatory network reconstruction were employed to identify stage-specific gene markers and their upstream regulators. Additionally, we constructed intercellular communication networks to evaluate signaling changes within the tumor microenvironment (TME) during LUAD progression. Results: Our analysis revealed that epithelial cells from stage IV tumors exhibited a distinct transcriptional profile compared to earlier stages, a separation not observed in immune or stromal cell populations. We identified a panel of gene markers that differentiated epithelial cells across disease stages and effectively stratified patients into subgroups with distinct survival outcomes and TME compositions. Regulatory network analysis uncovered key transcription factors, including ATF3, ATF4, HSF1, KLF4, and NFIC, as potential upstream regulators of these stage-specific genes. Moreover, cell–cell communication analysis revealed a significant increase in signaling originating from epithelial cells and a concomitant decrease in immune-derived signals in late-stage LUAD. We identified several signaling pathways enriched in stage-specific crosstalk, including Wnt, PTN, and PDGF pathways, which may play critical roles in LUAD progression. Conclusions: This study provides a comprehensive single-cell resolution map of LUAD progression, highlighting epithelial-driven regulatory programs and dynamic intercellular communication within the TME. Our findings uncover novel molecular markers and regulatory mechanisms with potential prognostic and therapeutic value for more precise treatment. Full article
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16 pages, 395 KiB  
Article
Sepsis-Induced Coagulopathy and Hypoalbuminemia: Endothelial Damage as Common Pathway and Clinical Implications on Mortality and Transfusion Risk
by Gianni Turcato, Arian Zaboli, Fabrizio Lucente, Lucia Filippi, Michael Maggi, Gloria Brigiari, Paolo Ferretto, Alessandro Cipriano, Lorenzo Ghiadoni and Christian J. Wiedermann
J. Clin. Med. 2025, 14(13), 4483; https://doi.org/10.3390/jcm14134483 - 24 Jun 2025
Viewed by 488
Abstract
Background: Sepsis-induced coagulopathy (SIC) and hypoalbuminemia represent distinct yet interrelated manifestations of endothelial dysfunction in sepsis. While both have been individually associated with increased mortality, their combined prognostic value remains unexplored. This study aimed to assess the relationship between the SIC score and [...] Read more.
Background: Sepsis-induced coagulopathy (SIC) and hypoalbuminemia represent distinct yet interrelated manifestations of endothelial dysfunction in sepsis. While both have been individually associated with increased mortality, their combined prognostic value remains unexplored. This study aimed to assess the relationship between the SIC score and serum albumin levels and to evaluate their integrated role in predicting mortality and bleeding risks in septic patients. Methods: We conducted a prospective observational study enrolling adult patients with community-acquired sepsis admitted to an Intermediate Medical Care Unit between January 2023 and June 2024. The primary outcome was 30-day all-cause mortality. The secondary outcome was the occurrence of ISTH-defined major bleeding. Multivariable logistic regression and Net Reclassification Improvement (NRI) analyses were performed to evaluate the predictive value of albumin when added to the SIC score. Results: A total of 413 patients were enrolled; 18.4% had a positive SIC score. The serum albumin and SIC score were inversely correlated (r = −0.189, p < 0.001). Both variables were independently associated with 30-day mortality and major bleeding. The addition of albumin significantly improved the predictive performance of the SIC score (NRI = 0.276 for mortality; NRI = 0.268 for bleeding; both p = 0.003). The cluster analysis identified distinct phenotypes based on albumin and SIC profiles, with differing clinical trajectories and transfusion needs. Conclusions: The combined assessment of the SIC score and serum albumin enhances early risk stratification in sepsis. This dual-parameter approach may support more accurate prognostication and individualized management in septic patients. Full article
(This article belongs to the Section Hematology)
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23 pages, 1564 KiB  
Review
DCIS Progression and the Tumor Microenvironment: Molecular Insights and Prognostic Challenges
by Karolina Prajzendanc
Cancers 2025, 17(12), 1925; https://doi.org/10.3390/cancers17121925 - 10 Jun 2025
Cited by 1 | Viewed by 934
Abstract
Ductal carcinoma in situ (DCIS) is the most common form of non-invasive breast cancer and a recognized precursor to invasive ductal carcinoma (IDC). Although DCIS itself is confined to the milk duct and not immediately life-threatening, its potential for progression to invasive disease [...] Read more.
Ductal carcinoma in situ (DCIS) is the most common form of non-invasive breast cancer and a recognized precursor to invasive ductal carcinoma (IDC). Although DCIS itself is confined to the milk duct and not immediately life-threatening, its potential for progression to invasive disease necessitates careful clinical management. The increased detection of DCIS due to advancements in imaging and widespread screening programs has raised critical questions regarding its classification, prognosis, and optimal treatment strategies. While most cases exhibit indolent behavior, others harbor molecular characteristics that drive malignant transformation. A key challenge lies in distinguishing low-risk DCIS, which may never progress, from aggressive cases requiring intervention. Tumor microenvironment dynamics, immune cell infiltration, and molecular alterations, including hormone receptor (HR) status, human epidermal growth factor 2 (HER2) expression, and genetic mutations, play crucial roles in determining disease trajectory. This review explores the biological and molecular mechanisms underlying DCIS progression, with an emphasis on myoepithelial cells, tumor-infiltrating lymphocytes, and microenvironmental factors. By integrating recent findings, this article aims to refine risk stratification approaches and guide future strategies for personalized DCIS management. Improved prognostic biomarkers and targeted therapeutic interventions could help optimize treatment decisions, balancing the need for effective cancer prevention while minimizing overtreatment in low-risk patients. Full article
(This article belongs to the Section Molecular Cancer Biology)
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23 pages, 744 KiB  
Review
Epigenetic Insights into Tuberous Sclerosis Complex, Von Hippel–Lindau Syndrome, and Ataxia–Telangiectasia
by Gavriel Hadjigavriel, Christina Stylianides, Evangelos Axarloglou, Maria Eleni Manthou, Efstratios Vakirlis, Paschalis Theotokis, Soultana Meditskou and Iasonas Dermitzakis
Epigenomes 2025, 9(2), 20; https://doi.org/10.3390/epigenomes9020020 - 9 Jun 2025
Viewed by 841
Abstract
Neurocutaneous syndromes represent a clinically and genetically heterogeneous group of disorders, with tuberous sclerosis complex (TSC), von Hippel–Lindau syndrome (VHL), and ataxia–telangiectasia (A-T) exemplifying some of the most complex entities within this category. These syndromes have traditionally been considered monogenic disorders, caused by [...] Read more.
Neurocutaneous syndromes represent a clinically and genetically heterogeneous group of disorders, with tuberous sclerosis complex (TSC), von Hippel–Lindau syndrome (VHL), and ataxia–telangiectasia (A-T) exemplifying some of the most complex entities within this category. These syndromes have traditionally been considered monogenic disorders, caused by germline mutations in tumor suppressor or regulatory genes. However, they exhibit a striking degree of phenotypic variability and divergent clinical trajectories that cannot be fully explained by their underlying genetic alterations alone. Increasingly, epigenetic regulatory mechanisms, such as DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA (ncRNA) activity, are recognized as key modulators of gene expression, cellular differentiation, and tissue-specific function. Disruption of these mechanisms has been implicated in disease pathogenesis, tumorigenesis, and neurodegeneration associated with TSC, VHL, and A-T. Aberrant epigenetic profiles may underlie the observed variability in clinical outcomes, even among individuals with identical mutations. This review consolidates current evidence on the epigenetic landscape of these syndromes, elucidating how these modifications may influence disease behavior and contribute to incomplete genotype–phenotype correlations. By integrating epigenetic insights with known molecular pathways, a more nuanced understanding of disease biology emerges, with potential implications for diagnostic stratification, prognostic assessment, and therapeutic innovation. Full article
(This article belongs to the Collection Feature Papers in Epigenomes)
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18 pages, 2292 KiB  
Article
Comprehensive Anatomical Staging Predicts Clinical Progression in Mild Cognitive Impairment: A Data-Driven Approach
by Raghav Tandon, Yajun Mei, James J. Lah and Cassie S. Mitchell
Int. J. Mol. Sci. 2025, 26(12), 5514; https://doi.org/10.3390/ijms26125514 - 9 Jun 2025
Viewed by 544
Abstract
Alzheimer’s disease (AD) presents significant challenges in clinical practice due to its heterogeneous manifestation and variable progression rates. This work develops a comprehensive anatomical staging framework to predict progression from mild cognitive impairment (MCI) to AD. Using the ADNI database, the scalable Subtype [...] Read more.
Alzheimer’s disease (AD) presents significant challenges in clinical practice due to its heterogeneous manifestation and variable progression rates. This work develops a comprehensive anatomical staging framework to predict progression from mild cognitive impairment (MCI) to AD. Using the ADNI database, the scalable Subtype and Stage Inference (s-SuStaIn) model was applied to 118 neuroanatomical features from cognitively normal (n = 504) and AD (n = 346) participants. The framework was validated on 808 MCI participants through associations with clinical progression, CSF and FDG-PET biomarkers, and neuropsychiatric measures, while adjusting for common confounders (age, gender, education, and APOE ε4 alleles). The framework demonstrated superior prognostic accuracy compared to traditional risk assessment (C-index = 0.73 vs. 0.62). Four distinct disease subtypes showed differential progression rates, biomarker profiles (FDG-PET and CSF Aβ42), and cognitive trajectories: Subtype 1, subcortical-first pattern; Subtype 2, executive–cortical pattern; Subtype 3, disconnection pattern; and Subtype 4, frontal–executive pattern. Stage-dependent changes revealed systematic deterioration across diverse cognitive domains, particularly in learning acquisition, visuospatial processing, and functional abilities. This data-driven approach captures clinically meaningful disease heterogeneity and improves prognostication in MCI, potentially enabling more personalized therapeutic strategies and clinical trial design. Full article
(This article belongs to the Special Issue Molecular Insight into Alzheimer’s Disease)
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12 pages, 1060 KiB  
Review
Role of B-Mode and Contrast-Enhanced Ultrasound in the Diagnostic Workflow of Gastro-Entero-Pancreatic Neuroendocrine Tumors (GEP-NETs)
by Linda Galasso, Maria Grazia Maratta, Valeria Sardaro, Giorgio Esposto, Irene Mignini, Raffaele Borriello, Antonio Gasbarrini, Maria Elena Ainora, Giovanni Schinzari and Maria Assunta Zocco
Cancers 2025, 17(11), 1879; https://doi.org/10.3390/cancers17111879 - 4 Jun 2025
Viewed by 588
Abstract
Gastro-entero-pancreatic neuroendocrine tumors (GEP-NETs) represent a rare and varied class of neoplasms, characterized by diverse clinical presentations and prognostic trajectories. Accurate and prompt diagnosis is vital to inform and optimize therapeutic decisions. Ultrasound, including standard B-mode imaging and advanced methods such as contrast-enhanced [...] Read more.
Gastro-entero-pancreatic neuroendocrine tumors (GEP-NETs) represent a rare and varied class of neoplasms, characterized by diverse clinical presentations and prognostic trajectories. Accurate and prompt diagnosis is vital to inform and optimize therapeutic decisions. Ultrasound, including standard B-mode imaging and advanced methods such as contrast-enhanced ultrasound (CEUS) and endoscopic ultrasound (EUS), serves as a key component in the diagnostic evaluation of these tumors. B-mode US and CEUS provide non-invasive, accessible methods for early detection and characterization. On B-mode imaging, GEP-NETs typically present as well-defined, hyperechoic, or iso-echoic lesions, while CEUS highlights their characteristic vascularity, marked by arterial-phase hyperenhancement and venous-phase washout. Compared to CT and MRI, ultrasound offers real-time, dynamic imaging without ionizing radiation or nephrotoxic contrast agents, making it particularly advantageous for patients requiring frequent monitoring or with contraindications to other imaging modalities. CT and MRI are widely regarded as the preferred methods for staging and surgical planning due to their detailed anatomical visualization. However, ultrasound, especially CEUS, provides a significant adjunctive role in both early detection and the follow-up on GEP-NETs. This analysis delves into the strengths, challenges, and innovations in ultrasound technology for diagnosing pancreatic NETs, focusing on its contribution to comprehensive imaging strategies and its impact on patient care decisions. Full article
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12 pages, 1605 KiB  
Article
BAG3 Positivity as Prognostic Marker in Head and Neck Squamous Cell Carcinoma
by Pietro De Luca, Francesco Antonio Salzano, Angelo Camaioni, Leopoldo Costarelli, Raul Pellini, Gerardo Petruzzi, Renato Covello, Luigi Vittori, Filippo Ricciardiello, Giuseppe Ricciardiello, Alessandro Iacobelli, Anna Lisa Cammarota, Paola Manzo, Jelena Dimitrov, Arianna Mauro, Margot De Marco, Liberato Marzullo and Alessandra Rosati
Cancers 2025, 17(11), 1843; https://doi.org/10.3390/cancers17111843 - 31 May 2025
Viewed by 620
Abstract
Background: Head and neck squamous cell carcinoma (HNSCC) exhibit considerable heterogeneity, complicating the prediction of disease progression and treatment response. Consequently, researchers are actively investigating reliable biomarkers to forecast disease trajectories and inform therapeutic decisions. This study examines the role of BAG3, a [...] Read more.
Background: Head and neck squamous cell carcinoma (HNSCC) exhibit considerable heterogeneity, complicating the prediction of disease progression and treatment response. Consequently, researchers are actively investigating reliable biomarkers to forecast disease trajectories and inform therapeutic decisions. This study examines the role of BAG3, a protein involved in cell survival and stress response, as a potential predictive marker in HNSCC. The objective is to analyze BAG3 expression across various HNSCC types and correlate it with disease-free survival (DFS), aiming to elucidate the influence of BAG3 positivity on cancer progression. Methods: A multi-institutional retrospective study was conducted by analyzing BAG3 expression by immunohistochemistry in 104 tissue samples from patients with head and neck squamous cell carcinoma (HNSCC). The data were then correlated with DFS to assess the impact of BAG3 positivity on prognosis. Results: Immunohistochemical analysis of primary tumor samples collected from therapy-naive patients showed that BAG3 positivity was widespread across different head and neck cancer sites, with no significant correlation to sex, smoking status, HPV infection, tumor location, grade, or TNM parameters. However, BAG3 high positive patients had shorter DFS (median 23.2 months) compared to BAG3-negative patients (median 31.3 months). Cox analysis revealed that BAG3 high expression by IHC was associated with a more than 3-fold increased risk of disease recurrence. Conclusions: This study is the first to explore BAG3 as a biomarker for HNSCC recurrence. While preliminary findings suggest a link between BAG3 positivity and increased recurrence risk, further research is needed to validate these results. Prospective studies could help establish BAG3’s prognostic value and potentially lead to more personalized treatment approaches for HNSCC. Full article
(This article belongs to the Special Issue New Biomarkers in Cancers 2nd Edition)
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16 pages, 4031 KiB  
Article
Oxidative DNA Damage and Repair Dynamics in Multiple Sclerosis: Insights from Comet Assay Kinetics, Base Excision Repair Gene Expression, and Genotype Analysis
by Beata Filipek, Anna Macieja, Aleksandra Binda, Rafal Szelenberger, Leslaw Gorniak, Elzbieta Miller, Mariola Swiderek-Matysiak, Mariusz Stasiolek, Ireneusz Majsterek and Tomasz Poplawski
Biomolecules 2025, 15(6), 756; https://doi.org/10.3390/biom15060756 - 24 May 2025
Cited by 1 | Viewed by 635
Abstract
Multiple sclerosis (MS) is a neuroinflammatory disease where oxidative stress and DNA damage may influence disease progression. We investigated whether defects in base excision repair (BER) pathways contribute to MS by combining functional DNA repair assays, gene expression profiling, and genotype analysis. We [...] Read more.
Multiple sclerosis (MS) is a neuroinflammatory disease where oxidative stress and DNA damage may influence disease progression. We investigated whether defects in base excision repair (BER) pathways contribute to MS by combining functional DNA repair assays, gene expression profiling, and genotype analysis. We collected peripheral blood mononuclear cells from 70 MS patients and 61 healthy controls. These cells were subjected to tert-butyl hydroperoxide (TBH)-induced oxidative stress, and comet assay kinetics were measured over a period of 60 min. Additionally, we quantified the mRNA expression of nine key BER genes and genotyped selected polymorphisms related to DNA repair capacity. Samples from MS patients exhibited significantly higher levels of TBH-induced DNA lesions and displayed a distinct repair trajectory over time, as indicated by area-under-the-curve (AUC) analyses (p < 0.001). The transcripts of MBD4 and NTHL1 were notably reduced in MS patients compared to those in the controls (p < 0.0001). A logistic regression analysis revealed an association between the specific BER-related single nucleotide polymorphisms (SNPs) rs3087404, rs4135054, and rs1052133 and ineffective DNA repair. Subset analyses of B cells, CD4+ cells, and CD8+ cells further supported the presence of altered repair kinetics in MS, even though some subsets exhibited similar baseline lesion levels. Our findings suggest that impaired oxidative DNA repair is present in MS, likely driven by functional deficits in repair kinetics and alterations in the expression of BER genes and polymorphisms. This integrated approach highlights DNA repair pathways as potential therapeutic or prognostic targets in MS. Full article
(This article belongs to the Special Issue DNA Damage, Mutagenesis, and Repair Mechanisms)
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23 pages, 3043 KiB  
Article
Evaluation of Acute Pancreatitis Severity and Prognosis Using the Aggregate Systemic Inflammation Index (AISI) as a New Marker: A Comparison with Other Inflammatory Indices
by Oğuzhan Zengin, Burak Göre, Oğuz Öztürk, Arap Merve Cengiz, Senanur Güler Kadıoğlu, Emra Asfuroğlu Kalkan and İhsan Ateş
J. Clin. Med. 2025, 14(10), 3419; https://doi.org/10.3390/jcm14103419 - 14 May 2025
Viewed by 1228
Abstract
Background/Objectives: Acute pancreatitis (AP) remains a pressing clinical challenge, largely due to its potential to lead to life-threatening complications and increased mortality. Over the years, numerous tools have been proposed to evaluate the intensity of AP and estimate likely health outcomes. Despite their [...] Read more.
Background/Objectives: Acute pancreatitis (AP) remains a pressing clinical challenge, largely due to its potential to lead to life-threatening complications and increased mortality. Over the years, numerous tools have been proposed to evaluate the intensity of AP and estimate likely health outcomes. Despite their usefulness, many of these assessment models are complex and rely on a wide array of clinical inputs, making them less practical in everyday healthcare settings. In contrast, the Aggregate Systemic Inflammation Index (AISI), which is calculated using routine blood count parameters, provides a simpler and more inclusive approach to measuring systemic inflammation. This research focuses on examining how effectively AISI can be used to gauge disease severity and project clinical trajectories in individuals affected by pancreatitis. Methods: This retrospective study reviewed the medical records of 412 individuals diagnosed with acute pancreatitis, all of whom received care at the Internal Medicine Clinic of Ankara Bilkent City Hospital between 1 April 2019 and 1 September 2024. The investigation encompassed a thorough analysis of patients’ demographic characteristics, lab parameters, and clinical findings, with special attention given to inflammatory markers, including the Aggregate Systemic Inflammation Index (AISI), its revised version, the Platelet-to-Lymphocyte Ratio (PLR), the Neutrophil-to-Lymphocyte Ratio (NLR), and the Systemic Inflammatory Response Index (SIRI). Comparative analyses between groups were performed using independent sample t-tests and one-way ANOVA, complemented by Tukey’s post hoc tests where appropriate. Correlations among continuous variables were determined through Pearson’s analysis, and the prognostic accuracy of both AISI and its modified form was assessed using Receiver Operating Characteristic (ROC) curve methodology. Results: The mean age among participants was 63.47 ± 17.92 years, while the average AISI value was calculated as 1183.89 ± 1067.42. Both the original and modified versions of the AISI index showed strong positive correlations with several key clinical measures, including prolonged hospitalization, a Glasgow score of 2 or above, BISAP, Ranson scoring, the revised Atlanta classification, and APACHE II. AISI was also significantly linked to the presence of complications and overall mortality (p < 0.01). Analysis through ROC curves demonstrated that an AISI level above 236.626 effectively predicted hospital stays exceeding 10 days, with a sensitivity of 94.40% and a specificity of 91.00%. Moreover, both AISI and its modified form reliably distinguished patients who had a Ranson score of zero, with high diagnostic accuracy. Conclusions: AISI and its modified version demonstrate a strong association with both the intensity and clinical course of acute pancreatitis. Thanks to their simplicity, low cost, and broad usability in healthcare settings, these indices hold considerable promise as practical and dependable tools for assessing the severity and likely outcomes of this increasingly prevalent disease. Full article
(This article belongs to the Section Gastroenterology & Hepatopancreatobiliary Medicine)
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