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.

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.

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.

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].

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 search for a TNBC vaccine: the guardian vaccine

Nearly 20 million people are diagnosed with cancer each year with breast cancer being the most common among women. Triple negative breast cancer (TNBC), defined by its no/low expression of ER and PR and lack of amplification of HER2, makes up 15-20% of all breast cancer cases. While patients overall have a higher response to chemotherapy, this subgroup is associated with the lowest survival rate indicating significant clinical and molecular heterogeneity demanding alternate treatment options. Therefore, new therapies have been explored, with a large focus on utilizing the immune system. A whole host of immunotherapies have been studied including immune checkpoint inhibitors, now standard of care for eligible patients, and possibly the most exciting and promising is that of a TNBC vaccine. While currently there are no approved TNBC vaccines, this review highlights many promising studies and points to an antigen, p53, which we believe is highly relevant for TNBC.

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.

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.

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.

Identification of genetic variants of the IL18R1 gene in association with COPD susceptibility

BACKGROUND

Although existing studies have identified some genetic loci associated with chronic obstructive pulmonary disease (COPD) susceptibility, many variants remain to be discovered. The aim of this study was to further explore the potential relationship between IL18R1 single nucleotide polymorphisms (SNPs) and COPD risk.

METHODS

Nine hundred and ninety-six subjects were recruited (498 COPD cases and 498 healthy controls). Five candidate SNPs of IL18R1 were selected and genotyped using MassARRAY iPLEX platform. Logistic regression analysis was performed to assess the association of these SNPs with COPD risk. Multifactor dimensionality reduction (MDR) software was applied to calculate the interaction of SNP-SNP on COPD risk.

RESULTS

IL18R1 rs9807989 (OR = 0.42, p < .001), rs3771166 (OR = 0.40, p < .001) and rs6543124 (OR = 0.44, p < .001) were associated with the reduced COPD risk, while rs2287037 (OR = 2.71, p < .001) and rs2058622 (OR = 2.06, p < .001) might be the risk-increasing factor for COPD occurrence in both the overall analysis and subgroup analysis (age, gender, drinking, and smoking). The best multi-locus model was the combination of rs2058622 and rs3771166.

CONCLUSION

Our study provided a reference and basis for investigating the association of IL18R1 polymorphisms with COPD risk.

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.

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.

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.

Research and developmental strategies to hasten the improvement of orphan crops

To feed the world's expanding population, crop breeders need to increase agricultural productivity and expand major crops base. Orphan crops are indigenously important crops with great potential because they are climate resilient, highly nutritious, contain nutraceutical compounds, and can improve the livelihood of smallholder farmers and consumers, but they have received little or no scientific attention. This review article examines several research and developmental strategies for hastening the improvement of these crops so that they can effectively play their role in securing food and nutrition. The integration of both research and developmental approaches will open up modern opportunities for crop improvement. We summarized ways in which advanced tools in phenotyping and genotyping, using high-throughput processes, can be used to accelerate their improvement. Finally, we suggest roles the genebanks can play in improving orphan crops, as the utilization of plant genetic resources is important for the genetic improvement of a crop.

Highly expressed cell wall genes contribute to robustness of sepal size

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

Global research trends in biological therapy for ankylosing spondylitis: A comprehensive visualization and bibliometric study (2004-2023)

Ankylosing spondylitis (AS) is a chronic inflammatory disease primarily affecting the spine and pelvic bones. Recently, many researchers have confirmed that biological therapy is effective for AS patients, which provides a new perspective for the treatment of AS. This study aimed to evaluate the characteristics of scientific research on AS and biological therapy worldwide and investigate research hotspots and the direction of future trends. Global literature on AS and biological therapy published from 2004 to 2023 was searched in the Web of Science, Scopus, and PubMed databases. Visualization and bibliometric analysis were carried out using the VOSviewer and CiteSpace software with the retrieved data regarding countries, institutions, journals, authors, and keywords. A total of 2,243 related articles were included, showing that the number of articles in this field has increased annually. The highest number of articles were from the USA (24.39%), followed by Italy (14.36%), England (12.19%), Germany (10.66%), and Spain (7.86%). Braun J was the most prolific author, with a h-index of 16. The institution with the most articles was Charite Universitatsmedizin Berlin, and the Rheumatology journal had the highest number of publications. "janus kinase inhibitor" and "secukinumab" displayed a notable citation burst in recent years, indicating IL-17i and JAKi are research hotspots. More and more attention has been paid to the association between AS and biological therapy in the past two decades. The USA plays a leading role, and China has made remarkable progress. This study has provided a valuable reference for future research in this field.

Prenatal diagnosis and pregnancy outcomes in fetuses with vertebral abnormalities

OBJECTIVE

To investigate the genetic risk and pregnancy outcomes of fetuses who had the sonographic diagnosis of vertebral abnormalities (VA).

METHODS

Fifty-two fetuses with sonographically detected VA (excluding neural tube defects) were included in the study. Data on prenatal ultrasound scan, prenatal genetic testing by amniocentesis, and pregnancy outcomes were collected and reviewed.

RESULTS

Four types of VA were identified among 52 fetuses: butterfly vertebrae (26.9%, 14/52), hemivertebrae (59.6%, 31/52), hemivertebrae combined with butterfly vertebrae (9.6%, 5/52), and block vertebrae (3.9%, 2/52). Of the 52 fetuses, 33 presented VA as the sole sonographic anomaly, while the remaining 19 had associated anomalies. The positive rate of prenatal diagnosis for fetuses with VA was 19.2% (10/52). Chromosomal analysis, including karyotyping and chromosomal microarray analysis (CMA), detected one case of mosaic trisomy 9 and six cases of (likely) pathogenic copy number variants (CNVs). Whole exome sequencing (WES) identified four likely pathogenic variants in three cases with negative CMA results, specifically c.5110-1G > A in FLNB, c.8366G > A in KMT2D, and c.1275_1283dup as well as c.870 + 2T > C in DLL3. Among the 10 cases with diagnostic genetic testing results, seven fetuses exhibited isolated VA. There was no significant difference in the diagnostic rates between the isolated VA group (21.2%, 7/33) and the non-isolated VA group (15.8%, 3/19) (odds ratio [OR] 0.696, 95% confidence interval [CI] 0.157-3.087, p = 0.910). However, the live birth rate was significantly higher in the isolated VA group (71.9%, 23/32) compared to the non-isolated VA group (38.9%, 7/18) (OR 4.016, 95% CI 1.184-13.622, p = 0.022). Among the 30 live birth cases, two underwent spinal surgery and another two were identified with additional abnormalities. Following appropriate interventions, no apparent abnormalities were observed in the growth and development of 30 live birth cases.

CONCLUSION

Invasive prenatal diagnosis is recommended for all fetuses diagnosed with VA, regardless of whether associated anomalies are present. WES can enhance the diagnostic yield for fetuses with negative CMA results. Fetuses with isolated VA can have favorable pregnancy outcomes when genetic testing results are negative. However, long-term follow-up remains necessary for the assessment of the prognosis of these fetuses.

Why do babies cry? Exploring the role of the gut microbiota in infantile colic, constipation, and cramps in the KOALA birth cohort study

Gastrointestinal symptoms are common during infancy, including infantile colic. Colic can be loosely defined as prolonged and recurrent crying without obvious cause. The cause indeed remains unclear despite much research. Results on infant nutrition are inconclusive, but prior work has linked maternal mental health to infant crying. Recently, several small studies have described associations between gut microbiota and colic. We used a larger cohort to examine the role of the microbiota in infant gastrointestinal health, while also accounting for other biopsychosocial factors. Using fecal 16S rRNA gene amplicon sequencing data from 1,012 infants in the KOALA birth cohort, we examined associations between the 1-month gut microbiota and parent-reported functional gastrointestinal symptoms throughout infancy, including colic, constipation, and cramps. These analyses were adjusted for biopsychosocial factors that were associated with symptoms in a broader analysis involving 2,665 participants. In 257 infants, we also explored associations between breastmilk human milk oligosaccharides (HMOs) and gastrointestinal symptoms. Higher relative abundance of Staphylococcus at one month was associated with less constipation in the first three months of life. Conversely, Ruminococcus gnavus group abundance was associated with more colicky symptoms, particularly between four and seven months. Breastmilk concentrations of the HMOs lacto-N-hexaose (LNH) and lacto-N-neohexaose (LNnH) were associated with less constipation in the first three months. Our results support the conclusion that gut microbiota are relevant in infantile colic and constipation. However more work is needed to elucidate the underlying mechanisms, and explore their interplay with other relevant biopsychosocial factors such as maternal mental health.

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.

Precision microbiota therapy for IBD: premise and promise

Inflammatory Bowel Disease (IBD) is a spectrum of chronic inflammatory diseases of the intestine that includes subtypes of ulcerative colitis (UC) and Crohn's Disease (CD) and currently has no cure. While IBD results from a complex interplay between genetic, environmental, and immunological factors, sequencing advances over the last 10-15 years revealed signature changes in gut microbiota that contribute to the pathogenesis of IBD. These findings highlight IBD as a disease target for microbiome-based therapies, with the potential to treat the underlying microbial pathogenesis and provide adjuvant therapy to the emerging spectrum of advanced therapies for IBD. Building on the success of fecal microbiota transplantation (FMT) for Clostridioides difficile infection, therapies targeting gut microbiota have emerged as promising approaches for treating IBD; however, unique aspects of IBD pathogenesis highlight the need for more precision in the approach to microbiome therapeutics that leverage aspects of recipient and donor selection, diet and xenobiotics, and strain-specific interactions to enhance the efficacy and safety of IBD therapy. This review focuses on both pre-clinical and clinical studies that support the premise for microbial therapeutics for IBD and aims to provide a framework for the development of precision microbiome therapeutics to optimize clinical outcomes for patients with IBD.

IGHG4: innovative diagnostic biomarkers for iron overload in β-thalassemia patients

OBJECTIVES

This study aims to investigate the serotransferrin (TF), complement C1s subcomponent (C1S), immunoglobulin heavy constant gamma 4 (IGHG4), hemoglobin subunit alpha (HBA1), and clusterin (CLU) contents in β-thalassemia patients, and explores their physiological role as potential non-invasive bioindicators for disease diagnosis and iron overload.

METHODS

A total of 62 children with β-thalassemia were recruited and categorized by genotype, along with 17 healthy pediatric volunteers for analysis. The circulating ferritin content was evaluated, and plasma levels of TF, C1S, IGHG4, HBA1, and CLU were assessed using ELISA. The primary outcome of this study was the correlation between the five protein marker levels and iron overload. Continuous variables were analyzed using the Student's t-test or the Mann-Whitney U test. A binary logistic regression model identified independent predictors of iron overload in patients with β-thalassemia. Receiver operating characteristics (ROC) were employed to evaluate the model's performance.

RESULTS

The IGHG4 protein content was significantly lower in β-thalassemia patients compared to healthy controls. The IGHG4 protein content was reduced in the β+/β0 and β0/β0 patient populations compared to controls, with no significant difference observed between the β+/β0 group and healthy controls. A strong inverse relationship was identified between the IGHG4 protein content and SF concentration (r = -0.322, p = 0.004). Finally, plasma IGHG4 levels demonstrated adequate diagnostic capability, as indicated by our ROC curve analysis.

CONCLUSION

In conclusion, decreased IGHG4 protein levels are significantly associated with the degree of iron overload in β-thalassemia patients and may serve as a possible biomarker for evaluating iron overload.

Interplay of replication timing, DNA repair, and translesion synthesis in UV mutagenesis in yeast

Replication timing during S-phase impacts mutation rates in yeast and human cancers; however, the exact mechanism involved remains unclear. Here, we analyze the impact of replication timing on UV mutagenesis in Saccharomyces cerevisiae. Our analysis indicates that UV mutations are enriched in early-replicating regions of the genome in wild-type cells, but in cells deficient in global genomic-nucleotide excision repair (GG-NER), mutations are enriched in late-replicating regions. Analysis of UV damage maps revealed that cyclobutane pyrimidine dimers are enriched in late-replicating regions, but this enrichment is almost entirely due to repetitive ribosomal DNA. Complex mutations typically associated with TLS activity are also elevated in late-replicating regions in GG-NER deficient cells. We propose that UV mutagenesis is higher in early-replicating regions in repair-competent cells because there is less time to repair the lesion prior to undergoing replication. However, in the absence of GG-NER, increased TLS activity promotes UV mutagenesis in late-replicating regions.

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.

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.

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.

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

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

An integral membrane constitutively active heparanase enhances the tumor infiltration capability of NK cells

Eradication of cancer cells by the immune system requires extravasation, infiltration and progression of immune cells through the tumor extracellular matrix (ECM). These are also critical determinants for successful adoptive cell immunotherapy of solid tumors. Together with structural proteins, such as collagens and fibronectin, heparan sulfate (HS) proteoglycans are major components of the ECM. Heparanase 1 (HPSE) is the only enzyme known to have endoglycosidase activity that degrades HS. HPSE is expressed at high levels in almost all hematopoietic cells, which suggests that it plays a relevant role in immune cell migration through solid tissues. Besides, tumor cells express also HPSE as a way to facilitate tumor cell resettlement and metastasis. Therefore, an increase in HPSE in the tumor ECM would be detrimental. Here, we analyzed the effects of constitutive expression of an active, membrane-bound HPSE on the ability of human natural killer (NK) cells to infiltrate tumors and eliminate tumor cells. We demonstrate that NK cells expressing a chimeric active form of HPSE on the cell surface as an integral membrane protein, display significantly enhanced infiltration capability into spheroids of various cancer cell lines, as well as into xenograft tumors in immunodeficient mice. As a result, tumor growth was significantly suppressed without causing noticeable side effects. Altogether, our results suggest that a constitutively expressed active HSPE on the surface of immune effector cells enhances their capability to access and eliminate tumor cells. This strategy opens new possibilities for improving adoptive immune treatments using NK cells.

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

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

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

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