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Article ; Online: Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren's Syndrome.

Arvidsson, Gustav / Czarnewski, Paulo / Johansson, Alina / Raine, Amanda / Imgenberg-Kreuz, Juliana / Nordlund, Jessica / Nordmark, Gunnel / Syvänen, Ann-Christine

Arthritis & rheumatology (Hoboken, N.J.)

2023 Volume 76, Issue 2, Page(s) 255–267

Abstract: Objective: B cells are important in the pathogenesis of primary Sjögren's syndrome (pSS). Patients positive for Sjögren's syndrome antigen A/Sjögren syndrome antigen B (SSA/SSB) autoantibodies are more prone to systemic disease manifestations and ... ...

Abstract	Objective: B cells are important in the pathogenesis of primary Sjögren's syndrome (pSS). Patients positive for Sjögren's syndrome antigen A/Sjögren syndrome antigen B (SSA/SSB) autoantibodies are more prone to systemic disease manifestations and adverse outcomes. We aimed to determine the role of B cell composition, gene expression, and B cell receptor usage in pSS subgroups stratified for SSA/SSB antibodies. Methods: Over 230,000 B cells were isolated from peripheral blood of patients with pSS (n = 6 SSA-, n = 8 SSA+ single positive and n = 10 SSA/SSB+ double positive) and four healthy controls and processed for single-cell RNA sequencing (scRNA-seq) and single-cell variable, diversity, and joining (VDJ) gene sequencing (scVDJ-seq). Results: We show that SSA/SSB+ patients present the highest and lowest proportion of naïve and memory B cells, respectively, and the highest up-regulation of interferon-induced genes across all B cell subtypes. Differential usage of IGHV showed that IGHV1-69 and IGHV4-30-4 were more often used in all pSS subgroups compared with controls. Memory B cells from SSA/SSB+ patients displayed a higher proportion of cells with unmutated VDJ transcripts compared with other pSS patient groups and controls, indicating altered somatic hypermutation processes. Comparison with previous studies revealed heterogeneous clonotype pools, with little overlap in CDR3 sequences. Joint analysis using scRNA-seq and scVDJ-seq data allowed unsupervised stratification of patients with pSS and identified novel parameters that correlated to disease manifestations and antibody status. Conclusion: We describe heterogeneity and molecular characteristics in B cells from patients with pSS, providing clues to intrinsic differences in B cells that affect the phenotype and outcome and allowing stratification of patients with pSS at improved resolution.
MeSH term(s)	Humans ; Sjogren's Syndrome ; B-Lymphocytes ; Autoantibodies ; Phenotype
Chemical Substances	Autoantibodies
Language	English
Publishing date	2023-12-18
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2756371-6
ISSN	2326-5205 ; 2326-5191
ISSN (online)	2326-5205
ISSN	2326-5191
DOI	10.1002/art.42683
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Article ; Online: Epigenetic alterations in primary Sjögren's syndrome - an overview.

Imgenberg-Kreuz, Juliana / Sandling, Johanna K / Nordmark, Gunnel

Clinical immunology (Orlando, Fla.)

2018 Volume 196, Page(s) 12–20

Abstract: Primary Sjögren's syndrome (pSS) is a chronic autoimmune rheumatic disease characterized by inflammation of exocrine glands, mainly salivary and lacrimal glands. In addition, pSS may affect multiple other organs resulting in systemic manifestations. ... ...

Abstract	Primary Sjögren's syndrome (pSS) is a chronic autoimmune rheumatic disease characterized by inflammation of exocrine glands, mainly salivary and lacrimal glands. In addition, pSS may affect multiple other organs resulting in systemic manifestations. Although the precise etiology of pSS remains elusive, pSS is considered to be a multi-factorial disease, where underlying genetic predisposition, environmental factors and epigenetic mechanisms contribute to disease development. Epigenetic mechanisms, such as DNA methylation, histone modifications and non-coding RNAs, may constitute a dynamic link between genome, environment and phenotypic manifestation by their modulating effects on gene expression. A growing body of studies reporting altered epigenetic landscapes in pSS suggests that epigenetic mechanisms play a role in the pathogenesis of pSS, and the reversible nature of epigenetic modifications suggests therapeutic strategies targeting epigenetic dysregulation in pSS. This article reviews our current understanding of epigenetic mechanisms in pSS and discusses implications for novel diagnostic and therapeutic approaches.
MeSH term(s)	DNA Methylation ; Epigenesis, Genetic ; Histone Code ; Humans ; Inflammation ; RNA, Untranslated ; Sjogren's Syndrome/genetics ; Sjogren's Syndrome/immunology
Chemical Substances	RNA, Untranslated
Language	English
Publishing date	2018-04-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1459903-x
ISSN	1521-7035 ; 1521-6616
ISSN (online)	1521-7035
ISSN	1521-6616
DOI	10.1016/j.clim.2018.04.004
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Article ; Online: Genetics and epigenetics in primary Sjögren's syndrome.

Imgenberg-Kreuz, Juliana / Rasmussen, Astrid / Sivils, Kathy / Nordmark, Gunnel

Rheumatology (Oxford, England)

2019 Volume 60, Issue 5, Page(s) 2085–2098

Abstract: Primary Sjögren's syndrome (pSS) is considered to be a multifactorial disease, where underlying genetic predisposition, epigenetic mechanisms and environmental factors contribute to disease development. In the last 5 years, the first genome-wide ... ...

Abstract	Primary Sjögren's syndrome (pSS) is considered to be a multifactorial disease, where underlying genetic predisposition, epigenetic mechanisms and environmental factors contribute to disease development. In the last 5 years, the first genome-wide association studies in pSS have been completed. The strongest signal of association lies within the HLA genes, whereas the non-HLA genes IRF5 and STAT4 show consistent associations in multiple ethnicities but with a smaller effect size. The majority of the genetic risk variants are found at intergenic regions and their functional impact has in most cases not been elucidated. Epigenetic mechanisms such as DNA methylation, histone modifications and non-coding RNAs play a role in the pathogenesis of pSS by their modulating effects on gene expression and may constitute a dynamic link between the genome and phenotypic manifestations. This article reviews the hitherto published genetic studies and our current understanding of epigenetic mechanisms in pSS.
MeSH term(s)	DNA Methylation ; Epigenesis, Genetic ; Genetic Predisposition to Disease ; Histone Code/genetics ; Humans ; Sjogren's Syndrome/genetics
Language	English
Publishing date	2019-01-19
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1464822-2
ISSN	1462-0332 ; 1462-0324
ISSN (online)	1462-0332
ISSN	1462-0324
DOI	10.1093/rheumatology/key330
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Article ; Online: Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.

Imgenberg-Kreuz, Juliana / Almlöf, Jonas Carlsson / Leonard, Dag / Sjöwall, Christopher / Syvänen, Ann-Christine / Rönnblom, Lars / Sandling, Johanna K / Nordmark, Gunnel

Frontiers in immunology

2019 Volume 10, Page(s) 1686

Abstract: Objectives: ...

Abstract	Objectives:
MeSH term(s)	Adult ; Aged ; CpG Islands/immunology ; DNA Methylation/immunology ; Female ; Genome, Human ; Humans ; Lupus Erythematosus, Systemic/genetics ; Lupus Erythematosus, Systemic/immunology ; Male ; Middle Aged ; Sjogren's Syndrome/genetics ; Sjogren's Syndrome/immunology
Language	English
Publishing date	2019-07-30
Publishing country	Switzerland
Document type	Clinical Trial ; Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2019.01686
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Article ; Online: DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome.

Imgenberg-Kreuz, Juliana / Sandling, Johanna K / Norheim, Katrine Brække / Johnsen, Svein Joar Auglænd / Omdal, Roald / Syvänen, Ann-Christine / Svenungsson, Elisabet / Rönnblom, Lars / Eloranta, Maija-Leena / Nordmark, Gunnel

Frontiers in immunology

2021 Volume 12, Page(s) 702037

Abstract: Primary Sjögren's syndrome (pSS) is an autoimmune inflammatory disease with profound clinical heterogeneity, where excessive activation of the type I interferon (IFN) system is considered one of the key mechanisms in disease pathogenesis. Here we present ...

Abstract	Primary Sjögren's syndrome (pSS) is an autoimmune inflammatory disease with profound clinical heterogeneity, where excessive activation of the type I interferon (IFN) system is considered one of the key mechanisms in disease pathogenesis. Here we present a DNA methylation-based IFN system activation score (DNAm IFN score) and investigate its potential associations with sub-phenotypes of pSS. The study comprised 100 Swedish patients with pSS and 587 Swedish controls. For replication, 48 patients with pSS from Stavanger, Norway, were included. IFN scores were calculated from DNA methylation levels at the IFN-induced genes RSAD2, IFIT1 and IFI44L. A high DNAm IFN score, defined as > mean
MeSH term(s)	DNA Methylation/immunology ; Female ; Humans ; Interferon Type I/immunology ; Lymphoma/immunology ; Male ; Middle Aged ; Phenotype ; RNA, Messenger/immunology ; Sjogren's Syndrome/immunology
Chemical Substances	Interferon Type I ; RNA, Messenger
Language	English
Publishing date	2021-07-16
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2021.702037
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Article ; Online: Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren’s syndrome

Marika Kvarnström / Ann-Christine Syvänen / Gunnel Nordmark / Albin Björk / Gudny Ella Thorlacius / Elina Richardsdotter Andersson / Juliana Imgenberg-Kreuz

RMD Open, Vol 6, Iss

2020 Volume 1

Abstract: ObjectiveStandard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in ... ...

Abstract	ObjectiveStandard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in the IFN-driven disease primary Sjögren’s syndrome (pSS).MethodsPatients with pSS seropositive or negative for anti-SSA/SSB and controls were included. Protein-based IFN (pIFN) scores were calculated from levels of PD-1, CXCL9 and CXCL10. DNA methylation-based (DNAm) IFN scores were calculated from DNAm levels at RSAD2, IFIT1 and IFI44L. Scores were compared with mRNA-based IFN scores measured by quantitative PCR (qPCR), Nanostring or RNA sequencing (RNAseq).ResultsmRNA-based IFN scores displayed strong correlations between B cells and monocytes (r=0.93 and 0.95, p<0.0001) and between qPCR and Nanostring measurements (r=0.92 and 0.92, p<0.0001). The pIFN score in plasma and serum was higher in patients compared with controls (p<0.0001) and correlated well with mRNA-based IFN scores (r=0.62–0.79, p<0.0001), as well as with each other (r=0.94, p<0.0001). Concordance of classification as ‘high’ or ‘low’ IFN signature between the pIFN score and mRNA-based IFN scores ranged from 79.5% to 88.6%, and the pIFN score was effective at classifying patients and controls (area under the curve, AUC=0.89–0.93, p<0.0001). The DNAm IFN score showed strong correlation to the RNAseq IFN score (r=0.84, p<0.0001) and performed well in classifying patients and controls (AUC=0.96, p<0.0001).ConclusionsWe describe novel methods of assessing IFN system activity in plasma, serum or DNA samples, which may prove particularly valuable in studies where RNA samples are not available.
Keywords	Medicine ; R
Subject code	616
Language	English
Publishing date	2020-05-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
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Article ; Online: Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome.

Björk, Albin / Richardsdotter Andersson, Elina / Imgenberg-Kreuz, Juliana / Thorlacius, Gudny Ella / Mofors, Johannes / Syvänen, Ann-Christine / Kvarnström, Marika / Nordmark, Gunnel / Wahren-Herlenius, Marie

RMD open

2020 Volume 6, Issue 1

Abstract: Objective: Standard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in ...

Abstract	Objective: Standard assessment of interferon (IFN) system activity in systemic rheumatic diseases depends on the availability of RNA samples. In this study, we describe and evaluate alternative methods using plasma, serum and DNA samples, exemplified in the IFN-driven disease primary Sjögren's syndrome (pSS). Methods: Patients with pSS seropositive or negative for anti-SSA/SSB and controls were included. Protein-based IFN (pIFN) scores were calculated from levels of PD-1, CXCL9 and CXCL10. DNA methylation-based (DNAm) IFN scores were calculated from DNAm levels at Results: mRNA-based IFN scores displayed strong correlations between B cells and monocytes (r=0.93 and 0.95, p<0.0001) and between qPCR and Nanostring measurements (r=0.92 and 0.92, p<0.0001). The pIFN score in plasma and serum was higher in patients compared with controls (p<0.0001) and correlated well with mRNA-based IFN scores (r=0.62-0.79, p<0.0001), as well as with each other (r=0.94, p<0.0001). Concordance of classification as 'high' or 'low' IFN signature between the pIFN score and mRNA-based IFN scores ranged from 79.5% to 88.6%, and the pIFN score was effective at classifying patients and controls (area under the curve, AUC=0.89-0.93, p<0.0001). The DNAm IFN score showed strong correlation to the RNAseq IFN score (r=0.84, p<0.0001) and performed well in classifying patients and controls (AUC=0.96, p<0.0001). Conclusions: We describe novel methods of assessing IFN system activity in plasma, serum or DNA samples, which may prove particularly valuable in studies where RNA samples are not available.
MeSH term(s)	Adult ; Aged ; Biomarkers/analysis ; Case-Control Studies ; DNA Methylation ; Female ; Humans ; Interferon Type I/genetics ; Interferon Type I/metabolism ; Male ; Middle Aged ; Proteins/genetics ; Proteins/metabolism ; RNA, Messenger/analysis ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, RNA ; Sjogren's Syndrome/genetics ; Sjogren's Syndrome/metabolism
Chemical Substances	Biomarkers ; Interferon Type I ; Proteins ; RNA, Messenger
Language	English
Publishing date	2020-01-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2812592-7
ISSN	2056-5933 ; 2056-5933
ISSN (online)	2056-5933
ISSN	2056-5933
DOI	10.1136/rmdopen-2019-000995
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Genetic variants at the

Norheim, Katrine Brække / Imgenberg-Kreuz, Juliana / Alexsson, Andrei / Johnsen, Svein Joar Auglænd / Bårdsen, Kjetil / Brun, Johan Gorgas / Dehkordi, Rezvan Kiani / Theander, Elke / Mandl, Thomas / Jonsson, Roland / Ng, Wan-Fai / Lessard, Christopher J / Rasmussen, Astrid / Sivilis, Kathy / Ronnblom, Lars / Omdal, Roald

RMD open

2021 Volume 7, Issue 3

Abstract: Objectives: Fatigue is common and severe in primary Sjögren's syndrome (pSS). The aim of this study was to identify genetic determinants of fatigue in pSS through a genome-wide association study.: Methods: Patients with pSS from Norway, Sweden, UK ... ...

Abstract	Objectives: Fatigue is common and severe in primary Sjögren's syndrome (pSS). The aim of this study was to identify genetic determinants of fatigue in pSS through a genome-wide association study. Methods: Patients with pSS from Norway, Sweden, UK and USA with fatigue and genotype data available were included. After genotype imputation and quality control, 682 patients and 4 966 157 genetic markers were available. Association analysis in each cohort using linear regression with fatigue as a continuous variable and meta-analyses between the cohorts were performed. Results: Meta-analysis of the Norwegian and Swedish cohorts identified five polymorphisms within the same linkage disequilibrium block at the receptor transporter protein 4 ( Conclusion: Genetic variations at
MeSH term(s)	Alleles ; Cohort Studies ; Fatigue/epidemiology ; Fatigue/genetics ; Genome-Wide Association Study ; Humans ; Mannose-Binding Protein-Associated Serine Proteases ; Sjogren's Syndrome/complications ; Sjogren's Syndrome/genetics
Chemical Substances	MASP1 protein, human (EC 3.4.21.-) ; Mannose-Binding Protein-Associated Serine Proteases (EC 3.4.21.-)
Language	English
Publishing date	2021-12-18
Publishing country	England
Document type	Journal Article ; Meta-Analysis ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2812592-7
ISSN	2056-5933 ; 2056-5933
ISSN (online)	2056-5933
ISSN	2056-5933
DOI	10.1136/rmdopen-2021-001832
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Article ; Online: Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.

Lundtoft, Christian / Pucholt, Pascal / Imgenberg-Kreuz, Juliana / Carlsson-Almlöf, Jonas / Eloranta, Maija-Leena / Syvänen, Ann-Christine / Nordmark, Gunnel / Sandling, Johanna K / Kockum, Ingrid / Olsson, Tomas / Rönnblom, Lars / Hagberg, Niklas

PLoS genetics

2020 Volume 16, Issue 10, Page(s) e1009199

Abstract: Interferons (IFNs) are cytokines that are central to the host defence against viruses and other microorganisms. If not properly regulated, IFNs may contribute to the pathogenesis of inflammatory autoimmune, or infectious diseases. To identify genetic ... ...

Abstract	Interferons (IFNs) are cytokines that are central to the host defence against viruses and other microorganisms. If not properly regulated, IFNs may contribute to the pathogenesis of inflammatory autoimmune, or infectious diseases. To identify genetic polymorphisms regulating the IFN system we performed an unbiased genome-wide protein-quantitative trait loci (pQTL) mapping of cell-type specific type I and type II IFN receptor levels and their responses in immune cells from 303 healthy individuals. Seven genome-wide significant (p < 5.0E-8) pQTLs were identified. Two independent SNPs that tagged the multiple sclerosis (MS)-protective HLA class I alleles A02/A68 and B*44, respectively, were associated with increased levels of IFNAR2 in B and T cells, with the most prominent effect in IgD-CD27+ memory B cells. The increased IFNAR2 levels in B cells were replicated in cells from an independent set of healthy individuals and in MS patients. Despite increased IFNAR2 levels, B and T cells carrying the MS-protective alleles displayed a reduced response to type I IFN stimulation. Expression and methylation-QTL analysis demonstrated increased mRNA expression of the pseudogene HLA-J in B cells carrying the MS-protective class I alleles, possibly driven via methylation-dependent transcriptional regulation. Together these data suggest that the MS-protective effects of HLA class I alleles are unrelated to their antigen-presenting function, and propose a previously unappreciated function of type I IFN signalling in B and T cells in MS immune-pathogenesis.
MeSH term(s)	Adult ; Aged ; Aged, 80 and over ; Alleles ; B-Lymphocytes/immunology ; B-Lymphocytes/pathology ; Female ; Flow Cytometry ; Genetic Predisposition to Disease ; HLA-A2 Antigen/genetics ; HLA-A2 Antigen/immunology ; Humans ; Interferon Type I/genetics ; Interferon Type I/immunology ; Interferon-gamma/genetics ; Interferon-gamma/immunology ; Killer Cells, Natural/immunology ; Male ; Middle Aged ; Multiple Sclerosis/epidemiology ; Multiple Sclerosis/genetics ; Multiple Sclerosis/immunology ; Multiple Sclerosis/pathology ; Polymorphism, Single Nucleotide/genetics ; Quantitative Trait Loci/genetics ; Receptor, Interferon alpha-beta/genetics ; Receptor, Interferon alpha-beta/immunology ; Receptors, Interferon/genetics ; Receptors, Interferon/immunology ; T-Lymphocytes/immunology ; T-Lymphocytes/pathology
Chemical Substances	HLA-A*02 antigen ; HLA-A2 Antigen ; Interferon Type I ; Receptors, Interferon ; interferon receptor, type II ; Receptor, Interferon alpha-beta (156986-95-7) ; Interferon-gamma (82115-62-6)
Language	English
Publishing date	2020-10-26
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2186725-2
ISSN	1553-7404 ; 1553-7390
ISSN (online)	1553-7404
ISSN	1553-7390
DOI	10.1371/journal.pgen.1009199
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.

Lupus science & medicine

2022 Volume 9, Issue 1

Abstract: Objective: Lupus nephritis (LN) is a common and severe manifestation of SLE. The genetic risk for nephritis and progression to end-stage renal disease (ESRD) in patients with LN remains unclear. Herein, we aimed to identify novel genetic associations ... ...

Abstract	Objective: Lupus nephritis (LN) is a common and severe manifestation of SLE. The genetic risk for nephritis and progression to end-stage renal disease (ESRD) in patients with LN remains unclear. Herein, we aimed to identify novel genetic associations with LN, focusing on subphenotypes and ESRD. Methods: We analysed genomic data on 958 patients with SLE (discovery cohort: LN=338) with targeted sequencing data from 1832 immunological pathway genes. We used an independent multiethnic cohort comprising 1226 patients with SLE (LN=603) as a replication dataset. Detailed functional annotation and functional epigenomic enrichment analyses were applied to predict functional effects of the candidate variants. Results: A genetic variant (rs56097910) within the Conclusion: We identified a novel genetic risk locus,
MeSH term(s)	Humans ; Protein-Tyrosine Kinases ; c-Mer Tyrosine Kinase/genetics ; Lupus Erythematosus, Systemic/complications ; Lupus Erythematosus, Systemic/genetics ; Lupus Nephritis/complications ; Lupus Nephritis/genetics ; Kidney Failure, Chronic/genetics
Chemical Substances	Protein-Tyrosine Kinases (EC 2.7.10.1) ; c-Mer Tyrosine Kinase (EC 2.7.10.1)
Language	English
Publishing date	2022-11-04
Publishing country	England
Document type	Meta-Analysis ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2779620-6
ISSN	2053-8790
ISSN	2053-8790
DOI	10.1136/lupus-2022-000752
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