Search Results (392)

Background: Rabies is among the oldest known zoonotic viral diseases and is caused by members of the Lyssavirus genus. The prototype species, Lyssavirus rabies, effectively evades the host immune response, allowing the infection to progress unnoticed until the onset of clinical signs. At this stage, the disease is irreversible and invariably fatal, with definitive diagnosis possible only post-mortem. Given the advances in modern proteomics, this study aimed to identify potential protein biomarkers for antemortem diagnosis of rabies in dogs, which are the principal reservoir hosts of the rabies virus. Methods: Two hundred and thirty-one samples (brain tissues (BT), cerebrospinal fluids (CSF), and serum (SR) samples) were collected from apparently healthy dogs brought for slaughter for human consumption in South-East and North-Central Nigeria. All the BT were subjected to a direct fluorescent antibody test to confirm the presence of lyssavirus antigen, and 8.7% (n = 20) were positive. Protein extraction, quantification, reduction, and alkylation were followed by on-bead (HILIC) cleanup and tryptic digestion. The resulting peptides from each sample were injected into the Evosep One LC system, coupled to the timsTOF HT MS, using the standard dia-PASEF short gradient data acquisition method. Data was processed using Spectronaut^TM (v19). An unpaired t-test was performed to compare identified protein groups (proteins and their isoforms) between the rabies-infected and uninfected BT, CSF, and SR samples. Results: The study yielded 54 significantly differentially abundant proteins for the BT group, 299 for the CSF group, and 280 for the SR group. Forty-five overlapping differentially abundant proteins were identified between CSF and SR, one between BT and CSF, and two between BT and SR; none were found that overlapped all three groups. Within the BT group, 33 proteins showed increased abundance, while 21 showed decreased abundance in the rabies-positive samples. In the CSF group, 159 proteins had increased abundance and 140 had decreased abundance in the rabies-positive samples. For the SR group, 215 proteins showed increased abundance, and 65 showed decreased abundance in the rabies-positive samples. Functional enrichment analysis revealed that pathways associated with CSF, spinocerebellar ataxia, and neurodegeneration were among the significant findings. Conclusion: This study identified canonical proteins in CSF and SR that serve as candidate biomarkers for rabies infection, offering insights into neuronal dysfunction and potential tools for early diagnosis. Full article

Rare genetic ocular diseases represent a heterogeneous group of disorders that significantly impair visual function and quality of life. Despite their clinical relevance, many of these conditions remain insufficiently characterized due to complex molecular mechanisms and diagnostic limitations. Recent advances in molecular diagnostics, particularly Next-Generation Sequencing (NGS), have enabled comprehensive and accurate identification of pathogenic variants, offering novel insights into genotype–phenotype correlations and supporting precision medicine approaches. In parallel, the use of alternative biological matrices such as tear fluid has emerged as a promising non-invasive strategy for biomarker discovery and disease monitoring. Tear-based omics, including proteomics and transcriptomics, have identified diagnostic signatures and pathogenic mediators such as non-coding RNAs, microRNAs, and tRNA-derived fragments (tRFs). Among these, tRF-1001 has shown potential both as a biomarker and therapeutic target in ocular neovascular conditions through its modulation of angiogenic pathways. The objective of this review is to show the integration of two rapidly advancing yet frequently isolated fields: next-generation sequencing-based genomics and tear-fluid molecular profiling, positioning them as complementary foundations of precision ophthalmology for rare inherited retinal and optic nerve disorders. Previous reviews have mainly concentrated on either genetic diagnosis or ocular surface biomarkers separately; however, we have introduced a convergent model wherein genomic data furnish diagnostic and prognostic clarity, while tear-omics deliver dynamic, minimally invasive assessments of disease activity, treatment efficacy, and persistent neurovascular stress. By explicitly connecting these two aspects, we have delineated how multi-matrix, multi-omics approaches can expedite early diagnosis, facilitate personalized longitudinal monitoring, and direct focused treatment interventions in rare ocular genetic illnesses. Full article

Alzheimer’s disease (AD) and dementia with Lewy bodies (DLB) are the two most common forms of dementia due to neurodegeneration. AD is characterized by extracellular amyloid-β (Aβ) plaques and intracellular tau neurofibrillary tangles, whereas DLB is defined by α-synuclein (α-Syn)-containing Lewy bodies. Although AD and DLB exhibit divergent core features, the disorders frequently co-occur and converge on shared endpoints. Co-pathology is common and linked to more severe cognitive decline, faster progression, and clinicopathological heterogeneity. Here, we discuss the current understanding of shared and unique clinical and neuropathological features of AD and DLB. We compare genetic risk and pathological drivers (Aβ and tau in AD; α-Syn in DLB) and their overlapping co-pathology, and review downstream mechanisms—mitochondrial dysfunction, oxidative stress, neuroinflammation, and cerebrovascular contributions, including cerebral amyloid angiopathy. We highlight recent findings from state-of-the-art multi-omics (transcriptomic, proteomic, metabolomic, and single-cell/spatial studies) that reveal convergent and disease-specific molecular signatures of AD and DLB. We outline a framework for emerging next-generation biomarkers—from blood-based and cerebrospinal fluid assays to imaging and digital measures—for diagnosis and stratification, and discuss potential translational implications. Together, these advances help to disentangle shared from disease-specific mechanisms, which is essential for improved diagnosis and the development of precise, disease-modifying therapies. Full article

The development of males and females of the cephalopod Amphioctopus fangsiao is asynchronous. The male produces sperm after maturity for storage in a spermatophore prior to mating. After mating, the sperm enter the female spermatheca for storage until ovulation occurs, a period that lasts for 8 months. This is a biologically uncommon phenomenon because sperm cells generally fail to maintain their ability to fertilize for a long time after being ejaculated. However, the molecular mechanisms of this phenomenon are still not clear. Sperm cells are stored in the male spermatophore and the female spermatheca, each of which provides a suitable environment. To determine the molecular basis of the sperm storage mechanisms in A. fangsiao, protein profiles from spermathecal fluid and seminal plasma were characterized separately using mass spectrometry-based proteomics. The antioxidant enzymes superoxide dismutase (SOD), glutathione S-transferase (GST), and Thioredoxin (Trx), and the glycolytic enzymes lactate dehydrogenase (LDH), hexokinase (HK), pyruvate dehydrogenase kinase (PDK), and ATP synthase were significantly enriched in the spermathecal fluid. Catalase (CAT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), triosephosphate isomerase (TIM), phosphoglycerate kinase (PGK), and Chitinase were significantly enriched in the seminal plasma. The antimicrobial proteins transforming growth factor beta regulator 1 (TBRG1) and interleukin enhancer binding factor 2 (ILF2) and the extracellular matrix-related proteins transforming growth factor beta induced protein (TGFBIp) and thrombospondin type-1 domain-containing protein 4 (THSD4) were also significantly expressed in the spermathecal fluid. These proteins may be crucial for successful long-term sperm storage. We measured the activities of four antioxidant enzymes based on the proteomic results, supporting the antioxidant mechanism during the sperm storage process. This study enhances our understanding of the sperm storage ability of A. fangsiao. Full article

Alzheimer’s Disease (AD) management is challenging due to limitations in detection methods. Currently, cerebrospinal fluid (CSF) biomarkers involve assessing β-amyloid (Aβ) and phosphorylated tau proteins. The lumbar puncture procedure to obtain CSF is invasive and sometimes causes significant anxiety in patients. In contrast, plasma biomarkers would allow rapid, accurate, and cost-effective diagnosis, while minimizing invasiveness and discomfort. Using a dataset involving 120 plasma proteins from clinically diagnosed AD patients versus cognitively normal subjects, we developed classification models by applying various machine learning algorithms (EBlasso, EBEN, XGBoost, LightGBM, TabNet, and TabPFN) to plasma proteomic measurements. Gene ontology and pathway enrichment, and a literature review were used to evaluate the potential relevance of the biomarkers identified in AD-related mechanisms. Biomarkers identified were also evaluated for the enrichment of aging-related biomarkers. The models developed yielded high AUROC and accuracy, mostly >0.9. Proteins selected as predictors by all the models included Angiopoietin-2 (ANG-2), epidermal growth factor (EGF), Interleukin 1α (IL-1α), and platelet growth factor subunit B (PDGF-BB). Ample previous literature supported their relevance in AD. The pool of all the biomarkers identified was significantly enriched with known aging-related biomarkers (p = 0.040). Applying cutting-edge algorithms is expected to be advantageous for developing AD prediction models with plasma proteomic data, and future large studies to externally validate the constructed models in other populations to assess their generalizability is important. The proteins uncovered may represent novel preventative or therapeutic targets. Full article

Alzheimer’s disease (AD) is one of the most widespread neurodegenerative disorders, primarily affecting individuals over the age of 65. It is characterized by severe cognitive impairment, memory loss, difficulties in performing daily activities, ventricular enlargement, and ultimately, dementia. AD is associated with the accumulation of amyloid $\beta \left(A\beta \right)$ protein plaques, intracellular neurofibrillary tangles (NFTs), progressive inflammation, and impairment of both synaptic transmission and mitochondrial function. Due to the limited diagnostic tools available for detecting the disease in its early stages, proteomic biomarkers have gained paramount importance, as they can monitor prodromal molecular alterations linked to AD. Furthermore, proteomic biomarkers can facilitate the longitudinal assessment of disease progression and contribute to the development of personalized therapeutic strategies before the devastating onset of dementia. Research has primarily focused on identifying proteomic biomarkers in cerebrospinal fluid (CSF) and plasma, as discussed in this review, but also in alternative matrices such as saliva and urine. These studies highlight both the high potential of proteomic approaches and the ongoing challenge of identifying clinically available, sensitive, and specific biomarkers for the various stages of the disease. Full article

Prostate cancer is one of the most common cancers affecting men, and finding better ways to detect and monitor it remains a top priority in oncology. In recent years, scientists have focused their attention on different classes of extracellular bodies, among them the small ones called exosomes. Exosomes are nanoscale extracellular vesicles (30–200 nm) released into body fluids, where they transport molecular cargo reflective of their cell of origin. Instead of serving as liquid biopsies themselves, exosomes present in accessible fluids such as plasma and urine can be analyzed as part of minimally invasive liquid biopsy strategies without the need for surgery or tissue sampling. In prostate cancer, exosomes are not just passive carriers: they actively influence how cancer grows, spreads, and responds to treatment. Exosomes can be extracted from simple fluid samples, opening the door to faster, safer, and more personalised approaches to diagnosis and care. Exosome content is analysed for the molecular profiling of tumours, including genomics, transcriptomics, proteomics, and metabolomics. This has led to the discovery of new biomarkers that may help detect prostate cancer earlier, predict its aggressiveness, and monitor the effectiveness of treatment. This review synthesizes current multi-omics data on exosomal cargo in prostate cancer, highlighting diagnostic, prognostic, and therapeutic implications as well as existing challenges to clinical translation. Full article

The way in which Aquaporin-4 (AQP4) is localized on the astrocytes’ surface—i.e., with AQP4 channels predominantly located on the endfeet of astrocytes near the blood vessels—represents an important structural element for maintaining brain fluid homeostasis. In addition to this structural function, AQP4 polarity also facilitates glymphatic transport, the maintenance of the blood–brain barrier (BBB) functions, ion buffering, and neurotransmitter removal, and helps regulate neurovascular communications. The growing body of literature suggests that the loss of AQP4 polarity—a loss in the organization of AQP4 channels to the perivascular membrane—is associated with increased vascular, inflammatory, and metabolic disturbances in the context of many neurological diseases. As a result, this review attempts to synthesize both experimental and clinical studies to highlight that AQP4 depolarization often occurs in conjunction with early signs of neurodegeneration and neuroinflammation; however, we are aware that the loss of AQP4 polarity is only one factor in a complex pathophysiological environment. This review examines the molecular structure responsible for maintaining the polarity of AQP4—such as dystrophin–syntrophin complexes, orthogonal particle arrays, lipid microdomains, trafficking pathways, and transcriptional regulators—and describes how the vulnerability of these systems to various types of vascular stress, inflammatory signals, energy deficits, and mechanical injury can lead to a loss of AQP4 polarity. Furthermore, we will explore how a loss of AQP4 polarity can lead to the disruption of perivascular fluid movement, changes in blood–brain barrier morphology, enhanced neuroimmune activity, changes in ionic and metabolic balance, and disruptions in the global neural network synchronization. Importantly, we recognize that each of these disruptions will likely occur in concert with other disease-specific mechanisms. Alterations in AQP4 polarity have been observed in a variety of neurological disorders including Alzheimer’s disease, Parkinson’s disease, multiple sclerosis, traumatic brain injury, and glioma; however, we also observe that the same alterations in fluid regulation occur across all of these different diseases, but that no single upstream event accounts for the alteration in polarity. Ultimately, we will outline emerging therapeutic avenues to restore perivascular fluid transport, and will include molecular-based therapeutic agents designed to modify the anchoring of AQP4, methods designed to modulate the state of astrocytes, biomaterials-based drug delivery systems, and therapeutic methods that leverage dynamic modulation of the neurovascular interface. Future advances in multi-omic profiling, spatial proteomics, glymphatic imaging, and artificial intelligence will allow for earlier identification of AQP4 polarity disturbances and potentially allow for the development of more personalized treatment plans. Ultimately, by linking these concepts together, this review aims to frame AQP4 polarity as a modifiable aspect of the “fluidic connectome”, and highlight its importance in maintaining overall brain health across disease states. Full article

Endometrial cancers (ECs) are mainly adenocarcinomas arising from the uterine endometrium. In this work, we employed data-independent acquisition (DIA) mass spectrometry (MS)-based label-free quantification (LFQ-MS) proteomics to analyze the proteome of tissue washings collected from 25 control (CTRL) subjects, 25 patients with low-grade type 1 endometrial cancer (EC), and 24 patients with high-grade type 1 EC. Following quantification and statistical analysis, we identified 42 proteins able to discriminate CTRL from EC patients, and 151 proteins differentiating high-grade EC cases from low-grade EC cases. Notably, PRRC2A and SYDE2 effectively distinguished both EC patients from controls and advanced EC cases from low-grade EC cases. Validation by Western blot analysis in an independent cohort comprising 19 CTRL patients, 19 patients with low-grade EC, and 19 patients with high-grade EC confirmed the upregulation of PRRC2A and SYDE2. These proteins are implicated in the translocation of SLC2A4, the regulation of MECP2, and extracellular matrix (ECM) proteoglycan pathways, all of which are associated with tumor growth. Our results demonstrate that DIA-based proteomic analysis of tissue washings enables the identification of potential biomarkers for endometrial cancer (EC). Moreover, this study highlights tissue washings as a promising biological fluid for biomarker discovery in EC. Full article

Susac Syndrome (SuS) is a rare autoimmune neurovascular disorder characterized by sudden visual loss, hearing disturbances, and encephalopathy. Pathology affects the small vessels of the brain, retina, and inner ear. Diagnosing SuS is challenging due to its rarity, complexity, and nonspecific symptoms. This single-case study presents a proteomic analysis of tear fluid from a patient with SuS, revealing upregulated proteins involved in immune dysregulation, cytoskeletal remodeling, and cellular repair. The activation of inflammatory proteins (e.g., S100), cytoskeletal and motility-related proteins (e.g., ezrin, radixin), and membrane transport proteins (e.g., aquaporin-5, chloride intracellular channel protein), together with activation of MAPK and NF-κB signaling pathways, highlights immune dysregulation and neurovascular damage in SuS. Hyperactivation of MAPK and NF-κB pathways leads to chronic neuroinflammation and decreased expression of neutrophil defensin 1, indicating a shift from a protective to a chronic inflammatory response. These findings from the personalized proteomic pattern of SuS support the potential of tear fluid proteomics for diagnosing SuS and offer valuable insights into its underlying molecular mechanisms. Full article

Several factors, including semen quality, can influence fertilisation success. Poor semen parameters may necessitate more frequent inseminations or the removal of males with consistently low fertility. This study evaluated turkey ejaculates (n = 37) with good fertility (GF) and impaired fertility (IF). The analyses included sperm motility parameters (total motility—TMOT, progressive motility—PMOT, curvilinear velocity—VCL, straight-line velocity—VSL, average path velocity—VAP, linearity—LIN, straightness—STR, amplitude of lateral head displacement—ALH, and beat cross frequency—BCF), plasma membrane integrity (PMI), mitochondrial membrane potential (MMP), and nitric oxide (NO) production, as well as enzymatic and biochemical assays of semen, such as superoxide dismutase (SOD), glutathione peroxidase (GPx), catalase (CAT) activities, glutathione (GSH) content, malondialdehyde (MDA) levels, and zinc (Zn²⁺) concentration. In parallel, the proteomes of seminal plasma and spermatozoa were separated using SDS- and Tricine-PAGE, and selected proteins were identified by nano LC-MS/MS. Spermatozoa derived from IF ejaculates exhibited significantly reduced TMOT (p = 0.002), VCL (p = 0.028), and PMI (p = 0.000), accompanied by elevated STR (p = 0.000) and NO production (p = 0.044). In the seminal plasma of IF males, a significant decrease was noted in SOD (p = 0.000) and GPx (p = 0.001) activities, whereas CAT activity was markedly higher (p = 0.014). Seminal fluid from IF ejaculates was also characterised by increased GSH (p = 0.014) and MDA (p = 0.014) concentrations, accompanied by reduced Zn²⁺ content (p = 0.014). In contrast, IF spermatozoa exhibited elevated SOD activity (p = 0.001), but reduced GPx (p = 0.000) and CAT (p = 0.012) activities. Sperm cells from IF ejaculates also had lower GSH levels (p = 0.000), higher MDA concentrations (p = 0.000), and increased Zn²⁺ content (p = 0.018) compared with those from GF ejaculates. A proteomic analysis revealed differences in fertility-associated proteins: peroxiredoxin 6 (PRDX6) was detected exclusively in GF semen, whereas alpha-enolase (ENO1), fatty acid-binding protein (FABP7), cytoplasmic aspartate aminotransferase (GOT1), and L-lactate dehydrogenase B (LDHB) were detected only in IF semen. Overall, the results demonstrate that both semen parameters and proteome composition may potentially affect the fertilisation outcomes in turkeys. Full article

Periodontitis (PD) is a multifactorial, progressive inflammatory disease affecting the teeth-supporting tissues, characterized by an imbalance of the oral microbiota and the presence of bacterial biofilms leading to host response. Nowadays, reliable biochemical markers for early and objective diagnosis, and for predicting disease progression, are still lacking. Our previous proteomic investigations revealed the significant overexpression of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in periodontal pocket tissue, gingival crevicular fluid (GCF), and tooth-surface-collected material (TSCM) from PD patients in comparison to periodontally healthy controls, proposing it as a possible biomarker of PD. This study aimed to evaluate the expression of GAPDH in saliva, a more accessible, non-invasive, and clinically relevant oral sample. The whole saliva was analyzed by a preliminary mass spectrometry-based proteomic approach, identifying significantly increased levels of GAPDH also in salivary samples from periodontal-affected subjects. These data were further validated by enzyme-linked-immunosorbent assay (ELISA). Additionally, protein–protein interaction networks were generated through the Human Protein Atlas database, using different datasets (OpenCell, IntAct, and BioGRID). Bioinformatic analysis provided noteworthy GAPDH-associated networks potentially relevant to periodontal pathology. The scientific significance of this study lies in the detection of salivary GAPDH as a novel strategy to advance periodontal clinical diagnostics from the perspective of a non-invasive screening test. In correlation with other protein markers, salivary GAPDH could constitute a promising set of distinctive and predictive targets to enhance early diagnosis of PD, disease monitoring, and treatment planning in periodontology. Full article

Ovarian follicular fluid (FF) is a metabolically active and biomarker-rich medium that mirrors the oocyte microenvironment. Its analysis is increasingly recognized in infertility diagnostics and assisted reproductive technologies (ART) for assessing oocyte competence, understanding reproductive disorders, and guiding personalized treatment. However, FF’s high viscosity, complex composition, and biochemical variability challenge reproducibility in sample preparation and molecular profiling. Sonication-based extraction has emerged as an effective approach to address these issues. By exploiting acoustic cavitation, sonication improves protein solubilization, metabolite release, and lipid recovery, while reducing solvent use and processing time. This review synthesizes recent advances in sonication-assisted FF analysis across proteomics, metabolomics, and lipidomics, emphasizing parameter optimization, integration with advanced mass spectrometry workflows, and emerging applications in microfluidics, automation, and point-of-care devices. Clinical implications are discussed in the context of enhanced biomarker discovery pipelines, real-time oocyte selection, and ART outcome prediction. Key challenges, such as preventing biomolecule degradation, standardizing protocols, and achieving inter-laboratory reproducibility, are addressed alongside regulatory considerations. Future directions highlight the potential of combining sonication with multi-omics strategies and AI-driven analytics, paving the way for high-throughput, standardized, and clinically actionable FF analysis to advance precision reproductive medicine. Full article

Non-small cell lung cancer (NSCLC) is a severe disease with a very poor prognosis. Some 30–80% of patients with NSCLC die within five years of cancer diagnosis. The main factors contributing to this condition are the lack of effective markers for diagnosing cancer at an early stage, as well as the complexity of the biological processes involved in tumorigenesis and progression. The development of knowledge regarding all aspects of NSCLC has provided information used in the detection, systemic anticancer therapy and monitoring of NSCLC, which has a significant impact on prognosis and quality of life. NSCLCs release various biological substances into the bloodstream. Liquid biopsies allow for the analysis of tumor components in body fluids, and the usefulness of these biopsy tests as a substitute for tumor tissue is increasing. In this article, we critically review the available literature on microRNAs, circulating cell-free DNA (cfDNA), tumor-educated platelets (TEPs), circulating tumor cells (CTCs), circulating extracellular vesicles (EVs), and metabolomic and proteomic markers in the diagnosis and monitoring of NSCLC. However, the usefulness of these new markers in clinical practice has significant limitations. Full article

Selenium, a crucial trace element, has garnered significant attention in functional food development due to its effective conversion into organic forms. This study systematically investigated the selenium enrichment potential and metabolic regulation mechanisms of 50 lactic acid bacteria (LAB) strains from Xinjiang. Through sodium selenite tolerance tests, eight core strains with over 80% selenium enrichment were selected, with optimal enrichment conditions being a 37 °C temperature, 2% sodium chloride concentration, and pH of 6.0 in MRS medium. Functional tests demonstrated that selenium-enriched strains exhibited a significantly enhanced antioxidant capacity (demonstrated by DPPH and ABTS free radical scavenging activities) and improved gastrointestinal fluid tolerance, with strain No.41 showing the most outstanding performance. Scanning electron microscopy combined with energy-dispersive X-ray spectroscopy (SEM-EDX) revealed nanoscale selenium (1.34 keV) on cell surfaces. Further characterization showed that 68.94% of selenium was incorporated into selenoproteins, 7.61% into nucleic acids, and 7.02% into polysaccharides. Integrated metabolomic and proteomic studies have shown that selenium reduces the content of L-cysteine primarily by replacing sulfur and competing for key sites in cysteine-S-conjugate-β-lyase, S-adenosyl-L-cysteine hydrolase, and homocysteine synthase, ultimately leading to the synthesis of selenocysteine and selenomethionine. A correlation analysis between differential metabolites and proteins revealed selenium’s significant impacts on the metabolic networks of LAB, antioxidant mechanisms, energy metabolism, and membrane stability. This research provides new insights for developing selenium-enriched probiotics for functional dairy products and health supplements. Full article