TY - JOUR
T1 - Altered methylation pattern in EXOC4 is associated with stroke outcome
T2 - an epigenome-wide association study
AU - Cullell, Natalia
AU - Soriano-Tárraga, Carolina
AU - Gallego-Fábrega, Cristina
AU - Cárcel-Márquez, Jara
AU - Muiño, Elena
AU - Llucià-Carol, Laia
AU - Lledós, Miquel
AU - Esteller, Manel
AU - de Moura, Manuel Castro
AU - Montaner, Joan
AU - Rosell, Anna
AU - Delgado, Pilar
AU - Martí-Fábregas, Joan
AU - Krupinski, Jerzy
AU - Roquer, Jaume
AU - Jiménez-Conde, Jordi
AU - Fernández-Cadenas, Israel
N1 - Funding Information:
We thank the International Stroke Genetics Consortium, the Spanish Stroke Genetics Consortium, the International Stroke Genetics Consortium, the Global Alliance for Stroke acute and long-term outcome, RETICS Network INVICTUS (RD16/0019/0002, RD16/0019/0010, RD16/0019/0011, RD16/0019/0021) and the RICORDS Stroke network.
Funding Information:
EPIGENESIS project (Carlos III Institute/Fondo Europeo de Desarrollo Regional (FEDER)- PI17/02089, Marató TV3 and Fundació MútuaTerrassa), MAESTRO project (Carlos III Institute/FEDER—PI18/01338), iBioStroke project (Eranet-Neuron, European research grants), the EPINEXO project- PI20/00678 (Carlos III Institute/FEDER), SEDMAN Study (Boehringer Ingelheim), APHAS Study (Pfizer/Bristol Myers), Fondo Europeo de Desarrollo Regional (FEDER), 2017SGR-1427 (AGAUR), the RETICS Network INVICTUS + and the RICORDS Stroke network. J. Cárcel-Márquez is supported by an AGAUR Contract (agència de gestió d'ajuts universitaris i de recerca; FI_DGR 2019, grant number 2019_FI_B 00853) co-financed by Fons Social Europeu (FSE). I. Fernandez is the recipient of a research contract from the Miguel Servet Program (CP12/03298) from the Carlos III Institute. M. Lledós is supported by a PFIS Contract (Contratos Predoctorales de Formación en Investigación en Salud): FI19/00309 C. Gallego-Fabrega is supported by a Sara Borrell Contract (CD20/00043) from Instituto de Salud Carlos III and Fondo Europeo de Desarrollo Regional (ISCIII-FEDER). E. Muiño is supported by a Río Hortega Contract (CM18/00198) from the Instituto de Salud Carlos III.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/9/30
Y1 - 2022/9/30
N2 - Background and purpose: The neurological course after stroke is highly variable and is determined by demographic, clinical and genetic factors. However, other heritable factors such as epigenetic DNA methylation could play a role in neurological changes after stroke. Methods: We performed a three-stage epigenome-wide association study to evaluate DNA methylation associated with the difference between the National Institutes of Health Stroke Scale (NIHSS) at baseline and at discharge (ΔNIHSS) in ischaemic stroke patients. DNA methylation data in the Discovery (n = 643) and Replication (n = 62) Cohorts were interrogated with the 450 K and EPIC BeadChip. Nominal CpG sites from the Discovery (p value < 10–06) were also evaluated in a meta-analysis of the Discovery and Replication cohorts, using a random-fixed effect model. Metabolic pathway enrichment was calculated with methylGSA. We integrated the methylation data with 1305 plasma protein expression levels measured by SOMAscan in 46 subjects and measured RNA expression with RT-PCR in a subgroup of 13 subjects. Specific cell-type methylation was assessed using EpiDISH. Results: The meta-analysis revealed an epigenome-wide significant association in EXOC4 (p value = 8.4 × 10–08) and in MERTK (p value = 1.56 × 10–07). Only the methylation in EXOC4 was also associated in the Discovery and in the Replication Cohorts (p value = 1.14 × 10–06 and p value = 1.3 × 10–02, respectively). EXOC4 methylation negatively correlated with the long-term outcome (coefficient = − 4.91) and showed a tendency towards a decrease in EXOC4 expression (rho = − 0.469, p value = 0.091). Pathway enrichment from the meta-analysis revealed significant associations related to the endocytosis and deubiquitination processes. Seventy-nine plasma proteins were differentially expressed in association with EXOC4 methylation. Pathway analysis of these proteins showed an enrichment in natural killer (NK) cell activation. The cell-type methylation analysis in blood also revealed a differential methylation in NK cells. Conclusions: DNA methylation of EXOC4 is associated with a worse neurological course after stroke. The results indicate a potential modulation of pathways involving endocytosis and NK cells regulation.
AB - Background and purpose: The neurological course after stroke is highly variable and is determined by demographic, clinical and genetic factors. However, other heritable factors such as epigenetic DNA methylation could play a role in neurological changes after stroke. Methods: We performed a three-stage epigenome-wide association study to evaluate DNA methylation associated with the difference between the National Institutes of Health Stroke Scale (NIHSS) at baseline and at discharge (ΔNIHSS) in ischaemic stroke patients. DNA methylation data in the Discovery (n = 643) and Replication (n = 62) Cohorts were interrogated with the 450 K and EPIC BeadChip. Nominal CpG sites from the Discovery (p value < 10–06) were also evaluated in a meta-analysis of the Discovery and Replication cohorts, using a random-fixed effect model. Metabolic pathway enrichment was calculated with methylGSA. We integrated the methylation data with 1305 plasma protein expression levels measured by SOMAscan in 46 subjects and measured RNA expression with RT-PCR in a subgroup of 13 subjects. Specific cell-type methylation was assessed using EpiDISH. Results: The meta-analysis revealed an epigenome-wide significant association in EXOC4 (p value = 8.4 × 10–08) and in MERTK (p value = 1.56 × 10–07). Only the methylation in EXOC4 was also associated in the Discovery and in the Replication Cohorts (p value = 1.14 × 10–06 and p value = 1.3 × 10–02, respectively). EXOC4 methylation negatively correlated with the long-term outcome (coefficient = − 4.91) and showed a tendency towards a decrease in EXOC4 expression (rho = − 0.469, p value = 0.091). Pathway enrichment from the meta-analysis revealed significant associations related to the endocytosis and deubiquitination processes. Seventy-nine plasma proteins were differentially expressed in association with EXOC4 methylation. Pathway analysis of these proteins showed an enrichment in natural killer (NK) cell activation. The cell-type methylation analysis in blood also revealed a differential methylation in NK cells. Conclusions: DNA methylation of EXOC4 is associated with a worse neurological course after stroke. The results indicate a potential modulation of pathways involving endocytosis and NK cells regulation.
KW - Brain Ischemia/genetics
KW - CpG Islands
KW - DNA Methylation
KW - Epigenesis, Genetic
KW - Epigenome
KW - Genome-Wide Association Study
KW - Humans
KW - RNA
KW - Stroke/genetics
KW - c-Mer Tyrosine Kinase/genetics
UR - http://www.scopus.com/inward/record.url?scp=85139198125&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/65b876f9-4c7d-379a-b1b8-9818cad60b44/
U2 - 10.1186/s13148-022-01340-5
DO - 10.1186/s13148-022-01340-5
M3 - Article
C2 - 36180927
AN - SCOPUS:85139198125
SN - 1868-7075
VL - 14
JO - Clinical Epigenetics
JF - Clinical Epigenetics
IS - 1
M1 - 124
ER -