Neuronal guidance signaling in neurodegenerative diseases: Key regulators that function at neuron-glia and neuroimmune interfaces

The nervous system processes a vast amount of information, performing computations that underlie perception, cognition, and behavior. During development, neuronal guidance genes, which encode extracellular cues, their receptors, and downstream signal transducers, organize neural wiring to generate the complex architecture of the nervous system. It is now evident that many of these neuroguidance cues and their receptors are active during development and are also expressed in the adult nervous system. This suggests that neuronal guidance pathways are critical not only for neural wiring but also for ongoing function and maintenance of the mature nervous system. Supporting this view, these pathways continue to regulate synaptic connectivity, plasticity, and remodeling, and overall brain homeostasis throughout adulthood. Genetic and transcriptomic analyses have further revealed many neuronal guidance genes to be associated with a wide range of neurodegenerative and neuropsychiatric disorders. Although the precise mechanisms by which aberrant neuronal guidance signaling drives the pathogenesis of these diseases remain to be clarified, emerging evidence points to several common themes, including dysfunction in neurons, microglia, astrocytes, and endothelial cells, along with dysregulation of neuron-microglia-astrocyte, neuroimmune, and neurovascular interactions. In this review, we explore recent advances in understanding the molecular and cellular mechanisms by which aberrant neuronal guidance signaling contributes to disease pathogenesis through altered cell-cell interactions. For instance, recent studies have unveiled two distinct semaphorin-plexin signaling pathways that affect microglial activation and neuroinflammation. We discuss the challenges ahead, along with the therapeutic potentials of targeting neuronal guidance pathways for treating neurodegenerative diseases. Particular focus is placed on how neuronal guidance mechanisms control neuron-glia and neuroimmune interactions and modulate microglial function under physiological and pathological conditions. Specifically, we examine the crosstalk between neuronal guidance signaling and TREM2, a master regulator of microglial function, in the context of pathogenic protein aggregates. It is well-established that age is a major risk factor for neurodegeneration. Future research should address how aging and neuronal guidance signaling interact to influence an individual's susceptibility to various late-onset neurological diseases and how the progression of these diseases could be therapeutically blocked by targeting neuronal guidance pathways.

Innovative gene delivery systems for retinal disease therapy

The human retina, a complex and highly specialized structure, includes multiple cell types that work synergistically to generate and transmit visual signals. However, genetic predisposition or age-related degeneration can lead to retinal damage that severely impairs vision or causes blindness. Treatment options for retinal diseases are limited, and there is an urgent need for innovative therapeutic strategies. Cell and gene therapies are promising because of the efficacy of delivery systems that transport therapeutic genes to targeted retinal cells. Gene delivery systems hold great promise for treating retinal diseases by enabling the targeted delivery of therapeutic genes to affected cells or by converting endogenous cells into functional ones to facilitate nerve regeneration, potentially restoring vision. This review focuses on two principal categories of gene delivery vectors used in the treatment of retinal diseases: viral and non-viral systems. Viral vectors, including lentiviruses and adeno-associated viruses, exploit the innate ability of viruses to infiltrate cells, which is followed by the introduction of therapeutic genetic material into target cells for gene correction. Lentiviruses can accommodate exogenous genes up to 8 kb in length, but their mechanism of integration into the host genome presents insertion mutation risks. Conversely, adeno-associated viruses are safer, as they exist as episomes in the nucleus, yet their limited packaging capacity constrains their application to a narrower spectrum of diseases, which necessitates the exploration of alternative delivery methods. In parallel, progress has also occurred in the development of novel non-viral delivery systems, particularly those based on liposomal technology. Manipulation of the ratios of hydrophilic and hydrophobic molecules within liposomes and the development of new lipid formulations have led to the creation of advanced non-viral vectors. These innovative systems include solid lipid nanoparticles, polymer nanoparticles, dendrimers, polymeric micelles, and polymeric nanoparticles. Compared with their viral counterparts, non-viral delivery systems offer markedly enhanced loading capacities that enable the direct delivery of nucleic acids, mRNA, or protein molecules into cells. This bypasses the need for DNA transcription and processing, which significantly enhances therapeutic efficiency. Nevertheless, the immunogenic potential and accumulation toxicity associated with non-viral particulate systems necessitates continued optimization to reduce adverse effects in vivo . This review explores the various delivery systems for retinal therapies and retinal nerve regeneration, and details the characteristics, advantages, limitations, and clinical applications of each vector type. By systematically outlining these factors, our goal is to guide the selection of the optimal delivery tool for a specific retinal disease, which will enhance treatment efficacy and improve patient outcomes while paving the way for more effective and targeted therapeutic interventions.

Novel insights into non-coding RNAs and their role in hydrocephalus

A large body of evidence has highlighted the role of non-coding RNAs in neurodevelopment and neuroinflammation. This evidence has led to increasing speculation that non-coding RNAs may be involved in the pathophysiological mechanisms underlying hydrocephalus, one of the most common neurological conditions worldwide. In this review, we first outline the basic concepts and incidence of hydrocephalus along with the limitations of existing treatments for this condition. Then, we outline the definition, classification, and biological role of non-coding RNAs. Subsequently, we analyze the roles of non-coding RNAs in the formation of hydrocephalus in detail. Specifically, we have focused on the potential significance of non-coding RNAs in the pathophysiology of hydrocephalus, including glymphatic pathways, neuroinflammatory processes, and neurological dysplasia, on the basis of the existing evidence. Lastly, we review the potential of non-coding RNAs as biomarkers of hydrocephalus and for the creation of innovative treatments.

Autophagy machinery as exploited by viruses

Viruses adapt and modulate cellular pathways to allow their replication in host cells. The catabolic pathway of macroautophagy, for simplicity referred to as autophagy, is no exception. In this review, we discuss anti-viral functions of both autophagy and select components of the autophagy machinery, and how viruses have evaded them. Some viruses use the membrane remodeling ability of the autophagy machinery to build their replication compartments in the cytosol or efficiently egress from cells in a non-lytic fashion. Some of the autophagy machinery components and their remodeled membranes can even be found in viral particles as envelopes or single membranes around virus packages that protect them during spreading and transmission. Therefore, studies on autophagy regulation by viral infections can reveal functions of the autophagy machinery beyond lysosomal degradation of cytosolic constituents. Furthermore, they can also pinpoint molecular interactions with which the autophagy machinery can most efficiently be manipulated, and this may be relevant to develop effective disease treatments based on autophagy modulation.

Mendelian randomisation studies for causal inference in chronic obstructive pulmonary disease: A narrative review

BACKGROUND AND OBJECTIVE

Most non-randomised controlled trials are unable to establish clear causal relationships in chronic obstructive pulmonary disease (COPD) due to the presence of confounding factors. This review summarises the evidence that the Mendelian randomisation method can be a powerful tool for performing causal inferences in COPD.

METHODS

A non-systematic search of English-language scientific literature was performed on PubMed using the following keywords: 'Mendelian randomisation', 'COPD', 'lung function', and 'GWAS'. No date restrictions were applied. The types of articles selected included randomised controlled trials, cohort studies, observational studies, and reviews.

RESULTS

Mendelian randomisation is becoming an increasingly popular method for identifying the risk factors of COPD. Recent Mendelian randomisation studies have revealed some risk factors for COPD, such as club cell secretory protein-16, impaired kidney function, air pollutants, asthma, and depression. In addition, Mendelian randomisation results suggest that genetically predicted factors such as PM2.5, inflammatory cytokines, growth differentiation factor 15, docosahexaenoic acid, and testosterone may have causal relationships with lung function.

CONCLUSION

Mendelian randomisation is a robust method for performing causal inferences in COPD research as it reduces the impact of confounding factors.

Haematopoietic gene therapy of non-conditioned patients with Fanconi anaemia-A: results from open-label phase 1/2 (FANCOLEN-1) and long-term clinical trials

BACKGROUND

Allogeneic haematopoietic stem-cell transplantation is the standard treatment for bone marrow failure (BMF) in patients with Fanconi anaemia, but transplantation-associated complications such as an increased incidence of subsequent cancer are frequent. The aim of this study was to evaluate the safety and efficacy of the infusion of autologous gene-corrected haematopoietic stem cells as an alternative therapy for these patients.

METHODS

This was an open-label, investigator-initiated phase 1/2 clinical trial (FANCOLEN-1) and long-term follow-up trial (up to 7 years post-treatment) in Spain. Mobilised peripheral blood (PB) CD34+ cells from nine patients with Fanconi anaemia-A in the early stages of BMF were transduced with a therapeutic FANCA-encoding lentiviral vector and re-infused without any cytotoxic conditioning treatment. The primary efficacy endpoint of FANCOLEN-1 was the engraftment of transduced cells, as defined by the detection of at least 0·1 therapeutic vector copies per nucleated cell of patient bone marrow (BM) or PB at the second year post-infusion, without this percentage having declined substantially over the previous year. The safety coprimary endpoint was adverse events during the 3 years after infusion. The completed open-label phase 1/2 and the ongoing long-term clinical trials are registered with ClinicalTrials.gov, NCT03157804; EudraCT, 2011-006100-12; and NCT04437771, respectively.

FINDINGS

There were eight evaluable treated patients with Fanconi anaemia-A. Patients were recruited between Jan 7, 2016 and April 3, 2019. The primary endpoint was met in five of the eight evaluable patients (62·50%). The median number of therapeutic vector copies per nucleated cell of patient BM and PB at the second year post-infusion was 0·18 (IQR 0·01-0·20) and 0·06 (0·01-0·19), respectively. No genotoxic events related to the gene therapy were observed. Most treatment-emergent adverse events (TEAEs) were non-serious and assessed as not related to therapeutic FANCA-encoding lentiviral vector. Nine serious adverse events (grade 3-4) were reported in six patients, one was considered related to medicinal product infusion, and all resolved without sequelae. Cytopenias and viral infections (common childhood illnesses) were the most frequently reported TEAEs.

INTERPRETATION

These results show for the first time that haematopoietic gene therapy without genotoxic conditioning enables sustained engraftment and reversal of BMF progression in patients with Fanconi anaemia.

FUNDING

European Commission, Instituto de Salud Carlos III, and Rocket Pharmaceuticals.

Acetaldehyde-driven mRNA methylation and expression changes in ethanol-metabolizing enzyme genes

This study examines how the alcohol metabolite acetaldehyde modulates mRNA methylation and expression of ethanol-metabolizing genes, uncovering its epigenetic role in ethanol metabolism. Using neuron-like (SH-SY5Y) and non-neuronal (SW620) cellular models, we examined the effects of chronic intermittent acetaldehyde (CIA) exposure and subsequent withdrawal (CIA+WD) on global RNA m6A modifications and the methylation and expression of three brain ethanol-metabolizing genes: CAT (catalase), CYP2E1 (cytochrome P450 2E1), and ALDH2 (aldehyde dehydrogenase 2). A 3-week CIA exposure, with or without 24-hour withdrawal, did not significantly alter global m6A methylation levels in either cell line. However, acetaldehyde exposure/withdrawal induced hypermethylation at the mRNA stop codon regions of ALDH2 (CIA: p = 0.002; CIA+WD: p = 0.055) and CAT (CIA: p = 0.077; CIA+WD: p = 0.036) in SH-SY5Y cells, but not in SW620 cells. Furthermore, ALDH2 mRNA expression was significantly upregulated in both cell types following exposure (SH-SY5Y: p = 0.073 [CIA] and 0.00002 [CIA+WD]; SW620: p = 0.0009 [CIA] and 0.00008 [CIA+WD]). In contrast, CYP2E1 mRNA methylation and the expression of CYP2E1 and CAT remained unchanged. These findings highlight the cell-specific epigenetic effects of acetaldehyde, particularly its role in modulating mRNA methylation and expression of ALDH2, a key enzyme in alcohol metabolism.

Epigenome-wide association study of perceived discrimination in the Multi-Ethnic Study of Atherosclerosis (MESA)

Perceived discrimination, recognized as a chronic psychosocial stressor, has adverse consequences on health. DNA methylation (DNAm) may be a potential mechanism by which stressors get embedded into the human body at the molecular level and subsequently affect health outcomes. However, relatively little is known about the effects of perceived discrimination on DNAm. To identify the DNAm sites across the epigenome that are associated with discrimination, we conducted epigenome-wide association analyses (EWAS) of three discrimination measures (everyday discrimination, race-related major discrimination, and non-race-related major discrimination) in 1,151 participants, including 565 non-Hispanic White, 221 African American, and 365 Hispanic individuals, from the Multi-Ethnic Study of Atherosclerosis (MESA). We conducted both race/ethnicity-stratified analyses as well as trans-ancestry meta-analyses. At false discovery rate of 10%, 7 CpGs and 4 differentially methylated regions (DMRs) containing 11 CpGs were associated with perceived discrimination exposures in at least one racial/ethnic group or in meta-analysis. Identified CpGs and/or nearby genes have been implicated in cellular development pathways, transcription factor binding, cancer and multiple autoimmune and/or inflammatory diseases. Of the identified CpGs (7 individual CpGs and 11 within DMRs), two CpGs and one CpG within a DMR were associated with expression of cis genes NDUFS5, AK1RIN1, NCF4 and ADSSL1. Our study demonstrated the potential influence of discrimination on DNAm and subsequent gene expression.

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.

Microbiota transplant therapy in inflammatory bowel disease: advances and mechanistic insights

Microbiota transplant therapy is an emerging therapy for inflammatory bowel disease, but factors influencing its efficacy and mechanism remain poorly understood. In this narrative review, we outline key elements affecting therapeutic outcomes, including donor factors (such as age and patient relationship), recipient factors, control selection, and elements impacting engraftment and its correlation with clinical response. We also examine potential mechanisms through inflammatory bowel disease trials, focusing on the interplay between the microbiota, host, and immune system. Finally, we briefly explore potential future directions for microbiota transplant therapy and promising emerging treatments.

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.

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.

Multidomain intervention for delaying aging in community-dwelling older adults (MIDA): study design and protocol

BACKGROUND

The exploration of interventions to delay aging is an emerging topic that promotes healthy aging. The multidomain intervention has the potential to be applied in the field of aging because it concentrates on the functional ability of older adults. There is currently no literature reporting on a multidomain intervention involving cognition, exercise and nutrition for delaying aging.

METHODS

The Multidomain Intervention for Delaying Aging in Community-dwelling Older Adults (MIDA) is a Zelen-design randomized controlled trial with a 6-month intervention duration. The multidomain intervention comprises cognitive training, exercise training, and nutritional guidance, delivered through both group sessions and individual family interventions. A total of 248 participants aged 60 to 85 years will be randomized to the intervention group or control group and followed up for 12 months. The primary outcome is the change in epigenetic age acceleration and pace of aging following the multidomain intervention. The secondary outcomes are the changes in frailty score and intrinsic capacity Z-score. Other outcomes include physical functions, body composition, aging biomarkers, inflammatory markers, haematology and biochemistry parameters, and lifestyle factors.

CONCLUSIONS

This study will explore the effects of the multidomain intervention on delaying aging in community-dwelling older adults. We aim to introduce a new approach to delaying aging and offer a practical multidomain intervention strategy for healthcare institutions.

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.

Genome wide landscaping of copy number variations for horse inter-breed variability

Copy number variations (CNVs) have become widely acknowledged as a significant source of genomic variability and phenotypic variance. To understand the genetic variants in horses, CNVs from six Indian horse breeds, namely, Manipuri, Zanskari, Bhutia, Spiti, Kathiawari and Marwari were discovered using Axiom™ Equine Genotyping Array. These breeds differed in agro-climatic adaptation with distinct phenotypic characters. A total of 2668 autosomal CNVs and 381 CNV regions (CNVRs) were identified with PennCNV tool. DeepCNV was employed to re-validate to get 883 autosomal CNVs, of which 9.06% were singleton type. A total of 180 CNVRs were identified after DeepCNV filtering with the estimated length of 3.12 Kb-4.90 Mb. The functional analysis showed the majority of the CNVRs genes enriched for sensory perception and olfactory receptor activity. An Equine CNVs database, EqCNVdb (http://backlin.cabgrid.res.in/eqcnvdb/) was developed which catalogues detailed information on the horse CNVs, CNVRs and gene content within CNVRs. Also, three random CNVRs were validated with real-time polymerase chain reaction. These findings will aid in the understanding the horse genome and serve as a preliminary foundation for future CNV association research with commercially significant equine traits. The identification of CNVs and CNVRs would lead to better insights into genetic basis of important traits.

Comparative genetic analysis of blood and semen samples in sperm donors from Hunan, China

OBJECTIVES

At present, most genetic tests or carrier screening are performed with blood samples, and the known carrier rate of disease-causing variants is also derived from blood. For semen donors, what is really passed on to offspring is the pathogenic variant in their sperm. This study aimed to determine whether pathogenic variants identified in the sperm of young semen donors are also present in their blood, and whether matching results for blood are consistent with results for sperm.

METHODS

We included 40 paired sperm and blood samples from 40 qualified semen donors at the Hunan Province Human Sperm Bank of China. All samples underwent exome sequencing (ES) analysis, and the pathogenicity was assessed according to the American College of Medical Genetics (ACMG) guidelines. Scoring for sperm donation matching, which was based on gene scoring and variant scoring, was also used to assess the consistency of sperm and blood genetic test results.

RESULTS

A total of 108 pathogenic (P)/likely pathogenic (LP) variants in 82 genes were identified. The highest carrier had 7 variants, and there was also one donor did not carry any P/LP variant. On average, each donor carried 2.7 P/LP variants. Among all the P/LP variants, missense mutation was the dominant type and most of them were located in exonic regions. Chromosome 1 harboured the largest number of variants and no pathogenic copy number variants (CNV) was identified in semen donors. The P/LP variant of all the 40 semen donors was consistent by comparing sperm and blood. Except for one case that was slightly different, the rest simulated matching results for blood were all consistent with results for sperm.

CONCLUSIONS

It is reasonable to choose either blood or sperm for genetic screening in semen donors.

Discovery of a selective PI3Kα inhibitor via structure-based virtual screening for targeted colorectal cancer therapy

Colorectal cancer (CRC) remains a leading cause of cancer-related mortality globally, driving an urgent need for effective therapies. A promising avenue of research focuses on the PI3K/AKT/mTOR signalling pathway, which is frequently disrupted by mutations in the PI3Kα subunit. Our cutting-edge study employed a structure-based virtual screening of ∼3000 compounds, leading to the discovery of F0608-0019, a highly potent and selective PI3Kα inhibitor. F0608-0019 demonstrated remarkable efficacy in suppressing HCT116 colorectal cancer cell proliferation, with an IC50 of 12.14 µM, while maintaining high selectivity by minimising activity against other PI3K isoforms. Advanced molecular dynamics simulations highlighted the stability of F0608-0019's binding interactions with key amino acids, such as TRP:780, ILE:932, and VAL:850, which are critical for its targeted action. These exciting findings reveal F0608-0019 as a leading candidate for innovative CRC therapies that selectively target PI3Kα dysregulation, offering promising new possibilities for effective CRC treatment.

A polyepigenetic glucocorticoid exposure score and HPA axis-related DNA methylation are associated with gestational epigenetic aging

Gestational epigenetic aging (GEA) is a novel approach for characterizing associations between prenatal exposures and postnatal risks. Psychosocial adversity in pregnancy may influence GEA, but the molecular mechanisms are not well understood. DNA methylation to glucocorticoid regulation and hypothalamic-pituitary-adrenal (HPA) axis genes are implicated but have not been fully examined in association with GEA. This study investigated whether a polyepigenetic glucocorticoid exposure score (PGES) and HPA axis gene (NR3C1, HSD11B2, FKBP5) methylation were associated with GEA, and whether associations were sex-specific. Participants were from a prospective cohort of racial/ethnic diverse and socially disadvantaged pregnant women and infants (n = 200). DNA methylation variables were estimated using umbilical cord blood. PGES was derived with CpGs shown to be sensitive to synthetic dexamethasone exposure. NR3C1, HSD11B2, and FKBP5 methylation was summarized via factor analysis. We found that PGES (β = -1.12, SE = 0.47, p = 0.02) and several NR3C1 and FKBP5 factor scores were associated with decelerated GEA (all p < 0.05). A significant sex interaction was observed for FKBP5 factor score 3 (β = -0.34, SE = 0.15, p = 0.02) suggesting decelerated GEA for males but not females. This study showed that glucocorticoid regulation-related DNA methylation was associated with a decelerated aging phenotype at birth that might indicate a neonatal risk.

SARS-CoV-2 epidemiology, kinetics, and evolution: A narrative review

Since winter 2019, SARS-CoV-2 has emerged, spread, and evolved all around the globe. We explore 4 y of evolutionary epidemiology of this virus, ranging from the applied public health challenges to the more conceptual evolutionary biology perspectives. Through this review, we first present the spread and lethality of the infections it causes, starting from its emergence in Wuhan (China) from the initial epidemics all around the world, compare the virus to other betacoronaviruses, focus on its airborne transmission, compare containment strategies ("zero-COVID" vs. "herd immunity"), explain its phylogeographical tracking, underline the importance of natural selection on the epidemics, mention its within-host population dynamics. Finally, we discuss how the pandemic has transformed (or should transform) the surveillance and prevention of viral respiratory infections and identify perspectives for the research on epidemiology of COVID-19.

Prp16 enables efficient splicing of introns with diverse exonic consensus elements in the short-intron rich Cryptococcus neoformans transcriptome

DEAH box splicing helicase Prp16 in budding yeast governs spliceosomal remodelling from the branching conformation (C complex) to the exon ligation conformation (C* complex). In this study, we examined the genome-wide functions of Prp16 in the short intron-rich genome of the basidiomycete yeast Cryptococcus neoformans. The presence of multiple introns per transcript with intronic features that are more similar to those of higher eukaryotes makes it a promising model for studying spliceosomal splicing. Using a promoter-shutdown conditional Prp16 knockdown strain, we uncovered genome-wide but substrate-specific roles in C. neoformans splicing. The splicing functions of Prp16 are dependent on helicase motifs I and II, which are conserved motifs for helicase activity. A small subset of introns spliced independent of Prp16 activity was investigated to discover that exonic sequences at the 5' splice site (5'SS) and 3' splice site (3'SS) with stronger affinity for U5 loop 1 are a common feature in these introns. Furthermore, short (60-100nts) and ultrashort introns (<60nts) prevalent in the C. neoformans transcriptome were more sensitive to Prp16 knockdown than longer introns, indicating that Prp16 is required for the efficient splicing of short and ultrashort introns. We propose that stronger U5 snRNA-pre-mRNA interactions enable efficient transition of the spliceosome from the first to the second catalytic confirmation in Prp16 knockdown, particularly for short introns and introns with suboptimal features. This study provides insights into fine-tuning spliceosomal helicase function with variations in cis-element features.

Crosstalk between macrophages and adjacent cells in AKI to CKD transition

Acute kidney injury (AKI), triggered by ischemia, sepsis, toxicity, or obstruction, is marked by a rapid impairment of renal function and could lead to the initiation and advancement of chronic kidney disease (CKD). The concept of AKI to CKD transition has gained much interest. Despite a series of studies highlighting the diverse roles of renal macrophages in the immune response following AKI, the intricate mechanisms of macrophage-driven cell-cell communication in AKI to CKD transition remains incompletely understood. In this review, we introduce the dynamic phenotype change of macrophages under the different stages of kidney injury. Importantly, we present novel perspectives on the extensive interaction of renal macrophages with adjacent cells, including tubular epithelial cells, vascular endothelial cells, fibroblasts, and other immune cells via soluble factors, extracellular vesicles, and direct contact, to facilitate the transition from AKI to CKD. Additionally, we summarize the potential therapeutic strategies based on the adverse macrophage-neighboring cell crosstalk.

tRNA modifications: greasing the wheels of translation and beyond

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

Highly expressed cell wall genes contribute to robustness of sepal size

Reproducibility in organ size and shape is a fascinating trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. Taking the sepal of Arabidopsis as a model, we investigated whether variability of gene expression plays a role in variation of organ size and shape. Previous work from our team identified cell-wall related genes as being enriched among the genes whose expression is highly variable. We then hypothesized that the variation of measured morphological parameters in cell-wall related single knockout mutants could be correlated with the variation in gene expression of the corresponding gene (the knocked-out gene) in wild-type plants. We analyzed sepal size and shape from 16 cell-wall mutants and found that sepal size variability correlates positively, not with gene expression variation, but with mean gene expression of the corresponding gene in wild type. These findings support a contribution of cell-wall related genes to the robustness of sepal size.

Histone modifications in the regulation of erythropoiesis

INTRODUCTION

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

DISCUSSION

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

miRNA-mRNA integrated analysis reveals candidate genes associated with salt stress response in Halophytic Sonneratia apetala

Sonneratia apetala is a pioneering species of mangrove plants, which has evolved various mechanisms to tolerate salt-stress due to their long-term exposure to a salinized environment as compared to the of terrestrial freshwater plants. However, limited attempt has been made to uncover the underlying molecular mechanism of their saline adaptation. Here, we integrated mRNA and microRNA (miRNA) sequencing to identify the genes and pathways that may be involved in salt stress-response in the roots of S. apetala. A comprehensive full‑length transcriptome containing 295,501 high‑quality unigenes was obtained by PacBio sequencing technology. Of these, 6,686 genes exhibited significantly differential accumulation after salt stress treatment (p < 0.001, Q < 0.01). They were mainly implicated in plant signal transduction and diverse metabolic pathways, such as those involving phenylpropanoid biosynthesis, plant-pathogen interaction and protein processing. Also, our results identified the regulatory interaction between miRNA-target counterparts during salt stress. Taken together, we present the first global overview of the transcriptome of S. apetala roots, and identify potentially important genes and pathways associated with salt tolerance for further investigation. This study is expected to deliver novel insights in understanding the regulatory mechanism in S. apetala response to salt stress.

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.

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.

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.

The genetic basis of male and female infertility

This review provides a comprehensive overview of the genetic factors underlying male and female infertility. Infertility affects an estimated one in six couples worldwide, with both male and female factors contributing equally to its prevalence. Approximately, 50% of infertility cases are attributed to genetic causes. We explore three main categories of genetic causes: chromosomal abnormalities, monogenic disorders, and syndromic conditions. Chromosomal causes, including numerical and structural aberrations, are discussed with a focus on their impact on gametogenesis and reproductive outcomes. We review key monogenic causes of infertility, highlighting recent discoveries in genes critical for gonadal development, gametogenesis, and hormonal regulation. Syndromic conditions affecting fertility are examined, highlighting their impact on reproductive function. Throughout the review, we address the challenges in identifying genetic mechanisms of infertility, particularly focusing on the intricate processes involved in oogenesis and spermatogenesis. We also discuss how advancements in genetic testing, such as next-generation sequencing (NGS) and genome-wide association studies (GWAS), have significantly enhanced our understanding of idiopathic infertility and promise further insights in the future. We also discuss the clinical implications of genetic diagnoses, including the role of preimplantation genetic testing (PGT) and genetic counseling in reproductive medicine. This review synthesizes current knowledge on the genetic basis of infertility, providing a comprehensive overview of chromosomal, monogenic, and syndromic causes. It aims to offer readers a solid foundation for understanding the complex genetic factors underlying reproductive disorders.

Comparing Campylobacter jejuni to three other enteric pathogens in OligoMM12 mice reveals pathogen-specific host and microbiota responses

Campylobacter jejuni, non-typhoidal Salmonella spp., Listeria monocytogenes and enteropathogenic/enterohemorrhagic Escherichia coli (EPEC/EHEC) are leading causes of food-borne illness worldwide. Citrobacter rodentium has been used to model EPEC and EHEC infection in mice. The gut microbiome is well-known to affect gut colonization and host responses to many food-borne pathogens. Recent progress has established gnotobiotic mice as valuable models to study how microbiota affect the enteric infections by S. Typhimurium, C. rodentium and L. monocytogenes. However, for C. jejuni, we are still lacking a suitable gnotobiotic mouse model. Moreover, the limited comparability of data across laboratories is often negatively affected by variations between different research facilities or murine microbiotas. In this study, we applied the standardized gnotobiotic OligoMM12 microbiota mouse model and compared the infections in the same facility. We provide evidence of robust colonization and significant pathological changes in OligoMM12 mice following infection with these pathogens. Moreover, we offer insights into pathogen-specific host responses and metabolite signatures, highlighting the advantages of a standardized mouse model for direct comparisons of factors influencing the pathogenesis of major food-borne pathogens. Notably, we reveal for the first time that C. jejuni stably colonizes OligoMM12 mice, triggering inflammation. Additionally, our comparative approach successfully identifies pathogen-specific responses, including the detection of genes uniquely associated with C. jejuni infection in humans. These findings underscore the potential of the OligoMM12 model as a versatile tool for advancing our understanding of food-borne pathogen interactions.

Klebsiella pneumoniae derived outer membrane vesicles mediated bacterial virulence, antibiotic resistance, host immune responses and clinical applications

Klebsiella pneumoniae is a gram-negative pathogen that can cause multiple diseases including sepsis, urinary tract infections, and pneumonia. The escalating detections of hypervirulent and antibiotic-resistant isolates are giving rise to growing public concerns. Outer membrane vesicles (OMVs) are spherical vesicles containing bioactive substances including lipopolysaccharides, peptidoglycans, periplasmic and cytoplasmic proteins, and nucleic acids. Emerging studies have reported various roles of OMVs in bacterial virulence, antibiotic resistance, stress adaptation, and host interactions, whereas knowledge on their roles in K. pneumoniae is currently unclear. In this review, we summarized recent progress on the biogenesis, components, and biological function of K. pneumoniae OMVs, the impact and action mechanism in virulence, antibiotic resistance, and host immune response. We also deliberated on the potential of K. pneumoniae OMVs in vaccine development, as diagnostic biomarkers, and as drug nanocarriers. In conclusion, K. pneumoniae OMVs hold great promise in the prevention and control of infectious diseases, which merits further investigation.

Advances in deciphering the mechanisms of salt tolerance in Maize

Maize (Zea mays L.) is a vital crop worldwide, serving as a cornerstone for food security, livestock feed, and biofuel production. However, its cultivation is increasingly jeopardized by environmental challenges, notably soil salinization, which severely constrains growth, yield, and quality. To combat salinity stress, maize employs an array of adaptive mechanisms, including enhanced antioxidant enzyme activity and modulated plant hormone levels, which work synergistically to maintain reactive oxygen species (ROS) balance and ion homeostasis. This review explores the intricate interactions among ROS, antioxidant systems, plant hormones, and ion regulation in maize under salt stress, providing a comprehensive understanding of the physiological and molecular basis of its tolerance. By elucidating these mechanisms, this study contributes to the development of salt-tolerant maize varieties and informs innovative strategies to sustain agricultural productivity under adverse environmental conditions, offering significant theoretical insights into plant stress biology and practical solutions for achieving sustainable agriculture amidst global climate challenges.

Roles of ABCA1 in Chronic Obstructive Pulmonary Disease

Chronic obstructive pulmonary disease (COPD) is one of the common chronic respiratory diseases, which causes a heavy burden to patients and society. Increasing studies suggest that ABCA1 plays an important role in COPD. ABCA1 belongs to a large class of ATP-binding (ABC) transporters. It is not only involved in the reverse transport of cholesterol, but also in the regulation of apoptosis, pyroptosis, cellular inflammation and cellular immunity. Meanwhile, ABCA1 is involved in several signaling pathways, such as SREBP pathway, LXR pathway, MAPK pathway, p62/mTOR pathway, CTRP1 pathway and so on. In addition, the ABCA1 participates in the disorder of lipid metabolism in COPD by regulating the formation of RCT and HDL, regulates the inflammation of COPD by removing excess cholesterol in macrophages, and promotes the differentiation of COPD phenotype into emphysema type. Accordingly, the ABCA1 may be a therapeutic target for COPD.

SIRT1/DNMT3B-mediated epigenetic gene silencing in response to phytoestrogens in mammary epithelial cells

We performed an integrated analysis of genome-wide DNA methylation and expression datasets in normal cells and healthy animals exposed to polyphenols with estrogenic activity (i.e. phytoestrogens). We identified that phytoestrogens target genes linked to disrupted cellular homeostasis, e.g. genes limiting DNA break repair (RNF169) or promoting ribosomal biogenesis (rDNA). Existing evidence suggests that DNA methylation may be governed by sirtuin 1 (SIRT1) deacetylase via interactions with DNA methylating enzymes, specifically DNMT3B. Since SIRT1 was reported to be regulated by phytoestrogens, we test whether phytoestrogens suppress genes related to disrupted homeostasis via SIRT1/DNMT3B-mediated transcriptional silencing. Human MCF10A mammary epithelial cells were treated with phytoestrogens, pterostilbene (PTS) or genistein (GEN), followed by analysis of cell growth, DNA methylation, gene expression, and SIRT1/DNMT3B binding. SIRT1 occupancy at the selected phytoestrogen-target genes, RNF169 and rDNA, was accompanied by consistent promoter hypermethylation and gene downregulation in response to GEN, but not PTS. GEN-mediated hypermethylation and SIRT1 binding were linked to a robust DNMT3B enrichment at RNF169 and rDNA promoters. This was not observed in cells exposed to PTS, suggesting a distinct mechanism of action. Although both SIRT1 and DNMT3B bind to RNF169 and rDNA promoters upon GEN, the two proteins do not co-occupy the regions. Depletion of SIRT1 abolishes GEN-mediated decrease in rDNA expression, suggesting SIRT1-dependent epigenetic suppression of rDNA by GEN. These findings enhance our understanding of the role of SIRT1-DNMT3B interplay in epigenetic mechanisms mediating the impact of phytoestrogens on cell biology and cellular homeostasis.

Correlation of extracellular vesicle Alu RNA with brain aging and neuronal injury: a potential biomarker for brain aging

BACKGROUND

Extracellular vesicles (EVs) are promising biomarkers for neurodegeneration. Alu elements are retrotransposons increasingly expressed with age and may be involved in aging-related diseases.

OBJECTIVE

To determine the potential of Alu RNA in plasma-derived EVs as a biomarker for brain aging and neuronal injury.

METHODS

EVs were isolated from plasma samples across different age groups. EV Alu RNA levels were measured and their associations with biomarkers of brain aging, including plasma neurofilament light chain (NfL), plasma amyloid-beta (Aβ42 and Aβ40), and plasma phosphorylated tau (p-Tau181), were analyzed.

RESULTS

EV Alu RNA levels were increased significantly with age and were strongly correlated with plasma NfL, suggesting a strong association between EV Alu RNA and neuronal injury. Significant correlations were also found between EV Alu RNA and plasma amyloid-beta levels, while no significant association was observed with tau pathology.

CONCLUSIONS

EV Alu RNA levels are elevated with age and associated with neuronal injury, highlighting their potential as a novel, non-invasive biomarker for brain aging and neurodegeneration.

EIciRNAs in focus: current understanding and future perspectives

Circular RNAs (circRNAs) are a unique class of covalently closed single-stranded RNA molecules that play diverse roles in normal physiology and pathology. Among the major types of circRNA, exon-intron circRNA (EIciRNA) distinguishes itself by its sequence composition and nuclear localization. Recent RNA-seq technologies and computational methods have facilitated the detection and characterization of EIciRNAs, with features like circRNA intron retention (CIR) and tissue-specificity being characterized. EIciRNAs have been identified to exert their functions via mechanisms such as regulating gene transcription, and the physiological relevance of EIciRNAs has been reported. Within this review, we present a summary of the current understanding of EIciRNAs, delving into their identification and molecular functions. Additionally, we emphasize factors regulating EIciRNA biogenesis and the physiological roles of EIciRNAs based on recent research. We also discuss the future challenges in EIciRNA exploration, underscoring the potential for novel functions and functional mechanisms of EIciRNAs for further investigation.

Etiology of nephrotic syndrome: insights from univariate and multivariate Mendelian randomization study

Nephrotic syndrome (NS) is a common cause of chronic glomerular disease. However, the precise way in which one or more risk exposure traits of renal injury lead to NS remains unclear. In this study, we systematically examined the causal relationships between NS and various exposure traits, including traits related to chronic hepatitis B/C infection, COVID-19 (hospitalized), general allergy status, herbal tea intake, immunoglobulin E, childhood obesity, and the human leukocyte antigen (HLA)-II histocompatibility DM α/DP β1/DQ α2 chain, via multivariate Mendelian randomization (MVMR). A previously reported exposure trait, ulcerative colitis, was also included to analyze the independent effect of each significant exposure on the risk of developing NS. In the univariable MR analysis, immunoglobulin E (OR = 5.62, 95% CI = 2.91-10.84, p = 2.67 × 10-7) and the HLA-II histocompatibility DQ α2 chain (OR = 0.70, 95% CI = 0.63-0.80, p = 2.83 × 10-7) were shown to have effect estimates consistent with a greater risk of developing NS. The reverse MR analysis showed no evidence of causal effect from NS to histocompatibility DQ α2 chain (p = 0.76). In MVMR, only the HLA-II histocompatibility DQ α2 chain retained a robust effect (OR = 0.71, 95% CI = 0.61-0.82; p = 9.39 × 10-6), and the estimate for immunoglobulin E was weakened (OR = 1.04, 95% CI = 0.60-2.13; p = 0.92). With two independent ulcerative colitis resources used for validation, ulcerative colitis was not significantly associated with NS. This study provides genetic evidence that the HLA-II histocompatibility DQ α2 chain has a predominant causal effect on the risk of developing NS. HLA-II histocompatibility-mediated immune abnormalities may lead to subtypes of NS and its pathological changes.

Childhood maltreatment and mental health: causal links to depression, anxiety, non-fatal self-harm, suicide attempts, and PTSD

Background: This study aims to elucidate the causal relationship between childhood maltreatment (CM) and subsequent mental health outcomes, including major depressive disorder (MDD), anxiety (ANX), post-traumatic stress disorder (PTSD), suicide attempts, and non-fatal self-harm. Utilising Mendelian Randomisation (MR) and genome-wide association studies (GWAS) data from individuals of European descent, this research applies a rigorous analytical methodology to large-scale datasets, overcoming the confounding variables inherent in previous observational studies.Methods: Genetic data were obtained from publicly available GWAS on individuals of European ancestry, focusing on Childhood Maltreatment (CM), Major Depressive Disorder (MDD), Anxiety (ANX), Post-Traumatic Stress Disorder (PTSD), Age at First Episode of Depression, Number of Depression Episodes, Non-fatal self-harm, and Suicide Attempts. Mendelian Randomisation (MR) analyses were conducted to investigate the causal impact of CM on these outcomes. Sensitivity analyses included IVW, MR Egger, WM, and MR-PRESSO. FDR corrections were applied to account for multiple testing. Results were presented as odds ratios (ORs) with confidence intervals (CIs).Results: Significant associations were identified between CM and the likelihood of developing MDD (IVW: OR = 2.28, 95% CI = 1.66-3.14, PFDR < .001), ANX (IVW: OR = 1.01, 95% CI = 1.00-1.02, PFDR =.032), and PTSD (IVW: OR = 2.29, 95% CI = 1.43-3.67, PFDR =.001). CM was also linked to increased non-fatal self-harm (IVW: OR = 1.06, 95% CI = 1.04-1.08, PFDR <.001), higher frequency of depressive episodes (IVW: β=0.31, 95% CI = 0.17-0.46, PFDR <.001), and earlier onset of depression (IVW: β=-0.17, 95% CI = -0.32 to - 0.02, PFDR =.033). No significant association was found between CM and suicide attempts (IVW: OR = 1.09, 95% CI = 0.81-1.45, PFDR =.573).Conclusion: This study provides robust evidence that CM is a significant causal factor for MDD, ANX, PTSD, and non-fatal self-harming behaviours. It is associated with a higher frequency of depressive episodes and earlier onset of depression. These findings highlight the need for early intervention and targeted prevention strategies to address the long-lasting psychological impacts of CM.

Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease

Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.

The role of peripheral blood microRNAs in the pathogenesis and treatment response of age-related macular degeneration

Age-related macular degeneration is a leading cause of vision loss in aging populations, driven by complex interactions between genetic, environmental, and molecular factors. MicroRNAs have emerged as crucial regulators of cellular processes such as oxidative stress, inflammation, and angiogenesis, all of which contribute to AMD pathogenesis. This narrative review aims to summarize the involvement of peripheral blood microRNAs in the pathogenesis of AMD, focusing on key pathways such as oxidative stress, inflammation, and angiogenesis. Additionally, it explores their potential as biomarkers for predicting treatment response, particularly to anti-VEGF therapies. The potential of miRNAs as noninvasive biomarkers for early diagnosis and personalized treatment strategies is also explored, highlighting future directions for research.

Alternative splicing of the Snap23 microexon is regulated by MBNL, QKI, and RBFOX2 in a tissue-specific manner and is altered in striated muscle diseases

The reprogramming of alternative splicing networks during development is a hallmark of tissue maturation and identity. Alternative splicing of microexons (small, genomic regions ≤ 51 nucleotides) functionally regulate protein-protein interactions in the brain and is altered in several neuronal diseases. However, little is known about the regulation and function of alternatively spliced microexons in striated muscle. Here, we investigated alternative splicing of a microexon in the synaptosome-associated protein 23 (Snap23) encoded gene. We found that inclusion of this microexon is developmentally regulated and tissue-specific, as it occurs exclusively in adult heart and skeletal muscle. The alternative region is highly conserved in mammalian species and encodes an in-frame sequence of 11 amino acids. Furthermore, we showed that alternative splicing of this microexon is mis-regulated in mouse models of heart and skeletal muscle diseases. We identified the RNA-binding proteins (RBPs) quaking (QKI) and RNA binding fox-1 homolog 2 (RBFOX2) as the primary splicing regulators of the Snap23 microexon. We found that QKI and RBFOX2 bind downstream of the Snap23 microexon to promote its inclusion, and this regulation can be escaped when the weak splice donor is mutated to the consensus 5' splice site. Finally, we uncovered the interplay between QKI and muscleblind-like splicing regulator (MBNL) as an additional, but minor layer of Snap23 microexon splicing control. Our results are one of the few reports detailing microexon alternative splicing regulation during mammalian striated muscle development.

Association between early heart rate trajectories in post-PCI STEMI patients and prognosis after hospital discharge

BACKGROUND

Timely percutaneous coronary intervention (PCI) is crucial for restoring myocardial blood supply in ST-segment elevation myocardial infarction (STEMI) patients, with the first 72 h being a critical period for early ventricular remodelling. The association between heart rate trajectories within this period and after hospital discharge outcomes in STEMI patients post-PCI remains unclear.

METHODS

We conducted a retrospective study involving STEMI patients who underwent successful PCI at three tertiary hospitals in Zhejiang Province, China. Heart rate data were collected every 8 h post-PCI through nursing records, along with intraoperative findings and biochemical markers. Using trajectory modelling, we identified heart rate patterns at 24, 48 and 72 h post-PCI, determined the optimal number of trajectory groups using Akaike information criterion (AIC) and Bayesian information criterion (BIC) criteria, and performed a minimum 3-month follow-up. Cox regression analysed the association between early heart rate trajectories and major adverse cardiovascular events (MACEs) post-discharge. The prognostic value of trajectory models was assessed using the area under the curve (AUC).

RESULTS

A total of 1257 patients were included, with an average follow-up duration of 28.72 ± 21.14 months and a mean age of 60.42 ± 14.19 years; 1013 (80.59%) were male. Growth mixture modelling identified four distinct heart rate trajectory groups at 24, 48 and 72 h post-PCI. Higher heart rate trajectories with rates greater than 80 bpm were strongly associated with MACEs, and the 72-hour heart rate trajectory showed a predictive value for MACEs (AUC = 0.745, 95% CI: 0.709-0.781).

CONCLUSIONS

Elevated heart rate trajectories exceeding 80 bpm within 72 h after PCI are associated with an increased risk of MACEs post-discharge. Heart rate management should be further emphasized in post-PCI STEMI patients.

Poly-epigenetic scores for cardiometabolic risk factors interact with demographic factors and health behaviors in older US Adults

Poly-epigenetic scores (PEGS) are surrogate measures that help capture individual-level risk. Understanding how the associations between PEGS and cardiometabolic risk factors vary by demographics and health behaviors is crucial for lowering the burden of cardiometabolic diseases. We used results from established epigenome-wide association studies to construct trait-specific PEGS from whole blood DNA methylation for systolic and diastolic blood pressure (SBP, DBP), body mass index (BMI), C-reactive protein (CRP), high- and low-density lipoprotein cholesterol (HDL-C, LDL-C), triglycerides (TG), and fasting glucose. Overall and race-stratified associations between PEGS and corresponding traits were examined in adults >50 years from the Health and Retirement Study (n = 3,996, mean age = 79.5 years). We investigated how demographics (age, sex, educational attainment) and health behaviors (smoking, alcohol consumption, physical activity) modified these associations. All PEGS were positively associated with their corresponding cardiometabolic traits (p < 0.05), and most associations persisted across all racial/ethnic groups. Associations for BMI, HDL-C, and TG were stronger in younger participants, and BMI and HDL-C associations were stronger in females. The CRP association was stronger among those with a high school degree. Finally, the HDL-C association was stronger among current smokers. These findings support PEGS as robust surrogate measures and suggest the associations may differ among subgroups.

Ferroptosis and hearing loss: from molecular mechanisms to therapeutic interventions

Hearing loss profoundly affects social engagement, mental health, cognition, and brain development, with sensorineural hearing loss (SNHL) being a major concern. Linked to ototoxic medications, ageing, and noise exposure, SNHL presents significant treatment challenges, highlighting the need for effective prevention and regeneration strategies. Ferroptosis, a distinct form of cell death featuring iron-dependent lipid peroxidation, has garnered interest due to its potential role in cancer, ageing, and neuronal degeneration, especially hearing loss. The emerging role of ferroptosis as a crucial mediator in SNHL suggests that it may offer a novel therapeutic target for otoprotection. This review aims to summarise the intricate connection between ferroptosis and SNHL, offering a fresh perspective for exploring targeted therapeutic strategies that could potentially mitigate cochlear cells damage and enhance the quality of life for individuals with hearing impairments.

RNA-binding proteins as therapeutic targets in cancer

RNA-binding proteins (RBPs) have emerged as critical regulators of cancer progression, influencing virtually all hallmarks of cancer. Their ability to modulate gene expression patterns that promote or inhibit tumorigenesis has positioned RBPs as promising targets for novel anti-cancer therapies. This mini-review summarizes the current state of RBP-targeted cancer treatments, focusing on five examples, eIF4F, FTO, SF3B1, RBM39 and nucleolin. We highlight the diversity of current targeting approaches and discuss ongoing challenges including the complexity of RBP regulatory networks, potential off-target effects and the need for more specific targeting methods. By assessing the future potential of novel therapeutic avenues, we provide insights into the evolving landscape of cancer treatment and the critical role RBPs may play in next-generation therapeutics.

Nucleolar ribosomal RNA synthesis continues in differentiating lens fiber cells until abrupt nuclear degradation required for ocular lens transparency

Cellular differentiation requires highly coordinated action of all three transcriptional systems to produce rRNAs, mRNAs and various 'short' and 'long' non-coding RNAs by RNA Polymerase I, II and III systems, respectively. RNA Polymerase I catalyzes transcription of about 400 copies of mammalian rDNA genes, generating 18S, 5.8S and 28S rRNA molecules. Lens fiber cell differentiation is a unique process to study transcriptional mechanisms of individual crystallin genes as their very high transcriptional outputs are directly comparable only to globin genes in erythrocytes. Importantly, both terminally differentiated lens fiber cells and mammalian erythrocytes degrade their nuclei through different mechanisms. In lens, the generation of the organelle-free zone (OFZ) includes the degradation of mitochondria, endoplasmic reticulum, Golgi apparatus and nuclei. Here, using RNA fluorescence in situ hybridization (FISH), we evaluated nascent rRNA transcription, located in the nucleoli, during the process of mouse lens fiber cell differentiation. Lens fiber cell nuclei undergo morphological changes including chromatin condensation prior to their denucleation. Remarkably, nascent rRNA transcription persists in all nuclei that are in direct proximity of the OFZ. Additionally, changes in both nuclei and nucleoli shape were evaluated via immunofluorescence detection of fibrillarin, nucleolin, UBF and other proteins. These studies demonstrate for the first time that highly condensed lens fiber cell nuclei have the capacity to support nascent rRNA transcription. Thus, we propose that 'late' production of rRNA molecules and consequently of ribosomes increases crystallin protein synthesis machinery within the mature lens fibers.

Inhibition of hepatic gluconeogenesis in type 2 diabetes by metformin: complementary role of nitric oxide

Metformin is the first-line treatment for type 2 diabetes mellitus. Type 2 diabetes mellitus is associated with decreased nitric oxide bioavailability, which has significant metabolic implications, including enhanced insulin secretion and peripheral glucose utilization. Similar to metformin, nitric oxide also inhibits hepatic glucose production, mainly by suppressing gluconeogenesis. This review explores the combined effects of metformin and nitric oxide on hepatic gluconeogenesis and proposes the potential of a hybrid metformin-nitric oxide drug for managing type 2 diabetes mellitus. Both metformin and nitric oxide inhibit gluconeogenesis through overlapping and distinct mechanisms. In hepatic gluconeogenesis, mitochondrial oxaloacetate is exported to the cytoplasm via various pathways, including the malate, direct, aspartate, and fumarate pathways. The effects of nitric oxide and metformin on the exportation of oxaloacetate are complementary; nitric oxide primarily inhibits the malate pathway, while metformin strongly inhibits the fumarate and aspartate pathways. Furthermore, metformin effectively blocks gluconeogenesis from lactate, glycerol, and glutamine, whereas nitric oxide mainly inhibits alanine-induced gluconeogenesis. Additionally, nitric oxide contributes to the adenosine monophosphate-activated protein kinase-dependent inhibition of gluconeogenesis induced by metformin. The combined use of metformin and nitric oxide offers the potential to mitigate common side effects. For example, lactic acidosis, a known side effect of metformin, is linked to nitric oxide deficiency, while the oxidative and nitrosative stress caused by nitric oxide could be counterbalanced by metformin's enhancement of glutathione. Metformin also amplifies nitric oxide -induced activation of adenosine monophosphate-activated protein kinase. In conclusion, a metformin-nitric oxide hybrid drug can benefit patients with type 2 diabetes mellitus by enhancing the inhibition of hepatic gluconeogenesis, decreasing the required dose of metformin for maintaining optimal glycemia, and lowering the incidence of metformin-associated lactic acidosis.

Identification of differentially expressed non-coding RNAs in the plasma of women with preterm birth

This study aimed to identify differentially expressed non-coding RNAs (ncRNAs) associated with preterm birth (PTB) and determine biological pathways being influenced in the context of PTB. We processed cell-free RNA sequencing data and identified seventeen differentially expressed (DE) ncRNAs that could be involved in the onset of PTB. Per the validation via customized RT-qPCR, the recorded variations in expressions of eleven ncRNAs were concordant with the in-silico analyses. The results of this study provide insights into the role of DE ncRNAs and their impact on pregnancy-related biological pathways that could lead to PTB. Further studies are required to elucidate the precise mechanisms by which these DE ncRNAs contribute to adverse pregnancy outcomes (APOs) and their potential as diagnostic biomarkers.

A tombus-like virus in patients with lower respiratory tract infection: an observational study based on meta-transcriptomic sequencing

The identification of a novel virus related to the family Tombusviridae, provisionally named human tombus-like virus (hTLV), is significant in the context of ongoing surveillance for respiratory pathogens. Meta-transcriptomic sequencing was utilized to detect respiratory pathogens in patients with lower respiratory tract infections (LRIs) in Jinan, China, from 2022 to 2023. The additional hTLV infections were identified through retrospective analysis of meta-transcriptome data collected in Beijing, China, from 2016 to 2019, prior to the COVID-19 outbreak. Phylogenetic analyzes indicated that hTLVs were clustered with a Jingmen tombus-like virus 2 but in a distinct clade. The hTLVs genomes consist of a single-stranded positive-sense RNA genomes of 4.7-4.8 kb in size, and contained four putative open reading frames (ORF1-4). The RNA-dependent RNA polymerase protein of hTLV shared significant sequence similarity containing three conserved motifs with 15, 24, and 15 amino acids, respectively. The hTLV genome included the canonical Gly376-Asp377-Asp378 (GDD) catalytic residues, which were a unifying feature of viruses in the family Tombusviridae. The main clinical manifestations of the 23 patients were fever, cough, expectoration and dyspnea, with varying degrees of lung infection or abnormalities in other laboratory indicators. Serological studies showed that fourfold rise in IgG titers in sera of a patient between acute and convalescent phase by ELISA. Identification of the pathogens for acute respiratory tract infections is essential for timely public health interventions and clinical management. The discovery of a novel virus, hTLV, in patients with LRIs highlights the continuous emergence of new respiratory pathogens in humans.

Mouse strain-specific responses along the gut-brain axis upon fecal microbiota transplantation from children with autism

Several factors are linked to the pathophysiology of autism spectrum disorders (ASD); however, the molecular mechanisms of the condition remain unknown. As intestinal problems and gut microbiota dysbiosis are associated with ASD development and severity, recent studies have focused on elucidating the microbiota-gut-brain axis' involvement. This study aims to explore mechanisms through which gut microbiota might influence ASD. Briefly, we depleted the microbiota of conventional male BALB/cAnNCrl (Balb/c) and C57BL/6J (BL/6) mice prior to human fecal microbiota transplantation (hFMT) with samples from children with ASD or their neurotypical siblings. We found mouse strain-specific responses to ASD hFMT. Notably, Balb/c mice exhibit decreased exploratory and social behavior, and show evidence of intestinal, systemic, and central inflammation accompanied with metabolic shifts. BL/6 mice show less changes after hFMT. Our results reveal that gut microbiota alone induce changes in ASD-like behavior, and highlight the importance of mouse strain selection when investigating multifactorial conditions like ASD.