Search Results (10,418)

Objective: Cerebral ischemia–reperfusion injury (IRI) is a distinct pathological phase that differs from permanent ischemia (IR) in that it triggers secondary damage despite the restoration of blood flow. The primary objective of this study is to comprehensively characterize and compare the molecular signatures—such as differential gene expression, protein activation, and metabolic alterations—between IRI and IR. By doing so, we aim to identify key pathways and biomarkers that specifically drive IRI and IR pathology, thereby providing novel therapeutic targets to mitigate reperfusion-induced damage in stroke and related neurological conditions. Methods: We employed an integrated transcriptomic and proteomic approach to compare a permanent ischemia model (IR, 24 h ischemia) with a reperfusion model (IRI, 1 h ischemia + 24 h reperfusion), using SHAM-operated animals as controls. Results: Our results demonstrate a profound decoupling between the transcriptome and proteome in IRI. While IRI induced extensive proteomic alterations (160 changed proteins in IRI vs. IR), transcriptional changes were minimal (3 genes), indicating dominant post-transcriptional regulation. Both IR and IRI activated shared inflammatory responses (e.g., Saa3, upregulated 14.33-fold in IRI/SHAM) and metabolic shifts (Gapdh, downregulated 4.03-fold). However, IRI uniquely upregulated neuroprotective genes (Arc, Npas4), activated a specific set of reperfusion-related pathways (72 proteins), and exhibited distinct extracellular matrix remodeling (Mmp3, upregulated 11.24-fold in IR/SHAM). The overall correlation between transcriptomic and proteomic dynamics was remarkably low (r = 0.014), underscoring the importance of translation and protein decay mechanisms. Conclusions: This study redefines IRI not merely as an exacerbation of ischemic damage but as a unique adaptive molecular trajectory. We identify Pisd-ps3 and Saa3 as potential therapeutic targets and show that proteomic signatures can stratify injury phases. These findings advance the prospects of precision therapeutics aimed at neuroprotection and immunomodulation in ischemic stroke. Full article

A growing body of work has linked the dysregulation of transmembrane (TMEM) proteins to the proliferation, metastasis, drug resistance, and tumor microenvironment remodeling of lung cancer, the leading global cause of cancer mortality. Renamed members such as STING1 (stimulator of interferon response cGAMP interactor 1, TMEM173), ANO1 (anoctamin-1, TMEM16A), ORAI1 (ORAI calcium release-activated calcium modulator 1, TMEM142A), ORAI3 (TMEM142C), and NDC1 (NDC1 transmembrane nucleoporin, TMEM48) are among the most extensively studied ones. Mechanisms of TMEM dysregulation in lung cancer span the modulation of Ca²⁺ influx, lysosomal exocytosis, ferroptosis, Wnt and β-catenin signaling, and immune cell infiltration and immune checkpoint rewiring, among others. Epigenetic silencing and targetable fusions (i.e., TMEM106B-ROS1 and TMEM87A-RASGRF1) create DNA-level vulnerabilities, while miRNA sponges offer RNA-level druggability. A subset of studies revealed context-specific expression (endothelial, B cell, and hypoxic EV) that can be exploited to remodel the tumor microenvironment. One study specifically focused on how isoform-specific expression and localization of TMEM88 determine its functional impact on tumor progression. Yet for most TMEMs, only pre-clinical or early-phase data exist, with many supported by a single study lacking independent validation. This review brings together scattered evidence on TMEM proteins in lung cancer, with the aim of guiding future work on their possible use as biomarkers or therapeutic targets. Full article

Background: Inflammatory activity in rheumatoid arthritis can be determined by normal blood count ratios such as Neutrophil Lymphocyte Ratio (NLR), Platelet Lymphocyte Ratio (PLR), Systemic Immune Inflammation Index (SII), and C-reactive Protein (CRP). Objective: The aim of this research is to determine how these markers change after therapy and whether their pre- and post-treatment differences follow patterns that allow for simple parametric analyses. Methods: A prospective cohort of 52 RA patients (30 females and 22 males) was examined. The patients’ blood samples were tested at baseline and at the end of their 6-month Infliximab treatment. Hematologic markers such as NLR, PLR, and SII were calculated from the complete blood count (CBC), and CRP levels were measured. The statistical methods of Shapiro–Wilk (SW), Kolmogorov–Smirnov (KS), and Anderson–Darling (AD) were used, and later, paired t-tests were used to generate statistics where necessary. Results: Post-treatment measurements were consistently lower for all four biomarkers. QQ-plots and formal tests revealed that the differences between findings were essentially normal, allowing for paired t-tests. The mean decreases were as follows: NLR −1.10 (95% CI −1.48 to −0.71), PLR −43.0 (−55.4 to −30.7), SII −299 (−388 to −211), and CRP −11.36 (−13.18 to −9.54), all p < 0.001. CRP showed the greatest drop, with significant decreases in PLR and SII and a moderate decline in NLR, indicating therapy-related attenuation of systemic inflammation. Conclusion: The study shows that six months of infliximab therapy results in a consistent post-treatment decrease in all four biomarkers: NLR, PLR, SII, and CRP. Because the pre-post differences were roughly normal, CRP revealed the greatest decrease, with significant decreases in PLR and SII and a moderate decrease in NLR, consistent with systemic inflammation reduction. When combined, the CBC-derived indices track with CRP and can serve as practical, low-cost markers for monitoring therapy response in RA, despite the single-arm design. Full article

Extracellular vesicles (EVs) are known as potential biomarkers for several diseases; nevertheless, the degree of technical and biological variability is not yet adequately characterized. Because pre-analytical factors such as blood collection time and EV subpopulation could confound biomarker studies, we performed a pilot study systematically quantifying methodological and biological variability including EV-Array (surface proteins), and proteome characterization of cargo. Plasma samples from six healthy adults were collected at two time points (morning and afternoon) and plasma was analyzed with EV-Array, and isolated EVs were analyzed using nanoparticle tracking analysis (NTA), and label-free mass spectrometry (LC-MS/MS). Methodological repeatability was high for NTA particle size (3.3% CV) and LC-MS (8.2% CV), and lower for EV-Array surface markers (22.6% CV). Variations between samples were reasonable for NTA-size, EV-Array and LC-MS/MS (5–21%) and substantially lower than between-subject variation. No evidence of systemic morning–afternoon shifts in particle size and concentration or EV cargo was observed, although small effects cannot be excluded. The same was true for most surface markers, but minor but statistically significant reductions in a few specific surface markers occurred in afternoon EV-Array samples. In this pilot we therefore do not observe any major systemic diurnal bias in healthy individuals in samples collected a.m. vs. p.m. Despite the small sample size, this study underscores the importance of accounting for individual variability and methodological standardization when designing EV-based biomarker research. Full article

An increasing number of stroke survivors are burdened by persistent disabilities, requiring long-term rehabilitation. However, the extent of functional gain is highly variable, severely impairing patients’ quality of life. This variability highlights a critical gap in current prognostic tools, which rely primarily on clinical and neuroimaging data. The aim of this review is to synthesize the current literature on serum biomarkers in stroke survivors and to evaluate their prognostic value for rehabilitation outcomes. Our synthesis indicates that biomarkers reflecting distinct pathophysiological processes are emerging as key prognostic indicators. Markers of inflammation such as Tumor Necrosis Factor-alpha (TNF-α), Interleukin-6 (IL-6), and Interleukin-1 beta (IL-1β), and neuro-glial injury, including S100 Calcium-Binding Protein B (S100B), Neuron-Specific Enolase (NSE), Glial Fibrillary Acidic Protein (GFAP), and Neurofilament Light Chain (NfL), are consistently associated with poorer functional outcomes. Conversely, markers of neuroplasticity, such as Brain-Derived Neurotrophic Factor (BDNF) and Insulin-like Growth Factor-1 (IGF-1), serve as potential indicators of recovery potential, although their predictive accuracy remains inconsistent across studies. Furthermore, emerging biomarkers of synaptic activity, such as Syntaxin-1a (STX1A) and Synaptosomal-Associated Protein, 25kDa (SNAP-25), and neuromuscular junction integrity, such as C-terminal Agrin Fragment (CAF), offer novel insights into brain–periphery communication, though their clinical utility is still under investigation. While promising, the translation of these biomarkers into clinical practice is hindered by methodological limitations, including assay heterogeneity and lack of large-scale validation. Future standardization of these molecular signatures is a critical step toward implementing precision medicine in stroke rehabilitation. Full article

This paper presents the optimization of surface modification for aptameric graphene nanosensors for the measurement of biomarkers in undiluted physiological media. In these sensors, graphene transduces the binding between an aptamer and the intended target biomarker into a measurable signal while being coated with a polyethylene glycol (PEG) nanolayer to minimize nonspecific adsorption of matrix molecules. We perform a systematic study of the aptamer and PEG attachment schemes and parameters, including the impact of the serial or parallel PEG–aptamer attachment scheme, PEG molecular weight and surface density, and aptamer surface density on the sensor behavior, such as the responsivity to biomarker concentration changes, and importantly, they are used for operation in physiological media and have the ability to reject nonspecific binding to interfering molecules. We then use the understanding from this parametric study to identify graphene nanosensor designs that are optimally functionalized with PEG and aptamers to be strongly responsive to target biomarkers and effectively reduce nonspecific adsorption of interferents, thereby enabling sensitive and specific biomarker measurements in undiluted physiological media. The experimental results show that nanosensors that were optimized via serial modification with 5000 Da PEG at 15 mM and a 94 nt DNA aptamer at 500 nM allowed specific measurement of C-reactive protein (CRP) in undiluted human serum with a limit of detection (LOD) down to 27 pM, representing an up to 1000-fold improvement compared to previously reported CRP measurements. Full article

Background/Objectives: Triple-negative breast cancer (TNBC) is an aggressive subtype, with limited diagnostic options and no targeted early detection tools. Liquid biopsy represents a minimally invasive approach for detecting tumor-derived molecular alterations in body fluids. This scoping review aimed to comprehensively synthesize all liquid biopsy-derived molecular biomarkers evaluated for the diagnosis of TNBC in adults. Methods: This review followed the Arksey and O’Malley framework and PRISMA-ScR guidelines. Systematic searches of PubMed, Scopus, Embase, and Web of Science identified primary human studies evaluating circulating molecular biomarkers for TNBC diagnosis. Non-TNBC, non-human, hereditary, treatment-response, and nonmolecular studies were excluded. Data on study design, patient characteristics, biospecimen type, analytical platforms, biomarker class, and diagnostic performance were extracted and synthesized descriptively by biomolecule class. Results: Thirty-two studies met the inclusion criteria, comprising 15 protein-based, 12 RNA-based, and 6 DNA-based studies (one reporting both protein and RNA). In total, 1532 TNBC cases and 3137 participants in the comparator group were analyzed. Protein biomarkers were the most frequently studied, although only APOA4 appeared in more than one study, with conflicting results. RNA-based biomarkers identified promising candidates, particularly miR-21, but validation cohorts were scarce. DNA methylation markers showed promising diagnostic accuracy yet lacked replication. Most studies were small retrospective case–control designs with heterogeneous comparators and inconsistent diagnostic reporting. Conclusions: Evidence for liquid biopsy-derived biomarkers in TNBC remains limited, heterogeneous, and insufficiently validated. No biomarker currently shows reproducibility suitable for clinical implementation. Robust, prospective, and standardized studies are needed to advance liquid biopsy-based diagnostics in TNBC. Full article

Conventional semen analysis fails to capture the molecular determinants underlying impaired reproductive function. Emerging evidence positions seminal plasma (SP) and extracellular vesicles (EVs) as dynamic regulators of sperm physiology, rather than passive transport components. SP, enriched with proteins, metabolites, hormones, and antioxidants, modulates sperm motility, capacitation, acrosome reaction, and immune tolerance. Complementarily, EVs, including prostasomes, epididymosomes, and testicular vesicles, deliver proteins, lipids, and small RNAs that remodel sperm membranes, protect against oxidative insults, and influence fertilization success. A critical dimension of the SP-EV axis is its role in balancing oxidative stress (OS) and endocrine signaling. Hormones and metabolic regulators within SP, together with EV-mediated transfer of receptors and regulatory RNAs, further integrate systemic metabolic health with local reproductive outcomes. Dysregulation of these networks, particularly in conditions such as varicocele, obesity, diabetes, and idiopathic infertility, compromises sperm function and reduces assisted reproductive technology (ART) success. This evidence-based review synthesizes current evidence on SP and EVs as ‘molecular gatekeepers’ in male infertility, emphasizing OS regulation, endocrine crosstalk, and their potential as biomarker reservoirs. By integrating proteomic, metabolomic, and transcriptomic insights, the translational opportunities for biomarker-informed diagnostics, prognostication, and therapeutic interventions are highlighted. Full article

Blood culture is the diagnostic gold standard for bacteremia in the emergency department (ED), but its turnaround time can delay appropriate antimicrobial therapy, highlighting the need for rapid, accessible biomarkers. We retrospectively analyzed adult ED patients from July 2023 to June 2024 who underwent blood culture testing and had complete data for monocyte distribution width (MDW), white blood cell count (WBC), C-reactive protein (CRP), and neutrophil-to-lymphocyte ratio (NLR). Discrimination was assessed using area under the receiver operating characteristic curve (AUROC) and diagnostic accuracy using sensitivity, specificity, and diagnostic odds ratio (DOR); combined models were compared with net reclassification improvement (NRI) and integrated discrimination improvement (IDI). Among 19,325 patients, 2011 (10.4%) had positive blood cultures. MDW had the highest AUROC (0.760) versus CRP (0.730), NLR (0.695), and WBC (0.642); at a cut-off of 22, MDW showed 0.72 sensitivity, 0.68 specificity, and DOR 5.46. The best combined model was MDW+NLR (AUROC 0.785; DOR 6.39; NRI 0.428; IDI 0.770). MDW is a rapid and effective marker for identifying bacteremia in the ED, and performance improves when combined with NLR. Full article

Background: Early recognition of renal allograft dysfunction requires biochemical markers capable of detecting molecular injury before functional decline becomes apparent. Serum creatinine, a late and nonspecific indicator of renal function, has limited value for early diagnosis. Protein biomarkers implicated in tubular injury, inflammation, and immune activation—including neutrophil gelatinase-associated lipocalin (NGAL), kidney injury molecule-1 (KIM-1), β2-microglobulin, interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α)—have emerged as promising alternatives. This study evaluated early post-transplant serum profiles of these biomarkers and their prognostic relevance for long-term graft outcomes. Methods: Nineteen adult recipients undergoing primary kidney transplantation were prospectively enrolled. Serum creatinine and protein biomarkers were measured 24 h post-transplant using validated immunochemical assays. Biomarker concentrations were compared with values from healthy controls, and correlations with renal function at 12 months were assessed. Receiver operating characteristic (ROC) analysis was used to evaluate predictive performance. Results: Significant biochemical alterations were observed at 24 h post-transplant. KIM-1 levels were markedly elevated compared with controls (74.50 ± 98.45 vs. 10.54 ± 17.19 ng/mL; p = 0.01), consistent with early tubular injury. IL-1β and NGAL showed upward trends without reaching statistical significance. β2-microglobulin and TNF-α levels did not differ substantially from control values. Serum KIM-1 correlated with serum creatinine both at 24 h (r = 0.35) and at 12 months (r = 0.40). ROC analysis identified a KIM-1 threshold of 24.5 ng/mL (AUC = 0.68) as a potential indicator of future graft dysfunction, outperforming serum creatinine (AUC = 0.64). Six patients experienced graft dysfunction at 12 months post-transplant, five of whom had serum creatinine values >5 mg/dL at 24 h. Based on early creatinine levels, patients were stratified into low-risk (creatinine <5 mg/dL; n = 10) and high-risk groups (creatinine >5 mg/dL; n = 9). Mean KIM-1 concentrations were significantly higher in the high-risk group (110.68 ± 115.29 vs. 26.67 ± 18.05 ng/mL; p = 0.05), consistent with more severe early tubular injury. Conclusions: Among the evaluated biomarkers, KIM-1 demonstrated the strongest potential as an early biochemical indicator of renal allograft dysfunction. Its rapid post-transplant elevation underscores its sensitivity to early tubular injury. Further prospective validation in larger, multicenter cohorts is warranted. Full article

Postoperative delirium (POD) is a frequent and serious complication among elderly surgical patients. Despite its clinical relevance, reliable biomarkers for early identification and pathophysiological insight remain limited. Recent evidence implicates systemic immune activation and complements dysregulation as contributors to cognitive decline after surgery. This study investigated the association between perioperative levels of selected complement pathway proteins and both the incidence and severity of POD. Methods: We performed a secondary analysis of 22 patients aged ≥ 60 years from the prospective CONFESS cohort undergoing elective spine surgery. Complement proteins (C1q, C2, C4), mannose-binding lectin (MBL), Factor D [FD], Factor B [FB], Factor I [FI] were quantified from blood samples collected at baseline, preoperatively, and on postoperative days 1 and 2. POD was assessed using the Nursing Delirium Screening Scale (Nu-DESC) and Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition criteria. Delirium severity was rated with the Confusion Assessment Method–Severity (CAM-S) scale. Associations were tested using univariate and multivariate regression analyses. Preoperative levels of FD and C2 were significantly elevated in patients who developed POD (FD: p = 0.023; C2: p = 0.044), while C4 levels trended lower. FD remained an independent predictor of POD in multivariate regression (p = 0.049), although cognitive performance was the only significant predictor when adjusted for surgery duration. Delirium severity was associated with perioperative reductions in C1q, FI, and FB and with increased MBL levels, explaining up to 43% of CAM-S score variance. These findings highlight the role of complement activation—particularly FD, C2, MBL—in the development and clinical expression of POD. Complement profiling may offer a novel approach for risk stratification and therapeutic targeting in perioperative neurocognitive disorders. Full article

C-reactive protein (CRP) and serum amyloid A (SAA) are classical acute-phase proteins that exemplify humoral innate immunity, the soluble arm of the host’s first-line defense. Beyond their traditional use as biomarkers of inflammation, both proteins function as active effectors against pathogens by binding microbial components, activating complements, and modulating inflammation. However, bacteria, viruses, and fungi have co-evolved diverse mechanisms to cope with or evade these host defenses. This review aims to summarize the current understanding of CRP and SAA as soluble innate immune effectors and to highlight pathogen strategies to counteract their antimicrobial pressure. We systematically surveyed and summarized evidence from experimental and clinical studies describing “function of CRP and SAA during infection”, “CRP and SAA in innate immune defense”, and “evasion mechanisms across bacterial, viral, and fungal pathogens”. CRP and SAA are rapidly upregulated in response to infection and contribute to pathogen recognition, opsonization, and inflammation. Pathogens, however, employ multiple coping strategies, including surface modification to block CRP binding, proteolytic degradation of acute-phase proteins, shielding within biofilms, and subversion of host signaling. These countermeasures enable microbes to reduce immune clearance and promote persistence. CRP and SAA represent central elements of humoral innate immunity, shaping the outcome of host–pathogen interactions. Pathogen adaptations to these proteins illustrate an ongoing evolutionary arms race between host defense and microbial survival. A deeper understanding of these processes may open avenues for novel therapeutic approaches, such as targeting microbial evasion factors or enhancing host acute-phase responses. Full article

Oxidative stress (OS) resulting from an imbalance between reactive oxygen species (ROS) generation and antioxidant defenses plays a pivotal role in vascular diseases such as atherosclerosis and hypertension. ROS derived from NADPH oxidase, mitochondria, and xanthine oxidase promote endothelial dysfunction by inducing lipid and protein oxidation, apoptosis, and pro-inflammatory signaling, thereby enhancing smooth muscle proliferation and atherogenesis. This review summarizes the molecular mechanisms linking OS to vascular injury and aims to systematically elucidate the role of OS in vascular diseases, with a specific focus on critiquing the current challenges in translating biomarkers to clinical practice and the emerging trends in personalized antioxidant therapy. Particular attention is given to biomarkers of oxidative stress, including those assessing antioxidant enzyme activity and oxidative damage products, which possess potential for clinical use. Therapeutic strategies targeting OS, including dietary and pharmacological antioxidants, show promise in improving vascular health, although clinical outcomes have been inconsistent and it is necessary to resolve the standardization and validation of these biomarkers, develop precise targeted therapies against specific ROS sources (e.g., NOX inhibitors, mitochondrial antioxidants), and explore personalized clinical trials based on redox stratification. Overall, OS is a central mediator in vascular pathology, and progress in biomarker validation and targeted therapies will be essential to translate current knowledge into effective prevention, diagnosis, and treatment of cardiovascular diseases. Personalized approaches based on accurate redox profiling may enhance efficacy. Full article

Background/Objectives: Tea and coffee, two of the most widely consumed beverages worldwide, play important roles in supporting overall health. Changes in the urine proteome reflect the changes in the body influenced by beverage consumption, rather than beverage metabolites. In this study, the effects of teas with different fermentation levels and black coffee on the body were explored via urine proteomics analysis. Methods: Urine samples were collected from rats before and after seven consecutive days of consuming green tea, oolong tea, black tea, Pu-erh tea, or black coffee. Both before-and-after comparisons and between-group comparisons were performed, and the samples were analyzed using liquid chromatography coupled with tandem mass spectrometry. Results: The urine proteome reflected the changes in rats after consumption of teas or black coffee for one week. Biological processes and pathways enriched with differential proteins included fat cell differentiation, lipid metabolism, glucose metabolism, fatty acid transport, and immune response. The effects of teas with different fermentation levels and black coffee on the body exhibited a high degree of specificity. Additionally, several identified differential proteins have been reported as biomarkers for diseases such as cancer and cardiovascular diseases. This suggests that beverage consumption, including tea and black coffee, should be considered in urine biomarker research. And the use of biomarker panels may be necessary to improve accuracy. Conclusions: The urine proteome provides a comprehensive and systematic reflection of the effects of all components in teas and black coffee on the body and allows for the distinction of changes in the body after consumption of teas with different fermentation levels and black coffee. Full article

Introduction: The global prevalence of chronic kidney disease (CKD) is increasing and it is associated with higher mortality rates. Transforming growth factor-beta (TGF-β) can serve as a novel biomarker for early prediction of chronic kidney disease (CKD) progression. Methods: This was a prospective longitudinal study among black patients with CKD who attended the Charlotte Maxeke Johannesburg Academic Hospital between September 2019 and March 2022. Patients provided urine and blood samples for laboratory investigations at study entry (0) and at 24 months follow up. Baseline serum and urine TGF-β1, TGF-β2 and TGF-β3 levels were measured using ELISAs. Multivariable logistic regression analysis was utilized to determine if TGF-β isoforms could predict CKD progression. Results: A total of 312 patients were enrolled at baseline, of whom 275 (88.1%) had early-stage CKD (Stage 1–3). A majority, 95.2% (297/312), of the patients completed the study after 2 years follow up. The prevalence of CKD progression was 47.8% when measured by a sustained decline in eGFR of >4 mL/min/1.73 m²/year or more and 51.9% when measured by a change in uPCR > 30%. The patients with CKD progression had significantly lower eGFR and increased urine protein–creatinine ratios compared to non-progressors. Furthermore, comparing progressors with non-progressors, the median serum TGF-β1 was 21210 (15915–25745) ng/L vs. 24200 (17570–29560) ng/L and the median urine TGF-β3 was 17.5 (5.4–76.2) ng/L vs. 2.8 (1.8–15.3) ng/L, respectively. Baseline serum and urine TGF-β isoforms were unable to discriminate between CKD progressors and non-progressors after multivariable logistic regression analysis. Conclusions: Despite the multiple roles of TGF-β isoforms in kidney disease, baseline levels were not predictive of chronic kidney disease progression. Full article