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.

Alpha-1 antitrypsin deficiency and Pi*S and Pi*Z SERPINA1 variants are associated with asthma exacerbations

INTRODUCTION AND OBJECTIVES

Asthma is a chronic inflammatory disease of the airways. Asthma patients may experience potentially life-threatening episodic flare-ups, known as exacerbations, which may significantly contribute to the asthma burden. The Pi*S and Pi*Z variants of the SERPINA1 gene, which usually involve alpha-1 antitrypsin (AAT) deficiency, had previously been associated with asthma. The link between AAT deficiency and asthma might be represented by the elastase/antielastase imbalance. However, their role in asthma exacerbations remains unknown. Our objective was to assess whether SERPINA1 genetic variants and reduced AAT protein levels are associated with asthma exacerbations.

MATERIALS AND METHODS

In the discovery analysis, SERPINA1 Pi*S and Pi*Z variants and serum AAT levels were analyzed in 369 subjects from La Palma (Canary Islands, Spain). As replication, genomic data from two studies focused on 525 Spaniards and publicly available data from UK Biobank, FinnGen, and GWAS Catalog (Open Targets Genetics) were analyzed. The associations between SERPINA1 Pi*S and Pi*Z variants and AAT deficiency with asthma exacerbations were analyzed with logistic regression models, including age, sex, and genotype principal components as covariates.

RESULTS

In the discovery, a significant association with asthma exacerbations was found for both Pi*S (odds ratio [OR]=2.38, 95% confidence interval [CI]= 1.40-4.04, p-value=0.001) and Pi*Z (OR=3.49, 95%CI=1.55-7.85, p-value=0.003)Likewise, AAT deficiency was associated with a higher risk for asthma exacerbations (OR=5.18, 95%CI=1.58-16.92, p-value=0.007) as well as AAT protein levels (OR= 0.72, 95%CI=0.57-0.91, p-value=0.005). The Pi*Z association with exacerbations was replicated in samples from Spaniards with two generations of Canary Islander origin (OR=3.79, p-value=0.028), and a significant association with asthma hospitalizations was found in the Finnish population (OR=1.12, p-value=0.007).

CONCLUSIONS

AAT deficiency could be a potential therapeutic target for asthma exacerbations in specific populations.

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.

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.

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.

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.

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.

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.

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

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

The vestibular and oculomotor dysfunction in Fabry disease: a cohort study in China

OBJECTIVE

Whereas a few studies have evaluated vestibular involvement in Fabry disease (FD), the relationship between vestibular/oculomotor abnormalities and disease-specific biomarkers remain unclear. Therefore, we seek to evaluate these quantitatively and analyze their relationship with disease phenotype and biomarkers in FD.

METHODS

This cohort study enrolled 37 Chinese FD patients registered in our center. The vestibular/oculomotor examinations were performed, including the videonystagmography, the caloric test and the video head-impulse test. Statistical analyses were made between different subgroups of patients.

RESULTS

Visuo-oculomotor dysfunctions were found in 30/37 (81.1%) patients. Vestibulo-oculomotor dysfunctions were revealed in 9/22 (40.9%) patients. Statistical tests showed: (1) significantly higher Mainz Severity Score Index in patients with prolonged saccade latency [20(18,33) VS 13(9,22), p = 0.008] and vestibulo-oculomotor dysfunction [23(20,31) VS 9(5.5,12.5), p = 0.024], (2) significantly higher total small-vessel disease score in subgroups with prolonged saccade latency [2.5(1,3.5) VS 1(0,2), p = 0.038], defective smooth pursuit [3(2,4) VS 1(0,2), p = 0.003], defective optokinetic nystagmus [4(2,4) VS 1(0.2), p = 0.009] and vestibulo-oculomotor dysfunction [1(1,3) VS 0(0,1), p = 0.028], (3) significantly lower α-Gal A activity (μmol/L/h) in subgroups with defective saccades [0.44(0.25,1.93) VS 1.85(0.75,5.52), p = 0.015] and defective smooth pursuit [0.30(0.17,0.44) VS 0.96(0.39,2.40), p = 0.008], and (4) significantly elevated plasma globotriaosylsphingosine (ng/ml) in patients with defective saccades [74.16(11.05,89.18) VS 10.64(7.08,36.32), p = 0.034], than in patients without those abnormalities.

CONCLUSION

A high incidence of extensive vestibular and oculomotor dysfunction was observed in patients with FD, with the neuro-otological dysfunction being closely related to the disease burden and biomarkers like α-Gal A activity and lyso-Gb3.

Aberrant regional neural fluctuations and functional connectivity in insomnia comorbid depression revealed by resting-state functional magnetic resonance imaging

Insomnia is a common mental illness seriously affecting people lives, that might progress to major depression. However, the neural mechanism of patients with CID comorbid MDD remain unclear. Combining fractional amplitude of low-frequency fluctuation (fALFF) and seed-based functional connectivity (FC), this study investigated abnormality in local and long-range neural activity of patients with CID comorbid MDD. Here, we acquired resting-state blood oxygenation level dependent (BOLD) data from 57 patients with CID comorbid MDD and 57 healthy controls (HC). Compared with the controls, patients with CID comorbid MDD exhibited abnormal functional activity in posterior cerebral cortex related to the visual cortex, including the middle occipital gyrus (MOG), the cuneus and the lingual gyrus, specifically, lower fALFF values in the right MOG, left cuneus, and right postcentral gyrus, increased FC between the right MOG and the left cerebellum, and decreased FC between the right MOG and the right lingual gyrus. Neuropsychological correlation analysis revealed that the decreased fALFF in the right MOG was negatively correlated with all the neuropsychological scores of insomnia and depression, reflecting common relationships with symptoms of CID and MDD. While the decreased fALFF of the left cuneus was distinctly correlated with the scores of depression related scales. The decreased FC between the right MOG and the right lingual gyrus was distinctly correlated with the scores of insomnia related scales. This study not only widened neuroimaging evidence that associated with insomnia and depressive symptoms of patients with CID comorbid MDD, but also provided new potential targets for clinical treatment.

Navigating the practical challenges and ethical dilemmas of surplus cryopreserved human embryos

Cryopreservation, the use of very low temperatures to preserve structurally intact living cells and tissues, has seen exponential growth in the field of in vitro fertilization (IVF). In the last decade, cryopreservation of embryos and freeze-all protocols have become an essential aspect and a prerequisite for a successful IVF outcome. Moreover, vitrification, which is a fast and safe cryopreservation method, has proved to be an effective choice for cryopreserving gametes and embryos. The increasing number of cryopreserved embryos worldwide in cryobanks and IVF clinics is an undisputable fact that raises important physiological, ethical, and moral considerations that merit careful examination and discussion. Many couples utilizing assisted reproduction will have a surplus of cryopreserved embryos, in other words they already have completed their family without exhausting all the embryos that were created and cryopreserved during the process. Additionally, the global IVF market has also experienced significant growth due to various factors, including advancements in technology, increased awareness about infertility treatments, and changing societal norms towards delayed parenthood. Thus, for the foreseeable future the number of cryopreserved embryos, and the phenomenon of surplus embryos will likely remain unresolved. In the present review, following a description of the cryopreservation method and the physiological changes during the cryopreservation of embryos, the bioethical issues raised by the surplus cryopreserved embryos will be discussed alongside possible solutions for resolving this phenomenon.

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.

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.

Alterations in mucosa branched N-glycans lead to dysbiosis and downregulation of ILC3: a key driver of intestinal inflammation

The perturbation of the symbiotic relationship between microbes and intestinal immune system contributes to gut inflammation and Inflammatory Bowel Disease (IBD) development. The host mucosa glycans (glycocalyx) creates a major biological interface between gut microorganisms and host immunity that remains ill-defined. Glycans are essential players in IBD immunopathogenesis, even years before disease onset. However, how changes in mucosa glycosylation shape microbiome and how this impact gut immune response and inflammation remains to be clarified. Here, we revealed that alterations in the expression of complex branched N-glycans at gut mucosa surface, modeled in glycoengineered mice, resulted in dysbiosis, with a deficiency in Firmicutes bacteria. Concomitantly, this mucosa N-glycan switch was associated with a downregulation of type 3 innate lymphoid cells (ILC3)-mediated immune response, leading to the transition of ILC3 toward an ILC1 proinflammatory phenotype and increased TNFα production. In addition, we demonstrated that the mucosa glycosylation remodeling through prophylactic supplementation with glycans at steady state was able to restore microbial-derived short-chain fatty acids and microbial sensing (by NOD2 expression) alongside the rescue of the expression of ILC3 module, suppressing intestinal inflammation and controlling disease onset. In a complementary approach, we further showed that IBD patients, often displaying dysbiosis, exhibited a tendency of decreased MGAT5 expression at epithelial cells that was accompanied by reduced ILC3 expression in gut mucosa. Altogether, these results unlock the effects of alterations in mucosa glycome composition in the regulation of the bidirectional crosstalk between microbiota and gut immune response, revealing host branched N-glycans/microbiota/ILC3 axis as an essential pathway in gut homeostasis and in preventing health to intestinal inflammation transition.

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.

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

BACKGROUND

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

METHODS

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

RESULTS

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

CONCLUSIONS

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

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

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

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

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

Dual roles of exostosin glycosyltransferase 1 in Zika virus infection

Many factors involved in heparan sulfate (HS) biosynthesis and metabolism have been reported to play roles in viral infection. However, the detailed mechanisms are still not fully understood. In this study, we report that exostosin glycosyltransferase 1 (EXT1), the HS polymerase, is a critical regulatory factor for Zika virus (ZIKV) infection. Knocking out EXT1 dramatically restricts ZIKV infection, which is not due to the inhibition of virus entry resulting from HS deficiency, but mediated by the downregulation of autophagy. Induction of autophagy promotes ZIKV infection, and attenuated autophagy is found in distinct EXT1 knockout (EXT1-KO) cell lines. Induction of autophagy by rapamycin can relieve the ZIKV production defect in EXT1-KO cells. While over-expressing EXT1 results in the reduction of ZIKV production by targeting the viral envelope (E) protein and non-structural protein NS3 in a proteasome-dependent degradation manner. The different roles of EXT1 in ZIKV infection are further confirmed by the data that knocking down EXT1 at the early stage of ZIKV infection represses viral infection, whereas the increase of ZIKV infection is observed when knocking down EXT1 at the late stage of viral infection. This study discovers previously unrecognized intricate roles of EXT1 in ZIKV infection.

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

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

Exome sequencing identifies a homozygous splice site variant in RP1 as the underlying cause of autosomal recessive retinitis pigmentosa in a Pakistani family

BACKGROUND

Mutations in RP1 gene are the third leading cause of inherited retinal dystrophies (IRDs) in Pakistani families.

PATIENTS

A two-generation consanguineous Pakistani family underwent both clinical and genetic analyses. Clinical examinations included visual acuity test, visual field, fundoscopy, and ocular coherence tomography (OCT). Whole exome sequencing (WES) was performed on the proband's DNA, and Sanger sequencing was performed to validate the WES findings. Splicing prediction tools such as Human Splicing Finder (HSF), NNSplice predictor, SpliceAI, MaxENTScan, and SpliceRover were used.

RESULTS

A nuclear family of seven children, comprising five affected individuals (four males and one female) and two healthy siblings, was recruited from northwestern Pakistan. The proband was a 49-years old male who was presented with complaints of decreased visual acuity and night blindness since early childhood. Upon clinical evaluation, the proband appeared to have severely reduced visual acuity of hand movement (HM), bilateral visual field constriction, a waxy pale disc with vascular attenuation, pigmentary bone spicules at the periphery associated with chorioretinal degeneration, diffuse macular atrophy, and horizontal nystagmus in both of his eyes. Exome sequencing (ES) in the proband identified a homozygous splice site variant (NM_006269.2: c.615 + 1G > A) in RP1 gene. In-silico analysis, genotype-phenotype co-segregation study, and literature survey strongly supported the causality of the detected variant.

CONCLUSIONS

We report a previously known pathogenic splice site variant of RP1 as the underlying cause of early-onset autosomal recessive retinitis pigmentosa (arRP) in a Pakistani family. We contemplate that the detected allele might constitute a mutational hotspot in RP1.

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.

Causal associations of metabolic dysfunction-associated steatotic liver disease with gestational hypertension and preeclampsia: a two-sample Mendelian randomization study

BACKGROUND

Hypertensive disorders of pregnancy (HDPs), which include gestational hypertension (GH) and preeclampsia (PE), are the primary causes of maternal morbidity and mortality worldwide. Recent studies have found a correlation between metabolic dysfunction-associated steatotic liver disease (MASLD) and HDPs, but the causality of this association remains to be identified. Therefore, this study aims to evaluate the causal relationship between MASLD and HDPs through Mendelian randomization (MR) analysis.

METHODS

The summary statistics from genome-wide association studies were employed to conduct a two-sample MR analysis. Five complementary MR methods, including inverse variance weighting (IVW), MR-Egger, weighted median, simple mode and weighted mode were performed to assess the causality of MASLD on GH and PE. Furthermore, we conducted various sensitivity analyses to ensure the stability and reliability of the results.

RESULTS

Genetically predicted MASLD significantly increased the risk of GH (IVW: OR = 1.138, 95% CI: 1.062-1.220, p < 0.001), while there was little evidence of a causal relationship between MASLD and PE (IVW: OR = 0.980, 95% CI: 0.910-1.056, p = 0.594). The sensitivity analyses indicated no presence of heterogeneity and horizontal pleiotropy.

CONCLUSION

This MR study provided evidence supporting the causal effect of MASLD on GH. Our findings underscore the significance of providing more intensive prenatal care and early intervention for pregnant women with MASLD to prevent potential adverse obstetric outcomes.

Novel role of FTO in regulation of gut-brain communication via Desulfovibrio fairfieldensis-produced hydrogen sulfide under arsenic exposure

Fat mass and obesity-associated protein (FTO) is the key demethylase that reverses the abnormally altered N6-methyladenosine (m6A) modification in eukaryotic cells under environmental pollutants exposure. Arsenic is an environmental metalloid and can cause severe symptoms in human mainly through drinking water. However, there is no specific treatment for its toxic effects due to the uncovered mechanisms. We previously revealed that exposure to arsenic increased the level of m6A via down-regulation of FTO, which might serve as a potential target for intervention against arsenic-related disorders. In this study, our results demonstrated that chronic exposure to arsenic significantly disrupted the intestinal barrier and microenvironment. Also, this administration resulted in the enhancement of m6A modification and the reduction of FTO expression in the intestine. By using both CRISPR/Cas9-based FTO knock-in strategy and adeno-associated virus (AAV)-mediated overexpression of FTO in the intestine, we established for the first time that up-regulation of FTO remarkably ameliorated arsenic-induced disruption of intestinal barriers and altered microenvironment of mice. We also firstly identified a dominant gut microbial species, Desulfovibrio fairfieldensis, which was sharply reduced in arsenic-exposed mice, was able to proceed arsenic-induced neurobehavioral impairments by declining the levels of its major metabolite hydrogen sulfide. Administration of Desulfovibrio fairfieldensis could significantly alleviate the neurotoxicity of arsenic. Intriguingly, the beneficial effects of FTO against arsenic neurotoxicity possibly occurred through a novel gut-brain communication via Desulfovibrio fairfieldensis and its produced hydrogen sulfide. Collectively, these findings will provide new ideas for understanding the mechanisms of arsenic-induced toxic effects from a gut-brain communication perspective, and will assist the development of explicit intervention strategy via regulation of a new potential target FTO for prevention and treatment against arsenic-related both intestinal and neurological disorders.

Glucocorticoid receptor epigenetic activity in the heart

The glucocorticoid receptor (GR) is a critical nuclear receptor that regulates gene expression in diverse tissues, including the heart, where it plays a key role in maintaining cardiovascular health. GR signaling influences essential processes within cardiomyocytes, including hypertrophy, calcium handling, and metabolic balance, all of which are vital for proper cardiac function. Dysregulation of GR activity has been implicated in various cardiovascular diseases (CVDs), highlighting the potential of GR as a therapeutic target. Remarkably, recent insights into GR's epigenetic regulation and its interaction with circadian rhythms reveal opportunities to optimize therapeutic strategies by aligning glucocorticoid administration with circadian timing. In this review, we provide an overview of the glucocorticoid receptor's role in cardiac physiology, detailing its genomic and non-genomic pathways, interactions with epigenetic and circadian regulatory mechanisms, and implications for cardiovascular disease. By dissecting these molecular interactions, this review outlines the potential of epigenetically informed and circadian-timed interventions that could change the current paradigms of CVD treatments in favor of precise and effective therapies.

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.

Genome-wide analysis of abnormal splicing regulators and alternative splicing involved in immune regulation in systemic lupus erythematosus

Systemic lupus erythematosus (SLE) is an autoimmune disease with complex clinical manifestations and no current cure. Alternative splicing (AS) plays a key role in SLE by regulating immune-related genes, but its genome-wide regulatory mechanisms remain unclear. To investigate the involvement of abnormal splicing regulators and AS events in the immune regulation of SLE. Transcriptome data from the SLE dataset GSE162828 were analyzed for differential gene expression and AS events using bioinformatics tools. Immune infiltration analysis was conducted with CIBERSORT, and co-expression of key splicing factors (SFs) and AS events was assessed using SUVA software. A total of 5144 differentially expressed genes and 73 SFs were identified. Significant immune cell differences were observed between SLE and controls, highlighting SFs such as HNRNPDL, RBM47, TIA1, SSB, and DHX15. Eighty-three AS events were identified, with IRF9 and PTPRC emerging as key regulatory events linked to SLE. Dysregulated SFs influence AS in immune-related genes, affecting immune cell composition and SLE progression. These findings offer potential new therapeutic targets for modulating the immune microenvironment in SLE.

Targeting γc family cytokines with biologics: current status and future prospects

Over the recent decades the market potential of biologics has substantially expanded, and many of the top-selling drugs worldwide are now monoclonal antibodies or antibody-like molecules. The common gamma chain (γc) cytokines, Interleukin (IL-)2, IL-4, IL-7, IL-9, IL-15, and IL-21, play pivotal roles in regulating immune responses, from innate to adaptive immunity. Dysregulation of cell signaling by these cytokines is strongly associated with a range of immunological disorders, which includes cancer as well as autoimmune and inflammatory diseases. Given the essential role of γc cytokines in maintaining immune homeostasis, the development of therapeutic interventions targeting these molecules poses unique challenges. Here, we provide an overview of current biologics targeting either single or multiple γc cytokines or their respective receptor subunits across a spectrum of diseases, primarily focusing on antibodies, antibody-like constructs, and antibody-cytokine fusions. We summarize therapeutic biologics currently in clinical trials, highlighting how they may offer advantages over existing therapies and standard of care, and discuss recent advances in this field. Finally, we explore future directions and the potential of novel therapeutic intervention strategies targeting this cytokine family.

Diagnostic significance of combined two-dimensional ultrasound and three-dimensional tomographic ultrasound imaging for cleft palate in fetus of 11-13 + 6 weeks: a prospective study

PURPOSE

Clinical screening for cleft palate in fetus currently focuses on weeks 20-24. It has been shown that cleft palate can be detected by ultrasound in first-trimester anatomy scan, but there are no large-scale samples to validate. This study was to confirm the ability of combined two-dimensional(2D)-ultrasound and three-dimensional(3D)-tomographic ultrasound imaging (TUI) to safely detect an fetal cleft palate at 11-13 + 6 weeks via large-scale samples.

METHODS

A prospective study was designed, involving 6870 pregnant women applying 2D-ultrasound transabdominal sweeps of the fetal face in the median sagittal and coronal views of the retronasal triangle with abnormalities of the palatal line detected, followed by an axial view of the superior alveolar eminence and 3D-TUI evaluation. The endpoints were the results of the fetal facial profile assessment for delivery and induction of labor. The accuracy, sensitivity, and specificity of ultrasound for diagnosing a cleft palate at 11-13 + 6 weeks were analyzed.

RESULTS

Among 6870 fetus, a total of 43 different cleft palate types were diagnosed by 2D-ultrasound in three-sections at the 11-13 + 6 weeks, and a total of 6827 cases were diagnosed of negative for cleft palate. Of the 43 cases diagnosed of positive for cleft palate, three cases were false positives compared to endpoint results, with a correct positive predictive value of 93.0%. Of the 6827 cases diagnosed of negative for cleft palate, five cases were false negatives compared to endpoint results, with a correct negative predictive value of 99.0%. The sensitivity and specificity of 2D-ultrasound screening for cleft palate were 84.4%, and 99.9%, respectively. The 43 cases received 3D-TUI scans, and the results showed that 37 cases of cleft palate detected, with a positive predictive value of 86.0%, which was lower than that of 2D ultrasonography (93.0%) (p < 0.05).

CONCLUSION

It may be feasible and accurate to diagnose cleft palate in fetus at 11-13 + 6 weeks by using combined 2D three sections ultrasound and 3D-TUI scans.

Association between caffeine intake and fat free mass index: a retrospective cohort study

BACKGROUND

Caffeine, identified as a central nervous system stimulant in foods, beverages (coffee, tea, chocolate), and medications, has been focused on its ergogenic properties, enhancing physical performance. The aim of this study was to investigate the association between the caffeine intake (from coffee) and fat-free mass index (FFMI).

MATERIALS AND METHODS

We carried out a cohort study that included 3,466 women and 3,145 men aged ≥20 years who were intaking caffeine. Caffeine intake from coffee were obtained from two 24-hour dietary recall interviews. The FFMI was calculated as FFM (kg) divided by height in m2. The caffeine intake was classified into quartiles and combined into 4 groups. Multiple linear regression model analysis and multiple logistic regression model analysis were used to assess associations between the caffeine and FFMI adjusted for potential confounders.

RESULTS

Among the 2,427 participants, males accounted for 52.4%, and females 47.6%. In multiple linear regression model, Model 1 (unadjusted Model (p = 0.041)) and Model 2 (adjusted for age, race, and BMI (p = 0.006)) in women showed a significant relationship between caffeine intake and FFMI. In multivariable models, caffeine intake and FFMI were significantly different (p < 0.05). In sex subgroups, among females, each quartile of caffeine intake was positively correlated with FFMI levels in the average FFMI group in Model 3 (p < 0.001). In age subgroups, each quartile of caffeine intake was positively correlated with FFMI levels in the average FFMI group in Model 3 for individuals aged 20-40 (p = 0.039) and those aged above 40 (p = 0.016). In drinking status subgroups, if they drunk alcohol, each quartile was positively correlated with FFMI levels in the average FFMI group in Model 3 (p < 0.001).

CONCLUSION

Caffeine intake was mainly positively associated with FFMI, especially in women with above levels of FFMI. Longitudinal studies and randomized controlled trials are needed to establish causality and provide evidence-based recommendations regarding caffeine intake to optimize muscle health.

A practical guide for nephrologist peer reviewers: understanding and appraising Mendelian randomization studies

Identifying risk factors for disease onset and progression has been a core focus in nephrology research. Mendelian Randomization (MR) has emerged as a powerful genetic epidemiological approach, utilizing genome-wide association studies (GWAS) to establish causal relationships between modifiable risk factors and kidney disease outcomes. MR uses genetic variants as instrumental variables to infer causal relationships between exposures and disease outcomes. This method leverages the natural randomization of genetic variants to balance confounders, akin to matched cohorts in observational research. The rapid increase in MR studies on kidney disease poses challenges for journals and peer reviewers, especially clinicians unfamiliar with the methodology. High-quality MR studies use strong, well-validated genetic instruments with clear biological relevance, thoroughly testing for pleiotropy and confounding factors using methods like MR-Egger. Sensitivity analyses, such as MR-PRESSO, should ensure findings remain consistent across various assumptions. Effect sizes with confidence intervals should be reported and discussed within established biological mechanisms. Additionally, limitations must be transparently addressed, with recommendations for replication in future studies, to strengthen findings. This article guides readers in understanding MR application in nephrology and identifying high-quality MR studies, helping peers avoid pitfalls while seizing new opportunities in advancing kidney disease research.

Zellweger syndrome; identification of mutations in PEX19 and PEX26 gene in Saudi families

BACKGROUND

Peroxisome biogenesis disorders (PBD) affect multiple organ systems. It is characterized by neurological dysfunction, hypotonia, ocular anomalies, craniofacial abnormalities, and absence of peroxisomes in fibroblasts. PBDs are associated with mutations in any of fourteen different PEX genes, which are involved in peroxisome biogenesis. Zellweger spectrum disorder (ZSD) is a severe form of PBD. More than 90% of the ZSD cases have mutations in PEX1, PEX6, PEX10, PEX12, and PEX26. Mutations in the PEX19 gene are rarely associated with PBD/ZSD; however, a large proportion of PEX26 mutations are associated with ZSD.

METHODS

We recruited two Saudi families with multiple affected individuals with dysmorphic features, including hypertelorism, large open fontanelles, generalized hypotonia, and epicanthal folds with poor reflexes since birth. Whole exome sequencing (WES) and Sanger sequencing was performed to identify the genetic cause. The frequency and pathogenicity of the identified mutations were assessed using various online bioinformatics tools.

RESULTS

WES identified a novel nonsense variant (c.367C > T) in the PEX19 gene in family A patients. This nonsense mutation was predicted to cause premature termination (p.Gln123*). A previously reported synonymous variant (c.228C > T; p.Gly76Gly) in PEX26 was found in a patient from family B. Both variants were segregating in an autosomal recessive manner in the respective families.

CONCLUSION

The present study has added a novel nonsense mutation to the mutation spectrum of PEX19, which is the second null mutation identified to date. Moreover, in this study, the importance of a synonymous exonic variant of PEX26 close to the splice donor site was explored in relation to pre-mRNA splicing and resulting disease manifestations.

Exploring the versatility of Drosophila melanogaster as a model organism in biomedical research: a comprehensive review

Drosophila melanogaster is a highly versatile model organism that has profoundly advanced our understanding of human diseases. With more than 60% of its genes having human homologs, Drosophila provides an invaluable system for modelling a wide range of pathologies, including neurodegenerative disorders, cancer, metabolic diseases, as well as cardiac and muscular conditions. This review highlights key developments in utilizing Drosophila for disease modelling, emphasizing the genetic tools that have transformed research in this field. Technologies such as the GAL4/UAS system, RNA interference (RNAi) and CRISPR-Cas9 have enabled precise genetic manipulation, with CRISPR-Cas9 allowing for the introduction of human disease mutations into orthologous Drosophila genes. These approaches have yielded critical insights into disease mechanisms, identified novel therapeutic targets and facilitated both drug screening and toxicological studies. Articles were selected based on their relevance, impact and contribution to the field, with a particular focus on studies offering innovative perspectives on disease mechanisms or therapeutic strategies. Our findings emphasize the central role of Drosophila in studying complex human diseases, underscoring its genetic similarities to humans and its effectiveness in modelling conditions such as Alzheimer's disease, Parkinson's disease and cancer. This review reaffirms Drosophila's critical role as a model organism, highlighting its potential to drive future research and therapeutic advancements.

Brief biology and pathophysiology of Tekt bundles

Tektins, a family of microtubule-stabilizing proteins, are critical for cilia and flagella assembly in mammals. They maintain doublet microtubule stability and ciliary/flagellar motility. Loss of Tekt1-5 causes microtubule instability, impaired motility, and diseases like infertility, retinal degeneration, Mainzer-Saldino syndrome, and diabetic nephropathy. Pathophysiological stimuli regulate Tektin expression through transcriptional, posttranscriptional, translational, and posttranslational modifications. This review summarizes the latest findings on Tektin functions and their role in diseases.

Frontiers of premature ovarian insufficiency research: an analysis from the top 100 most influential articles in the field

Objectives: Premature ovarian insufficiency (POI) is a serious condition that affects women worldwide, In recent years, the number of research publications on POI has increased over the last decades because of the advancement of cutting-edge research in gynecology and the deepening of disciplinary interactions. At the same time, there is a more urgent need to systematically analyze and review existing studies to generalize the research paradigm and disciplinary structure of the field under technological changes.

Materials and methods: We selected the top 100 most cited papers in the Web of Science (WOS) SCI-Expanded database. Knowledge graphs were constructed through the VOS viewer, Cite Space, and Scimago Graphica software, and then relevant information retrieved from the literature was edited using Excel to assess research priorities and trends in the field.

Results: A total of 53 periodicals from 34 different nations and regions published the 100 most-cited publications between 1999 and 2024. The Journal of Clinical Endocrinology & Metabolism published the majority of the papers, while The Lancet had the highest average number of citations per piece. The United States of America produced the highest contribution in terms of publications, with China and France closely trailing after. In terms of total publications, Erasmus MC, Shanghai Jiao Tong University, and Shandong University each contributed the highest number of papers. The main categories were obstetrics and gynecology, endocrinology and metabolism, and reproductive biology. The top five keywords were: failure, women, ANTI-MULLERIAN HORMONE, NATURAL MENOPAUSE, and AGE. The study of HERITAGE AND GENETICS, CARDIOVASCULAR DISEASES, and CELL BIOLOGY AND IMMUNOGENETICS is becoming more and more popular in POI, as shown by cluster analysis.

Conclusions: Bibliometric analysis enables POI researchers to efficiently and visibly pinpoint the cutting-edge areas and focal points of their study. Potential topics of future study may include genetic and molecular biological pathways, cardiovascular pathology, and immunology.

Autism spectrum disorder: difficulties in diagnosis and microRNA biomarkers

We performed a PubMed search for microRNAs in autism spectrum disorder that could serve as diagnostic biomarkers in patients and selected 17 articles published from January 2008 to December 2023, of which 4 studies were performed with whole blood, 4 with blood plasma, 5 with blood serum, 1 with serum neural cell adhesion molecule L1-captured extracellular vesicles, 1 with blood cells, and 2 with peripheral blood mononuclear cells. Most of the studies involved children and the study cohorts were largely males. Many of the studies had performed microRNA sequencing or quantitative polymerase chain reaction assays to measure microRNA expression. Only five studies had used real-time polymerase chain reaction assay to validate microRNA expression in autism spectrum disorder subjects compared to controls. The microRNAs that were validated in these studies may be considered as potential candidate biomarkers for autism spectrum disorder and include miR-500a-5p, -197-5p, -424-5p, -664a-3p, -365a-3p, -619-5p, -664a-3p, -3135a, -328-3p, and -500a-5p in blood plasma and miR-151a-3p, -181b-5p, -320a, -328, -433, -489, -572, -663a, -101-3p, -106b-5p, -19b-3p, -195-5p, and -130a-3p in blood serum of children, and miR-15b-5p and -6126 in whole blood of adults. Several important limitations were identified in the studies reviewed, and need to be taken into account in future studies. Further studies are warranted with children and adults having different levels of autism spectrum disorder severity and consideration should be given to using animal models of autism spectrum disorder to investigate the effects of suppressing or overexpressing specific microRNAs as a novel therapy.

Small heat shock protein B8: from cell functions to its involvement in diseases and potential therapeutic applications

Heat shock protein family B (small) member 8 (HSPB8) is a 22 kDa ubiquitously expressed protein belonging to the family of small heat shock proteins. HSPB8 is involved in various cellular mechanisms mainly related to proteotoxic stress response and in other processes such as inflammation, cell division, and migration. HSPB8 binds misfolded clients to prevent their aggregation by assisting protein refolding or degradation through chaperone-assisted selective autophagy. In line with this function, the pro-degradative activity of HSPB8 has been found protective in several neurodegenerative and neuromuscular diseases characterized by protein misfolding and aggregation. In cancer, HSPB8 has a dual role being capable of exerting either a pro- or an anti-tumoral activity depending on the pathways and factors expressed by the model of cancer under investigation. Moreover, HSPB8 exerts a protective function in different diseases by modulating the inflammatory response, which characterizes not only neurodegenerative diseases, but also other chronic or acute conditions affecting the nervous system, such as multiple sclerosis and intracerebellar hemorrhage. Of note, HSPB8 modulation may represent a therapeutic approach in other neurological conditions that develop as a secondary consequence of other diseases. This is the case of cognitive impairment related to diabetes mellitus, in which HSPB8 exerts a protective activity by assuring mitochondrial homeostasis. This review aims to summarize the diverse and multiple functions of HSPB8 in different pathological conditions, focusing on the beneficial effects of its modulation. Drug-based and alternative therapeutic approaches targeting HSPB8 and its regulated pathways will be discussed, emphasizing how new strategies for cell and tissue-specific delivery represent an avenue to advance in disease treatments.

Functions of nuclear factor Y in nervous system development, function and health

Nuclear factor Y is a ubiquitous heterotrimeric transcription factor complex conserved across eukaryotes that binds to CCAAT boxes, one of the most common motifs found in gene promoters and enhancers. Over the last 30 years, research has revealed that the nuclear factor Y complex controls many aspects of brain development, including differentiation, axon guidance, homeostasis, disease, and most recently regeneration. However, a complete understanding of transcriptional regulatory networks, including how the nuclear factor Y complex binds to specific CCAAT boxes to perform its function remains elusive. In this review, we explore the nuclear factor Y complex's role and mode of action during brain development, as well as how genomic technologies may expand understanding of this key regulator of gene expression.

Biological and translational attributes of mitochondrial DNA copy number: Laboratory perspective to clinical relevance

The mitochondrial DNA copy number (mtDNAcn) plays a vital role in cellular energy metabolism and mitochondrial health. As mitochondria are responsible for adenosine triphosphate production through oxidative phosphorylation, maintaining an appropriate mtDNAcn level is vital for the overall cellular function. Alterations in mtDNAcn have been linked to various diseases, including neurodegenerative disorders, metabolic conditions, and cancers, making it an important biomarker for understanding the disease pathogenesis. The accurate estimation of mtDNAcn is essential for clinical applications. Quantitative polymerase chain reaction and next-generation sequencing are commonly employed techniques with distinct advantages and limitations. Clinically, mtDNAcn serves as a valuable indicator for early diagnosis, disease progression, and treatment response. For instance, in oncology, elevated mtDNAcn levels in blood samples are associated with tumor aggressiveness and can aid in monitoring treatment efficacy. In neurodegenerative diseases such as Alzheimer’s and Parkinson’s, altered mtDNAcn patterns provide insights into disease mechanisms and progression. Understanding and estimating mtDNAcn are critical for advancing diagnostic and therapeutic strategies in various medical fields. As research continues to uncover the implications of mtDNAcn alterations, its potential as a clinical biomarker is likely to expand, thereby enhancing our ability to diagnose and manage complex diseases.

Reduced mesencephalic astrocyte-derived neurotrophic factor expression by mutant androgen receptor contributes to neurodegeneration in a model of spinal and bulbar muscular atrophy pathology

JOURNAL/nrgr/04.03/01300535-202509000-00027/figure1/v/2024-11-05T132919Z/r/image-tiff Spinal and bulbar muscular atrophy is a neurodegenerative disease caused by extended CAG trinucleotide repeats in the androgen receptor gene, which encodes a ligand-dependent transcription factor. The mutant androgen receptor protein, characterized by polyglutamine expansion, is prone to misfolding and forms aggregates in both the nucleus and cytoplasm in the brain in spinal and bulbar muscular atrophy patients. These aggregates alter protein-protein interactions and compromise transcriptional activity. In this study, we reported that in both cultured N2a cells and mouse brain, mutant androgen receptor with polyglutamine expansion causes reduced expression of mesencephalic astrocyte-derived neurotrophic factor. Overexpression of mesencephalic astrocyte-derived neurotrophic factor ameliorated the neurotoxicity of mutant androgen receptor through the inhibition of mutant androgen receptor aggregation. Conversely, knocking down endogenous mesencephalic astrocyte-derived neurotrophic factor in the mouse brain exacerbated neuronal damage and mutant androgen receptor aggregation. Our findings suggest that inhibition of mesencephalic astrocyte-derived neurotrophic factor expression by mutant androgen receptor is a potential mechanism underlying neurodegeneration in spinal and bulbar muscular atrophy.

Glucocorticoid receptor signaling in the brain and its involvement in cognitive function

The hypothalamic-pituitary-adrenal axis regulates the secretion of glucocorticoids in response to environmental challenges. In the brain, a nuclear receptor transcription factor, the glucocorticoid receptor, is an important component of the hypothalamic-pituitary-adrenal axis's negative feedback loop and plays a key role in regulating cognitive equilibrium and neuroplasticity. The glucocorticoid receptor influences cognitive processes, including glutamate neurotransmission, calcium signaling, and the activation of brain-derived neurotrophic factor-mediated pathways, through a combination of genomic and non-genomic mechanisms. Protein interactions within the central nervous system can alter the expression and activity of the glucocorticoid receptor, thereby affecting the hypothalamic-pituitary-adrenal axis and stress-related cognitive functions. An appropriate level of glucocorticoid receptor expression can improve cognitive function, while excessive glucocorticoid receptors or long-term exposure to glucocorticoids may lead to cognitive impairment. Patients with cognitive impairment-associated diseases, such as Alzheimer's disease, aging, depression, Parkinson's disease, Huntington's disease, stroke, and addiction, often present with dysregulation of the hypothalamic-pituitary-adrenal axis and glucocorticoid receptor expression. This review provides a comprehensive overview of the functions of the glucocorticoid receptor in the hypothalamic-pituitary-adrenal axis and cognitive activities. It emphasizes that appropriate glucocorticoid receptor signaling facilitates learning and memory, while its dysregulation can lead to cognitive impairment. This provides clues about how glucocorticoid receptor signaling can be targeted to overcome cognitive disability-related disorders.

Acquired sensorineural hearing loss, oxidative stress, and microRNAs

Hearing loss is the third leading cause of human disability. Age-related hearing loss, one type of acquired sensorineural hearing loss, is largely responsible for this escalating global health burden. Noise-induced, ototoxic, and idiopathic sudden sensorineural are other less common types of acquired hearing loss. The etiology of these conditions is complex and multi-factorial involving an interplay of genetic and environmental factors. Oxidative stress has recently been proposed as a likely linking cause in most types of acquired sensorineural hearing loss. Short non-coding RNA sequences known as microRNAs (miRNAs) have increasingly been shown to play a role in cellular hypoxia and oxidative stress responses including promoting an apoptotic response. Sensory hair cell death is a central histopathological finding in sensorineural hearing loss. As these cells do not regenerate in humans, it underlies the irreversibility of human age-related hearing loss. Ovid EMBASE, Ovid MEDLINE, Web of Science Core Collection, and ClinicalTrials.gov databases over the period August 1, 2018 to July 31, 2023 were searched with "hearing loss," "hypoxamiRs," "hypoxia," "microRNAs," "ischemia," and "oxidative stress" text words for English language primary study publications or registered clinical trials. Registered clinical trials known to the senior author were also assessed. A total of 222 studies were thus identified. After excluding duplicates, editorials, retractions, secondary research studies, and non-English language articles, 39 primary studies and clinical trials underwent full-text screening. This resulted in 11 animal, in vitro , and/or human subject journal articles and 8 registered clinical trial database entries which form the basis of this narrative review. MiRNAs miR-34a and miR-29b levels increase with age in mice. These miRNAs were demonstrated in human neuroblastoma and murine cochlear cell lines to target Sirtuin 1/peroxisome proliferator-activated receptor gamma coactivator-1-alpha (SIRT1/PGC-1α), SIRT1/p53, and SIRT1/hypoxia-inducible factor 1-alpha signaling pathways resulting in increased apoptosis. Furthermore, hypoxia and oxidative stress had a similar adverse apoptotic effect, which was inhibited by resveratrol and a myocardial inhibitor-associated transcript, a miR-29b competing endogenous mRNA. Gentamicin reduced miR-182-5p levels and increased cochlear oxidative stress and cell death in mice - an effect that was corrected by inner ear stem cell-derived exosomes. There is ongoing work seeking to determine if these findings can be effectively translated to humans.

Modulation of the Nogo signaling pathway to overcome amyloid-β-mediated neurite inhibition in human pluripotent stem cell-derived neurites

JOURNAL/nrgr/04.03/01300535-202509000-00026/figure1/v/2024-11-05T132919Z/r/image-tiff Neuronal cell death and the loss of connectivity are two of the primary pathological mechanisms underlying Alzheimer's disease. The accumulation of amyloid-β peptides, a key hallmark of Alzheimer's disease, is believed to induce neuritic abnormalities, including reduced growth, extension, and abnormal growth cone morphology, all of which contribute to decreased connectivity. However, the precise cellular and molecular mechanisms governing this response remain unknown. In this study, we used an innovative approach to demonstrate the effect of amyloid-β on neurite dynamics in both two-dimensional and three-dimensional culture systems, in order to provide more physiologically relevant culture geometry. We utilized various methodologies, including the addition of exogenous amyloid-β peptides to the culture medium, growth substrate coating, and the utilization of human-induced pluripotent stem cell technology, to investigate the effect of endogenous amyloid-β secretion on neurite outgrowth, thus paving the way for potential future applications in personalized medicine. Additionally, we also explore the involvement of the Nogo signaling cascade in amyloid-β-induced neurite inhibition. We demonstrate that inhibition of downstream ROCK and RhoA components of the Nogo signaling pathway, achieved through modulation with Y-27632 (a ROCK inhibitor) and Ibuprofen (a Rho A inhibitor), respectively, can restore and even enhance neuronal connectivity in the presence of amyloid-β. In summary, this study not only presents a novel culture approach that offers insights into the biological process of neurite growth and inhibition, but also proposes a specific mechanism for reduced neural connectivity in the presence of amyloid-β peptides, along with potential intervention points to restore neurite growth. Thereby, we aim to establish a culture system that has the potential to serve as an assay for measuring preclinical, predictive outcomes of drugs and their ability to promote neurite outgrowth, both generally and in a patient-specific manner.

Mitophagy in acute central nervous system injuries: regulatory mechanisms and therapeutic potentials

Acute central nervous system injuries, including ischemic stroke, intracerebral hemorrhage, subarachnoid hemorrhage, traumatic brain injury, and spinal cord injury, are a major global health challenge. Identifying optimal therapies and improving the long-term neurological functions of patients with acute central nervous system injuries are urgent priorities. Mitochondria are susceptible to damage after acute central nervous system injury, and this leads to the release of toxic levels of reactive oxygen species, which induce cell death. Mitophagy, a selective form of autophagy, is crucial in eliminating redundant or damaged mitochondria during these events. Recent evidence has highlighted the significant role of mitophagy in acute central nervous system injuries. In this review, we provide a comprehensive overview of the process, classification, and related mechanisms of mitophagy. We also highlight the recent developments in research into the role of mitophagy in various acute central nervous system injuries and drug therapies that regulate mitophagy. In the final section of this review, we emphasize the potential for treating these disorders by focusing on mitophagy and suggest future research paths in this area.

Small molecule inhibitor DDQ-treated hippocampal neuronal cells show improved neurite outgrowth and synaptic branching

JOURNAL/nrgr/04.03/01300535-202509000-00024/figure1/v/2024-11-05T132919Z/r/image-tiff The process of neurite outgrowth and branching is a crucial aspect of neuronal development and regeneration. Axons and dendrites, sometimes referred to as neurites, are extensions of a neuron's cellular body that are used to start networks. Here we explored the effects of diethyl (3,4-dihydroxyphenethylamino)(quinolin-4-yl) methylphosphonate (DDQ) on neurite developmental features in HT22 neuronal cells. In this work, we examined the protective effects of DDQ on neuronal processes and synaptic outgrowth in differentiated HT22 cells expressing mutant Tau (mTau) cDNA. To investigate DDQ characteristics, cell viability, biochemical, molecular, western blotting, and immunocytochemistry were used. Neurite outgrowth is evaluated through the segmentation and measurement of neural processes. These neural processes can be seen and measured with a fluorescence microscope by manually tracing and measuring the length of the neurite growth. These neuronal processes can be observed and quantified with a fluorescent microscope by manually tracing and measuring the length of the neuronal HT22. DDQ-treated mTau-HT22 cells (HT22 cells transfected with cDNA mutant Tau) were seen to display increased levels of synaptophysin, MAP-2, and β-tubulin. Additionally, we confirmed and noted reduced levels of both total and p-Tau, as well as elevated levels of microtubule-associated protein 2, β-tubulin, synaptophysin, vesicular acetylcholine transporter, and the mitochondrial biogenesis protein-peroxisome proliferator-activated receptor-gamma coactivator-1α. In mTau-expressed HT22 neurons, we observed DDQ enhanced the neurite characteristics and improved neurite development through increased synaptic outgrowth. Our findings conclude that mTau-HT22 (Alzheimer's disease) cells treated with DDQ have functional neurite developmental characteristics. The key finding is that, in mTau-HT22 cells, DDQ preserves neuronal structure and may even enhance nerve development function with mTau inhibition.