Search Results (815)

Accounting for 15–30% of colorectal cancer cases, the serrated pathway remains poorly characterized compared to the adenoma–carcinoma sequence. It involves sessile serrated lesions as precursors and is characterized by BRAF mutations (BRAF^V600E), CpG island hypermethylation, and microsatellite instability (MSI). Using label-free proteomics, we compared normal tissue margins from patients with diverticular disease, sessile serrated lesions, low-grade adenomas, and high-grade adenomas. We identified S100A14 as significantly overexpressed in sessile serrated lesions compared to low-grade adenomas, high-grade adenomas, and normal tissues. This overexpression was confirmed by immunohistochemical scoring in an independent cohort. Gene expression analyses of public datasets showed higher S100A14 expression in BRAF^V600E-mutated and MSI-H colorectal cancers compared to microsatellite stable BRAF^wt tumors. This finding was confirmed by immunohistochemical scoring in an independent colorectal cancer cohort. Furthermore, single-cell RNA sequencing analysis from the Human Colon Cancer Atlas revealed that S100A14 expression in tumor cells positively correlated with the abundance of tumoral CD8⁺ cytotoxic T cells, particularly the CD8⁺ CXCL13⁺ subset, known for its association with a favorable response to immunotherapy. Collectively, our results demonstrate for the first time that S100A14 is a potential biomarker of serrated neoplasia and further suggests its potential role in predicting immunotherapy responses in colorectal cancer. Full article

The diagnosis of opioid use disorder (OUD) is prevalent due to increased prescribing of opioids. Long-term oxycodone self-administration can lead to addiction-like behavioral responses in rats. Herein, we sought to identify molecular pathways consequent to long-term exposure to oxycodone self-administration. Towards that end, we used male Sprague Dawley rats that self-administered oxycodone for 20 days according to short-(ShA, 3 h) and long-access (LgA, 9 h) paradigms. LgA rats escalated their oxycodone intake and developed into 2 phenotypes, labeled Long-access High (LgA-H) and Long-access Low (LgA-L) rats, based on their escalation. RNA sequencing analysis revealed the LgA-H has significantly different DEGs in comparison to other groups. DAVID analysis revealed the participation of LgA-H DEGs in potassium transport. RT-PCR analysis of striatal samples validated the increased levels of potassium channels. Since these increases correlated with oxycodone intake, we believe potassium channels are potential targets for the treatment of oxycodone use disorder Full article

Background: Lysosomal-associated membrane protein 1 (LAMP1), typically localized to the lysosomal membrane, is increasingly implicated as a marker of cancer aggressiveness and metastasis when expressed on the cell surface. This study aimed to develop a LAMP1-targeted antibody-based PET tracer and assess its efficacy in mouse models of human breast and colon adenocarcinoma. Methods: To determine the source of LAMP1 expression, we utilized human single-cell RNA sequencing and spatial transcriptomics, complemented by in-house flow cytometry on xenografted mouse models. Tissue microarrays of multiple epithelial cancers and normal tissue were stained for LAMP-1, and staining was quantified. An anti-LAMP1 monoclonal antibody was conjugated with desferrioxamine (DFO) and labeled with zirconium-89 (⁸⁹Zr). Human triple-negative breast cancer (MDA-MB-231) and colon cancer (Caco-2) cell lines were implanted in nude mice. PET/CT imaging was conducted at 24, 72, and 168 h post-intravenous injection of ⁸⁹Zr-DFO-anti-LAMP1 and ⁸⁹Zr-DFO-IgG (negative control), followed by organ-specific biodistribution analyses at the final imaging time point. Results: Integrated single-cell and spatial RNA sequencing demonstrated that LAMP1 expression was localized to myeloid-derived suppressor cells (MDSCs) and cancer-associated fibroblasts (CAFs) in addition to the cancer cells. Tissue microarray showed significantly higher staining for LAMP-1 in tumor tissue compared to normal tissue (3986 ± 2635 vs. 1299 ± 1291, p < 0.001). Additionally, xenograft models showed a significantly higher contribution of cancer cells than the immune cells to cell surface LAMP1 expression. In vivo, PET imaging with ⁸⁹Zr-DFO-anti-LAMP1 PET/CT revealed detectable tumor uptake as early as 24 h post-injection. The ⁸⁹Zr-DFO-anti-LAMP1 tracer demonstrated significantly higher uptake than the control ⁸⁹Zr-DFO-IgG in both models across all time points (MDA-MB-231 SUV_max at 168 h: 12.9 ± 5.7 vs. 4.4 ± 2.4, p = 0.003; Caco-2 SUV_max at 168 h: 8.53 ± 3.03 vs. 3.38 ± 1.25, p < 0.01). Conclusions: Imaging of cell surface LAMP-1 in breast and colon adenocarcinoma is feasible by immuno-PET. LAMP-1 imaging can be expanded to adenocarcinomas of other origins, such as prostate and pancreas. Full article

Exosomes are nanoscale extracellular vesicles (EVs) that carry biomolecular signatures reflective of their parent cells, making them powerful tools for non-invasive diagnostics and therapeutic monitoring. Despite their potential, clinical application is hindered by challenges such as low abundance, heterogeneity, and the complexity of biological samples. To address these limitations, plasmonic biosensing technologies—particularly propagating surface plasmon resonance (PSPR), localized surface plasmon resonance (LSPR), and surface-enhanced Raman scattering (SERS)—have been developed to enable label-free, highly sensitive, and multiplexed detection at the single-vesicle level. This review outlines recent advancements in nanoplasmonic platforms for exosome detection and profiling, emphasizing innovations in nanostructure engineering, microfluidic integration, and signal enhancement. Representative applications in oncology, neurology, and immunology are discussed, along with the increasingly critical role of artificial intelligence (AI) in spectral interpretation and diagnostic classification. Key technical and translational challenges—such as assay standardization, substrate reproducibility, and clinical validation—are also addressed. Overall, this review highlights the synergy between exosome biology and plasmonic nanotechnology, offering a path toward real-time, precision diagnostics via sub-femtomolar detection of exosomal miRNAs through next-generation biosensing strategies. Full article

Translation initiation site (TIS) prediction in mRNA sequences constitutes an essential component of transcriptome annotation, playing a crucial role in deciphering gene expression and regulation mechanisms. Numerous computational methods have been proposed and achieved acceptable prediction accuracy. In our previous work, we developed NeuroTIS, a novel method for TIS prediction based on a hybrid dependency network combined with a deep learning framework that explicitly models label dependencies both within coding sequences (CDSs) and between CDSs and TISs. However, this method has limitations in fully exploiting the primary structural information within mRNA sequences. First, it only captures label dependency within three neighboring codon labels. Second, it neglects the heterogeneity of negative TISs originating from different reading frames, which exhibit distinct coding features in their vicinity. In this paper, under the framework of NeuroTIS, we propose its enhanced version, NeuroTIS+, which allows for more sophisticated codon label dependency modeling via temporal convolution and homogenous feature building through an adaptive grouping strategy. Tests on transcriptome-wide human and mouse datasets demonstrate that the proposed method yields excellent prediction performance, significantly surpassing the existing state-of-the-art methods. Full article

Anseriformes (waterfowl) and Charadriiformes (shorebirds) are well-recognized natural reservoirs of low pathogenic (LP) influenza A viruses (IAVs). Historically, LP IAVs circulate among healthy individuals during seasonal, and often transcontinental, migrations. However, following the introduction of clade 2.3.4.4b highly pathogenic (HP) A/Goose/Guangdong/1/1996 lineage H5 IAV to North America in 2021, countless wild birds succumbed to fatal infections across the Western Hemisphere. Due to their small size and cryptic plumage patterns, opportunities for carcass recovery and postmortem evaluation in sanderlings (Calidris alba) and other shorebirds are rare. A multispecies mortality event in coastal Virginia, USA, in March–April 2024 included sanderlings among other wild bird species. Nine sanderlings underwent postmortem evaluation and clade 2.3.4.4b H5 IAV RNA was detected in pooled oropharyngeal-cloacal swabs from 11/11 individuals by real-time reverse transcription polymerase chain reaction. Histopathology was similar to that in waterfowl and included necrosis in the pancreas and brain and less commonly in the gonad, adrenal gland, spleen, liver, and intestine. Immunohistochemistry revealed IAV antigen labeling in necrotic neurons of the brain (neurotropism) and epithelial cells of the pancreas, gonad, and adrenal gland (epitheliotropism). Describing HP IAV-attributed pathology in shorebirds is key to understanding ecoepidemiology and population health threats in order to further document and compare pathogenesis among avian species. Full article

MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression and have emerged as critical biomarkers in various diseases, including cancer. Their stability in bodily fluids and role as oncogenes or tumor suppressors make them attractive targets for non-invasive diagnostics. However, conventional detection methods, such as Northern blotting, RT-PCR, and microarrays, are limited by low sensitivity, lengthy protocols, and limited specificity. Electrochemical biosensors offer a promising alternative, providing high sensitivity, rapid response times, portability, and cost-effectiveness. These biosensors translate miRNA hybridization events into quantifiable electrochemical signals, often leveraging redox-active labels, mediators, or intercalators. Recent advancements in nanomaterials and signal amplification strategies have further enhanced detection capabilities, enabling sensitive, label-free miRNA quantification. This review provides a comprehensive overview of the recent advances in electrochemical biosensing of miRNAs, emphasizing innovative redox-based detection strategies, probe immobilization techniques, and hybridization modalities. The critical challenges and future perspectives in advancing electrochemical miRNA biosensors toward clinical translation and point-of-care diagnostics are discussed. Full article

The synthesis of novel biodegradable polymers as non-viral vectors remains one of the challenging tasks in the field of gene delivery. In this study, the synthesis of the polysaccharide-g-polypeptide copolymers, namely, hyaluronic acid-g-polylysine (HA-g-PLys), using a copper-free strain-promoted azide-alkyne cycloaddition reaction was proposed. For this purpose, hyaluronic acid was modified with dibenzocyclooctyne moieties, and poly-L-lysine with a terminal azido group was obtained using ring-opening polymerization of N-carboxyanhydride of the corresponding protected amino acid, initiated with the amino group azido-PEG₃-amine. Two HA-g-PLys samples with different degrees of grafting were synthesized, and the structures of all modified and synthesized polymers were confirmed using ¹H NMR and FTIR spectroscopy. The HA-g-PLys samples obtained were able to form nanoparticles in aqueous media due to self-assembly driven by electrostatic interactions. The binding of DNA and model siRNA by copolymers to form polyplexes was analyzed using ethidium bromide, agarose gel electrophoresis, and SybrGreen I assays. The hydrodynamic diameter of polyplexes was ˂300 nm (polydispersity index, PDI ˂ 0.3). The release of a model fluorescently-labeled oligonucleotide in the complex biological medium was significantly higher in the case of HA-g-PLys as compared to that in the case of PLys-based polyplexes. In addition, the cytotoxicity in normal and cancer cells, as well as the ability of HA-g-PLys to facilitate intracellular delivery of anti-GFP siRNA to NIH-3T3/GFP+ cells, were evaluated. Full article

The major objective was to investigate the protective capabilities of endophytic bacterial strains isolated from a number of medicinal plant species towards Aspergillus spp. secured from the internal tissues of fungi-infected peanuts. Among 32 fungal isolates surveyed for mycotoxin production in various culture media (PDA, RBCA, YES, CA), 10 isolates qualitatively producing AFB₁, besides 10 OTA-producers, were assayed by HPLC for quantitative toxin production. Aspergillus spp. isolate Be 13 produced an extraordinary quantity of 1859.18 μg mL⁻¹ AFB₁, against the lowest toxin level of 280.40 μg mL⁻¹ produced by the fungus isolate IS 4. The estimated amounts of OTA were considerably lower and fell in the range 0.88–6.00 μg mL⁻¹; isolate Sa 1 was superior, while isolate Be 7 seemed inferior. Based on ITS gene sequencing, the highly toxigenic Aspergillus spp. isolates Be 13 and Sa 1 matched the description of A. novoparasiticus and A. ochraceus, respectively, ochraceus, respectively, which are present in GenBank with identity exceeding 99%. According to 16S rRNA gene sequencing, these antagonists labeled Ar6, Ma27 and So34 showed the typical characteristics of Pseudomonas aeruginosa, Bacillus subtilis and Bacillus velezensis, respectively, with similarity percentages of 99–100. The plant growth-promoting activity measurements of the identified endophytes indicated the production of 16.96–80.00 μg/100 mL culture medium of IAA. Phosphate-solubilizing capacity varied among endophytes from 2.50 to 21.38 μg/100 mL. The polysaccharide production pool of bacterial strains ranged between 2.74 and 6.57 mg mL⁻¹. P. aeruginosa Ar6 and B. velezensis successfully produced HCN, but B. subtilis failed. The in vitro mycotoxin biodegradation potential of tested bacterial endophytes indicated the superiority of B. velezensis in degrading both mycotoxins (AFB₁-OTA) with average percentage of 88.7; B. subtilis ranked thereafter (85.6%). The 30-day old peanut (cv. Giza 6) seedlings grown in gnotobiotic system severely injured due to infection with AFB₁/OTA-producing fungi, an effect expressed in significant reductions in shoot and root growth traits. Simultaneous treatment with the endophytic antagonists greatly diminished the harmful impact of the pathogens; B. velezensis was the pioneer, not P. aeruginosa Ar6. In conclusion, these findings proved that several endophytic bacterial species have the potential as alternative tools to chemical fungicides for protecting agricultural commodities against mycotoxin-producing fungi. Full article

Kisspeptin (Kiss1) and kisspeptin 1 receptor (Kiss1R) are vital in regulating various functions across many species, primarily those relating to reproduction. The kisspeptin system has recently attracted clinical interest as a potential therapeutic treatment for patients with hypoactive sexual desire disorder. This study maps the distribution of Kiss1 and Kiss1R mRNA in the Syrian hamster forebrain using dual-labeled RNAscope. In our study, the distributions of kisspeptin and its receptor were mapped across adult males and females on day 1 or day 2 of their estrous cycle. Conditioned place preference was used to observe the potential effect of kisspeptin on sexual reward in female hamsters. The expression of kisspeptin was greater in females than males, with the estrous cycle having no effect on expression. A comparison of these findings to those in other species revealed that the expression in Syrian hamsters was similar to that reported for other species, demonstrating the conservation of expression. Kisspeptin did not influence sexual reward in females, nor did it affect measures of their primary sexual behavior. These findings provide additional insights into the expression and function of kisspeptin across novel species and add to ongoing research in understanding how kisspeptin may influence sexual desire in animals, including humans. Full article

This study aims to investigate the effect of the Pd(II) complex on HeLa cells using computational biology and proteomic analysis. [Pd(dach)Cl₂]-treated HeLa cells were subjected to comparative proteomics analysis using label-free data-independent liquid chromatography-tandem mass spectrometry (LC-MS/MS). In parallel, the informational spectrum method (ISM) was used to predict potential protein interactors of the [Pd(dach)Cl₂] complex in HeLa cells. Proteomics analysis revealed 121 differentially abundant proteins (DAPs). Enrichment analysis of Gene Ontology (GO) annotations revealed ATP hydrolysis and RNA/protein binding as the top molecular functions and RNA splicing and protein–RNA complex organization as the top biological processes. Enrichment analysis of altered canonical pathways pointed out spliceosome and ribosome pathways. The top hub proteins with potential regulatory importance encompassed ribosomal proteins, translational and transcriptional factors, and components of the ribosome assembly machinery. ISM and cross-spectral analysis identified the nucleoplasm and sensor of the single-stranded DNA (SOSS DNA) complex. Proteome analysis showed that [Pd(dach)Cl₂] targets proteins involved in ribosomal biogenesis and RNA splicing, whereas theoretical prediction implies also potential effect on p53 signaling pathway, and thus, alterations of the expression of regulatory proteins involved in cell survival and proliferation. These findings underscore the potential of Pd(II) complexes as anti-cancer agents, warranting further exploration and detailed functional validation. Full article

Background: Cell-penetrating peptides cross cell membrane barriers while carrying cargoes in a functional form. Our work identified two novel lung-targeting peptides, S7A and R11A. Here, we present studies on biodistribution, the cell types targeted, and an in vitro proof of application. Methods: Studies were performed in human bronchial epithelial cells (HBECs) with and without various endocytic inhibitors, and coincubation with fluorescently labeled transferrin or endocytic markers. Cyclic R11A (cR11A) was conjugated to siRNA duplexes and anti-viral activity against SARS-CoV-2 was tested. Biodistribution studies were performed by injecting wild-type mice with fluorescently labeled peptides, and various circulation times were allowed for, as well as cross-staining of lung sections or isolated single cells with various cellular markers, followed by fluorescence-activated cell sorting or confocal microscopy. Results: cR11A showed peak uptake in 15 min, with the highest uptake in airway epithelial type II (ATII) cells, followed by p63+ basal cells and ionocytes. Cyclization increased transduction efficiencies ~100-fold. Endocytosis studies showed a decrease in peptide uptake by pre-treatment with Pitstop2 but not Amiloride or Nystatin. Endocytic marker Lamp1 showed colocalization at the earliest time point, with the escape of the peptide from endocytic vesicles later. cR11A conjugated to ant-spike and anti-envelop proteins showed anti-viral effects with an EC₉₀ of 0.6 μM and 1.0 µM, respectively. Conclusions: We have identified a novel peptide, cR11A, that targets ATII, basal cells, and ionocytes, the cyclization of which increased transduction efficiency in vitro and in vivo. The uptake mechanism appears to be via clathrin-mediated endocytosis with escape from endocytic vesicles. cR11A can act as a vector to deliver anti-viral siRNA to epithelial cells. Full article

Background: The emergence of checkpoint inhibitors (CPIs) has significantly improved survival outcomes in later-stage melanoma. However, the efficacy of these treatments remains limited, with around 50% of later-stage melanoma patients experiencing recurrence. As variable response rates to CPIs persist, the development of cancer vaccines has emerged as a potential strategy to augment antitumor immune responses. Results: This review compares two promising personalized therapeutic cancer vaccine trials in advanced melanoma: Elios Therapeutics’ Tumor Lysate (TL) vaccine and Moderna’s mRNA-4157 vaccine. The TL vaccine, which utilizes yeast cell wall particles (YCWPs) loaded with autologous tumor lysate, and the mRNA-4157 vaccine, which encodes up to 34 patient-specific neoantigens, both aim to stimulate robust tumor-specific immune responses. Both trials were phase 2b randomized studies, with Elios Therapeutics’ trial employing a double-blind, placebo-controlled design, while Moderna’s was open-label. Both trials had roughly equivalent sample sizes (n = 187 and n = 157, respectively) with similar demographics and disease characteristics. The TL trial reported improvements in disease-free survival (DFS) with a hazard ratio (HR) of 0.52 (p < 0.01) over 36 months, whereas the mRNA-4157 trial demonstrated improvements in recurrence-free survival (RFS) with an HR of 0.56 (p = 0.053) over 18 months. The TL vaccine exhibited lower rates of related grade 3 adverse events (<1%) compared to the mRNA vaccine (12%). Key differences between the two trials include the use of CPIs, with 100% of patients in the mRNA trial receiving pembrolizumab versus 37% of the patients in the TL trial receiving either an anti-PD-1 or anti-CTLA-4. The production processes also varied significantly, with the mRNA vaccine requiring individualized sequencing and a 9-week production time, while the TL vaccine utilized tumor lysate with a 1–3-day production time. Conclusions: While both vaccines demonstrated promising efficacy, future phase 3 trials are needed to further evaluate their potential as adjuvant therapies for melanoma. This review highlights the comparative strengths and limitations of these vaccine platforms, providing insight into the evolving landscape of adjuvant cancer vaccines. Full article

Chondrocytes maintain cartilage integrity through coordinated regulation of extracellular matrix (ECM) synthesis and remodeling. These processes depend on ECM dynamic interactions, mediated by integrin-based focal adhesions and associated cytoskeletal components. While the roles of core adhesion proteins are well described, the involvement of sarcoglycans (SGs) remains unclear in chondrocytes. Drawing parallels from striated muscle, where the SG subcomplex stabilizes the sarcolemma, we hypothesized that SGs similarly integrate into chondrocyte adhesion complexes. This study investigated the SGs (α, β, γ, δ) expression with cytoskeletal and adhesion proteins, including actin and vinculin, in human chondrocytes cultured by immunofluorescence, qPCR, and siRNA-mediated silencing. All four SG isoforms were expressed in the cytoplasmic and membrane domains, with enrichment at focal adhesion sites. Double labeling revealed SG colocalization with F-actin stress fibers and vinculin, indicating integration into the core adhesion complex. Silencing of each SG resulted in disrupted actin stress fibers, diffuse vinculin distribution, reduced focal plaque number, and a change in cell morphology. These findings support the hypothesis that SGs regulate actin cytoskeletal dynamics and focal contact stabilization. Loss of SG function compromises chondrocyte shape and adhesion, highlighting the importance of these glycoproteins also in non-muscle cells. Full article

Recent studies on myogenic satellite cells (SCs) in Duchenne muscular dystrophy (DMD) documented altered division capacities and impaired regeneration potential of SCs in DMD patients and animal models. It remains unknown, however, if SC-intrinsic effects trigger these deficiencies at pre-contractile stages of myogenesis rather than resulting from the pathologic environment. In this study, we isolated SCs from a porcine DMD model and age-matched wild-type (WT) piglets for comprehensive analysis. Using immunofluorescence, differentiation assays, traction force microscopy (TFM), RNA-seq, and label-free proteomic measurements, SCs behavior was characterized, and molecular changes were investigated. TFM revealed significantly higher average traction forces in DMD than WT SCs (90.4 ± 10.5 Pa vs. 66.9 ± 8.9 Pa; p = 0.0018). We identified 1390 differentially expressed genes and 1261 proteins with altered abundance in DMD vs. WT SCs. Dysregulated pathways uncovered by gene ontology (GO) enrichment analysis included sarcomere organization, focal adhesion, and response to hypoxia. Multi-omics factor analysis (MOFA) integrating transcriptomic and proteomic data, identified five factors accounting for the observed variance with an overall higher contribution of the transcriptomic data. Our findings suggest that SC impairments result from their inherent genetic abnormality rather than from environmental influences. The observed biological changes are intrinsic and not reactive to the pathological surrounding of DMD muscle. Full article