Targets For Intervention Research Articles

Feasibility, acceptability, and preliminary efficacy of a self-directed online psychosocial intervention for women with metastatic breast cancer: Finding My Way-Advanced

PurposeFew digital interventions target patients with advanced cancer. Hence, we feasibility-tested Finding My Way-Advanced (FMW-A), a self-guided program for women with metastatic breast cancer.MethodsA single-site randomised controlled pilot trial was conducted. Participants were recruited through clinicians, professional networks, and social media and randomised to intervention or usual-care control. Participants were randomly allocated to either the intervention (FMW-A; a 6-week, 6-module CBT-based online self-directed psychosocial program for women with MBC + usual care resources) or control (usual care resources: BCNA’s Hope and Hurdles kit). Feasibility outcomes included rates of recruitment, uptake, engagement, and attrition. Distress, QOL, and unmet needs were evaluated for signals of efficacy, and qualitative feedback was collected to assess acceptability.ResultsDue to COVID-19 and funding constraints, the target recruitment of 40 was not reached (n = 60 approached; n = 55 eligible; n = 35 consented). Uptake was high (n = 35/55; 63.6%), engagement modest (median 3/6 modules per user), and attrition acceptable (66% completed post-treatment). Efficacy signals were mixed: compared to controls, FMW-A participants experienced small improvements in fear of progression (d = 0.21) and global QOL (d = 0.22) and demonstrated a trend towards improvements in cancer-specific distress (d = 0.13) and role functioning (d = 0.18). However, FMW-A participants experienced small-to-moderate deteriorations in general distress (d = 0.23), mental QOL (d = 0.51), and social functioning (d = 0.27), whereas controls improved. Qualitatively, participants (n = 4) were satisfied with the program, perceived it as appropriate, but noted some sections could evoke transient distress.ConclusionThe study demonstrated feasibility (high uptake and acceptable retention) and generated realistic recruitment estimates. While FMW-A appears promising for targeting cancer-specific distress and fear of progression, the mixed findings in quality of life and general distress warrant further revisions and testing.

Elucidating macrophage scavenger receptor 1's mechanistic contribution as a shared molecular mediator in obesity and thyroid cancer pathogenesis via bioinformatics analysis.

Obesity is a disease characterized by the excessive accumulation of fat. Concurrently, thyroid carcinoma (THCA) stands as the foremost endocrine malignancy. Despite the observed escalation in concurrent prevalence of both conditions, the underlying interconnections remain elusive. This indicates the need to identify potential biomarkers to predict the pathways through which obesity and THCA coexist. The study employed a variety of methods, including differential gene expression analysis, Weighted Gene Co-expression Network Analysis (WGCNA), and gene enrichment analysis. It was also supplemented with immunohistochemical data from the Human Protein Atlas (HPA), advanced machine learning techniques, and related experiments such as qPCR, to identify important pathways and key genes shared between obesity and THCA. Through differential gene expression analysis, WGCNA, and machine learning methods, we identified three biomarkers (IL6R, GZMB, and MSR1) associated with obesity. After validation analysis using THCA-related datasets and biological experiments, we selected Macrophage Scavenger Receptor 1 (MSR1) as a key gene for THCA analysis. The final analysis revealed that MSR1 is closely related to the degree of immune cell infiltration in patients with obesity and THCA, suggesting that this gene may be a potential intervention target for both obesity and THCA. Our research indicates that MSR1 may influence the occurrence and development of obesity and THCA by regulating the infiltration level of immune cells. This lays the foundation for future research on targeted therapies based on their shared mechanisms.

Gut Microbiome as a Target of Intervention in Inflammatory Bowel Disease Pathogenesis and Therapy

Inflammatory bowel disease (IBD) is a chronic complicated inflammatory gut pathological disorder and is categorized into ulcerative colitis (UC) and Crohn’s disease (CD). Although the cause of IBD is unclear, dysbiosis of the gut microbiota is thought to be a key factor in the disease’s progression. The gut microbiome serves as a metabolic organ and promotes wellness by carrying out several biological activities. Any modification in the makeup of the gut microbiome leads to several pathological conditions, including IBD. In this review, we emphasize the key metabolic processes that control host–microbiome interaction and its impact on host health. We also discuss the association between microbiome dysbiosis (bacteriome, virome, and mycobiome) and the progression of IBD. Finally, we will highlight microbiome-based therapy as a novel and promising strategy to treat and manage IBD.

RNA sequencing uncovers key players of cartilage calcification: potential implications for osteoarthritis pathogenesis.

Osteoarthritis (OA) is a joint disease linked with pathologic cartilage calcification, caused by the deposition of calcium-containing crystals by chondrocytes. Despite its clinical significance, the precise mechanisms driving calcification remain elusive. This study aimed to identify crucial players in cartilage calcification, offering insights for future targeted interventions against OA. Primary murine chondrocytes were stimulated with secondary calciprotein particles (CPP2) or left untreated (NT) for 6 h. Calcification was assessed by alizarin red staining. RNA was analyzed by Bulk RNA sequencing. Differentially expressed (DE) genes were identified (cutoff: abs(LogFC)>1 and adj.p-val < 0.05), and top 50 DE genes were cross-referenced with human OA datasets from previous studies (ie healthy vs OA cartilage, or undamaged vs damaged cartilage). RNA from NT and CPP2-stimulated primary human OA chondrocytes were used to validate genes by qPCR. CPP2 induced crystal formation by chondrocytes and significantly modulated 1466 genes. Out of the top 50 DE genes in CPP2, 27 were confirmed in published OA cartilage datasets. Of those genes, some are described in calcification and/or OA (Errfi1, Ngf, Inhba, Col9a1). Two additional ones (Rcan1, Tnfrsf12a) appear novel and interesting in the context of calcification and OA. We validated modulation of these six genes in calcifying human chondrocytes from 5 patients. Ultimately, we unveiled two distinct gene families modulated by CPP2: the first comprised cytoskeletal genes (Actb, Tpm1, Cfl1, Tagln2, Lmna), while the second encompassed extracellular matrix genes (Fmod, Sparc, Col9a1, Cnmd). CPP2 modulates genes in chondrocytes that could represent new targets for therapeutic interventions in OA.

High-cost users after sepsis: a population-based observational cohort study.

High-cost users (HCU) represent important targets for health policy interventions. Sepsis is a life-threatening syndrome that is associated with high morbidity, mortality, and economic costs to the healthcare system. We sought to estimate the effect of sepsis on being a subsequent HCU. Using linked health-administrative databases, we conducted a population-based, propensity score-weighted cohort study of adults who survived a hospitalization in Ontario, Canada between January 2016 and December 2017. Sepsis was identified using a validated algorithm. The primary outcome was being a persistent HCU after hospital discharge (in the top 5% or 1% of total health care spending for 90 consecutive days), and the proportion of follow-up time since discharge as a HCU. We identified 927,057 hospitalized individuals, of whom 79,065 had sepsis. Individuals who had sepsis were more likely to be a top 5% HCU for 90 consecutive days at any time after discharge compared to those without sepsis (OR 2.24; 95% confidence interval [CI] 2.04-2.46) and spent on average 42.3% of their follow up time as a top 5% HCU compared to 28.9% of time among those without sepsis (RR 1.46; 95% CI 1.45-1.48). Individuals with sepsis were more likely to be a top 1% HCU for 90 consecutive days compared to those without sepsis (10% versus 5.1%, OR 2.05 [95% CI 1.99-2.11]), and spent more time as a top 1% HCU (18.5% of time versus 10.8% of time, RR 1.68 [95% CI 1.65-1.70]). The sequelae of sepsis result in higher healthcare costs with important economic implications. After discharge, individuals who experienced sepsis are more likely to be a HCU and spend more time as a HCU compared to individuals who did not experience sepsis during hospitalization.

Collagen Type VII (COL7A1) as a Longevity Mediator in Caenorhabditis elegans: Anti-Aging Effects on Healthspan Extension and Skin Collagen Synthesis

Longevity genes and senescence-related signaling proteins are crucial targets in aging research, which aims to enhance the healthy period and quality of life. Identifying these target proteins remains challenging because of the need for precise categorization and validation methods. Our multifaceted approach combined bioinformatics with transcriptomic data to identify collagen as a key element associated with the lifespan of the model organism, Caenorhabditis elegans. By analyzing transcriptomic data from long-lived mutants that involved mechanisms such as antioxidation, dietary restriction, and genetic background, we identified collagen as a common longevity-associated gene. We validated these findings by confirming that collagen peptides positively affect lifespan, thereby strengthening the validity of the target. Further verification through healthspan factors in C. elegans and functional assays in skin fibroblasts provided additional evidence of the role of collagen in organismal aging. Specifically, our study revealed that collagen type VII is a significant target protein for mitigating age-related decline. By validating these findings across different aging models and cell-based studies, we present compelling evidence for the anti-aging effects of collagen type VII, highlighting its potential as a target for promoting healthy aging. This study proposes that collagen not only serves as an indicative marker of organismal longevity across various senescence-related signaling pathways, but also offers a mechanistic understanding of skin degeneration. Consequently, collagen is an effective target for interventions aimed at mitigating skin aging. This study underscores the potential of collagen type VII (bonding collagen T7) as a therapeutic target for enhancing skin health and overall longevity.

SEC14L3 knockdown inhibited clear cell renal cell carcinoma proliferation, metastasis and sunitinib resistance through an SEC14L3/RPS3/NFκB positive feedback loop

BackgroundClear cell renal cell carcinoma (ccRCC) arises from the renal parenchymal epithelium and is the predominant malignant entity of renal cancer, exhibiting increasing incidence and mortality rates over time. SEC14-like 3 (SEC14L3) has emerged as a compelling target for cancer intervention; nevertheless, the precise clinical implications and molecular underpinnings of SEC14L3 in ccRCC remain elusive.MethodsBy leveraging clinical data and data from the TCGA-ccRCC and GEO datasets, we investigated the association between SEC14L3 expression levels and overall survival rates in ccRCC patients. The biological role and mechanism of SEC14L3 in ccRCC were investigated via in vivo and in vitro experiments. Moreover, siRNA-SEC14L3@PDA@MUC12 nanoparticles (SSPM-NPs) were synthesized and assessed for their therapeutic potential against SEC14L3 through in vivo and in vitro assays.ResultsOur investigation revealed upregulated SEC14L3 expression in ccRCC tissues, and exogenous downregulation of SEC14L3 robustly suppressed the malignant traits of ccRCC cells. Mechanistically, knocking down SEC14L3 facilitated the ubiquitination-mediated degradation of ribosomal protein S3 (RPS3) and augmented IκBα accumulation in ccRCC. This concerted action thwarted the nuclear translocation of P65, thereby abrogating the activation of the nuclear factor kappa B (NFκB) signaling pathway and impeding ccRCC cell proliferation and metastasis. Furthermore, diminished SEC14L3 levels exerted a suppressive effect on NFKB1 expression within the NFκB signaling cascade. NFKB1 functions as a transcriptional regulator capable of binding to the SEC14L3 enhancer and promoter, thereby promoting SEC14L3 expression. Consequently, the inhibition of SEC14L3 expression was further potentiated, thus forming a positive feedback loop. Additionally, we observed that downregulation of SEC14L3 significantly increased the sensitivity of ccRCC cells to sunitinib. The evaluation of SSPM-NPs nanotherapy highlighted its effectiveness in combination with sunitinib for inhibiting ccRCC growth.ConclusionOur findings not only underscore the promise of SEC14L3 as a therapeutic target but also unveil an SEC14L3/RPS3/NFκB positive feedback loop that curtails ccRCC progression. Modulating SEC14L3 expression to engage this positive feedback loop might herald novel avenues for ccRCC treatment.

The reverse transsulfuration pathway affects the colonic microbiota and contributes to colitis in mice

Cystathionine γ-lyase (CTH) is a critical enzyme in the reverse transsulfuration pathway, the major route for the metabolism of sulfur-containing amino acids, notably converting cystathionine to cysteine. We reported that CTH supports gastritis induced by the pathogen Helicobacter pylori. Herein our aim was to investigate the role of CTH in colonic inflammation. First, we found that CTH is induced in the colon mucosa in mice with dextran sulfate sodium-induced colitis. Expression of CTH was completely absent in the colon of Cth–/– mice. We observed that clinical and histological parameters are ameliorated in Cth-deficient mice compared to wild-type animals. However, Cth deletion had no effect on tumorigenesis and the level of dysplasia in mice treated with azoxymethane-DSS, as a reliable model of colitis-associated carcinogenesis. Mechanistically, we determined that the deletion of the gene Slc7a11 encoding for solute carrier family 7 member 11, the transporter of the anionic form of cysteine, does not affect DSS colitis. Lastly, we found that the richness and diversity of the fecal microbiota were significantly increased in Cth–/– mice compared to both WT and Slc7a11–/– mice. In conclusion, our data suggest that the enzyme CTH represents a target for clinical intervention in patients with inflammatory bowel disease, potentially by beneficially reshaping the composition of the gut microbiota.

Cognitive Health Benefits of Everyday Physical Activity in a Diverse Sample of Middle-Aged Adults.

Physical activity has been associated with a wide range of health benefits including long-term benefits for cognitive and brain health. Whether episodes of everyday physical activity are associated with immediate cognitive benefits remains unknown. The purpose of the current study was to examine whether episodes of physical activity, occurring over the course of participants' daily lives, are associated with short-term improvements in cognitive health. Participants completed a 9-day ecological momentary assessment protocol involving 5 daily assessments of self-reported physical activity and ambulatory cognitive assessments of processing speed and visuospatial working memory. Data were analyzed in a multilevel modeling framework to explore changes in performance on each task associated with physical activity during the period leading up to the assessment as well as individual differences in average frequency of physical activity. Results of MLMs indicated that engaging in physical activity during the period (~3.5hr) leading up to an assessment was associated with improvements in processing speed equivalent to 4 years of cognitive aging. Such improvements were observed for both light and moderate-to-vigorous physical activity levels. No association was observed for visuospatial working memory accuracy; however, response time during the working memory task reliably mirrored the association observed for processing speed. The short-term benefits were observed, particularly, for individuals with an overall higher frequency of reported physical activity. Our findings suggest that engaging in everyday physical activity of any intensity level may have short-term, acute benefits for cognitive health and point to new potential targets for intervention. NCT03240406.

Burnt out and still single: Susceptibility to dating app burnout over time

Despite the ubiquity of dating apps, there is little longitudinal research examining the mental health and well-being of dating app users. To fill this void, this study takes a social compensation approach to exploring dating app users’ burnout experiences (i.e., emotional exhaustion, inefficacy, and depersonalization) over time. Four hundred ninety-three active single dating app users were surveyed over four waves across 12 weeks, with a final sample of 190. Multilevel growth curve models showed that dating app users experienced increased emotional exhaustion and inefficacy over time. Furthermore, depression, anxiety, and loneliness predicted more emotional exhaustion and inefficacy, while problematic dating app use predicted more emotional exhaustion and less inefficacy. The results suggest that dating apps may exacerbate existing difficulties with relationship initiation among vulnerable users by increasing their risk of burnout. Dating app burnout is a potential intervention target to improve users’ dating success.

Soybean isoflavones protect dopaminergic neurons from atrazine damage by inhibiting VPS13A to increase autophagy

Atrazine (ATR) is a broad-spectrum herbicide with dopaminergic (DAergic) neurotoxicity that can cause Parkinson’s disease (PD)-like syndrome. However, research on preventing ATR neurotoxicity is unclear. Soybean isoflavones (SI) are natural plant compounds with neuroprotective effects. In this study, we found that pre-administration of SI prevented ATR-induced motor dysfunction and substantia nigra pathological damage. RNA-seq datasets revealed that the neuroprotective effect of SI was related to autophagy. Further experiments showed that ATR inhibited autophagy, and SI pre-administration before ATR exposure increased autophagy. In addition, single-cell data analysis combined with experimental verification showed that the gene VPS13A was a key target by which SI protected DAergic neurons from ATR damage, and inhibiting VPS13A-induced autophagy was a key mechanism enabling SI prevention of neuron damage. Together, these findings provide new insights for the development of preventive measures and intervention targets protecting against functional neuronal damage caused by ATR and other herbicides.

Hyperbaric oxygen-induced acute lung injury: A mouse model study on pathogenic characteristics and recovery dynamics.

Oxygen is an essential substance for the maintenance of human life. It is also widely used in clinical and diving medicine. Although oxygen is crucial for survival, too much oxygen can be harmful. Excessive oxygen inhalation in a short period of time can lead to injury, and the lung is one of the main target organs. Acute lung injury (ALI) induced by hyperbaric oxygen (HBO) is notably more severe than that caused by normobaric oxygen, yet systematic research on such injury and its regression is scarce. In this study, two independent experiments were designed. In the first experiment, mice were exposed to 2 atmospheres absolute (ATA), ≥95% oxygen for 2, 4, 6, and 8 h. Changes in lung histopathology, inflammation and expression of chemokines, alveolar-capillary barrier, and 8-OHdG were detected before and after the exposure. In the second experiment, these parameters were measured at 0 h, 12 h, and 24 h following 6 h of exposure to 2 ATA of ≥95% oxygen. Research indicates that ALI induced by HBO is characterized histologically by alveolar expansion, atelectasis, inflammatory cell infiltration, and hemorrhage. At 2 ATA, significant changes in the alveolar-capillary barrier were observed after more than 95% oxygen exposure for 4 h, as evidenced by increased Evans blue (EB) extravasation (p = 0.0200). After 6 h of HBO exposure, lung tissue pathology scores, 8-OHdG levels, and inflammatory and chemotactic factors (such as Il6, CCL2, CCL3, CXCL5, and CXCL10), intercellular adhesion molecule 1 (ICAM1), and vascular cell adhesion molecule 1 (VCAM1) were significantly elevated. Compared to lung injury caused by normobaric oxygen, the onset time of injury was significantly shortened. Additionally, it was observed that these markers continued to increase after leaving the HBO environment, peaking at 12 h and starting to recover at 24 h, indicating that the peak of inflammatory lung injury occurs within 12 h post-exposure, with recovery beginning at 24 h. This contradicts the common belief that lung injury is alleviated upon removal from a high-oxygen environment. However, EB levels, which reflect damage to the alveolar-capillary barrier, and VE-Cadherin (VE-Cad), tight junction protein 1 (ZO-1), ICAM1, and VCAM1 remained significantly altered 24 h after leaving the HBO environment. This suggests that the alveolar-capillary barrier is the most sensitive and slowest recovering part of the lung injury induced by HBO. These findings can provide insights into the pathogenesis and progression of lung injury caused by HBO and offer references for identifying corresponding intervention targets.

The development of the Negative Mental Imagery Questionnaire (MIQ-N).

Mental imagery plays a key role in the onset and maintenance of psychological disorders, and has become the target of psychological interventions for the treatment of several anxiety-related conditions. However, there are currently no transdiagnostic measures designed to assess the varied dimensions of mental imagery relevant to psychopathology. To develop and validate a new measure assessing the experiences and appraisals of negative mental imagery. The initial item pool was generated through a comprehensive literature review and interviews with subject-matter experts. An online community sample provided data for the exploratory (n=345) and confirmatory (n=325) factor analyses. The new 16-item Negative Mental Imagery Questionnaire demonstrated four subscales (Intrusiveness, Controllability, Beliefs about Mental Imagery, and Realness). Reliability and validity were good to excellent for both the full- and sub-scales. Appraisals of mental imagery captured by the new measure are consistent with previous research on mental imagery and psychopathology.

Chromatin interaction maps identify oncogenic targets of enhancer duplications in cancer.

As a major type of structural variants, tandem duplication plays a critical role in tumorigenesis by increasing oncogene dosage. Recent work has revealed that noncoding enhancers are also affected by duplications leading to the activation of oncogenes that are inside or outside of the duplicated regions. However, the prevalence of enhancer duplication and the identity of their target genes remains largely unknown in the cancer genome. Here, by analyzing whole-genome sequencing data in a non-gene-centric manner, we identify 881 duplication hotspots in 13 major cancer types, most of which do not contain protein-coding genes. We show that the hotspots are enriched with distal enhancer elements and are highly lineage-specific. We develop a HiChIP-based methodology that navigates enhancer-promoter contact maps to prioritize the target genes for the duplication hotspots harboring enhancer elements. The methodology identifies many novel enhancer duplication events activating oncogenes such as ESR1, FOXA1, GATA3, GATA6, TP63, and VEGFA, as well as potentially novel oncogenes such as GRHL2, IRF2BP2, and CREB3L1 In particular, we identify a duplication hotspot on Chromosome 10p15 harboring a cluster of enhancers, which skips over two genes, through a long-range chromatin interaction, to activate an oncogenic isoform of the NET1 gene to promote migration of gastric cancer cells. Focusing on tandem duplications, our study substantially extends the catalog of noncoding driver alterations in multiple cancer types, revealing attractive targets for functional characterization and therapeutic intervention.

NLRP10 maintains epidermal homeostasis by promoting keratinocyte survival and P63-dependent differentiation and barrier function

Atopic dermatitis (AD) is a common chronic inflammatory skin disorder characterized by disrupted epidermal barrier function and aberrant immune responses. Despite recent developments in new therapeutics for AD, there is still a large unmet medical need for disease management due to the complex and multifactorial nature of AD. Recent genome-wide association studies (GWAS) have identified NLRP10 as a susceptible gene for AD but the physiological role of NLRP10 in skin homeostasis and AD remains unknown. Here we show that NLRP10 is downregulated in AD skin samples. Using an air-lift human skin equivalent culture, we demonstrate that NLRP10 promotes keratinocyte survival and is required for epidermal differentiation and barrier function. Mechanistically, NLRP10 limits cell death by preventing the recruitment of caspase-8 to the death inducing signaling complex (DISC) and by inhibiting its subsequent activation. NLRP10 also stabilizes p63, the master regulator of keratinocyte differentiation, to drive proper keratinocyte differentiation and to reinforce the barrier function. Our findings underscore NLRP10 as a key player in atopic dermatitis pathogenesis, highlighting NLRP10 as a potential target for therapeutic intervention to restore skin barrier function and homeostasis in AD.

Identification of Potential Drug Targets for Sleep Apnea Through Mendelian Randomization

Background: Sleep apnea is a significant health impediment, and it presently lacks efficacious therapeutic interventions. Thus, it is imperative to discover novel therapeutic targets that could guide clinical treatment strategies. Objective: This study aims to utilize an integrative analytic approach to unearth previously unappreciated protein-encoding genes implicated in sleep apnea susceptibility. Methods: Through the Multi-Marker Analysis of Genomic Annotation (MAGMA), we aligned Single-Nucleotide Polymorphism (SNP) summary statistics from Genome-Wide Association Studies (GWAS) of gene bodies to discern potential risk genes. Following the MAGMA results, we conducted a round of Transcriptome-Wide Association Studies (TWAS) and Proteome-Wide Association Studies (PWAS) to expedite the conversion of genetic associations into probable protein targets. Mendelian Randomization (MR) and co-localization analysis were employed to ascertain the causal linkage between the candidate target genes and sleep apnea. Finally, a mediation analysis was undertaken to explore the possible intermediary role of 150 inflammatory metabolites and 1,124 proteins. Results: The MAGNA analysis revealed 2,819 genes in association with sleep apnea. TWAS and PWAS analyses indicated that cis-regulation of nine particular genes could play a role in sleep apnea onset via blood protein level alterations. MR and co-localization analyses also suggested a causal relationship with sleep apnea for three genes (ACADVL, CCDC134, UPP1). Consistent associations were found between genetically predicted biomarkers and Albumin, HCC-1, N-acetyl carnosine, and RELT, pointing towards their potential mediating roles in sleep apnea's etiological pathway. result: The MAGNA analysis revealed 2,819 genes in association with sleep apnea. TWAS and PWAS analyses indicated that cis-regulation of nine particular genes could play a role in sleep apnea onset via blood protein level alterations. MR and co-localization analyses also suggested a causal relationship with sleep apnea for three genes (ACADVL, CCDC134, UPP1). Consistent associations were found between genetically predicted biomarkers and Albumin, HCC-1, N-acetylcarnosine, and RELT, pointing towards their potential mediating roles in sleep apnea&amp;#039;s etiological pathway. Conclusion: Our findings indicate that ACADVL, CCDC134, and UPP1 genes are potentially significant targets for further functional investigation and therapeutic interventions for sleep apnea.

Integrated temporal transcriptional and epigenetic single-cell analysis reveals the intrarenal immune characteristics in an early-stage model of IgA nephropathy during its acute injury.

Kidney inflammation plays a crucial role in the pathogenesis of IgA nephropathy (IgAN), yet the specific phenotypes of immune cells involved in disease progression remain incompletely understood. Utilizing joint profiling through longitudinal single-cell RNA-sequencing (scRNAseq) and single-cell assay for transposase-accessible chromatin sequencing (scATACseq) can provide a comprehensive framework for elucidating the development of cell subset diversity and how chromatin accessibility regulates transcription. We aimed to characterize the dynamic immune cellular landscape at a high resolution in an early IgAN mouse model with acute kidney injury (AKI). A murine model was utilized to mimic 3 immunological states -"immune stability (IS), immune activation (IA) and immune remission (IR)" in early human IgAN-associated glomerulopathy during AKI, achieved through lipopolysaccharide (LPS) injection. Urinary albumin to creatinine ratio (UACR) was measured to further validate the exacerbation and resolution of kidney inflammation during this course. Paired scRNAseq and scATACseq analysis was performed on CD45+ immune cells isolated from kidney tissues obtained from CTRL (healthy vehicle), IS, IA and IR (4 or 5 mice each). The analyses revealed 7 major cell types and 24 clusters based on 72304 single-cell transcriptomes, allowing for the identification and characterization of various immune cell types within each cluster. Our data offer an impartial depiction of the immunological characteristics, as the proportions of immune cell types fluctuated throughout different stages of the disease. Specifically, these analyses also revealed novel subpopulations, such as a macrophage subset (Nlrp1b Mac) with distinct epigenetic features and a unique transcription factor motif profile, potentially exerting immunoregulatory effects, as well as an early subset of Tex distinguished by their effector and cytolytic potential (CX3CR1-transTeff). Furthermore, in order to investigate the potential interaction between immune cells and renal resident cells, we conducted single-cell RNA sequencing on kidney cells obtained from a separate cohort of IS and IA mice without isolating immune cells. These findings underscored the diverse roles played by macrophages and CD8+ T cells in maintaining homeostasis of endothelial cells (ECs) under stress. This study presents a comprehensive analysis of the dynamic changes in immune cell profiles in a model of IgAN, identifying key cell types and their roles and interactions. These findings significantly contribute to the understanding of the pathogenesis of IgAN and may provide potential targets for therapeutic intervention.

Pathogenic Mutation ΔK280 Promotes Hydrophobic Interactions Involving Microtubule-Binding Domain and Enhances Liquid-Liquid Phase Separation of Tau.

Liquid-liquid phase separation (LLPS) of tau protein can initiate its aggregation which is associated with Alzheimer's disease. The pathogenic mutation ΔK280 can enhance the aggregation of K18, a truncated tau variant comprising the microtubule-binding domain. However, the impact of ΔK280 on K18 LLPS and underlying mechanisms are largely unexplored. Herein, the conformational ensemble and LLPS of ΔK280 K18 through multiscale molecular simulations and microscopy experiments are investigated. All-atom molecular dynamic simulations reveal that ΔK280 significantly enhances the collapse degree and β-sheet content of the K18 monomer, indicating that ΔK280 mutation may promote K18 LLPS, validated by coarse-grained phase-coexistence simulations and microscopy experiments. Importantly, ΔK280 mutation promotes β-sheet formation of six motifs (especially PHF6), increases the hydrophobic solvent exposure of PHF6* and PHF6, and enhances hydrophobic, hydrogen bonding, and cation-π interactions involving most of the motifs, thus facilitating the phase separation of K18. Notably, ΔK280 alters the interaction network among the six motifs, inducing the formation of K18 conformations with high β-sheet contents and collapse degree. Coarse-grained simulations on full-length tau reveal that ΔK280 promotes tau LLPS by enhancing the hydrophobic interactions involving the microtubule-binding domain. These findings offer detailed mechanistic insights into ΔK280-induced tau pathogenesis, providing potential targets for therapeutic intervention.

Application of large-scale and multicohort plasma proteomics data to discover novel causal proteins in gastric cancer

PurposesGastric cancer (GC) is one of the most common malignant tumors threatening human beings and has a poor prognosis. Therefore, exploring unveiled biomarkers or therapeutic targets for the diagnosis and treatment of GC is crucial.MethodsA total of 5772 protein quantitative trait loci (pQTL) were aggregated from four latest large-scale proteomics cohorts. Two-sample Mendelian randomization (two-sample MR) was utilized to identify the causal effect of blood plasma proteins on GC. Heterogeneity, pleiotropy, and directionality analyses were employed to evaluate proteins identified via two-sample MR. The robustness of results was further validated via colocalization. The drug targets of proteins were evaluated to reveal the compounds that can interfere with these proteins.ResultsTen proteins with potential causations in relation to GC were identified: LY6D, SLURP1, MLN, PSCA, THSD1, CFTR, PPM1B, KDM3A, TSC1, and HCG22. Among these proteins, LY6D, SLURP1, and THSD1 were considered as the most reliable biomarkers of GC due to their significant H4 posterior probabilities in colocalization analysis and absence of pleiotropy. Compound 35, nitrosamide, and 0175029-0000 were potential drugs or small molecules targeting LY6D, SLURP1, and THSD1, respectively.ConclusionThis study identified several plasma proteins as potential biomarkers of GC and provided data support and new insights into the early diagnosis, intervention, and therapeutic targets of GC.

DNA methylation at AHRR as a master predictor of smoke exposure and a biomarker for sleep and exercise

BackgroundDNA methylation profiling may provide a more accurate measure of the smoking status than self-report and may be useful in guiding clinical interventions and forensic investigations. In the current study, blood DNA methylation profiles of nearly 800 Polish individuals were assayed using Illuminia EPIC and the inference of smoking from epigenetic data was explored. In addition, we focused on the role of the AHRR gene as a top marker for smoking and investigated its responsiveness to other lifestyle behaviors.ResultsWe found > 450 significant CpGs associated with cigarette consumption, and overrepresented in various biological functions including cell communication, response to stress, blood vessel development, cell death, and atherosclerosis. The model consisting of cg05575921 in AHRR (p = 4.5 × 10–32) and three additional CpGs (cg09594361, cg21322436 in CNTNAP2 and cg09842685) was able to predict smoking status with a high accuracy of AUC = 0.8 in the test set. Importantly, a gradual increase in the probability of smoking was observed, starting from occasional smokers to regular heavy smokers. Furthermore, former smokers displayed the intermediate DNA methylation profiles compared to current and never smokers, and thus our results indicate the potential reversibility of DNA methylation after smoking cessation. The AHRR played a key role in a predictive analysis, explaining 21.5% of the variation in smoking. In addition, the AHRR methylation was analyzed for association with other modifiable lifestyle factors, and showed significance for sleep and physical activity. We also showed that the epigenetic score for smoking was significantly correlated with most of the epigenetic clocks tested, except for two first-generation clocks.ConclusionsOur study suggests that a more rapid return to never-smoker methylation levels after smoking cessation may be achievable in people who change their lifestyle in terms of physical activity and sleep duration. As cigarette smoking has been implicated in the literature as a leading cause of epigenetic aging and AHRR appears to be modifiable by multiple exogenous factors, it emerges as a promising target for intervention and investment.