Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients

Sunjay Jude Fernandes; Matilda Ericsson; Mohsen Khademi; Maja Jagodic; Tomas Olsson; David Gomez-Cabrero; Ingrid Kockum; Jesper Tegner

doi:10.2217/epi-2021-0205

Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients

Sunjay Jude Fernandes, Matilda Ericsson, Mohsen Khademi, Maja Jagodic, Tomas Olsson, David Gomez-Cabrero, Ingrid Kockum, Jesper Tegner

Research output: Contribution to journal › Article › peer-review

4 Scopus citations

Abstract

Background: The putative involvement of chromatin states in multiple sclerosis (MS) is thus far unclear. Here we determined the association of chromatin-accessibility with concurrent genetic, epigenetic and transcriptional events. Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-seq profiles from sorted blood immune CD4$^{+}$ and CD8$^{+}$ T cells, CD14$^{+}$ monocytes and CD19$^{+}$ B cells from healthy controls (HCs) and MS patients. Results: We identified differentially accessible regions between MS and HCs, primarily in CD4$^{+}$ and CD19$^{+}$. CD4$^{+}$ regions were enriched for MS-associated single nucleotide polymorphisms and differentially methylated loci. In the vicinity of differentially accessible regions of CD4$^{+}$ cells, 42 differentially expressed genes were identified. The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1. Conclusion: These findings provide new insight into the primary role of CD4$^{+}$ and CD19$^{+}$ cells in MS.

Original language	English (US)
Journal	Epigenomics
DOIs	https://doi.org/10.2217/epi-2021-0205
State	Published - Oct 22 2021

Bibliographical note

KAUST Repository Item: Exported on 2021-10-25
Acknowledgements: The authors thank all the multiple sclerosis patients who have been willing to take part in this study. The authors also thank the healthy donors for contributing their blood to this study. The authors acknowledge P Noori for the extraction of RNA from sorted cells.

ASJC Scopus subject areas

Genetics
Cancer Research

UN SDGs

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10.2217/epi-2021-0205

Cite this

@article{b7e21800dbdf460791bb4f2db94376d7,

title = "Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients",

abstract = "Background: The putative involvement of chromatin states in multiple sclerosis (MS) is thus far unclear. Here we determined the association of chromatin-accessibility with concurrent genetic, epigenetic and transcriptional events. Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-seq profiles from sorted blood immune CD4$^{+}$ and CD8$^{+}$ T cells, CD14$^{+}$ monocytes and CD19$^{+}$ B cells from healthy controls (HCs) and MS patients. Results: We identified differentially accessible regions between MS and HCs, primarily in CD4$^{+}$ and CD19$^{+}$. CD4$^{+}$ regions were enriched for MS-associated single nucleotide polymorphisms and differentially methylated loci. In the vicinity of differentially accessible regions of CD4$^{+}$ cells, 42 differentially expressed genes were identified. The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1. Conclusion: These findings provide new insight into the primary role of CD4$^{+}$ and CD19$^{+}$ cells in MS.",

author = "Fernandes, {Sunjay Jude} and Matilda Ericsson and Mohsen Khademi and Maja Jagodic and Tomas Olsson and David Gomez-Cabrero and Ingrid Kockum and Jesper Tegner",

note = "KAUST Repository Item: Exported on 2021-10-25 Acknowledgements: The authors thank all the multiple sclerosis patients who have been willing to take part in this study. The authors also thank the healthy donors for contributing their blood to this study. The authors acknowledge P Noori for the extraction of RNA from sorted cells.",

year = "2021",

month = oct,

day = "22",

doi = "10.2217/epi-2021-0205",

language = "English (US)",

journal = "Epigenomics",

issn = "1750-1911",

publisher = "Future Medicine",

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TY - JOUR

T1 - Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients

AU - Fernandes, Sunjay Jude

AU - Ericsson, Matilda

AU - Khademi, Mohsen

AU - Jagodic, Maja

AU - Olsson, Tomas

AU - Gomez-Cabrero, David

AU - Kockum, Ingrid

AU - Tegner, Jesper

N1 - KAUST Repository Item: Exported on 2021-10-25 Acknowledgements: The authors thank all the multiple sclerosis patients who have been willing to take part in this study. The authors also thank the healthy donors for contributing their blood to this study. The authors acknowledge P Noori for the extraction of RNA from sorted cells.

PY - 2021/10/22

Y1 - 2021/10/22

N2 - Background: The putative involvement of chromatin states in multiple sclerosis (MS) is thus far unclear. Here we determined the association of chromatin-accessibility with concurrent genetic, epigenetic and transcriptional events. Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-seq profiles from sorted blood immune CD4$^{+}$ and CD8$^{+}$ T cells, CD14$^{+}$ monocytes and CD19$^{+}$ B cells from healthy controls (HCs) and MS patients. Results: We identified differentially accessible regions between MS and HCs, primarily in CD4$^{+}$ and CD19$^{+}$. CD4$^{+}$ regions were enriched for MS-associated single nucleotide polymorphisms and differentially methylated loci. In the vicinity of differentially accessible regions of CD4$^{+}$ cells, 42 differentially expressed genes were identified. The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1. Conclusion: These findings provide new insight into the primary role of CD4$^{+}$ and CD19$^{+}$ cells in MS.

AB - Background: The putative involvement of chromatin states in multiple sclerosis (MS) is thus far unclear. Here we determined the association of chromatin-accessibility with concurrent genetic, epigenetic and transcriptional events. Material & methods: We generated paired assay for transposase-accessible chromatin sequencing and RNA-seq profiles from sorted blood immune CD4$^{+}$ and CD8$^{+}$ T cells, CD14$^{+}$ monocytes and CD19$^{+}$ B cells from healthy controls (HCs) and MS patients. Results: We identified differentially accessible regions between MS and HCs, primarily in CD4$^{+}$ and CD19$^{+}$. CD4$^{+}$ regions were enriched for MS-associated single nucleotide polymorphisms and differentially methylated loci. In the vicinity of differentially accessible regions of CD4$^{+}$ cells, 42 differentially expressed genes were identified. The top two dysregulated genes identified in this multilayer analysis were CCDC114 and SERTAD1. Conclusion: These findings provide new insight into the primary role of CD4$^{+}$ and CD19$^{+}$ cells in MS.

UR - http://hdl.handle.net/10754/672937

UR - https://www.futuremedicine.com/doi/10.2217/epi-2021-0205

U2 - 10.2217/epi-2021-0205

DO - 10.2217/epi-2021-0205

M3 - Article

C2 - 34676774

SN - 1750-1911

JO - Epigenomics

JF - Epigenomics

ER -

Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients

Abstract

Bibliographical note

ASJC Scopus subject areas

UN SDGs

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