Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome

Primary Sjogren’s syndrome (pSS) is a complex systemic autoimmune disease, which is difficult to accurately diagnose due to symptom diversity in patients, especially at earlier stages. We tried to find potential single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and related signal...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Xuan Qi, Xi-Qin Wang, Lu Jin, Li-Xia Gao, Hui-Fang Guo
Formato:	article
Lenguaje:	EN
Publicado:	Taylor & Francis Group 2021
Materias:	primary sjogren’s syndrome whole-exome sequencing single nucleotide variants copy number variations signaling pathway sanger sequencing in vitro validation Biotechnology TP248.13-248.65
Acceso en línea:	https://doaj.org/article/49f9848ab32445fa92d93c0edaac7568
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:49f9848ab32445fa92d93c0edaac7568
record_format	dspace
spelling	oai:doaj.org-article:49f9848ab32445fa92d93c0edaac75682021-11-26T11:19:49ZUncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome2165-59792165-598710.1080/21655979.2021.2000245https://doaj.org/article/49f9848ab32445fa92d93c0edaac75682021-12-01T00:00:00Zhttp://dx.doi.org/10.1080/21655979.2021.2000245https://doaj.org/toc/2165-5979https://doaj.org/toc/2165-5987Primary Sjogren’s syndrome (pSS) is a complex systemic autoimmune disease, which is difficult to accurately diagnose due to symptom diversity in patients, especially at earlier stages. We tried to find potential single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and related signaling pathways. Genomic DNA was extracted from peripheral blood of 12 individuals (7 individuals from 3 pSS pedigrees and 5 sporadic cases) for whole-exome sequencing (WES) analysis. SNPs and CNVs were identified, followed by functional annotation of genes with SNPs and CNVs. Gene expression profile (involving 64 normal controls and 166 cases) was downloaded from the Gene Expression Omnibus database (GEO) dataset for differentially expression analysis. Sanger sequencing and in vitro validation was used to validate the identified SNPs and differentially expressed genes, respectively. A total of 5 SNPs were identified in both pedigrees and sporadic cases, such as FES, PPM1J, and TRAPPC9. A total of 3402 and 19 CNVs were identified in pedigrees and sporadic cases, respectively. Fifty-one differentially expressed genes were associated with immunity, such as BATF3, LAP3, BATF2, PARP9, and IL15RA. AMPK signaling pathway and cell adhesion molecules (CAMs) were the most significantly enriched signaling pathways of identified SNPs. Identified CNVs were associated with systemic lupus erythematosus, mineral absorption, and HTLV-I infection. IL2-STAT5 signaling, interferon-gamma response, and interferon-alpha response were significantly enriched immune related signaling pathways of identified differentially expressed genes. In conclusion, our study found some potential SNPs, CNVs, and related signaling pathways, which could be useful in understanding the pathological mechanism of pSS.Xuan QiXi-Qin WangLu JinLi-Xia GaoHui-Fang GuoTaylor & Francis Grouparticleprimary sjogren’s syndromewhole-exome sequencingsingle nucleotide variantscopy number variationssignaling pathwaysanger sequencingin vitro validationBiotechnologyTP248.13-248.65ENBioengineered, Vol 12, Iss 2, Pp 9313-9331 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	primary sjogren’s syndrome whole-exome sequencing single nucleotide variants copy number variations signaling pathway sanger sequencing in vitro validation Biotechnology TP248.13-248.65
spellingShingle	primary sjogren’s syndrome whole-exome sequencing single nucleotide variants copy number variations signaling pathway sanger sequencing in vitro validation Biotechnology TP248.13-248.65 Xuan Qi Xi-Qin Wang Lu Jin Li-Xia Gao Hui-Fang Guo Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome
description	Primary Sjogren’s syndrome (pSS) is a complex systemic autoimmune disease, which is difficult to accurately diagnose due to symptom diversity in patients, especially at earlier stages. We tried to find potential single nucleotide polymorphisms (SNPs), copy number variations (CNVs) and related signaling pathways. Genomic DNA was extracted from peripheral blood of 12 individuals (7 individuals from 3 pSS pedigrees and 5 sporadic cases) for whole-exome sequencing (WES) analysis. SNPs and CNVs were identified, followed by functional annotation of genes with SNPs and CNVs. Gene expression profile (involving 64 normal controls and 166 cases) was downloaded from the Gene Expression Omnibus database (GEO) dataset for differentially expression analysis. Sanger sequencing and in vitro validation was used to validate the identified SNPs and differentially expressed genes, respectively. A total of 5 SNPs were identified in both pedigrees and sporadic cases, such as FES, PPM1J, and TRAPPC9. A total of 3402 and 19 CNVs were identified in pedigrees and sporadic cases, respectively. Fifty-one differentially expressed genes were associated with immunity, such as BATF3, LAP3, BATF2, PARP9, and IL15RA. AMPK signaling pathway and cell adhesion molecules (CAMs) were the most significantly enriched signaling pathways of identified SNPs. Identified CNVs were associated with systemic lupus erythematosus, mineral absorption, and HTLV-I infection. IL2-STAT5 signaling, interferon-gamma response, and interferon-alpha response were significantly enriched immune related signaling pathways of identified differentially expressed genes. In conclusion, our study found some potential SNPs, CNVs, and related signaling pathways, which could be useful in understanding the pathological mechanism of pSS.
format	article
author	Xuan Qi Xi-Qin Wang Lu Jin Li-Xia Gao Hui-Fang Guo
author_facet	Xuan Qi Xi-Qin Wang Lu Jin Li-Xia Gao Hui-Fang Guo
author_sort	Xuan Qi
title	Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome
title_short	Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome
title_full	Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome
title_fullStr	Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome
title_full_unstemmed	Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome
title_sort	uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary sjogren’s syndrome
publisher	Taylor & Francis Group
publishDate	2021
url	https://doaj.org/article/49f9848ab32445fa92d93c0edaac7568
work_keys_str_mv	AT xuanqi uncoveringpotentialsinglenucleotidepolymorphismscopynumbervariationsandrelatedsignalingpathwaysinprimarysjogrenssyndrome AT xiqinwang uncoveringpotentialsinglenucleotidepolymorphismscopynumbervariationsandrelatedsignalingpathwaysinprimarysjogrenssyndrome AT lujin uncoveringpotentialsinglenucleotidepolymorphismscopynumbervariationsandrelatedsignalingpathwaysinprimarysjogrenssyndrome AT lixiagao uncoveringpotentialsinglenucleotidepolymorphismscopynumbervariationsandrelatedsignalingpathwaysinprimarysjogrenssyndrome AT huifangguo uncoveringpotentialsinglenucleotidepolymorphismscopynumbervariationsandrelatedsignalingpathwaysinprimarysjogrenssyndrome
_version_	1718409465988907008

Uncovering potential single nucleotide polymorphisms, copy number variations and related signaling pathways in primary Sjogren’s syndrome

Ejemplares similares