Search Results (290)

Liquid biopsy has become an integral component of precision oncology, with circulating tumor DNA serving as the dominant analyte for genomic profiling and disease monitoring. However, DNA-based approaches are intrinsically limited in their ability to capture dynamic cellular states, functional adaptation, and tumor–host interactions. Circulating RNA has emerged as a complementary class of liquid biopsy biomarkers that reflects active transcriptional programs and systemic biological responses. In this review, we conceptualize circulating RNA as a liquid transcriptome and propose a structured classification framework based on physical carriers, RNA biotypes, and layers of biological interpretation. We describe how circulating RNA signals encode tissue-of-origin information, cell-state dynamics, and host immune responses, thereby enabling system-level insight into cancer biology beyond mutation-centric analyses. Recent large-scale profiling efforts and advances in extracellular RNA characterization further support the biological relevance and analytical feasibility of circulating RNA across diverse biofluids. We discuss emerging applications of circulating RNA across the cancer continuum, including early cancer detection and multi-cancer screening, tissue-of-origin inference, longitudinal monitoring of treatment response, detection of adaptive resistance, and immunotherapy stratification. In parallel, we critically examine key technical, analytical, and computational challenges that currently limit reproducibility and clinical translation, emphasizing the importance of standardized workflows, transparent reporting, and multi-center validation. Finally, we outline future directions for integrating circulating RNA with genomic and proteomic biomarkers, supported by advances in artificial intelligence and machine learning. Collectively, this review positions circulating RNA as a functionally informative and clinically promising component of next-generation liquid biopsy strategies in oncology. Full article

This study evaluated the effects of the dietary administration of a glycosylated form of active vitamin D (calcitriol, 1,25(OH)₂D₃) combined with ursolic acid (UA) and oleanolic acid (OA) triterpenes on sow health and productivity. Twenty-four third-parity Landrace × Large White sows were allocated at day 108 of gestation into three groups: a control group receiving 1800 IU/kg of vitamin D₃, and two treatment groups receiving the control diet supplemented with either 0.64 µg/kg (ACTD1) or 0.96 µg/kg (ACTD2) of glycosylated 1,25(OH)₂D₃ plus 140 or 210 µg/kg of UA + OA (4:1 ratio), respectively. Diets were administered from late gestation through the end of lactation. Farrowing duration, sow body weight, backfat thickness, and litter growth were recorded. Blood samples collected at key physiological stages were analyzed for pro-inflammatory cytokines, mineral homeostasis, endocrine markers, and serum proteome. Farrowing time was reduced in both treatment groups compared with the control (p < 0.05). Treated sows exhibited lower backfat thickness at the end of lactation and improved litter weights at farrowing, after cross-fostering, and at weaning (p < 0.05). Plasma pro-inflammatory cytokines (TNF-α, IL-1α, and IL-1β) were reduced at the end of lactation in ACTD1 and ACTD2 sows, with TNF-α and IL-1β already decreased after farrowing (p < 0.05). Treated sows also displayed decreased plasma parathormone concentrations at the end of lactation, along with increased circulating 1,25(OH)₂D₃ and calcium concentrations after farrowing and at lactation end (p < 0.05), while plasma phosphate levels remained unchanged. Proteomic analysis supported the systemic availability of the supplemented compounds and their involvement in metabolic and inflammatory pathways rather than calcium transport or vitamin D binding mechanisms. Overall, this nutritional strategy influenced the immune modulation while maintaining mineral homeostasis via modest endocrine adaptations. Larger-scale trials are warranted to confirm these results and to evaluate their practical applicability under commercial production conditions. Full article

Antimicrobial resistance (AMR) remains a serious public health concern, and methicillin-resistant Staphylococcus aureus (MRSA) continues to limit treatment options. This laboratory-based comparative study evaluated antibiotic resistance patterns and nanoparticle (NP) susceptibility among 110 S. aureus isolates recovered from human skin and soft tissue infections (n = 80) and camel milk (n = 30). Proteomic identification utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) was carried out for all isolates under study. Phenotypic differentiation between MRSA and methicillin-sensitive S. aureus (MSSA) was performed via the cefoxitin disk diffusion method, and antimicrobial susceptibility testing was carried out using the disk diffusion method as stated in international guidelines. Multidrug resistance (MDR) was defined by established criteria. The antibacterial activity of silver nanoparticles (AgNPs) and gold nanoparticles (AuNPs) was detected by broth microdilution to determine minimum inhibitory concentration values (MIC₅₀ and MIC₉₀). The ability to develop reduced susceptibility was evaluated through ten serial sub-inhibitory passages followed by stability testing without using nanoparticles. MRSA prevalence was 52.5% among human isolates and 70% among camel milk isolates. Overall, 56.4% of isolates met MDR criteria, with a significantly higher MDR rate among MRSA compared with MSSA. Both human and camel isolates showed similar resistance patterns. AgNPs exhibited strong antibacterial activity, with MIC₅₀ and MIC₉₀ values of 0.0078 mg/mL and 0.0156 mg/mL, respectively; nevertheless, AuNPs demonstrated higher MIC values. Response to NPs was similar between isolates, independent of methicillin resistance or MDR. Serial sub-inhibitory exposure resulted in increased MIC values in all tested isolates, and stable resistance persisted in 50% of cases. These results indicate ongoing MRSA circulation in human and animal settings and reinforce the need for careful and controlled use of NP-based antimicrobials. Full article

While PCOS research has extensively explored genomic, transcriptomic, proteomic, and metabolomic milieus, our study examines the plasma glycome, comparing women with PCOS to age-matched healthy controls. In this observational study, n = 47 women with PCOS were screened and enrolled at the UC Davis Health campus; the comparator group constituted of n = 25 age-matched healthy women. During a study visit, body weight and body composition were measured, and fasted plasma samples were obtained to measure glucose, insulin, circulating lipids, and leptin, among other parameters, in both groups. In addition, in the PCOS group, circulating androgens and other endocrine hormones were measured. The plasma glycome was measured using a UHPLC-MS protocol. As expected, women with PCOS had higher body weight (p < 0.01), body fat (p = 0.004), fasting leptin (p = 0.01), insulin (p = 0.003), and glucose (p = 0.004). Hybrid-type glycans were reduced (p = 0.019), while tetraantennary (glycans with four branches) were modestly increased (p = 0.05) in women with PCOS compared to healthy controls. SVEM–LASSO (bootstrapped) regression models further supported a higher tetraantennary and lower hybrid glycan profile as representative of women with PCOS (AUROC: 0.81, accuracy: 82), even when adjusted for body weight (AUROC: 0.89, accuracy: 80) and body fat mass (AUROC: 0.89, accuracy: 86). Furthermore, in women with PCOS, total testosterone was positively correlated with tetraantennary glycans (r = 0.322, p = 0.029). We report novel findings of elevated tetraantennary and reduced hybrid-type N-glycans in PCOS, and a potential association between circulating androgens and protein glycosylation. Given the pilot nature of this study, larger cohort investigations are required to validate these observations. Full article

Background: Heart failure (HF) is a clinical syndrome that involves multiple interconnected pathways. Circulating biomarkers in HF emerged as powerful tools for risk stratification, diagnostic confirmation, prognostic assessment, and monitoring of treatment efficacy. The aim of the present study was to evaluate circulating levels of biomarkers in elderly patients with improved HF ejection fraction, previously with left ventricular ejection fraction (LVEF) <40%, after six months of drug therapy optimisation. Methods: We enrolled 100 HFimpEF outpatients. All patients provided medical history and underwent physical examination at baseline and after six months of follow-up. The serum values of circulating biomarkers were assessed with an ELISA test. Proteomic analysis was performed on serum samples collected from a subset of 13 patients at baseline and after six months of follow-up. Results: At follow-up, we observed significant improvements in glycometabolic, renal and inflammatory profiles (p < 0.001). Proteomic analysis revealed selective changes in key cardiovascular (CV)-related proteins, such as insulin-like growth factor-binding protein 4 (IBP4), thrombospondin-4 (TSP4), intercellular adhesion molecule 1 (ICAM1), and syndecan-4 (SDC4). Conclusions: This study demonstrates significant improvements across multiple CV biomarkers after six months of therapy optimisation in HFimpEF patients, providing evidence for comprehensive therapeutic effects targeting inflammation, oxidative stress, neurohormonal activation, and thrombotic risk. Full article

Background: SARS-CoV-2 vaccination is crucial for protecting against severe COVID-19 disease; however, patients with haematological malignancies (HM) respond poorly to vaccination due to immunosuppression driven by chemotherapy, targeted cell depletion, and immune dysregulation. We sought to define novel biomarkers that predict effective vaccination in patients with HM. Methods: HM patients and healthy controls received SARS-CoV-2 vaccines and were followed for six months post-vaccination. Virus-specific humoral and cellular immune responses were analysed in serum and whole blood pre- and post-vaccination, and serum proteomics was analysed pre-vaccination to identify potential biomarkers for vaccine response. Results: HM patients displayed delayed antibody seroconversion, and 37.5% failed to seroconvert. Baseline proteomic and cellular immune profiles revealed that T-cell-associated chemokines CXCL13 and CRTAM were differentially expressed, with decreased levels seen in vaccine non-responders. Vaccine response was also associated with a reduced frequency of circulating monocytes, greater numbers of B-cells, and a trend toward greater numbers of CD4+ helper cell phenotypes, including T peripheral helper cells pre-vaccination. In vitro generation of COVID-19-specific T-cells from a subset of participants trended towards increased cytotoxic CD4+ and CD8+ T-cell activity in seroconverters and dysfunctional COVID-19-specific T-cell responses in non-seroconverters. Conclusions: These results suggest that HM patients have impaired T-cell immunity, and non-responders may be identified by low levels of serum CXCL13 and CRTAM. This allows for the identification of at-risk patients who would benefit from alternative COVID-19 prophylaxis strategies. Full article

Calprotectin in blood has been identified as a potential biomarker for severe COVID-19 and sepsis. As a knowledge gap remains regarding the biological role of calprotectin, we aimed to investigate the association between serum calprotectin and the circulating proteome in patients with COVID-19 as a model for viral sepsis. In this observational study, serum samples were collected from 160 hospitalized adult patients with COVID-19. The samples were analyzed for calprotectin using a routine turbidimetric assay and for proteomics using the Olink Explore 1536 platform. Patients were classified as having severe or moderate COVID-19 according to oxygen supply on the day of blood sampling. The median calprotectin level was significantly higher in patients with severe compared to moderate COVID-19. In relation to proteomics, calprotectin levels were associated with a neutrophil-centered inflammatory proteomic signature, characterized by upregulation of cytokine and danger-signaling pathways. S100A12 showed the strongest correlation to calprotectin. In conclusion, calprotectin is associated with disease severity in COVID-19, and high levels reflect a neutrophil-driven inflammatory proteomic profile, particularly involving S100A12. These findings support calprotectin as a biomarker of neutrophil-mediated hyperinflammation in viral sepsis. Full article

Background: The ACE Y215C mutation is a common, functionally damaging missense variant (~1.5% allele frequency) associated with reduced plasma ACE levels and increased Alzheimer’s disease (AD) risk. In CHO and HEK cell models, this mutation caused a ~3–6-fold decrease in ACE surface expression, soluble ACE levels, and ACE enzymatic activity compared to those of wild-type ACE. Methods: Circulating ACE levels and activity were measured in EDTA plasma obtained from 84 carriers of the ACE Y215C mutation using a set of mAbs to the ACE. The mAbs 5B3/1G12 binding ratio was revealed as a sensitive marker for the circulating Y215C ACE mutant. Whole-exome and whole-genome sequencing (WES/WGS) were performed to identify genetic variants potentially modifying circulating ACE levels. In parallel, published sequencing and proteomic data from 35,559 Icelanders participants were analyzed to identify genes influencing ACE shedding. Sequence comparison was performed between carriers with elevated and reduced ACE concentrations to identify the potential protective variants that may compensate for decreased ACE levels due to the Y215C mutation itself. Results: Most carriers of the Y215C ACE mutation demonstrated significantly decreased ACE levels (median is 62% of control ACE levels). However, substantial inter-individual variability was observed in plasma ACE activity among carriers. Comparative sequencing analysis revealed 9648 variants unique to individuals with elevated ACE, mapping to 5779 protein-coding genes and enriched for pathways related to intracellular and transmembrane transport. Conclusions: The presence of the damaging ACE mutation Y215C does not invariably result in low plasma ACE or, likely, elevated AD risk. Therefore, combined blood ACE phenotyping and whole-exome sequencing are recommended to more accurately assess ACE-related AD susceptibility in mutation carriers. Full article

The total cavopulmonary anastomosis (Fontan procedure), a palliative procedure for single-ventricle congenital heart disease, improves survival but is associated with progressive multiorgan complications and high long-term morbidity. Prior blood-based proteomic studies in adults have been limited to targeted antibody-based panels or focused on methodological comparisons. Systemic molecular alterations in younger, clinically heterogeneous patients, particularly in untargeted pathways, remain incompletely characterized. Serum samples from 48 Fontan patients and 48 age- and sex-matched healthy controls were analyzed using mass spectrometry with TMT labeling. 2228 proteins were quantified, of which 124 were significantly differentially abundant (fold change > 1.5 or <0.67, FDR-adjusted p < 0.05). Network analysis identified three major functional clusters: extracellular matrix (ECM) organization (predominantly increased), actin cytoskeleton organization, and platelet-related pathways (both predominantly decreased). Stratified analyses showed reduced ECM protein abundance in high-risk patients, suggesting a shift from active remodeling toward a more established fibrotic state, and uniquely elevated cytochrome b5 reductase 3 (CYB5R3), implicating altered redox homeostasis, nitric oxide metabolism, and cellular aging. Overall, our findings extend prior targeted analyses, reveal potential biomarkers such as CYB5R3 and underscore the complexity of the Fontan circulation, with implications for risk stratification and therapeutic targeting. Full article

Feline calicivirus (FCV) is a highly variable RNA virus that infects domestic cats and circulates endemically within feline populations, causing a wide spectrum of clinical manifestations, from asymptomatic infections to severe disease. Genomic analysis of 69 FCV strains revealed a high prevalence of the virus across multiple provinces in China. In vitro infection of CRFK cells with laboratory isolates FCV-BJ616 and FCV-BJDX40 resulted in significant cytotoxic effects. Serum proteomic analysis identified 221 upregulated and 123 downregulated proteins following infection with FCV-BJ616, and 233 upregulated and 165 downregulated proteins following infection with FCV-BJDX40. Among these, 215 proteins exhibited shared differential expression. Functional analyses revealed enriched pathways, including TNF signaling and ferroptosis. Notably, upregulation of Acyl-CoA Synthetase Long-Chain Family Member 4 (ACSL4) was correlated with lung injury, while downregulation of S100 Calcium Binding Protein A2 (S100A2) was associated with poor prognosis in FCV-associated oral disease. The differential expression of ACSL4 and S100A2 was further validated through Western blot analysis. These results suggest that ACSL4 and S100A2 are promising candidate biomarkers for monitoring FCV infection and disease progression, laying a foundation for future diagnostic and prognostic applications. Full article

Although neurological disease is common in people with human immunodeficiency virus (HIV) (PWH), the contributing factors and underlying inflammatory mechanisms remain challenging to identify. Extracellular vesicles (EVs) constitute a relatively uncharacterized modality of intercellular communication and bioactive cargo transport in the setting of viral infection and pathogenesis. EVs carry inflammatory mediators to areas of the periphery during antiretroviral therapy (ART) suppression but are understudied in the brain. Using a biologically relevant simian–human immunodeficiency chimeric virus with a clade D HIV envelope (SHIV.D)-infected rhesus macaque (RM) model of HIV persistence in the central nervous system (CNS), we investigate circulating EV populations and the protein cargo of myeloid-derived EVs during SHIV infection. Using EV flow cytometry to quantify specific EV subpopulations, we found a significant increase in TMEM119+ microglial EVs and CD171+ neuronal EVs in RM plasma during viremia and ART suppression. Using primary RM monocyte-derived macrophages (MDMs), we determined that MDMs increased EV production after SHIV infection. Whole proteomic analysis of these EVs demonstrated that myeloid EVs isolated from SHIV.D-infected MDMs carried significantly increased levels of neuropathogenic and inflammatory proteins. Altogether, these studies improve our understanding of the contribution of myeloid EVs to neurological disease during SHIV/HIV infection. Full article

Endometriosis is traditionally conceptualized as a pelvic lesion–centered disease; however, mounting evidence indicates it is a chronic, systemic, and multifactorial inflammatory disorder. This review examines the molecular dialog between ectopic endometrial tissue, the immune system, and peripheral organs, highlighting mechanisms that underlie disease chronicity, symptom variability, and therapeutic resistance. Ectopic endometrium exhibits distinct transcriptomic and epigenetic signatures, disrupted hormonal signaling, and a pro-inflammatory microenvironment characterized by inflammatory mediators, prostaglandins, and matrix metalloproteinases. Immune-endometrial crosstalk fosters immune evasion through altered cytokine profiles, extracellular vesicles, immune checkpoint molecules, and immunomodulatory microRNAs, enabling lesion persistence. Beyond the pelvis, systemic low-grade inflammation, circulating cytokines, and microRNAs reflect a molecular spillover that contributes to chronic pain, fatigue, hypothalamic–pituitary–adrenal axis dysregulation, and emerging gut–endometrium interactions. Furthermore, circulating biomarkers—including microRNAs, lncRNAs, extracellular vesicles, and proteomic signatures—offer potential for early diagnosis, patient stratification, and monitoring of therapeutic responses. Conventional hormonal therapies demonstrate limited efficacy, whereas novel molecular targets and delivery systems, including angiogenesis inhibitors, immune modulators, epigenetic regulators, and nanotherapeutics, show promise for precision intervention. A systems medicine framework, integrating multi-omics analyses and network-based approaches, supports reconceptualizing endometriosis as a systemic inflammatory condition with gynecologic manifestations. This perspective emphasizes the need for interdisciplinary collaboration to advance diagnostics, therapeutics, and individualized patient care, ultimately moving beyond a lesion-centered paradigm toward a molecularly informed, holistic understanding of endometriosis. Full article

Intervertebral disc (IVD) herniation is a complex and multifactorial condition with a challenging diagnosis and limited therapeutic options, highlighting the need for reliable biomarkers to improve clinical decision-making. The aim of this study was to identify circulating prognostic biomarkers of IVD herniation regression. The plasma proteomic profile and the expression of circulating non-coding RNAs were analysed in a rat model of IVD herniation and were correlated with herniation size. Four candidate proteins (TNC, COPS3, JUP, and GNAI2) were significantly correlated with herniation size, with TNC further validated by ELISA. Additionally, miR-143-3p, miR-10b-5p, miR-27a-3p, miR-140-5p, miR-155-5p, miR-146a-5p, and miR-21-5p were positively correlated with herniation size. Moreover, TNC, COPS3, JUP, and GNAI2 were found to be potential targets of miR-155-5p. This study provides the first combined proteomic and miRNA account of preclinical plasma biomarkers of IVD herniation size, where TNC-miR-155-5p emerge as promising elements of a regulatory module with IVD herniation prognostic potential. Full article

Extracellular RNAs are released from cells and circulate stably in biofluids such as blood, cerebrospinal fluid, saliva, and urine via carriers including extracellular vesicles, RNA-binding proteins and lipoproteins. Because transcriptional and metabolic disturbances—notably mitochondrial dysfunction and oxidative stress—often precede protein aggregation, synaptic loss, and structural change in many brain diseases, exRNAs offer minimally invasive access to early disease biology. Mechanistic studies demonstrate selective RNA packaging and delivery: transferred mRNAs can be translated and miRNAs can modulate targets, indicating exRNAs both report intracellular programs and actively influence recipient cells. Clinical and preclinical data support a dual role for exRNAs as biomarkers and as mediators of pathology. Key technical hurdles—pre-analytical variability, isolation heterogeneity, and uncertain cellular origin—limit reproducibility; recommended solutions include standardized workflows, carrier- and cell type-specific enrichment, multimodal integration with proteomics/metabolomics and neuroimaging, and large, longitudinal validation studies. We synthesize mechanistic and clinical evidence for exRNA utility in early detection, prognosis, and therapeutic targeting and outline a roadmap to translate exRNA findings into robust clinical assays and interventions for neurodegenerative and brain disorders. Full article

Nintedanib is an anti-fibrotic medication endowed with a multi-kinase inhibitor profile and approved for the treatment of Idiopathic Pulmonary Fibrosis (IPF). Nintedanib is believed to inhibit mainly Vascular Endothelial Growth Factor (VEGF), Platelet-Derived Growth Factor (PDGF), and Fibroblast Growth Factor (FGF) receptor kinases. The main objective was to identify potential tissue and/or circulating biomarkers to demonstrate Nintedanib’s target engagement and support its in vivo pharmacodynamic activity, consistent with its proposed mechanism(s) of action. In four independent experiments of bleomycin (BLM)-induced lung fibrosis model in rats, animals received Nintedanib (oral, 100 mg/kg/day) from day 7 post-BLM for 3 weeks. As expected, Nintedanib significantly reduced lung weight, the levels of lung fibrotic markers, and fibrotic areas. Moreover, Nintedanib-treated animals expressed lower levels of FGF2 in lung homogenates and higher plasma and lung levels of VEGF (≥3-fold, p < 0.05) compared to control animals. Lung proteomic analysis revealed the inhibition of receptor tyrosine kinases signaling in Nintedanib-treated animals. Circulating and lung levels of Nintedanib confirmed an optimal tissue distribution in the rat, consistent with the data reported for humans. Although VEGF ligand levels are elevated in the lungs of Nintedanib-treated animals, the VEGF signaling pathway remained functionally downregulated, strongly suggesting compensatory VEGF feedback delivery to its receptor blockade by Nintedanib. In summary, based on the present experimental findings in rats and supporting clinical preliminary evidence, increased VEGF levels can be reasonably considered an indicator of target engagement for Nintedanib and potentially for other VEGF modulators. Full article