A targeted sequencing approach to find novel pathogenic genes associated with sporadic aortic dissection

Relationship Between RNF213 p.R4810K and Echocardiographic Findings in Patients with Cerebrovascular Diseases: A Multicenter Prospective Cohort Study

BACKGROUND

RING finger protein 213 (RNF213) p.R4810K is an established risk factor for moyamoya disease and intracranial artery stenosis in East Asian people. Recent evidence suggests its potential association with extracranial cardiovascular diseases, including pulmonary hypertension. We hypothesized that insidious abnormal cardiac functions are detected in RNF213 p.R4810K carriers with cerebrovascular diseases.

METHODS AND RESULTS

We investigated patients registered in the National Cerebral and Cardiovascular Center Genome Registry between May 2017 and August 2021 who underwent echocardiography. All patients had cerebrovascular diseases. Patients with a medical history of chronic heart or pulmonary diseases were excluded. RNF213 p.R4810K was genotyped in all the patients. Of 2089 patients registered in the registry, 71 carriers and 1241 noncarriers were eligible for our analyses. The carriage of RNF213 p.R4810K emerged as a significant predictor for longer right ventricular outflow tract acceleration time in multivariable linear regression analysis (β=8.33 [95% CI, 0.92-15.74]; P=0.028). Additionally, the carriers showed increased odds of having right ventricular outflow tract acceleration time values ≥150 milliseconds (odds ratio, 2.22 [95% CI, 1.18-4.18]; P=0.014) in multivariable logistic regression analysis.

CONCLUSIONS

A longer right ventricular outflow tract acceleration time may reflect an increased pulmonary vascular bed induced by abnormal vascular collateral networks and dilation of capillary vessels in peripheral pulmonary arteries in the preclinical stage of RNF213-related pulmonary hypertension. Thus, the right ventricular outflow tract acceleration time marker in RNF213 p.R4810K carriers suggests a biphasic course from the presymptomatic to symptomatic phase. Furthermore, vascular neurologists should carefully examine multiple organs because RNF213-related vasculopathy covers systemic cardiovascular diseases.

REGISTRATION

URL: https://www.umin.ac.jp; Unique identifier: UMIN000050750.

Exploring RNF213 in Ischemic Stroke and Moyamoya Disease: From Cellular Models to Clinical Insights

Advances in stroke genetics have highlighted the critical role of rare genetic variants in cerebrovascular diseases, with RNF213 emerging as a key player in ischemic stroke and Moyamoya disease (MMD). Initially identified as the primary susceptibility gene for MMD, RNF213-notably the p.R4810K variant-has been strongly linked to intracranial artery stenosis (ICAS) and various ischemic stroke subtypes, particularly in East Asian populations. This gene encodes an E3 ubiquitin ligase with diverse roles in angiogenesis, vascular remodeling, lipid metabolism, and cerebral blood flow regulation, yet its exact mechanisms in cerebrovascular pathology remain incompletely understood. This review synthesizes findings from genetic studies, as well as cellular and animal models, to provide a holistic understanding of RNF213's involvement in cerebrovascular diseases. Key mechanisms by which RNF213 variants contribute to disease pathogenesis are explored, alongside discussions on their clinical utility as biomarkers and therapeutic targets. Additionally, we address the gene's implications for disease prediction, risk assessment, and cascade screening. By integrating evidence across disciplines, this review identifies critical knowledge gaps, including the biological pathways underlying RNF213's pathogenicity. These insights lay the groundwork for future research and underscore the potential of RNF213 in driving personalized approaches to cerebrovascular disease management.

Downregulation of LILRB4 Promotes Human Aortic Smooth Muscle Cell Contractile Phenotypic Switch and Apoptosis in Aortic Dissection

Aortic dissection (AD) is a severe vascular disease with high rates of mortality and morbidity. However, the underlying molecular mechanisms of AD remain unclear. Differentially expressed genes (DEGs) were screened by bioinformatics methods. Alterations of histopathology and inflammatory factor levels in β-aminopropionitrile (BAPN)-induced AD mouse model were evaluated through Hematoxylin-Eosin (HE) staining and Enzyme-linked immunosorbent assay (ELISA), respectively. Reverse transcription quantitative real-time polymerase chain reaction was performed to detect DEGs expression. Furthermore, the role of LILRB4 in AD was investigated through Cell Counting Kit-8 (CCK-8), wound healing, and flow cytometry. Western blotting was employed to assess the phenotypic switch and extracellular matrix (ECM)-associated protein expressions in platelet-derived growth factor-BB (PDGF-BB)-stimulated in vitro model of AD. In the AD mouse model, distinct dissection formation was observed. TNF-α, IL-1β, IL-8, and IL-6 levels were higher in the AD mouse model than in the controls. Six hub genes were identified, including LILRB4, TIMP1, CCR5, CCL7, MSR1, and CLEC4D, all of which were highly expressed. Further exploration revealed that LILRB4 knockdown inhibited the cell vitality and migration of PDGF-BB-induced HASMCs while promoting apoptosis and G0/G1 phase ratio. More importantly, LILRB4 knockdown promoted the protein expression of α-SMA and SM22α, while decreasing the expression of Co1, MMP2, and CTGF, which suggested that LILRB4 silencing promoted contractile phenotypic transition and ECM stability. LILRB4 knockdown inhibits the progression of AD. Our study provides a new potential target for the clinical treatment of AD.

A harmful MYH11 variant detected in a family with thoracic aortic dissection and patent ductus arteriosus

Thoracic aortic dissection (TAD) is an important cause of sudden cardiac death and is characterized by high morbidity, mortality, and a poor prognosis. Patent ductus arteriosus (PDA) is a common congenital heart disease. The pathogenesis of both TAD and PDA has been reported to be related to genetic factors. The MYH11 gene, which encodes myosin heavy chain 11, has been reported in individuals with both TAD and PDA. Herein, we first detected a harmful MYH11 missense variant (c. T3728C, p. L1243P) in a TAD and PDA family. This missense variant co-segregated with the TAD/PDA phenotype in this family of four individuals, providing evidence of its harmfulness. Histopathological examinations revealed the presence of fragmented, broken, and lessened elastic fibers and the deposition of proteoglycans in the median of aortic dissection. Moreover, the immunofluorescence results showed that the labeled MYH11 protein in the tissue of the aortic dissection was weaker than that in the normal aorta. We present this familial case to stress the necessity of postmortem genetic testing in such cases among forensic practices. Identifying those culprit gene variants can direct effective genetic counseling and personalized health management in family members (especially first-degree relatives) with high-risk genotypes.

Genetic architecture of thoracic aortic dissection in the female population

BACKGROUND

Sex-related differences in cardiovascular disease are now gaining much more attention and their importance is increasingly being recognized, but little is known about the genetic distribution, genotype-phenotype correlation, and outcomes in the female population with thoracic aortic dissection (TAD).

METHODS

One hundred seventy-nine Chinese female probands with TAD were enrolled from Tongji Hospital between October 2009 and October 2020. Genetic analysis was performed among 12 genes, and participants were subsequently followed up for a median of 38.2 months for TAD-related death.

RESULTS

We identified 18 pathogenic or likely pathogenic variants among 18 (10.1%) probands and 21 variants of uncertain significance in 21 (11.7%) patients. Individuals with positive variants presented with a significant risk of TAD (OR: 12.0, 95% CI: 5.87-26.8), and an association between FBN1 (p = 2.60E-11, OR = 19.8), MYLK (p = 0.006, OR = 14.0) variants and an increased risk for female TAD was identified as well. Furthermore, nearly half of the variants were found in the FBN1 gene, which was significantly linked to early aortic dissection and tended to cause death at a young age.

CONCLUSION

This study revealed the monogenic contribution of known TAD genes to the female TAD population with East Asian ancestry. Patients who tested positive for FBN1 were significantly younger at the time of aortic dissection and had a higher probability of dying at an early age.

RNF213-Associated Vascular Disease: A Concept Unifying Various Vasculopathies

The ring finger protein 213 gene (RNF213) encodes a 590 kDa protein that is thought to be involved in angiogenesis. This gene was first recognized as a vasculopathy-susceptibility locus through genome-wide association studies undertaken in a Japanese population, demonstrating that heterozygotes for RNF213 p.Arg4810Lys (c.14429G>A, rs112735431) had a greatly increased risk of moyamoya disease. The association of RNF213 p.Arg4810Lys as a susceptibility variant of moyamoya disease was reproduced in Korean and Chinese individuals and, later, in Caucasians. Variants of the RNF213 gene have been linked to a number of vascular diseases such as moyamoya disease, intracranial major artery stenosis, pulmonary arterial hypertension, and peripheral pulmonary artery stenosis, and have also been associated with co-occurrent diseases and vascular disease in different organs. Based on the findings that we have reported to date, our paper proposes a new concept of “RNF213-associated vascular disease” to unify these conditions with the aim of capturing patients with multiple diseases but with a common genetic background. This concept will be highly desirable for clarifying all of the diseases in the RNF213-associated vascular disease category by means of global epidemiological investigations because of the possibility of such diseases appearing asymptomatically in some patients.

Comparative analysis of aneurysm subtypes associated genes based on protein-protein interaction network

The arterial aneurysm refers to localized dilation of blood vessel wall and is common in general population. The majority of aneurysm cases remains asymptomatic until a sudden rupture which is usually fatal and of extremely high mortality (~ 50-60%). Therefore, early diagnosis, prevention and management of aneurysm are in urgent need. Unfortunately, current understanding of disease driver genes of various aneurysm subtypes is still limited, and without appropriate biomarkers and drug targets no specialized drug has been developed for aneurysm treatment. In this research, aneurysm subtypes were analyzed based on protein-protein interaction network to better understand aneurysm pathogenesis. By measuring network-based proximity of aneurysm subtypes, we identified a relevant closest relationship between aortic aneurysm and aortic dissection. An improved random walk method was performed to prioritize candidate driver genes of each aneurysm subtype. Thereafter, transcriptomes of 6 human aneurysm subtypes were collected and differential expression genes were identified to further filter potential driver genes. Functional enrichment of above driver genes indicated a general role of ubiquitination and programmed cell death in aneurysm pathogenesis. Especially, we further observed participation of BCL-2-mediated apoptosis pathway and caspase-1 related pyroptosis in the development of cerebral aneurysm and aneurysmal subarachnoid hemorrhage in corresponding transcriptomes.

Identification of COL3A1 variants associated with sporadic thoracic aortic dissection: a case-control study

Thoracic aortic dissection (TAD) without familial clustering or syndromic features is known as sporadic TAD (STAD). So far, the genetic basis of STAD remains unknown. Whole exome sequencing was performed in 223 STAD patients and 414 healthy controls from the Chinese Han population (N = 637). After population structure and genetic relationship and ancestry analyses, we used the optimal sequence kernel association test to identify the candidate genes or variants of STAD. We found that COL3A1 was significantly relevant to STAD (P = 7.35 × 10^-6) after 10 000 times permutation test (P = 2.49 × 10^-3). Moreover, another independent cohort, including 423 cases and 734 non-STAD subjects (N = 1157), replicated our results (P = 0.021). Further bioinformatics analysis showed that COL3A1 was highly expressed in dissected aortic tissues, and its expression was related to the extracellular matrix (ECM) pathway. Our study identified a profile of known heritable TAD genes in the Chinese STAD population and found that COL3A1 could increase the risk of STAD through the ECM pathway. We wanted to expand the knowledge of the genetic basis and pathology of STAD, which may further help in providing better genetic counseling to the patients.

COL5A1 Variants Cause Aortic Dissection by Activating TGF-β-Signaling Pathway

Background

Aortic dissection (AD) is one of the most life‐threatening cardiovascular diseases that exhibit high genetic heterogeneity. However, it is unclear whether variants within the COL5A1 gene can cause AD. Therefore, we intend to determine whether COL5A1 is a causative gene of AD.

Methods and Results

We performed targeted sequencing in 702 patients with unrelated sporadic AD and 163 matched healthy controls using a predesigned panel with 152 vessel matrix‐related genes. As a result, we identified that 11 variants in COL5A1 caused AD in 11 out of the 702 patients with AD. Furthermore, Col5a1 knockout (Col5a1^+/−) rats were generated through the CRISPR/Cas9 system. Although there was no spontaneous AD, electron microscopy revealed a fracture of elastic fibers and disarray of collagenous fibers in 6‐week‐old Col5a1^+/− rats, but not in WT rats (93.3% versus 0.0%, P<0.001). Three‐week‐old rats were used to induce the AD phenotype with β‐aminopropionitrile monofumarate for 4 weeks followed by angiotensin II for 72 hours. The β‐aminopropionitrile monofumarate and angiotensin II‐treated rat model confirmed that Col5a1^+/− rats had considerably higher AD incidence than WT rats. Subsequent mechanism analyses demonstrated that the transforming growth factor‐β‐signaling pathway was significantly activated in Col5a1^+/− rats.

Conclusions

Our findings, for the first time, revealed a relationship between variants in COL5A1 and AD via targeted sequencing in 1.57% patients with sporadic aortic dissection. The Col5a1 knockout rats exhibited AD after an intervention, indicating that COL5A1 is a causative gene of AD. Activation of the transforming growth factor‐β‐signaling pathway may be implicated in the pathogenesis of this kind of AD.

[Gene mutation analysis of 19 Uighur families with aortic disease in Kashgar, China]

OBJECTIVE

To explore genetic mutation types and their correlation with clinical phenotypes in Uighur patients with aortic disease in Kashgar (Xinjiang Uighur Autonomous Region, China).

METHODS

We examined 37 pathogenic genes in 19 Uighur families with aortic diseases including Marfan syndrome from Kashgar using next generation sequencing, and the results were confirmed by Sanger sequence in the first relatives.

RESULTS

This study included 19 families with aortic diseases, in whom a total of 23 variants were identified, and 11 (57.89%) probands had one or more variants. Among them, definite pathogenic mutation was detected in one patient (5.26%), variants of uncertain significance (VUS) were found in 8 (42.11%), and benign/likely benign variants were detected in 7 (36.84%). The 23 variants identified included one (5.26%) pathogenic variant, 14 (60.87%) VUS, and 8 (34.78%) benign/likely benign variants. The 14 VUS were analyzed by prediction with SIFT and Polyphen2 HDIV, which identified 6 (42.86%) variants as deleterious/possibly damaging; all the 8 benign/likely benign variants were predicted to be deleterious/possibly damaging.

CONCLUSIONS

We detected 23 genetic variants in the 19 Uighur families with aortic diseases, and 22 of these variants remain to be verified by more patient data in future studies.

Sequencing barcode construction and identification methods based on block error-correction codes

Multiplexed sequencing relies on specific sample labels, the barcodes, to tag DNA fragments belonging to different samples and to separate the output of the sequencers. However, the barcodes are often corrupted by insertion, deletion and substitution errors introduced during sequencing, which may lead to sample misassignment. In this paper, we propose a barcode construction method, which combines a block error-correction code with a predetermined pseudorandom sequence to generate a base sequence for labeling different samples. Furthermore, to identify the corrupted barcodes for assigning reads to their respective samples, we present a soft decision identification method that consists of inner decoding and outer decoding. The inner decoder establishes the hidden Markov model (HMM) for base insertion/deletion estimation with the pseudorandom sequence, and adapts the forward-backward (FB) algorithm to output the soft information of each bit in the block code. The outer decoder performs soft decision decoding using the soft information to effectively correct multiple errors in the barcodes. Simulation results show that the proposed methods are highly robust to high error rates of insertions, deletions and substitutions in the barcodes. In addition, compared with the inner decoding algorithm of the barcodes based on watermarks, the proposed inner decoding algorithm can greatly reduce the decoding complexity.

Exploring the genetic pathogenicity of aortic dissection from 72 Han Chinese individuals using next-generation sequencing

Aortic dissection (AD) is a heterogeneous genetic disease with high morbidity and mortality. Although many genes predispose patients to AD, the pathogenic spectrum remains incomplete. This study aims to (a) investigate whether genotype differences exist between Stanford A and B AD individuals, and (b) broaden the pathogenic genetic spectrum of AD and reported novel variants of AD-associated genes. The DNA of 72 unrelated Han Chinese individuals with AD was tested by whole-exome sequencing. Of 142 AD-associated genes, 10 pathogenic variants, and 48 likely pathogenic variants in 36 genes were identified among 39 cases. The diagnostic yield was 54.2%. Of the 58 positive variants, 27 were novel. FBN1 was the most frequently positive gene in both Stanford A and Stanford B. Twenty-seven positive variants from 18 COL family genes were distributed in 36.8% of Stanford A and 6.7% of Stanford B cases. We emphasize that positive variants of COL family genes show distribution predominance and strong pathogenicity in Stanford A, while positive variants of smooth muscle cell pathway genes present distribution advantages mainly in Stanford B cases. Our findings provide a new perspective for both the pathogenic mechanism and the treatment of AD.

Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data

Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.

FBN1 gene mutations in 26 Hungarian patients with suspected Marfan syndrome or related fibrillinopathies

Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder mainly affecting the cardiovascular, ocular and musculo-skeletal systems. FBN1 gene mutations lead to MFS and related connective tissue disorders. In this work we described clinical and molecular data of 26 unrelated individuals with suspected MFS who were referred for FBN1 mutation analysis. FBN1 gene sequencing was performed by next generation sequencing and Sanger sequencing methods. We identified 23 causal or potentially causal (including variants of uncertain significance) FBN1 variants, seven of them was novel (˜30%). About 30% of the cases were sporadic. FBN1 mutations were associated with MFS in the majority of the patients, in two cases with severe and early onset manifestation of the syndrome. Missense mutations were detected in 69.6% (16/23), the majority of them were located in one of the cbEGF motifs and ˜70% of them substituted conserved cystein residues. Small deletions/duplications were identified in 13% of the cases (3/23), while splice site variants were detected in 17.4% (4/23). In three unrelated patients a low frequency recurrent silent variant (c.3294C > T (p.Asp1098=) was identified. FBN1 mRNA analysis showed that the mutation does not lead to aberrant splicing, based on available data the mutation was classified as benign.