Frontiers in Molecular Biosciences最新文献

Background: Chronic liver disease due to alcohol-related liver disease and chronic viral hepatitis pose a substantial burden on healthcare systems. Chronic liver disease may predispose to hepatocellular carcinoma, for which therapeutic options are limited. This study aimed to explore the immune cell characteristics of the clinical conditions.

Methods: Explant liver samples were collected from 25 patients for bulk RNA sequencing and flow cytometry analysis. Immune cell populations were characterized by flow cytometry from isolated hepatic and peripheral mononuclear cells.

Results: Significant differences in immune cell characteristics were observed among patients with three clinical conditions. Viral hepatitis and peri-tumor samples exhibited higher hepatic B cell counts compared to alcohol-related liver disease. Additionally, chronic liver disease patients showed higher levels of CD57⁺ T cells, suggestive of T cell differentiation. Differential expression analysis identified several genes associated with immune regulation, including downregulation of CD27 and upregulation of granzyme B in ARLD, consistent with a highly differentiated phenotype. LAG3 and PDCD1 were upregulated in peri-tumor samples. The NK cell count was lower in peri-tumor liver specimens compared to ARLD, and an upregulation of TIGIT, an inhibitory marker, was observed in those peri-tumor specimens.

Conclusion: This study contributes to the understanding of immune dynamics in chronic liver disease among different etiologies. B lymphocytes are relatively reduced in alcohol-related liver disease compared to other groups, and T cells exhibit a more differentiated subtype. The peritumor microenvironment in HCC suggests a relatively diminished presence of NK cells and a potential tendency toward increased inhibitory characteristics.

Inflammatory Bowel Disease (IBD), which includes Ulcerative Colitis (UC) and Crohn's Disease (CD), is marked by dysbiosis of the gut microbiome. Despite therapeutic interventions with biological agents like Vedolizumab, Ustekinumab, and anti-TNF agents, the variability in clinical, histological, and molecular responses remains significant due to inter-individual and inter-population differences. This study introduces a novel approach using Individual Specific Networks (ISNs) derived from faecal microbial measurements of IBD patients across multiple cohorts. These ISNs, constructed from baseline and follow-up data post-treatment, successfully predict therapeutic outcomes based on endoscopic remission criteria. Our analysis revealed that ISNs characterised by core gut microbial families, including Lachnospiraceae and Ruminococcaceae, are predictive of treatment responses. We identified significant changes in abundance levels of specific bacterial genera in response to treatment, confirming the robustness of ISNs in capturing both linear and non-linear microbiota signals. Utilising network topological metrics, we further validated these findings, demonstrating that critical microbial features identified through ISNs can differentiate responders from non-responders with respect to various therapeutic outcomes. The study highlights the potential of ISNs to provide individualised insights into microbiota-driven therapeutic responses, emphasising the need for larger cohort studies to enhance the accuracy of molecular biomarkers. This innovative methodology paves the way for more personalised and effective treatment strategies in managing IBD.

Introduction: This study applies NMR-based metabolomics to investigate neovascular age-related macular degeneration (nAMD), addressing challenges in patient management, disease progression evaluation, and treatment response assessment. A two-year follow-up of 29 nAMD patients undergoing treatment provided 231 time points for analysis.

Methods: Over the two-year period, 11 males and 18 females (aged 61-92 years) were monitored, yielding 231 time points. At each time point, blood samples for NMR metabolomics analysis, clinical measurements (e.g., lactate, glucose levels, HDL/LDL cholesterol, and blood pH), and optical coherence tomography (OCT) images were collected to evaluate the progression of choroidal neovascularization. 1H-NMR metabolomic analysis led to the quantification of over 60 metabolites and of the major lipoprotein fractions. Both multivariate and univariate statistical approaches tailored for longitudinal data were employed to identify biomarkers correlating metabolomic changes with ocular alterations during disease progression.

Results and discussion: Despite a rigorous analytical workflow enabling precise quantification of over 60 metabolites and the application of advanced statistical tools for longitudinal data, achieving consistent results across the cohort proved challenging. The dataset's heterogeneity, reflecting real-world clinical practice, complicated the derivation of global conclusions. Personalized analyses on a patient-by-patient basis successfully identified individual correlation models, but a universal model remained elusive. This study highlights the inherent challenges of translating findings from controlled settings into clinical practice, where factors such as visit frequency, treatment variability, and disease heterogeneity limit data uniformity. We emphasize the importance of experimental design in longitudinal studies, particularly when dealing with incomplete and variable datasets. We are therefore confident that, considering both the challenges and difficulties identified in this work and the preliminary results presented here, it is possible to develop predictive and individualized models for monitoring patients with nAMD. Such models could greatly assist clinicians in providing better care for these patients.

Aging and cancer are intricately linked through shared molecular processes that influence both the onset of malignancy and the progression of age-related decline. As organisms age, cellular stress, genomic instability, and an accumulation of senescent cells create a pro-inflammatory environment conducive to cancer development. Autophagy, a cellular process responsible for degrading and recycling damaged components, plays a pivotal role in this relationship. While autophagy acts as a tumor-suppressive mechanism by preventing the accumulation of damaged organelles and proteins, cancer cells often exploit it to survive under conditions of metabolic stress and treatment resistance. The interplay between aging, cancer, and autophagy reveals key insights into tumorigenesis, cellular senescence, and proteostasis dysfunction. This review explores the molecular connections between these processes, emphasizing the potential for autophagy-targeted therapies as strategies that could be further explored in both aging and cancer treatment. Understanding the dual roles of autophagy in suppressing and promoting cancer offers promising avenues for therapeutic interventions aimed at improving outcomes for elderly cancer patients while addressing age-related deterioration.

Oral cancer (OC) is a prevalent malignancy with high mortality rates, largely attributed to late diagnosis and limited therapeutic advancements. MicroRNAs (miRNAs), as critical regulators of gene expression, have emerged as key players in modulating plethora of cellular mechanisms. This study analyzed miRNA and gene expression profiles in OC using publicly available datasets from the Gene Expression Omnibus (GEO) to explore their roles in tumorigenesis. A total of 23 differentially expressed miRNAs (DEmiRs) and 1,233 differentially expressed genes (DEGs) were identified. Functional annotation and pathway enrichment analyses highlighted significant involvement of DEmiRs and their target genes in cell cycle-related processes, including enrichment in the nucleus, transcription factor activity, regulation of nucleosides, nucleotide and nucleic acids, cell growth and/or maintenance, mitotic cell cycle, mitotic M-M/G1 phases an DNA replication. Furthermore, different signaling cascades such as IGF signaling, PDGF signaling and LKB1 signaling and PLK1 signaling pathways were also found associated with DEmiR-related regulation of OC progression. Protein-protein interaction (PPI) network analysis identified key molecular hubs associated with DEmiR and DEGs in OC. Notably, most of these hub genes such as NEK2, NDC80, NUF2, PLK1, SMAD2, TP53, TPX2, TTK, UBE2C, WDHD1, WTAP, YWHAZ are directly or indirectly associated with cell cycle progression, underscoring the role of DEmiRs in driving tumor proliferation and survival in OC via dysregulating cell cycle. This study offers insights into the molecular mechanisms underlying OC and highlights miRNAs as potential biomarkers and therapeutic targets to disrupt the cancerous cell cycle and improve treatment outcomes.

Introduction: Although the role of tumor immune microenvironment (TIME) in thyroid cancer is well established, little data exists about the differences in immune cell presence in thyroid adenomas and carcinomas. We assume that immune cell density could be an additional diagnostic criterion for differentiating benign and malignant tumors in thyroid aspirates.

Aim: The current study compared the immune contexture of thyroid adenoma (TA) and thyroid carcinoma (TC) in histological and cytological specimens of III-V categories.

Materials and methods: This pilot study included 72 cases (36 of TA and 36 of TC) with verified histological diagnosis and pre-operative cytology corresponding to categories III, IV and V according to the Bethesda system for reporting thyroid cytology. The number of CD8+, CD68+ and CD163+ cells was assessed in histological samples of TA and TC with further comparison to cytological specimens. Besides, the expression of STAT6 and SMAD4 as potential regulators of TIME was evaluated in the study.

Results: TC demonstrated an immune-rich profile representing abundant tumor-associated CD8+ lymphocytes, CD68 and CD163+ macrophages. In contrast, TA represented mostly a low immune cell infiltration. The higher immunogenicity of TC was accompanied by the more profound expression of STAT6 and SMAD4 in tumor cells. The number of immune cells in cytological specimens correlated with CD8+ (r = 0.693; p < 0.001) and CD163+ cells (r = 0.559; p < 0.001) in histological samples, reflecting the differences in the tumor immune microenvironment between benign and malignant thyroid neoplasms.

Conclusion: TC demonstrated high immunogenicity compared to TA, which correlated to the number of immune cells in cytological specimens. The number of immune cells in thyroid cytology samples could be an additional criterion in cytological diagnostics for III-V Bethesda categories. Further investigations are needed to validate the findings of the study.

Iron uptake in the intestinal epithelium is associated with transport of ferrous iron via the DMT1 transporter (SLC11a2; NRAMP2). In later years, uptake of iron from complex sources, such as nanoparticles, has been found to be mediated through endocytosis. Here we propose that iron from the simple salt ferrous fumarate, a common iron supplement, can be absorbed by clathrin-mediated endocytosis. We used siRNA to silence DMT1 transporter expression, pharmacological inhibition of endocytosis, and Time-of-Flight Secondary Ion Mass Spectrometry (ToF-SIMS) to show that iron uptake from ferrous fumarate can be mediated by both transport via DMT1 and by clathrin-dependent endocytosis in Hutu-80 cells. Iron uptake (ferritin L) from ferrous fumarate (0.5 mM, 24 h) in DMT1 silenced cells was significantly decreased (60% ± 11%) in comparison to iron controls while a 1-h dose of ferrous fumarate (0.5 mM) significantly decreased ferritin L formation in the presence of the clathrin inhibitor chlorpromazine (61% ± 10%, in post-confluent cells and 37% ± 9% in non-confluent cells). A pilot showed a similar trend for Ferritin (H) levels (confluent cells) and for total cellular iron load (non-confluent cells). ToF-SIMS analysis revealed diminished membrane-associated iron load in endocytosis-inhibited ferrous fumarate treated cells. The reported results support a clathrin-mediated endocytosis mechanism for uptake of iron from ferrous fumarate in addition to iron uptake by DMT1. More studies are needed to understand what determines which uptake mechanism are employed and to which extent.

Introduction: Machine learning methods were applied to analyze pharmacophore features derived from four protein-binding sites, aiming to identify key features associated with ligand-specific protein conformations.

Methods: Using molecular dynamics simulations, we generated an ensemble of protein conformations to capture the dynamic nature of their binding sites. By leveraging pharmacophore descriptors, the AI/ML framework prioritized features uniquely associated with ligand-selected conformations, enabling a mechanism-driven understanding of binding interactions. This novel approach integrates biophysical insights with machine learning, focusing on pharmacophoric properties such as charge, hydrogen bonding, hydrophobicity, and aromaticity.

Results: Results showed significant enrichment of true positive ligands-improving database enrichment by up to 54-fold compared to random selection-demonstrating the robustness of this approach across diverse proteins.

Conclusion: Unlike conventional structure-based or ligand-based screening methods, this work emphasizes the role of specific protein conformations in driving ligand binding, making the process highly interpretable and actionable for drug discovery. The key innovation lies in identifying pharmacophore features tied to conformations selected by ligands, offering a predictive framework for optimizing drug candidates. This study illustrates the potential of combining ML and pharmacophoric analysis to develop intuitive and mechanism-driven tools for lead optimization and rational drug design.

Purpose: PEXS was first described in 1917, yet its etiology still needs clarification. An imbalance between oxidants and antioxidants plays a significant role. PEXS leads to various ocular complications, including increased risk during cataract surgery due to weak zonules, lens dislocation, and reduced visual outcomes. Our study investigates whether metabolomics can provide insights into this ocular pathology.

Methods: The study included 183 patients undergoing cataract surgery at Pauls Stradins Clinical University Hospital. 104 patients did not have PEXS, while 79 were diagnosed with the condition. Intraocular fluid samples from these patients were analyzed using targeted metabolite analysis, performed through HILIC liquid chromatography coupled with mass spectrometry detection.

Results: The aqueous humor of PEXS patients contains statistically significant higher levels of cystine (p < 0.001), citrulline (p < 0.001), phenylalanine (p = 0.041), tyrosine (p = 0.025), serine (p = 0.030), arginine (p = 0.017), lactic acid (p = 0.055), tryptophan (p = 0.055), and creatinine (p = 0.022). These results suggest a potential link to ferroptosis.

Conclusion: Ferroptosis is a form of programmed cell death characterized by iron-dependent LPO. The inhibition of the antiporter system X_c ^- leads to increased oxidative stress, suggesting that the changes seen in PEXS could be linked to ferroptosis. Our findings indicate that cysteine synthesis occurs via the transsulfation pathway, attributable to inhibiting the antiporter system X_c ^-. Treatment of pseudoexfoliation should lower the oxidative stress inside the anterior chamber by reducing the uptake of PUFAs, lower iron levels, and cysteine supplementation.

[This retracts the article DOI: 10.3389/fmolb.2020.00126.].