Dissecting the polygenic basis of atherosclerosis via disease-associated cell state signatures

Transcriptomic signatures of atheroresistance in the human atrium and ventricle highlight potential candidates for targeted atherosclerosis therapeutics

Atherosclerosis risk is not uniform throughout the cardiovascular system. This study therefore aimed to compare the transcriptomes of atheroresistant human atrium and ventricle with atheroprone coronary arteries to identify transcriptomic signatures of atheroresistance and potential targets for atherosclerosis therapeutics. Using publicly available gene read counts, differentially expressed genes between the atrium, ventricle, and coronary artery were identified for each contrast and validated against the Swiss Institute of Bioinformatics' Bgee database. Over-representation analysis and active-subnetwork-oriented enrichment assessment then identified enriched terms, which were grouped into endothelial dysfunction-related processes. Potential biological significance was further explored with pathway analysis. Among 21474 features, 12656 differentially expressed genes were identified across the three contrasts and associated with 1215 enriched terms. There were 315 down-regulated and 133 up-regulated genes associated with endothelial dysfunction-related processes across the contrasts, including immune modulators, cell adhesion molecules, and lipid metabolism- and coagulation-related molecules. Differentially expressed genes were associated with six down-regulated Kyoto Encyclopedia of Genes and Genomes pathways, related to immune cell and associated endothelium functions. Review of regulated genes associated with endothelial dysfunction-related processes and included in these pathways, indicate immune cell-associated B cell scaffold protein with ankyrin repeats 1, as well as arterial endothelial cell-associated vascular cell adhesion molecule 1 and cadherin 5, as potential atherosclerosis targets.

Macrophage WEE1 Directly Binds to and Phosphorylates NF-κB p65 Subunit to Induce Inflammatory Response and Drive Atherosclerosis

Atherosclerosis has an urgent need for new therapeutic targets. Protein kinases orchestrate multiple cellular events in atherosclerosis and may provide new therapeutic targets for atherosclerosis. Here, a protein kinase, WEE1 G2 checkpoint kinase (WEE1), promoting inflammation in atherosclerosis is identified. Kinase enrichment analysis and experimental evidences reveal macrophage WEE1 phosphorylation at S642 in human and mouse atherosclerotic tissues. RNA-seq analysis, combined with experiment studies using mutant WEE1 plasmids, shows that WEE1 phosphorylation, rather than WEE1 expression, mediated oxLDL-induced inflammation in macrophages. Macrophage-specific deletion of WEE1 or pharmacological inhibition of WEE1 kinase activity attenuates atherosclerosis by reducing inflammation in mice. Mechanistically, RNA-seq and co-immunoprecipitation followed by proteomics analysis are used to explore the mechanism and substrate of WEE1. p-WEE1 promoted inflammatory response through activating NF-κB shown and further revealed that WEE1 can directly bind to the p65 subunit. It is confirmed that p-WEE1 directly interacts with the RHD domain of p65 and phosphorylates p65 at S536, thereby facilitating subsequent NF-κB activation and inflammatory response in macrophages. The findings demonstrate that macrophage WEE1 drives NF-κB activation and atherosclerosis by directly phosphorylating p65 at S536. This study identifies WEE1 as a new upstream kinase of p65 and a potential therapeutic target for atherosclerosis.

Female-biased vascular smooth muscle cell gene regulatory networks predict MYH9 as a key regulator of fibrous plaque phenotype

Atherosclerosis, a chronic inflammatory condition driving coronary artery disease (CAD), manifests in two primary plaque types: unstable atheromatous plaques and stable fibrous plaques. While significant research has focused on atheromatous plaques, recent studies emphasize the growing importance of fibrous plaques, particularly in females under 50 years of age, where erosion on fibrous plaques significantly contributes to coronary thrombosis. The molecular mechanisms underlying sex differences in atherosclerotic plaque characteristics, including vascular smooth muscle cell (VSMC) contributions, remain understudied. Therefore, we utilized sex-specific gene regulatory networks (GRNs) derived from VSMC gene expression data from 119 male and 32 female heart transplant donors to identify molecular drivers of fibrous plaques. GRN analysis revealed two female-biased networks in VSMC, GRN floralwhite and GRN yellowgreen , enriched for inflammatory signaling and actin remodeling pathways, respectively. Single-cell RNA sequencing of carotid plaques from female and male patients confirmed the sex specificity of these networks in VSMCs. Further sub cellular phenotyping of the single-cell RNA sequencing revealed a sex-specific gene expression signature within GRN yellowgreen for VSMCs enriched for contractile and vasculature development pathways. Bayesian network modeling of the GRN yellowgreen identified MYH9 as a key driver gene. Indeed, elevated MYH9 protein expression in atherosclerotic plaques was associated with higher smooth muscle cell content and lower lipid content in female plaques, suggesting its involvement in fibrous plaque formation. Further proteomic analysis confirmed MYH9's upregulation in female fibrous plaques only and its correlation with stable plaque features. These findings provide novel insights into sex-specific molecular mechanisms regulating fibrous plaque formation.

Integrative analysis of single-cell transcriptomics and genetic associations identify cell states associated with vascular disease

BACKGROUND

Vascular diseases are accompanied by alterations in cellular phenotypes which underlie disease pathogenesis, with single-cell technologies aiding in the discovery of cellular heterogeneity among endothelial cell (EC) and vascular smooth muscle cell (VSMC) populations. In atherosclerotic disease, VSMCs are hypothesized to transition between contractile and synthetic states; however, the specific vascular subpopulations and intermediate cell states responsible for early vascular dysfunction remain unclear.

METHODS

We integrated newly generated and published single-nuclear RNA-sequencing (snRNA-seq) datasets to analyze normal (n = 7), aneurysmal (n = 9), and atherosclerotic (n = 2) flash-frozen human ascending thoracic aortas. Cell types and subtypes were defined using both top marker genes and canonical gene markers. Disease enrichment and relevant cell types were identified using newly developed computational tools to integrate GWAS data from multiple vascular disease-relevant studies with the single nuclei aortic expression profiles.

RESULTS

Nuclear dissociation and snRNA-seq identified ten distinct transcriptomic clusters from the integrated analysis representing all major vascular cell populations. Three distinct VSMC populations emerged that exhibited differential expression of extracellular matrix, contractile and pro-proliferative genes. Aneurysmal specimens were enriched for one fibroblast and one VSMC subpopulation compared to healthy tissue. RNA-trajectory analysis inferred a phenotypic continuum of gene expression between VSMC A and VSMC B or C and between two of the identified fibroblast types. VSMCs and Fibroblast C exhibited the greatest cell type-specific enrichment of genes mapped to GWAS loci for coronary artery disease (CAD), blood pressure, and migraine. Cell type-specific enrichment scores were more robust among the transcriptional profiles from non-diseased vascular tissue.

CONCLUSIONS

Our use of single-cell isolation and new computational methods prioritizes the cell types that most contribute to vascular disease pathogenesis. Specifically, tissue dissociation and single-nuclear transcriptomics better represent all vascular cell types, from which we demonstrate enrichment of pro-proliferative VSMCs in TAA and further implicate phenotypic switching as a likely pathologic mechanism. Integrated analysis of cell-specific gene expression and vascular disease GWAS data implicate genes and pathways associated with fibroblast and VSMC cell-state transitions.

Enhancing polygenic scores for cardiometabolic traits through tissue- and cell-type-specific functional annotations

Functional genomic annotations can improve polygenic scores (PGS) within and between genetic ancestry groups. While general annotations are commonly used in PGS development, tissue- and cell-type-specific annotations derived from open chromatin and gene expression experiments may further enhance PGS for cardiometabolic traits. We developed PGS for 14 cardiometabolic traits in the UK Biobank using SBayesRC. We integrated GWAS summary statistics from FinnGen and GLGC with three annotation sources: (1) Baseline-LD model version 2.2 (general annotations), (2) cell-type-specific snATAC-seq peaks, and (3) tissue-specific eQTLs/sQTLs. We created PGS using two EUR LD reference panels (1.2 million [1.2M] HapMap3 variants and 7M imputed variants). Tissue- and cell-type-specific annotations showed stronger heritability enrichment than Baseline-LD annotations on average, particularly coronary snATAC-seq peaks and fine-mapped eQTLs. Without annotations, HapMap3 and 7M variant PGS performed similarly. However, with all annotations, 7M variant PGS outperformed HapMap3 variant PGS (8% average increase in relative performance in EUR). Compared to using no annotations, modeling Baseline-LD annotations improved performance by 5% for HapMap3 and 11% for 7M variant PGS, while modeling all annotations yielded improvements of 5% and 13%, respectively. Although annotations provided greater relative improvement for cross-ancestry prediction, they did not decrease the disparity in PGS performance between genetic ancestry groups. In conclusion, functional annotations improved PGS for cardiometabolic traits. Despite strong heritability enrichment, tissue- and cell-type-specific snATAC-seq and eQTL annotations provided marginal performance gains beyond general genomic annotations.

Distinct inflammatory pathways shape atherosclerosis in different vascular beds

Studies suggest varying atherosclerotic cardiovascular disease (ASCVD) prevalence across arterial beds. Factors such as smoking expedite ASCVD progression in the abdominal aorta, while diabetes accelerates plaque development in lower limb arteries, and hypertension plays a significant role in ASCVD development in the coronary and carotid arteries. Moreover, superficial femoral atherosclerosis advances slower compared with atherosclerosis in coronary and carotid arteries. Furthermore, femoral atherosclerosis exhibits higher levels of ossification and calcification, but lower cholesterol concentrations compared with atherosclerotic lesions of other vascular beds. Such disparities exemplify the diverse progression of ASCVD across arterial beds, pointing towards differential mechanistic pathways in each vascular bed. Hence, this review summarizes current literature on immune-inflammatory mechanisms in various arterial beds in ASCVD to advance our understanding of this disease in an aging society with increased need of vascular bed and patient-specific treatment options.

Epigenetic regulation of vascular smooth muscle cell phenotypes in atherosclerosis

Vascular smooth muscle cells (VSMCs) in adult arteries maintain substantial phenotypic plasticity, which allows for the reversible cell state changes that enable vascular remodelling and homeostasis. In atherosclerosis, VSMCs dedifferentiate in response to lipid accumulation and inflammation, resulting in loss of their characteristic contractile state. Recent studies showed that individual, pre-existing VSMCs expand clonally and can acquire many different phenotypes in atherosclerotic lesions. The changes in gene expression underlying this phenotypic diversity are mediated by epigenetic modifications which affect transcription factor access and thereby gene expression dynamics. Additionally, epigenetic mechanisms can maintain cellular memory, potentially facilitating reversion to the contractile state. While technological advances have provided some insight, a comprehensive understanding of how VSMC phenotypes are governed in disease remains elusive. Here we review current literature in light of novel insight from studies at single-cell resolution. We also discuss how lessons from epigenetic studies of cellular regulation in other fields could help in translating the potential of targeting VSMC phenotype conversion into novel therapies in cardiovascular disease.

Identification of ALEKSIN as a novel multi-IRF inhibitor of IRF- and STAT-mediated transcription in vascular inflammation and atherosclerosis

Cardiovascular diseases (CVDs) include atherosclerosis, which is an inflammatory disease of large and medium vessels that leads to atherosclerotic plaque formation. The key factors contributing to the onset and progression of atherosclerosis include the pro-inflammatory cytokines interferon (IFN)α and IFNγ and the pattern recognition receptor (PRR) Toll-like receptor 4 (TLR4). Together, they trigger the activation of IFN regulatory factors (IRFs) and signal transducer and activator of transcription (STAT)s. Based on their promoting role in atherosclerosis, we hypothesized that the inhibition of pro-inflammatory target gene expression through multi-IRF inhibitors may be a promising strategy to treat CVDs. Using comparative in silico docking of multiple IRF-DNA-binding domain (DBD) models on a multi-million natural compound library, we identified the novel multi-IRF inhibitor, ALEKSIN. This compound targets the DBD of IRF1, IRF2, and IRF8 with the same affinity and simultaneously inhibits the expression of multiple IRF target genes in human microvascular endothelial cells (HMECs) in response to IIFNα and IFNγ. Under the same conditions, ALEKSIN also inhibited the phosphorylation of STATs, potentially through low-affinity STAT-SH2 binding but with lower potency than the known multi-STAT inhibitor STATTIC. This was in line with the common inhibition of ALEKSIN and STATTIC observed on the genome-wide expression of pro-inflammatory IRF/STAT/NF-κB target genes, as well as on the migration of HMECs. Finally, we identified a novel signature of 46 ALEKSIN and STATTIC commonly inhibited pro-atherogenic target genes, which was upregulated in atherosclerotic plaques in the aortas of high-fat diet-fed ApoEKO mice and associated with inflammation, proliferation, adhesion, chemotaxis, and response to lipids. Interestingly, the majority of these genes could be linked to macrophage subtypes present in aortic plaques in HFD-fed LDLR-KO mice. Together, this suggests that ALEKSIN represents a novel class of multi-IRF inhibitors, which inhibits IRF-, STAT-, and NF-κB-mediated transcription and could offer great promise for the treatment of CVDs. Furthermore, the ALEKSIN and STATTIC commonly inhibited pro-inflammatory gene signature could help monitor plaque progression during experimental atherosclerosis.

Genomic Drivers of Coronary Artery Disease and Risk of Future Outcomes After Coronary Angiography

Importance

Disease characteristics of genetically mediated coronary artery disease (CAD) on coronary angiography and the association of genomic risk with outcomes after coronary angiography are not well understood.

Objective

To assess the angiographic characteristics and risk of post-coronary angiography outcomes of patients with genomic drivers of CAD: familial hypercholesterolemia (FH), high polygenic risk score (PRS), and clonal hematopoiesis of indeterminate potential (CHIP).

Design, Setting, and Participants

A retrospective cohort study of 3518 Mass General Brigham Biobank participants with genomic information who underwent coronary angiography was conducted between July 18, 2000, and August 1, 2023.

Exposures

The presence of a genomic risk factor of CAD, defined as FH variant, high CAD PRS, or CHIP driver variation.

Main Outcomes and Measures

Coronary artery disease presentation (stable or acute), angiographic CAD characteristics (severity and burden), angiographic outcomes (repeat angiogram, revascularization, and in-stent restenosis), and clinical outcomes (heart failure and all-cause mortality).

Results

Among 3518 participants (2467 [70.1%] male; median age, 64.0 [IQR, 55.0-72.0] years), 1509 (42.9%) had at least 1 genomic driver of CAD (26 FH, 1191 high CAD PRS, and 466 CHIP) that was associated with the presentation of acute coronary syndromes (adjusted odds ratio, 2.67; 95% CI, 2.19-3.26) and with the presence, burden, and severity of angiographic CAD. This association was driven by FH and CAD PRS. One SD of CAD PRS was associated with a 12.51-point higher Gensini score. During 9 years of follow-up, there was an increased risk among FH carriers for a repeat angiogram (adjusted hazard ratio [AHR], 1.70; 95% CI, 1.02-2.83), and revascularization (AHR, 1.97; 95% CI, 1.02-3.80), and among people with high CAD PRS (repeat angiogram: AHR, 1.79; 95% CI, 1.45-2.22; revascularization: AHR, 1.85; 95% CI, 1.37-2.50; and in-stent restenosis: AHR, 3.89; 95% CI, 2.16-7.01). CHIP carriers had no significant increase in angiographic outcomes but were at higher risk of heart failure (AHR, 1.58; 95% CI, 1.04-2.40) and all-cause mortality (AHR, 1.78; 95% CI, 1.47-2.16).

Conclusions and Relevance

The findings of this study suggest that germline monogenic and polygenic risk are associated with acute coronary syndromes presentation, severity and burden of atherosclerosis, and risk of repeat angiogram, revascularization, and in-stent restenosis. CHIP variant status is associated with incident heart failure and mortality after coronary angiography.

Risk of major vascular events in patients without traditional risk factors after transient ischemic attack or minor ischemic stroke: An international prospective cohort

INTRODUCTION

To investigate the clinical characteristics in patients without traditional risk factors (TRFs) after transient ischemic attack or minor ischemic stroke, who were recruited in the TIAregistry.org.

PATIENTS AND METHODS

A total of 3847 patients were analyzed. TRFs included hypertension, diabetes, hypercholesterolemia, current smoking, and atrial fibrillation. Background characteristics and outcomes at 1 and 5 years in patients without TRFs were compared to those in patients with TRFs. The primary outcome was major cardiovascular event (MACE), which was non-fatal stroke, non-fatal acute coronary syndrome, or vascular death. To evaluate the causes, we applied the ASCOD (atherosclerosis, small vessel disease, cardiac pathology, other causes or dissection) grading system.

RESULTS

One-year risk of MACE (5.3% vs 6.3%, hazard ratio (HR) 0.84, 95% confidence interval (CI) 0.53-1.31) was comparable between patients without TRFs (n = 402) and those with TRFs (n = 3445). Five-year risk of MACE was significantly lower in patients without TRFs than in those with TRFs (7.9% vs 13.9%, HR 0.57, 95% CI 0.39-0.82). In patients without TRFs, causal atherosclerosis was a potent risk factor (HR 5.67, 95% CI 2.68-12.02) and ipsilateral extra- or intra-cranial arterial stenosis was only significant predictor of MACE (interaction p = 0.0046) at 5 years.

CONCLUSION AND DISCUSSION

The 5-year risk of MACE was lower in patients without TRFs than those with TRFs, although a certain level of risk persisted in the absence of TRFs. The most significant predictor of MACE in patients without TRFs was arterial stenosis.

GWAS breakthroughs: mapping the journey from one locus to 393 significant coronary artery disease associations

Coronary artery disease (CAD) poses a substantial threat to global health, leading to significant morbidity and mortality worldwide. It has a significant genetic component that has been studied through genome-wide association studies (GWAS) over the past 17 years. These studies have made progress with larger sample sizes, diverse ancestral backgrounds, and the discovery of multiple genomic regions related to CAD risk. In this review, we provide a comprehensive overview of CAD GWAS, including information about the genetic makeup of the disease and the importance of ethnic diversity in these studies. We also discuss challenges of identifying causal genes and variants within GWAS loci with a focus on non-coding regions. Additionally, we highlight tissues and cell types relevant to CAD, and discuss clinical implications of GWAS findings including polygenic risk scores, sex-specific differences in CAD genetics, ethnical aspects of personalized interventions, and GWAS guided drug development.

Genetic relations between type 1 diabetes, coronary artery disease and leukocyte counts

AIMS/HYPOTHESIS

Type 1 diabetes is associated with excess coronary artery disease (CAD) risk even when known cardiovascular risk factors are accounted for. Genetic perturbation of haematopoiesis that alters leukocyte production is a novel independent modifier of CAD risk. We examined whether there are shared genetic determinants and causal relationships between type 1 diabetes, CAD and leukocyte counts.

METHODS

Genome-wide association study summary statistics were used to perform pairwise linkage disequilibrium score regression and heritability estimation from summary statistics (ρ-HESS) to respectively estimate the genome-wide and local genetic correlations, and two-sample Mendelian randomisation to estimate the causal relationships between leukocyte counts (335,855 healthy individuals), type 1 diabetes (18,942 cases, 501,638 control individuals) and CAD (122,733 cases, 424,528 control individuals). A latent causal variable (LCV) model was performed to estimate the genetic causality proportion of the genetic correlation between type 1 diabetes and CAD.

RESULTS

There was significant genome-wide genetic correlation (rg) between type 1 diabetes and CAD (rg=0.088, p=8.60 × 10-3) and both diseases shared significant genome-wide genetic determinants with eosinophil count (rg for type 1 diabetes [rg(T1D)]=0.093, p=7.20 × 10-3, rg for CAD [rg(CAD)]=0.092, p=3.68 × 10-6) and lymphocyte count (rg(T1D)=-0.052, p=2.76 × 10-2, rg(CAD)=0.176, p=1.82 × 10-15). Sixteen independent loci showed stringent Bonferroni significant local genetic correlations between leukocyte counts, type 1 diabetes and/or CAD. Cis-genetic regulation of the expression levels of genes within shared loci between type 1 diabetes and CAD was associated with both diseases as well as leukocyte counts, including SH2B3, CTSH, MORF4L1, CTRB1, CTRB2, CFDP1 and IFIH1. Genetically predicted lymphocyte, neutrophil and eosinophil counts were associated with type 1 diabetes and CAD (lymphocyte OR for type 1 diabetes [ORT1D]=0.67, p=2.02-19, ORCAD=1.09, p=2.67 × 10-6; neutrophil ORT1D=0.82, p=5.63 × 10-5, ORCAD=1.17, p=5.02 × 10-14; and eosinophil ORT1D=1.67, p=5.45 × 10-25, ORCAD=1.07, p=2.03 × 10-4. The genetic causality proportion between type 1 diabetes and CAD was 0.36 ± 0.16 (pLCV=1.30 × 10-2), suggesting a possible intermediary causal variable.

CONCLUSIONS/INTERPRETATION

This study sheds light on shared genetic mechanisms underlying type 1 diabetes and CAD, which may contribute to their co-occurrence through regulation of gene expression and leukocyte counts and identifies cellular and molecular targets for further investigation for disease prediction and potential drug discovery.

Proliferation capability of natural killer cells upon cytokines stimulation correlated negatively with serum lactate dehydrogenase level in coronary artery disease patients

Background

Natural killer (NK) cells are proposed to participate in coronary artery disease (CAD) development. However, little is known about how CAD patients' NK cells respond to different stimulatory factors in terms of proliferation capability.

Methods and results

Twenty-nine CAD patients' peripheral blood NK cells were isolated and individually treated with IL-2, IL-12, IL-15, IL-18, IL-21, cortisone acetate, hydrocortisone, or ascorbic acid for 36 hours, followed by cell cycle analysis using flow cytometry. The ratio of S and G2/M phase cell number to total cell number was defined as a proliferation index (PrI) and used for proliferative capability indication. The results showed that these eight factors resulted in different life cycle changes in the 29 NK cell samples. Remarkably, 28 out of 29 NK cell samples showed an obvious increase in PrI upon ascorbic acid treatment. The serum lactate dehydrogenase (LDH) level of the 29 CAD patients was measured. The results showed a negative correlation between serum LDH level and the CAD patients' NK cell PrI upon stimulation of interleukins, but not the non-interleukin stimulators. Consistently, a retrospective analysis of 46 CAD patients and 32 healthy donors showed that the circulating NK cell number negatively correlated with the serum LDH level in CAD patients. Unexpectedly, addition of LDH to NK cells significantly enhanced the production of IFN-γ, IL-10 and TNF-α, suggesting a strong regulatory role on NK cell's function.

Conclusion

Ascorbic acid could promote the proliferation of the CAD patients' NK cells; LDH serum level may function as an indicator for NK cell proliferation capability and an immune-regulatory factor.

TAT-beclin1 treatment accelerates the development of atherosclerotic lesions in ApoE-deficient mice

The importance of autophagy in atherosclerosis has garnered significant attention regarding the potential applications of autophagy inducers. However, the impact of TAT-Beclin1, a peptide inducer of autophagy, on the development of atherosclerotic plaques remains unclear. Single-cell omics analysis indicates a notable reduction in GAPR1 levels within fibroblasts, stromal cells, and macrophages during atherosclerosis. Tat-beclin1 (T-B), an autophagy-inducing peptide derived from Beclin1, could selectively bind to GAPR1, relieving its inhibition on Beclin1 and thereby augmenting autophagosome formation. To investigate its impact on atherosclerosic plaque progression, we established the ApoE-/- mouse model of carotid atherosclerotic plaques. Surprisingly, intravenous administration of Tat-beclin1 dramatically accelerated the development of carotid artery plaques. Immunofluorescence analysis suggested that macrophage aggregation and autophagosome formation within atherosclerotic plaques were significantly increased upon T-B treatment. However, immunofluorescence and transmission electron microscopy (TEM) analysis revealed a reduction in autophagy flux through lysosomes. In vitro, the interaction between T-B and GAPR1 was confirmed in RAW264.7 cells, resulting in the increased accumulation of p62/SQSTM1 and LC3-II in the presence of ox-LDL. Additionally, T-B treatment elevated the protein levels of p62/SQSTM1, LC3-II, and cleaved caspase 1, along with the secretion of IL-1β in response to ox-LDL exposure. In summary, our study underscores that T-B treatment amplifies abnormal autophagy and inflammation, consequently exacerbating atherosclerotic plaque development in ApoE-/- mice.

Translatome profiling reveals Itih4 as a novel smooth muscle cell-specific gene in atherosclerosis

AIMS

Vascular smooth muscle cells (SMCs) and their derivatives are key contributors to the development of atherosclerosis. However, studying changes in SMC gene expression in heterogeneous vascular tissues is challenging due to the technical limitations and high cost associated with current approaches. In this paper, we apply translating ribosome affinity purification sequencing to profile SMC-specific gene expression directly from tissue.

METHODS AND RESULTS

To facilitate SMC-specific translatome analysis, we generated SMCTRAP mice, a transgenic mouse line expressing enhanced green fluorescent protein (EGFP)-tagged ribosomal protein L10a (EGFP-L10a) under the control of the SMC-specific αSMA promoter. These mice were further crossed with the atherosclerosis model Ldlr-/-, ApoB100/100 to generate SMCTRAP-AS mice and used to profile atherosclerosis-associated SMCs in thoracic aorta samples of 15-month-old SMCTRAP and SMCTRAP-AS mice. Our analysis of SMCTRAP-AS mice showed that EGFP-L10a expression was localized to SMCs in various tissues, including the aortic wall and plaque. The TRAP fraction demonstrated high enrichment of known SMC-specific genes, confirming the specificity of our approach. We identified several genes, including Cemip, Lum, Mfge8, Spp1, and Serpina3, which are known to be involved in atherosclerosis-induced gene expression. Moreover, we identified several novel genes not previously linked to SMCs in atherosclerosis, such as Anxa4, Cd276, inter-alpha-trypsin inhibitor-4 (Itih4), Myof, Pcdh11x, Rab31, Serpinb6b, Slc35e4, Slc8a3, and Spink5. Among them, we confirmed the SMC-specific expression of Itih4 in atherosclerotic lesions using immunofluorescence staining of mouse aortic roots and spatial transcriptomics of human carotid arteries. Furthermore, our more detailed analysis of Itih4 showed its link to coronary artery disease through the colocalization of genome-wide association studies, splice quantitative trait loci (QTL), and protein QTL signals.

CONCLUSION

We generated a SMC-specific TRAP mouse line to study atherosclerosis and identified Itih4 as a novel SMC-expressed gene in atherosclerotic plaques, warranting further investigation of its putative function in extracellular matrix stability and genetic evidence of causality.

Schizophrenia polygenic risk scores, clinical variables and genetic pathways as predictors of phenotypic traits of bipolar I disorder

AIM

We investigated the predictive value of polygenic risk scores (PRS) derived from the schizophrenia GWAS (Trubetskoy et al., 2022) (SCZ3) for phenotypic traits of bipolar disorder type-I (BP-I) in 1878 BP-I cases and 2751 controls from Romania and UK.

METHODS

We used PRSice-v2.3.3 and PRS-CS for computing SCZ3-PRS for testing the predictive power of SCZ3-PRS alone and in combination with clinical variables for several BP-I subphenotypes and for pathway analysis. Non-linear predictive models were also used.

RESULTS

SCZ3-PRS significantly predicted psychosis, incongruent and congruent psychosis, general age-of-onset (AO) of BP-I, AO-depression, AO-Mania, rapid cycling in univariate regressions. A negative correlation between the number of depressive episodes and psychosis, mainly incongruent and an inverse relationship between increased SCZ3-SNP loading and BP-I-rapid cycling were observed. In random forest models comparing the predictive power of SCZ3-PRS alone and in combination with nine clinical variables, the best predictions were provided by combinations of SCZ3-PRS-CS and clinical variables closely followed by models containing only clinical variables. SCZ3-PRS performed worst. Twenty-two significant pathways underlying psychosis were identified.

LIMITATIONS

The combined RO-UK sample had a certain degree of heterogeneity of the BP-I severity: only the RO sample and partially the UK sample included hospitalized BP-I cases. The hospitalization is an indicator of illness severity. Not all UK subjects had complete subphenotype information.

CONCLUSION

Our study shows that the SCZ3-PRS have a modest clinical value for predicting phenotypic traits of BP-I. For clinical use their best performance is in combination with clinical variables.

Multifaceted roles of Meg3 in cellular senescence and atherosclerosis

BACKGROUND AND AIMS

Long noncoding RNAs are involved in the pathogenesis of atherosclerosis. As long noncoding RNAs maternally expressed gene 3 (Meg3) prevents cellular senescence of hepatic vascular endothelium and obesity-induced insulin resistance, we decided to examine its role in cellular senescence and atherosclerosis.

METHODS AND RESULTS

By analyzing our data and human and mouse data from the Gene Expression Omnibus database, we found that Meg3 expression was reduced in humans and mice with cardiovascular disease, indicating its potential role in atherosclerosis. In Ldlr-/- mice fed a Western diet for 12 weeks, Meg3 silencing by chemically modified antisense oligonucleotides attenuated the formation of atherosclerotic lesions by 34.9% and 20.1% in male and female mice, respectively, revealed by en-face Oil Red O staining, which did not correlate with changes in plasma lipid profiles. Real-time quantitative PCR analysis of cellular senescence markers p21 and p16 revealed that Meg3 deficiency aggravates hepatic cellular senescence but not cellular senescence at aortic roots. Human Meg3 transgenic mice were generated to examine the role of Meg3 gain-of-function in the development of atherosclerosis induced by PCSK9 overexpression. Meg3 overexpression promotes atherosclerotic lesion formation by 29.2% in Meg3 knock-in mice independent of its effects on lipid profiles. Meg3 overexpression inhibits hepatic cellular senescence, while it promotes aortic cellular senescence likely by impairing mitochondrial function and delaying cell cycle progression.

CONCLUSIONS

Our data demonstrate that Meg3 promotes the formation of atherosclerotic lesions independent of its effects on plasma lipid profiles. In addition, Meg3 regulates cellular senescence in a tissue-specific manner during atherosclerosis. Thus, we demonstrated that Meg3 has multifaceted roles in cellular senescence and atherosclerosis.

The disruptive role of LRG1 on the vasculature and perivascular microenvironment

The establishment of new blood vessels, and their subsequent stabilization, is a critical process that facilitates tissue growth and organ development. Once established, vessels need to diversify to meet the specific needs of the local tissue and to maintain homeostasis. These processes are tightly regulated and fundamental to normal vessel and tissue function. The mechanisms that orchestrate angiogenesis and vessel maturation have been widely studied, with signaling crosstalk between endothelium and perivascular cells being identified as an essential component. In disease, however, new vessels develop abnormally, and existing vessels lose their specialization and function, which invariably contributes to disease progression. Despite considerable research into the vasculopathic mechanisms in disease, our knowledge remains incomplete. Accordingly, the identification of angiocrine and angiopathic molecules secreted by cells within the vascular microenvironment, and their effect on vessel behaviour, remains a major research objective. Over the last decade the secreted glycoprotein leucine-rich α-2 glycoprotein 1 (LRG1), has emerged as a significant vasculopathic molecule, stimulating defective angiogenesis, and destabilizing the existing vasculature mainly, but not uniquely, by altering both canonical and non-canonical TGF-β signaling in a highly cell and context dependent manner. Whilst LRG1 does not possess any overt homeostatic role in vessel development and maintenance, growing evidence provides a compelling case for LRG1 playing a pleiotropic role in disrupting the vasculature in many disease settings. Thus, LRG1 has now been reported to damage vessels in various disorders including cancer, diabetes, chronic kidney disease, ocular disease, and lung disease and the signaling processes that drive this dysfunction are being defined. Moreover, therapeutic targeting of LRG1 has been widely proposed to re-establish a quiescent endothelium and normalized vasculature. In this review, we consider the current status of our understanding of the role of LRG1 in vascular pathology, and its potential as a therapeutic target.

Unraveling the intercellular communication disruption and key pathways in Alzheimer's disease: an integrative study of single-nucleus transcriptomes and genetic association

BACKGROUND

Recently, single-nucleus RNA-seq (snRNA-seq) analyses have revealed important cellular and functional features of Alzheimer's disease (AD), a prevalent neurodegenerative disease. However, our knowledge regarding intercellular communication mediated by dysregulated ligand-receptor (LR) interactions remains very limited in AD brains.

METHODS

We systematically assessed the intercellular communication networks by using a discovery snRNA-seq dataset comprising 69,499 nuclei from 48 human postmortem prefrontal cortex (PFC) samples. We replicated the findings using an independent snRNA-seq dataset of 56,440 nuclei from 18 PFC samples. By integrating genetic signals from AD genome-wide association studies (GWAS) summary statistics and whole genome sequencing (WGS) data, we prioritized AD-associated Gene Ontology (GO) terms containing dysregulated LR interactions. We further explored drug repurposing for the prioritized LR pairs using the Therapeutic Targets Database.

RESULTS

We identified 190 dysregulated LR interactions across six major cell types in AD PFC, of which 107 pairs were replicated. Among the replicated LR signals, we found globally downregulated communications in the astrocytes-to-neurons signaling axis, characterized, for instance, by the downregulation of APOE-related and Calmodulin (CALM)-related LR interactions and their potential regulatory connections to target genes. Pathway analyses revealed 44 GO terms significantly linked to AD, highlighting Biological Processes such as 'amyloid precursor protein processing' and 'ion transmembrane transport,' among others. We prioritized several drug repurposing candidates, such as cromoglicate, targeting the identified dysregulated LR pairs.

CONCLUSIONS

Our integrative analysis identified key dysregulated LR interactions in a cell type-specific manner and the associated GO terms in AD, offering novel insights into potential therapeutic targets involved in disrupted cell-cell communication in AD.

Unveiling the role of ABI3 and hub senescence-related genes in macrophage senescence for atherosclerotic plaque progression

BACKGROUND

Atherosclerosis, characterized by abnormal arterial lipid deposition, is an age-dependent inflammatory disease and contributes to elevated morbidity and mortality. Senescent foamy macrophages are considered to be deleterious at all stages of atherosclerosis, while the underlying mechanisms remain largely unknown. In this study, we aimed to explore the senescence-related genes in macrophages diagnosis for atherosclerotic plaque progression.

METHODS

The atherosclerosis-related datasets were retrieved from the Gene Expression Omnibus (GEO) database, and cellular senescence-associated genes were acquired from the CellAge database. R package Limma was used to screen out the differentially expressed senescence-related genes (DE-SRGs), and then three machine learning algorithms were applied to determine the hub DE-SRGs. Next, we established a nomogram model to further confirm the clinical significance of hub DE-SRGs. Finally, we validated the expression of hub SRG ABI3 by Sc-RNA seq analysis and explored the underlying mechanism of ABI3 in THP-1-derived macrophages and mouse atherosclerotic lesions.

RESULTS

A total of 15 DE-SRGs were identified in macrophage-rich plaques, with five hub DE-SRGs (ABI3, CAV1, NINJ1, Nox4 and YAP1) were further screened using three machine learning algorithms. Subsequently, a nomogram predictive model confirmed the high validity of the five hub DE-SRGs for evaluating atherosclerotic plaque progression. Further, the ABI3 expression was upregulated in macrophages of advanced plaques and senescent THP-1-derived macrophages, which was consistent with the bioinformatics analysis. ABI3 knockdown abolished macrophage senescence, and the NF-κB signaling pathway contributed to ABI3-mediated macrophage senescence.

CONCLUSION

We identified five cellular senescence-associated genes for atherogenesis progression and unveiled that ABI3 might promote macrophage senescence via activation of the NF-κB pathway in atherogenesis progression, which proposes new preventive and therapeutic strategies of senolytic agents for atherosclerosis.

Unraveling the intercellular communication disruption and key pathways in Alzheimer's disease: An integrative study of single-nucleus transcriptomes and genetic association

Background

Recently, single-nucleus RNA-seq (snRNA-seq) analyses have revealed important cellular and functional features of Alzheimer's disease (AD), a prevalent neurodegenerative disease. However, our knowledge regarding intercellular communication mediated by dysregulated ligand-receptor (LR) interactions remains very limited in AD brains.

Methods

We systematically assessed the intercellular communication networks by using a discovery snRNA-seq dataset comprising 69,499 nuclei from 48 human postmortem prefrontal cortex (PFC) samples. We replicated the findings using an independent snRNA-seq dataset of 56,440 nuclei from 18 PFC samples. By integrating genetic signals from AD genome-wide association studies (GWAS) summary statistics and whole genome sequencing (WGS) data, we prioritized AD-associated Gene Ontology (GO) terms containing dysregulated LR interactions. We further explored drug repurposing for the prioritized LR pairs using the Therapeutic Targets Database.

Results

We identified 316 dysregulated LR interactions across six major cell types in AD PFC, of which 210 pairs were replicated. Among the replicated LR signals, we found globally downregulated communications in astrocytes-to-neurons signaling axis, characterized, for instance, by the downregulation of APOE-related and Calmodulin (CALM)-related LR interactions and their potential regulatory connections to target genes. Pathway analyses revealed 60 GO terms significantly linked to AD, highlighting Biological Processes such as 'amyloid precursor protein processing' and 'ion transmembrane transport', among others. We prioritized several drug repurposing candidates, such as cromoglicate, targeting the identified dysregulated LR pairs.

Conclusions

Our integrative analysis identified key dysregulated LR interactions in a cell type-specific manner and the associated GO terms in AD, offering novel insights into potential therapeutic targets involved in disrupted cell-cell communication in AD.