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.

Stress granules: Guardians of cellular health and triggers of disease

Stress granules are membraneless organelles that serve as a protective cellular response to external stressors by sequestering non-translating messenger RNAs (mRNAs) and regulating protein synthesis. Stress granules formation mechanism is conserved across species, from yeast to mammals, and they play a critical role in minimizing cellular damage during stress. Composed of heterogeneous ribonucleoprotein complexes, stress granules are enriched not only in mRNAs but also in noncoding RNAs and various proteins, including translation initiation factors and RNA-binding proteins. Genetic mutations affecting stress granule assembly and disassembly can lead to abnormal stress granule accumulation, contributing to the progression of several diseases. Recent research indicates that stress granule dynamics are pivotal in determining their physiological and pathological functions, with acute stress granule formation offering protection and chronic stress granule accumulation being detrimental. This review focuses on the multifaceted roles of stress granules under diverse physiological conditions, such as regulation of mRNA transport, mRNA translation, apoptosis, germ cell development, phase separation processes that govern stress granule formation, and their emerging implications in pathophysiological scenarios, such as viral infections, cancer, neurodevelopmental disorders, neurodegeneration, and neuronal trauma.

Investigation of epilepsy-related genes in a Drosophila model

Complex genetic architecture is the major cause of heterogeneity in epilepsy, which poses challenges for accurate diagnosis and precise treatment. A large number of epilepsy candidate genes have been identified from clinical studies, particularly with the widespread use of next-generation sequencing. Validating these candidate genes is emerging as a valuable yet challenging task. Drosophila serves as an ideal animal model for validating candidate genes associated with neurogenetic disorders such as epilepsy, due to its rapid reproduction rate, powerful genetic tools, and efficient use of ethological and electrophysiological assays. Here, we systematically summarize the advantageous techniques of the Drosophila model used to investigate epilepsy genes, including genetic tools for manipulating target gene expression, ethological assays for seizure-like behaviors, electrophysiological techniques, and functional imaging for recording neural activity. We then introduce several typical strategies for identifying epilepsy genes and provide new insights into gene‒gene interactions in epilepsy with polygenic causes. We summarize well-established precision medicine strategies for epilepsy and discuss prospective treatment options, including drug therapy and gene therapy for genetic epilepsy based on the Drosophila model. Finally, we also address genetic counseling and assisted reproductive technology as potential approaches for the prevention of genetic epilepsy.

Synaptic and synchronic impairments in subcortical brain regions associated with early non-cognitive dysfunction in Alzheimer's disease

For many decades, Alzheimer's disease research has primarily focused on impairments within cortical and hippocampal regions, which are thought to be related to cognitive dysfunctions such as memory and language deficits. The exact cause of Alzheimer's disease is still under debate, making it challenging to establish an effective therapy or early diagnosis. It is widely accepted that the accumulation of amyloid-beta peptide in the brain parenchyma leads to synaptic dysfunction, a critical step in Alzheimer's disease development. The traditional amyloid cascade model is initiated by accumulating extracellular amyloid-beta in brain areas essential for memory and language. However, while it is possible to reduce the presence of amyloid-beta plaques in the brain with newer immunotherapies, cognitive symptoms do not necessarily improve. Interestingly, recent studies support the notion that early alterations in subcortical brain regions also contribute to brain damage and precognitive decline in Alzheimer's disease. A body of recent evidence suggests that early Alzheimer's disease is associated with alterations (e.g., motivation, anxiety, and motor impairment) in subcortical areas, such as the striatum and amygdala, in both human and animal models. Also, recent data indicate that intracellular amyloid-beta appears early in subcortical regions such as the nucleus accumbens, locus coeruleus, and raphe nucleus, even without extracellular amyloid plaques. The reported effects are mainly excitatory, increasing glutamatergic transmission and neuronal excitability. In agreement, data in Alzheimer's disease patients and animal models show an increase in neuronal synchronization that leads to electroencephalogram disturbances and epilepsy. The data indicate that early subcortical brain dysfunctions might be associated with non-cognitive symptoms such as anxiety, irritability, and motivation deficits, which precede memory loss and language alterations. Overall, the evidence reviewed suggests that subcortical brain regions could explain early dysfunctions and perhaps be targets for therapies to slow disease progression. Future research should focus on these non-traditional brain regions to reveal early pathological alterations and underlying mechanisms to advance our understanding of Alzheimer's disease beyond the traditionally studied hippocampal and cortical circuits.

Polymorphisms and haplotypes of TOLLIP and MUC5B are associated with susceptibility and survival in patients with fibrotic hypersensitivity pneumonitis

INTRODUCTION AND OBJECTIVES

Hypersensitivity pneumonitis (HP) is an interstitial lung disease with diverse clinical features that can present a fibrotic phenotype similar to idiopathic pulmonary fibrosis (IPF) in genetically predisposed individuals. While several single nucleotide polymorphisms (SNPs) have been associated with IPF, the genetic factors contributing to fibrotic HP (fHP) remain poorly understood. This study investigated the association of MUC5B and TOLLIP variants with susceptibility, clinical presentation and survival in Portuguese patients with fHP.

MATERIAL AND METHODS

A case-control study was undertaken with 97 fHP patients and 112 controls. Six SNPs residing in the MUC5B and TOLLIP genes and their haplotypes were analyzed. Associations with risk, survival, and clinical, radiographic, and pathological features of fHP were probed through comparisons among patients and controls.

RESULTS

MUC5B rs35705950 and three neighboring TOLLIP variants (rs3750920, rs111521887, and rs5743894) were associated with increased susceptibility to fHP. Minor allele frequencies were greater among fHP patients than in controls (40.7% vs 12.1%, P<0.0001; 52.6% vs 40.2%, P = 0.011; 22.7% vs 13.4%, P = 0.013; and 23.2% vs 12.9%, P = 0.006, respectively). Haplotypes formed by these variants were also linked to fHP susceptibility. Moreover, carriers of a specific haplotype (G-T-G-C) had a significant decrease in survival (adjusted hazard ratio 6.92, 95% CI 1.73-27.64, P = 0.006). Additional associations were found between TOLLIP rs111521887 and rs5743894 variants and decreased lung function at baseline, and the MUC5B SNP and radiographic features, further highlighting the influence of genetic factors in fHP.

CONCLUSION

These findings suggest that TOLLIP and MUC5B variants and haplotypes may serve as valuable tools for risk assessment and prognosis in fibrotic hypersensitivity pneumonitis, potentially contributing to its patient stratification, and offer insights into the genetic factors influencing the clinical course of the condition.

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.

Defective exercise-related expiratory muscle recruitment in patients with PHOX2B mutations: A clue to neural determinants of the congenital central hypoventilation syndrome

INTRODUCTION AND OBJECTIVES

The human congenital central hypoventilation syndrome (CCHS) is caused by mutations in the PHOX2B (paired-like homeobox 2B) gene. Genetically engineered PHOX2B rodents exhibit defective development of the brainstem retrotrapezoid nucleus (RTN), a carbon dioxide sensitive structure that critically controls expiratory muscle recruitment. This has been linked to a blunted exercise ventilatory response. Whether this can be extrapolated to human CCHS is unknown and represents the objective of this study.

MATERIALS AND METHODS

Thirteen adult CCHS patients and 13 healthy participants performed an incremental symptom-limited cycle cardiopulmonary exercise test. Responses were analyzed using guideline approaches (ventilation V'E, tidal volume VT, breathing frequency, oxygen consumption, carbon dioxide production) complemented by a breathing pattern analysis (i.e. expiratory and inspiratory reserve volume, ERV and IRV).

RESULTS

A ventilatory response occurred in both study groups, as follows: V'E and VT increased in CCHS patients until 40 W and then decreased, which was not observed in the healthy participants (p<0.001). In the latter, exercise-related ERV and IRV decreases attested to concomitant expiratory and inspiratory recruitment. In the CCHS patients, inspiratory recruitment occurred but there was no evidence of expiratory recruitment (absence of any ERV decrease, p<0.001).

CONCLUSIONS

Assuming a similar organization of respiratory rhythmogenesis in humans and rodents, the lack of exercise-related expiratory recruitment observed in our CCHS patients is compatible with a PHOX2B-related defect of a neural structure that would be analogous to the rodents' RTN. Provided corroboration, ERV recruitment could serve as a physiological outcome in studies aiming at correcting breathing control in CCHS.

Effect of vitamin D supplementation on frozen embryo transfer cycle outcomes

The role of serum 25-OH D3 (D3) in the physiology and regulation of the female genital system has gained significant research interest. Recent data have suggested that sufficient D3 levels are associated with improved outcomes of in vitro fertilization (IVF), although other studies failed to confirm so. Screening for D3 levels before IVF is becoming common practice in many IVF centres, and D3 insufficiency is treated with supplements before treatment. However, little is known about the effect of this intervention on D3 levels during endometrial preparation for frozen-embryo transfer (FET) cycles, especially regarding clinical outcomes. To examine the effect of vitamin D supplementation and the impact of vitamin D status in women undergoing FET cycles, a prospective study of infertile women undergoing FET cycles was carried out. Initial screening of D3 levels was performed in 252 infertile women before a FET cycle, and where insufficiency was found (<30 ng/mL) [115 (45.6%)], supplements were prescribed according to a standardized protocol. Serum D3 levels were measured at three distinct time-points: at the initiation of endometrial preparation (T1), embryo transfer (T2), and beta-hCG testing (T3). We found no significant difference in ongoing pregnancy [40 (34.8%) vs. 51 (37.2%); odds ratio (OR) 0.90, 95% confidence interval (CI) 0.54-1.51; adjusted OR 1.04, 95% CI 0.58-1.83], live birth, positive β-hCG, clinical pregnancy, miscarriage, and ectopic pregnancy rates between D3-insufficient participants at T1 receiving vitamin D and D3-replete ones not receiving any supplementation (p-values >0.05). We also found no significant difference in ongoing pregnancy [21 (30.9%) vs. 66 (40.2%), and 17 (34.0%) vs. 51 (41.5%)] and the rest of the outcomes between D3-insufficient and replete participants at T2 and T3, respectively (p-values >0.05). In conclusion, this prospective cohort study of women undergoing FET cycles found no significant difference in ongoing pregnancy rates between D3-insufficient participants receiving supplementation at the beginning of endometrial preparation and replete ones receiving no supplementation. Large, high-quality trials are required to further investigate this hypothesis and compare the IVF outcomes between replete participants, insufficient participants receiving no supplementation, and insufficient participants receiving supplementation.

Novel digital droplet inverse PCR assay shows that natural clearance of hepatitis B infection is associated with fewer viral integrations

Hepatitis B virus (HBV) DNA integration into the host cell genome is reportedly a major cause of liver cancer, and a source of hepatitis B surface antigen (HBsAg). High HBsAg levels can alter immune responses which therefore contributes to the progression of HBV-related disease. However, to what extent integration leads to the persistent circulating HBsAg is unclear. Here, we aimed to determine if the extent of HBV DNA integration is associated with the persistence of circulating HBsAg in people exposed to HBV. We established a digital droplet quantitative inverse PCR (dd-qinvPCR) method to quantify integrated HBV DNA in patients who had been exposed to HBV (anti-HBc positive and HBeAg-negative). Total DNA extracts from both liver resections (n = 32; 14 HBsAg-negative and 18 HBsAg-positive) and fine-needle aspirates (FNA, n = 10; 2 HBsAg-negative and 8 HBsAg-positive) were analysed. Using defined in vitro samples for assay establishment, we showed that dd-qinvPCR could detect integrations within an input of <80 cells. The frequency of integrated HBV DNA in those who had undergone HBsAg loss (n = 14, mean ± SD of 1.514 × 10-3 ± 1.839 × 10-3 integrations per cell) was on average 9-fold lower than those with active HBV infection (n = 18, 1.16 × 10-2 ± 1.76 × 10-2 integrations per cell; p = 0.0179). In conclusion, we have developed and validated a highly precise, sensitive and quantitative PCR-based method for the quantification of HBV integrations in clinical samples. Natural clearance of HBV is associated with fewer viral integrations. Future studies are needed to determine if dynamics of integrated HBV DNA can inform the development of curative therapies.

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

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

RARB genetic variants might contribute to the risk of chronic obstructive pulmonary disease based on a case-control study

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a progressive respiratory disease that severely impairs patients' respiratory function and quality of life. RARB is involved in COPD progression by affecting inflammatory reactions, cell proliferation, and apoptosis. The impact of single nucleotide polymorphisms (SNPs) within RARB on COPD susceptibility remains unclear. Here, we aimed to evaluate the association between RARB SNPs and COPD risk.

METHODS

A total of 270 COPD patients and 271 healthy controls were enrolled. The MassARRAY iPLEX platform tested the genotype of the SNPs. The association was analyzed using logistic regression analysis. The false-positive report probability (FPRP) analysis was performed to validate the significant findings. The relationship between SNPs and RARB expression was evaluated using the GTEx database.

RESULTS

Our study found a significant association between rs6799734 and COPD susceptibility (OR 1.88, p = 0.008, p (FDR) = 0.047). The stratified analysis revealed that this association was particularly pronounced among individuals aged ≤ 71 years (OR 2.34, p = 0.011, p (FDR) = 0.045), males (OR 2.60, p = 0.002, p (FDR) = 0.013), those with a BMI ≥ 24 (OR 3.95, p = 0.018, p (FDR) = 0.108), and smokers (OR 2.48, p = 0.020, p (FDR) = 0.120). Additionally, rs1286641 and rs1881706 showed significant associations with COPD risk in females and smokers. These associations were further validated by FPRP analysis. Preliminary mechanism studies indicated that rs1286641 and rs1881706 were related to RARB expression.

CONCLUSION

Our findings suggest a potential role of RARB SNPs in influencing COPD risk.

An integrative approach to identifying NPC1 as a susceptibility gene for gestational diabetes mellitus

OBJECTIVE

The objective of this study was to identify a novel gene and its potential mechanisms associated with susceptibility to gestational diabetes mellitus (GDM) through an integrative approach.

METHODS

We analyzed data from genome-wide association studies (GWAS) of GDM in the FinnGen R11 dataset (16,802 GDM cases and 237,816 controls) and Genotype Tissue Expression v8 expression quantitative trait locus data. We used summary-data-based Mendelian randomization to determine associations between transcript levels and phenotypes, transcriptome-wide association studies to provide insights into gene-trait associations, multi-marker analysis of genomic annotation to perform gene-based analysis, genome-wide complex trait analysis-multivariate set-based association test-combo to determine gene prioritization, and polygenic priority scores to prioritize the causal genes to screen candidate genes. Subsequent Mendelian randomization analysis was performed to infer causality between the candidate genes and GDM and phenome-wide association study (PheWAS) analysis was used to explore the associations between selected genes and other characteristics. Furthermore, to gain a deeper understanding of the functional implications of these susceptibility genes, GeneMANIA analysis was used to determine the fundamental biological functions of the therapeutic targets and protein-protein interaction network analysis was performed to identify intracellular protein interactions.

RESULTS

We identified two novel susceptibility genes associated with GDM: NPC1 and KIAA1191. Magnetic resonance imaging revealed a strong correlation between NPC1 expression levels and a lower incidence of GDM (odds ratio: 0.922, 95% confidence interval: 0.866-0.981, p = 0.011). PheWAS at the gene level indicated that NPC1 was not associated with any other trait. The biological significance of this gene was evidenced by its strong association with sterol metabolism.

CONCLUSION

Our study identified NPC1 as a novel gene whose predicted expression level is linked to a reduced risk of GDM, providing new insights into the genetic framework of this disease.

Pathogenicity and virulence of Pseudomonas aeruginosa: Recent advances and under-investigated topics

Pseudomonas aeruginosa is a model for the study of quorum sensing, protein secretion, and biofilm formation. Consequently, it has become one of the most intensely reviewed pathogens, with many excellent articles in the current literature focusing on these aspects of the organism's biology. Here, though, we aim to take a slightly different approach and consider some less well appreciated (but nonetheless important) factors that affect P. aeruginosa virulence. We start by reminding the reader of the global importance of P. aeruginosa infection and that the "virulome" is very niche-specific. Overlooked but obvious questions such as "what prevents secreted protein products from being digested by co-secreted proteases?" are discussed, and we suggest how the nutritional preference(s) of the organism might dictate its environmental reservoirs. Recent studies identifying host genes associated with genetic predisposition towards P. aeruginosa infection (and even infection by specific P. aeruginosa strains) and the role(s) of intracellular P. aeruginosa are introduced. We also discuss the fact that virulence is a high-risk strategy and touch on how expression of the two main classes of virulence factors is regulated. A particular focus is on recent findings highlighting how nutritional status and metabolism are as important as quorum sensing in terms of their impact on virulence, and how co-habiting microbial species at the infection site impact on P. aeruginosa virulence (and vice versa). It is our view that investigation of these issues is likely to dominate many aspects of research into this WHO-designated priority pathogen over the next decade.

Chromatin accessibility profiling of Treg cells in acute urticaria

Acute urticaria can be a presenting symptom of anaphylaxis characterized by transient red swellings or fulminant wheals, often accompanied by severe pruritus. Numerous studies have substantiated the important involvement of regulatory T cells (Tregs) in the occurrence of allergic diseases and autoimmune diseases. However, the role of Tregs in the pathogenesis of acute urticaria is unclear. In this study, we found that the frequency of Tregs in peripheral blood mononuclear cells (PBMCs) was decreased in patients with acute urticaria compared with normal controls by flow cytometry. Analysis of Assay for transposase-accessible chromatin with sequencing (ATAC-seq) data identified 28 differentially accessible regions comparing Tregs from healthy individuals and patients with acute urticaria, all showing increased chromatin accessibility in the Tregs from acute urticaria. IL-1b was highly expressed in sera of patients with acute urticaria and the level of IL-1b was moderately positively related to white blood cell count. The elevated expression of IL-1b may be due to the diminished immune-suppressive function following the decline of Tregs in this study. We found that IL1B gene expression was also significantly increased in the skin lesions of both chronic spontaneous urticaria and solar urticaria compared to healthy controls. IL1B might play a key role in the development of acute urticaria and IL1B could be a potential prognostic biomarker and therapeutic target in urticaria.

Heterologous expression of SpsTAC2 in Arabidopsis affected branch angle and secondary vascular system development

To investigate the biological functions of Tiller Angle Control 2 (TAC2) in Salix psammophila. In this study, TAC2 was cloned from Salix psammophila, and an overexpression and subcellular localization expression vector for the SpsTAC2 gene was constructed. The SpsTAC2 gene was overexpressed in Arabidopsis and analyzed for phenotypic changes. The subcellular localization of SpsTAC2 was analyzed via Agrobacterium-mediated transient expression in onion (Allium cepa L.) epidermal cells. Phenotypic characterization of SpsTAC2 overexpressing Arabidopsis strains revealed that the branching angle of the transgenic strains was significantly greater than that of the wild type, and the anatomical structures of the stems and hypocotyls of the transgenic strains indicated that the vascular system of the transgenic strains developed more slowly than did that of the wild type. The subcellular localization of the SpsTAC2 gene revealed that the localization signals of the SpsTAC2 gene were mainly in the nucleus, and weak signals also appeared in the cell membrane, suggesting that the SpsTAC2 gene was mainly expressed mainly in the nucleus, with a small amount of expression in the cell membrane. This findings suggest that the SpsTAC2 gene influences the development of the branching angle of plants and xylem, and exerts its effects mainly in the nucleus and membrane. This study can help to characterize the regulatory effect of the TAC gene on the branching angle and explore its effect on the branching angle and vascular system development, and also help to explore the possible molecular regulatory mechanism, which can provide a theoretical basis for further elucidation of the mechanism of action of the IGT gene family.

Closing the loops: chromatin loop dynamics after DNA damage

Chromatin is a dynamic polymer in constant motion. These motions are heterogeneous between cells and within individual cell nuclei and are profoundly altered in response to DNA damage. The shifts in chromatin motions following genomic insults depend on the temporal and physical scales considered. They are also distinct in damaged and undamaged regions. In this review, we emphasize the role of chromatin tethering and loop formation in chromatin dynamics, with the view that pulsing loops are key contributors to chromatin motions. Chromatin tethers likely mediate micron-scale chromatin coherence predicted by polymer models and measured experimentally, and we propose that remodeling of the tethers in response to DNA breaks enables uncoupling of damaged and undamaged chromatin regions.

The causal relationship between gut microbiota and preterm birth: a two-sample Mendelian randomization study

BACKGROUND

Preterm birth, a significant global health concern, has been associated with alterations in the gut microbiota. However, the causal nature of this relationship remains uncertain due to the limitations inherent in observational studies.

PURPOSE

To investigate the potential causal relationship between gut microbiota imbalances and preterm birth.

METHODS

We conducted a two-sample Mendelian randomization (MR) study using genome-wide association study (GWAS) data from the MiBioGen consortium focusing on microbiota and preterm birth. Single nucleotide polymorphisms (SNPs) associated with the microbiota were selected as instrumental variables. The inverse variance weighting (IVW) method was used to estimate causality. We confirmed pleiotropy and identified and excluded outlier SNPs using MR-PRESSO and MR-Egger regression. Cochran's Q test was applied to assess heterogeneity among SNPs, and a leave-one-out analysis was performed to evaluate the influence of individual SNPs on overall estimates.

RESULTS

Our findings provide evidence for a causal link between specific components of the gut microbiota and preterm birth, with the identification of relevant metabolites.

CONCLUSION

This study highlights the causal role of gut microbiota imbalances in preterm birth, offering novel insights into the development of preterm birth and potential targets for prevention strategies.

Mendelian randomization analysis of blood uric acid and risk of preeclampsia: based on GWAS and eQTL data

BACKGROUND

The causal association between blood uric acid and preeclampsia (Preeclampsia, PE) has not been conclusively established based on the literature reviewed to date. This bi-directional Mendelian randomization study aimed to investigate the bi-directional causal association between blood uric acid concentration and PE at different genetic levels.

METHODS

Pooled data on preeclampsia (sample size = 82,085) and blood uric acid (sample size = 129,405) were conducted based on publicly available genome-wide association analysis (Genome-Wide Association Study, GWAS) on the East Asian populations regarding preeclampsia and blood uric acid, respectively. We assessed blood uric acid and PE associations using two-sample Mendelian randomization (TSMR) analyses based on GWAS pooled statistics using inverse variance weighted (Inverse variance weighted), MR-Egger, and Weighted median (Weighted median) to examine the association between blood uric acid and pre-eclampsia. Causal relationship between blood uric acid and pre-eclampsia.Cochran's Q statistic was used to quantify the heterogeneity of instrumental variables among other methods. Subsequently, we extracted the expression quantitative trait loci (eQCTL, Expression quantitative trait loci) data corresponding to each gene as the instrumental variables using the genes corresponding to the intersecting instrumental variables of the exposure and the outcome in the respective analyses of the forward and backward TSMR respectively, so as to analyze the genetic causality of the genes with the different forward and backward TSMR methods further. Inverse variance weighted (IVW) was used to analyze the genetic causality of genes with different positive and negative outcomes.

RESULTS

Genetically determined blood uric acid level IVW method, ratio (OR) 1.30, 95% confidence interval (CI): [0.6, 2.83], p = 0.51 was not risk associated with PE. In addition according to the inverse MR analysis, we found an OR of 0.99, 95% CI [0.99, 1.0], p = 0.999) for PE on blood uric acid level IVW method and no significant heterogeneity in instrumental variables or level polytropy was found. (ii) Although GWAS data suggested no risk association between PE and uric acid, gene association analysis of eQTL data at blood uric acid levels with PE suggested a risk effect of the TP53INP1 gene for PE (IVW, OR = 11.476, 95% CI 2.511-52.452, p = 1.648 × 10-3) and a protective effect of CTSZ (IVW, OR = 0.011, 95% CI 0.001-0.189, p = 1.804 × 10-3), while a risk effect of ETV7 on hyperuricemia was suggested in a genetic association analysis of PE eQTL data with blood uric acid levels (OR = 1.018, 95% CI 1.007-1.029, p = 1.289 × 10-3).

CONCLUSION

Our MR (Mendelian Randomization) study based on the GWAS database did not support a bidirectional causal effect between blood uric acid levels and PE, whereas MR based on quantitative trait loci suggested that TP53INP1, which affects uric acid levels, has a risk association for PE, whereas CTSZ is protective against preeclampsia. Among the genes affecting PE the ETV7 gene may play a positive role in elevating uric acid levels.

The impact of trauma and how to intervene: a narrative review of psychotraumatology over the past 15 years

To mark 15 years of the European Journal of Psychotraumatology, editors reviewed the past 15-year years of research on trauma exposure and its consequences, as well as developments in (early) psychological, pharmacological and complementary interventions. In all sections of this paper, we provide perspectives on sex/gender aspects, life course trends, and cross-cultural/global and systemic societal contexts. Globally, the majority of people experience stressful events that may be characterized as traumatic. However, definitions of what is traumatic are not necessarily straightforward or universal. Traumatic events may have a wide range of transdiagnostic mental and physical health consequences, not limited to posttraumatic stress disorder (PTSD). Research on genetic, molecular, and neurobiological influences show promise for further understanding underlying risk and resilience for trauma-related consequences. Symptom presentation, prevalence, and course, in response to traumatic experiences, differ depending on individuals' age and developmental phase, sex/gender, sociocultural and environmental contexts, and systemic socio-political forces. Early interventions have the potential to prevent acute posttraumatic stress reactions from escalating to a PTSD diagnosis whether delivered in the golden hours or weeks after trauma. However, research on prevention is still scarce compared to treatment research where several evidence-based psychological, pharmacological and complementary/ integrative interventions exist, and novel forms of delivery have become available. Here, we focus on how best to address the range of negative health outcomes following trauma, how to serve individuals across the age spectrum, including the very young and old, and include considerations of sex/gender, ethnicity, and culture in diverse contexts, beyond Western, Educated, Industrialized, Rich, and Democratic (WEIRD) countries. We conclude with providing directions for future research aimed at improving the well-being of all people impacted by trauma around the world. The 15 years EJPT webinar provides a 90-minute summary of this paper and can be downloaded here [http://bit.ly/4jdtx6k].

Perinuclear organelle trauma at the nexus of cardiomyopathy pathogenesis arising from loss of function LMNA mutation

Over the past 25 years, nuclear envelope (NE) perturbations have been reported in various experimental models with mutations in the LMNA gene. Although the hypothesis that NE perturbations from LMNA mutations are a fundamental feature of striated muscle damage has garnered wide acceptance, the molecular sequalae provoked by the NE damage and how they underlie disease pathogenesis such as cardiomyopathy (LMNA cardiomyopathy) remain poorly understood. We recently shed light on one such consequence, by employing a cardiomyocyte-specific Lmna deletion in vivo in the adult heart. We observed extensive NE perturbations prior to cardiac function deterioration with collateral damage in the perinuclear space. The Golgi is particularly affected, leading to cytoprotective stress responses that are likely disrupted by the progressive deterioration of the Golgi itself. In this review, we discuss the etiology of LMNA cardiomyopathy with perinuclear 'organelle trauma' as the nexus between NE damage and disease pathogenesis.

Preclinical development of ozuriftamab vedotin (BA3021), a novel ROR2-specific conditionally active biologic antibody-drug conjugate

Receptor tyrosine kinase-like orphan receptor (ROR2) has been identified as a highly relevant tumor-associated antigen in a variety of cancer indications of high unmet medical need, including melanoma, renal cell carcinoma, osteosarcoma, gastrointestinal stromal tumor, colorectal cancer, pancreatic ductal adenocarcinoma, and non-small cell lung cancer. Overexpression of ROR2 often correlates with advanced disease or poor prognosis, making it an attractive target for cancer therapy. We developed a novel, conditionally active biologic (CAB) antibody-drug conjugate (ADC), ozuriftamab vedotin (BA3021), which binds to ROR2 only in the acidic tumor microenvironment. In healthy tissue, binding to ROR2 is greatly reduced by a novel selection mechanism using physiological chemicals as protein-associated chemical switches (PaCS). The CAB anti-ROR2 ADC displays the anticipated binding properties and mediates potent lysis of ROR2-positive cancer cell lines. In vivo, BA3021 has potent and durable antitumor activity in human cancer xenograft mouse models, including patient-derived xenograft models. In non-human primates, BA3021 was well tolerated at doses of up to 10 mg/kg and showed excellent stability in vivo. These preclinical results indicate that CAB anti-ROR2 ADC is efficacious and well tolerated and may be a promising treatment for cancer patients with ROR2-expressing tumors.

Evaluation of causal relationships between genetic liability to inflammatory bowel disease and autism spectrum disorder by Mendelian randomization analysis

BACKGROUND

Emerging observational studies have indicated the association between autism spectrum disorder (ASD) and IBD, including Crohn's disease (CD) and ulcerative colitis (UC), whereas the causality remains unknown.

METHODS

Summary-level data from large-scale genome-wide association (GWAS) studies of IBD and ASD were retrieved. Mendelian randomisation analyses were performed with a series of sensitivity tests.

RESULTS

Genetic predisposition to ASD was not associated with the risk of IBD (odds ratio [OR] = 0.99, 95% confidence interval [CI = 0.91-1.06, p = 0.70; OR [95% CI]: 1.03 [0.93-1.13], p = 0.58 for CD; OR [95% CI]: 0.96 [0.87-1.05], p = 0.37 for UC) in the IIBDGC dataset. In the FinnGen dataset, their causal effects were unfounded (OR [95% CI]: 1.04 [0.94-1.15], p = 0.49 for IBD; OR [95% CI]: 1.08 [0.89-1.31], p = 0.42 for CD; OR [95% CI]: 1.00 [0.88-1.13], p = 0.95 for UC). In the meta-analysis of two datasets, the OR was 1.01 (95% CI 0.96-1.07, p = 0.45). For the risk of ASD under genetic liability to IBD, the OR from meta-analysis was 1.03 (95% CI 1.01-1.05, p = 0.01).

CONCLUSION

Our findings indicate genetic predisposition to ASD might not increase the risk of IBD, whereas genetic liability to IBD is associated with an increased risk of ASD. Further investigations using more powerful datasets are warranted.

Molecular signaling pathways in osteoarthritis and biomaterials for cartilage regeneration: a review

Osteoarthritis is a prevalent degenerative joint disease characterized by cartilage degradation, synovial inflammation, and subchondral bone alterations, leading to chronic pain and joint dysfunction. Conventional treatments provide symptomatic relief but fail to halt disease progression. Recent advancements in biomaterials, molecular signaling modulation, and gene-editing technologies offer promising therapeutic strategies. This review explores key molecular pathways implicated in osteoarthritis, including fibroblast growth factor, phosphoinositide 3-kinase/Akt, and bone morphogenetic protein signaling, highlighting their roles in chondrocyte survival, extracellular matrix remodeling, and inflammation. Biomaterial-based interventions such as hydrogels, nanoparticles, and chitosan-based scaffolds have demonstrated potential in enhancing cartilage regeneration and targeted drug delivery. Furthermore, CRISPR/Cas9 gene editing holds promise in modifying osteoarthritis-related genes to restore cartilage integrity. The integration of regenerative biomaterials with precision medicine and molecular therapies represents a novel approach for mitigating osteoarthritis progression. Future research should focus on optimizing biomaterial properties, refining gene-editing efficiency, and developing personalized therapeutic strategies. The convergence of bioengineering and molecular science offers new hope for improving joint function and patient quality of life in osteoarthritis management.

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.

Genomic islands and molecular mechanisms relating to drug-resistance in Clostridioides (Clostridium) difficile PCR ribotype 176

OBJECTIVES

To analyse characteristics of Clostridioides difficile PCR ribotype 176 clinical isolates from Poland, the Czech Republic and Slovakia with regard to the differences in its epidemiology.

METHODS

Antimicrobial susceptibility testing and whole genome sequencing were performed on a selected group of 22 clonally related isolates as determined by multilocus variable-number tandem repeat analysis (n = 509). Heterologous expression and functional analysis of the newly identified methyltransferase were performed.

RESULTS

Core genome multilocus sequence typing found 10-37 allele differences. All isolates were resistant to fluoroquinolones (gyrA_p. T82I), aminoglycosides with aac(6')-Ie-aph(2'')-Ia in six isolates. Erythromycin resistance was detected in 21/22 isolates and 15 were also resistant to clindamycin with ermB gene. Fourteen isolates were resistant to rifampicin with rpoB_p. R505K or p. R505K/H502N, and five to imipenem with pbp1_p. P491L and pbp3_p. N537K. PnimBG together with nimB_p. L155I were detected in all isolates but only five were resistant to metronidazole on chocolate agar. The cfrE, vanZ1 and cat-like genes were not associated with linezolid, teicoplanin and chloramphenicol resistance, respectively. The genome comparison identified six transposons carrying antimicrobial resistance genes. The ermB gene was carried by new Tn7808, Tn6189 and Tn6218-like. The aac(6')-Ie-aph(2'')-Ia were carried by Tn6218-like and new Tn7806 together with cfrE gene. New Tn7807 carried a cat-like gene. Tn6110 and new Tn7806 contained an RlmN-type 23S rRNA methyltransferase, designated MrmA, associated with high-level macrolide resistance in isolates without ermB gene.

CONCLUSIONS

Multidrug-resistant C. difficile PCR ribotype 176 isolates carry already described and unique transposons. A novel mechanism for erythromycin resistance in C. difficile was identified.

The impact of leisure sedentary behaviors on risk of chronic kidney disease, diabetes, and related complications: Mendelian randomization study

BACKGROUND

The causal relationship between leisure sedentary behaviors (LSBs) and chronic kidney disease, diabetes and related complications is still equivocal. In this study, we performed two-sample Mendelian randomization for declaring the potential causal association between LSBs and these diseases and summarized the causal estimates.

METHODS

In this study, we used GWAS summary statistics from the public database for exposures (LSB: television watching, computer use, and driving) and outcomes (chronic kidney diseases, diabetes mellitus, and related complications). To ensure reliable results for this study, we applied several methods including IVW, MR-Egger, and weighted median for the regression process; MR-Egger intercept test, Cochran's Q test, 'leave-one-out' analysis and MR-PRESSO test were used to detect horizontal pleiotropy and heterogeneity for sensitivity analysis.

RESULTS

Television watching was harmful of CKD (OR = 1.26, 95%CI 1.09-1.44; p = 0.0011), T2D (OR = 1.82, 95%CI 1.48-2.24; p = 1.67e - 08) and DM (OR = 2.26, 95%CI 1.75-2.93; p = 6.44e - 10). No horizontal pleiotropy was detected in MR-Egger intercept test (p value > 0.05) and there were no influential SNPs based on 'leave-one-out' analysis.

CONCLUSIONS

Mendelian randomization estimates in our study genetically predicted the causal effect between television watching and CKD, T2D, and DM. However, we cannot get the definitive causal effect of television watching and other related complications, further studies need to be done to explore the mechanism of action of sedentary behavior on the complications of diabetes and chronic kidney disease.

Bidirectional Mendelian Randomization analysis of iron status and uremia: no evidence of a causal relationship

Iron status and uremia have been linked, but the causality remains ambiguous. This bidirectional study aimed to explore the causal association between genetically predicted iron status and uremia. Utilizing summary data from genome-wide association studies (GWAS) of iron status and uremia, a two-sample Mendelian Randomization (MR) design was employed. Iron status was assessed through serum iron (SI), serum ferritin (SF), total iron-binding capacity (TIBC), and transferrin saturation (TS), while uremia included renal failure and dialysis. The primary analysis was conducted using the Inverse Variance Weighted (IVW) method. Additional MR evaluation included the weighted median, weighted mode, simple mode, and MR-Egger regression methods. Sensitivity analysis included MR-Egger for pleiotropy, MR-PRESSO for detecting outliers, Cochran's Q test for heterogeneity, and leave-one-out analysis for robustness. Genetically determined iron status did not have a causal effect on the risk of uremia (renal failure or dialysis). The primary IVW results indicated no statistically significant relationship between iron status and uremia (all p > 0.05). Consistent results were found through various methods. Similarly, there were no significant causal effects of uremia on iron status (all p > 0.05). Heterogeneity was observed in some associations, but pleiotropy was generally not evident. This bidirectional MR study provides no evidence for a causal relationship between genetically predicted iron status and the risk of uremia. These findings challenge prior observational associations and highlight the need for further mechanistic and interventional studies to elucidate the complex interplay between iron metabolism and kidney disease.

A rare deleterious missense mutation in the AXIN2 gene in Chinese women with polycystic ovary syndrome

BACKGROUND

Polycystic ovary syndrome (PCOS) is an endocrine disorders and characterized by polycystic ovary morphology and oligomenorrhea, affecting fertility and health condition of female around the world. The causative factors of PCOS are complex, and genetic structure remains a long-standing medical challenge in genetics. Previous genome-wide association study (GWAS) showed that Wing-less-related integration site (Wnt) signaling is the most affected pathway among PCOS-related risk genes, and genetic mutations in the Wnt/β-catenin signaling may lead to abnormal development of PCOS.

OBJECTIVE

To explore the possibility of axis inhibitor-2 (AXIN2) variants in Chinese women with PCOS and assess their pathogenicities.

METHODS

A total of 365 Chinese women with PCOS and 905 women without PCOS as control were recruited from Jiangxi Provincial Maternal and Child Health Hospital, All of the 11 exons and flanking regions of the AXIN2 gene were amplified by polymerase chain reaction (PCR), the potential variants were analyzed by Sanger sequencing. The evolutionary conservation analysis of the identified Axin-2 mutant was analyzed among 15 vertebrates from human to zebrafish. The protein structure change was analyzed between the wild-type and mutation-type. The pathogenicity of AXIN2 variant was further analyzed in silico.

RESULTS

We totally identified 7 genetic variants of AXIN2 in this study, including 4 synonymous and 3 missense. Among them, we find a rare deleterious missense variant [p.R714W (c.2140C > T)]. The allele frequencies of this variant were 0.82% and 0.17% in PCOS cases and matched controls, respectively. And it was ranging from 7.89e-5 to 1.47e-4 in public databases. Fisher's exact test indicated that the allele frequencies in PCOS were p < 0.05 compared to both the controls and the databases. Especially, the mutant amino acid site is highly conserved in vertebrates, while the mutation changed the 714th arginine to tryptophan resulting in significant change in the protein structural of Axin-2.

CONCLUSION

In this study, we identified a rare deleterious missense AXIN2 mutation [p.R714W (c.2140C > T)] in Chinese women with PCOS, and this mutant is probably pathogenic. This study may provide a new perspective on revealing the genetic variation of PCOS.

Prognostic significance of neutrophil extracellular trap-related genes in childhood acute lymphoblastic leukemia: insights from multi-omics and in vitro experiment

BACKGROUND

This study aimed to develop a prognostic model based on extracellular trap-related genes (NETRGs) for patients with cALL.

METHODS

Data from the TARGET-ALL-P2 and TARGET-ALL-P3 cohorts in the Genomic Data Commons database, the transcriptome dataset GSE26713, the single-cell transcriptome dataset GSE130116 from the Gene Expression Omnibus database and 306 NETRGs identified were analysed. Differentially expressed genes (DEGs) were identified from GSE26713 and differentially expressed NETRGs (DE-NETRGs) were obtained by overlapping DEGs with NETRGs. Functional analyses were conducted. Key feature genes were identified through univariate and least absolute shrinkage and selection operator (LASSO) regression. Prognostic genes were determined via multivariate Cox regression analysis, followed by the construction and validation of a risk model and nomogram. Additional analyses included immune profiling, drug sensitivity, functional differences, cell-type-specific expression, enrichment analysis and RT-qPCR.

RESULTS

A total of 1,270 DEGs were identified in GSE26713, of which 74 overlapped with NETRGs. Seven prognostic genes were identified using univariate, LASSO and multivariate Cox regression analyses. Survival analysis revealed lower survival rates in the high-risk group. Independent prognostic analysis identified risk scores and primary diagnosis as independent predictors of prognosis. Immune cell profiling showed significant differences in cell populations such as aDCs, eosinophils and Th2 cells between risk groups. Six cell subtypes were annotated, with prognostic genes predominantly expressed in myeloid cells. RT-qPCR revealed that PTAFR, FCGR2A, RETN and CAT were significantly downregulated, while TLR2 and S100A12 were upregulated in cALL.

CONCLUSION

TLR2, PTAFR, FCGR2A, RETN, S100A12 and CAT may serve as potential therapeutic targets.

Comparative genomics of Salmonella enterica serovars Paratyphi A, Typhi and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance and defense systems repertoire

Salmonella enterica (S. enterica) is a highly ubiquitous and diverse animal and human pathogen. Distinct S. enterica serovars may present varying host-specificity and cause different diseases. While the human-restricted serovars S. Typhi (STY) and S. Paratyphi A (SPA) cause in humans a systemic life-threatening enteric fever, the host-generalist serovar, S. Typhimurium (STM) causes in immunocompetent individuals a self-limited gastroenteritis. Here, we have performed whole-genome sequencing and hybrid assembly of new SPA and STY typhoidal strains and took a comparative genomics approach to examine their phylogeny, pangenome structure and accessory genome content in comparison to the reference non-typhoidal serovar, STM. Our results identified previously uncharacterized lineages of SPA and refined the presence and distribution of core pseudogenes in typhoidal serovars. Pangenome analysis showed that while these serovars have a relatively similar core-genome size, the accessory genome of STM is more than four times larger than those of typhoidal Salmonellae and that STY and SPA display a more closed pangenome than STM. Unexpectedly, we demonstrate that STY and SPA present distinct differences in their pangenome composition, with a noticeable lower number of prophages, conjugative elements and antimicrobial genes per genome in SPA vs. STY. These results suggest that although SPA and STY are closely related at the DNA level, share a similar lifestyle and cause a symptomatic-indistinguishable disease, their genomic evolution and accessory genomes are markedly different. Moreover, these results may provide genomic explanation to phenotypic and epidemiological differences in antimicrobial resistance profiles associated with these serovars globally.

Autosomal dominant polycystic kidney disease: an overview of recent genetic and clinical advances

Autosomal Dominant Polycystic Kidney Disease (ADPKD) is the most common inherited kidney disease, characterized by the progressive development of multiple kidney cysts, leading to a gradual decline in kidney function. ADPKD is also the fourth leading cause of kidney failure (KF) in adults. In addition to kidney manifestations, ADPKD is associated with various extrarenal features, including liver cysts, cardiovascular abnormalities, intracranial aneurysms, and chronic pain with significant impact on patients' quality of life. While several disease-modifying agents have been tested in ADPKD, tolvaptan remains the only approved drug by the US Food and Drug Administration. The Mayo Imaging Classification is currently the most practical tool for predicting rate of kidney disease progression in ADPKD. This review provides a comprehensive overview of ADPKD, focusing on its genetics, pathophysiology, clinical presentation, management, and prognostic tools. Advances in diagnostic imaging and genetic testing have improved the early detection of ADPKD, allowing better classification of patients and prediction of KF. The review also discusses current therapeutic approaches to ADPKD, including tolvaptan, a vasopressin V2-receptor antagonist. Additionally, we address specific issues in children and pregnant individuals with ADPKD. Despite substantial progress in understanding ADPKD, there is a large need for additional effective treatments and prognostic markers to provide a more personalized care for these patients.

Prolonged sitting time and all-cause mortality: the mediating and predictive role of kidney function markers

OBJECTIVE

To investigate the association between daily sitting time and all-cause mortality, with a focus on the mediating effect and predictive value of the makers relating to kidney.

METHODS

The cross-sectional study utilized data from the National Health and Nutrition Examination Survey (NHANES) from 2003 to 2020. The makers relating to kidney were assessed through estimated glomerular filtration rate (eGFR), urine albumin creatinine ratio (UACR), and other relevant markers.

RESULTS

A total of 9,707 adults were included in the analysis. There was a significant increase in the levels of blood urea nitrogen (BUN), creatinine, uric acid, osmolality, and UACR with extended daily sitting time, while eGFR significantly decreased. Notably, individuals sitting ≥ 8 h per day exhibited a 67% higher risk of all-cause mortality (HR = 1.67, 95% CI: 1.43-1.94). A nonlinear (L-shaped) relationship was observed between eGFR (p < 0.001) or UACR (p < 0.001) and all-cause mortality. Mediation analysis revealed that eGFR accounted for 20.98% of the association between sitting time and mortality (p < 0.01). An addition of eGFR or UACR would increase the AUC from 0.585 to 0.762 and 0.656, respectively(p < 0.001). The main mortality caused by daily sitting time included chronic lower respiratory diseases, diabetes mellitus, cerebrovascular diseases and heart diseases.

CONCLUSIONS

Prolonged daily sitting time is significantly associated with an increased risk of all-cause mortality, potentially mediated by impaired kidney function. Incorporating kidney function markers such as eGFR and UACR enhances the predictive value for mortality risk assessment in sedentary populations.

The causal relationship between circulating metabolites and gestational hypertension, pre-eclampsia, eclampsia: A bidirectional two-sample Mendelian randomization study

OBJECTIVE

Gestational hypertension, pre-eclampsia, and eclampsia pose significant risks to maternal and fetal health, yet their underlying causes remain unclear. This study investigates the associations between 233 metabolites and these conditions.

METHODS

We analyzed data from the Genome-Wide Association Studies (GWAS) database for gestational hypertension, pre-eclampsia, and eclampsia. The bidirectional two-sample MR analysis examined causal relationships using inverse variance weighting as the primary method, supplemented by MR-Egger, weighted median, simple mode, and weighted mode. Sensitivity analyses assessed robustness, heterogeneity, and horizontal pleiotropy.

RESULTS

In the forward Mendelian randomization analysis, a reduction in citrate levels (OR = 0.906, 95% CI = 0.829-0.990, p = .029) is associated with an increased risk of gestational hypertension. The ratio of conjugated linoleic acid to total fatty acids (OR = 1.172, 95% CI = 1.026-1.339, p = .019) is associated with an increased risk of gestational hypertension. The ratio of conjugated linoleic acid to total fatty acids (OR = 1.288, 95% CI = 1.064-1.560, p = .009) is associated with an increased risk of preeclampsia and eclampsia. The phospholipids to total lipids ratio in large HDL (OR = 1.227, 95% CI = 1.120-1.344, p = 9.91 × 10^-6) is associated with an increased risk of preeclampsia and eclampsia. The total cholesterol to total lipids ratio in chylomicrons and extremely large VLDL (OR = 0.884, 95% CI = 0.789-0.990, p = .033) is associated with an increased risk of preeclampsia and eclampsia. In the reverse Mendelian randomization analysis, the occurrence of gestational hypertension is associated with a reduction in Cholesteryl esters to total lipids ratio in very large VLDL (OR = 0.987, 95% CI = 0.975-0.999, p = .044). The occurrence of preeclampsia and eclampsia is associated with a reduction in total choline levels (OR = 0.989, 95% CI = 0.979-0.998, p = .029), and with a reduction in total phosphoglycerides levels (OR = 0.988, 95% CI = 0.978-0.997, p = .012). Sensitivity analysis did not detect significant heterogeneity or pleiotropy.

CONCLUSION

This research elucidates the causal links between specific metabolites and gestational hypertension, pre-eclampsia, and eclampsia, potentially informing new clinical approaches for diagnosis and treatment.

A machine learning approach to risk-stratification of gastric cancer based on tumour-infiltrating immune cell profiles

BACKGROUND

Gastric cancer (GC) is a highly heterogeneous disease, and the response of patients to clinical treatment varies substantially. There is no satisfactory strategy for predicting curative effects to date. We aimed to explore a new method for predicting the clinical efficacy of GC treatment based on immune variables detected via flow cytometry.

METHODS

We collected 394 tumour tissues from GC patients for flow cytometry analysis and gating analysis of tumour-infiltrating immune cells (TIICs). Unsupervised consensus clusters were generated from the cohort to classify patients into different phenogroups, and their clinical characteristics were examined. The derived model was evaluated via principal component analysis and t-distributed stochastic neighbourhood embedding analysis. Kaplan-Meier's curves were used to determine the prognosis during a 920-day-long median follow-up period (interquartile range: 834-1071 days). Adjusted multivariate Cox regression analysis was used to evaluate the association of clusters with disease-free survival (DFS) and recurrence.

RESULTS

All patients were classified based on their TIIC profiles into the C1 (characterized by low CD45 negative cell, high lymphocyte, high neutrophil and low CD3 + T cell levels), C2 (characterized by high CD8 + CD279+ cell and low CD4+ Th and CD8+ Tc cell numbers) and C3 (characterized by high CD4 + CD25+ and Treg cell levels) phenogroups. Patients from the three clusters had varied pathologies, MMR statuses and TIIC distribution patterns (p < .05). Kaplan-Meier's analysis showed that the prognosis of C3 was inferior compared to C1 and C2 (p = .0025). Adjusted Cox proportional hazard models helped us identify that C1 and C2 exhibited a favourable factor of recurrence after surgery, compared to C3. Kaplan-Meier's analysis showed that C1 and C2 were associated with a better DFS than C3 in some GC patient subgroups.

CONCLUSIONS

The machine learning model developed was found to be effective model at predicting the prognosis of patients with GC and their TIIC profiles for risk stratification in clinical settings.

Optic disc changes in Chinese patients with NLRP3-associated autoinflammatory disease

OBJECTIVE

To investigate the optic disc changes (ODC) in Chinese patients with NLRP3-associated autoinflammatory disease (NLRP3-AID).

METHODS

Patients who were diagnosed with NLRP3-AID at the Department of Rheumatology, Peking Union Medical College Hospital between April 2015 and December 2022 were retrospectively reviewed and analyzed.

RESULTS

A total of 20 patients were enrolled in this retrospective study. All 20 patients had a moderate MWS NLRP3-AID phenotype. Thirteen patients (65%) had ocular involvements. The interval between symptoms onset and diagnosis was significantly longer in patients with ocular involvement than in patients without (p = 0.044). The incidence of hearing loss was significantly higher in patients with ocular involvement (p = 0.017), while the incidence of abdominal pain was significantly lower when compared to patients without ocular involvement (p = 0.007). Optic disc swelling (ODS) (50%) was the most common ODC. All of the four T348M mutation carriers within our cohort exhibited ODS with visual-field defects. There was a significant difference between patients with/without ODS regarding the number of patients carrying T348M mutation (p = 0.014). The occurrence of hearing loss and CNS involvement was significantly higher in the group with ODS compared to the group without (p = 0.0014, p = 0.0198). Of the eight patients who underwent lumbar puncture, five presented with intracranial hypertension (IH). ODS was observed in all patients with IH. The serum inflammatory markers were significantly higher in patients with ODS than in those without. Two patients receiving regular subcutaneous IL-1 inhibitor treatment showed improvements in ODC.

CONCLUSIONS

ODC is common among Chinese patients with NLRP3-AID, with ODS being the most common manifestation. Hearing loss and CNS involvement often accompany the occurrence of ODS. The serum inflammatory markers are associated with ODS. The T348M mutation is more likely to lead to ODC with visual-field defects.

Unveiling causal pathways in autoimmune diseases: a multi-omics approach

Autoimmune diseases (ADs), such as Graves' disease (GD), Hashimoto's thyroiditis (HT), psoriasis, systemic lupus erythematosus (SLE), and type 1 diabetes (T1D), involve complex immune and inflammatory responses. This study employed Mendelian randomization (MR) analysis using genome-wide association study (GWAS) data to examine the causal relationships among 91 circulating inflammatory proteins, 41 cytokines, 211 gut microbiota, and 731 immune cell traits in relation to ADs. Additionally, we integrated mediation and bioinformatics analyses, including protein-protein interaction (PPI) networks, Gene Ontology (GO) enrichment, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis. Subnetwork discovery and key protein identification were performed using the Molecular Complex Detection (MCODE) plugin, alongside colocalization analysis and drug target exploration to identify potential mechanisms. MR analysis identified significant causal relationships between various circulating inflammatory proteins, cytokines, gut microbiota species, immune cells, and ADs, with certain relationships retaining significance after false discovery rate (FDR) correction. Mediation analysis demonstrated that inflammatory proteins mediate pathogenic pathways linking immune cells to psoriasis and gut microbiota to Hashimoto's thyroiditis. PPI and bioinformatics analyses highlighted 22 key proteins involved in ADs, while subnetwork analysis identified 15 central proteins. Fms-related tyrosine kinase 3 ligand (FLT3LG) exhibited strong colocalization evidence. Molecular docking confirmed several proteins as viable drug targets. This comprehensive multi-omics study advances our understanding of ADs, identifies novel therapeutic targets, and offers valuable insights for developing new treatment strategies.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

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.

Causal associations between premature ovarian insufficiency and cardiovascular diseases: a Mendelian randomization study

To date, there remains a paucity of prospective studies examining the association between premature ovarian insufficiency (POI) and cardiovascular diseases (CVD). The objective of this study was to investigate the potential association between POI and CVD utilizing the method of Mendelian randomization (MR). MR analyses utilized summary statistics from the most extensive genome-wide association studies (GWAS) on POI and CVD extracted from European ancestry cohorts and the FinnGen biobank. The inverse variance-weighted (IVW) method was the primary MR analysis technique. Supplementary analyses were performed using MR-Robust Adjusted Profile Score (MR-RAPS). Cochran's Q statistic, MR-Egger, and weighted median MR models were employed to further assess heterogeneity and horizontal pleiotropy. Causal effects of POI on coronary heart disease (odds ratio [OR] = 1.048, 95% confidence interval [CI]: 1.006-1.091; p = 0.023)] and ischemic stroke (OR = 1.010, 95% CI: 1.000-1.020; p = 0.0498) were found. However, we did not observe a significant correlation between POI and hypertension (OR = 0.999, 95% CI: 0.994-1.004, p = 0.691), heart failure (OR = 1.009, 95% CI: 0.999-1.020, p = 0.0725), atrial fibrillation (OR = 0.995, 95% CI: 0.986-1.004, p = 0.3035), and myocardial infarction (OR = 1.002, 95% CI: 0.991-1.013, p = 0.7061). POI was causally associated with coronary heart disease and ischemic stroke, with no apparent impact on hypertension, heart failure, atrial fibrillation, or myocardial infarction. The causal relationship between POI and CVD underscores the imperative for proactive cardiovascular risk management in individuals with POI.

Bridging-mediated compaction of mitotic chromosomes

Within living cells, chromosome shapes undergo a striking morphological transition, from loose and uncondensed fibers during interphase to compacted and cylindrical structures during mitosis. ATP driven loop extrusion performed by a specialized protein complex, condensin, has recently emerged as a key driver of this transition. However, while this mechanism can successfully recapitulate the compaction of chromatids during the early stages of mitosis, it cannot capture structures observed after prophase. Here we hypothesize that a condensin bridging activity plays an additional important role, and review evidence - obtained largely through molecular dynamics simulations - that, in combination with loop extrusion, it can generate compact metaphase cylinders. Additionally, the resulting model qualitatively explains the unusual elastic properties of mitotic chromosomes observed in micromanipulation experiments and provides insights into the role of condensins in the formation of abnormal chromosome structures associated with common fragile sites.

Glucagon-like peptide-1 receptor agonists, inflammation, and kidney diseases: evidence from Mendelian randomization

OBJECTIVE

It has been proved that glucagon-like peptide-1 receptor (GLP1R) agonists have positive effects on renal outcomes in diabetic patients. However, it remains unknown whether GLP1R agonists could provide similar protection against other kidney diseases.

METHODS

We performed two-sample Mendelian randomization (MR) analyses to determine the causal effects of GLP1R agonists on multiple kidney diseases. Exposure to GLP1R agonist was proxied by the available cis-eQTLs for GLP1R. Primary outcomes included the risk assessment for diabetic nephropathy, IgA nephropathy, membranous nephropathy, nephrotic syndrome, chronic kidney disease, acute glomerulonephritis, chronic glomerulonephritis and calculus of kidney/ureter. Type 2 diabetes and body mass index were used as positive control. Two-stage network MR analyses were conducted to assess the mediation effect of inflammatory proteins on the relationships between GLP1R agonists and kidney diseases.

RESULTS

After meta-analyses of both discovery and validation cohorts, genetically proxied GLP1R agonist was found to significantly associated with a decreased risk of diabetic nephropathy (OR = 0.72, 95%CI = 0.54-0.97, p = 0.031) and IgA nephropathy (OR = 0.58, 95%CI = 0.36-0.94, p = 0.027). Two-stage network MR revealed that there was an indirect effect of GLP1R agonist on IgA nephropathy through signaling lymphocytic activation molecule family member 1 (SLAMF1), with a mediated proportion of 34.27% (95% CI, 1.47-67.03%, p = 0.041) of the total effect.

CONCLUSIONS

The findings of current study presented genetic proof for the potential protective effects of GLP1R agonists in the development of diabetic nephropathy and IgA nephropathy, offering a novel sight for future mechanistic and clinical applications.

The impact of rising peripheral blood naïve CD8+ T cell levels on chronic kidney disease onset: a Mendelian randomization study

BACKGROUND

The global incidence of chronic kidney disease (CKD) is rising rapidly. Immune cells play a crucial role in the onset and progression of CKD, however, the causal relationships and underlying immunological mechanisms remain incompletely elucidated. This deficiency hinders the development and application of early interventions and immunotherapies for CKD.

METHODS

In this study, we hypothesize that alterations in immune cell phenotypes (ICPs) in the blood may influence the onset of CKD. We collated Genome Wide Association Studies (GWAS) data for 731 ICPs, alongside summary data for CKD and estimated glomerular filtration rate (eGFR). Utilizing bidirectional mendelian randomization analysis (MR), we identified the impact of ICPs on the onset of CKD.

RESULTS

Preliminary MR analyses revealed three ICPs positively associated with CKD onset: the absolute number of CD45RA+ CD28- CD8+ T cells (p = 1.209 × 10-15, 95% CI: 1.0002-1.0003), the percentage of CD28+ CD45RA+ CD8+ T cells of total T cells (p = 5.831 × 10-6, 95% CI: 1.0028-1.0070), and the percentage of CD45RA- CD28- CD8+ T cells of total T cells (p = 4.292 × 10-5, 95% CI: 1.0005-1.0015). After conducting sensitivity and reverse MR analyses, only the percentage of CD28+ CD45RA+ CD8+ T cells (naïve CD8+ T Cells) was found to have a sufficiently robust causal impact on CKD.

CONCLUSION

We are the first to demonstrate a significant positive association between the percentage of naïve CD8+ T cells and CKD onset. This finding offers new insights for early prevention and treatment of CKD.

Deciphering the causal link between gut microbiota and membranous nephropathy: insights into potential inflammatory mechanisms

BACKGROUND

Membranous nephropathy (MN), a leading cause of adult nephrotic syndrome and renal failure, has been linked to gut microbiota (GM) and their metabolites. However, direct causal relationships and therapeutic implications remain unclear.

METHODS

We utilized a comprehensive GWAS dataset that encompasses GM, metabolites, and MN through two-sample Mendelian randomization (MR) analyses, bidirectional MR evaluations, and detailed sensitivity tests.

RESULTS

We identified strong causal associations between nine specific types of GM, including class Clostridia (OR = 1.816, 95%CI: 1.021-3.236, p = .042), class Melainabacteria (OR = 0.661, 95%CI: 0.439-0.996, p = .048), order Gastranaerophilales (OR = 0.689, 95%CI: 0.480-0.996, p = .044), genus Alistipes (OR = 0.480, 95%CI: 0.223-0.998, p = .049), genus Butyricicoccus (OR = 0.464, 95%CI: 0.216-0.995, p = .048), genus Butyrivibrio (OR = 0.799, 95%CI: 0.639-0.998, p = .048), genus Ruminococcaceae UCG003 (OR = 0.563, 95%CI: 0.362-0.877, p = .011), genus Streptococcus (OR = 0.619, 95%CI: 0.393-0.973, p = .038), and genus Oscillibacter (OR = 1.90, 95%CI: 1.06-3.40, p = .031). Additionally, the metabolite tryptophan also exhibited a significant causal influence on MN (OR = 0.852, 95%CI: 0.754-0.963, p = .010). Sensitivity and reverse MR analyses confirmed the robustness of these findings. Further exploration using gutMGene database suggests that GM may influence MN by affecting the release of inflammatory factors and modulating inflammatory pathways.

CONCLUSION

This study offers a comprehensive understanding of the causal links between GM, their metabolites, and MN, which highlight potential pathways for developing new preventive and therapeutic strategies for this condition.

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.

Causal relationship between chronic kidney disease, renal function, and venous thromboembolism: a bidirectional Mendelian randomization study

BACKGROUND

Chronic kidney disease (CKD) and impaired renal function have been implicated in venous thromboembolism (VTE), but their causal relationships remain uncertain. This study employs Mendelian randomization (MR) to elucidate the potential bidirectional causal effects between CKD, renal function biomarkers, and VTE.

METHODS

We collated datasets from genome-wide association studies conducted among European individuals to perform MR analyses. The primary method utilized was the random-effect inverse variance-weighted (IVW) approach, with MR-Egger and the weighted median approaches employed as supplemental techniques. Several sensitivity studies were performed to assess the findings' robustness.

RESULTS

We identified a link between elevated serum creatinine levels and both VTE (OR: 1.14, 95% CI: 1.05-1.24, p = 0.001) and PE (OR: 1.20, 95% CI: 1.08-1.33, p = 0.001). After outlier removal and Bonferroni correction, the Cr-VTE association lost significance (p = 0.005). A suggestive causal relationship was found between eGFR and VTE (OR: 0.38, 95% CI: 0.20-0.73, p = 0.004), DVT (OR: 0.37, 95% CI: 0.16-0.87, p = 0.022), and PE (OR: 0.29, 95% CI: 0.12-0.66, p = 0.004). No causal effects of CKD or BUN on VTE or its subtypes were observed. Reverse causality inferences did not reveal any meaningful results.

CONCLUSIONS

This MR analysis provides evidence that elevated serum creatinine is associated with a higher risk of VTE and PE, while reduced eGFR may be a potential risk factor for VTE and its subtypes. These findings highlight the need for proactive monitoring and preventive strategies in individuals with impaired renal function. Further studies are warranted to confirm these associations and explore underlying mechanisms.

A novel clustered-based binary grey wolf optimizer to solve the feature selection problem for uncovering the genetic links between non-Hodgkin lymphomas and rheumatologic diseases

The growing incidence of Non-Hodgkin lymphomas (NHL) in recent times has brought attention to the need for thorough investigations of their genetic associations with autoimmune and rheumatologic conditions, such as systemic lupus, celiac disease, and Sjögren's syndrome. Our study is the first of its type in this field since it uses machine learning to investigate these relationships in great detail. Firstly, we have developed a new genetic dataset, specifically designed to uncover the genetic intricacies of NHL and rheumatologic diseases, offering unprecedented insights into their molecular mechanisms. Following this, we introduced the Clustered-Based Binary Grey Wolf Optimizer (CB-BGWO), a novel method that significantly revolutionizes the feature selection process in genetic analysis. This optimizer significantly improves the accuracy and efficiency of identifying important genetic variables affecting the interaction between rheumatologic and NHL illnesses. This methodological advance not only increases the analytical power but also creates a new standard for genetic research methods. Our findings address a significant gap in the literature and offer valuable insights that could positively support future treatment strategies and research paths. By illuminating the complex genetic connections between NHL and significant rheumatologic conditions, this work contributes to a better understanding and treatment of these complex diseases.

Construction of a novel radioresistance-related signature for prediction of prognosis, immune microenvironment and anti-tumour drug sensitivity in non-small cell lung cancer

BACKGROUND

Non-small cell lung cancer (NSCLC) is a fatal disease, and radioresistance is an important factor leading to treatment failure and disease progression. The objective of this research was to detect radioresistance-related genes (RRRGs) with prognostic value in NSCLC.

METHODS

The weighted gene coexpression network analysis (WGCNA) and differentially expressed genes (DEGs) analysis were performed to identify RRRGs using expression profiles from TCGA and GEO databases. The least absolute shrinkage and selection operator (LASSO) regression and random survival forest (RSF) were used to screen for prognostically relevant RRRGs. Multivariate Cox regression was used to construct a risk score model. Then, Immune landscape and drug sensitivity were evaluated. The biological functions exerted by the key gene LBH were verified by in vitro experiments.

RESULTS

Ninety-nine RRRGs were screened by intersecting the results of DEGs and WGCNA, then 11 hub RRRGs associated with survival were identified using machine learning algorithms (LASSO and RSF). Subsequently, an eight-gene (APOBEC3B, DOCK4, IER5L, LBH, LY6K, RERG, RMDN2 and TSPAN2) risk score model was established and demonstrated to be an independent prognostic factor in NSCLC on the basis of Cox regression analysis. The immune landscape and sensitivity to anti-tumour drugs showed significant disparities between patients categorized into different risk score subgroups. In vitro experiments indicated that overexpression of LBH enhanced the radiosensitivity of A549 cells, and knockdown LBH reversed the cytotoxicity induced by X-rays.

CONCLUSION

Our study developed an eight-gene risk score model with potential clinical value that can be adopted for choice of drug treatment and prognostic prediction. Its clinical routine use may assist clinicians in selecting more rational practices for individuals, which is important for improving the prognosis of NSCLC patients. These findings also provide references for the development of potential therapeutic targets.

Mediated roles of oxidative stress and kidney function to leukocyte telomere length and prognosis in chronic kidney disease

BACKGROUND

Few studies have focused on the correlation between leukocyte telomere length (LTL) and cancer-related mortality or identified potential factors that mediate the relationship between LTL and mortality among chronic kidney disease (CKD) patients. Our study aimed to explore the associations between LTL and all-cause and cause-specific mortality and to identify the underlying mediators.

METHODS

CKD patients were obtained from the National Health and Nutrition Examination Survey (NHANES) 1999-2002. Cox regression analysis and restricted cubic spline analysis were used to explore the associations between LTL and all-cause or specific-cause mortality and their nonlinear connections. Stratified analyses were executed to assess the relationships among the different subgroups. The latent mediated factors were confirmed using mediation analysis. Sensitivity analyses were used to evaluate the robustness of our findings.

RESULTS

Longer LTL associated with the lower risk of all-cause mortality, cardiovascular disease (CVD) and cancer-related mortality, and U-shaped relationships were detected. Patients younger than 65 years with greater LTL or who had hypertension had better prognoses. Age and history of hypertension were associated with LTL and overall mortality. In addition, estimated glomerular filtration rate (eGFR), albumin, and total bilirubin mediated the association, and the proportions of indirect effects were 7.81%, 3.77%, and 2.50%, respectively. Six sensitivity analyses confirmed the robustness of our findings.

CONCLUSIONS

This study revealed that LTL was a protective factor for survival among patients with CKD and emphasized the mediating roles of oxidative stress and kidney function.