P2RY8 plays essential roles in human B cell tolerance and prevents lupus

Samples were obtained from Renji Hospital Biobank, Shanghai Jiaotong University School of medicine (Ethical approval number: [2013] 126). All donors signed the informed consent. Genomic DNA was isolated from blood using QIAamp DNA Blood kit (QIAGEN) and was sequenced by Illumina platform (Novogene, Beijing). Bioinformatic analysis were performed at China-Australia Centre for Personalised Immunology (CACPI). Relatedness was checked using Peddy45. Identified variants were scored based upon a predesigned algorithm incorporating frequency of SNP, potential consequence of resulting amino acid changes, in silico predictions of damage (Polyphen, SIFT, and CADD), and function of domains bearing mutation. All variants of interest in P2RY8 were further confirmed by Sanger sequencing. Whole exome sequencing (WES) of 61 trios in which the proband had childhood-onset SLE identified a novel heterozygous missense P2RY8 variant L257F (c.769C>T) (Fig.1a and Extended Data Fig. 1a). The girl suffered from lupus, glomerulonephritis (histological class V), iron-deficiency anemia, and multiple bone infarcts affecting knees, femur, tibia, and fibula. Sanger sequencing of both parents coupled with relatedness check established that the L257F variant occurred de novo (it was not present in either parent) (Fig.1c and Extended Data Fig. 1b,c). WES of an additional cohort of 118 Chinese SLE patients identified (Fig.1a) an additional rare heterozygous P2RY8 variant E323G (c.968A>G) in two adult-onset SLE patients, which was Sanger-validated (Fig.1d). Both P2RY8 L257F and E323G variants were predicted to be pathogenic according to SIFT and CADD score, and the L257F variant was also predicted to be damaging by polyphen (Fig.1b). Variant frequency databases including Exome Aggregation Consortium (ExAC) and the Genome Aggregation Database (gnomAD) indicated the L257F variant was novel, and the E323G variant minor allele frequency was less than 0.3% (ExAC = 0.00021) (Fig.1b). The L257F variant occurs in a highly conserved transmembrane region (Fig.1e,f). The E323 site is located in the C-terminus, and is also conserved in multiple species (Fig.1e,f).
Type
Collection
Title
P2RY8 plays essential roles in human B cell tolerance and prevents lupus
Collection Type
Dataset
Access Privileges
Australian Phenomics Facility
DOI - Digital Object Identifier
10.25911/5f1f7040d40ab
Metadata Language
English
Data Language
English
Significance Statement
Here we identify a P2RY8 loss-of-function (LOF) variant and a partial LOF variant in Chinese SLE kindreds and demonstrate these variants cause B cell hyperactivity and disrupt B cell tolerance.
Full Description
Samples were obtained from Renji Hospital Biobank, Shanghai Jiaotong University School of medicine (Ethical approval number: [2013] 126). All donors signed the informed consent. Genomic DNA was isolated from blood using QIAamp DNA Blood kit (QIAGEN) and was sequenced by Illumina platform (Novogene, Beijing). Bioinformatic analysis were performed at China-Australia Centre for Personalised Immunology (CACPI). Relatedness was checked using Peddy45. Identified variants were scored based upon a predesigned algorithm incorporating frequency of SNP, potential consequence of resulting amino acid changes, in silico predictions of damage (Polyphen, SIFT, and CADD), and function of domains bearing mutation. All variants of interest in P2RY8 were further confirmed by Sanger sequencing. Whole exome sequencing (WES) of 61 trios in which the proband had childhood-onset SLE identified a novel heterozygous missense P2RY8 variant L257F (c.769C>T) (Fig.1a and Extended Data Fig. 1a). The girl suffered from lupus, glomerulonephritis (histological class V), iron-deficiency anemia, and multiple bone infarcts affecting knees, femur, tibia, and fibula. Sanger sequencing of both parents coupled with relatedness check established that the L257F variant occurred de novo (it was not present in either parent) (Fig.1c and Extended Data Fig. 1b,c). WES of an additional cohort of 118 Chinese SLE patients identified (Fig.1a) an additional rare heterozygous P2RY8 variant E323G (c.968A>G) in two adult-onset SLE patients, which was Sanger-validated (Fig.1d). Both P2RY8 L257F and E323G variants were predicted to be pathogenic according to SIFT and CADD score, and the L257F variant was also predicted to be damaging by polyphen (Fig.1b). Variant frequency databases including Exome Aggregation Consortium (ExAC) and the Genome Aggregation Database (gnomAD) indicated the L257F variant was novel, and the E323G variant minor allele frequency was less than 0.3% (ExAC = 0.00021) (Fig.1b). The L257F variant occurs in a highly conserved transmembrane region (Fig.1e,f). The E323 site is located in the C-terminus, and is also conserved in multiple species (Fig.1e,f).
Contact Email
yuke.he@anu.edu.au; carola.vinuesa@anu.edu.au
Contact Address
Co-Director, Centre for Personalised Immunology, NHMRC Centre of Research Excellence College of Health & Medicine The Australian National University
Contact Phone Number
+61 (0) 432 130556
Fields of Research
119999 - Medical and Health Sciences not elsewhere classified
Socio-Economic Objective
9201 - Clinical Health (Organs, Diseases and Abnormal Conditions)
Keywords
P2RY8; autoimmunity; SLE; lupus; B cells
Type of Research Activity
Strategic basic research
Year of data publication
2020
Creator(s) for Citation
Yuke
He
Carola
Vinuesa
Nan
Shen
National Human Genetic Resources Sharing Service Platform
Publisher for Citation
Centre for Personalised Immunology (CACPI)
Related Websites
https://cacpi.org/
中澳个体化免疫学中心 China - Australia Centre for personalised Immunology
Access Rights Type
Restricted
Retention Period
Indefinitely
Data Size
298 MB
Data Management Plan
No
Status: Published
Published to:
  • Australian National University
  • Australian National Data Service
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