DNA Methylation Regulates Gene Expression in Intracranial Aneurysms

doi:10.1016/j.wneu.2017.04.064

World Neurosurgery

Volume 105, September 2017, Pages 28-36

https://doi.org/10.1016/j.wneu.2017.04.064 Get rights and content

Background

Different gene expression profiles are observed in intracranial aneurysm tissues. Understanding these genes and what regulates their expression will provide insight into the pathogenesis of intracranial aneurysms. We investigated whether differences in DNA methylation regulate gene expression in intracranial aneurysms.

Methods

We compared 20 intracranial aneurysm tissue specimens with 20 matched specimens from the superficial temporal artery as controls. We identified the gene expression profiles in these samples using the GeneChip Human U133 Plus 2.0 array and evaluated DNA methylation modifications using the Infinium HumanMethylation450 BeadChip Kit.

Results

A total of 11,022 differentially methylated sites between aneurysm tissues and matched control tissues were identified, and 2142 differentially expressed gene transcripts were detected based on the 2 gene expression profiles. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses and verification analysis showed that the MYH11, LIFR, and TLR4 genes were associated with the occurrence and development of intracranial aneurysms. These genes mainly encode cell adhesion molecules or are involved in the NF-κB, JAK-STAT, and ERK/JNK signaling pathways.

Conclusions

In the development of intracranial aneurysms, DNA methylation plays an important role in the regulation of genetic expression involved in immune and inflammatory reactions, cell function, cell maintenance, and cell signal transduction.

Introduction

Intracranial aneurysmal subarachnoid hemorrhage is associated with high mortality and morbidity.¹ The risk factors for intracranial aneurysms include genetic factors, smoking, drinking, aging, female sex, hypertension, drug abuse, and use of medications that can lead to arteriosclerosis and hypertension,² of which genetic factors are the most important. These factors can lead to changes in hemodynamics, artery structure, inflammation, and autoimmune function, all of which are linked to the occurrence of intracranial aneurysms.3, 4, 5, 6 Many single nucleotide polymorphisms that participate in the formation and development of sporadic intracranial aneurysms have been identified7, 8, 9, 10; however, identification of pathogenic genes is difficult owing to regional and ethnic differences. Therefore, understanding gene expression and regulatory factors in intracranial aneurysm remains crucial for understanding its pathogenesis.

Previous research has confirmed that the expression patterns of genes involved in inflammatory reactions, extracellular matrix components, extracellular matrix renewal, cell adhesion and antiadhesion, cytokinesis, and cell migration are different in intracranial aneurysm tissue compared to controls.11, 12, 13, 14 In previous work, we compared the gene expression profiles in 15 intracranial aneurysm tissues with 17 superficial temporal artery tissue samples and found significant differences in genes involved in immune and inflammatory reactions, cell migration, cell function and maintenance, signal transduction and interaction, cell growth and proliferation, cell development, immune cell trafficking, development and function of the hematologic system, organization morphology, humoral immune response, and cardiovascular system development.¹⁵ These gene expression abnormalities may be caused by environmental factors.

Environmental factors can change DNA methylation levels, affecting DNA conformation, stability, and ability to interact with proteins. Given that DNA methylation is a common epigenetic modification and an important regulator of gene expression, we aimed to investigate whether gene methylation modification affects the gene expression profiles in intracranial aneurysms.¹⁶ We used microarrays to compare the methylation levels and gene expression profiles in tissue samples from intracranial aneurysms with matched tissue samples from the superficial temporal artery, and evaluated methylation modification as a potential mechanism for the observed gene expression changes in intracranial aneurysms.

Section snippets

Patients

All experiments performed in this study were reviewed and approved in advance by the Ethics Committee of the Beijing Tiantan Hospital, which is affiliated with Capital Medical University. All subjects provided written consent for participation in this study.

The study cohort comprised 20 patients with intracranial aneurysms who underwent intracranial aneurysm clip resection at Beijing Tiantan Hospital between March 2013 and June 2014. The inclusion criteria were Han ethnicity and a diagnosis of

Patients' Clinical Information and Methylation Detection

We collected 20 intracranial aneurysm tissue specimens and 20 matched specimens from the superficial temporal artery, including 13 unruptured aneurysms and 7 ruptured aneurysms, from 8 male and 12 female patients (male:female ratio, 1:1.5). The patients ranged in age from 6 to 69 years, with an average age of 50.89 ± 9.29 years (males, 42.25 ± 13.18 years; females, 55.92 ± 4.43 years). Two aneurysms were located in the right anterior communicating artery, 3 were in the left internal carotid

Discussion

To better understand the pathophysiological processes of intracranial aneurysms, we detected the DNA methylation levels and gene expression profiles in intracranial aneurysm tissue compared with matched superficial temporal artery tissue using microarrays. Because the intracranial aneurysm and superficial temporal artery tissues were obtained from the same individual, the genome was identical in the paired samples; however, we observed differences in the gene methylation and expression

Conclusion

DNA methylation is an important regulatory mechanism leading to differential gene expression in intracranial aneurysms. Our findings indicate that the gene expression is regulated by methylation modification, and has vital roles in the development of intracranial aneurysms through the signaling pathway. Intracranial aneurysm tissue showed a distinct DNA methylation and gene expression pattern compared with control tissue, especially for genes involved in immune and inflammatory reactions, cell

Acknowledgments

We thank all of the participants for their support of this research.

References (23)

B.V. Nahed et al.
Mapping a Mendelian form of intracranial aneurysm to 1p34.3-p36.13
Am J Hum Genet
(2005)
B. Krischek et al.
Network-based gene expression analysis of intracranial aneurysm tissue reveals role of antigen presenting cells
Neuroscience
(2008)
S. Xu et al.
LIFRα-CT3 induces differentiation of a human acute myelogenous leukemia cell line HL-60 by suppressing miR-155 expression through the JAK/STAT pathway
Leuk Res
(2014)
M. Renard et al.
Novel MYH11 and ACTA2 mutations reveal a role for enhanced TGFβ signaling in FTAAD
Int J Cardiol
(2013)
D.G. Peters et al.
Molecular anatomy of an intracranial aneurysm: coordinated expression of genes involved in wound healing and tissue remodeling
Stroke
(2001)
M. Clarke
Systematic review of reviews of risk factors for intracranial aneurysms
Neuroradiology
(2008)
Y.M. Ruigrok et al.
Genome-wide linkage in a large Dutch family with intracranial aneurysms: replication of two loci for intracranial aneurysms to chromosome 1p36.11-p36.13 and Xp22.2-p22.32
Stroke
(2008)
Y.B. Roos et al.
Genome-wide linkage in a large Dutch consanguineous family maps a locus for intracranial aneurysms to chromosome 2p13
Stroke
(2004)
T. Santiago-Sim et al.
Genomewide linkage in a large Caucasian family maps a new locus for intracranial aneurysms to chromosome 13q
Stroke
(2009)
S.K. Low et al.
Genome-wide association study for intracranial aneurysm in the Japanese population identifies three candidate susceptible loci and a functional genetic variant at EDNRA
Hum Mol Genet
(2012)

W. Osman et al.

A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma

Hum Mol Genet

(2012)

Cited by (29)

Impinging Flow Induces Expression of Monocyte Chemoattractant Protein-1 in Endothelial Cells Through Activation of the c-Jun N-terminal Kinase/c-Jun/p38/c-Fos Pathway
2022, World Neurosurgery
Citation Excerpt :
A comparison of genes that were differentially expressed in IA and normal superficial temporal artery tissues revealed that the ERK pathway might play an important role in IA formation and development. Thus, the possible involvement of ERK in the regulation of endothelial dysfunction (via other biological pathways) requires further study.58 Flow impingement regulates the inflammatory response of HUVECs by activating JNK and p38, which may be involved in the formation and development of IA by regulating endothelial dysfunction.
Monocyte chemoattractant protein-1 (MCP-1) is an important regulator of the formation and development of intracranial aneurysms. This study explored the molecular mechanisms underlying the induction of MCP-1 and related inflammatory factors in human umbilical vein endothelial cells (HUVECs) under hemodynamic conditions.
A modified T chamber was used to simulate fluid flow at the bifurcation of the artery and wall shear stress on HUVECs in vitro. Changes in HUVECs were analyzed in response to impinging flow. And HUVECs without impinging flow were used as the control group. Protein expression levels of extracellular signal–regulated kinase (ERK), c-Jun N-terminal kinase (JNK), p38, activator protein-1, and MCP-1 were detected by Western blot, and the messenger RNA expression levels of MCP-1, interleukin (IL)-1β, and IL-6 were determined by quantitative reverse transcription polymerase chain reaction.
Under impinging flow, the phosphorylation levels of ERK, JNK, and p38, as well as the protein levels of MCP-1, c-Jun, and c-Fos, increased. The messenger RNA expression of MCP-1, IL-1β, and IL-6 also increased in HUVECs. Pretreatment of the HUVECs with inhibitors of JNK and p38 significantly attenuated the increased expression of MCP-1, IL-1β, and IL-6, while ERK inhibitors had no obvious effect.
Under impinging flow, MCP-1 and inflammatory factors are regulated through the JNK/c-Jun/p38/c-Fos pathway and participate in EC inflammation.
Correlation Between Altered DNA Methylation of Intergenic Regions of ITPR3 and Development of Delayed Cerebral Ischemia in Patients with Subarachnoid Hemorrhage
2019, World Neurosurgery
Citation Excerpt :
Accordingly, hypermethylation of the IGR located upstream of ITPR3 can be involved in DCI development, and not the age-related DNA methylation change. Yu et al.36 investigated the difference in DNA methylation gene expression between intracranial aneurysm wall tissues and control specimens from the superficial temporal arteries. Several CpG sites of such genes as MYH11, LIFR, and TLR4 were related to aneurysm development.
Delayed cerebral ischemia (DCI) is related to the major causes of morbidity and mortality in patients following subarachnoid hemorrhage (SAH); however, little is known about the role of epigenetics in the pathogenesis of DCI. We investigated the specific DNA methylation profile that may affect the expression of inositol 1-,4-,5-trisphosphate receptor (ITPR3) responsible for cerebral vasospasm following SAH.
We prospectively studied patients with SAH between March 2015 and October 2018. The degree of methylation in the distal intergenic region (IGR) located on ITPR3 and gene expression were measured using methylation-specific polymerase chain reaction (MSP) and quantitative real-time polymerase chain reaction (qPCR). To investigate the regulatory mechanims of DNA hypermethylation, we further analyzed the mRNA expression of DNA methyltransferase (DNMT1) and ten-eleven translocation enzymes (TET1, TET2, and TET3).
A total of 42 patients were included in our analysis. Patients with SAH and DCI had significantly higher levels of methylation intensity of distal IGR upstream of ITPR3 than those without DCI (median, 0.941 [interquartile range (IQR), 0.857–0.984] versus (0.670 [IQR, 0.543–0.761]; P < 0.001). In addition, patients with DCI showed decreased mRNA expression of ITPR3 compared with patients without DCI (median, 0.039 [IQR, 0.030–0.045] vs. 0.047 [IQR, 0.038–0.064]; P = 0.0328). Patients with DCI had higher DNMT1 expression (P < 0.001) and lower TET1 expression (P = 0.040) than those without DCI; however, differences in TET2 and TET3 levels between the 2 groups were not statistically significant.
Hypermethylation of the distal IGR located upstream of ITPR3 is related to greater DCI development in patients with SAH. Further studies of the precise mechanisms of methylation degree and DCI development using in vitro and in vivo models are needed.
Genetics of intracranial aneurysm
2019, Bulletin de l'Academie Nationale de Medecine
Les anévrismes intracrâniens (AIC) se définissent par une hernie acquise de la paroi artérielle survenant préférentiellement à une bifurcation artérielle avec une prédilection topographique caractéristique au niveau des vaisseaux de la base du crâne. La détection fortuite en scanner ou IRM d’un AIC est une situation fréquente, ces examens étant de plus en plus pratiqués. Les facteurs de risque modifiables de rupture d’AIC sont bien définis, et les antécédents familiaux d’AIC constituent le principal facteur de risque pour la présence d’AIC. De nombreuses affections héréditaires sont associées à la formation d’AIC, mais ces syndromes représentent moins de 1 % de l’ensemble des AIC. Aucun test diagnostique basé sur la génétique n’est actuellement disponible pour identifier les mutations et les patients qui présentent un risque plus élevé de développer des AIC. La détection de ces mutations permettrait une meilleure compréhension des voies moléculaires impliquées dans la formation et la rupture des AIC ainsi que le développement de thérapies ciblées.
Intracranial Aneurysms (IA) are defined by an acquired hernia of the arterial wall arising mainly on arterial bifurcations. There is a characteristic topographical predilection for the vessels of the skull base. Detection of an IA is a common finding in MRI practice. Nowadays, the incidence of unruptured IA seems to be increasing with the continuous evolution of imaging techniques. Important modifiable risk factors for SAH are well defined, but familial history of IA is the best risk marker for the presence of IA. Numerous heritable conditions are associated with IA formation but these syndromes account for less than 1% of all IAs in the population. No reliable diagnostic genetic test is currently available to identify theses mutations and patients who are at higher risk for developing IAs. In the longer term, a more comprehensive understanding of independent and interdependent molecular pathways germane to IA formation and rupture may guide the physician in developing targeted therapies and optimizing prognostic risk assessment.
Advancing stroke genomic research in the age of Trans-Omics big data science: Emerging priorities and opportunities
2017, Journal of the Neurological Sciences
Citation Excerpt :
For instance, transcriptome study observed that genes regulated in large-vessel atherosclerotic stroke are expressed in platelets and monocytes and modulate hemostasis while genes regulated in cardioembolic stroke are expressed in neutrophils and modulate immune responses to infectious-like stimuli [70]. In the development of intracranial aneurysms, genomic DNA methylation has been found to play an important role in the genetic expression regulation involved in immune and inflammatory reactions, cell function, cell maintenance, and cell signal transduction [71]. In ischemic stroke patients, CDKN2B methylation in peripheral blood leukocytes was found to be associated with carotid artery calcification [72].
We systematically reviewed the genetic variants associated with stroke in genome-wide association studies (GWAS) and examined the emerging priorities and opportunities for rapidly advancing stroke research in the era of Trans-Omics science.
Using the PRISMA guideline, we searched PubMed and NHGRI- EBI GWAS catalog for stroke studies from 2007 till May 2017.
We included 31 studies. The major challenge is that the few validated variants could not account for the full genetic risk of stroke and have not been translated for clinical use. None of the studies included continental Africans. Genomic study of stroke among Africans presents a unique opportunity for the discovery, validation, functional annotation, Trans-Omics study and translation of genomic determinants of stroke with implications for global populations. This is because all humans originated from Africa, a continent with a unique genomic architecture and a distinctive epidemiology of stroke; as well as substantially higher heritability and resolution of fine mapping of stroke genes.
Understanding the genomic determinants of stroke and the corresponding molecular mechanisms will revolutionize the development of a new set of precise biomarkers for stroke prediction, diagnosis and prognostic estimates as well as personalized interventions for reducing the global burden of stroke.
Influence of DNA Methylation on Vascular Smooth Muscle Cell Phenotypic Switching
2024, International Journal of Molecular Sciences
The Role of Epigenetics in Brain Aneurysm and Subarachnoid Hemorrhage: A Comprehensive Review
2024, International Journal of Molecular Sciences

View all citing articles on Scopus

: Conflict of interest statement: This work was supported by Research on the Genetics and Pathogenesis of Intracranial Aneurysm and Arteriovenous Malformation, a cooperative project of the Science and Technology Ministry of China and the National Research Council of Canada (2010DFB30850) and by the National Key Technology Research and Development Program of the Ministry of Science and Technology of China (2015BAI12B04). The authors declare that the article content was composed in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

View full text

Original ArticleDNA Methylation Regulates Gene Expression in Intracranial Aneurysms

Background

Methods

Results

Conclusions

Introduction

Section snippets

Patients

Patients' Clinical Information and Methylation Detection

Discussion

Conclusion

Acknowledgments

Am J Hum Genet

Neuroscience

Leuk Res

Int J Cardiol

Molecular anatomy of an intracranial aneurysm: coordinated expression of genes involved in wound healing and tissue remodeling

Stroke

Systematic review of reviews of risk factors for intracranial aneurysms

Neuroradiology

Genome-wide linkage in a large Dutch family with intracranial aneurysms: replication of two loci for intracranial aneurysms to chromosome 1p36.11-p36.13 and Xp22.2-p22.32

Stroke

Genome-wide linkage in a large Dutch consanguineous family maps a locus for intracranial aneurysms to chromosome 2p13

Stroke

Genomewide linkage in a large Caucasian family maps a new locus for intracranial aneurysms to chromosome 13q

Stroke

Genome-wide association study for intracranial aneurysm in the Japanese population identifies three candidate susceptible loci and a functional genetic variant at EDNRA

Hum Mol Genet

A genome-wide association study in the Japanese population confirms 9p21 and 14q23 as susceptibility loci for primary open angle glaucoma

Hum Mol Genet

Original Article
DNA Methylation Regulates Gene Expression in Intracranial Aneurysms