Is age-related myelinodegenerative change an initial risk factor of neurodegenerative diseases?

Myelination, the continuous ensheathment of neuronal axons, is a lifelong process in the nervous system that is essential for the precise, temporospatial conduction of action potentials between neurons. Myelin also provides intercellular metabolic support to axons. Even minor disruptions in the integrity of myelin can impair neural performance and increase susceptibility to neurological diseases. In fact, myelin degeneration is a well-known neuropathological condition that is associated with normal aging and several neurodegenerative diseases, including multiple sclerosis and Alzheimer's disease. In the central nervous system, compact myelin sheaths are formed by fully mature oligodendrocytes. However, the entire oligodendrocyte lineage is susceptible to changes in the biological microenvironment and other risk factors that arise as the brain ages. In addition to their well-known role in action potential propagation, oligodendrocytes also provide intercellular metabolic support to axons by transferring energy metabolites and delivering exosomes. Therefore, myelin degeneration in the aging central nervous system is a significant contributor to the development of neurodegenerative diseases. Interventions that mitigate age-related myelin degeneration can improve neurological function in aging individuals. In this review, we investigate the changes in myelin that are associated with aging and their underlying mechanisms. We also discuss recent advances in understanding how myelin degeneration in the aging brain contributes to neurodegenerative diseases and explore the factors that can prevent, slow down, or even reverse age-related myelin degeneration. Future research will enhance our understanding of how reducing age-related myelin degeneration can be used as a therapeutic target for delaying or preventing neurodegenerative diseases.

In vitro co-culture of Fasciola hepatica newly excysted juveniles (NEJs) with 3D HepG2 spheroids permits novel investigation of host-parasite interactions

Fasciola hepatica, or liver fluke, causes fasciolosis in humans and livestock. Following ingestion of vegetation contaminated with encysted parasites, metacercariae, newly excysted juveniles (NEJ) excyst in the small intestine and cross the intestinal wall. After penetrating the liver, the parasite begins an intra-parenchymal migratory and feeding phase that not only drives their rapid growth and development but also causes extensive haemorrhaging and immune pathology. Studies on infection are hindered by the difficulty in accessing these microscopic juvenile parasites in vivo. Thus, a simple and scalable in vitro culture system for parasite development is needed. Here, we find that two-dimensional (2D) culture systems using cell monolayers support NEJ growth to a limited extent. By contrast, co-culture of F. hepatica NEJ with HepG2-derived 3D spheroids, or "mini-livers," that more closely mimic the physiology and microenvironment of in vivo liver tissue, promoted NEJ survival, growth, and development. NEJ grazed on the peripheral cells of the spheroids, and they released temporally regulated digestive cysteine proteases, FhCL3, and FhCL1/2, similar to in vivo parasites. The 3D co-culture induced development of the NEJ gut and body musculature, and stimulated the tegument to elaborate spines and a variety of surface sensory/tango/chemoreceptor papillae (termed S1, S2, and S3); these were especially pronounced around the oral and ventral suckers that sense host chemical cues and secure the parasite in tissue. HepG2 3D spheroid/parasite co-culture methodologies should accelerate investigations into the understanding of F. hepatica NEJ developmental biology and studies on host-parasite interactions, and streamline the search for new anti-parasite interventions.

Proteomics reveals the key transcription-related factors mediating obstructive nephropathy in pediatric patients and mice

BACKGROUND

Obstructive nephropathy is one of the leading causes of kidney injury in infants and children. Increasing evidence has shown that transcription-related factors (TRFs), including transcription factors and cofactors, are associated with kidney diseases. However, a global landscape of dysregulated TRFs in pediatric patients with obstructive nephropathy is lacking.

METHODS

We mined the data from our previous proteomic study for the TRF profile in pediatric patients with obstructive nephropathy and unilateral ureteral obstruction (UUO) mice. Gene ontology (GO) analysis was performed to determine pathways that were enriched in the dysregulated TRFs. We then took advantage of kidney samples from patients and UUO mice to verify the selected TRFs by immunoblots.

RESULTS

The proteomes identified a total of 140 human TRFs with 28 upregulated and 1 downregulated, and 160 murine TRFs with 88 upregulated and 1 downregulated (fold change >2 or <0.5). These dysregulated TRFs were enriched in the inflammatory signalings, such as janus kinase/signal transducer and activator of transcription (JAK-STAT) and tumor necrosis factor (TNF) pathways. Of note, the transforming growth factor (TGF)-β signaling pathway, which is the master regulator of organ fibrosis, was enriched in both patients and mice. Cross-species analysis showed 16 key TRFs that might mediate obstructive nephropathy in patients and UUO mice. Moreover, we verified a significant dysregulation of three previously unexplored TRFs; prohibitin (PHB), regulatory factor X 1 (RFX1), and activity-dependent neuroprotector homeobox protein (ADNP), in patients and mice.

CONCLUSIONS

Our study uncovered key TRFs in the obstructed kidneys and provided additional molecular insights into obstructive nephropathy.

tRNA modifications: greasing the wheels of translation and beyond

Transfer RNA (tRNA) is one of the most abundant RNA types in cells, acting as an adaptor to bridge the genetic information in mRNAs with the amino acid sequence in proteins. Both tRNAs and small fragments processed from them play many nonconventional roles in addition to translation. tRNA molecules undergo various types of chemical modifications to ensure the accuracy and efficiency of translation and regulate their diverse functions beyond translation. In this review, we discuss the biogenesis and molecular mechanisms of tRNA modifications, including major tRNA modifications, writer enzymes, and their dynamic regulation. We also summarize the state-of-the-art technologies for measuring tRNA modification, with a particular focus on 2'-O-methylation (Nm), and discuss their limitations and remaining challenges. Finally, we highlight recent discoveries linking dysregulation of tRNA modifications with genetic diseases.

Deciphering novel enzymatic and non-enzymatic lysine lactylation in Salmonella

Lysine lactylation, a novel post-translational modification, is involved in multiple cellular processes. The role of lactylation remains largely unknown, especially in bacteria. Here, we identified 1090 lactylation sites on 469 proteins by mass spectrometry in Salmonella Typhimurium. Many proteins involved in metabolic processes, protein translation, and other biological functions are lactylated, with lactylation levels varying according to the growth phase or lactate supplementation. Lactylation is regulated by glycolysis, and inhibition of L-lactate utilization can enhance lactylation levels. In addition to the known lactylase in E. coli, the acetyltransferase YfiQ can also catalyse lactylation. More importantly, L-lactyl coenzyme A (L-La-CoA) and S,D-lactoylglutathione (LGSH) can directly donate lactyl groups to target proteins for chemical lactylation. Lactylation is involved in Salmonella invasion of eukaryotic cells, suggesting that lactylation is crucial for bacterial virulence. Collectively, we have comprehensively investigated protein lactylome and the regulatory mechanisms of lactylation in Salmonella, providing valuable insights into studying lactylation function across diverse bacterial species.

Histone modifications in the regulation of erythropoiesis

INTRODUCTION

The pathogenesis of anemia and other erythroid dysphasia are mains poorly understood, primarily due to limited knowledge about the differentiation processes and regulatory mechanisms governing erythropoiesis. Erythropoiesis is a highly complex and precise biological process, that can be categorized into three distinct stages: early erythropoiesis, terminal erythroid differentiation, and reticulocyte maturation, and this complex process is tightly controlled by multiple regulatory factors. Emerging evidence highlights the crucial role of epigenetic modifications, particularly histone modifications, in regulating erythropoiesis. Methylation and acetylation are two common modification forms that affect genome accessibility by altering the state of chromatin, thereby regulating gene expression during erythropoiesis.

DISCUSSION

This review systematically examines the roles of histone methylation and acetylation, along with their respective regulatory enzymes, in regulating the development and differentiation of hematopoietic stem/progenitor cells (HSPCs) and erythroid progenitors. Furthermore, we discuss the involvement of these histone modifications in erythroid-specific developmental processes, including hemoglobin switching, chromatin condensation, and enucleation.Conclusions This review summarizes the current understanding of the role of histone modifications in erythropoiesis based on existing research, as a foundation for further research the mechanisms of epigenetic regulatory in erythropoiesis.

Key RNA-binding proteins in renal fibrosis: a comprehensive bioinformatics and machine learning framework for diagnostic and therapeutic insights

BACKGROUND

Renal fibrosis is a critical factor in chronic kidney disease progression, with limited diagnostic and therapeutic options. Emerging evidence suggests RNA-binding proteins (RBPs) are pivotal in regulating cellular mechanisms underlying fibrosis.

METHODS

Utilizing an extensive GEO dataset (175 renal fibrosis and 99 normal kidney samples), we identified and validated key RBPs through integrated bioinformatics and machine learning approaches, including lasso and logistic regression models. Differentially expressed genes were analyzed for pathway enrichment using Gene Ontology and KEGG. Single-cell RNA sequencing delineated cell-specific RBP expression, and a murine unilateral ureteral obstruction (UUO) model provided experimental validation.

RESULTS

A diagnostic model incorporating five RBPs (FKBP11, DCDC2, COL6A3, PLCB4, and GNB5) achieved high accuracy (AUC = 0.899) and robust external validation. These RBPs are implicated in immune-mediated pathways such as cytokine signaling and inflammatory responses. Single-cell analysis highlighted their expression in specific renal cell populations, underscoring functional diversity. Immunofluorescence linked FKBP11 with macrophage infiltration, suggesting its potential as a therapeutic target.

CONCLUSION

his study identifies novel RBPs associated with renal fibrosis, advancing the understanding of its pathogenesis and offering actionable biomarkers and therapeutic targets. The integration of bioinformatics and machine learning emphasizes their translational potential in kidney care.

Helicobacter pylori infection induces DNA double-strand breaks through the ACVR1/IRF3/POLD1 signaling axis to drive gastric tumorigenesis

Helicobacter pylori (H. pylori) infection plays a pivotal role in gastric carcinogenesis through inflammation-related mechanisms. Activin A receptor type I (ACVR1), known for encoding the type I receptor for bone morphogenetic proteins (BMPs), has been identified as a cancer diver gene across various tumors. However, the specific role of AVCR1 in H. pylori-induced gastric tumorigenesis remains incompletely understood. We conducted a comprehensive analysis of the clinical relevance of ACVR1 by integrating data from public databases and our local collection of human gastric tissues. In vitro cell cultures, patient-derived gastric organoids, and transgenic INS-GAS mouse models were used for Western blot, qRT-PCR, immunofluorescence, immunohistochemistry, luciferase assays, ChIP, and comet assays. Furthermore, to investigate the therapeutic potential, we utilized the ACVR1 inhibitor DM3189 in our in vivo studies. H. pylori infection led to increased expression of ACVR1 in gastric epithelial cells, gastric organoid and gastric mucosa of INS-GAS mice. ACVR1 activation led to DNA double-strand break (DSB) accumulation by inhibiting POLD1, a crucial DNA repair enzyme. The activation of POLD1 was facilitated by the transcription factor IRF3, with identified binding sites. Additionally, treatment with the ACVR1 inhibitor DM3189 significantly ameliorated H. pylori-induced gastric pathology and reduced DNA damage in INS-GAS mice. Immunohistochemistry analysis showed elevated levels of ACVR1 in H. pylori-positive gastritis tissues, showing a negative correlation with POLD1 expression. This study uncovers a novel signaling axis of AVCR1/IRF3/POLD1 in the pathogenesis of H. pylori infection. The upregulation of ACVR1 and the suppression of POLD1 upon H. pylori infection establish a connection between the infection, genomic instability, and the development of gastric carcinogenesis.

Recent advances in nuclear actin research

Actin was first observed in the nucleus more than sixty years ago but research on nuclear actin did not receive significant attention for the next forty years. It only started to accelerate around the year 2000, when the first convincing experimental data emerged indicating that actin participates in essential nuclear processes. Today, we know that actin is involved in transcription, replication, DNA repair, chromatin remodeling, and participates in the determination of nuclear shape and size. In this paper we review the results of the last five years of increasingly intensive research on nuclear actin, because on one hand, the field has expanded with several new directions during this time, and on the other hand, the enrichment of our picture of nuclear actin will certainly provide a more solid foundation and new impetus for its future investigation.

Verification of biological markers of subacute cutaneous lupus erythematosus via TMT labelling proteomics combined with transcriptome data

OBJECTIVE

This study aimed to investigate biological markers in subacute cutaneous lupus erythematosus (SCLE).

METHODS

The tandem mass tag (TMT)-labelling proteomics method was used to explore differentially expressed proteins between SCLE lesions and normal skin tissues. The differences in transcriptomic data between SCLE tissues and normal skin tissues were analysed from the GEO database (GSE81071, GSE109248 and GSE112943). The differences in transcriptomic data from peripheral blood mononuclear cells (PBMCs) of patients with systemic lupus erythematosus (SLE) and normal controls were analysed (GSE81622 and GSE154851). The 35 healthy controls, 30 SCLE patients, 35 SLE patients and 30 lupus nephritis (LN) patients were diagnosed and enrolled. The serum expression levels of IFI44 and EPSTI1 were detected. Data were presented as the mean ± standard deviation or frequency and were analysed using Student's t-test, Chi-square test and one-way ANOVA between the groups. Receiver operating characteristic (ROC) curves were used to analyse the clinical efficacy of IFI44 and EPSTI1 in distinguishing SCLE from SLE.

RESULTS

In a comparative analysis of SCLE lesions and normal skin tissues, proteomics studies identified 376 proteins that exhibited significant differential expression. In GO and KEGG analyses, the enriched terms mainly included the interferon-gamma-mediated signalling pathway (p < .001), immune receptor activity (p < .001) and cell adhesion molecules (p < .001). The top 10 hub genes were screened in SCLE as follows: CD8A, CXCL10, IFI44, CD7, CCL5, TLR4, EPSTI1, ISG15, KLRD1 and SELL using Cytoscape (3.10.1) software. The 15 common proteins/genes between proteomics and three datasets results were found, including CXCL10, OAS1, DDX60L, CFB, IFI6, HERC6, IFI44L, GBP1, EPSTI1, OAS2, CXCL11, TYMP, IFI44, ISG15 and IFIT3. The 61 differentially expressed genes in GSE81622 and the top 100 differentially expressed genes in GSE154851, alongside the 15 identified genes described above through Venn diagram analysis. Four common genes, IFI44L, IFI44, EPSTI1 and OAS1, were identified. Two common genes, IFI44 and EPSTI1, were found in hub genes from the proteomics results. The serum levels of IFI44 and EPSTI1 in LN were significantly higher than those in SLE patients (p < .05). ROC curve analysis demonstrated that serum levels of IFI44 and EPSTI1 could differentiate SCLE from SLE with an area under the curve (AUC) of 0.898 and 0.847, respectively.

CONCLUSIONS

The IFI44 and EPSTI1 proved to be closely involved in the progression from SCLE to SLE, and can represent new candidate diagnostic molecular markers of occurrence and progression of SCLE.

Non-stochastic reassembly of a metabolically cohesive gut consortium shaped by N-acetyl-lactosamine-enriched fibers

Diet is one of the main factors shaping the human microbiome, yet our understanding of how specific dietary components influence microbial consortia assembly and subsequent stability in response to press disturbances - such as increasing resource availability (feeding rate) - is still incomplete. This study explores the reproducible re-assembly, metabolic interplay, and compositional stability within microbial consortia derived from pooled stool samples of three healthy infants. Using a single-step packed-bed reactor (PBR) system, we assessed the reassembly and metabolic output of consortia exposed to lactose, glucose, galacto-oligosaccharides (GOS), and humanized GOS (hGOS). Our findings reveal that complex carbohydrates, especially those containing low inclusion (~1.25 gL-1) components present in human milk, such as N-acetyl-lactosamine (LacNAc), promote taxonomic, and metabolic stability under varying feeding rates, as shown by diversity metrics and network analysis. Targeted metabolomics highlighted distinct metabolic responses to different carbohydrates: GOS was linked to increased lactate, lactose to propionate, sucrose to butyrate, and CO2, and the introduction of bile salts with GOS or hGOS resulted in butyrate reduction and increased hydrogen production. This study validates the use of single-step PBRs for reliably studying microbial consortium stability and functionality in response to nutritional press disturbances, offering insights into the dietary modulation of microbial consortia and their ecological dynamics.

Isolation of derivatives from the food-grade probiotic Lactobacillus johnsonii CNCM I-4884 with enhanced anti-Giardia activity

Giardiasis, a widespread intestinal parasitosis affecting humans and animals, is a growing concern due to the emergence of drug-resistant strains of G. intestinalis. Probiotics offer a promising alternative for preventing and treating giardiasis. Recent studies have shown that the probiotic Lactobacillus johnsonii CNCM I-4884 inhibits G. intestinalis growth both in vitro and in vivo. This protective effect is largely mediated by bile salt hydrolase (BSH) enzymes, which convert conjugated bile acids (BAs) into free forms that are toxic to the parasite. The objective of this study was to use adaptive evolution to develop stress-resistant derivatives of L. johnsonii CNCM I-4884, with the aim of improving its anti-Giardia activity. Twelve derivatives with enhanced resistance to BAs and reduced autolysis were generated. Among them, derivative M11 exhibited the highest in vitro anti-Giardia effect with enhanced BSH activity. Genomic and proteomic analyses of M11 revealed two SNPs and the upregulation of the global stress response by SigB, which likely contributed to its increased BAs resistance and BSH overproduction. Finally, the anti-Giardia efficacy of M11 was validated in a murine model of giardiasis. In conclusion, our results demonstrate that adaptive evolution is an effective strategy to generate robust food-grade bacteria with improved health benefits.

The physiological limits of bispecific monoclonal antibody tissue targeting specificity

Bispecific monoclonal antibodies (bsmAbs) are expected to provide targeted drug delivery that overcomes the dose-limiting toxicities often accompanying antibody-drug conjugates (ADC) in clinical practice. Much attention has been paid in the past to target selection, mAb affinities and the payload linker design, but challenges remain. Here, we demonstrate, by physiologically based pharmacokinetic (PBPK) in silico modeling and simulation, that the tissue-targeting accuracy of mono- and bispecific antibody therapeutics is substantially limited by normal physiological characteristics like organ volumes, blood flow rates, lymphatic circulation, and rates of extravasation. Only a small fraction of blood flows through solid tumor, where the diffusion-driven extravasation is relatively slow compared with many other organs. EGFR and HER2 are used as model antigens based on their experimentally measured tissue and tumor expression levels, but the approach is generic and can account for the cellular expression variation of targets. The model confirms experimental observations that only about 0.1-1% of the dosed mAb is likely to reach the tumor, while the rest ends up in healthy tissues due to target-mediated internalization and nonspecific uptake. The model suggests that the dual-positive tumor cell targeting specificity with bispecific antibodies is likely to be higher at lower drug concentrations and doses. However, this can be offset by elevated drug exposure in more accessible healthy tissues, primarily endothelium. The balance of exposure can be shifted toward tumor cells by using higher doses, albeit at the expense of more extensive target engagement elsewhere in the body, suggesting the need to adapt the toxicity of the payload if ADCs are considered. We suggest that PBPK modeling can guide and support biologics and bsmAb development, from target evaluation and drug optimization to therapeutic dose selection.

Extracellular vesicles in the pathogenesis and future diagnostics of oral squamous cell carcinoma

Extracellular vesicles are a group of heterogeneous particles secreted during both physiological and pathological conditions which serve in intercellular communication and play a role in the development and progression of oral squamous cell carcinoma, the most common malignant tumor of the head and neck with a high mortality rate. Extensive research is being conducted in order to determine the precise role of extracellular vesicles in oncogenic processes and to explore the possible application of extracellular vesicles as early tumor biomarkers. In this review, we aimed to systematize observed roles extracellular vesicles might play in organizing of tumor microenvironment, tumor invasion and metastasis, as well as the impact of extracellular vesicles on immune dysregulation and development of resistance to chemotherapeutics. Additionally, we summarized findings involving the potential use of extracellular vesicles cargo proteins as early disease biomarkers.

Advancing precision medicine in hepatocellular carcinoma: current challenges and future directions in liquid biopsy, immune microenvironment, single nucleotide polymorphisms, and conversion therapy

Hepatocellular carcinoma (HCC) remains a health concern characterized by heterogeneity and high mortality. Surgical resection, radiofrequency ablation, trans-arterial chemoembolization, and liver transplantation offer potentially curative treatments for early-stage disease, but recurrence remains high. Most patients present with advanced-stage HCC, where locoregional therapies are less effective, and systemic treatments-primarily multi-kinase inhibitors and immune checkpoint inhibitors-often yield limited responses. Precision medicine aims to tailor therapy to molecular and genetic profiles, yet its adoption in HCC is hindered by inter-/intra-tumoral heterogeneity and limited biopsy availability. Advances in molecular diagnostics support reintroducing tissue sampling to better characterize genetic, epigenetic, and immunological features. Liquid biopsy offers a minimally invasive method for capturing real-time tumor evolution, overcoming spatial and temporal heterogeneity. Artificial intelligence and machine learning are revolutionizing biomarker discovery, risk stratification, and treatment planning by integrating multi-omics data. Immunological factors such as tumor-infiltrating lymphocytes, natural killer cells, macrophages, and fibroblasts have emerged as determinants of HCC progression and treatment response. Conversion therapy-combining systemic agents with locoregional treatments-has showndemonstrated promise in downstaging unresectable HCC. Ongoing efforts to refine biomarker-driven approaches and optimize multi-modality regimens underscore precision medicine's potential to improve outcomes. PubMed (January 2002-February 2025) was searched for relevant studies.

Expression characteristics of CsESA1 in citrus and analysis of its interacting protein

The most damaging disease affecting citrus globally is Huanglongbing (HLB), primarily attributed to the infection by 'Candidatus Liberibacter asiaticus' (CaLas). Based on comparative transcriptome data, two cellulose synthase (CESA) genes responsive to CaLas infection induction were screened, and one gene cloned with higher differential expression level was selected and named CsCESA1. we verified the interaction between CsCESA1 and citrus exopolysaccharide 2 (CsEPS2) proteins. Subcellular localization in tobacco indicated that both CsCESA1 and CsEPS2 proteins are primarily located in the nucleus and cytoplasm. RT-qPCR analysis indicated that the expression levels of CsCESA1 and CsEPS2 were associated with variety tolerance, tissue site, and symptom development. Furthermore, we generated CsCESA1 and CsEPS2 silencing plants and obtained CsCESA1 and CsEPS2 silencing and overexpressing hairy roots. The analysis of hormone content and gene expression also showed that CsCESA1 and CsEPS2 are involved in transcriptional regulation of genes involved in systemic acquired resistance (SAR) response. In conclusion, our results suggested that CsCESA1 and CsEPS2 could serve as potential resistance genes for HLB disease, offering insights into the plant's defense mechanisms against HLB.

Overexpression of ST8Sia1 inhibits tumor progression by TGF-β1 signaling in rectal adenocarcinoma and promotes the tumoricidal effects of CD8+ T cells by granzyme B and perforin

BACKGROUND

Rectal adenocarcinoma (READ) involves the dysregulated expression of alpha 2,8-Sialyltransferase1 (ST8Sia1) although its role during READ's progression is unclear.

METHODS

The mRNA level of ST8Sia1 was analyzed based on The Cancer Genome Atlas (TCGA), Gene Expression Omnibus (GEO), and Tumor Immune Estimation Resource (TIMER) 2.0. Furthermore, the prognostic and significance of ST8Sia1 in READ was assessed through Kaplan-Meier curve, univariate, multivariate Cox regression, and receiver operating characteristic (ROC) methods. The role of ST8Sia1 in the READ immune microenvironment was explored using ESTIMATE analysis and TIMER databases. Furthermore, the expression of ST8Sia1 in tissues was analyzed using real-time quantitative polymerase chain reaction (RT-qPCR), western blotting (WB), and immunohistochemistry (IHC). Perforin and Granzyme B secretion by CD8+ T cells, as well as tumor cell apoptosis, were detected after co-culturing CD8+ T cells with READ tumor cells and ST8Sia1-overexpression (ST8Sia1-OE) tumor cells. Furthermore, we examined the interaction between ST8Sia1 and TGF-β1 in READ cells.

RESULTS

ST8Sia1 exhibited excellent diagnostic capability for READ, with positive correlations to immune response and negative correlations to tumor purity. Increased levels of perforin and Granzyme B from CD8+ T cells were observed in vitro, enhancing tumor cell apoptosis. ST8Sia1 interacts with TGF-β1, mediating its inhibitory effects on READ development.

CONCLUSIONS

ST8Sia1 is a potential diagnostic biomarker and therapeutic target for READ, enhancing CD8+ T cell function and possibly improving patient outcomes through cellular immunotherapy.

Coupling mechanisms coordinating mRNA translation with stages of the mRNA lifecycle

Gene expression involves a series of consequential processes, beginning with mRNA synthesis and culminating in translation. Traditionally studied as a linear sequence of events, recent findings challenge this perspective, revealing coupling mechanisms that coordinate key steps of gene expression, even when spatially and temporally distant. In this review, we focus on translation, the final stage of gene expression, and examine its coupling with key stages of mRNA metabolism: synthesis, processing, export, and decay. For each of these processes, we provide an overview of known instances of coupling with translation. Furthermore, we discuss the role of high-throughput technologies in uncovering these intricate interactions on a genome-wide scale. Finally, we highlight key challenges and propose future directions to advance our understanding of how coupling mechanisms orchestrate robust and adaptable gene expression programs.

Neutralizing antibodies against SARS-CoV-2 of vaccinated healthcare workers in Taiwan

BACKGROUND

Vaccination is one of the best ways to control the SARS-CoV-2 outbreak. In Taiwan, healthcare workers were prioritized for vaccination, but the effectiveness of these vaccines for them remains unclear. Thus, it's essential to examine their neutralizing antibodies after prime-boost vaccinations.

METHODS

In this prospective observational study, 514 healthcare workers from Chang Gung Memorial hospitals in Taiwan were included between 19 March 2021 and 21 August 2021. The two doses of COVID-19 vaccines were either a match or a mixing of AZD1222 and mRNA-1273, e.g. AZD1222 + AZD1222 (n = 406), mRNA-1273 + mRNA-1273 (n = 62), and AZD1222 + mRNA-1273 (n = 46). Blood specimens were drawn after two doses of vaccines, defined as post-vaccine days [median 34.00 days and interquartile range (IQR) 29.00-42.00 days], and examined for the neutralizing antibodies via SARS-CoV-2 neutralization kits. The results were analyzed as a percentage of inhibition based on the negative control.

RESULTS

After 2 vaccination doses, subjects with AZD1222 + mRNA-1273 (median 97.15%, IQR 96.06-98.06%) and mRNA-1273 + mRNA-1273 (median 97.47%, IQR 96.75-97.89%) exhibited higher neutralizing antibodies than those receiving AZD1222 + AZD1222 vaccines (median 71.28%, IQR 49.39-89.70%) (the percentage was referred to inhibition of surrogate virus). The post-vaccination days negatively impacted the neutralizing antibodies, except for the mRNA-1273 + mRNA-1273 group. The presence of fever, headache, and myalgia after the second dosage was reflected in the higher neutralizing antibodies (median of no fever 76.00% vs. fever 97.00%, p < 0.0001; median of no headache 76.00% vs. headache 95.00%, p < 0.0001; median of no myalgia 75.50% vs. myalgia 96.00%, p < 0.0001). The subjects with underlying diseases, including hypertension and cancer showed lower neutralizing antibodies (median of no hypertension 81.00% vs. hypertension 56.00%, p = 0.0029; median of no cancer 81.00% vs. cancer 56.00%, p = 0.0143).

CONCLUSION

Heterologous prime-boost vaccines (AZD1222 + mRNA-1273) and two doses of mRNA vaccines are recommended. For future directions, we need to investigate the effectiveness of the vaccination against new SARS-CoV-2 variants.

Calcium bridges built by mitochondria-associated endoplasmic reticulum membranes: potential targets for neural repair in neurological diseases

The exchange of information and materials between organelles plays a crucial role in regulating cellular physiological functions and metabolic levels. Mitochondria-associated endoplasmic reticulum membranes serve as physical contact channels between the endoplasmic reticulum membrane and the mitochondrial outer membrane, formed by various proteins and protein complexes. This microstructural domain mediates several specialized functions, including calcium (Ca 2+ ) signaling, autophagy, mitochondrial morphology, oxidative stress response, and apoptosis. Notably, the dysregulation of Ca 2+ signaling mediated by mitochondria-associated endoplasmic reticulum membranes is a critical factor in the pathogenesis of neurological diseases. Certain proteins or protein complexes within these membranes directly or indirectly regulate the distance between the endoplasmic reticulum and mitochondria, as well as the transduction of Ca 2+ signaling. Conversely, Ca 2+ signaling mediated by mitochondria-associated endoplasmic reticulum membranes influences other mitochondria-associated endoplasmic reticulum membrane-associated functions. These functions can vary significantly across different neurological diseases-such as ischemic stroke, traumatic brain injury, Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease-and their respective stages of progression. Targeted modulation of these disease-related pathways and functional proteins can enhance neurological function and promote the regeneration and repair of damaged neurons. Therefore, mitochondria-associated endoplasmic reticulum membranes-mediated Ca 2+ signaling plays a pivotal role in the pathological progression of neurological diseases and represents a significant potential therapeutic target. This review focuses on the effects of protein complexes in mitochondria-associated endoplasmic reticulum membranes and the distinct roles of mitochondria-associated endoplasmic reticulum membranes-mediated Ca 2+ signaling in neurological diseases, specifically highlighting the early protective effects and neuronal damage that can result from prolonged mitochondrial Ca 2+ overload or deficiency. This article provides a comprehensive analysis of the various mechanisms of Ca 2+ signaling mediated by mitochondria-associated endoplasmic reticulum membranes in neurological diseases, contributing to the exploration of potential therapeutic targets for promoting neuroprotection and nerve repair.

Post sleeve gastrectomy-enriched gut commensal Clostridia promotes secondary bile acid increase and weight loss

The gut microbiome is altered after bariatric surgery and is associated with weight loss. However, the commensal bacteria involved and the underlying mechanism remain to be determined. We performed shotgun metagenomic sequencing in obese subjects before and longitudinally after sleeve gastrectomy (SG), and found a significant enrichment in microbial species in Clostridia and bile acid metabolizing genes after SG treatment. Bile acid profiling further revealed decreased primary bile acids (PBAs) and increased conjugated secondary bile acids (C-SBAs) after SG. Specifically, glycodeoxycholic acid (GDCA) and taurodeoxycholic acid (TDCA) were increased at different follow-ups after SG, and were associated with the increased abundance of Clostridia and body weight reduction. Fecal microbiome transplantation with post-SG feces increased SBA levels, and alleviated body weight gain in the recipient mice. Furthermore, both Clostridia-enriched spore-forming bacteria and GDCA supplementation increased the expression of genes responsible for lipolysis and fatty acid oxidation in adipose tissue and reduced adiposity via Takeda G-protein-coupled receptor 5 (TGR5) signaling. Our findings reveal post-SG gut microbiome and C-SBAs as contributory to SG-induced weight loss, in part via TGR5 signaling, and suggest SBA-producing gut microbes as a potential therapeutic target for obesity intervention.

Precursor of H-type II histo-blood group antigen and subterminal sialic acids on gangliosides are significantly implicated in cell entry and infection by a porcine P[11] rotavirus

Rotaviruses, non-enveloped viruses with a double-stranded RNA genome, are the leading etiological pathogen of acute gastroenteritis in young children and animals. The P[11] genotype of rotaviruses exhibits a tropism for neonates. In the present study, a binding assay using synthetic oligosaccharides demonstrated that the VP8* protein of P[11] porcine rotavirus (PRV) strain 4555 binds to lacto-N-neotetraose (LNnT) with the sequence Galβ1,4-GlcNAcβ1,3-Galβ1,4-Glc, one of the core parts of histo-blood group antigen (HBGA) and milk glycans. However, infections were significantly inhibited by blocking of endogenous monosialoganglioside (GM) GM1a with cholera toxin B subunit and preincubation of the virus with exogenous GM1a, suggesting that GM1a is involved in the infection of P[11] PRV 4555. In addition to GM1a, preincubation of the virus with exogenous disialogangliosides (GD) GD1a, GD1b, and trisialoganglioside (GT) GT1b also prevented infection. In contrast, exogenous ganglioside GM3 only inhibited infections at an early time point, and exogenous asyalosphingolipids GA1 and LacCer did not show any inhibitory effect on infections. This indicates that P[11] PRV 4555 preferentially utilizes gangliosides containing subterminal sialic acids. Further experiments revealed that P[11] PRV 4555 infections were prevented by preincubation of the virus with Neu5Ac and Neu5Gc. These results confirmed that sialic acids are essential for P[11] PRV 4555 cell entry, despite the classification as NA-resistant strain. Overall, our results proved that P[11] rotavirus not only binds to the Gal-GlcNAc motif but also utilizes gangliosides containing subterminal sialic acids.

Integrative metagenomics and metabolomics reveal age-associated gut microbiota and metabolite alterations in a hamster model of COVID-19

Aging is a key contributor of morbidity and mortality during acute viral pneumonia. The potential role of age-associated dysbiosis on disease outcomes is still elusive. In the current study, we used high-resolution shotgun metagenomics and targeted metabolomics to characterize SARS-CoV-2-associated changes in the gut microbiota from young (2-month-old) and aged (22-month-old) hamsters, a valuable model of COVID-19. We show that age-related dysfunctions in the gut microbiota are linked to disease severity and long-term sequelae in older hamsters. Our data also reveal age-specific changes in the composition and metabolic activity of the gut microbiota during both the acute phase (day 7 post-infection, D7) and the recovery phase (D22) of infection. Aged hamsters exhibited the most notable shifts in gut microbiota composition and plasma metabolic profiles. Through an integrative analysis of metagenomics, metabolomics, and clinical data, we identified significant associations between bacterial taxa, metabolites and disease markers in the aged group. On D7 (high viral load and lung epithelial damage) and D22 (body weight loss and fibrosis), numerous amino acids, amino acid-related molecules, and indole derivatives were found to correlate with disease markers. In particular, a persistent decrease in phenylalanine, tryptophan, glutamic acid, and indoleacetic acid in aged animals positively correlated with poor recovery of body weight and/or lung fibrosis by D22. In younger hamsters, several bacterial taxa (Eubacterium, Oscillospiraceae, Lawsonibacter) and plasma metabolites (carnosine and cis-aconitic acid) were associated with mild disease outcomes. These findings support the need for age-specific microbiome-targeting strategies to more effectively manage acute viral pneumonia and long-term disease outcomes.

An updated proteomic analysis of Drosophila haemolymph after bacterial infection

Using an in-depth Mass Spectrometry-based proteomics approach, we provide a comprehensive characterization of the hemolymphatic proteome of adult flies upon bacterial infection. We detected and quantified changes in abundance of several known immune regulators and effectors, including multiple antimicrobial peptides, peptidoglycan-binding proteins and serine proteases. Comparison to previously published transcriptomic analyses reveals a partial overlap with our dataset, indicating that many proteins released into the haemolymph upon infection may not be regulated at the transcript level. Among them, we identify a set of muscle-derived proteins released into the haemolymph upon infection. Finally, our analysis reveals that infection induces major changes in the abundance of proteins associated with mitochondrial respiration. This study uncovers a large number of previously undescribed proteins potentially involved in the immune response.

The impact of gut microbial short-chain fatty acids on colorectal cancer development and prevention

Cancer is a long-term illness that involves an imbalance in cellular and immune functions. It can be caused by a range of factors, including exposure to environmental carcinogens, poor diet, infections, and genetic alterations. Maintaining a healthy gut microbiome is crucial for overall health, and short-chain fatty acids (SCFAs) produced by gut microbiota play a vital role in this process. Recent research has established that alterations in the gut microbiome led to decreased production of SCFA's in lumen of the colon, which associated with changes in the intestinal epithelial barrier function, and immunity, are closely linked to colorectal cancer (CRC) development and its progression. SCFAs influence cancer progression by modifying epigenetic mechanisms such as DNA methylation, histone modifications, and non-coding RNA functions thereby affecting tumor initiation and metastasis. This suggests that restoring SCFA levels in colon through microbiota modulation could serve as an innovative strategy for CRC prevention and treatment. This review highlights the critical relationship between gut microbiota and CRC, emphasizing the potential of targeting SCFAs to enhance gut health and reduce CRC risk.

Development of ketobenzothiazole-based peptidomimetic TMPRSS13 inhibitors with low nanomolar potency

TMPRSS13, a member of the Type II Transmembrane Serine Proteases (TTSP) family, is involved in cancer progression and in respiratory virus cell entry. To date, no inhibitors have been specifically developed for this protease. In this study, a chemical library of 65 ketobenzothiazole-based peptidomimetic molecules was screened against a proteolytically active form of recombinant TMPRSS13 to identify novel inhibitors. Following an initial round of screening, subsequent synthesis of additional derivatives supported by molecular modelling revealed important molecular determinants involved in TMPRSS13 inhibition. One inhibitor, N-0430, achieved low nanomolar affinity towards TMPRSS13 activity in a cellular context. Using a SARS-CoV-2 pseudovirus cell entry model, we further demonstrated the ability of N-0430 to block TMPRSS13-dependent entry of the pseudovirus. The identified peptidomimetic inhibitors and the molecular insights into their potency gained from this study will aid in the development of specific TMPRSS13 inhibitors.

Identification of TTLL8, POTEE, and PKMYT1 as immunogenic cancer-associated antigens and potential immunotherapy targets in ovarian cancer

Most high-grade serous ovarian cancers (OC) do not respond to current immunotherapies. To identify potential new actionable tumor antigens in OC, we performed immunopeptidomics on a human OC cell line expressing the HLA-A02:01 haplotype, which is commonly expressed across many racial and ethnic groups. From this dataset, we identified TTLL8, POTEE, and PKMYT1 peptides as candidate tumor antigens with low expression in normal tissues and upregulated expression in OC. Using tissue microarrays, we assessed the protein expression of TTLL8 and POTEE and their association with patient outcomes in a large cohort of OC patients. TTLL8 was found to be expressed in 56.7% of OC and was associated with a worse overall prognosis. POTEE was expressed in 97.2% of OC patients and had no significant association with survival. In patient TILs, increases in cytokine production and tetramer-positive populations identified antigen-specific CD8 T cell responses, which were dependent on antigen presentation by HLA class I. Antigen-specific T cells triggered cancer cell killing of antigen-pulsed OC cells. These findings suggest that TTLL8, POTEE, and PKMYT1 are potential targets for the development of antigen-targeted immunotherapy in OC.

P-Pev: micelle-like complexes transformed from tumor extracellular vesicles by PEG-PE for personalized therapeutic tumor vaccine

The clinical benefits of personalized therapeutic tumor vaccines are mainly challenged by the need to identify immunogenic neoantigens promptly, given the rapid pace of tumor mutations. An increasing body of literature addresses the potential of tumor-derived extracellular vesicles (TEVs) as an anti-tumor "cell-free" vaccine due to their substantial presence of neoantigens. However, their immunosuppression and limited presentation efficiency of dendritic cells (DCs) restrict their further application. Here, we have developed a novel tumor-personalized vaccine, termed P-Pev, based on remodeled TEVs by polymeric surfactant polyethylene glycol-phosphatidyleolamine (PEG-PE) and adjuvant monophosphoryl lipid A (MPLA). Our results show that PEG-PE transforms TEVs into micelle-like complexes by disrupting the original structure, facilitating antigens delivery to the cytoplasm, and cross-presentation by DCs. P-Pev particularly prevents the immunosuppressive impacts of TEVs on the ability of DCs to prime CD8+ T cells and eliminates the potency of TEVs to promote lung metastasis through their membrane-bound PD-L1. Finally, the P-Pev effectively induces neoantigen-specific cytotoxic T lymphocytes (CTLs) responses and exhibits excellent therapeutic effects in various murine tumor models. Also, the P-Pev induces neoantigen-specific antibodies, suggesting the involvement of humoral immunity in its anti-tumor effects. More importantly, it has been shown that P-Pev prepared by mutated tumor cells can retard these mutated tumor cell-established syngeneic tumors better than P-Pev prepared by original tumor cells, indicating the feasibility that leverages TEVs to prepare personalized tumor vaccines, and it is synergistically enhanced by PD-1 mAb combination. Collectively, we present a general strategy that offers a streamlined, cost-effective, and time-consuming approach to preparing personalized therapeutic tumor vaccines.

Comparative proteomic analysis of plasma exosomes reveals the functional contribution of N-acetyl-alpha-glucosaminidase to Parkinson's disease

JOURNAL/nrgr/04.03/01300535-202510000-00029/figure1/v/2024-11-26T163120Z/r/image-tiff Parkinson's disease is the second most common progressive neurodegenerative disorder, and few reliable biomarkers are available to track disease progression. The proteins, DNA, mRNA, and lipids carried by exosomes reflect intracellular changes, and thus can serve as biomarkers for a variety of conditions. In this study, we investigated alterations in the protein content of plasma exosomes derived from patients with Parkinson's disease and the potential therapeutic roles of these proteins in Parkinson's disease. Using a tandem mass tag-based quantitative proteomics approach, we characterized the proteomes of plasma exosomes derived from individual patients, identified exosomal protein signatures specific to patients with Parkinson's disease, and identified N-acetyl-alpha-glucosaminidase as a differentially expressed protein. N-acetyl-alpha-glucosaminidase expression levels in exosomes from the plasma of patients and healthy controls were validated by enzyme-linked immunosorbent assay and western blot. The results demonstrated that the exosomal N-acetyl-alpha-glucosaminidase concentration was not only lower in Parkinson's disease, but also decreased with increasing Hoehn-Yahr stage, suggesting that N-acetyl-alpha-glucosaminidase could be used to rapidly evaluate Parkinson's disease severity. Furthermore, western blot and immunohistochemistry analysis showed that N-acetyl-alpha-glucosaminidase levels were markedly reduced both in cells treated with 1-methyl-4-phenylpyridinium and cells overexpressing α-synuclein compared with control cells. Additionally, N-acetyl-alpha-glucosaminidase overexpression significantly increased cell viability and inhibited α-synuclein expression in 1-methyl-4-phenylpyridinium-treated cells. Taken together, our findings demonstrate for the first time that exosomal N-acetyl-alpha-glucosaminidase may serve as a biomarker for Parkinson's disease diagnosis, and that N-acetyl-alpha-glucosaminidase may reduce α-synuclein expression and 1-methyl-4-phenylpyridinium-induced neurotoxicity, thus providing a new therapeutic target for Parkinson's disease.

Enhanced l-serine synthesis in Corynebacterium glutamicum by exporter engineering and Bayesian optimization of the medium composition

l-serine is a versatile, high value-added amino acid, widely used in food, medicine and cosmetics. However, the low titer of l-serine has limited its industrial production. In this study, a cell factory without plasmid for efficient production of l-serine was constructed based on transport engineering. Firstly, the effects of l-serine exporter SerE overexpression and deletion on the cell growth and l-serine titer were investigated in Corynebacterium glutamicum (C. glutamicum) A36, overexpression of s erE using a plasmid led to a 15.1% increase in l-serine titer but also caused a 15.1% decrease in cell growth. Subsequently, to increase the export capacity of SerE, we conducted semi-rational design and bioinformatics analysis, combined with alanine mutation and site-specific saturation mutation. The mutant E277K was obtained and exhibited a 53.2% higher export capacity compared to wild-type SerE, resulting in l-serine titer increased by 39.6%. Structural analysis and molecular dynamics simulations were performed to elucidate the mechanism. The results showed that the mutation shortened the hydrogen bond distance between the exporter and l-serine, enhanced complex stability, and reduced the binding energy. Finally, Bayesian optimization was employed to further improve l-serine titer of the mutant strain C-E277K. Under the optimized conditions, 47.77 g/L l-serine was achieved in a 5-L bioreactor, representing the highest reported titer for C. glutamicum to date. This study provides a basis for the transformation of l-serine export pathway and offers a new strategy for increasing l-serine titer.

Black rice bran improved lipid metabolism in hyperlipidemia mice via steroid hormone biosynthesis and PPAR signaling pathway

This study was aimed to explore the alleviating effect of black rice (BR), black peeled rice (BPR), and black rice bran (BRB) on lipid metabolism disorders in hyperlipidemia mice caused by high fat and cholesterol diet (HFCD). Combined untargeted metabolomics and RNA-seq transcriptomics analysis was used to demonstrate the potential mechanism regulated by BR, BPR and BRB. The untargeted metabolomics analysis indicated that BR especially BRB significantly increased Deoxycholic acid, 5-Dehydroavenasterol, scyllo-Inositol, Phloretin, 5-KETE, Lipoxin B4, 3,4-Dihydroxybenzeneacetic acid levels, while BRB significantly regulated PPAR signaling pathway, Arachidonic acid metabolism, Regulation of lipolysis in adipocytes, Steroid biosynthesis, and Sphingolipid signaling pathway, which closely linked to lipid metabolism. Furthermore, RNA-seq transcriptomics analysis showed that BRB obviously regulated Steroid hormone biosynthesis (Cyp2b9, Cyp2b13 and Cyp2c38) and PPAR signaling pathway (Pparg, Fabp4, Cd36 and Plin4), which were closely associated with inflammation and lipid metabolism. Moreover, quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) analysis validated this. The obtaining results were hoping to reveal the detailed mechanism of BRB in alleviating hyperlipidemia and provide some insights for developing a new kind of natural anti-hyperlipidemia drug.

DNA aptamer targeting zinc transporters ZIP10 and ZIP6 on cancer cells

Cell-SELEX is an effective method for generating aptamers that specifically bind molecules in their native state on live cells. It not only uncovers novel potential biomarkers but also provides robust molecular recognition tools for a wide spectrum of applications. In this work, we generate a high affinity aptamer, HL15, through Cell-SELEX. A refined sequence HL15a demonstrated a strong binding affinity to target cells, with a minimal dissociation constant (Kd) of just 1.90 ± 0.49 nM. Subsequent truncation and mutation assays revealed that the core sequence of HL15a forms an antiparallel G-quadruplex structure. Furthermore, the target proteins of aptamer HL15a were identified and confirmed to be ZIP10 and ZIP6, both members of the zinc transporter ZIP family with high homology. Using HL15a as a molecular probe, we detected a range of universal binding affinities to the majority of tumor cells in the 48 cell lines evaluated. Furthermore, HL15a was effectively applied to distinguish high malignancy cancer tissues from both normal and low malignancy tissues in the pathological sections of breast and prostate cancers. Given that ZIP10 and ZIP6 play crucial roles in regulating zinc homeostasis and are implicated in numerous diseases, the aptamer HL15a offers a powerful tool for the study and potential therapeutic intervention of these two proteins.

Protein arginine methyltransferase-6 regulates heterogeneous nuclear ribonucleoprotein-F expression and is a potential target for the treatment of neuropathic pain

JOURNAL/nrgr/04.03/01300535-202509000-00029/figure1/v/2024-11-05T132919Z/r/image-tiff Protein arginine methyltransferase-6 participates in a range of biological functions, particularly RNA processing, transcription, chromatin remodeling, and endosomal trafficking. However, it remains unclear whether protein arginine methyltransferase-6 modifies neuropathic pain and, if so, what the mechanisms of this effect. In this study, protein arginine methyltransferase-6 expression levels and its effect on neuropathic pain were investigated in the spared nerve injury model, chronic constriction injury model and bone cancer pain model, using immunohistochemistry, western blotting, immunoprecipitation, and label-free proteomic analysis. The results showed that protein arginine methyltransferase-6 mostly co-localized with β-tubulin III in the dorsal root ganglion, and that its expression decreased following spared nerve injury, chronic constriction injury and bone cancer pain. In addition, PRMT6 knockout (Prmt6-/-) mice exhibited pain hypersensitivity. Furthermore, the development of spared nerve injury-induced hypersensitivity to mechanical pain was attenuated by blocking the decrease in protein arginine methyltransferase-6 expression. Moreover, when protein arginine methyltransferase-6 expression was downregulated in the dorsal root ganglion in mice without spared nerve injury, increased levels of phosphorylated extracellular signal-regulated kinases were observed in the ipsilateral dorsal horn, and the response to mechanical stimuli was enhanced. Mechanistically, protein arginine methyltransferase-6 appeared to contribute to spared nerve injury-induced neuropathic pain by regulating the expression of heterogeneous nuclear ribonucleoprotein-F. Additionally, protein arginine methyltransferase-6-mediated modulation of heterogeneous nuclear ribonucleoprotein-F expression required amino acids 319 to 388, but not classical H3R2 methylation. These findings indicated that protein arginine methyltransferase-6 is a potential therapeutic target for the treatment of peripheral neuropathic pain.

Isotope-coded hydrazide tags for MALDI-MS based quantitative glycomics

The detection of glycosylation alterations is essential for elucidating the roles of glycan functions in biological processes and identifying potential disease biomarkers. Stable isotopic chemical labeling, coupled with mass spectrometry (MS), represents a powerful approach in quantitative glycomics. In this study, we synthesized a novel isotopic hydrazide pair, 2,6-Dimethyl-4-chinolincarbohydrazid (DMQCH) and its deuterium isomer DMQCH-d4, via an efficient and cost-effective method, and applied it for the first time in MALDI-MS-based quantitative glycomics. The hydrazide tags, DMQCH/DMQCH-d4, enabled stable mass shifts through reductive-terminal reactions with glycans, allowing for differential mass tagging of two samples without additional purification after derivatization. This DMQCH/DMQCH-d4 pair exhibited high derivatization efficiency (including on-target derivatization), substantial improvements in MS signal intensity (a 15-fold increase for maltoheptaose, high reproducibility (CV < 13.6 %), and excellent linearity (R2 > 0.99) over two orders of magnitude in dynamic range for the relative quantitative analysis of maltoheptaose. Furthermore, this isotopic hydrazide pair was validated by successfully measuring changes in serum N-glycan profiles from individuals with healthy human serum control and ovarian cancer, highlighting its potential in quantitative glycomics for clinical applications.

Alcohol-based solvents as mobile phases for LC-MS characterization of therapeutic proteins

Acetonitrile (ACN) is currently the preferred solvent in reversed phase (RP) chromatography for protein characterization through peptide mapping. Despite its effective performance, ACN poses toxicity risks to humans and has adverse effects on environmental sustainability. In the current work, we developed a novel alcohol-based solvent system for peptide mapping by systematic evaluation of parameters such as organic eluent composition, solvent gradient, flow rate, and column temperature. We compared the chromatographic performance and MS response of peptides between the standard (ACN based) and the new developed solvent systems (EtOH/IPA based). The results of our study show that the EtOH/IPA based solvent system improves selectivity factor (α) and resolution (R), while the standard ACN based solvent system provides a lower peak width and hence a higher peak height. The majority of the analysed peptides exhibited shorter retention times, whereas hydrophobic peptides eluted later when using the EtOH/IPA solvent system. Several critical quality attributes (CQA) of a monoclonal antibody (mAb) were successfully characterized by this method without compromising the chromatographic separations and MS response of the peptides. Furthermore, the suitability of the new approach for LC-UV assessment of a mAb as part of an identity test of therapeutic proteins was demonstrated. Our proposed approach, which prioritizes safety, non-toxicity, and compatibility with all LC-MS instruments, offers significant support to a broad community of academic and biopharmaceutical scientists in their pursuit of a bottom-up green strategy.

Investigation of the protein corona and biodistribution profile of polymeric nanoparticles for intra-amniotic delivery

When exposed to the biological environment, nanoparticles (NPs) form a protein corona that influences delivery profile. We present a study of protein corona formation and NP biodistribution in amniotic fluid (AF) for poly(lactic-co-glycolic acid) (PLGA) and poly(lactic-acid) (PLA) NPs, with and without polyethylene glycol (PEG), as well as poly(amine-co-ester)-PEG (PACE-PEG) NPs. The presence of surface PEG and polyvinyl alcohol (PVA) were characterized to investigate surfactant role in determining protein corona formation. The surface density of PEG groups demonstrated an inverse correlation with the total amount of protein surface adsorption. All PEGylated NPs exhibited a dense brush conformation and demonstrated higher levels of stability in AF than non-PEGylated NPs. The protein corona composition varied by core polymer, while the amount of protein adsorption varied by PEGylation status. In A549 cells, in vitro cellular association of each NP type correlated with the amount of albumin that was found in the protein corona. In vivo, only PEGylated NPs were able successfully distribute to fetal organs, likely due to the enhanced stability imparted by PEG. PLGA-PEG and PACE-PEG NPs had both high levels of albumin in the protein corona and high biodistribution to the fetal lung, consistent with the association with lung cells in vitro. PLA-PEG NPs distributed exclusively to the fetal bowel, which we propose is associated with known gastrointestinal targeting keratin proteins. By furthering our understanding of polymeric NP behavior in AF, this novel study provides a basis for optimization of intra-amniotic NP delivery systems targeting congenital pulmonary and gastrointestinal diseases.

The inflammasome adaptor pycard is essential for immunity against Mycobacterium marinum infection in adult zebrafish

Inflammasomes regulate the host response to intracellular pathogens including mycobacteria. We have previously shown that the course of Mycobacterium marinum infection in adult zebrafish (Danio rerio) mimics the course of tuberculosis in human. To investigate the role of the inflammasome adaptor pycard in zebrafish M. marinum infection, we produced two zebrafish knockout mutant lines for the pycard gene with CRISPR/Cas9 mutagenesis. Although the zebrafish larvae lacking pycard developed normally and had unaltered resistance against M. marinum, the loss of pycard led to impaired survival and increased bacterial burden in the adult zebrafish. Based on histology, immune cell aggregates, granulomas, were larger in pycard-deficient fish than in wild-type controls. Transcriptome analysis with RNA sequencing of a zebrafish haematopoietic tissue, kidney, suggested a role for pycard in neutrophil-mediated defence, haematopoiesis and myelopoiesis during infection. Transcriptome analysis of fluorescently labelled, pycard-deficient kidney neutrophils identified genes that are associated with compromised resistance, supporting the importance of pycard for neutrophil-mediated immunity against M. marinum. Our results indicate that pycard is essential for resistance against mycobacteria in adult zebrafish.

Identification and characterization of tubulin as Ga(III)-binding protein in T24 cells

Gallium-based metallic drugs and agents have been widely applied for the diagnosis and treatment of diseases such as non-Hodgkin's lymphoma (NHL), but there are few reports on the potential Ga(III)-binding proteins and the related cytotoxic mechanisms for Ga(III). Herein, by using human urinary bladder cancer T24 cells as a model, we identify and report that tubulin is a Ga(III)-binding protein target in T24 cells. Our analyses, including the employment of a series of methods based on immobilized metal affinity chromatography (IMAC), cellular thermal shift assay (CETSA), and immunofluorescence experiments, collectively explained this finding. Our results suggest that the binding of Ga(III) to tubulin led to significant changes in the morphology and distribution of microtubules in cells. The blocked microtubule formation or microtubule depolymerization as a result of the binding of Ga(III) to tubulin may be an important molecular mechanism by which Ga(III) exerts its cytotoxic effects in T24 cells to inhibit tumor cell growth.

Pasteurization and lyophilization affect membrane proteins of pomegranate-derived nanovesicles reducing their functional properties and cellular uptake

Plant-derived nanovesicles (PDNVs) are promising therapeutic agents, valued for their bioactive compound content and as drug delivery systems. However, the effects of industrial food processing techniques on PDNVs remain underexplored. This study evaluated the impact of lyophilization and pasteurization on the properties and uptake efficiency of pomegranate-derived nanovesicles (PgNVs). PgNVs were isolated from pomegranate juice using tangential flow filtration and size exclusion chromatography. Treated PgNVs were analyzed via transmission electron microscopy, nanoparticle tracking analysis, and LC-MS/MS, assessing their functional properties and cellular uptake. High-purity PgNVs were obtained, although both treatments reduced their yield. Pre-treated PgNVs displayed diminished anti-inflammatory and wound-healing capacities, though antioxidant activity remained unaffected. Treated PgNVs also exhibited lower internalization by human macrophages compared to untreated PgNVs. Proteomic analyses revealed that the damage of membrane proteins, such as Tetraspanin-8, might be responsible for these effects. Our findings emphasize the need of optimizing processing to preserve PDNV therapeutic potential.

Exploring the molecular modifications and allergenicity of the egg white protein matrix during boiling

Hen's egg allergy is the second most common food allergy in young children, with the major allergens ovalbumin and ovomucoid found in egg white. While many egg-allergic children can tolerate baked or hard-boiled eggs, there is limited understanding of how heating affects allergen structure and allergenicity within the egg white protein matrix. This study investigated the impact of egg white boiling for 10 or 45 min on the structure and allergenicity of the main egg white allergens. Our results showed that 45 min of boiling led to significant structural changes and a strong reduction in egg white allergenicity, while 10 min of boiling had a minor effect. Gastric digestion further reduced allergenicity, especially in 45 min boiled eggs. These findings highlight how increasing the boiling time of egg white can reduce allergenicity through structural changes in the main egg white allergens.

Production and characterization of novel antioxidant peptides from mulberry leaf ferment using B. subtilis H4 and B. amyloliquefaciens LFB112

The objective of this study was to isolate and characterize antioxidant peptides from mulberry leaves fermented with Bacillus subtilis H4 and Bacillus amyloliquefaciens LFB112. The results indicated that fraction F4 (<1 kDa) exhibited superior DPPH activity compared to the F1 (>10 kDa), F2 (3-10 kDa), and F3 (1-3 kDa) fractions, and cytoprotective effect against lipopolysaccharides (LPS)-induced oxidative stress in RAW264.7 cells. Three novel peptides, FRFDP, RFGG, and GPPLAFGGGP, were identified in the F4 fraction of the mulberry leaf ferment, and docking results showed that these peptides could form stable carbon (covalent) and hydrogen bonds to the active sites of Keap1, thus regulating the Keap1-Nrf2 pathway by blocking the Nrf2 binding sites on Keap1. These peptides significantly upregulated the mRNA expression of Nrf2, HO-1, and NQO1, providing indirect evidence of their potential to enhance cellular antioxidant defense via the possible activation of Keap1-Nrf2 pathway. Furthermore, these peptides showed good DPPH and ABTS scavenging activities, indicating their potential as antioxidant peptides. This study offers valuable insights into the integration of these novel peptides in developing mulberry leaf ferment as a functional food and their potential use as a feed additive.

Exomeres and supermeres: Current advances and perspectives

Recent studies have revealed a great diversity and complexity in extracellular vesicles and particles (EVPs). The developments in techniques and the growing awareness of the particle heterogeneity have spurred active research on new particle subsets. Latest discoveries highlighted unique features and roles of non-vesicular extracellular nanoparticles (NVEPs) as promising biomarkers and targets for diseases. These nanoparticles are distinct from extracellular vesicles (EVs) in terms of their smaller particle sizes and lack of a bilayer membrane structure and they are enriched with diverse bioactive molecules particularly proteins and RNAs, which are widely reported to be delivered and packaged in exosomes. This review is focused on the two recently identified membraneless NVEPs, exomeres and supermeres, to provide an overview of their biogenesis and contents, particularly those bioactive substances linked to their bio-properties. This review also explains the concepts and characteristics of these nanoparticles, to compare them with other EVPs, especially EVs, as well as to discuss their isolation and identification methods, research interests, potential clinical applications and open questions.

Buffer 4-Ethylmorpholinium/Acetate: Exploring a New Alternative Buffer for Native Mass Spectrometry

RATIONALE

To perform native mass spectrometry (MS) studies, there are a limited number of volatile and electrospray ionization (ESI)-MS compatible solutions, such as ammonium bicarbonate and ammonium acetate (AA). These solutions could induce the unfolding of proteins due to the formation of CO2 bubbles or induced acidification during ESI. Hence, it was important to introduce a buffer suitable to preserve the native form of proteins while simulating physiological conditions.

METHODS

The 4-ethylmorpholinium/acetate (4EM/A) buffer was compared to AA for the analysis of proteins and protein complexes with mass ranges from 5 to 103 kDa and isoelectric points (pI) between 3 and 11. The evaluations were conducted by comparing the native-MS profiles, CCS values, arrival time distributions (ATDs), and proteins bioactivities. The human cardiac troponin complex (cTn complex) and its subunit cardiac troponin T (cTnT) were analyzed as proof of the applicability of this buffer for challenging proteins and protein complexes.

RESULTS

4EM/A led to lower charge states compared to AA, supporting the likelihood of preserving protein folding during nano-ESI and in a high vacuum environment of MS. Ion mobility measurements revealed that proteins in 4EM/A exhibit a lower degree of conformational variation compared to AA, suggesting enhanced conformational stability and potential retention of natural-like compactness. Additionally, testing the impact of 4EM/A on bioactivity, lysozyme showed increased biological activity in 4EM/A relative to AA, highlighting the buffer's potential for real-time assessment of protein interaction kinetics and bioactivity. The 4EM/A buffer enabled native-MS analysis of cTnT for the first time.

CONCLUSION

We introduced 4EM/A, with pKa of 7.72/4.76, as a promising buffer for native-MS studies to maintain protein and protein complex bioactivity and conformational integrity.

FGFR2 residence in primary cilia is necessary for epithelial cell signaling

Primary cilium projects from cells to provide a communication platform with neighboring cells and the surrounding environment. This is ensured by the selective entry of membrane receptors and signaling molecules, producing fine-tuned and effective responses to the extracellular cues. In this study, we focused on one family of signaling molecules, the fibroblast growth factor receptors (FGFRs), their residence within cilia, and its role in FGFR signaling. We show that FGFR1 and FGFR2, but not FGFR3 and FGFR4, localize to primary cilia of the developing mouse tissues and in vitro cells. For FGFR2, we demonstrate that the ciliary residence is necessary for its signaling and expression of target morphogenic genes. We also show that the pathogenic FGFR2 variants have minimal cilium presence, which can be rescued for the p.P253R variant associated with the Apert syndrome by using the RLY-4008 kinase inhibitor. Finally, we determine the molecular regulators of FGFR2 trafficking to cilia, including IFT144, BBS1, and the conserved T429V430 motif within FGFR2.

Phosphorylation-dependent regional motility of the ciliary kinesin OSM-3

Kinesin motor proteins, vital for intracellular microtubule-based transport, display region-specific motility within cells, a phenomenon that remains molecularly enigmatic. This study focuses on the localized activation of OSM-3, an intraflagellar transport kinesin crucial for the assembly of ciliary distal segments in Caenorhabditis elegans sensory neurons. Fluorescence lifetime imaging microscopy unveiled an extended, active conformation of OSM-3 in the ciliary base and middle segments, where OSM-3 is conveyed as cargo by kinesin-II. We demonstrate that NEKL-3, a never in mitosis kinase-like protein, directly phosphorylates the motor domain of OSM-3, inhibiting its in vitro activity. NEKL-3 and NEKL-4, localized at the ciliary base, function redundantly to restrict OSM-3 activation. Elevated levels of protein phosphatase 2A at the ciliary transition zone or middle segments triggered premature OSM-3 motility, while its deficiency resulted in reduced OSM-3 activity and shorter cilia. These findings elucidate a phosphorylation-mediated mechanism governing the regional motility of kinesins.

The proximity proteome of pre-40S pre-ribosomal particle components PNO1 and NOB1 using turboID proximity labeling technology

BACKGROUND

The ribosome assembly factors PNO1 and NOB1 play crucial roles in the maturation of the 40S ribosomal small subunit. TurboID is an efficient biotin ligase that can biotinylate proteins in proximity to the target protein and is widely used to study complex biological processes within cells. In this study, we employed this technology to investigate the complex proximity network of PNO1 and NOB1 within the cell, further revealing their key roles in ribosome biogenesis.

RESULTS

Firstly, through immunofluorescence experiments, we observed that PNO1 and NOB1 have different localizations within the cell. Subsequently, by analyzing the proximal proteins labeled by PNO1-TurboID and NOB1-TurboID, we identified 871 proximal proteins for PNO1 and 1044 for NOB1, with 663 overlapping proteins. Functional analysis revealed that these proximal proteins are predominantly enriched in biological processes related to ribosome assembly, rRNA processing, and translation, all of which are closely linked to ribosome biogenesis. Notably, we validated the mass spectrometry-identified proteins through co-IP experiments and found that PNO1 and NOB1 interact with the translation-related proteins EIF4B and EIF4G2.

CONCLUSION

Our study constructed the protein network environment of ribosome assembly factors PNO1 and NOB1 within the cell and found that their neighboring proteins are primarily involved in key biological processes such as ribosome processing, mRNA translation, and the cell cycle, all of which are critical for ribosome biogenesis. These findings provide a valuable foundation for further understanding the roles of PNO1 and NOB1 in ribosome biogenesis and how they regulate this process.

Prognostic gene expression profile of colorectal cancer

Colorectal cancer is a major global health burden, with significant heterogeneity in clinical outcomes among patients. Identifying robust prognostic gene expression signatures can help stratify patients, guide treatment decisions, and improve clinical management. This review provides an overview of current prognostic gene expression profiles in colorectal cancer research. We have synthesized evidence from numerous published studies investigating the association between tumor gene expression patterns and patient survival outcomes. The reviewed literature reveals several promising gene signatures that have demonstrated the ability to predict disease-free survival and overall survival in CRC patients, independent of standard clinicopathological risk factors. These genes are crucial in fundamental biological processes, including cell cycle control, epithelial-mesenchymal transition, and immune regulation. The implementation of prognostic gene expression tests in clinical practice holds great potential for enabling more personalized management strategies for colorectal cancer.

Diagnostic platforms for snakebite: Current approaches and challenges in medically important species

Diagnosing snakebite envenoming is a critical aspect of managing this life-threatening condition. Achieving the impacts and clinical applications of the diagnosis of snakebites is important to help clarify the challenges faced in identifying venomous snakebites and implementing effective treatment strategies. The complexity of the envenomation requires a comprehensive diagnostic approach, considering both clinical symptoms and laboratory findings. Despite advances in diagnostic technologies, the lack of standardized tools represents a significant obstacle to obtaining accurate and timely assessments. This paper analyzes the state-of-the-art snakebite diagnosis, emphasizing the need for methodologies for differential diagnosis of snakebites. Furthermore, it investigates the far-reaching consequences of late or incorrect diagnoses, emphasizing their role in the potential development of serious morbidity and even mortality. The discussion extends to the global health burden caused by snakebite envenoming, emphasizing the importance of personalized diagnostic methods in regions with diverse snake species. Furthermore, the review explores recent advances in the global scale diagnosis of snakebite venom. The clinical applications of these innovations are explored, highlighting their potential to revolutionize snakebite management in resource-limited settings. By addressing the multifaceted challenges in snakebite diagnosis, this summary contributes to ongoing efforts to mitigate the global impact of snakebite envenoming by highlighting the critical need for collaborative research, standardization, and accessibility of diagnostic tools.

Host cell protein-mediated adjuvanticity and immunogenicity risks of biotherapeutics

Host cell proteins (HCPs) are process-related impurities of biotherapeutic production that might affect product quality and/or patient safety. In a few cases, adverse events were attributed to HCPs present in the administered biotherapeutic. HCP-associated immune risks include adjuvanticity and immunogenicity with potential cross-reactivity. Based on the published data, some HCPs can act as adjuvants increasing the immunogenicity of the biotherapeutic as a bystander effect. HCPs may also induce immunogenicity against themselves, resulting in anti-HCP T cell responses and anti-HCP antibody formation. Depending on sequence similarities, these anti-HCP immune responses might theoretically be cross-reactive to the biotherapeutic or human endogenous proteins. In this review, we examine HCP-associated immune-related risks reported from non-clinical and clinical studies. We also discuss the potential and limitations of in vitro and in silico methods to evaluate the adjuvanticity and immunogenicity potential of HCPs. A risk-based assessment of the safety impact of HCPs may include the identity of the HCP and similarity to the biotherapeutic and human proteins, as well as product, treatment-, and patient-related factors.