Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis

Summary: Low reproducibility in gene expression profiles has been observed in transcriptome studies, and this often limits applying findings to clinical practice. Here, we show time-of-day effects on gene expression and analytical schemes to increase the reproducibility in expression patterns. We re...

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Autores principales:	Suihong Huang, Tan Wu, Alexander Y. Lau, Cheryl Au, Hao Huang, Xin Wang, Jin Young Kim
Formato:	article
Lenguaje:	EN
Publicado:	Elsevier 2021
Materias:	Biological sciences Neuroscience Clinical neuroscience Omics Transcriptomics Science Q
Acceso en línea:	https://doaj.org/article/2ef2ecb9cb3e4014ae75c18ba779c1e2
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spelling	oai:doaj.org-article:2ef2ecb9cb3e4014ae75c18ba779c1e22021-11-20T05:08:50ZAttention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis2589-004210.1016/j.isci.2021.103247https://doaj.org/article/2ef2ecb9cb3e4014ae75c18ba779c1e22021-11-01T00:00:00Zhttp://www.sciencedirect.com/science/article/pii/S2589004221012165https://doaj.org/toc/2589-0042Summary: Low reproducibility in gene expression profiles has been observed in transcriptome studies, and this often limits applying findings to clinical practice. Here, we show time-of-day effects on gene expression and analytical schemes to increase the reproducibility in expression patterns. We recruited patients with relapsing-remitting multiple sclerosis (RRMS) and healthy subjects and collected blood from individuals twice a day, day (2 pm) and night (9 pm). RNA sequencing analyses found that gene expression in RRMS in relapse (Relapse) is significantly changed at night compared with either Relapse at day or RRMS in remission (Remission). Gene set overrepresentation analysis demonstrated that gene sets significantly changed in Relapse at night are enriched to immune responses related to MS pathology. In those gene sets, 68 genes are significantly changed expression in Relapse at night compared with Relapse at day and Remission. This supports that times of sample collections should be standardized to obtain reproducible gene expression patterns.Suihong HuangTan WuAlexander Y. LauCheryl AuHao HuangXin WangJin Young KimElsevierarticleBiological sciencesNeuroscienceClinical neuroscienceOmicsTranscriptomicsScienceQENiScience, Vol 24, Iss 11, Pp 103247- (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biological sciences Neuroscience Clinical neuroscience Omics Transcriptomics Science Q
spellingShingle	Biological sciences Neuroscience Clinical neuroscience Omics Transcriptomics Science Q Suihong Huang Tan Wu Alexander Y. Lau Cheryl Au Hao Huang Xin Wang Jin Young Kim Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis
description	Summary: Low reproducibility in gene expression profiles has been observed in transcriptome studies, and this often limits applying findings to clinical practice. Here, we show time-of-day effects on gene expression and analytical schemes to increase the reproducibility in expression patterns. We recruited patients with relapsing-remitting multiple sclerosis (RRMS) and healthy subjects and collected blood from individuals twice a day, day (2 pm) and night (9 pm). RNA sequencing analyses found that gene expression in RRMS in relapse (Relapse) is significantly changed at night compared with either Relapse at day or RRMS in remission (Remission). Gene set overrepresentation analysis demonstrated that gene sets significantly changed in Relapse at night are enriched to immune responses related to MS pathology. In those gene sets, 68 genes are significantly changed expression in Relapse at night compared with Relapse at day and Remission. This supports that times of sample collections should be standardized to obtain reproducible gene expression patterns.
format	article
author	Suihong Huang Tan Wu Alexander Y. Lau Cheryl Au Hao Huang Xin Wang Jin Young Kim
author_facet	Suihong Huang Tan Wu Alexander Y. Lau Cheryl Au Hao Huang Xin Wang Jin Young Kim
author_sort	Suihong Huang
title	Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis
title_short	Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis
title_full	Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis
title_fullStr	Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis
title_full_unstemmed	Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis
title_sort	attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis
publisher	Elsevier
publishDate	2021
url	https://doaj.org/article/2ef2ecb9cb3e4014ae75c18ba779c1e2
work_keys_str_mv	AT suihonghuang attentiontotimeofdayvariabilityimprovesthereproducibilityofgeneexpressionpatternsinmultiplesclerosis AT tanwu attentiontotimeofdayvariabilityimprovesthereproducibilityofgeneexpressionpatternsinmultiplesclerosis AT alexanderylau attentiontotimeofdayvariabilityimprovesthereproducibilityofgeneexpressionpatternsinmultiplesclerosis AT cherylau attentiontotimeofdayvariabilityimprovesthereproducibilityofgeneexpressionpatternsinmultiplesclerosis AT haohuang attentiontotimeofdayvariabilityimprovesthereproducibilityofgeneexpressionpatternsinmultiplesclerosis AT xinwang attentiontotimeofdayvariabilityimprovesthereproducibilityofgeneexpressionpatternsinmultiplesclerosis AT jinyoungkim attentiontotimeofdayvariabilityimprovesthereproducibilityofgeneexpressionpatternsinmultiplesclerosis
_version_	1718419532975964160

Attention to time-of-day variability improves the reproducibility of gene expression patterns in multiple sclerosis

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