Sign in to use this feature.

Years

Between: -

Subjects

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Journals

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Article Types

Countries / Regions

remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline
remove_circle_outline

Search Results (2,964)

Search Parameters:
Keywords = cell cycle control

Order results
Result details
Results per page
Select all
Export citation of selected articles as:
23 pages, 1594 KB  
Article
Metabolomics of Multiple System Atrophy Patient-Derived Striatal Medium Spiny Neurons
by Nadine J. Smandzich, Heike Bähre, Thomas Gschwendtberger, Stephan Greten, Lan Ye, Martin Klietz, Alessio Di Fonzo, Lisa M. Henkel and Florian Wegner
Biomolecules 2026, 16(2), 190; https://doi.org/10.3390/biom16020190 - 26 Jan 2026
Abstract
In multiple system atrophy (MSA), the fatal movement disorder, cell populations of the striatum and other subcortical brain regions degenerate, leading to a rapidly progressive, atypical Parkinsonian syndrome. The pathophysiology of neurons and glial cells shows misfolding, aggregation, and increased release of the [...] Read more.
In multiple system atrophy (MSA), the fatal movement disorder, cell populations of the striatum and other subcortical brain regions degenerate, leading to a rapidly progressive, atypical Parkinsonian syndrome. The pathophysiology of neurons and glial cells shows misfolding, aggregation, and increased release of the protein α-synuclein. In addition, neuronal hypoexcitability, a reduction in the activity of the mitochondrial respiratory chain, and a dysregulation of the enzymes involved in the biosynthesis of coenzyme Q10 were observed in human stem-cell models. In this study, untargeted and targeted metabolome analyses were performed with MSA patient-derived GABAergic striatal medium spiny neurons focusing on the citrate cycle and mitochondrial respiratory chain. The results indicate a significant decrease in succinate and ATP as well as an imbalanced NAD+/NADH ratio of MSA cell lines compared to matched healthy controls, suggesting alterations in mitochondrial processes which may facilitate neurodegeneration. Full article
(This article belongs to the Special Issue Advances in Metabolomics in Health and Disease)
17 pages, 4317 KB  
Article
Natural Genetic Variation Impacts Stress-Induced Quiescence and Regeneration in Response to Rapamycin
by Sahiti Peddibhotla, Miriam Gonzaga, Tricia Zhang, Yasha Goel, Jun Sun, Benjamin R. Harrison, Daniel E. L. Promislow and Hannele Ruohola-Baker
Cells 2026, 15(3), 236; https://doi.org/10.3390/cells15030236 - 26 Jan 2026
Abstract
In response to ionizing radiation (IR), both adult and cancer stem cells enter reversible cell cycle arrest at the G1/S transition to evade apoptosis and subsequently re-enter the cell cycle to regenerate damaged tissue. Entry into and exit from this arrest, known as [...] Read more.
In response to ionizing radiation (IR), both adult and cancer stem cells enter reversible cell cycle arrest at the G1/S transition to evade apoptosis and subsequently re-enter the cell cycle to regenerate damaged tissue. Entry into and exit from this arrest, known as “quiescence,” is governed by the inhibition of mTORC1. The pharmacological suppression of mTORC1 with rapamycin prevents quiescent stem cells from re-entering the cell cycle and impairs tissue regeneration. Rapamycin holds great therapeutic promise in preventing tumor regrowth from dormant cancer stem cells. Yet the extent to which genetic background impacts the known variation in the pharmacological response of rapamycin remains unknown. Here, we show that natural genetic variation across the Drosophila Genetics Reference Panel (DGRP) drives substantial differences in the rapamycin-mediated suppression of post-IR quiescence and regeneration. To define the basis of this differential sensitivity, we examined mitochondrial turnover and DNA damage repair—processes controlling IR-induced dormancy. Our analyses reveal that variation in rapamycin sensitivity is more strongly associated with differences in mitochondrial dynamics than with DNA damage response following radiation. Together, these findings demonstrate that genetic background is a critical determinant of rapamycin efficacy and identify mitochondrial regulation as a key mechanism underlying differential therapeutic response. Full article
(This article belongs to the Special Issue Genetics and Gene Regulation)
Show Figures

Figure 1

31 pages, 706 KB  
Article
Applying Action Research to Developing a GPT-Based Assistant for Construction Cost Code Verification in State-Funded Projects in Vietnam
by Quan T. Nguyen, Thuy-Binh Pham, Hai Phong Bui and Po-Han Chen
Buildings 2026, 16(3), 499; https://doi.org/10.3390/buildings16030499 - 26 Jan 2026
Abstract
Cost code verification in state-funded construction projects remains a labor-intensive and error-prone task, particularly given the structural heterogeneity of project estimates and the prevalence of malformed codes, inconsistent units of measurement (UoMs), and locally modified price components. This study evaluates a deterministic GPT-based [...] Read more.
Cost code verification in state-funded construction projects remains a labor-intensive and error-prone task, particularly given the structural heterogeneity of project estimates and the prevalence of malformed codes, inconsistent units of measurement (UoMs), and locally modified price components. This study evaluates a deterministic GPT-based assistant designed to automate Vietnam’s regulatory verification. The assistant was developed and iteratively refined across four Action Research cycles. Also, the system enforces strict rule sequencing and dataset grounding via Python-governed computations. Rather than relying on probabilistic or semantic reasoning, the system performs strictly deterministic checks on code validity, UoM alignment, and unit price conformity in material (MTR), labor (LBR), and machinery (MCR), given the provincial unit price books (UPBs). Deterministic equality is evaluated either on raw numerical values or on values transformed through explicitly declared, rule-governed operations, preserving auditability without introducing tolerance-based or inferential reasoning. A dedicated exact-match mechanism, which is activated only when a code is invalid, enables the recovery of typographical errors only when a project item’s full price vector well matches a normative entry. Using twenty real construction estimates (16,100 rows) and twelve controlled error-injection cases, the study demonstrates that the assistant executes verification steps with high reliability across diverse spreadsheet structures, avoiding ambiguity and maintaining full auditability. Deterministic extraction and normalization routines facilitate robust handling of displaced headers, merged cells, and non-standard labeling, while structured reporting provides line-by-line traceability aligned with professional verification workflows. Practitioner feedback confirms that the system reduces manual tracing effort, improves evaluation consistency, and supports documentation compliance with human judgment. This research contributes a framework for large language model (LLM)-orchestrated verification, demonstrating how Action Research can align AI tools with domain expectations. Furthermore, it establishes a methodology for deploying LLMs in safety-critical and regulation-driven environments. Limitations—including narrow diagnostic scope, unlisted quotation exclusion, single-province UPB compliance, and sensitivity to extreme spreadsheet irregularities—define directions for future deterministic extensions. Overall, the findings illustrate how tightly constrained LLM configurations can augment, rather than replace, professional cost verification practices in public-sector construction. Full article
(This article belongs to the Special Issue Knowledge Management in the Building and Construction Industry)
Show Figures

Figure 1

25 pages, 9799 KB  
Article
Design and Validation of a Multi-Modal Bioreactor System: Assessing the Effects of Perfusion and Cyclic Tensile Stimulation on Mechanical and Biological Properties of 3D-Printed Missing-Rib Auxetic Scaffolds
by Tavila Sharmin, Sakhawat Hossan and Rohan A. Shirwaiker
Bioengineering 2026, 13(2), 140; https://doi.org/10.3390/bioengineering13020140 - 26 Jan 2026
Abstract
Bioreactors used for the maturation of cell-seeded tissue-engineered scaffolds should essentially mimic the dynamic in vivo environments experienced by the native tissues they intend to substitute. In addition to perfusion of growth medium to facilitate continuous mass transfer, application of appropriate mechanical stimulation [...] Read more.
Bioreactors used for the maturation of cell-seeded tissue-engineered scaffolds should essentially mimic the dynamic in vivo environments experienced by the native tissues they intend to substitute. In addition to perfusion of growth medium to facilitate continuous mass transfer, application of appropriate mechanical stimulation is important to enhance cellular responses in scaffolds for tissues such as tendons, skin, and cardiac muscle that experience dynamic loading. This study focuses on the development of a multi-modal custom bioreactor capable of applying cyclic tensile stimulation and perfusion within physiologically relevant ranges while minimizing shear stress detrimental to cells seeded on scaffolds. To validate the bioreactor design and operation, we assessed the effects of tensile stimulation (0.1 Hz, 2000 cycles/day) and perfusion (media flow rate = 0.15 mL/min) over 21 days on the biofunctional performance of 3D-bioplotted polycaprolactone (PCL) auxetic scaffolds with a representative design (missing-rib pattern) characterized by negative Poisson’s ratio similar to the aforementioned soft tissues. The scaffold had a tensile yield strain of 9.14%, yield strength of 0.25 MPa, elastic modulus of 2.85 MPa, and ultimate tensile strength (UTS) of 1.32 MPa. The application of perfusion and tensile stimulation (0–5% cyclic strain) for 21 days did not adversely affect the yield strength and elastic modulus of the scaffold but affected its UTS (22.5% decrease) compared to the control cultured without perfusion or stimulation. Notably, it resulted in significantly improved fibroblast cellular responses (DNA = 29 µg/g sample and collagen = 371.78 µg/g sample) compared to the control (7.52 µg/g sample and 163.51 µg/g sample, respectively). These results validate the bioreactor system operation and the ability of multi-modal stimulation to control biofunctional responses of auxetic scaffolds, which will serve as the basis for future studies that will optimize auxetic scaffold design and dynamic culture parameters for NPR tissue-specific applications. Full article
Show Figures

Figure 1

35 pages, 2059 KB  
Review
Phage Therapy in Plant Disease Management: 110 Years of History, Current Challenges, and Future Trends
by Botond Zsombor Pertics, Lóránt Király, Zoltán Bozsó, Dániel Krüzselyi, Judit Kolozsváriné Nagy, András Künstler, Ferenc Samu and Ildikó Schwarczinger
Plants 2026, 15(3), 368; https://doi.org/10.3390/plants15030368 - 24 Jan 2026
Viewed by 54
Abstract
Bacteriophages, or phages, are viruses that specifically infect and lyse bacterial cells. Since their discovery 110 years ago, they have held a unique place in microbiology, medicine, and agriculture as both scientific tools and potential therapeutic agents. The concept of employing phages to [...] Read more.
Bacteriophages, or phages, are viruses that specifically infect and lyse bacterial cells. Since their discovery 110 years ago, they have held a unique place in microbiology, medicine, and agriculture as both scientific tools and potential therapeutic agents. The concept of employing phages to combat bacterial infections, known as phage therapy, predates the antibiotic era and has undergone cycles of enthusiasm, neglect, and revival. Initially explored in the early 20th century, phage therapy offered a targeted biological approach to bacterial disease control. However, the widespread adoption of antibiotics led to a significant reduction in phage research, which only regained momentum in recent decades owing to the global rise of antibiotic-resistant bacteria and increasing demand for environmentally sustainable disease management strategies. This review traces the complete timeline of this history, highlighting key milestones in phage discovery, molecular microbiology, the antibiotic era, and the resulting critical events that spurred the modern phage renaissance in plant disease management. Finally, the significance of cutting-edge integration of synthetic biology, advanced phage delivery systems, and artificial intelligence (AI), which could drive the development of next-generation biopesticides, is also discussed. Full article
Show Figures

Figure 1

23 pages, 6517 KB  
Article
Molecular Characterization of Muscle-Invasive Bladder Cancer: Key MicroRNAs, Transcription Factors, and Differentially Expressed Genes
by Venhar Gurbuz Can
Genes 2026, 17(2), 122; https://doi.org/10.3390/genes17020122 - 24 Jan 2026
Viewed by 53
Abstract
Background: The present study set out to identify key miRNAs, TFs and signaling pathways associated with bladder cancer, with a view to elucidating the networks of miRNA-TF-gene interactions that may serve as potential molecular biomarkers for disease diagnosis. Methods: An integrative analysis was [...] Read more.
Background: The present study set out to identify key miRNAs, TFs and signaling pathways associated with bladder cancer, with a view to elucidating the networks of miRNA-TF-gene interactions that may serve as potential molecular biomarkers for disease diagnosis. Methods: An integrative analysis was conducted using the publicly available microarray dataset GSE130598. Expression profanalyzede analyzed from 42 muscle-invasive bladder cancer (MIBC) tissues and 42 matched adjacent normal bladder tissues. After data preprocessing and normalization, differentially expressed genes (DEGs) were identified. To identify the associated biological processes and signaling pathways, functional enrichment analyses were conducted using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Protein–protein interaction (PPI) network analysis was then employed to identify hub genes and key molecular interaction modules associated with bladder cancer. Results: MYC, TP53, SP1, E2F1, E2F3, NFKB1, and TWIST1 were identified as central transcriptional regulators, indicating their roles in controlling genes involved in cell cycle regulation, DNA damage response, and tumor progression. Several miRNA families, including miR-200, miR-17, miR-29, miR-141, and miR-548, have been identified as key post-transcriptional regulators, suggesting their involvement in oncogenic signaling and cellular differentiation. PPI network analysis revealed MAPK3, AKT1, CHEK1, CDK1, AURKA, and AURKB as hub genes associated with cell proliferation, mitotic control, and intracellular signaling. Conclusions: Fundamental molecular processes underlying bladder cancer pathogenesis include cell cycle control, signal transduction, and genomic stability. These findings provide insight into the molecular regulatory landscape of MIBC and highlight potential targets for diagnostic and prognostic applications. Full article
(This article belongs to the Section Molecular Genetics and Genomics)
Show Figures

Figure 1

16 pages, 14226 KB  
Article
Preparation of a Magnetic Ti-IMAC Material Based on Thiol-Ene Click Reaction and the Application in Intact Phosphoprotein Enrichment
by Yan Lu, Sen Zhang, Hong-Yan Ge, Han-Yue Yang, Feng Zhang, Yi-Fan Pan and Hong-Zhen Lian
Molecules 2026, 31(3), 396; https://doi.org/10.3390/molecules31030396 - 23 Jan 2026
Viewed by 149
Abstract
Protein phosphorylation is a crucial post-translational modification that regulates protein activity, cellular signaling, transcriptional regulation, and cell cycle control. However, the analysis of phosphoproteins in biological samples is often compromised by complex sample matrices and interference from high-abundance proteins. While the top-down phosphoproteomics [...] Read more.
Protein phosphorylation is a crucial post-translational modification that regulates protein activity, cellular signaling, transcriptional regulation, and cell cycle control. However, the analysis of phosphoproteins in biological samples is often compromised by complex sample matrices and interference from high-abundance proteins. While the top-down phosphoproteomics strategy enables comprehensive analysis of post-translational modifications based on intact proteins, its requirement for higher protein purity due to low protein ionization efficiency poses stern challenges. Consequently, developing appropriate enrichment methods for phosphoproteins in practical samples becomes essential. Immobilized metal ion affinity chromatography (IMAC) represents a common strategy for phosphorylated protein separation and enrichment. Among metal ions, Ti4+ has gained widespread application as IMAC chelating ligands due to its capacity to form multiple coordination networks and its high selectivity for phosphorylated protein enrichment, leveraging the strong chelating ability of phosphate groups toward metal ions. This paper presents the design and preparation of a novel magnetic Ti-IMAC nanocomposite, MNP@MPTMS–VPA–Ti(IV). The material is modified with phosphate groups via facile thiol-ene click chemistry and then immobilizes Ti4+, enabling selective enrichment of intact phosphoproteins through IMAC affinity. The efficiency of enrichment was evaluated using subsequent matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for detection and analysis. This Ti-IMAC material-based magnetic solid-phase extraction (MSPE)-MALDI-TOF MS protocol has been successfully applied to enrich intact phosphoproteins in milk and eel mucus with high selectivity, sensitivity, and suitability. Full article
(This article belongs to the Section Analytical Chemistry)
Show Figures

Figure 1

17 pages, 4757 KB  
Article
Antiviral Activity of Eugenol Against Chinese Rice-Field Eel Rhabdovirus in Monopterus albus
by Jingwen Jiang, Mingyang Xue, Wenzhi Liu, Yong Zhou, Yiqun Li and Yuding Fan
Animals 2026, 16(2), 315; https://doi.org/10.3390/ani16020315 - 20 Jan 2026
Viewed by 106
Abstract
Chinese rice-field eel rhabdovirus (CrERV) is a serious epidemic pathogen of Chinese rice-field eel and causes severe economic losses to aquaculture. However, there are no commercial drugs presently available to control CrERV infection. Eugenol is a bioactive compound extracted from clove plants and [...] Read more.
Chinese rice-field eel rhabdovirus (CrERV) is a serious epidemic pathogen of Chinese rice-field eel and causes severe economic losses to aquaculture. However, there are no commercial drugs presently available to control CrERV infection. Eugenol is a bioactive compound extracted from clove plants and exhibits potential antiviral activity. In the study, the antiviral activity of eugenol against CrERV was investigated in Chinese rice-field eel (Monopterus albus). Eugenol reached the highest inhibition rate of 96.6% at 40 mg/L in Chinese rice-field eel kidney cells (CrEK). Notably, eugenol exhibits antiviral activity by directly targeting CrERV and additionally confers prophylactic effects against infection via its action on CrEK cells. The results of exploring the viral invasion cycle demonstrated that eugenol primarily exerted its antiviral effect during the middle stage and late stage (12 h and 24 h) of viral infection. In addition, eugenol inhibited CrERV-induced apoptosis of CrEK cells, maintained mitochondrial membrane potential levels, maintained physiological cellular morphology and structure, and protected cells from loss of cellular morphology, formation of apoptotic vesicles, and cell fragmentation. For the in vivo study, eugenol increased the survival rate of CrERV-infected rice-field eel by 56% and 48%, in prevention experiments and treatment experiments, respectively. Concurrently, eugenol significantly reduced viral loads and induced the upregulation of anti-inflammatory and antioxidant genes, indicating its potential for immunoregulation. In summary, eugenol holds potential for both preventing and treating CrERV infections in the aquaculture context. Full article
(This article belongs to the Section Aquatic Animals)
Show Figures

Figure 1

24 pages, 8647 KB  
Article
Mechanical Insights into the Distinct Effects of Ovariectomy Versus Adrenalectomy on Age-Related Thymic Atrophy in Female Mice
by Junan Chen, Xudong Zhou, Ling Wei, Zixuan Tian, Haozhe Zeng, Fei Yan, Junhua Zhou, Xianyin Zeng, Fengyan Meng, Xiaohan Cao, Haozhou Li and Xingfa Han
Int. J. Mol. Sci. 2026, 27(2), 1022; https://doi.org/10.3390/ijms27021022 - 20 Jan 2026
Viewed by 108
Abstract
Age-related thymic atrophy, a hallmark of immunosenescence linked to age-related diseases, involves gonadal and adrenal steroid hormones, but their distinct roles and mechanisms in this process remain unclear. Through biochemical, histological, and RNA-seq analyses, we comprehensively explored the mechanisms underpinning age-related thymic atrophy [...] Read more.
Age-related thymic atrophy, a hallmark of immunosenescence linked to age-related diseases, involves gonadal and adrenal steroid hormones, but their distinct roles and mechanisms in this process remain unclear. Through biochemical, histological, and RNA-seq analyses, we comprehensively explored the mechanisms underpinning age-related thymic atrophy in response to ovariectomy (OVX) versus adrenalectomy (ADX) in female mice. Compared to the sham controls, OVX overtly ameliorated age-related thymic atrophy, as evidenced by increased thymus mass, a larger gross thymus area, and denser cortex cellularity. In contrast, ADX evidently accelerated age-related thymic atrophy, characterized by increased adipose infiltration and decreased cortex/medulla ratio, obscure cortico-medullary junctions, and sparser thymic cortical cells. Unexpectedly, combined OVX and ADX displayed a more pronounced effect than OVX alone in ameliorating age-related thymic atrophy. Mechanistically, OVX decreased while ADX increased the circulating 17β-estradiol levels in female mice, which drove these opposing outcomes potentially by promoting Pparg-mediated thymic fat deposition and blocking Cdk1-dependent thymocyte cell cycle progression. Although OVX eliminated gonadal 17β-estradiol production, it appeared to trigger a compensatory adrenal-dependent estrogen biosynthesis, whereas combined OVX and ADX nearly eliminated all estrogen sources, thus leading to a more pronounced effect than OVX alone in ameliorating age-related thymic atrophy in female mice. Notably, OVX increased while ADX decreased serum corticosterone levels, but these alterations exerted minimal impacts on age-related thymic atrophy, highlighting a pivotal role of estrogens over glucocorticoids in accelerating age-related thymic atrophy in females. Undesirably, although OVX ameliorated age-related thymic atrophy, it appeared to simultaneously increase autoimmune susceptibility by downregulating thymic Cd74 expression. Taken together, our results indicate that OVX ameliorates while ADX accelerates age-related thymic atrophy in females. Estrogens rather than glucocorticoids act as the predominant regulator of this process, potentially via promoting Pparg-dependent fat deposition and blocking Cdk1-dependent thymocyte cycle progression. However, OVX-induced estrogen depletion also elevated autoimmune risk, emphasizing the need to balance benefits and risks in regulating thymic aging. Full article
(This article belongs to the Section Molecular Endocrinology and Metabolism)
Show Figures

Figure 1

9 pages, 1389 KB  
Case Report
Progressive Destructive Hypothyroidism Associated with Sunitinib Therapy: A Three-Year Case Analysis
by Marcin Nosal
J. Clin. Med. 2026, 15(2), 788; https://doi.org/10.3390/jcm15020788 - 19 Jan 2026
Viewed by 78
Abstract
Sunitinib, a tyrosine kinase inhibitor (TKI) targeting vascular endothelial growth factor receptors (VEGFRs) and platelet-derived growth factor receptors (PDGFRs), is widely used in renal cell carcinoma. A broad spectrum of thyroid dysfunctions has been observed during TKI therapy, yet their mechanisms and clinical [...] Read more.
Sunitinib, a tyrosine kinase inhibitor (TKI) targeting vascular endothelial growth factor receptors (VEGFRs) and platelet-derived growth factor receptors (PDGFRs), is widely used in renal cell carcinoma. A broad spectrum of thyroid dysfunctions has been observed during TKI therapy, yet their mechanisms and clinical progression remain only partially explained. A longitudinal case analysis of a woman with metastatic clear-cell renal cell carcinoma treated with cyclical sunitinib therapy (4 weeks on, 2 weeks off) was performed. Thyroid function tests, clinical symptoms, and ultrasound imaging findings were evaluated over time and compared with treatment exposure and dose adjustments. Baseline thyroid function was normal. During the third cycle, thyroid-stimulating hormone (TSH) increased markedly (33.44–41.26 mIU/L), with free thyroid hormones initially remaining within reference limits. TSH fluctuations corresponded to treatment intervals before stabilising into persistent hypothyroidism requiring levothyroxine replacement. Thyroid ultrasound revealed progressive parenchymal destruction and a reduction in gland volume from 18 mL to approximately 2 mL over three years. Endocrine management enabled maintenance of biochemical euthyroidism, and systemic oncological treatment continued without interruption. Sunitinib treatment may lead to progressive destructive hypothyroidism. Routine surveillance of thyroid function is essential, and timely levothyroxine therapy facilitates continued anticancer treatment and symptom control. Full article
(This article belongs to the Section Endocrinology & Metabolism)
Show Figures

Figure 1

20 pages, 1619 KB  
Article
Ensemble Machine Learning on Bulk RNA-Seq Identifies 17-Gene Signature Predicting Neoadjuvant Chemotherapy Response in Breast Cancer
by Stelios Lamprou, Styliana Georgiou, Triantafyllos Stylianopoulos and Chrysovalantis Voutouri
Curr. Issues Mol. Biol. 2026, 48(1), 94; https://doi.org/10.3390/cimb48010094 - 16 Jan 2026
Viewed by 176
Abstract
Predicting neoadjuvant chemotherapy response in breast cancer remains critical for optimizing treatment strategies, yet robust predictive biomarkers are lacking. This study implemented an ensemble machine learning approach to identify a gene expression signature predicting pathological complete response (pCR) versus residual disease (RD) using [...] Read more.
Predicting neoadjuvant chemotherapy response in breast cancer remains critical for optimizing treatment strategies, yet robust predictive biomarkers are lacking. This study implemented an ensemble machine learning approach to identify a gene expression signature predicting pathological complete response (pCR) versus residual disease (RD) using bulk RNA-sequencing data from GSE163882 (138 RD, 80 pCR). We employed TMM normalization with differential expression analysis (250 genes, FDR < 0.05, |log2FC| ≥ 1), ensemble feature selection across five classifiers (Random Forest, Gradient Boosting, SVM, k-NN, and Neural Network) with 10-fold repeated cross-validation, and stacked ensemble development. Consensus selection identified a 17-gene signature consistently ranked across algorithms. The stacked ensemble achieved 0.97 AUC post-testing on hold-out test data. External validation on the independent GSE240671 cohort (37 pCR, 25 RD) following ComBat batch correction achieved ROC AUC of 0.78 and PR AUC of 0.85 with isotonic calibration, demonstrating balanced accuracy of 0.71 and 0.86 sensitivity for pCR detection. Pathway enrichment revealed associations with cell cycle regulation (E2F3, MKI67), DNA repair (BRCA2), and transcriptional control (MED1), with six priority genes (MED1, BRCA2, E2F3, PITPNB, H1-1, and FARP2) showing established breast cancer relevance. This externally validated 17-gene signature provides a biologically grounded tool for NAC response prediction in precision oncology. Full article
(This article belongs to the Special Issue Gene Expression and Regulation in Cancer)
Show Figures

Figure 1

16 pages, 10343 KB  
Article
Circulating Naïve Regulatory T Cell Subset Displaying Increased STAT5 Phosphorylation During Controlled Ovarian Hyperstimulation Is Associated with Clinical Pregnancy and Progesterone Levels
by Ksenija Rakić, Aleš Goropevšek, Nejc Kozar, Borut Kovačič, Sara Čurič, Andreja Zakelšek, Evgenija Homšak and Milan Reljič
Int. J. Mol. Sci. 2026, 27(2), 922; https://doi.org/10.3390/ijms27020922 - 16 Jan 2026
Viewed by 101
Abstract
Regulatory T cells (Tregs), particularly their phenotypically distinct subpopulations, are critical for the establishment of maternal immune tolerance during embryo implantation. Despite advances in assisted reproductive technologies, implantation failure remains a frequent and often unexplained clinical challenge. Variations in Treg frequency and phenotype [...] Read more.
Regulatory T cells (Tregs), particularly their phenotypically distinct subpopulations, are critical for the establishment of maternal immune tolerance during embryo implantation. Despite advances in assisted reproductive technologies, implantation failure remains a frequent and often unexplained clinical challenge. Variations in Treg frequency and phenotype have been proposed to influence implantation success, particularly under differing hormonal conditions. This study aimed to investigate peripheral blood Treg levels and their subpopulations on the day of blastocyst transfer in both stimulated in vitro fertilization (IVF/ICSI) cycles involving controlled ovarian hyperstimulation (COH) and true natural cycles with frozen embryo transfer (FET), and to examine their associations with systemic hormone levels and anti-Müllerian hormone (AMH). A prospective observational study was conducted including women undergoing IVF/ICSI with fresh embryo transfer (ET) and women undergoing natural cycle FET. Peripheral blood samples were collected on the day of ET and analyzed using 13-colour flow cytometry, enabling detailed subdivision of Tregs into multiple subpopulations based on the expression of differentiation and chemokine markers, including CXCR5. In addition, because common γ-chain cytokines may influence pregnancy success by modulating the balance between suppressive Treg and non-Treg subsets, intracellular STAT5 signaling was assessed using phospho-specific flow cytometry. Serum estradiol, progesterone, FSH, LH, and AMH levels were measured in parallel. Significant differences were observed in Treg subpopulation distributions between women who conceived and those who did not. Higher frequencies of naïve CXCR5 Tregs were associated with clinical pregnancy, independent of age, and correlated with serum progesterone levels. Moreover, both naïve Treg frequency and enhanced IL-7-dependent STAT5 signaling in naïve Tregs from women undergoing COH were associated with AMH levels, suggesting a link between ovarian reserve and Treg homeostasis mediated by signal transducer and activator of transcription 5 (STAT5) signaling. In conclusion, Treg subpopulations, particularly CXCR5 naïve Tregs, appear to play a central role in implantation success following ET. Their distribution differs between stimulated and natural cycles and is influenced by systemic progesterone levels and STAT5 signaling. These findings suggest that peripheral Treg profiling may represent a potential biomarker of implantation competence and could inform personalized approaches in assisted reproduction. Full article
(This article belongs to the Section Molecular Biology)
Show Figures

Figure 1

14 pages, 633 KB  
Article
Genomic Landscape of Thymic Carcinoma: A Large-Scale Analysis of Somatic Mutations, Demographic Disparities, and Metastatic Drivers from the AACR Project GENIE® Cohort
by Aden V. Chudziak, Tyson J. Morris, David Maliy, Grace S. Saglimbeni, Akaash Surendra, Beau Hsia, Huijun Li and Abubakar Tauseef
Curr. Issues Mol. Biol. 2026, 48(1), 90; https://doi.org/10.3390/cimb48010090 - 16 Jan 2026
Viewed by 212
Abstract
Thymic carcinoma (TC) is a rare and aggressive malignancy with poor prognosis, and its genomic landscape remains incompletely defined. Identifying the somatic alterations that shape TC biology is essential for improving diagnostic precision, developing targeted therapies, and informing early detection strategies. We performed [...] Read more.
Thymic carcinoma (TC) is a rare and aggressive malignancy with poor prognosis, and its genomic landscape remains incompletely defined. Identifying the somatic alterations that shape TC biology is essential for improving diagnostic precision, developing targeted therapies, and informing early detection strategies. We performed a retrospective genomic analysis of 141 TC tumor specimens from 134 patients using de-identified data from the American Association for Cancer Research (AACR) Project GENIE® database. Somatic mutations and copy number alterations (CNAs) were characterized, and statistical analyses were conducted to evaluate associations with patient demographics (sex, race) and tumor site (primary vs. metastatic). The cohort was predominantly male (56.7%) and White (56.7%). The most frequently altered genes were TP53 (27.7%), CYLD (17.6%), and CDKN2A (12.1%). Recurrent homozygous deletions at chromosome 9p21.3 involving CDKN2A and CDKN2B were common. Sex-stratified analysis revealed several significant male-specific alterations. Although the Pacific Islander subgroup was small (n = 2), preliminary analysis suggested enrichment of alterations in key cancer-associated genes, including TP53, BRCA1, and STAT5B, underscoring the need for diverse representation in TC genomics. Notably, MTOR mutations were significantly enriched in a subset of local recurrences and lymph node metastases (n = 3; q = 0.013), suggesting a potential role in disease progression. This large-scale genomic analysis reinforces the central involvement of TP53, cell-cycle control, and chromatin-modifying pathways in TC. The identification of sex-associated and race-associated mutational patterns, together with the enrichment of MTOR alterations in recurrent and metastatic disease, highlights biologically plausible mechanisms of progression and potential therapeutic vulnerabilities. These findings support the value of comprehensive genomic profiling in TC and emphasize the need for prospective, multi-omic studies to validate these observations and guide the development of more personalized treatment strategies. Full article
(This article belongs to the Special Issue Linking Genomic Changes with Cancer in the NGS Era, 3rd Edition)
Show Figures

Figure 1

14 pages, 436 KB  
Article
Real-World Clinical Experience of First-Line Ribociclib Combined with an Aromatase Inhibitor in Metastatic Breast Cancer
by Ana S. Cvetanović, Kristina B. Jankovic, Ana S. Stojković, Nikola D. Živković, Miloš S. Kostić and Lazar S. Popović
Cancers 2026, 18(2), 242; https://doi.org/10.3390/cancers18020242 - 13 Jan 2026
Viewed by 373
Abstract
Background/Objectives: Despite initial sensitivity to ET, most patients with HR+/HER2− breast cancer develop resistance. A key molecular mechanism of endocrine resistance in HR+ breast cancer involves dysregulation of the cyclin D–CDK4/6–Rb signaling axis, which controls the transition from the G1 to S phase [...] Read more.
Background/Objectives: Despite initial sensitivity to ET, most patients with HR+/HER2− breast cancer develop resistance. A key molecular mechanism of endocrine resistance in HR+ breast cancer involves dysregulation of the cyclin D–CDK4/6–Rb signaling axis, which controls the transition from the G1 to S phase of the cell cycle. Introducing cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i) has changed therapeutic paradigms in HR+/HER2− breast cancer, as their synergistic use with endocrine therapy significantly prolongs progression-free survival (PFS) and effectively mitigates clinically relevant endocrine resistance in this patient population compared to ET alone. The aim of our study was to evaluate patients’ clinical characteristics, the clinical effectiveness of treatment, measured by progression-free survival (PFS), and the safety profile of combined ribociclib (CDK4/6i) and standard endocrine therapy (aromatase inhibitor) as a first-line treatment for patients with HR+/HER2− advanced or metastatic breast cancer at the Clinic of Oncology, University Clinical Centre Nis, Serbia. Methods: In this study, we present a retrospective prospective analysis of all patients with metastatic HR+/HER2− breast cancer treated with a combination of ribociclib and aromatase inhibitors in the first-line treatment of metastatic HR+/HER2− BC between June 2022 and January 2025, with a follow-up completed in October 2025. A total of 132 patients who met the criteria were included. Results: The median progression-free survival (PFS) in the entire group was 30 months, while the 12-, 24-, and 36-month PFS were 82.15%, 72.24%, and 28.75%, respectively. The overall response rate (ORR) was 41.7%, while the clinical benefit rate (CBR) was 89.3%. There was no statistically significant difference in PFS with respect to tumor grade (p = 0.54), Ki 67 level (<20% vs. >20%, p = 0.83), or the type of adjuvant endocrine therapy used (tamoxifen vs. AI) It is important to emphasize that female patients who had not previously received chemotherapy had a better response to ribociclib compared to those who had (33 m vs. 28 m, p = 0.05). Although a numerical difference in PFS was found in patients with bone-only metastases compared to those with metastases in other organs, the difference was not statistically significant (PFS 33 m vs. 30 m, p = 0.27;), and efficacy was consistent across menopausal status groups. The most common adverse effect was neutropenia, occurring in 89.4% of patients, 47.7% of whom presented with grade 3 or 4. As for hepatotoxicity, transaminase increase occurred in 25 patients (18.8%), 5 of whom (3.8%) were grade 3–4, and QTc interval prolongation occurred in 5.3% of patients. Conclusions: The results in terms of PFS and AEs are consistent with those of pivotal studies and real clinical practice data, but a direct comparison is not possible due to differences in patient populations. Ribociclib once again demonstrated efficacy in all patient subgroups and remains the gold standard, alongside ET, for first-line HR+/HER2-negative mBC. Full article
(This article belongs to the Special Issue Breast Cancer and Hormone-Related Therapy: 2nd Edition)
Show Figures

Figure 1

30 pages, 711 KB  
Review
A Systematic Review on GLP-1 Receptor Agonists in Reproductive Health: Integrating IVF Data, Ovarian Physiology and Molecular Mechanisms
by Charalampos Voros, Fotios Chatzinikolaou, Ioannis Papapanagiotou, Spyridon Polykalas, Despoina Mavrogianni, Aristotelis-Marios Koulakmanidis, Diamantis Athanasiou, Vasiliki Kanaka, Kyriakos Bananis, Antonia Athanasiou, Aikaterini Athanasiou, Georgios Papadimas, Charalampos Tsimpoukelis, Dimitrios Vaitsis, Athanasios Karpouzos, Maria Anastasia Daskalaki, Nikolaos Kanakas, Marianna Theodora, Nikolaos Thomakos, Panagiotis Antsaklis, Dimitrios Loutradis and Georgios Daskalakisadd Show full author list remove Hide full author list
Int. J. Mol. Sci. 2026, 27(2), 759; https://doi.org/10.3390/ijms27020759 - 12 Jan 2026
Viewed by 481
Abstract
Women of reproductive age, especially those with polycystic ovarian syndrome (PCOS), often use glucagon-like peptide-1 receptor agonists (GLP-1RAs) to improve their metabolic functions. A growing body of evidence suggests that GLP-1R signaling may directly affect ovarian physiology, influencing granulosa cell proliferation, survival pathways, [...] Read more.
Women of reproductive age, especially those with polycystic ovarian syndrome (PCOS), often use glucagon-like peptide-1 receptor agonists (GLP-1RAs) to improve their metabolic functions. A growing body of evidence suggests that GLP-1R signaling may directly affect ovarian physiology, influencing granulosa cell proliferation, survival pathways, and steroidogenic production, in addition to its systemic metabolic effects. Nonetheless, there is a limited comprehension of the molecular mechanisms that regulate these activities and their correlation with menstrual function, reproductive potential, and assisted reproduction. This comprehensive review focuses on ovarian biology, granulosa cell signaling networks, steroidogenesis, and translational fertility outcomes, integrating clinical, in vivo, and in vitro information to elucidate the effects of GLP-1 receptor agonists on reproductive health. We conducted a thorough search of PubMed, Scopus, and Web of Science for randomized trials, prospective studies, animal models, and cellular experiments evaluating the effects of GLP-1RA on reproductive or ovarian outcomes, in accordance with PRISMA criteria. The retrieved data included metabolic changes, androgen levels, monthly regularity, ovarian structure, granulosa cell growth and death, FOXO1 signaling, FSH-cAMP-BMP pathway activity, and fertility or IVF results. Clinical trials shown that GLP-1 receptor agonists improve menstrual regularity, decrease body weight and central adiposity, increase sex hormone-binding globulin levels, and lower free testosterone in overweight and obese women with PCOS. Liraglutide, when combined with metformin, significantly improved IVF pregnancy rates, whereas exenatide increased natural conception rates. Mechanistic studies demonstrate that GLP-1R activation affects FOXO1 phosphorylation, hence promoting granulosa cell proliferation and anti-apoptotic processes. Incretin signaling altered steroidogenesis by reducing the levels of StAR, P450scc, and 3β-HSD, so inhibiting FSH-induced progesterone synthesis, while simultaneously enhancing BMP-Smad signaling. Animal studies demonstrated both beneficial (enhanced follicular growth, anti-apoptotic effects) and detrimental results (oxidative stress, granulosa cell death, uterine inflammation), indicating a context- and dose-dependent response. GLP-1 receptor agonists influence female reproductive biology by altering overall physiological processes and specifically impacting the ovaries via FOXO1 regulation, steroidogenic enzyme expression, and BMP-mediated FSH signaling. Preliminary clinical data indicate improved reproductive function in PCOS, as seen by increased pregnancy rates in both natural and IVF cycles; nevertheless, animal studies reveal a potential risk of ovarian and endometrial damage. These results highlight the need for controlled human research to clarify reproductive safety, molecular pathways, and optimum therapy timing, particularly in non-PCOS patients and IVF settings. Full article
(This article belongs to the Special Issue Molecular Research on Reproductive Physiology and Endocrinology)
Show Figures

Figure 1

Back to TopTop