The Role of Autophagy and Cell Communication in COPD Progression: Insights from Bioinformatics and scRNA-seq

Chronic obstructive pulmonary disease (COPD) is characterized by restricted airflow that leads to significant respiratory difficulties. This progressive disease often results in diminished pulmonary function and the onset of additional respiratory conditions. Autophagy, a critical cellular homeostasis mechanism, plays a significant role in the exacerbation of COPD. In this study, we utilized various bioinformatics tools to identify autophagy-related genes activated by smoking in individuals with COPD. Furthermore, we explored the immune landscape of COPD through these genes, analyzing cell communication patterns using scRNA-seq data. This analysis focused on key pathways between epithelial cells and other cellular subpopulations with different autophagy scores, essential for understanding the initiation and progression of COPD.

ELAV/Hu RNA-binding protein family: key regulators in neurological disorders, cancer, and other diseases

The ELAV/Hu family represents a crucial group of RNA-binding proteins predominantly expressed in neurons, playing significant roles in mRNA transcription and translation. These proteins bind to AU-rich elements in transcripts to regulate the expression of cytokines, growth factors, and the development and maintenance of neurons. Elav-like RNA-binding proteins exhibit remarkable molecular weight conservation across different species, highlighting their evolutionary conservation. Although these proteins are widely expressed in the nervous system and other cell types, variations in the DNA sequences of the four Elav proteins contribute to their distinct roles in neurological disorders, cancer, and other Diseases . Elavl1, a ubiquitously expressed family member, is integral to processes such as cell growth, ageing, tumorigenesis, and inflammatory diseases. Elavl2, primarily expressed in the nervous and reproductive systems, is critical for central nervous system and retinal development; its dysregulation has been implicated in neurodevelopmental disorders such as autism. Both Elavl3 and Elavl4 are restricted to the nervous system and are involved in neuronal differentiation and excitability. Elavl3 is essential for cerebellar function and has been associated with epilepsy, while Elavl4 is linked to neurodegenerative diseases, including Parkinson's and Alzheimer's diseases. This paper provides a comprehensive review of the ELAV/Hu family's role in nervous system development, neurological disorders, cancer, and other diseases.

CAVIN-2 positively correlates with diabetic PAD and promotes LDL transcytosis by inhibiting eNOS activation

OBJECTIVE

Caveolae are closely linked to the onset and progression of atherosclerosis. The pivotal involvement of caveolin-1 (CAV1) within the caveolae in atherosclerosis development has been consistently supported. However, the potential contributions of additional caveolae proteins to atherosclerosis necessitate further exploration. Therefore, this research aimed to afford clinical evidence linking CAVIN-2 to diabetic peripheral artery disease (PAD) and its role in low-density lipoprotein (LDL) transcytosis.

METHODS

Blood samples were collected from a total of 115 participants, including 36 patients without diabetes (ND), 26 patients with type 2 diabetes mellitus (T2DM), and 53 patients with T2DM and PAD (DM-PAD). The plasma levels of CAV1, CAVIN-1, and CAVIN-2 were measured by ELISA. The correlation between CAV1, CAVIN-1, CAVIN-2, and diabetic PAD was examined using Spearman correlation analysis. The predictive effect of CAV1 and CAVIN-2 were analyzed by receiver operating characteristic (ROC) curves. Cellular experiments were used to investigate the effect and mechanism of CAVIN-2 on LDL transcytosis.

RESULTS

Elevated CAV1 and CAVIN-2 levels were observed in T2DM and DM-PAD groups, with a positive correlation to DM-PAD and PAD severity. Both CAV1 and CAVIN-2 emerged as predictors of DM-PAD. In vitro, CAVIN-2 knockdown decreased LDL transcytosis, while CAVIN-2 overexpression increased it. Additionally, CAVIN-2 was found to inhibit eNOS activation and nitric oxide (NO) production, thereby promoting LDL transcytosis and atherosclerosis progression.

CONCLUSION

CAVIN-2 was positively correlated with DM-PAD and promoted LDL transcytosis through the inhibition of eNOS activation, contributing to atherosclerosis development. This study provided clinical evidence linking CAVIN-2 to diabetic PAD and suggested its potential as a biomarker for disease progression.

Exploring RNA modifications in infectious non-coding circular RNAs

Viroids, small circular non-coding RNAs, act as infectious pathogens in higher plants, demonstrating high stability despite consisting solely of naked RNA. Their dependence of replication on host machinery poses the question of whether RNA modifications play a role in viroid biology. Here, we explore RNA modifications in the avocado sunblotch viroid (ASBVd) and the citrus exocortis viroid (CEVd), representative members of viroids replicating in chloroplasts and the nucleus, respectively, using LC - MS and Oxford Nanopore Technology (ONT) direct RNA sequencing. Although no modification was detected in ASBVd, CEVd contained approximately one m6A per RNA molecule. ONT sequencing predicted three m6A positions. Employing orthogonal SELECT method, we confirmed m6A in two positions A353 and A360, which are highly conserved among CEVd variants. These positions are located in the left terminal region of the CEVd rod-like structure where likely RNA Pol II and and TFIIIA-7ZF bind, thus suggesting potential biological role of methylation in viroid replication.

Interkingdom signaling between gastrointestinal hormones and the gut microbiome

The interplay between the gut microbiota and gastrointestinal hormones plays a pivotal role in the health of the host and the development of diseases. As a vital component of the intestinal microecosystem, the gut microbiota influences the synthesis and release of many gastrointestinal hormones through mechanisms such as modulating the intestinal environment, producing metabolites, impacting mucosal barriers, generating immune and inflammatory responses, and releasing neurotransmitters. Conversely, gastrointestinal hormones exert feedback regulation on the gut microbiota by modulating the intestinal environment, nutrient absorption and utilization, and the bacterial biological behavior and composition. The distributions of the gut microbiota and gastrointestinal hormones are anatomically intertwined, and close interactions between the gut microbiota and gastrointestinal hormones are crucial for maintaining gastrointestinal homeostasis. Interventions leveraging the interplay between the gut microbiota and gastrointestinal hormones have been employed in the clinical management of metabolic diseases and inflammatory bowel diseases, such as bariatric surgery and fecal microbiota transplantation, offering promising targets for the treatment of dysbiosis-related diseases.

Maternal-infant probiotic transmission mitigates early-life stress-induced autism in mice

Autism, a disorder influenced by both genetic and environmental factors, presents significant challenges for prevention and treatment. While maternal-infant gut microbiota has been a focus in autism research, preventive strategies targeting maternal gut microbiota remain underexplored. This study demonstrates that prenatal probiotic intake can effectively prevent maternal separation-induced autistic-like behaviors in offspring without altering the embryonic neurodevelopment in mice. Using specific PCR primers and cross-fostering experiments, we traced the vertical transmission of probiotics, primarily via fecal/vaginal contamination. Early probiotic colonization conferred resilience against stress-induced gut pathogenic microbes and Th17-mediated peripheral inflammation while significantly inhibiting hypermyelination and neuroinflammation linked to systemic inflammation. Microbial metabolites like tyrosol and xanthurenic acid alleviated neuroinflammation and hypermyelination in vitro, though the causal relationship among neuroinflammation, hypermyelination, and autism in vivo requires further validation. These findings underscore the importance of the maternal-infant microbiota transmission window in autism prevention and highlight the clinical potential of prenatal probiotic interventions.

Synergistic and off-target effects of bacteriocins in a simplified human intestinal microbiome: implications for Clostridioides difficile infection control

Clostridioides difficile is a major cause of nosocomial diarrhea. As current antibiotic treatment failures and recurrence of infections are highly frequent, alternative strategies are needed for the treatment of this disease. This study explores the use of bacteriocins, specifically lacticin 3147 and pediocin PA-1, which have reported inhibitory activity against C. difficile. We engineered Lactococcus lactis strains to produce these bacteriocins individually or in combination, aiming to enhance their activity against C. difficile. Our results show that lacticin 3147 and pediocin PA-1 display synergy, resulting in higher anti-C. difficile activity. We then evaluated the effects of these L. lactis strains in a Simplified Human Intestinal Microbiome (SIHUMI-C) model, a bacterial consortium of eight diverse human gut species that includes C. difficile. After introducing the bacteriocin-producing L. lactis strains into SIHUMI-C, samples were collected over 24 hours, and the genome copies of each species were assessed using qPCR. Contrary to expectations, the combined bacteriocins increased C. difficile levels in the consortium despite showing synergy against C. difficile in agar-based screening. This can be rationally explained by antagonistic inter-species interactions within SIHUMI-C, providing new insights into how broad-spectrum antimicrobials might fail to control targeted species in complex gut microbial communities. These findings highlight the need to mitigate off-target effects in complex gut microbiomes when developing bacteriocin-based therapies with potential clinical implications for infectious disease treatment.

Staphylococcus warneri dampens SUMOylation and promotes intestinal inflammation

Gut bacteria play key roles in intestinal physiology, via the secretion of diversified bacterial effectors. Many of these effectors remodel the host proteome, either by altering transcription or by regulating protein post-translational modifications. SUMOylation, a ubiquitin-like post-translational modification playing key roles in intestinal physiology, is a target of gut bacteria. Mutualistic gut bacteria can promote SUMOylation, via the production of short- or branched-chain fatty acids (SCFA/BCFA). In contrast, several pathogenic bacteria were shown to dampen SUMOylation in order to promote infection. Here, we demonstrate that Staphylococcus warneri, a natural member of the human gut microbiota, decreases SUMOylation in intestinal cells. We identify that Warnericin RK, a hemolytic toxin secreted by S. warneri, targets key components of the host SUMOylation machinery, leading to the loss of SUMO-conjugated proteins. We further demonstrate that Warnericin RK promotes inflammation in intestinal and immune cells using both SUMO-dependent and SUMO-independent mechanisms. We finally show that Warnericin RK regulates the expression of genes involved in intestinal tight junctions. Together, these results highlight the diversity of mechanisms used by bacteria from the gut microbiota to manipulate host SUMOylation. They further highlight that changes in gut microbiota composition may impact intestinal inflammation, by altering the equilibrium between bacterial effectors promoting or dampening SUMOylation.

Higher serum Metrnl levels are associated with increased vascular calcification in hemodialysis patients

BACKGROUND

Meteorin-like (Metrnl) is a newly identified secreted protein that plays important roles in metabolic and inflammation-related diseases. Our study aimed to evaluate serum Metrnl levels and establish their relationship with vascular calcification (VC) in hemodialysis (HD) patients.

METHODS

In total, 313 HD patients and 41 healthy individuals, as controls, were included. Serum levels of Metrnl and other clinical and laboratory parameters were compared. VC was evaluated based on the abdominal aortic calcification (AAC) scores. HD patients were divided into a high-AAC score group (AAC score ≥ 4) and a low-AAC score group (AAC score < 4).

RESULTS

HD patients had higher serum Metrnl levels than the controls (0.52 ± 0.26 ng/ml vs. 0.24 ± 0.11 ng/ml, p < 0.001). Serum Metrnl concentrations were significantly higher in HD patients in the high-AAC score group than in those in the low-AAC score group (0.55 ± 0.27 vs. 0.49 ± 0.24 ng/ml, p = 0.041). Multivariate logistic regression revealed that serum Metrnl, age, diabetes mellitus, serum total carbon dioxide (tCO2) and serum intact parathyroid hormone (iPTH) were significant independent determinants of high AAC scores.

CONCLUSION

The results herein provide the first clinical evidence of the association between serum Metrnl and VC in HD patients. Higher Metrnl levels, older age, diabetes mellitus, and higher serum tCO2 and iPTH levels are independent determining factors for high AAC scores in HD patients.

The critical role of ferroptosis in virus-associated hematologic malignancies and its potential value in antiviral-antitumor therapy

Epstein-Barr Virus (EBV), Kaposi's sarcoma-associated herpesvirus (KSHV), and human T-cell leukemia virus type 1 (HTLV-1) are key infectious agents linked to the development of various hematological malignancies, including Hodgkin's lymphoma, non-Hodgkin's lymphoma, and adult T-cell leukemia/lymphoma. This review highlights the critical knowledge gaps in understanding the role of ferroptosis, a novel form of cell death, in virus-related tumors. We focus on how ferroptosis influences the host cell response to these viral infections, revealing groundbreaking mechanisms by which the three viruses differentially regulate core pathways of ferroptosis, such as iron homeostasis, lipid peroxidation, and antioxidant systems, thereby promoting malignant transformation of host cells. Additionally, we explore the potential of antiviral drugs and ferroptosis modulators in the treatment of virus-associated hematological malignancies.

Immune checkpoint inhibitors in cancer patients with autoimmune disease: Safety and efficacy

The utilization of immune-checkpoint inhibitors (ICIs) in cancer immunotherapy frequently leads to the occurrence of immune-related adverse events (irAEs), making it generally not recommended for patients with preexisting autoimmune diseases. Hence, we conducted a meta-analysis on safety and efficacy of ICIs in cancer patients with preexisting autoimmune diseases to provide further insights. PubMed, EMBASE, and Cochrane Library were systematically searched until December 20, 2024. The main summary measures used were pooled rate and risk ratio (RR) with 95% confidential interval (CI), which were analyzed using R statistic software. A total of 52 articles were included in the study. When cancer patients with preexisting autoimmune diseases received ICIs treatment, the overall incidence was 0.610 (95% CI: 0.531-0.686) for any grade irAEs, 0.295 (95% CI: 0.248-0.343) for flares, 0.325 (95% CI: 0.258-0.396) for de novo irAEs, 0.238 (95% CI: 0.174-0.309) for grade ≥3 irAEs, and 0.143 (95% CI: 0.109-0.180) for discontinuation due to immunotoxicity. Compared with those without autoimmune diseases, cancer patients with autoimmune diseases experienced a higher risk of any-grade irAEs (RR: 1.23, 95% CI: 1.12-1.35) and discontinuation due to immunotoxicity (1.40, 95% CI: 1.11-1.78). However, no statistically significant differences were observed in the incidence of grade ≥3 irAEs, objective response rate (ORR), disease control rate (DCR), overall survival (OS), and progression-free survival (PFS) between the two groups. During ICIs treatment, irAEs are common among cancer patients with autoimmune diseases, but severe irAEs is relatively low. ICIs are effective in this population, but should be strictly monitored when used to avoid immunotoxicity.

Germ granule-mediated mRNA storage and translational control

Germ cells depend on specialized post-transcriptional regulation for proper development and function, much of which is mediated by dynamic RNA granules. These membrane-less organelles form through the condensation of RNA and proteins, governed by multivalent biomolecular interactions. RNA granules compartmentalize cellular components, selectively enriching specific factors and modulating biochemical reactions. Over recent decades, various types of RNA granules have been identified in germ cells across species, with extensive studies uncovering their molecular roles and developmental significance. This review explores the mRNA regulatory mechanisms mediated by RNA granules in germ cells. We discuss the distinct spatial organization of specific granule components and the variations in material states of germ granules, which contribute to the regulation of mRNA storage and translation. Additionally, we highlight emerging research on how changes in these material states, during developmental stages, reflect the dynamic nature of germ granules and their critical role in development.

Patient-specific HLA-I subtypes predict response to immune checkpoint blockade

Specific shared HLA-I alleles were linked to the response to immune checkpoint blockade (ICB). We aimed to identify the HLA-A subtypes associated with maximum benefit from ICB. We compiled a clinical dataset of patients who underwent a CLIA-approved germline HLA status testing as part of various advanced immune and cell therapy trials undertaken at the Christie NHS Foundation Trust. A total of 285 patients were eligible for final analysis. We identified 15 HLA-A subtypes, the most common alleles being HLA-A02, HLA-A01, and HLA-A03. A02:01 showed a tumor lineage-specific distribution. One hundred and forty patients received ICB and had evaluable response status. Patients with A01 were associated with better clinical outcomes. No significant associations were observed between HLA-A subtypes and the incidence of immune-related adverse effects. HLA genotyping should be incorporated early in the diagnostic work-up of patients with solid cancers as a predictive and selective biomarker.

Novel human coronavirus in an infant patient with pneumonia, Republic of Korea

Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequently found among patients with respiratory infections. To date, limited attention has been directed towards alphacoronaviruses due to their low prevalence and fatality rates. Nasal swab and serum samples were collected from a paediatric patient, and an epidemiological survey was conducted. Retrospective surveillance investigated the molecular prevalence of CoV in 880 rodents collected in the Republic of Korea (ROK) from 2018 to 2022. Next-generation sequencing (NGS) and phylogenetic analyses characterized the novel HCoV and closely related CoVs harboured by Apodemus spp. On 15 December 2022, a 103-day-old infant was admitted with fever, cough, sputum production, and rhinorrhea, diagnosed with human parainfluenza virus 1 (HPIV-1) and rhinovirus co-infection. Elevated AST/ALT levels indicated transient liver dysfunction on the fourth day of hospitalization. Metagenomic NGS (mNGS) identified a novel HCoV in nasal swab and serum samples. Retrospective rodent surveillance and phylogenetic analyses showed the novel HCoV was closely related to alphacoronaviruses carried by Apodemus spp. in the ROK and China. This case highlights the potential of mNGS to identify emerging pathogens and raises awareness of possible extra-respiratory manifestations, such as transient liver dysfunction, associated with novel HCoVs. While the liver injury in this case may be attributable to the novel HCoV, further research is necessary to elucidate its clinical significance, epidemiological prevalence, and zoonotic origins.

Gene prediction of the relationship between iron deficiency anemia and immune cells

BACKGROUND

Observational studies have shown a potential link between immune factors and the risk of iron deficiency anemia (IDA), yet the causal relationship between immune cells and IDA remains enigmatic. Herein, we used Mendelian randomization (MR) to assess whether this association is causal.

METHODS

We selected IDA genetic variants, including 8376 samples and 9810691 single nucleotide polymorphisms, and immune cells from a large open genome-wide association study (GWAS) for a bidirectional MR study. The primary method was inverse variance weighting (IVW), and auxiliary analyses were MR-Egger, weighted median, simple mode and weighted mode. The reliability of the results was subsequently verified by heterogeneity and sensitivity analysis.

RESULTS

IVW method showed that 19 types of immune cells may be the risk factors of IDA, whereas 15 types of immune cells are the protective factors of IDA. Reverse MR analysis suggested that immune cells from upstream etiology of IDA are not involved in follow-up immune activities. Next, we selected 731 immune cell types as the results. The research revealed that IDA may result in a rise in 23 kinds of immune cells and a reduction in 12 kinds of immune cells. In addition, sensitivity analysis demonstrated no evidence of heterogeneity or horizontal pleiotropy.

CONCLUSIONS

From a genetic standpoint, our study suggests that specific immune cells may be involved in the occurrence of IDA. Inversely, IDA may also contribute to immune dysfunction, thus guiding future clinical investigations.

A single mutation at position 214 of influenza B hemagglutinin enhances cross-neutralization

High variability of influenza B virus (IBV) hemagglutinin (HA) impairs the cross- neutralization ability of vaccines, leading to reduce efficacy. We identified significant differences in cross-neutralization between IBV strains B/Wyoming/06/2014 and B/Brisbane/60/2008, which differ in only three amino acid residues. The 214 T point mutation was found to dramatically enhance cross-neutralization (>10-fold). Antibody-based reverse validation also revealed that this mutation significantly increased the neutralization capacity (500-62,500-fold). Furthermore, monitoring revealed that the mutation rate at this site has reached its highest level in nearly 20 years, with a prevalence exceeding 80% in sequences submitted from certain regions. Our findings provide new evidence for the selection of vaccine strains with improved cross- neutralization effects, which will aid the development of broad-spectrum vaccines by modifying minimal antigenic epitopes.

Unveiling the impact of competition weight loss on gut microbiota: alterations in diversity, composition, and predicted metabolic functions

BACKGROUND

Competitive sports and sports nutrition, popular among amateur athletes aiming for a lean physique, have limited research on gut microbiota.

METHODS

We conducted a 46-week study to analyze the consequences of fat loss and diet restrictions in 23 fitness athletes who prepared for a physique competition. Body composition, dietary intakes, serum cytokines and chemokines, and fecal samples were analyzed.

RESULTS

Fat loss through caloric restriction and aerobic exercise led to an increased phylogenetic diversity of gut microbiota and changes in the composition of gut microbiota, with Faecalibacterium, Lachnospiraceae, Bacteroides, and Intestinimonas showing altered abundances. Fat loss also changed the predicted microbial functions responsible for the metabolism of carbohydrates and amino acids. Consumption of energy, carbohydrates, fiber, vitamins and minerals, and various fatty acids decreased during the preparation for the competition, which was partly associated with changes in gut microbiota. Several cytokine levels decreased (IL1a, IL1b, IL10, and TFNα), and certain chemokine levels increased (GROa and RANTES). During the 23-week regain period after the competition, gut microbiota showed signs of recovery, with increased diversity compared to pre- and post-competition measurements. Most taxonomic changes returned to their baseline levels after the regain period.

CONCLUSIONS

The study highlights the dynamic nature of gut microbiota and its response to fat loss and regain in non-obese fitness/physique competitors and provides novel insights into how competitive sports and sports nutrition can influence the gut ecosystem.

Proteins of the SubB family provide multiple mechanisms of serum resistance in Yersinia pestis

The serum complement system is a cornerstone element of the innate immune response. Bacterial resistance to this system is a multifaceted process involving various proteins and molecular mechanisms. Here, we report several genes required for the growth of Yersinia pestis in serum. Among them, we found that ypo0337 encodes an outer-membrane-associated lectin that recruits factor H, C4BP and hemopexin, conferring resistance to the serum complement system. YPO0337 displays high sequence similarity with the SubB subunit of the AB5 toxin from Escherichia coli, as well as other SubB-like proteins, and subB from E. coli restores the ability of Y. pestis Δypo0337 mutant to resist to serum complement. Altogether, the data suggest that at least two members of the SubB protein family function as virulence factors, conferring resistance to serum complement through a unique mode of action.

Deciphering the role of APOE in cerebral amyloid angiopathy: from genetic insights to therapeutic horizons

Cerebral amyloid angiopathy (CAA), characterized by the deposition of amyloid-β (Aβ) peptides in the walls of medium and small vessels of the brain and leptomeninges, is a major cause of lobar hemorrhage in elderly individuals. Among the genetic risk factors for CAA that continue to be recognized, the apolipoprotein E (APOE) gene is the most significant and prevalent, as its variants have been implicated in more than half of all patients with CAA. While the presence of the APOE ε4 allele markedly increases the risk of CAA, the ε2 allele confers a protective effect relative to the common ε3 allele. These allelic variants encode three APOE isoforms that differ at two amino acid positions. The primary physiological role of APOE is to mediate lipid transport in the brain and periphery; however, it has also been shown to be involved in a wide array of biological functions, particularly those involving Aβ, in which it plays a known role in processing, production, aggregation, and clearance. The challenges posed by the reliance on postmortem histological analyses and the current absence of an effective intervention underscore the urgency for innovative APOE-targeted strategies for diagnosing CAA. This review not only deepens our understanding of the impact of APOE on the pathogenesis of CAA but can also help guide the exploration of targeted therapies, inspiring further research into the therapeutic potential of APOE.

Small molecules targeting the eubacterial β-sliding clamp discovered by combined in silico and in vitro screening approaches

Antibiotic resistance stands as the foremost post-pandemic threat to public health. The urgent need for new, effective antibacterial treatments is evident. Protein-protein interactions (PPIs), owing to their pivotal role in microbial physiology, emerge as novel and attractive targets. Particularly promising is the α-subunit/β-sliding clamp interaction, crucial for the replicative competence of bacterial DNA polymerase III holoenzyme. Through pharmacophore-based virtual screening, we identified 4,000 candidate small molecule inhibitors targeting the β-clamp binding pocket. Subsequently, these candidates underwent evaluation using the BRET assay in yeast cells. Following this, three hits and 28 analogues were validated via Protein Thermal Shift and competitive ELISA assays. Among them, thiazolo[4,5-d]-pyrimidinedione and benzanilide derivatives exhibited micromolar potency in displacing the β-clamp protein partner and inhibiting DNA replication. This screening campaign unveiled new chemical classes of α/β-clamp PPI disruptors capable of inhibiting DNA polymerase III activity, which lend themselves for further optimisation to improve their antibacterial efficacy.

Regulation of dentate gyrus pattern separation by hilus ectopic granule cells

The dentate gyrus (DG) in hippocampus is reported to perform pattern separation, converting similar inputs into different outputs and thus avoiding memory interference. Previous studies have found that human and mice with epilepsy have significant pattern separation defects and a portion of adult-born granule cells (abGCs) migrate abnormally into the hilus, forming hilus ectopic granule cells (HEGCs). For the lack of relevant pathophysiological experiments, how HEGCs affect pattern separation remains unclear. Therefore, in this paper, we will construct the DG neuronal circuit and focus on discussing effects of HEGCs on pattern separation numerically. The obtained results showed that HEGCs impaired pattern separation efficiency since the sparse firing of granule cells (GCs) was destroyed. We provided new insights into the underlining mechanisms of HEGCs impairing pattern separation through analyzing two excitatory circuits: GC-HEGC-GC and GC-Mossy cell (MC)-GC, both of which involve the participation of HEGCs within the DG. It is revealed that the recurrent excitatory circuit GC-HEGC-GC formed by HEGCs mossy fiber sprouting significantly enhanced GCs activity, consequently disrupted pattern separation. However, another excitatory circuit had negligible effects on pattern separation due to the direct and indirect influences of MCs on GCs, which in turn led to the GCs sparse firing. Thus, HEGCs impair DG pattern separation mainly through the GC-HEGC-GC circuit and therefore ablating HEGCs may be one of the effective ways to improve pattern separation in patients with epilepsy.

Lactobacillus intestinalis facilitates tumor-derived CCL5 to recruit dendritic cell and suppress colorectal tumorigenesis

Gut microbes play a crucial role in regulating the tumor microenvironment (TME) of colorectal cancer (CRC). Nevertheless, the deep mechanism between the microbiota-TME interaction has not been well explored. In this study, we for the first time discovered that Lactobacillus intestinalis (L. intestinalis) effectively suppressed tumor growth both in the AOM/DSS-induced CRC model and the ApcMin/+ spontaneous adenoma model. Our investigation revealed that L. intestinalis increased the infiltration of immune cells, particularly dendritic cells (DC), in the TME. Mechanically, the tumor-derived CCL5 induced by L. intestinalis recruited DC chemotaxis through the NOD1/NF-κB signaling pathway. In clinical samples and datasets, we found positive correlation between L. intestinalis, CCL5 level, and the DC-related genes. Our study provided a new strategy for microbial intervention for CRC and deepened the understanding of the interaction between tumor cells and the immune microenvironment modulated by gut microbes.

Age-related changes in the immune system and challenges for the development of age-specific vaccines

BACKGROUND

A better understanding of how the immune system evolves with age and how vaccines work in older people has led to increasing focus on the development of vaccines aimed specifically at older age groups. We discuss strategies used to improve vaccine immunogenicity for older adults, focusing on licensed adjuvants.

FINDINGS

With age-related immune decline (immunosenescence), older adults face increased vulnerability to infections and severe complications. Immunosenescence affects T-cell and B-cell populations and innate immunity, leading to reduced chemotaxis, cytotoxicity, and altered cytokine production. This contributes to inflammaging-low-grade, chronic inflammation linked to aging. However, immune responses vary due to genetics and life-long exposures, making chronological age an imperfect indicator of immune health. Vaccination remains key to prevention, yet immune dysfunction complicates vaccine efficacy. Strategies to enhance responses in older adults include mRNA vaccines, high-antigen content vaccines, intradermal administration, and adjuvants. mRNA COVID-19 vaccines generated strong immune responses in older adults, though lower than in younger groups. High-antigen content influenza vaccines have shown superior efficacy compared to standard vaccination. Adjuvants offer a well-established approach to boosting vaccine responses by enhancing innate immunity.

CONCLUSIONS

Of various strategies used to improve immunogenicity of vaccines for older adults, adjuvants have been the most consistently effective and practical. More recently, mRNA vaccines have also shown great promise.

Functional characterization of four soybean C2H2 zinc-finger genes in Phytophthora resistance

Soybean (Glycine max) is one of the most important industrial and oilseed crops; however, the yield is threatened by the invasion of various pathogens. Soybean stem and root rot, caused by Phytophthora sojae, is a destructive disease that significantly damages soybean production worldwide. C2H2 zinc finger protein (C2H2-ZFP) is a large transcription factor family in plants that plays crucial roles in stress response and hormone signal transduction. Given its importance, we analyzed the expression patterns of C2H2-ZFP family genes in response to P. sojae infection and selected four candidate genes to explore their molecular characteristics and functions related to P. sojae resistance. Subcellular localization analysis indicated that three ZFPs (GmZFP2, GmZFP3, and GmZFP4) were localized in the nucleus, while GmZFP1 was found in both the nucleus and plasma membrane. Dual-luciferase transient expression analysis revealed that all four ZFPs possessed transcriptional repression activation. Further transient expression in N. benthamiana leaves demonstrated that GmZFP2 induced significant cell death and reactive oxygen species (ROS) accumulation. GmZFP2 significantly enhanced the resistance to Phytophthora pathogens in N. benthamiana leaves and soybean hairy roots. This study provides insights in to the functional characterization of soybean ZFPs in Phytophthora resistance and demonstrates that GmZFP2 plays a positive role in P. sojae resistance in soybeans.

Integrated bioinformatics analysis identifies neutrophils and villous cytotrophoblasts infiltration characterized by BLC6 upregulation as associated with the co-occurrence of gestational diabetes mellitus and pre-eclampsia

BACKGROUND

Gestational diabetes mellitus (GDM) patients are one of the important high-risk groups for the development of pre-eclampsia (PE). The pathogenesis of PE in GDM patients is not fully understood. This study aims to identify hub genes and pathways associated with the co-occurrence of GDM and PE.

METHODS

The matrix files of GDM and PE datasets were downloaded from GEO to identify differentially expressed genes (DEGs). The common DEGs were predicted for functional analysis through GO and KEGG analysis. A protein-protein interaction (PPI) network was constructed to determine the common hub genes for GDM and PE. Diagnostic hub genes were obtained through regression modeling and ROC analysis, and validated in publicly available datasets. The differences in immune infiltration between GDM and PE were analyzed. The expression and role of common hub genes in the co-occurrence of GDM and PE were explored through analysis of single-cell sequencing data.

RESULTS

A total of 104 DEGs were identified between GDM and PE. These common DEGs were found to be involved in mucosal immune response and the JAK-STAT signaling pathway. A total of 27 common hub genes were identified for both GDM and PE. BCL6, DNAH9, and SCG2 were identified as potential diagnostic biomarkers for PE. BCL6 showed high expression in neutrophils and villous cytotrophoblasts (VCTs) in both PE and GDM.

CONCLUSION

This study identified BCL6, DNAH9, and SCG2 as common hub genes in GDM and PE. BCL6 is expected to be a new target for the diagnosis and treatment of GDM concurrent with PE.

Role of the C-terminal domain in modifying pH-dependent regulation of Cav1.4 Ca2+ channels

In the retina, Ca2+ influx through Cav1.4 Ca2+ channels triggers neurotransmitter release from rod and cone photoreceptors. Changes in extracellular pH modify channel opening, enabling a feedback regulation of photoreceptor output that contributes to the encoding of color and contrast. However, the mechanisms underlying pH-dependent modulation of Cav1.4 are poorly understood. Here, we investigated the role of the C-terminal domain (CTD) of Cav1.4 in pH-dependent modulation of Ba2+ currents (IBa) in HEK293T cells transfected with the full length CaV1.4 (FL) or variants lacking portions of the CTD due to alternative splicing (Δe47) or a disease-causing mutation (K1591X). While extracellular alkalinization caused an increase in IBa for each variant, the magnitude of this increase was significantly diminished (~40-50%) for both CTD variants; K1591X was unique in showing no pH-dependent increase in maximal conductance. Moreover, the auxiliary α2δ-4 subunit augmented the pH sensitivity of IBa, as compared to α2δ-1 or no α2δ, for FL and K1591X but not Δe47. We conclude that the CTD and α2δ-4 are critical determinants of pH-dependent modulation of Cav1.4 and may influence the processing of visual information in normal and diseased states of the retina.

Severe postoperative complications after minimally invasive esophagectomy reduce the long-term prognosis of well-immunonutrition patients with locally advanced esophageal squamous cell carcinoma

BACKGROUND

While severe postoperative complications (SPCs) impact cancer prognosis, their effect on locally advanced esophageal squamous cell carcinoma (ESCC) patients with varying immunonutritional statuses after minimally invasive esophagectomy (MIE) is unclear.

METHODS

This retrospective study analyzed 442 patients with locally advanced ESCC who underwent MIE, investigating the relationship between SPCs and survival based on preoperative immunonutritional status, determined by the prognostic nutritional index (PNI). Nomograms were developed for patients with preserved immunonutritional status using Cox regression, and their performance was assessed.

RESULTS

Of the patients, 102 (23.1%) experienced SPCs after MIE. Five-year overall survival (OS) and disease-free survival (DFS) were significantly different between SPCs and non-SPCs groups (p < 0.001). In the preserved immunonutritional group, SPCs significantly reduced 5-year OS (p = 0.008) and DFS (p = 0.011), but not in the poor immunonutritional group (OS p = 0.152, DFS p = 0.098). Multivariate Cox regression identified SPCs as an independent risk factor for OS (HR = 1.653, p = 0.013) and DFS (HR = 1.476, p = 0.039). A nomogram for predicting OS and DFS in preserved immunonutritional patients demonstrated excellent performance.

CONCLUSIONS

SPCs significantly affect prognosis in ESCC patients with preserved immunonutritional status after MIE. Nomograms based on SPCs can predict OS and DFS in these patients.

A fast in situ hybridization chain reaction method in Drosophila embryos and ovaries

The in situ hybridization chain reaction (isHCR) is a powerful method for visualizing mRNA in many species. We present a rapid isHCR method for Drosophila embryos and ovaries. Ethylene carbonate was added to the hybridization buffer to facilitate the hybridization reaction, and a modified short hairpin DNA was used in the amplification reaction; these modifications decreased the RNA staining time from 3 days to 1 day. This method is compatible with immunohistochemistry and can detect multiple mRNAs. The proposed method could significantly reduce staining time for Drosophila researchers using isHCR.

Arginine depletion-induced autophagy and metabolic dysregulation are involved in the disease severity of hand, foot, and mouth disease

Amino acid metabolism provides significant insight into the development and prevention of many viral diseases. Therefore, the present study aimed to compare the amino acid profiles of hand, foot, and mouth disease (HFMD) patients with those of healthy individuals and to further reveal the molecular mechanisms of HFMD severity. Using UPLC-MS/MS, we determined the plasma amino acid expression profiles of pediatric patients with HFMD (mild, n = 42; severe, n = 43) and healthy controls (n = 25). Brain tissues from CVA6-infected mice were examined using untargeted metabolomics. Several amino acids were significantly different between the three groups. Pathway analysis revealed that arginine, proline, and tryptophan metabolism are implicated in the pathogenesis of HFMD. A similar arginine depletion was observed in the brain tissues of CVA6-infected mice. Importantly, L-arginine supplementation improved the survival rate of CVA6-infected mice, inhibited virus multiplication, and reduced pathological autophagy associated with mTOR-autophagy pathway in the brain. Collectively, arginine, as the hub amino acid metabolite of the mammalian target of rapamycin (mTOR) signaling pathway affecting autophagy, plays an important role in the pathogenesis of severe HFMD. L-arginine supplementation may serve as a potential therapeutic option for critical patients with HFMD.

Aba-induced active stomatal closure in bulb scales of Lanzhou lily

Abscisic acid (ABA) mediated stomatal closure is a highly effective mode of active stomatal regulation under drought stress. Previous studies on stomatal regulation have primarily focused on the leaves of vascular plants, while research on the stomatal behavior of bulbous plants remains unknown. In addition, ABA-induced stomatal regulation in bulbs has yet to be explored. Therefore, we aim to investigate the ABA-induced active regulation in the bulb of the Lanzhou lily (Lilium davidii var. unicolor). The morphological characteristics of epidermal strips were analyzed along with a stomatal aperture assay to investigate the bulb's stomatal response to ABA. Moreover, the mechanism of ABA signaling was explored using treatments with ABA signaling chemicals and corresponding scavengers. This study revealed that stomata are mainly distributed on the upper part and outer surface of the bulb. The guard cells of the lily bulb are inflated, and the stomata have a nearly circular shape with relatively low stomatal density. Exogenous ABA was found to induce varying degrees of stomatal closure in a dose-dependent manner, with significant stomatal aperture reduction observed after treatment with 10 µM ABA. Overall, the study indicated that both hydrogen peroxide (H2O2) and nitric oxide (NO) are involved in the ABA-induced stomatal closure process, with H2O2 functioning as an upstream component of NO.

E. coli genetically modified for purine nucleobase release promotes butyrate generation and colonic wound healing during DSS insult

The gut microbiota transforms energy stored as undigestible carbohydrates into a remarkable number of metabolites that fuel intestinal bacterial communities and the host tissue. Colonic epithelial cells at the microbiota-host interface depend upon such microbiota-derived metabolites (MDMs) to satisfy their energy requisite. Microbial dysbiosis eliciting MDM loss contributes to barrier dysfunction and mucosal disease. Recent work has identified a role for microbiota-sourced purines (MSPs), notably hypoxanthine, as an MDM salvaged by the colonic epithelium for nucleotide biogenesis and energy balance. Here, we investigated the role of MSPs in mice during disease-modeled colonic energetic stress using a strain of E. coli genetically modified for enhanced purine nucleobase release (E. coli Mutant). E. coli Mutant colonization protected against DSS-induced tissue damage and permeability while promoting proliferation for wound healing. Metabolite and metagenomic analyses suggested a colonic butyrate-purine nucleobase metabolic axis, wherein the E. coli Mutant provided purine substrate for Clostridia butyrate production and host purine salvage, altogether supplying the host substrate for efficient nucleotide biogenesis and energy balance.

Unraveling the anoikis-cancer nexus: a bibliometric analysis of research trends and mechanisms

BACKGROUND

Cancer, influenced by genetics and the environment, involves anoikis, a cell death mechanism upon extracellular matrix detachment crucial for metastasis. Understanding this relationship is key for therapy. We analyze cancer and anoikis trends using bibliometrics.

METHODS

A search was conducted from Web of Science Core, PubMed, Scopus and non-English databases such as the CNKI (inception- 21 December 2024). Data analysis employed Microsoft Excel, VOSviewer, CiteSpace, R software, and the online platform (https://bibliometric.com/).

RESULTS

2510 publications were retrieved, with a significant increase in the last decade. China led, the University of Texas system was productive, and the Oncogene Journal was popular. Breast, and colorectal cancers were frequently studied. Among them, representative tumor-related mechanisms were identified, commonalities such as (EMT, ECM, autophagy) and respective specific mechanisms were summarized.

CONCLUSION

This bibliometric analysis highlights rapid advances in anoikis research in cancer, emphasizing EMT and FAK pathways' translational potential, guiding targeted therapies, and improving cancer treatment outcomes.

The regulatory roles of RNA-binding proteins in the tumour immune microenvironment of gastrointestinal malignancies

The crosstalk between the tumour immune microenvironment (TIME) and tumour cells promote immune evasion and resistance to immunotherapy in gastrointestinal (GI) tumours. Post-transcriptional regulation of genes is pivotal to GI tumours progression, and RNA-binding proteins (RBPs) serve as key regulators via their RNA-binding domains. RBPs may exhibit either anti-tumour or pro-tumour functions by influencing the TIME through the modulation of mRNAs and non-coding RNAs expression, as well as post-transcriptional modifications, primarily N6-methyladenosine (m6A). Aberrant regulation of RBPs, such as HuR and YBX1, typically enhances tumour immune escape and impacts prognosis of GI tumour patients. Further, while targeting RBPs offers a promising strategy for improving immunotherapy in GI cancers, the mechanisms by which RBPs regulate the TIME in these tumours remain poorly understood, and the therapeutic application is still in its early stages. This review summarizes current advances in exploring the roles of RBPs in regulating genes expression and their effect on the TIME of GI tumours, then providing theoretical insights for RBP-targeted cancer therapies.

Gut microbiota shift in Ghanaian individuals along the migration axis: the RODAM-Pros cohort

Migration is associated with a substantial change in environmental exposures and health outcomes. We aimed to investigate the shift in gut microbiota composition and the associations with cardiometabolic outcomes in the RODAM-Pros cohort spanning multiple research sites across continents. We determined gut microbiota composition of 1,177 Ghanaian participants in rural Ghana, urban Ghana, and Amsterdam, the Netherlands, using 16S rRNA sequencing. We observed a clear gradient in gut microbiota composition and alpha and beta diversity from rural Ghana to urban Ghana, to Amsterdam. We used pairwise XGBoost machine learning classification models to identify which microbes were most distinct between locations in prevalence and abundance. The associations between these microbes and the locations could partly be explained by differences in confounders such as dietary intake. Groups of microbes that emerged or disappeared along the migration axis were associated with cardiometabolic outcomes, including higher body mass index, higher HbA1c and higher diastolic blood pressure. Concluding, we identified associations between a shift in gut microbiota composition and cardiometabolic risk along the migration axis, underscoring the relevance of gut health in the context of migration-associated adverse health outcomes.

Comprehensive characterization of the molecular feature of T cells in laryngeal cancer: evidence from integrated single-cell and bulk RNA sequencing data using multiple machine learning approaches

BACKGROUND

The clinical relevance of T cell-related molecules at single-cell resolution in laryngeal cancer (LC) has not been clarified.

MATERIALS AND METHODS

Three LC tissues and matching adjoining normal tissues from the hospital were used to perform 10X single-cell RNA sequencing. Hub T cell-related genes (TCRGs) were detected by applying ten machine learning (ML) techniques based TCGA and GEO databases, which were also utilized to create a prediction model (TCRG classifier) and a multicenter validation model. Lastly, we conducted a comprehensive analysis of the TCRG's correlation with immunological properties.

RESULTS

The analysis of single-cell RNA-seq data revealed that T cells are the primary components of the tumor microenvironment (TME), are significantly involved in cell differentiation pathways, and play a considerable role in intercellular communication. Based on 10 ML approaches, TCRG classifier were identified to develop and validate. The TCRG classifier exhibited excellent prognostic values with a mean C-index of 0.66 in six cohorts, serving as an independent risk factor (p < 0.01). Additionally, the TCRG exhibited a significant relationship with immune score, immune cell infiltration, immune-associated pathways, immune checkpoint inhibitors, human leukocyte antigen, and immunogenicity. Lastly, IPS, TCIC, TIDE, and IMvigor210 cohort analysis illustrated that the immunotherapy response may be accurately predicted using TCRG.

CONCLUSION

A TCRG classifier is an excellent resource for predicting a patient's prognosis, potentially guiding the preservation of laryngeal function, and identifying patients who may have a positive response to immunotherapy, which might have profound effects on therapeutic practice.

Cross-feeding-based rational design of a probiotic combination of Bacterides xylanisolvens and Clostridium butyricum therapy for metabolic diseases

The human gut microbiota has gained interest as an environmental factor that contributes to health or disease. The development of next-generation live biotherapeutic products (LBPs) is a promising strategy to modulate the gut microbiota and improve human health. In this study, we identified a novel cross-feeding interaction between Bacteroides xylanisolvens and Clostridium butyricum and developed their combination into a novel LBP for treating metabolic syndrome. Using in-silico analysis and in vitro experiments, we demonstrated that B. xylanisolvens supported the growth and butyrate production of C. butyricum by supplying folate, while C. butyricum reciprocated by providing pABA for folate biosynthesis. Animal gavage experiments showed that the two-strain combination LBP exhibited superior therapeutic efficacy against metabolic disorders in high-fat diet-induced obese (DIO) mice compared to either single-strain treatment. Further omics-based analyses revealed that the single-strain treatments exhibited distinct taxonomic preferences in modulating the gut microbiota, whereas the combination LBP achieved more balanced modulation to preserve taxonomic diversity to a greater extent, thereby enhancing the stability and resilience of the gut microbiome. Moreover, the two-strain combinations more effectively restored gut microbial functions by reducing disease-associated pathways and opportunistic pathogen abundance. This work demonstrates the development of new LBP therapy for metabolic diseases from cross-feeding microbial pairs which exerted better self-stability and robust efficacy in complex intestinal environments compared to conventional single-strain LBPs.

Impact of complement C3 levels on the development of healthcare-associated infections in intensive care patients: a retrospective case-control study

PURPOSE

The immune system serves as a critical line of defence against pathogenic microorganisms. To investigate the impact of immune markers, measured within the first 48 h of intensive care unit (ICU) admission, on the incidence of healthcare-associated infections (HAIs) in ICU patients.

METHODS

This case-control study included 364 patients admitted from 1 January 2020 to 30 November 2023, receiving immune marker testing within 48 h of ICU admission. Cox proportional hazard models and propensity score matching evaluated immune markers' association with HAIs risk. Log-rank tests compared time-to-event by C3 levels. All data processing and analysis were performed using R version 4.2.0 (R Foundation for Statistical Computing, Vienna, Austria) and Python version 3.11 (Python Software Foundation, Wilmington, DE).

RESULTS

In total, 258 patients without HAIs (mean [SD] age, 67.24 [17.79] years) and 106 patients with HAIs (mean [SD] age, 73.80 [14.93] years) were included in the final analysis. The HAIs group had older age, longer hospital stay, lower Sequential Organ Failure Assessment (SOFA) scores, and a higher rate of comorbid infections than the non-HAIs group. Also, the HAIs group had a higher proportion of basophils, lymphocytes, monocytes and T suppressor cells (CD3 + CD8+), while the proportion of neutrophils and B cells (CD19+) was lower. After Cox regression analysis and propensity score adjustment, we found that C3 complement levels (HR: 0.40; 95%CI, 0.16-0.98; p = .044) influenced the incidence of HAIs. Patients were then divided into high C3 and low C3 groups based on a cut-off value of 0.455 for C3. A time-to-event plot showed that the median time to HAIs occurrence was nine days in the high C3 group and six days in the low C3 group (p = .048).

CONCLUSIONS

Elevated complement C3 levels may associat with a reduced incidence of HAIs in ICU patients.

The mechanistic action of mogroside V in the alleviation of oxidative aging

INTRODUCE

Diseases related to oxidative ageing are becoming increasingly evident in younger individuals. In this study, we investigated the mechanisms underlying the actions of mogroside V when used to treat anti-oxidative ageing.

METHODS

We used D-galactose-induced LO2 cells and C57BL/6J mice as models to investigate the molecular mechanisms of mogroside V (MV) for the treatment of oxidative ageing. Network pharmacology was used to predict the targets of MV for the treatment of oxidative ageing.

RESULTS

By down-regulating the EGFR/p38/JNK pathway, MV significantly inhibited oxidative ageing and apoptosis in cells, reduced the levels of SA-β-galactosidase. In mice, compared with the model group, MV treatment (100 mg/kg·d) reduced MDA levels and significantly increased the levels of GSH and SOD; furthermore, the size and structure of the liver leaflet and glomeruli was arranged in a regular manner; the small intestine glands had decreased in size. Moreover, the expression levels of Ptp1b mRNA had increased significantly while the levels of c-Jun mRNA and protein were significantly reduced. MV also increased the proportion of beneficial bacteria in the small intestine, including Bacteroidales and Lactobacillaceae.

CONCLUSION

Our analyses revealed that MV can significantly reduce oxidative ageing caused by the accumulation of D-galactose.

Nanoscale warriors against viral invaders: a comprehensive review of Nanobodies as potential antiviral therapeutics

Viral infections remain a significant global health threat, with emerging and reemerging viruses causing epidemics and pandemics. Despite advancements in antiviral therapies, the development of effective treatments is often hindered by challenges, such as viral resistance and the emergence of new strains. In this context, the development of novel therapeutic modalities is essential to combat notorious viruses. While traditional monoclonal antibodies are widely used for the treatment of several diseases, nanobodies derived from heavy chain-only antibodies have emerged as promising "nanoscale warriors" against viral infections. Nanobodies possess unique structural properties that enhance their ability to recognize diverse epitopes. Their small size also imparts properties, such as improved bioavailability, solubility, stability, and proteolytic resistance, making them an ideal class of therapeutics for viral infections. In this review, we discuss the role of nanobodies as antivirals against various viruses. Techniques used for developing nanobodies, delivery strategies are covered, and the challenges and opportunities associated with their use as antiviral therapies are discussed. We also offer insights into the future of nanobody-based antiviral research to support the development of new strategies for managing viral infections.

Gut microbiota and microbial metabolites for osteoporosis

Osteoporosis is an age-related bone metabolic disease. As an essential endocrine organ, the skeletal system is intricately connected with extraosseous organs. The crosstalk between bones and other organs supports this view. In recent years, the link between the gut microecology and bone metabolism has become an important research topic, both in preclinical studies and in clinical trials. Many studies have shown that skeletal changes are accompanied by changes in the composition and structure of the gut microbiota (GM). At the same time, natural or artificial interventions targeting the GM can subsequently affect bone metabolism. Moreover, microbiome-related metabolites may have important effects on bone metabolism. We aim to review the relationships among the GM, microbial metabolites, and bone metabolism and to summarize the potential mechanisms involved and the theory of the gut‒bone axis. We also describe existing bottlenecks in laboratory studies, as well as existing challenges in clinical settings, and propose possible future research directions.

Deciphering the interplay between SETD2 mediated H3K36me3 and RNA N6-methyladenosine in clear cell renal cell carcinoma (ccRCC)

RNA N6-methyladenosine (m6A) plays diverse roles in RNA metabolism and its deregulation contributes to tumor initiation and progression. Clear cell renal cell carcinoma (ccRCC) is characterized by near ubiquitous loss of VHL followed by mutations in epigenetic regulators PBRM1, SETD2, and BAP1. Mutations in SETD2, a histone H3 lysine 36 trimethylase (H3K36me3), are associated with reduced survival, greater metastatic propensity, and metabolic reprogramming. While m6A and H3K36me3 deregulation are separately implicated in renal tumorigenesis, H3K36me3 may participate directly in m6A targeting, but the m6A-H3K36me3 interplay has not been investigated in the context of ccRCC. Using RCC-relevant SETD2 isogenic knockout and rescue cell line models, we demonstrate a dynamic redistribution of m6A in the SETD2 depleted transcriptome, with a subset of transcripts involved in metabolic reprogramming demonstrating SETD2 dependent m6A and expression level changes. Using a panel of six histone modifications we show that m6A redistributes to regions enriched in gained active enhancers upon SETD2 inactivation. Finally, we demonstrate a reversal of transcriptomic programs involved in SETD2 loss mediated metabolic reprogramming, and reduced cell viability through pharmacologic inhibition or genetic ablation of m6A writer METTL3 specific to SETD2 deficient cells. Thus, targeting m6A may represent a novel therapeutic vulnerability in SETD2 mutant ccRCC.

Immune infiltration landscape and potential drug-targeted implications for hepatocellular carcinoma with 'progression/hyper-progression' recurrence

BACKGROUND AND AIMS

Hepatocellular carcinoma (HCC) recurrence was previously characterized into four types, and patients with progression/hyper-progression recurrence (type III-IV) have an extremely poor prognosis. However, the immune background of resectable HCC, particularly in patients who experience recurrence, remains underexplored. Therefore, this study aimed to describe the immune landscape of resectable HCC, especially postoperative type III-IV recurrent HCC, and explore potential immune-targeted anti-relapse strategies for treated populations.

METHODS

The differences in gene expression in patients with recurrent HCC (type I-II (solitary or multi-intrahepatic oligo recurrence) vs. type III-IV) were investigated using bulk sequencing. Multiple immune infiltration methods (single-sample gene set enrichment analysis (GSEA), Microenvironment Cell Populations-counter and ESTIMATE) were used, and patients were divided into four groups to identify four distinct immune subtypes: immune-enrichment/matrix-poor (IE1), immune-enrichment/matrix-rich (IE2), immune intermediate/matrix-rich (ITM) and immune desert/matrix-poor (ID). Co-expression and protein interaction analyses were used to identify characteristic genes in ITM closely associated with type III-IV recurrence, which was matched with drug targets for Huaier granules (HG) and lenvatinib. Virtual docking was used to identify potential therapeutic targets, and the results were verified using single-nuclei RNA sequencing and histological analysis.

RESULTS

ITM was closely related to type III-IV recurrence and exhibited immunotherapy potential. The potential efficacy of inhibiting CCNA2, VEGFA, CXCL8, PLK2, TIMP1, ITGB2, ALDOA, ANXA5 and CSK in ITM reversal was determined. Molecular docking demonstrated that the proteins of these genes could bind to HG or lenvatinib. The immunohistochemical findings demonstrated differential VEGFA (p < .01) and PLK2 (p < .001) expression in ITM type and ID in type III-IV recurrent HCC.

CONCLUSIONS

Three primary immunotypes of resectable HCC (IE2, ITM and ID) were identified, and HG and lenvatinib could potentially overcome immune checkpoint blockade (ICB) resistance in ITM patients with HCC, particularly those classified as type III-IV.

Discussion on the mechanism of HER2 resistance in esophagogastric junction and gastric cancer in the era of immunotherapy

Human epidermal growth factor receptor 2 (HER2) is a critical biomarker and therapeutic target in gastric/gastroesophageal junction (G/GEJ) cancers, despite the initial success of HER2-targeted therapies, such as trastuzumab, resistance to these drugs has emerged as a major impediment to effective long-term treatment. This review examines the mechanisms of drug resistance in HER2-positive G/GEJ cancer, the primary mechanisms of resistance explored include alterations in the HER2 receptor itself, such as mutations and changes in expression levels, as well as downstream signaling pathways, and interactions with the tumor microenvironment (TME). Furthermore, the review discusses the Novel therapeutic approaches, including the use of antibody-drug conjugates (ADCs) and combination therapies are assessed for their potential to enhance outcomes. By integrating recent research findings and clinical trials, this review aims to provide oncologists and researchers with insights into developing more effective treatments for patients with drug-resistant HER2-positive G/GEJ cancer.

The role of the early-life gut microbiome in childhood asthma

Asthma is a chronic disease affecting millions of children worldwide, and in severe cases requires hospitalization. The etiology of asthma is multifactorial, caused by both genetic and environmental factors. In recent years, the role of the early-life gut microbiome in relation to asthma has become apparent, supported by an increasing number of population studies, in vivo research, and intervention trials. Numerous early-life factors, which for decades have been associated with the risk of developing childhood asthma, are now being linked to the disease through alterations of the gut microbiome. These factors include cesarean birth, antibiotic use, breastfeeding, and having siblings or pets, among others. Association studies have highlighted several specific microbes that are altered in children developing asthma, but these can vary between studies and disease phenotype. This demonstrates the importance of the gut microbial ecosystem in asthma, and the necessity of well-designed studies to validate the underlying mechanisms and guide future clinical applications. In this review, we examine the current literature on the role of the gut microbiome in childhood asthma and identify research gaps to allow for future microbial-focused therapeutic applications in asthma.

The role of non-malignant B cells in malignant hematologic diseases

The tumor microenvironment (TME) represents a heterogeneous, complicated ecosystem characterized by intricate interactions between tumor cells and immune cells. During the past decade, immune cells especially T cells were found to play an important role in the progression of tumor and many related immune checkpoints drugs were created. In recent years, more and more scientists revealed the critical role of B-cells within the TME, particularly various populations of non-malignant B cells. Some studies indicated that non-malignant B cells may exert a 'double-edged sword' role in solid tumors. However, there has been comparatively less focus on the role of non-malignant B cells in hematologic malignancies. In this review, we characterized the development of B cells and summarized its functions of antitumor immunity within TME, with an emphasis on elucidating the roles and potential mechanisms of non-malignant B cells in the progression of hematologic diseases including classical Hodgkin's lymphoma, non-Hodgkin's B-cell lymphoma, non-Hodgkin's T-cell lymphoma, leukemia and multiple myeloma.

Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential

Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown. Here, we show that adolescents exhibit significant gut microbiome and metabolome shifts several months after laparoscopic vertical sleeve gastrectomy (VSG), with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited a potentially inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG. We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.

Normal bronchial field basal cells show persistent methylome-wide impact of tobacco smoking, including in known cancer genes

Lung carcinogenesis is causally linked to cigarette smoking, in part by epigenetic changes. We tested whether accumulated epigenetic change in smokers is apparent in bronchial basal cells as cells of origin of squamous cell carcinoma. Using an EM-seq platform covering 53.8 million CpGs (96% of the entire genome) at an average of 7.5 sequencing reads per CpG site at a single base resolution, we evaluated cytology-normal basal cells bronchoscopically brushed from the in situ tobacco smoke-exposed 'bronchial epithelial field' and isolated by short-term primary culture from 54 human subjects. We found that mean methylation was globally lower in ever (former and current) smokers versus never smokers (p = 0.0013) across promoters, CpG shores, exons, introns, 3'-UTRs, and intergenic regions, but not in CpG islands. Among 6mers with dinucleotides flanking CpG, those containing CGCG showed no effect from smoking, while those flanked with TT and AA displayed the strongest effects. At the gene level, smoking-related differences in methylation level were observed in CDKL1, ARTN, EDC3, CYP1B1, FAM131A, and MAGI2. Among candidate cancer genes, smoking reduced the methylation level in KRAS, ROS1, CDKN1A, CHRNB4, and CADM1. We conclude that smoking reduces long-term epigenome-wide methylation in bronchial stem cells, is impacted by the flanking sequence, and persists indefinitely beyond smoking cessation.

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.

Defining enteric bacterial pathogenesis using organoids: Citrobacter rodentium uses EspC, an atypical mucinolytic protease, to penetrate mouse colonic mucus

Enteric bacterial pathogens pose significant threats to human health; however, the mechanisms by which they infect the mammalian gut in the face of daunting host defenses remain to be fully defined. For the attaching and effacing (A/E) bacterial family member and murine pathogen Citrobacter rodentium, its virulence strategy appears to involve penetration of the colonic mucus barrier to reach the underlying epithelium. To better define these interactions, we grew colonoids under air-liquid interface (ALI) conditions, producing a thick mucus layer that mimicked in vivo mucus composition and glycosylation. C. rodentium's penetration of ALI-derived mucus was dramatically enhanced upon exposure to sialic acid, in concert with the secretion of two serine protease autotransporter of Enterobacteriaceae (SPATE) proteins, Pic and EspC. Despite Pic being a class II SPATE, and already recognized as a mucinase, it was EspC, a class I SPATE family member, that degraded ALI-derived mucus, despite class I SPATEs not previously shown to possess mucinase activity. Confirming this finding, E. coli DH5α carrying a plasmid that expresses C. rodentium-derived EspC was able to degrade the mucus. Moreover, recombinant EspC alone also displayed mucinolytic activity in a dose-dependent manner. Collectively, our results reveal the utility of ALI-derived mucus in modeling microbe-host interactions at the intestinal mucosal surface, as well as identify EspC as an atypical class I SPATE that shows significant mucinolytic activity toward ALI-derived mucus.

Limosilactobacillus reuteri - a probiotic gut commensal with contextual impact on immunity

The gut microbiome plays a key role in human health, influencing various biological processes and disease outcomes. The historical roots of probiotics are traced back to Nobel Laureate Élie Metchnikoff, who linked the longevity of Bulgarian villagers to their consumption of sour milk fermented by Lactobacilli. His pioneering work led to the global recognition of probiotics as beneficial supplements, now a multibillion-dollar industry. Modern probiotics have been extensively studied for their immunomodulatory effects. Limosilactobacillus reuteri (L. reuteri), a widely used probiotic, has garnered significant attention for its systemic immune-regulatory properties, particularly in relation to autoimmunity and cancer. This review delves into the role of L. reuteri in modulating immune responses, with a focus on its impact on systemic diseases.