Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.

[Application of synthetic MRI in predicting isocitrate dehydrogenase 1 genotypes in gliomas]

This study analyzed the clinical and imaging data of 81 glioma patients who underwent brain synthetic MRI and diffusion weighted imaging (DWI) examination in the General Hospital of Ningxia Medical University from August 2020 to September 2021 to explore the value of synthetic MRI relaxation quantitative value in predicting the genotype of isocitrate dehydrogenase 1 (IDH1) in gliomas. There were 44 males and 37 females, those patients with an aged 50.0 (36.5, 59.0) years. The tumor pre-T1, pre-T2, pre-PD, post-T1 and ADC values were obtained by outlining the region of interest (ROI). Univariate analysis was used to compare the differences of parameter values between groups, and the receiver operating characteristic was used to evaluate the diagnostic efficacy of each parameter value in predicting glioma IDH1 genotype. The results showed that the pre-T1 and pre-PD values [M (Q1, Q3)] of IDH1m glioma were lower than those of IDH1w glioma [1 462.75 (1 306.41, 1 567.75) ms vs 1 532.83 (1 434.67, 1 617.67) ms, 84.18 (82.28, 86.41) pu vs 85.85 (84.65, 86.90) pu] (all P<0.05). The post-T1 and ADC values of IDH1m glioma were higher than those of IDH1w glioma [1 054.50 (631.92, 1 262.63) ms vs 669.67 (535.17, 823.33) ms, 1.20 (0.86, 1.35) ×10-3 mm2/s vs 0.80 (0.76, 0.93) ×10-3 mm2/s] (all P<0.05). The AUC of the combined model (pre-T1+pre-PD+post-T1+ADC+Age) is 0.828 (95%CI:0.729-0.903). Synthetic MRI relaxation quantitative values are helpful to distinguish IDH1 genotypes in glioma. The diagnostic efficacy of the multi-parameter combined model based on pre-T1, pre-PD, post-T1, ADC, and age is better than that of the single parameter, and it can be used as an effective strategy to improve the differential diagnosis ability of gliomas molecular markers.

Cardiovascular utility of single cell RNA-Seq

PURPOSE OF REVIEW

Cardiovascular diseases remain the leading causes of morbidity and mortality globally. Single-cell RNA sequencing has the potential to improve diagnostics, risk stratification, and provide novel therapeutic targets that have the potential to improve patient outcomes.

RECENT FINDINGS

Here, we provide an overview of the basic processes underlying single-cell RNA sequencing, including library preparation, data processing, and downstream analyses. We briefly discuss how the technique has been adapted to related medical disciplines, including hematology and oncology, with short term translational impact. We discuss potential applications of this technology within cardiology as well as recent innovative research within the field. We also discuss future directions to translate this technology to other high impact clinical areas.

SUMMARY

The use of single-cell RNA sequencing technology has made significant advancements in the field of cardiology, with ongoing growth in terms of applications and uptake. Most of the current research has focused on structural or atherosclerotic heart disease. Future areas that stand to benefit from this technology include cardiac electrophysiology and cardio-oncology.

Integrative multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

Genome-wide association studies (GWAS) have identified hundreds of genetic risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWAS and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotype information to identify quantitative trait loci (QTL) for gene expression and splicing in coronary arteries obtained from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary arteries and 19% exhibited cell-type-specific expression. Colocalization analysis with GWAS identified subgroups of eGenes unique to CAD and blood pressure. Fine-mapping highlighted additional eGenes of interest, including TBX20 and IL5 . Splicing (s)QTLs for 1,690 genes were also identified, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing events to accurately identify disease-relevant gene expression. Our work provides the first human coronary artery eQTL resource from a patient sample and exemplifies the necessity of diverse study populations and multi-omic approaches to characterize gene regulation in critical disease processes.

Study Design Overview

The meningeal transcriptional response to traumatic brain injury and aging

Emerging evidence suggests that the meningeal compartment plays instrumental roles in various neurological disorders, however, we still lack fundamental knowledge about meningeal biology. Here, we utilized high-throughput RNA sequencing (RNA-seq) techniques to investigate the transcriptional response of the meninges to traumatic brain injury (TBI) and aging in the sub-acute and chronic time frames. Using single-cell RNA sequencing (scRNA-seq), we first explored how mild TBI affects the cellular and transcriptional landscape in the meninges in young mice at one-week post-injury. Then, using bulk RNA-seq, we assessed the differential long-term outcomes between young and aged mice following TBI. In our scRNA-seq studies, we highlight injury-related changes in differential gene expression seen in major meningeal cell populations including macrophages, fibroblasts, and adaptive immune cells. We found that TBI leads to an upregulation of type I interferon (IFN) signature genes in macrophages and a controlled upregulation of inflammatory-related genes in the fibroblast and adaptive immune cell populations. For reasons that remain poorly understood, even mild injuries in the elderly can lead to cognitive decline and devastating neuropathology. To better understand the differential outcomes between the young and the elderly following brain injury, we performed bulk RNA-seq on young and aged meninges 1.5 months after TBI. Notably, we found that aging alone induced upregulation of meningeal genes involved in antibody production by B cells and type I IFN signaling. Following injury, the meningeal transcriptome had largely returned to its pre-injury signature in young mice. In stark contrast, aged TBI mice still exhibited upregulation of immune-related genes and downregulation of genes involved in extracellular matrix remodeling. Overall, these findings illustrate the dynamic transcriptional response of the meninges to mild head trauma in youth and aging.

PlaqView 2.0: A comprehensive web portal for cardiovascular single-cell genomics

Single-cell RNA-seq (scRNA-seq) is a powerful genomics technology to interrogate the cellular composition and behaviors of complex systems. While the number of scRNA-seq datasets and available computational analysis tools have grown exponentially, there are limited systematic data sharing strategies to allow rapid exploration and re-analysis of single-cell datasets, particularly in the cardiovascular field. We previously introduced PlaqView, an open-source web portal for the exploration and analysis of published atherosclerosis single-cell datasets. Now, we introduce PlaqView 2.0 (www.plaqview.com), which provides expanded features and functionalities as well as additional cardiovascular single-cell datasets. We showcase improved PlaqView functionality, backend data processing, user-interface, and capacity. PlaqView brings new or improved tools to explore scRNA-seq data, including gene query, metadata browser, cell identity prediction, ad hoc RNA-trajectory analysis, and drug-gene interaction prediction. PlaqView serves as one of the largest central repositories for cardiovascular single-cell datasets, which now includes data from human aortic aneurysm, gene-specific mouse knockouts, and healthy references. PlaqView 2.0 brings advanced tools and high-performance computing directly to users without the need for any programming knowledge. Lastly, we outline steps to generalize and repurpose PlaqView's framework for single-cell datasets from other fields.

Single-nucleus chromatin accessibility profiling highlights regulatory mechanisms of coronary artery disease risk

Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across cell types. Genome-wide association studies (GWAS) have identified over 200 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis-regulatory elements (CREs). Here, we applied single-nucleus ATAC-seq to profile 28,316 nuclei across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped ~320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants. . We identified elements in smooth muscle cell (SMC) transition states (e.g. fibromyocytes) and functional variants predicted to alter SMC and macrophage-specific regulation of MRAS (3q22) and LIPA (10q23), respectively. We further nominated key driver transcription factors such as PRDM16 and TBX2. Together, this single nucleus atlas provides a critical step towards interpreting regulatory mechanisms across the continuum of CAD risk.

Intersecting single-cell transcriptomics and genome-wide association studies identifies crucial cell populations and candidate genes for atherosclerosis

Aims

Genome-wide association studies (GWASs) have discovered hundreds of common genetic variants for atherosclerotic disease and cardiovascular risk factors. The translation of susceptibility loci into biological mechanisms and targets for drug discovery remains challenging. Intersecting genetic and gene expression data has led to the identification of candidate genes. However, previously studied tissues are often non-diseased and heterogeneous in cell composition, hindering accurate candidate prioritization. Therefore, we analysed single-cell transcriptomics from atherosclerotic plaques for cell-type-specific expression to identify atherosclerosis-associated candidate gene–cell pairs.

Methods and results

We applied gene-based analyses using GWAS summary statistics from 46 atherosclerotic and cardiovascular disease, risk factors, and other traits. We then intersected these candidates with single-cell RNA sequencing (scRNA-seq) data to identify genes specific for individual cell (sub)populations in atherosclerotic plaques. The coronary artery disease (CAD) loci demonstrated a prominent signal in plaque smooth muscle cells (SMCs) (SKI, KANK2, and SORT1) P-adj. = 0.0012, and endothelial cells (ECs) (SLC44A1, ATP2B1) P-adj. = 0.0011. Finally, we used liver-derived scRNA-seq data and showed hepatocyte-specific enrichment of genes involved in serum lipid levels.

Conclusion

We discovered novel and known gene–cell pairs pointing to new biological mechanisms of atherosclerotic disease. We highlight that loci associated with CAD reveal prominent association levels in mainly plaque SMC and EC populations. We present an intuitive single-cell transcriptomics-driven workflow rooted in human large-scale genetic studies to identify putative candidate genes and affected cells associated with cardiovascular traits. Collectively, our workflow allows for the identification of cell-specific targets relevant for atherosclerosis and can be universally applied to other complex genetic diseases and traits.

Enhanced single-cell RNA-seq workflow reveals coronary artery disease cellular cross-talk and candidate drug targets

BACKGROUND AND AIMS

The atherosclerotic plaque microenvironment is highly complex, and selective agents that modulate plaque stability are not yet available. We sought to develop a scRNA-seq analysis workflow to investigate this environment and uncover potential therapeutic approaches. We designed a user-friendly, reproducible workflow that will be applicable to other disease-specific scRNA-seq datasets.

METHODS

Here we incorporated automated cell labeling, pseudotemporal ordering, ligand-receptor evaluation, and drug-gene interaction analysis into a ready-to-deploy workflow. We applied this pipeline to further investigate a previously published human coronary single-cell dataset by Wirka et al. Notably, we developed an interactive web application to enable further exploration and analysis of this and other cardiovascular single-cell datasets.

RESULTS

We revealed distinct derivations of fibroblast-like cells from smooth muscle cells (SMCs), and showed the key changes in gene expression along their de-differentiation path. We highlighted several key ligand-receptor interactions within the atherosclerotic environment through functional expression profiling and revealed several avenues for future pharmacological development for precision medicine. Further, our interactive web application, PlaqView (www.plaqview.com), allows lay scientists to explore this and other datasets and compare scRNA-seq tools without prior coding knowledge.

CONCLUSIONS

This publicly available workflow and application will allow for more systematic and user-friendly analysis of scRNA datasets in other disease and developmental systems. Our analysis pipeline provides many hypothesis-generating tools to unravel the etiology of coronary artery disease. We also highlight potential mechanisms for several drugs in the atherosclerotic cellular environment. Future releases of PlaqView will feature more scRNA-seq and scATAC-seq atherosclerosis-related datasets to provide a critical resource for the field, and to promote data harmonization and biological interpretation.

Abstract 113: Cell-specific Chromatin Landscape Of Human Coronary Artery Resolves Mechanisms Of Disease Risk

Coronary artery disease (CAD) is a complex inflammatory disease involving genetic influences across several cell types. Genome-wide association studies (GWAS) have identified over 170 loci associated with CAD, where the majority of risk variants reside in noncoding DNA sequences impacting cis -regulatory elements (CREs). Here, we applied single-cell ATAC-seq to profile 28,316 cells across coronary artery segments from 41 patients with varying stages of CAD, which revealed 14 distinct cellular clusters. We mapped over 320,000 accessible sites across all cells, identified cell type-specific elements, transcription factors, and prioritized functional CAD risk variants via quantitative trait locus and sequence-based predictive modeling. Using differential peak analyses we identified a number of candidate mechanisms for smooth muscle cell transition states (e.g. fibromyocytes). By integrating these profiles with GWAS meta-analysis summary data we resolved cell type-specific putative binding sites for the majority of CAD risk variants. In particular, we prioritized functional variants predicted to alter MEF2 binding in smooth muscle cells at the MRAS locus. We also identify variants predicted to alter macrophage-specific regulation of LIPA. We further employed DNA to gene linkage to nominate disease-associated key driver transcription factors such as PRDM16 and TBX2. Together, this single cell atlas provides a critical step towards interpreting cis -regulatory mechanisms in the vessel wall across the continuum of CAD risk.

[Clinical features and prognosis of patients with leptomeningeal metastases]

Objective: To describe the clinical manifestations, neuroimaging, cerebrospinal fluid(CSF) cytology and prognosis of Leptomeningeal metastases(LM). Methods: The clinical manifestations, imaging features and CSF cytology of LM patients admitted to Henan Provincial People's Hospital from May 1, 2015 to May 31, 2020 were retrospectively analyzed. The overall survival (OS) was evaluated by the time from the diagnosis of LM to death. Results: A total of 88 patients with LM were enrolled in the study, and the median age was 59 years (range:28-78 years). There were 42 males (47.7%) and 46 females (52.3%). According to the pathological classification, it was lung cancer in 58 cases (65.9%), gastric cancer in 13 cases (14.8%), breast cancer in 7 cases (8.0%), melanoma in 1 case, esophageal cancer in 1 case, gallbladder cancer in 1 case, renal cell carcinoma in 1 case, double source cancer in 2 cases, and unknown source in 4 cases. The median Karnofsky Performance Scale (KPS) score was 50. LM was the initial manifestation of cancer in 34 patients. All patients had LM-related clinical symptoms, including headache in 73 cases (83.0%), nausea and vomiting in 63 cases (71.6%), abnormal physical and mental behaviors in 37 cases (42.0%), seizure in 41 cases (46.6%). Cranial nerve involvement was observed in 23 patients (39.0%) and spinal nerve involvement in 20(33.9%). There were 61 patients (83.6%) who showed neuroimaging features of LM. Tumor cells or atypical cells were found in 90.8% of patients for the first time, and activated monocytes in 47 cases (54.7%). The median OS was 13.0 weeks (95%CI:2.9-23.1) with the 1-year survival rate of 19.1%. Univariate analysis of survival indicated that lung cancer, lower KPS score, tyrosine kinase inhibitors (TKIs) and whole brain radiotherapy were favorable predictors of survival (P<0.05). Conclusions: The overall prognosis of LM is poor. Good physical condition, TKIs treatment and whole brain radiotherapy might improve clinical outcomes of LM patients.

Pan-Cancer Analysis Shows TP53 Mutations Modulate the Association of NOX4 with Genetic Programs of Cancer Progression and Clinical Outcome

Previously, we have shown TGF-β-induced NOX4 expression is involved in the epithelial-to-mesenchymal transition (EMT), a process critical for cancer metastasis, and that wild-type (WT) and mutant (Mut) p53 have divergent effects on TGF-β induction of NOX4: WT-p53 suppresses whereas Mut-p53 augments NOX4 mRNA and protein production in several tumor cell models. We sought to validate and extend our model by analyzing whole-exome data of primary tumor samples in The Cancer Genome Atlas (TCGA). We constructed a Pan-Cancer dataset from 23 tumor types and explored NOX4 expression patterns in relation to EMT and patient survival. NOX4 mRNA levels increase as a function of cancer progression in several cancers and correlate with Mut-p53 mRNA and genes involved in programs of EMT, cellular adhesion, migration, and angiogenesis. Tumor macrophages appear to be a source of NOX2, whose association with genetic programs of cancer progression emulate that of NOX4. Notably, increased NOX4 expression is linked to poorer survival in patients with Mut-TP53, but better survival in patients with WT-TP53. NOX4 is negatively associated with markers of apoptosis and positively with markers of proliferation in patients with Mut-TP53, consistent with their poorer survival. These findings suggest that TP53 mutations could “switch” NOX4 from being protective and an indicator of good prognosis to deleterious by promoting programs favoring cancer progression.

Histone modifications affect differential regulation of TGFβ- induced NADPH oxidase 4 (NOX4) by wild-type and mutant p53

Previously, we showed wild-type (WT) and mutant (mut) p53 differentially regulate reactive oxygen species (ROS) generation by NADPH oxidase-4 (NOX4): p53-WT suppresses TGFβ-induced NOX4, ROS and cell migration, whereas tumor-associated mut-p53 proteins enhance NOX4 expression and cell migration. Here, we extended our findings on the effects of p53 on NOX4 in several tumors and examined the basis of NOX4 transcriptional regulation by p53 and SMAD3. Statistical analysis of expression data from primary tumors available from The Cancer Genome Atlas (TCGA) detected correlations between mut-p53 and increased NOX4 expression. Furthermore, by altering p53 levels in cell culture models we showed several common tumor-associated mutant forms support TGFβ/SMAD3-dependent NOX4 expression. Deletion analysis revealed two critical SMAD3 binding elements (SBE) required for mut-p53-dependent NOX4 induction, whereas p53-WT caused dose-dependent suppression of NOX4 transcription. ChIP analysis revealed SMAD3 and p53-WT or mut-p53 associate with SBEs and p53 response elements in a TGFβ-dependent manner. Interestingly, the repressive effects of p53-WT on NOX4 were relieved by mutation of its transactivation domain or histone deacetylase (HDAC) inhibitor treatment. Overexpression of p300, a transcriptional co-regulator and histone acetyltransferase (HAT), enhanced p53-mediated NOX4 induction, whereas HAT-inactive p300 reduced NOX4 expression. Mut-p53 augmented TGFβ-stimulated histone acetylation within the NOX4 promoter. Finally, wound assays demonstrated NOX4 and p300 promote TGFβ/mut-p53-mediated cell migration. Our studies provide new insight into TGFβ/SMAD3 and mut-p53-mediated NOX4 induction involving epigenetic control of NOX4 in tumor cell migration, suggesting NOX4 is a potential therapeutic target to combat tumor progression and metastasis.

A novel recombinant protein TAT-GFP-KDEL with dual-function of penetrating cell membrane and locating at endoplasm reticulum

Although the potential value of phenotypic/functional knockout technology with intrabody/kine in prevention and cure of some serious diseases, such as AIDS and cancer, is being regarded, there are still several technical difficulties. One of the the most critical problems is how to directly deliver the intrabody/kine proteins into endoplasm reticulum (ER). In this study, a novel recombinant protein, TAT-GFP-KDEL, was designed and constructed. In this recombinant protein, HIV-derived TAT (47-57) and an ER retention four-peptide sequence KDEL were fused at the N-terminal and C-terminal of GFP respectively. The results showed that TAT-GFP-KDEL had been successfully expressed in bacteria BL21 and its purity reached to 95%. Moreover, we observed that this recombinant protein was able to efficiently transduce into MOLT-4 cells and accurately locate at ER. This study may provide an available strategy to promote the transmembrane delivery and ER localization of protein-based intrabody/kine.

[The impact of caring experiences of the patients with borderline personality disorder on psychiatric nurses]

The purpose of this qualitative study was to explore the subjective perceptions of the impact of caring with the hospitalized patients with borderline personality disorder (BPD) on psychiatric nurses. A purposive sample of psychiatric nurses with experiences of caring with at least one hospitalized BPD patient was obtained at one leading psychiatric hospital in northern Taiwan. A semi-structured interview guide and audio-taped recording skill was employed, and data were analyzed by qualitative content analysis. Thirteen female nurses participated in this project. Eighty percent of them were aged between 26-35 (mean +/- SD = 31.77 +/- 4.92). Thirty-eight percent of nurses were registered professional nurses; 54% worked as psychiatric nurses for 5-7 years; and 69% ever took care of 3-4 subjects with BPD. Several impacts of the caring experiences on nurses were identified. They are as follows: (1) becoming more knowledgeable about the BPD patients' characteristics and the related nursing care; (2) having positive or negative motivation of nursing profession; (3) changing nurses' attitudes of interpersonal relationship; (4) valuing nurses' personal belongings; and (5) enhancing nurses' understanding and facilitating their personal growth. The result of this study may empower psychiatric nurses to better understand the BPD patients, and to increase nurses' motivation of caring them. It may also enhance the quality care for these patients and the nurses' sense of satisfaction.

[Clinical and experimental study on rapid bladder ultrasound developer of Chinese medicinal herbs]

OBJECTIVE

To seek for a rapid type B ultrasound developer of Chinese medicinal herbs, so that the bladder and pelvic cavity developed clearly and pelvic cavity diseases could be diagnosed rapidly.

METHODS

One hundred and twenty-two patients were observed clinically and animal experiments were performed. The rapid bladder ultrasonography developer (RBUD-1, a preparation of Chinese herbal medicine) alone was used in Group 1, composite prescription of Western and Chinese medicine was used in group 2. The control groups were using lasix or mineral water.

RESULTS

Rapid diuresis and the decrease of the bladder capacity needed for development could be realized by Chinese medical herbs preparation, the difference between Group 1 and control group in developing time and bladder capacity were very significant. Results of animal experiments, which were referred to clinical grouping, showed the diuretic intensity of RBUD-1 within one hour was significantly higher than that in the other groups. Toxicological study showed the RBUD-1 was a non-toxic preparation.

CONCLUSION

RBUD-1 could effectively develop bladder and pelvic cavity, it would help to diagnose in time, on the other hand, it would also contribute for the combination imaging of Chinese and Western medicine.

Direct genotyping and prenatal diagnosis of beta-thalassemia in Chinese by polymerase chain reaction mediated restriction fragment length polymorphism method

The molecular basis of beta-thalassemia is predominantly point mutations in the beta-globin gene. Frameshift 41-42 (-CTTT), IVS-2 position 654 (C-->T) mutation, nonsense codon 17 (A-->T), TATA box position -28 (A-->G) mutation and frameshift 71-72 (+A) account for more than 95% of beta-thalassemia alleles in the population of South China. We have developed a polymerase chain reaction (PCR)-mediated restriction fragment length polymorphism (RFLP) method for the identification of these alleles. In this method, artificial mispairing bases in PCR-amplified products were created to distinguish normal from mutant alleles on the basis of RFLPs. The size of the five PCR-amplified DNA fragments that may potentially contain the above five types of mutations is 93 or 89 bp (codons 41-42), 221 bp (IVS-2 nt 654), 110 bp (codon 17), 123 bp (TATA box nt -28), and 97 or 98 bp (codons 71-72). After these fragments were digested with Hinc II, Mae III, Nhe I, EcoR I, and Dde I, respectively, the allele-specific RFLPs produced were analyzed by gel electrophoresis. DNA samples of 24 patients with the above five types of beta-thalassemia were investigated with the present method and allele-specific oligonucleotide (ASO) probing simultaneously. We used this method in the prenatal diagnosis of 14 Chinese families for beta-thalassemia. The results obtained by the present method correspond well with those by the ASO probe test.