The role and function of lncRNA in ageing-associated liver diseases

Liver diseases are a significant global health issue, characterized by elevated levels of disorder and death. The substantial impact of ageing on liver diseases and their prognosis is evident. Multiple processes are involved in the ageing process, which ultimately leads to functional deterioration of this organ. The process of liver ageing not only renders the liver more susceptible to diseases but also compromises the integrity of other organs due to the liver's critical function in metabolism regulation. A growing body of research suggests that long non-coding RNAs (lncRNAs) play a significant role in the majority of pathophysiological pathways. They regulate gene expression through a variety of interactions with microRNAs (miRNAs), messenger RNAs (mRNAs), DNA, or proteins. LncRNAs exert a major influence on the progression of age-related liver diseases through the regulation of cell proliferation, necrosis, apoptosis, senescence, and metabolic reprogramming. A concise overview of the current understanding of lncRNAs and their potential impact on the development of age-related liver diseases will be provided in this mini-review.

With great power, comes great responsibility: the importance of broadly measuring Fc-mediated effector function early in the antibody development process

The field of antibody therapeutics is rapidly growing, with over 210 antibodies currently approved or in regulatory review and ~ 1,250 antibodies in clinical development. Antibodies are highly versatile molecules that, with strategic design of their antigen-binding domain (Fab) and the domain responsible for mediating effector functions (Fc), can be used in a wide range of therapeutic indications. Building on many years of progress, the biopharmaceutical industry is now advancing innovative research and development by exploring new targets and new formats and using antibody engineering to fine-tune functions tailored to specific disease requirements. In addition to considering the target and the disease context, however, the unique features of each therapeutic antibody trigger a diverse set of Fc-mediated effector functions. To avoid unexpected results on safety and efficacy outcomes during the later stages of the development process, it is crucial to measure the impact of antibody design on Fc-mediated effector function early in the antibody development process. Given the breadth of effector functions antibodies can deploy and the close interplay between the antibody Fab and Fc functional domains, it is important to conduct a comprehensive evaluation of Fc-mediated functions using an array of antigen-specific biophysical and cell-mediated functional assays. Here, we review antibody and Fc receptor properties that influence Fc effector functions and discuss their implications on development of safe and efficacious antibody therapeutics.

Restriction of mitochondrial oxidation of glutamine or fatty acids enhances intracellular growth of Mycobacterium abscessus in macrophages

Mycobacterium abscessus (Mab), a nontuberculous mycobacterium, is increasing in prevalence worldwide and causes treatment-refractory pulmonary diseases. However, how Mab rewires macrophage energy metabolism to facilitate its survival is poorly understood. We compared the metabolic profiles of murine bone marrow-derived macrophages (BMDMs) infected with smooth (S)- and rough (R)-type Mab using extracellular flux technology. Mab infection shifted BMDMs towards a more energetic phenotype, marked by increased oxidative phosphorylation (OXPHOS) and glycolysis, with a significantly greater enhancement in OXPHOS. This metabolic adaptation was characterized by enhanced ATP production rates, particularly in cells infected with S-type Mab, highlighting OXPHOS as a key energy source. Notably, Mab infection also modulated mitochondrial substrate preferences, increasing fatty acid oxidation capabilities while revealing significant changes in glutamine dependency and flexibility. R-type Mab infections exhibited a marked decrease in glutamine reliance but enhanced metabolic flexibility and capacity. Furthermore, targeting metabolic pathways related to glutamine and fatty acid oxidation exacerbated Mab growth within macrophages, suggesting these pathways play a protective role against infection. These insights advance our understanding of Mab's impact on host cell metabolism and propose a novel avenue for therapeutic intervention. By manipulating host mitochondrial metabolism, we identify a potential host-directed therapeutic strategy against Mab, offering a promising alternative to conventional treatments beleaguered by drug resistance. This study underscores the importance of exploring metabolic interventions to combat Mab infection, paving the way for innovative approaches in the fight against this formidable pathogen.

The gut microbiota predicts and time-restricted feeding delays experimental colitis

The etiology of inflammatory bowel disease (IBD) remains unclear, treatment options unsatisfactory and disease development difficult to predict for individual patients. Dysbiosis of the gastrointestinal microbiota and disruption of the biological clock have been implicated and studied as diagnostic and therapeutic targets. Here, we examine the relationship of IBD to biological clock and gut microbiota by using the IL-10 deficient (IL-10-/-) mouse model for microbiota-dependent spontaneous colitis in combination with altered (4 h/4 h) light/dark cycles to disrupt and time-restricted feeding (TRF) to restore circadian rhythmicity. We show that while altered light/dark cycles disrupted the intestinal clock in wild type (WT) mice, IL-10-/- mice were characterized by altered microbiota composition, impaired intestinal clock, and microbiota rhythmicity irrespective of external clock disruption, which had no consistent colitis-promoting effect on IL-10-/- mice. TRF delayed colitis onset reduced the expression of inflammatory markers and increased the expression of clock genes in the intestine, and increased gut microbiota rhythmicity in IL-10-/- mice. Compositional changes and reduced rhythmicity of the fecal microbiota preceded colitis and could predict colitis symptoms for individual IL-10-/- mice across different experiments. Our findings provide perspectives for new diagnostic and TRF-based, therapeutic applications in IBD that should be further explored.

CEACAM5 exacerbates asthma by inducing ferroptosis and autophagy in airway epithelial cells through the JAK/STAT6-dependent pathway

OBJECTIVES

Asthma, a prevalent chronic disease, poses significant health threats and burdens healthcare systems. This study focused on the role of bronchial epithelial cells in asthma pathophysiology.

METHODS

Bioinformatics was used to identify key asthmarelated genes. An ovalbumin-sensitized mouse model and an IL-13-stimulated Beas-2B cell model were established for further investigation.

RESULTS

Carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5) was identified as a crucial gene in asthma. CEACAM5 expression was elevated in asthmatic mouse lung tissues and IL-13-stimulated Beas-2B cells, primarily in bronchial epithelial cells. CEACAM5 induced reactive oxygen species (ROS), lipid peroxidation, and ferroptosis. Interfering with CEACAM5 reduced ROS, malondialdehyde levels, and enhanced antioxidant capacity, while inhibiting iron accumulation and autophagy. Overexpression of CEACAM5 in IL-13-stimulated cells activated the JAK/STAT6 pathway, which was necessary for CEACAM5-induced autophagy, ROS accumulation, lipid peroxidation, and ferroptosis.

CONCLUSION

CEACAM5 promotes ferroptosis and autophagy in airway epithelial cells via the JAK/STAT6 pathway, exacerbating asthma symptoms. It represents a potential target for clinical treatment.

miR-301a-mediated crosstalk between the Hedgehog and HIPPO/YAP signaling pathways promotes pancreatic cancer

Pancreatic ductal adenocarcinoma (PDAC) poses a significant challenge in oncology due to its dismal prognosis and limited therapeutic options. In this study, we investigated the role of miR-301a in facilitating crosstalk between the Hedgehog (Hh) and HIPPO/YAP signaling pathways during the progression of PDAC. Our findings revealed that miR-301a served as a central regulatory node, targeting Gli1 within the Hh pathway and STK4 within the HIPPO/YAP pathway. Immunohistochemical and molecular analyses confirmed dysregulation of pathway components in pancreatic cancer, underscoring the pivotal role of miR-301a. Functional assays demonstrated the impact of miR-301a on cell proliferation and apoptosis, particularly in synergy with TNF-α. Overall, our study elucidated the intricate interplay between the Hh and HIPPO/YAP pathways mediated by miR-301a, providing valuable insights into potential therapeutic strategies for intervening in PDAC.

Transcriptome-wide study of mRNAs modified by m6A RNA methylation in the testis development of dairy goats

N6-methyladenosine (m6A) is an important epigenetic modification in RNA, playing a crucial role in regulating the production and aging of animal testicular sperm. This study extracted mRNA from the testicular tissue of male goats before and after sexual maturity, generating a methylation map through preliminary experiments and methylation immunoprecipitation sequencing. The results showed that during the development of dairy goats, the expression levels of marker genes related to testicular development and methylation-related enzymes changed significantly. A total of 36,602 peaks and 11,223 genes were identified in the two groups, including 2989 differential peaks (427 upregulated and 2562 downregulated) and 1457 differentially expressed genes (833 upregulated and 624 downregulated). The abundance of m6A was positively correlated with gene expression levels. This study reports for the first time the mRNA profiles of m6A modifications across the entire transcriptome during testicular development in Guanzhong dairy goats, providing a new perspective for genetic improvement in goats.

Fusobacterium nucleatum upregulates the immune inhibitory receptor PD-L1 in colorectal cancer cells via the activation of ALPK1

Fusobacterium nucleatum is a Gram-negative oncobacterium that is associated with colorectal cancer. The molecular mechanisms utilized by F. nucleatum to promote colorectal tumor development have largely focused on adhesin-mediated binding to the tumor tissue and on the pro-inflammatory capacity of F. nucleatum. However, the exact manner in which F. nucleatum promotes inflammation in the tumor microenvironment and subsequent tumor promotion remains underexplored. Here, we show that both living F. nucleatum and sterile F. nucleatum-conditioned medium promote CXCL8 release from the intestinal adenocarcinoma HT-29 cell line. We determined that the observed pro-inflammatory effect was ALPK1-dependent in both HEK293 and HT-29 cells and that the released F. nucleatum molecule had characteristics that match those of the pro-inflammatory ALPK1 ligand ADP-heptose or related heptose phosphates. In addition, we determined that not only F. nucleatum promoted an ALPK1-dependent pro-inflammatory environment but also other Fusobacterium species such as F. varium, F. necrophorum and F. gonidiaformans generated similar effects, indicating that ADP-heptose or related heptose phosphate secretion is a conserved feature of the Fusobacterium genus. By performing transcriptional analysis of ADP-heptose stimulated HT-29 cells, we found several inflammatory and cancer-related pathways to be differentially regulated, including DNA mismatch repair genes and the immune inhibitory receptor PD-L1. Finally, we show that stimulation of HT-29 cells with F. nucleatum resulted in an ALPK1-dependent upregulation of PD-L1. These results aid in our understanding of the mechanisms by which F. nucleatum can affect tumor development and therapy and pave the way for future therapeutic approaches.

Early life gut microbiome and its impact on childhood health and chronic conditions

The development of the gut microbiome is crucial to human health, particularly during the first three years of life. Given its role in immune development, disturbances in the establishment process of the gut microbiome may have long term consequences. This review summarizes evidence for these claims, highlighting compositional changes of the gut microbiome during this critical period of life as well as factors that affect gut microbiome development. Based on human and animal data, we conclude that the early-life microbiome is a determinant of long-term health, impacting physiological, metabolic, and immune processes. The early-life gut microbiome field faces challenges. Some of these challenges are technical, such as lack of standardized stool collection protocols, inconsistent DNA extraction methods, and outdated sequencing technologies. Other challenges are methodological: small sample sizes, lack of longitudinal studies, and poor control of confounding variables. To address these limitations, we advocate for more robust research methodologies to better understand the microbiome's role in health and disease. Improved methods will lead to more reliable microbiome studies and a deeper understanding of its impact on health outcomes.

Nuclear envelope and chromatin choreography direct cellular differentiation

The nuclear envelope plays an indispensable role in the spatiotemporal organization of chromatin and transcriptional regulation during the intricate process of cell differentiation. This review outlines the distinct regulatory networks between nuclear envelope proteins, transcription factors and epigenetic modifications in controlling the expression of cell lineage-specific genes during differentiation. Nuclear lamina with its associated nuclear envelope proteins organize heterochromatin via Lamina-Associated Domains (LADs), proximal to the nuclear periphery. Since nuclear lamina is mechanosensitive, we critically examine the impact of extracellular forces on differentiation outcomes. The nuclear envelope is spanned by nuclear pore complexes which, in addition to their central role in transport, are associated with chromatin organization. Furthermore, mutations in the nuclear envelope proteins disrupt differentiation, resulting in developmental disorders. Investigating the underlying nuclear envelope controlled regulatory mechanisms of chromatin remodelling during lineage commitment will accelerate our fundamental understanding of developmental biology and regenerative medicine.

Mini-review on the therapeutic vaccines targeting chronic infectious diseases: Evaluation system of therapeutic vaccines targeting HPV and EBV-related cancers

Chronic infectious diseases are threatening human health today, and their public health severity is increasing. The efficacy issues of drugs and the increase in drug-resistant pathogens require new response strategies for chronic infectious diseases, and therapeutic vaccines have recently been proposed as an effective alternative. However, research on therapeutic vaccines is still relatively underdeveloped. To solve this problem, an accurate understanding of the status and the challenge at hand of therapeutic vaccines targeting chronic infectious diseases is needed. In the present review, we provide an overview of the latest research trends in therapeutic vaccines targeting chronic infectious diseases and summarize the development status of therapeutic vaccines currently undergoing clinical research, focusing on the cases of human papillomavirus (HPV) and Epstein-Barr virus (EBV) as representative examples. We highlight the importance of standard methods for the evaluation of therapeutic vaccine, focusing on the cell-mediated immune response, which might accelerate therapeutic vaccine development.

Serum metabolomic characteristics of COVID-19 patients co-infection with echovirus

Currently, the Omicron variant of the Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate globally. In our multiplex respiratory pathogen detection, we identified numerous instances of co-infection with Echovirus (ECHO) among Coronavirus Disease 2019 (COVID-19) patients, which exacerbated the clinical symptoms of these patients. Such co-infections are likely to impact the subsequent medical treatment. To date, there are no reports on the pathogenic mechanisms related to COVID-19 co-infected with ECHO. Therefore, this study employed the TM Widely-Targeted metabolomics approach to analyze the serum metabolomes of COVID-19 patients with single SARS-CoV-2 infection (COVID-19), COVID-19 patients co-infected with ECHO (COVID-19  +  ECHO), and healthy individuals (Control) recruited from routine physical examinations during the same period. Concurrent clinical laboratory tests were performed on the patients to reveal the differences in metabolomic characteristics between the COVID-19 patients and the COVID-19  +  ECHO patients, as well as to explore potential metabolic pathways that may exacerbate disease progression. Our findings indicate that both clinical examination indicators and the pathways enriched by differential metabolites confirm that patients with dual infection exhibit higher inflammatory and immune responses compared to those with single COVID-19 infections. This difference is likely reflected through abnormalities in the glycerophospholipid metabolic pathway, with the metabolite Sn-Glycero-3-Phosphocholine playing a crucial role in this process. Finally, we established a diagnostic model based on logistic regression using five differential metabolites, which accurately differentiates between the dual infection population and the single COVID-19 infection population (AUC = 0.828).

Porcine cGAS-STING signalling induced apoptosis negatively regulates STING downstream IFN response and autophagy via different mechanisms

The innate immune cGAS-STING signalling pathway recognizes double-stranded DNA and induces the interferon (IFN) response, autophagy and apoptosis, exerting a broad antiviral effect. However, the mechanisms and interrelationship between STING induced downstream IFN, autophagy, and apoptosis in livestock have not been fully elucidated. Our previous study defined porcine STING (pSTING) induced IFN, autophagy and apoptosis, and showed that IFN does not affect autophagy and apoptosis, whereas autophagy inhibits both IFN and apoptosis, likely by promoting pSTING degradation. In this study, we further explored the underlying mechanism of pSTING induced apoptosis and the regulation of IFN and autophagy by apoptosis. First, pSTING induces endoplasmic reticulum (ER) stress and mitochondrial damage to activate caspases 9, 3, and 7, which drive intrinsic apoptosis. Second, pSTING triggered apoptosis inhibits the IFN response by activating caspase 7, which cleaves pIRF3 at the species specific D197/D198 site. Third, pSTING activated apoptotic caspases 9, 3, and 7 reduce the expression of ATG proteins, and cleave the ATG5-ATG12L1 complex, effectively inhibiting autophagy. Fourth, knockout of pSTING activated apoptosis heightens the IFN response and autophagy, while suppressing the replication of Herpes Simplex Virus type 1 (HSV-1), Vesicular Stomatitis Virus (VSV) and Pseudorabies Virus (PRV). This study sheds light on the molecular mechanisms of innate immunity in pigs.

The molybdate transport protein ModA regulates nitrate reductase activity to increase the intestinal colonization and extraintestinal dissemination of Klebsiella pneumoniae in the inflamed gut

The mammalian intestine is a major site of colonization and a starting point of severe infections by Klebsiella pneumoniae. Inflammatory bowel disease (IBD) is an inflammatory disorder of the gut, and host-derived nitrate in IBD confers a luminal growth advantage upon Escherichia coli and Salmonella typhimurium through nitrate respiration in the inflamed gut. However, the impact of nitrate on the growth and pathogenicity of K. pneumoniae in this microenvironment is poorly understood. In this study, we used oral administration of dextran sodium sulphate to induce IBD in mouse models. We then analysed the colonization levels of K. pneumoniae wild-type (WT), the nitrate reductase gene mutant strains (ΔnarG, ΔnarZ and ΔnarGΔnarZ), and the molybdate uptake gene mutant strain (ΔmodA) in the inflamed intestinal tract. Results showed that the growth, intestinal colonization, and extraintestinal dissemination of K. pneumoniae were increased in the intestines of dextran sulphate sodium (DSS)-treated mice. Nitrate in the inflamed bowel conferred a growth advantage to K. pneumoniae through nitrate respiration. The molybdate transport protein ModA regulated nitrate reductase activity to increase the growth, intestinal colonization, and extraintestinal dissemination of K. pneumoniae. Tungstate will be a promising antibacterial agent to tackle K. pneumoniae infections in IBD patients.

Natural product as a lead for impairing mitochondrial respiration in cancer cells

The impact of the isoxazole derivative of usnic acid, ISOXUS (formerly known as 2b) on cancer and non-cancerous cell metabolism was investigated. ISOXUS significantly reduced the utilisation of most metabolic substrates that produce NADH or FADH2, mitochondrial electron flow and oxygen consumption rate (OCR) in MCF-7 breast cancer cells in contrast to HB2 normal epithelial cells. Molecular docking revealed that ISOXUS inhibits mitochondrial respiratory chain complex II, which was confirmed experimentally. Disturbance of electron flow in MCF-7 cells resulted in increased reactive oxygen species (ROS) production. They appeared crucial for ISOXUS-induced cancer cell vacuolization and a drop in survival as an antioxidant, α-tocopherol, protected against these processes. These findings indicate that ISOXUS is a metabolic inhibitor that targets mitochondrial complex II in breast cancer cells resulting in diminished ATP production and increased ROS formation which translates into reduced cell viability.

MERTK inhibition improves therapeutic efficacy of immune checkpoint inhibitors in hepatocellular carcinoma

Immunotherapy with immune checkpoint inhibitors (ICI) in hepatocellular carcinoma (HCC) patients only achieves response rates of 25%-30%, indicating the necessity of new therapies for non-responder patients. Since myeloid-related suppressive factors are associated with poor responses to ICI in a subgroup of HCC patients, modulation of these targets may improve response rates. Our aim was to characterize the expression of the efferocytosis receptor MERTK in HCC and to analyze its potential as a new therapeutic target. In HCC patients, MERTK was expressed by myeloid cells and was associated with poorer survival. In a murine HCC model with progressive myeloid cell infiltration, MERTK was detected in dendritic cells and macrophages with an activated phenotype, which overexpressed the checkpoint ligand PD-L1. Concomitant expression of PD-1 in tumor T-cells suggested the pertinence of combined PD-1/PD-L1 and MERTK blockade. In vivo experiments in mice showed that inhibition of MERTK improved the therapeutic effect promoted by anti-PD-1 or by ICI combinations currently approved for HCC. This effect was associated with enhanced tumor infiltration and superior activity of antigen presenting cells and effector lymphocytes. Our results indicate that MERTK may behave as a relevant target for immunotherapeutic combinations in those HCC patients with tumors enriched in a myeloid component.

Study on the mechanism of Xanthoceras sorbifolia Bunge oil in the treatment of Alzheimer's disease by an integrated "network pharmacology-metabolomics" strategy

BACKGROUND

Xanthoceras sorbifolia Bunge oil (XSBO) has garnered significant interest from researchers due to its distinctive anti-Alzheimer's disease (AD) properties. However, the underlying molecular mechanism remain unclear. This study aims to investigate the potential mechanisms by which XSBO may exert therapeutic effects on AD by employing a combination of network pharmacology analysis and experimental validation.

METHODS

The chemical composition and absorbed compounds of XSBO were identified using GC-MS and LC-MS. Network pharmacology analysis was performed using various computational tools to identify hub genes and construct compound-target-pathway networks. Subsequently, both in vitro and in vivo experiments were conducted to confirm the mechanisms by which XSBO may treat AD.

RESULTS

The results identified 43 active compounds in XSBO, targeting a total of 223 genes, of which 191 were associated with AD. Network analysis indicated that the active constituents in XSBO, such as 9,12-octadecadienoic acid, linoelaidic acid and 11-octadecenoic acid, interact with targets including MAPK1, MAPK3, AKT1, RXRA, RXRB, PPARD and PPARA to modulate inflammation-related signalling pathways and the sphingolipid signalling pathway. In vitro investigations corroborated that XSBO can significantly influence the viability of Aβ25-35-induced SH-SY5Y cells via the MAPK pathway.

CONCLUSIONS

This study demonstrated that XSBO has the potential to mitigate inflammation network disorders through the MAPK pathway and to restore sphingolipid metabolite levels in AD rats, thereby laying a groundwork for future studies.

A small RNA from Streptococcus suis epidemic ST7 strain promotes bacterial survival in host blood and brain by enhancing oxidative stress resistance

Streptococcus suis is a Gram-positive pathogen causing septicaemia and meningitis in pigs and humans. However, how S. suis maintains a high bacterial load in the blood and brain is poorly understood. In this study, we found that a small RNA rss03 is predominantly present in S. suis, Streptococcus parasuis, and Streptococcus ruminantium, implying a conserved biological function. rss03 with a size of 303 nt mainly exists in S. suis sequence type (ST) 1 and epidemic ST7 strains that are responsible for human infections in China. Using MS2-affinity purification coupled with RNA sequencing (MAPS), proteomics analysis, and CopraRNA prediction, 14 direct targets of rss03 from an ST7 strain were identified. These direct targets mainly involve substance transport, transcriptional regulation, rRNA modification, and stress response. A more detailed analysis reveals that rss03 interacts with the coding region of glpF mRNA, and unexpectedly rss03 protects glpF mRNA from degradation by RNase J1. The GlpF protein is an aquaporin, contributes to S. suis oxidative stress resistance by H2O2 efflux, and facilitates bacterial survival in murine macrophages RAW264.7. Finally, we showed that rss03 and GlpF are required to maintain a high bacterial load in mouse blood and brain. Our study presents the first sRNA targetome in streptococci, enriches the knowledge of sRNA regulation in streptococci, and identifies pathways contributing to S. suis pathogenesis.

A face-off between Smaug and Caspar modulates primordial germ cell count and identity in Drosophila embryos

Proper formation and specification of Primordial Germ Cells (PGCs) is of special significance as they gradually transform into Germline Stem Cells (GSCs) that are ultimately responsible for generating the gametes. Intriguingly, not only the PGCs constitute the only immortal cell type but several specific determinants also underlying PGC specification such as Vasa, Nanos and Germ-cell-less are conserved through evolution. In Drosophila melanogaster, PGC formation and specification depends on two independent factors, the maternally deposited specialized cytoplasm (or germ plasm) enriched in germline determinants, and the mechanisms that execute the even partitioning of these determinants between the daughter cells. Prior work has shown that Oskar protein is necessary and sufficient to assemble the functional germ plasm, whereas centrosomes associated with the nuclei that invade the germ plasm are responsible for its equitable distribution. Our recent data suggests that Caspar, the Drosophila orthologue of human Fas-associated factor-1 (FAF1) is a novel regulator that modulates both mechanisms that underlie the determination of PGC fate. Consistently, early blastoderm embryos derived from females compromised for caspar display reduced levels of Oskar and defective centrosomes.

Flavonoids from Polypodium hastatum as neuroprotective agents attenuate cerebral ischemia/reperfusion injury in vitro and in vivo via activating Nrf2

OBJECTIVES

Cerebral ischemic stroke is a leading cause of death worldwide. Though timely reperfusion reduces the infarction size, it exacerbates neuronal apoptosis due to oxidative stress. Nuclear factor erythroid 2-related factor 2 (Nrf2) is a transcription factor regulating the expression of antioxidant enzymes. Activating Nrf2 gives a therapeutic approach to ischemic stroke.

METHODS

Herein we explored flavonoids identified from Polypodium hastatum as Nrf2 activators and their protective effects on PC12 cells injured by oxygen and glucose deprivation/restoration (OGD/R) as well as middle cerebral artery occlusion (MCAO) mice.

RESULTS

The results showed among these flavonoids, AAKR significantly improved the survival of PC12 cells induced by OGD/R and activated Nrf2 in a Keap1-dependent manner. Further investigations have disclosed AAKR attenuated oxidative stress, mitochondrial dysfunction and following apoptosis resulting from OGD/R. Meanwhile, activation of Nrf2 by AAKR was involved in the protective effects. Finally, it was found that AAKR could protect MCAO mice brains against ischemia/reperfusion injury via activating Nrf2.

DISCUSSION

This investigation could provide lead compounds for the discovery of novel Nrf2 activators targeting ischemia/reperfusion injury.

DEELE-Rad: exploiting deep radiomics features in deep learning models using COVID-19 chest X-ray images

Purpose

Deep learning-based radiomics techniques have the potential to aid specialists and physicians in performing decision-making in COVID-19 scenarios. Specifically, a Deep Learning (DL) ensemble model is employed to classify medical images when addressing the diagnosis during the classification tasks for COVID-19 using chest X-ray images. It also provides feasible and reliable visual explicability concerning the results to support decision-making.

Methods

Our DEELE-Rad approach integrates DL and Machine Learning (ML) techniques. We use deep learning models to extract deep radiomics features and evaluate its performance regarding end-to-end classifiers. We avoid successive radiomics approach steps by employing these models with transfer learning techniques from ImageNet, such as VGG16, ResNet50V2, and DenseNet201 architectures. We extract 100 and 500 deep radiomics features from each DL model. We also placed these features into well-established ML classifiers and applied automatic parameter tuning and a cross-validation strategy. Besides, we exploit insights into the decision-making behavior by applying a visual explanation method.

Results

Experimental evaluation on our proposed approach achieved 89.97% AUC when using 500 deep radiomics features from the DenseNet201 end-to-end classifier. Besides, our ensemble DEELE-Rad method improves the results up to 96.19% AUC for the 500 dimensions. To outperform, ML DEELE-Rad reached the best results with an Accuracy of 98.39% and 99.19% AUC for the same setup. Our visual assessment employs additional possibilities for specialists and physicians to decision-making.

Conclusion

The results reflect that the DEELE-Rad approach provides robustness and confidence to the images' analysis. Our approach can benefit healthcare specialists when employed at clinical routines and respective decision-making procedures. For reproducibility, our code is available at https://github.com/usmarcv/deele-rad.

Emerging West African Genotype Chikungunya Virus in Mosquito Virome

We studied the viromes of three dominant mosquito species in Wenzhou, a coastal city in Zhejiang Province, using metavirome sequencing, with 18 viral families identified. Viral sequences were verified by RT-PCR. The JEV E gene was most closely related to the 1988 Korean strain. DENV sequences were most closely related to the 1997 Australian strain. CHIKV-E1-1 was most closely related to the 1983 Senegal strain and belonged to West African genotype CHIKV. Remarkably, this is the first time that a West African genotype of CHIKV has been detected in Zhejiang Province. Mutations in the CHIKV-E1-1 protein A226V may increase infectivity in Ae. albopictus. Three non-conservative mutations of CHIKV-E1-1 (D45H, D70H and V290D) may have an impact on the function. In conclusion, our study reveals the diversity of mosquito-borne viruses and potential emerging outbreaks in the southeast coastal region of China, providing new perspectives for mining the ecological characterization of other important arboviruses.

Prediction of protein biophysical traits from limited data: a case study on nanobody thermostability through NanoMelt

In-silico prediction of protein biophysical traits is often hindered by the limited availability of experimental data and their heterogeneity. Training on limited data can lead to overfitting and poor generalizability to sequences distant from those in the training set. Additionally, inadequate use of scarce and disparate data can introduce biases during evaluation, leading to unreliable model performances being reported. Here, we present a comprehensive study exploring various approaches for protein fitness prediction from limited data, leveraging pre-trained embeddings, repeated stratified nested cross-validation, and ensemble learning to ensure an unbiased assessment of the performances. We applied our framework to introduce NanoMelt, a predictor of nanobody thermostability trained with a dataset of 640 measurements of apparent melting temperature, obtained by integrating data from the literature with 129 new measurements from this study. We find that an ensemble model stacking multiple regression using diverse sequence embeddings achieves state-of-the-art accuracy in predicting nanobody thermostability. We further demonstrate NanoMelt's potential to streamline nanobody development by guiding the selection of highly stable nanobodies. We make the curated dataset of nanobody thermostability freely available and NanoMelt accessible as a downloadable software and webserver.

Rotenone inhibited osteosarcoma metastasis by modulating ZO-2 expression and location via the ROS/Ca2+/AMPK pathway

BACKGROUND

Pulmonary metastases in osteosarcoma (OS) are associated with a poor prognosis. Rotenone has shown anti-cancer activity. However, its effects on metastasis and the underlying mechanisms remain unknown. This study investigated the potential use of Rotenone for OS treatment.

METHODS

The effect of Rotenone and ROS/Ca2+/AMPK/ZO-2 pathway on metastasis and EMT was evaluated by Western blot, Transwell and Wound healing. Flow cytometer was employed to measure the intracellular Ros and Ca2+ levels. The subcellular location of ZO-2 was detected by IF, interaction between AMPK and ZO-2 were examined by Co-IP. Then, subcutaneous tumor and metastasis models were used to evaluate the function of Rotenone in OS metastasis.

RESULTS

Rotenone-induced ROS led to increased intracellular Ca2+, which promoted the EMT of OS cells through activation of AMPK and ZO-2 nuclear translocation. Inhibition of ROS production decreased intracellular Ca2+, restraining AMPK activity. Knock-down of ZO-2 significantly suppressed the anti-metastasis effects of Rotenone in OS cells. Moreover, Rotenone elevated p-AMPK and ZO-2 expression but inhibited EMT and lung metastasis in vivo.Conclusion These results provide evidence supporting an anti-metastatic effect of Rotenone. These findings support the use of Rotenone in the prevention of OS metastasis.

Individual responses to encapsulated caffeine and caffeine chewing gum on strength and power in strength-trained males

BACKGROUND

Liquid-dissolved and encapsulated powder are two popular ways to consume caffeine for performance-enhancing effects. Caffeine in other delivery methods, such as chewing gums, orally dissolvable strips, gels, mouthwashes, energy drinks, and nasal sprays, is believed to be absorbed more quickly into the bloodstream. Inter-individual responses to caffeine's enhancing effects are recognized. The present study examined the inter-individual responses to the acute effects of encapsulated caffeine and caffeinated chewing gum on the lower-body isokinetic and isometric strength and power in strength-trained males.

METHOD

A randomized, cross-over, placebo-controlled study was conducted with 15 strength-trained males (age: 25  ±  4 years, height: 176  ±  7 cm, weight: 75  ±  11 kg, habitual caffeine intake: 66  ±  15 mg·day-1). Participants were randomly assigned to three conditions: i) caffeinated chewing gum (CG), ii) caffeine capsule (CC), and iii) starch capsule as a placebo (PLA). Participants consumed approximately 3 to 4.5 mg·kg-1 of caffeine 60 minutes before testing. The washout period between conditions was one week. Participants performed the Sargent jump test, followed by a 5-minute active recovery (walking). Subsequently, isokinetic strength and power (60°/s and 180°/s) and isometric strength (45° and 60°) parameters were measured for knee extensor and flexor muscles. Data were analyzed using one-way repeated measures ANOVA and Bonferroni post hoc tests, with significance set at p ≤ 0.05. Responders to the caffeine conditions were identified using the smallest worthwhile change (SWC) analysis.

RESULTS

In knee extensors, 1) average peak torque and power at 60°/s were higher in CC (p = 0.045; + 11.2% and p = 0.038; + 14.1%) and CG (p = 0.044; + 7.3% and p = 0.015; + 11.4%) compared to PLA with a co-response rate of 60% and 66%, 2) maximum voluntary isometric contraction at 45° (MVIC-45°) was higher in CC compared to PLA (p = 0.031; + 10.1%), and 3) MVIC-60° was higher in CG compared to PLA (p = 0.037; + 10.1%) with a co-response rate of 60%. In knee flexors, 1) time to peak torque at 60°/s was higher in CG compared to PLA (p = 0.011; + 18.2%) with a co-response rate of 46%, 2) average rate of force development at 60°/s was higher in CC (p = 0.007; + 24.1%) and CG (p = 0.050; + 20.6%) compared to PLA with a co-response rate of 53%, and 3) average power at 180°/s was higher in CC compared to PLA (p = 0.033; + 18%) with a co-response rate of 46%. However, there were no differences between other strength indicators in the knee extensors and flexors between the different conditions. Vertical jump height (VJH) was higher in CC (p = 0.001; + 5.5%) and CG (p = 0.001; + 6.) compared to PLA, with a co-response rate of 53%.

CONCLUSION

Caffeine supplementation in CC and CG forms significantly enhanced lower-body strength, power, and vertical jump height in strength-trained males, with over  ~50% of participants exceeding the SWC thresholds across key performance metrics. CC showed slightly higher responder rates for strength parameters, while CG excelled in time-dependent measures, supporting their use as effective and flexible ergogenic aids.

Release and degradation of dissolved environmental RNAs from zebrafish cells

The sources and degradation profiles of dissolved environmental RNAs from fish in water remain unknown. In this study, laboratory experiments and mathematical modelling were conducted to investigate the permeability of RNA extracted from zebrafish cells through filters, the release of dissolved environmental RNAs from live and dying zebrafish cells, and the degradation of RNA extracted from zebrafish cells in a non-sterile aqueous environment. This research aimed to provide biological and ecological insights into fish RNAs dissolved in water. The results showed that most of the RNA extracted from zebrafish cells was detected in the filtrates after passage through 0.45 µm filters. Over the course of the 6-day experiment, dynamic levels of the RNAs in the liquid environment containing live or dying zebrafish cells were determined. The release and degradation rates of dissolved environmental RNA from zebrafish cells were calculated using mathematical modelling. RNA extracted from zebrafish cells degraded in non-sterile water in the tubes, and after 2 months, more than 15% of the RNAs in the water remained detectable. The half-life of the RNA in the tubes was approximately 20 ~ 43 days. The modelling results suggest that the levels of the dissolved environmental fish RNAs in natural waters or aquariums could be so low that it would be difficult to detect them using current techniques. The results obtained in this study will help develop new methods for measuring the dynamics of dissolved environmental fish RNAs in water and determining their significance.

Identification of host genetic factors modulating β-lactam resistance in Escherichia coli harbouring plasmid-borne β-lactamase through transposon-sequencing

Since β-lactam antibiotics are widely used, emergence of bacteria with resistance to them poses a significant threat to society. In particular, acquisition of genes encoding β-lactamase, an enzyme that degrades β-lactam antibiotics, has been a major contributing factor in the emergence of bacteria that are resistant to β-lactam antibiotics. However, relatively few genetic targets for killing these resistant bacteria have been identified to date. Here, we used a systematic approach called transposon-sequencing (Tn-Seq), to screen the Escherichia coli genome for host genetic factors that, when mutated, affect resistance to ampicillin, one of the β-lactam antibiotics, in a strain carrying a plasmid that encodes β-lactamase. This approach enabled not just the isolation of genes previously known to affect β-lactam resistance, but the additional loci skp, gshA, phoPQ and ypfN. Individual mutations in these genes modestly but consistently affected antibiotic resistance. We have identified that these genes are not only implicated in β-lactam resistance by itself but also play a crucial role in conditions associated with the expression of β-lactamase. GshA and phoPQ appear to contribute to β-lactam resistance by regulating membrane integrity. Notably, the overexpression of the uncharacterized membrane-associated protein, ypfN, has been shown to significantly enhance β-lactam resistance. We applied the genes identified from the screening into Salmonella Typhimurium and Pseudomonas aeruginosa strains, both critical human pathogens with antibiotic resistance, and observed their significant impact on β-lactam resistance. Therefore, these genes can potentially be utilized as therapeutic targets to control the survival of β-lactamase-producing bacteria.

Role of gut microbiome in suppression of cancers

The pathogenesis of cancer is closely related to the disruption of homeostasis in the human body. The gut microbiome plays crucial roles in maintaining the homeostasis of its host throughout lifespan. In recent years, a large number of studies have shown that dysbiosis of the gut microbiome is involved in the entire process of cancer initiation, development, and prognosis by influencing the host immune system and metabolism. Some specific intestinal bacteria promote the occurrence and development of cancers under certain conditions. Conversely, some other specific intestinal bacteria suppress the oncogenesis and progression of cancers, including inhibiting the occurrence of cancers, delaying the progression of cancers and boosting the therapeutic effect on cancers. The promoting effects of the gut microbiome on cancers have been comprehensively discussed in the previous review. This article will review the latest advances in the roles and mechanisms of gut microbiome in cancer suppression, providing a new perspective for developing strategies of cancer prevention and treatment.

Evolution of the RNA alternative decay cis element into a high-affinity target for the immunomodulatory protein Roquin

RNA cis elements play pivotal roles in regulatory processes, e.g. in transcriptional and translational regulation. Two stem-looped cis elements, the constitutive and alternative decay elements (CDE and ADE, respectively) are shape-specifically recognized in mRNA 3' untranslated regions (UTRs) by the immune-regulatory protein Roquin. Roquin initiates mRNA decay and contributes to balanced transcript levels required for immune homoeostasis. While the interaction of Roquin with several CDEs is described, our knowledge about ADE complex formation is limited to the mRNA of Ox40, a gene encoding a T-cell costimulatory receptor. The Ox40 3'UTR comprises both a CDE and ADE, each sufficient for Roquin-mediated control. Opposed to highly conserved and abundant CDE structures, ADEs are rarer, but predicted to exhibit a greater structural heterogeneity. This raises the question of how and when two structurally distinct cis elements evolved as equal target motifs for Roquin. Using an interdisciplinary approach, we here monitor the evolution of sequence and structure features of the Ox40 ADE across species. We designed RNA variants to probe en-detail determinants steering Roquin-RNA complex formation. Specifically, those reveal the contribution of a second RNA-binding interface of Roquin for recognition of the ADE basal stem region. In sum, our study sheds light on how the conserved Roquin protein selected ADE-specific structural features to evolve a second high-affinity mRNA target cis element relevant for adaptive immune regulation. As our findings also allow expanding the RNA target spectrum of Roquin, the approach can serve a paradigm for understanding RNA-protein specificity through back-tracing the evolution of the RNA element.

A translational review of hyperthermia biology

This review was written to be included in the Special Collection 'Therapy Ultrasound: Medicine's Swiss Army Knife?' The purpose of this review is to provide basic presentation and interpretation of the fundamentals of hyperthermia biology, as it pertains to uses of therapeutic ultrasound. The fundamentals are presented but in the setting of a translational interpretation and a view toward the future. Subjects that require future research and development are highlighted. The effects of hyperthermia are time and temperature dependent. Because intra-tumoral temperatures are non-uniform in tumors, one has to account for differential biologic effects in different parts of a tumor that occur simultaneously during and after hyperthermia.

The haemagglutinin gene of bovine-origin H5N1 influenza viruses currently retains receptor-binding and pH-fusion characteristics of avian host phenotype

Clade 2.3.4.4b H5N1 high pathogenicity avian influenza virus (HPAIV) has caused a panzootic affecting all continents except Australia, expanding its host range to several mammalian species. In March 2024, H5N1 HPAIV was first detected in dairy cattle and goats in the United States. Over 891 dairy farms across 16 states have tested positive until 25 December 2024, with zoonotic infections reported among dairy workers. This raises concerns about the virus undergoing evolutionary changes in cattle that could enhance its zoonotic potential. The Influenza glycoprotein haemagglutinin (HA) facilitates entry into host cells through receptor binding and pH-induced fusion with cellular membranes. Adaptive changes in HA modulate virus-host cell interactions. This study compared the HA genes of cattle and goat H5N1 viruses with the dominant avian-origin clade 2.3.4.4b H5N1 in the United Kingdom, focusing on receptor binding, pH fusion, and thermostability. All the tested H5N1 viruses showed binding exclusively to avian-like receptors, with a pH fusion of 5.9, outside the pH range associated with efficient human airborne transmissibility (pH 5.0-5.5). We further investigated the impact of emerging HA substitutions seen in the ongoing cattle outbreaks, but saw little phenotypic difference, with continued exclusive binding to avian-like receptor analogues and pHs of fusion above 5.8. This suggests that the HA genes from the cattle and goat outbreaks do not pose an enhanced threat compared to circulating avian viruses. However, given the rapid evolution of H5 viruses, continuous monitoring and updated risk assessments remain essential to understanding virus zoonotic and pandemic risks.

Revealing the role of natural killer cells in ankylosing spondylitis: identifying diagnostic biomarkers and therapeutic targets

BACKGROUND

Ankylosing spondylitis (AS) is a chronic autoimmune disease that primarily affects the axial joints. Immune cells play a key role in the pathogenesis of AS. This study integrated bioinformatics methods with experimental validation to explore the role of natural killer (NK) cells in AS.

METHODS

Two microarray datasets, GSE25101 and GSE73754, were selected, and the scRNA-seq data were obtained from GSE194315 and Liu's research. Differentially expressed genes (DEGs) and functional enrichment analysis were performed respectively. Weighted gene co-expression network analysis (WGCNA) was conducted to identify key modules of co-expressed genes and genes involved in NK cell function. The diagnostic value of the identified key genes was evaluated using ROC curves, logistic regression analysis, and a nomogram. Real-time PCR (RT-PCR) was used to quantified the expression of genes. Statistical analysis was conducted using the R software package, and a p-value of less than 0.05 was considered statistically significant.

RESULTS

Pathways enrichment analysis revealed the involvement of NK cell-mediated immune pathways and regulation of the innate immune response, indicating the crucial role of innate immunity, especially NK cells, in AS pathogenesis. The construction of a co-expression network revealed that the MElightyellow module was most relevant to the NK cell-mediated immune pathway. IL2RB, CD247, PLEKHF1, EOMES, S1PR5, FGFBP2 from the MElightyellow module were identified as key genes involved in NK cell-mediated immune response and served as potential diagnostic biomarkers for AS, with moderate to high diagnostic values based on AUC values. Further analysis using scRNA-seq profiling revealed the higher expression level of IL2RB, CD247, PLEKHF1, S1PR5, FGFBP2 in NK cells compared to that in other cell types. CD247, PLEKHF1, EOMES, S1PR5, and FGFBP2 were reduced expressed in AS patients as compare to control group verified by scRNA-seq data, CD247, EOMES, FGFBP2, IL2RB and S1PR5 were reduced expressed verified by RT-PCR, and PLEKHF1, S1PR5, and FGFBP2 was upregulated after TNF-α blocker therapy.

CONCLUSION

The study revealed the potential role of NK cells and identified IL2RB, CD247, PLEKHF1, EOMES, S1PR5, and FGFBP2 as key genes associated with NK cells in the pathogenesis of AS.

Effect of extracellular vesicle ZNF280B derived from lung cancer stem cells on lung cancer progression

OBJECTIVE

The purpose of this research was to investigate the role of extracellular vesicles derived from lung cancer stem cells (lung CSCs-EVs) in lung cancer and to explore their potential mechanisms.

METHODS

Lung CSCs were first isolated and verified using flow cytometry and RT-qPCR assays. Lung CSCs-EVs were extracted through ultracentrifugation and further characterized using transmission electron microscopy and Western blotting. The interaction between lung CSCs-EVs and lung cancer cells was observed through PKH67 staining. Subsequently, we analyzed the differentially expressed genes in lung CSCs using bioinformatics data analysis and evaluated the prognostic value of ZNF280B in lung cancer with the Kaplan-Meier Plotter. RT-qPCR was utilized to assess the mRNA expression levels of these genes, while Western blotting was used to evaluate the protein expression levels of ZNF280B and P53. Next, CCK-8 and colony formation assays were conducted to assess the effects of lung CSCs-EVs and ZNF280B on cancer cell proliferation, migration (via wound healing assay), and invasion (using transwell assay). Additionally, subcutaneous tumor-bearing experiments in nude mice were performed to evaluate the roles of lung CSCs-EVs in lung cancer progression in vivo.

RESULTS

The results indicated that lung CSCs-EVs accelerated the progression of lung cancer. Mechanistically, these lung CSCs-EVs transferred ZNF280B into cancer cells, leading to the inhibition of P53 expression.

CONCLUSIONS

In summary, the manuscript first describes the molecular mechanism by which lung CSCs-EVs promote pro-cancer functions in lung cancer through the ZNF280B/P53 axis.

From chaos to order: optimizing fecal microbiota transplantation for enhanced immune checkpoint inhibitors efficacy

The integration of fecal microbiota transplantation (FMT) with immune checkpoint inhibitors (ICIs) presents a promising approach for enhancing cancer treatment efficacy and overcoming therapeutic resistance. This review critically examines the controversial effects of FMT on ICIs outcomes and elucidates the underlying mechanisms. We investigate how FMT modulates gut microbiota composition, microbial metabolite profiles, and the tumor microenvironment, thereby influencing ICIs effectiveness. Key factors influencing FMT efficacy, including donor selection criteria, recipient characteristics, and administration protocols, are comprehensively discussed. The review delineates strategies for optimizing FMT formulations and systematically monitoring post-transplant microbiome dynamics. Through a comprehensive synthesis of evidence from clinical trials and preclinical studies, we elucidate the potential benefits and challenges of combining FMT with ICIs across diverse cancer types. While some studies report improved outcomes, others indicate no benefit or potential adverse effects, emphasizing the complexity of host-microbiome interactions in cancer immunotherapy. We outline critical research directions, encompassing the need for large-scale, multi-center randomized controlled trials, in-depth microbial ecology studies, and the integration of multi-omics approaches with artificial intelligence. Regulatory and ethical challenges are critically addressed, underscoring the imperative for standardized protocols and rigorous long-term safety assessments. This comprehensive review seeks to guide future research endeavors and clinical applications of FMT-ICIs combination therapy, with the potential to improve cancer patient outcomes while ensuring both safety and efficacy. As this rapidly evolving field advances, maintaining a judicious balance between openness to innovation and cautious scrutiny is crucial for realizing the full potential of microbiome modulation in cancer immunotherapy.

Nuclear envelope components in vascular mechanotransduction: emerging roles in vascular health and disease

The vascular network, uniquely sensitive to mechanical changes, translates biophysical forces into biochemical signals for vessel function. This process relies on the cell's architectural integrity, enabling uniform responses to physical stimuli. Recently, the nuclear envelope (NE) has emerged as a key regulator of vascular cell function. Studies implicate nucleoskeletal elements (e.g. nuclear lamina) and the linker of nucleoskeleton and cytoskeleton (LINC) complex in force transmission, emphasizing nucleo-cytoskeletal communication in mechanotransduction. The nuclear pore complex (NPC) and its component proteins (i.e. nucleoporins) also play roles in cardiovascular disease (CVD) progression. We herein summarize evidence on the roles of nuclear lamina proteins, LINC complex members, and nucleoporins in endothelial and vascular cell mechanotransduction. Numerous studies attribute NE components in cytoskeletal-related cellular behaviors to insinuate dysregulation of nucleocytoskeletal feedback and nucleocytoplasmic transport as a mechanism of endothelial and vascular dysfunction, and hence implications for aging and vascular pathophysiology.

PMA1-containing extracellular vesicles of Candida albicans triggers immune responses and colitis progression

Candida albicans (C. albicans) exhibits aberrant changes in patients with colitis, and it has been reported to dominate the colonic mucosal immune response. Here, we found that PMA1 expression was significantly increased in C. albicans from patients with IBD compared to that in healthy controls. A Crispr-Cas9-based fungal strain editing system was then used to knock out PMA1 expression in C. albicans. Compared to WT-C.a, ΔPMA1-C.a could not aggravate colitis. Proteomic analysis showed that PMA1 was transported by extracellular vesicles (EVs) of C. albicans. PMA1-containing EVs aggravated colitis, modulated the migration of cDC2 from the lamina propria to mesenteric lymph nodes, and induced TH17 cell differentiation. Moreover, the adaptor protein CARD9 was critical in PMA1-containing EV-induced colitis, and CARD9-deficient DCs did not induce TH17 cell differentiation or IL-17A production. Mechanically, CARD9 combines with the glycolytic protein GAPDH (aa2-146 domain) through its CARD region. CARD9 deficiency led to decreased enzyme activity of GAPDH and decreased glycolysis of DCs. These findings indicate that PMA1 is a potential virulence factor responsible for the pathogenesis of C. albicans colitis.

Opportunities and challenges of immuno-oncology: A bibliometric analysis from 2014 to 2023

The emergence of immuno-oncology (IO) has led to revolutionary changes in the field of cancer treatment. Despite notable advancements in this field, a thorough exploration of its full depth and extent has yet to be performed. This study provides a comprehensive overview of publications pertaining to IO. Publications on IO from 2014 to 2023 were retrieved by searching the Web of Science Core Collection database (WoSCC). VOSviewer software and Citespace software were used for the visualized analysis. A total of 1,874 articles have been published in the IO domain. The number of publications and citations has been increasing annually. This study also examines the primary research directions within the field of IO. In conclusion, this study offers a comprehensive overview of the opportunities and challenges associated with IO, illuminating the current status of research and indicating potential future trajectories in this rapidly progressing field. This study provides a comprehensive survey of the current research status and hot spots within the field of IO. It will assist researchers in comprehending the current research emphasis and development trends in this field and offers guidance for future research directions.

Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection

An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1 but had positive correlations with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effects of ART on virome and cytokine profiles in HIV-1-infected individuals.

Tumor organoids in cancer medicine: from model systems to natural compound screening

CONTEXT

The advent of tissue engineering and biomedical techniques has significantly advanced the development of three-dimensional (3D) cell culture systems, particularly tumor organoids. These self-assembled 3D cell clusters closely replicate the histopathological, genetic, and phenotypic characteristics of primary tissues, making them invaluable tools in cancer research and drug screening.

OBJECTIVE

This review addresses the challenges in developing in vitro models that accurately reflect tumor heterogeneity and explores the application of tumor organoids in cancer research, with a specific focus on the screening of natural products for antitumor therapies.

METHODS

This review synthesizes information from major databases, including Chemical Abstracts, Medicinal and Aromatic Plants Abstracts, ScienceDirect, Google Scholar, Scopus, PubMed and Springer Link. Publications were selected without date restrictions, using terms such as 'organoid', 'natural product', 'pharmacological', 'extract', 'nanomaterial' and 'traditional uses'. Articles related to agriculture, ecology, synthetic work or published in languages other than English were excluded.

RESULTS AND CONCLUSIONS

The review identifies key challenges related to the efficiency and variability of organoid generation and discusses ongoing efforts to enhance their predictive capabilities in drug screening and personalized medicine. Recent studies utilizing patient-derived organoid models for natural compound screening are highlighted, demonstrating the potential of these models in developing new classes of anticancer agents. The integration of natural products with patient-derived organoid models presents a promising approach for discovering novel anticancer compounds and elucidating their mechanisms of action.

TET-mediated 5hmC in breast cancer: mechanism and clinical potential

Breast cancer is the most common cancer among women, with differences in clinical features due to its distinct molecular subtypes. Current studies have demonstrated that epigenetic modifications play a crucial role in regulating the progression of breast cancer. Among these mechanisms, DNA demethylation and its reverse process have been studied extensively for their roles in activating or silencing cancer related gene expression. Specifically, Ten-Eleven Translocation (TET) enzymes are involved in the conversion process from 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which results in a significant difference in the global level of 5hmC in breast cancer compared with normal tissues. In this review, we summarize the functions of TET proteins and the regulated 5hmC levels in the pathogenesis of breast cancer. Discussions on the clinical values of 5hmC in early diagnosis and the prediction of prognosis are also mentioned.

Effects of Hsa-miR-4741/LILRB2 on Senescence of Nucleus Pulposus Cells and Their Prognostic Values in Lumbar Disc Herniation

BACKGROUND

The incidence of lumbar disk herniation (LDH) is usually caused by lumbar disk degeneration. Surgery is a common treatment strategy for LDH, but it can recur, resulting in recurrent disk herniation (RDH).

PURPOSE

To explore the predictive value of hsa-miR-4741 and LILRB2 in the prognosis of LDH surgery and the mechanism of nucleus pulposus senescence.

METHOD

The ROC curves of RDH based on hsa-miR-4741 and LILRB2 were constructed to evaluate their predictive values in the prognosis of LDH surgery. Human nucleus pulposus cells (NPC) was treated by TNF-α to construct a cell senescence model, studying the senescence mechanism. Oxidative stress and senescence markers were detected after overexpression of hsa-miR-4741 and LILRB2 to evaluate their effects on the senescence of NPC. Dual luciferase assay and the transfection of hsa-miR-4741 mimics or inhibitor were used to investigate the targeted regulation of it to LILRB2.

RESULTS

The combination of hsa-miR-4741 and LILRB2 showed higher accuracy in predicting the outcome of RDH (AUC = 0.9367), compared with a single molecule. Overexpression of hsa-miR-4741 enhanced TNF-α-induced oxidative stress and senescence, while LILRB2 overexpression had the opposite effect. Hsa-miR-4741 mimics attenuated the luciferase activity of NPC transfected with wt-LILRB2 vector and significantly down-regulated LILRB2 expression. In addition, the antioxidant NAC reversed the promotion of hsa-miR-4741 on NPC senescence.

CONCLUSION

The combination of hsa-miR-4741 and LILRB2 was a good predictor of LDH prognosis. Hsa-miR-4741 promoted oxidative stress-induced NPC senescence by negatively regulating LILRB2.

Biofilm-associated proteins: from the gut biofilms to neurodegeneration

Human microbiota form a biofilm with substantial consequences for health and disease. Numerous studies have indicated that microbial communities produce functional amyloids as part of their biofilm extracellular scaffolds. The overlooked interplay between bacterial amyloids and the host may have detrimental consequences for the host, including neurodegeneration. This work gives an overview of the biofilm-associated amyloids expressed by the gut microbiota and their potential role in neurodegeneration. It discusses the biofilm-associated proteins (BAPs) of the gut microbiota, maps the amyloidogenic domains of these proteins, and analyzes the presence of bap genes within accessory genomes linked with transposable elements. Furthermore, the evidence supporting the existence of amyloids in the gut are presented. Finally, it explores the potential interactions between BAPs and α-synuclein, extending the literature on amyloid cross-kingdom interactions. Based on these findings, this study propose that BAP amyloids act as transmissible catalysts, facilitating the misfolding, accumulation, and spread of α-synuclein aggregates. This review contributes to the understanding of complex interactions among the microbiota, transmissible elements, and host, which is crucial for developing novel therapeutic approaches to combat microbiota-related diseases and improve overall health outcomes.

Lessons for medical countermeasure development from unforeseen outbreaks

The unanticipated emergence of the COVID-19 pandemic and the rapid spread of the mpox epidemic in 2022 and 2024 brought unforeseen challenges to public health. While distinct in nature, these outbreaks share some similarities and offer valuable insights into responding to novel virus dissemination in vulnerable populations. In light of these two experiences, we aim to discern the prioritization of medical countermeasures (MCM) among antivirals, antibodies, and vaccines. Comparative analysis of MCMs reveals that while antivirals serve essential roles as therapeutic tools, monoclonal antibodies can be used for both prevention and treatment, and vaccines remain of paramount importance for controlling epidemics as mass or targeted prophylaxis. Variability in production processes, administration methods, logistics, and costs distinguish these countermeasures. Vaccines, by inducing long-lasting immunity and ideally promoting herd effects, exhibit substantial advantages over other options. To enhance future pandemic readiness, proactive measures must include ready-to-use vaccine platforms with regulatory approval and manufacturing capacities, as well as prototype vaccines for representative pathogens and preexisting protocols to evaluate their efficacies and side effects. The comparison underscores the challenges of social acceptance and equity, particularly in vaccine production and distribution. As the world faces unknown agents, the three major types of MCMs do not have equal and symmetrical effects in terms of epidemic control. Thus, a vaccine-oriented strategy with a community-centered approach, proves essential for effective pandemic preparedness, encouraging continued innovation in vaccinology.

Dual nanobody-redirected and Bi-specific CD13/TIM3 CAR T cells eliminate AML xenografts without toxicity to human HSCs

Adoptive cell therapy including chimeric antigen receptor (CAR) T cells targeting CD19 has been approved by FDA to treat B cell-derived malignancies with remarkable success. The success has not yet been expanded to treating Acute Myeloid Leukemia (AML). We previously showed that a nanobody and single-chain fragment variable (scFv) CD13 (Nanobody)/TIM-3 (scFv) directed bispecific split CAR (bissCAR) T cells, while effective in eliminating AML in preclinical models, also caused substantial toxicity to human hematopoietic stem cells (HSCs) and other lineages. To maintain the bissCART specificity and efficacy, yet reduce toxicity to normal cells including HSCs, we generated new anti-TIM-3 nanobodies and constructed new cognate nanobodies-directed CD13/41BB and TIM3/CD3zeta nbiCARTs. The resultant nbiCARTs showed strong antitumor activity to CD13/TIM3 positive leukemic cells in vitro and in preclinical models. Importantly, the 3rd generation of nbiCARTs had little toxicity to human bone marrow-derived colony forming progenitors ex vivo and the human HSCs in mice with a humanized immune system. Together, the current studies generated novel and 3rd G CD13/TIM-3 nbiCARTs that displayed stronger antitumor activity yet minimal toxicity to normal tissues like HSCs that express a moderate level of CD13, paving the way to further evaluate the novel CD13/TIM-3CARTs in treating aggressive and refractory AML in clinical studies.

Assessing the relationship between serum vitamin A, C, E, D, and B12 levels and preeclampsia

OBJECTIVE

Micronutrients play an important role in maintaining physiological functions while preventing complications associated with pregnancy. The main aim of this study was to evaluate the possible associations between vitamins A, C, D, E, B12, and preeclampsia using a retrospective analytical approach.

METHODS

This retrospective study enrolled pregnant women who attended routine antenatal checkups between January 2021 and January 2023 at the Obstetrics and Gynecology Hospital of Fudan University. One thousand pregnant women aged 18-50 years whose serum vitamin assessments were conducted during 12-20 weeks of gestation were enrolled. Inclusion criteria: women with preeclampsia, singleton pregnancies, and no previous history of hypertension or preeclampsia. Exclusion criteria: metabolic disorders, multiple pregnancies, and other specified exclusions. Approval of the hospital's ethics committee; all participants gave written informed consent. Demographic data analyzed include age, BMI, and gestational age, showing no significant differences in age span between groups (p > .05).

RESULTS

In the preeclampsia group, the serum level of vitamin A stands at 1.08 ± 0.29 μmol/L, which is lower than the control group of 1.13 ± 0.31 μmol/L (p < .05). Mean serum levels of vitamin C in preeclampsia are 51.81 ± 13.15 μmol/L, which was lower than in the control group, where it was 59.67 ± 16.40 μmol/L (p < .05). The mean serum vitamin B12 level in preeclampsia is 158.28 ± 46.77 pmol/L, lower than the 165.61 ± 40.99 pmol in the control group (p < .05). The two groups had no significant difference in serum vitamin E and vitamin D levels (p > .05).

CONCLUSION

Serum vitamins A, C, and B12 at 12 to 20 weeks of pregnancy might be important predisposing factors for preeclampsia. They can be used as indicators of preeclampsia severity and offer clinical detection even before the patient presents with symptoms.

Stress hyperglycemia ratio: a novel predictor of left ventricular dysfunction in peripartum cardiomyopathy

OBJECTIVE

This study aims to assess the predictive value of the stress hyperglycemia ratio (SHR) for left ventricular (LV) systolic dysfunction in patients with peripartum cardiomyopathy (PPCM).

METHODS

We conducted a retrospective analysis of 78 consecutive PPCM patients from January 2007 to March 2023. Their clinical, laboratory, and auxiliary examination data were collected. The estimated average glucose (eAG) was calculated using the formula: eAG = [1.59 × hemoglobin A1c (%) -%2.59]. The SHR was determined by the formula: SHR = (blood glucose at admission)/eAG. The primary outcome measured was the recovery of LV systolic function. A receiver operating characteristic (ROC) curve was used to evaluate the SHR. Logistic regression analysis was performed to identify risk factors for LV systolic dysfunction in PPCM patients.

RESULTS

The mean random blood glucose level in the PPCM patients was 6.38 mmol/L, with an SHR of 1.16. Among these patients, 37 (47.4%) exhibited persistent LV systolic dysfunction during follow-up. The SHR was significantly higher in the non-recovery group than in the recovery group (1.45 vs. 0.91, p < .001). An SHR cutoff of 1.079 predicted persistent LV systolic dysfunction with a sensitivity of 81.1% and a specificity of 90.2%, yielding a Youden index of 0.713. Logistic regression identified an SHR ≥ 1.079, a left ventricular end-diastolic diameter (LVEDD) > 55 mm, and digoxin usage as risk factors for LV systolic dysfunction.

CONCLUSIONS

PPCM patients with an SHR of 1.079 or higher should receive increased scrutiny for persistent LV systolic dysfunction.

Engineered bacteria as an orally administered anti-viral treatment and immunization system

The emergence of new viral pathogens necessitates innovative antiviral therapies and vaccines. Traditional approaches, such as monoclonal antibodies and vaccines, are often hindered by resistance, limited effectiveness, and high costs. Here, we develop an engineered probiotic-based antiviral platform using Escherichia coli Nissle 1917 (EcN), capable of providing both mucosal and systemic immunity via oral administration. EcN was engineered to display anti-spike nanobodies or express the Spike-Receptor Binding Domain on its surface. Our findings reveal that EcN with nanobodies effectively inhibits the interaction between spike protein-expressing pseudoviruses and the ACE2 receptor. Furthermore, we observed the translocation of nanobodies to distant organs, facilitated by outer membrane vesicles (OMVs). The oral administration of EcN expressing spike proteins induced a robust immune response characterized by the production of both IgG and IgA, antibodies that blocked the pseudovirus-ACE2 interaction. While SARS-CoV-2 served as a model, this versatile probiotic platform holds potential for developing customizable biotherapeutics against a wide range of emerging pathogens such as influenza virus or respiratory syncytial virus (RSV) by engineering EcN to express viral surface protein or neutralizing nanobodies demonstrating its versatility as a next-generation mucosal vaccine strategy.

Sodium butyrate alleviates DSS-induced inflammatory bowel disease by inhibiting ferroptosis and modulating ERK/STAT3 signaling and intestinal flora

BACKGROUND

Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), can seriously impact patients' quality of life. Sodium butyrate (NaB), a product of dietary fiber fermentation, has been shown to alleviate IBD symptoms. Some studies have shown that it is related to ferroptosis. However, the precise mechanism linking NaB, IBD, and ferroptosis is not clear.

OBJECTIVE

This study aimed to demonstrate that NaB suppresses ferroptosis, thereby alleviating inflammatory bowel disease (IBD) through modulation of the extracellular regulated protein kinases/signal transducer and activator of transcription 3 (ERK/STAT3) signaling pathway and intestinal flora.

METHODS

An IBD model was established using 2.5% (w/v) dextran sulfate sodium (DSS). Mice were orally administered low-dose NaB, high-dose NaB , or 5-aminosalicylic acid (5-ASA). Ferroptosis-related molecules were measured using specific kits, and western blotting (WB) and real-time polymerase chain reaction (RT-qPCR) were used to determine the levels of the target molecules.

RESULTS

NaB alleviated symptoms in IBD mice, including reduced weight loss, prolonged colon length, reduced disease activity index (DAI), and reduced spleen index and mRNA expression of inflammatory factors. Additionally, NaB reduced the content of Fe2+ and myeloperoxidase (MPO) and increased the content of GSH and the activity of superoxide dismutase (SOD), which reflected NaB-inhibited ferroptosis. Moreover, western blotting showed that NaB enhanced STAT3 and ERK phosphorylation. In addition, NaB regulates the composition and functions of flora related to IBD.

CONCLUSION

NaB alleviates IBD by inhibiting ferroptosis and modulating ERK/STAT3 signaling and the intestinal flora.

Gut microbiota and derived metabolites mediate obstructive sleep apnea induced atherosclerosis

Obstructive sleep apnea (OSA) is characterized by intermittent hypoxia/hypercapnia (IHC), affects predominantly obese individuals, and increases atherosclerosis risk. Since we and others have implicated gut microbiota and metabolites in atherogenesis, we dissected their contributions to OSA-induced atherosclerosis. Atherosclerotic lesions were compared between conventionally-reared specific pathogen free (SPF) and germ-free (GF) Apoe-/- mice following a high fat high cholesterol diet (HFHC), with and without IHC conditions. The fecal microbiota and metabolome were profiled using 16S rRNA gene amplicon sequencing and untargeted tandem mass spectrometry (LC-MS/MS) respectively. Phenotypic data showed that HFHC significantly increased atherosclerosis as compared to regular chow (RC) in both aorta and pulmonary artery (PA) of SPF mice. IHC exacerbated lesions in addition to HFHC. Differential abundance analysis of gut microbiota identified an enrichment of Akkermansiaceae and a depletion of Muribaculaceae (formerly S24-7) family members in the HFHC-IHC group. LC-MS/MS showed a dysregulation of bile acid profiles with taurocholic acid, taurodeoxycholic acid, and 12-ketodeoxycholic acid enriched in the HFHC-IHC group, long-chain N-acyl amides, and phosphatidylcholines. Interestingly, GF Apoe-/- mice markedly reduced atherosclerotic formation relative to SPF Apoe-/- mice in the aorta under HFHC/IHC conditions. In contrast, microbial colonization did not show a significant impact on the atherosclerotic progression in PA. In summary, this research demonstrated that (1) IHC acts cooperatively with HFHC to induce atherosclerosis; (2) gut microbiota modulate atherogenesis, induced by HFHC/IHC, in the aorta not in PA; (3) different analytical methods suggest that a specific imbalance between Akkermansiaceae and Muribaculaceae bacterial families mediate OSA-induced atherosclerosis; and (4) derived bile acids, such as deoxycholic acid and lithocholic acid, regulate atherosclerosis in OSA. The knowledge obtained provides novel insights into the potential therapeutic approaches to prevent and treat OSA-induced atherosclerosis.

Impact of FcRn antagonism on vaccine-induced protective immune responses against viral challenge in COVID-19 and influenza mouse vaccination models

Antagonism of the neonatal Fc receptor through an engineered antibody Fc fragment, such as efgartigimod, results in a decrease in immunoglobulin G levels. This approach is being evaluated as a therapeutic strategy for the treatment of IgG-mediated autoimmune diseases. Our goal was to evaluate the impact of mFc-ABDEG, a mouse-adapted antibody Fc fragment with a mode of action highly similar to efgartigimod, on vaccine-induced protective immune responses against viral infections. Therefore, mouse vaccination models for COVID-19 and influenza were employed, utilizing an mRNA COVID-19 vaccine (COMIRNATY) and an adjuvanted, inactivated quadrivalent influenza vaccine (Seqirus+AddaVax), respectively. In both models, vaccination induced robust humoral responses. As expected, animals treated with mFc-ABDEG had lower levels of virus-specific IgG, while virus-specific IgM responses remained unaffected. The COVID-19 vaccine induced a strong Th1-type T cell response irrespective of mFc-ABDEG treatment. Influenza vaccination resulted in a poor T cell induction, regardless of mFc-ABDEG treatment, due to the Th2-biased response that inactivated influenza vaccines typically induce. Importantly, mFc-ABDEG treatment had no effect on protective immunity against live viral challenges in both models. Vaccinated animals treated with mFc-ABDEG were equally protected as the non-treated vaccinated controls. These non-clinical data demonstrate that FcRn antagonism with mFc-ABDEG did not affect the generation of vaccine-induced protective humoral and cellular responses, or protection against viral challenges. These data substantiate the clinical observations that, although IgG titers were reduced, FcRn antagonism with efgartigimod did not impair the ability to generate new specific IgG responses, regardless of the timing of vaccination.