POS0096 SJÖGREN’S DISEASE AND SYSTEMIC LUPUS ERYTHEMATOSUS DDX6-CXCR5 RISK INTERVALS REVEAL COMMON SNPS WITH FUNCTIONAL SIGNIFICANCE IN IMMUNE AND SALIVARY GLAND CELLS

Background

Sjögren’s Disease (SjD) and Systemic Lupus Erythematosus (SLE) are autoimmune diseases with several shared characteristics and similar genome-wide significant associations with the DDX6-CXCR5 locus. DDX6 suppresses interferon-stimulated gene expression and CXCR5 regulates T cell functions implicated in autoimmunity.

Objectives

To identify and characterize functional SNPs in the DDX6-CXCR5 interval.

Methods

ImmunoChip data from European populations (3785 SLE cases; 1916 SjD cases; 6893 controls) were imputed and SNP-trait associations tested. Bayesian statistics defined a credible SNP set that was refined using bioinformatic analyses (RegulomeDB, Haploreg, ENCODE, promoter capture Hi-C, eQTLs, etc.). Electrophoretic mobility shift assays (EMSAs) and luciferase expression assays were used to test allele-specific SNP function in EBV-transformed B (EBV B) cells, Daudi B cells, Jurkat T cells, THP1 monocytes, and A253 salivary gland cell lines. Chromatin conformation capture with quantitative PCR (3C-qPCR) was used to assess long-range chromatin interactions.

Results

Fine mapping of the SjD and SLE associations found similar SNP associations. Bioinformatic analyses identified 5 common SNPs with strong evidence of functionality in immune cell types: rs57494551 in an intron of DDX6, and rs4938572, rs4936443, rs7117261, and rs4938573 in the promoter/enhancer region of DDX6 and CXCR5. EMSAs and luciferase experiments showed cell type-specific differences in protein binding and promoter or enhancer activity, respectively, at each SNP. Risk allele of rs57494551 increased enhancer activity in B cells and A253 cells (p<0.001), but decreased promoter activity in T cells and A253 cells (p<0.01). SNP rs4938572 is an eQTL of DDX6 in T cells, and the risk allele significantly increased protein binding, promoter and enhancer activity in T cells (p<0.01). Risk allele of rs4938572 also increased promoter activity in A253 cells (p<0.001), but had no effect on promoter or enhancer activity in B cells. SNP rs4936443 showed no promoter or enhancer activity in immune cells, but the risk allele showed significant promoter and enhancer (p<0.001) activity in A253 cells. SNP rs7117261 showed decreased enhancer activity in EBV B cells, T cells, and A253 cells (p<0.05) and increased promoter activity in A253 cells (p<0.001). SNP rs4938573 showed decreased promoter activity in EBV B cells, T cell and A253 cells (p<0.05), decreased promoter activity in EBV B cells (p<0.05), and increased enhancer activity in A253 cells (p<0.0001). Overall, A253 cells exhibited more allele-specific effects on promoter and enhancer activity across the five SNPs compared to tested immune cells. In addition to DDX6 and CXCR5, rs57494551 and/or rs4938572 are reported eQTLs for several other genes of interest in the local chromatin regulatory network: IL10RA in T cells, TRAPPC4 in salivary gland and activated macrophages, and long non-coding (lnc)RNA AP002954.1 in T cells and whole blood. 3C-qPCR in EBV B and A253 cells showed that the two regulatory regions carrying rs4938572 or rs57494551 interacted with a region upstream of DDX6 that includes AP002954.1. Hi-C data showed looping between AP002954.1 and the regulatory region carrying rs4938572 and rs57494551 in T cells.

Conclusion

SjD and SLE share similar genomic architecture across the DDX6-CXCR5 risk interval with several common SNPs showing immune and salivary gland cell type-specific allelic effects on protein binding and/or enhancer/promoter activity. Extensive bioinformatic analyses suggest that the SNPs likely work within the local chromatin regulatory network to regulate cell type-specific expression of several genes on the interval. Ongoing studies will use 3C-qPCR to assess allele-specific chromatin interactions between the SNPs and these genes in different cells types, and CRISPR to determine how the risk alleles alters expression.

Disclosure of Interests

Mandi M Wiley: None declared, Bhuwan Khatri: None declared, Kandice L Tessneer: None declared, Michelle L Joachims: None declared, Anna M Stolarczyk: None declared, Anna Nagel: None declared, Astrid Rasmussen: None declared, Simon J. Bowman Consultant of: Abbvie, Galapagos, and Novartis in 2020-2021, Lida Radfar: None declared, Roald Omdal: None declared, Marie Wahren-Herlenius: None declared, Blake M Warner: None declared, Torsten Witte: None declared, Roland Jonsson: None declared, Maureen Rischmueller: None declared, Patrick M Gaffney: None declared, Judith A. James: None declared, Lars Ronnblom: None declared, R Hal Scofield: None declared, Xavier Mariette: None declared, Wan Fai Ng: None declared, Kathy Sivils Employee of: current employee of Janssen., Gunnel Nordmark: None declared, Betty Tsao: None declared, Christopher Lessard: None declared

POS0456 AUTOPHAGY-RELATED RISK LOCI IN SLE AND THEIR ROLE IN NEUTROPHILS

Background

Systemic lupus erythematous (SLE) is an autoimmune disease with ~150 established susceptibility risk loci. Genome wide-association (GWA) studies in SLE cases and controls of Korean ancestry identified the SLE risk locus ATG16L2-P2RY2, and rs11235604 as a SLE-associated missense variant (R220W) of Autophagy Related 16 Like 2 (ATG16L2) [1]. PRDM1-ATG5 is also an SLE risk locus in European populations that is implicated in autophagy. Autophagy plays a crucial role in neutrophil extracellular trap (NET) formation, degranulation, and limiting autoantigens in blood. Dysregulated autophagy has been implicated in SLE pathology and poor disease outcomes. The function of ATG16L2 is unknown, but evidence suggests it may function as a negative regulator of autophagosome formation [2].

Objectives

To identify autophagy-related SLE risk variants shared across different ancestry populations and define the role of ATG16L2 in SLE and autophagy.

Methods

SLE case-control GWA scans from European (7568 cases; 1082 controls), African American (4336 cases; 935 controls), Hispanic (3752 cases; 1840 controls), and Korean (1173 cases; 4213 controls) populations were imputed and SNP associations tested. Meta-analysis was performed, then Bayesian statistics were used to define a credible SNP set. Bioinformatic analyses (RegulomeDB, promoter capture Hi-C, eQTLs, etc.) further prioritized SNPs based on predicted functionality. The functional significance of autophagy SLE risk genes, ATG16L1, ATG16L,2 and ATG5, were tested by CRISPR knockout (KO) in PLB-985 cell line. CRISPR-targeted single cell clones were screened for ATG16L1, ATG16L2 or ATG5 deletion using qPCR, NanoPore sequencing, and Western blotting. Changes in autophagy were assessed by Western blotting and confocal microscopy.

Results

Transracial fine-mapping of PRDM1-ATG5 locus identified two SNP associations shared across the credible sets in all populations: rs56886418 (p=1.38x10-5) located in the intron of PRDM1 and rs77791277 (p=1.38x10-5) that tagged a group of SNPs in strong linkage disequilibrium. Cross comparison of the credible SNP sets and bioinformatic analyses of shared SNPs identified rs533733 and rs9373843 as additional likely functional variants. Bioinformatic analyses prioritized rs56886418, an eQTL for ATG5 (p=0.05) and PRDM1 (p=4.75x10-7) in blood cells positioned in a topologically associated domain (TAD) that may interact with ATG5 and PRDM1 promoters in EBV-transformed B cells. SNP rs533733 is an eQTL for ATG5 in neutrophils (p=0.006) and is in a TAD 6.4kb 3’ of PRDM1 that interacts with the ATG5 promoter region where rs9373843 (eQTL of ATG5 in neutrophils (p=0.04)) is positioned. These data suggest that risk SNPs on the PRDM1-ATG5 locus may modulate ATG5 expression and autophagy in specific cell types by modulating the local chromatin regulatory network.

To assess the roles of ATG5, ATG16L1 and ATG16L2 in autophagy, PMA/I-induced hallmarks of autophagy, LC3-I and LC3-II conversion and p62 protein aggregation, were assessed in homozygous and heterozygous ATG5, ATG16L1, or ATG16L2 CRISPR KO PLB-985 cells by Western blotting and confocal microscopy. Loss of ATG5 or ATG16L1 impaired PMA/I-induced autophagosome formation in myeloid-like and differentiated neutrophil-like PLB-985 cells. In contrast, loss of ATG16L2 elevated the conversion of LC3-I to LC3-II and p62 protein aggregation in both cell types, suggesting that ATG16L2 may inhibit autophagy.

Conclusion

Functional characterization of SNPs on the PRDM1-ATG5 and ATG16L2-P2RY2 loci, and the functional characterization of ATG16L2 in myeloid and neutrophil cell lines, provide new insights into the mechanisms that regulate autophagy in health and disease. Ongoing studies will focus on in vitro validation of predicted functional SNPs and will introduce ATG16L2 rs11235604 risk variant in PLB-985 cells to assess its importance in autophagy.

References

[1]Lessard CJ, et al. Arthritis Rheumatol. 2016; 68(5):1197-1209.

[2]Wible DJ, et al. Cell Discov. 2019; 5:42.

Disclosure of Interests

None declared.

OP0111 INTEGRATION OF GWAS AND EPIGENETIC STUDIES IDENTIFIES NOVEL GENES THAT ALTER EXPRESSION IN THE MINOR SALIVARY GLAND IN SJÖGREN’S DISEASE

Background

Sjogren’s disease (SjD) is an autoimmune disease characterized by reduced function of exocrine glands (i.e., salivary and lacrimal glands). Epithelial cell damage resulting from lymphocytic infiltration has been implicated in SjD etiology [1]. How genetic and epigenetic changes influence epithelial-immune cell interactions in SjD pathogenesis remain understudied.

Objectives

Evaluate the role of SjD risk loci in salivary gland tissue to gain insights into the potential genes involved in salivary gland dysfunction.

Methods

SNPs from 16 regions with SNP-SjD associations (P<5x10-8) in our GWAS study (3232 SjD cases) and meta-analysis of ImmunoChip data (619 SjD cases) [2] were interrogated for eQTLs using Genotype-Tissue Expression (GTEx) minor salivary gland data. Subsequent analysis identified genes that were both eQTLs in the minor salivary gland and significantly expressed in RNA-seq and ATAC-seq data from the submaxillary salivary gland epithelial cell line, A253. Pathway enrichment analysis was performed using gProfiler on the genes where coalescence of eQTL, RNA-seq, and ATAC-seq data was observed. To further validate the results, we performed transcriptome-wide association study (TWAS) analysis using GWAS summary statistics and minor salivary gland eQTL GTEx data.

Results

In total, 5884 genome-wide significant SNPs from 16 SjD risk loci were identified as potential minor salivary gland eQTLs using two discovery thresholds: p(FDR)<0.05 provided by eQTL study (3566 SNPs) and p(FDR)>0.05 and p<0.05 in eQTL study (2318 SNPs). Further analysis revealed 10 SjD risk loci with SNPs that were minor salivary gland eQTLs for a total of 155 unique genes that had a coalescence of RNA- and ATAC-seq data in A253 cells. Many SNPs altered the expression of the nearest gene to the risk allele (i.e., index gene), such as IRF5 and TNPO3 on chromosome 7 at 128Mb; however, this locus had 12 additional genes that were eQTLs in minor salivary gland. In contrast, other loci had no reported eQTLs for the index gene, but several reported eQTLs for other genes, such TYK2 on chromosome 19 at 10Mb that showed no change in TYK2 expression but eQTLs for 8 distant genes, including ICAM1. Pathway enrichment analysis revealed an enrichment in Butyrophilin (BTN) family interactions (R-HSA-8851) (PAdj=1.564x10-5), including the BTN2A1, BTN2A2, BTN3A1, BTN3A2 and BTN3A3 gene cluster in the MHC region. In further support, TWAS of the minor salivary gland and the SjD GWAS summary statistics (after Bonferroni correction) showed association between SjD and BTN3A2 (p=1.24x10-42), as well as many other loci in the MHC region. In addition, several long non-coding (lnc) RNAs on chromosome 17 were significant, peaking at RP11-259G18.1 (p=4.43x10-10).

Conclusion

This study shows that SjD-associated risk alleles influence disease by altering gene expression in immune cells and minor salivary glands. Further, our analysis suggests that altered gene expression in the minor salivary gland expands beyond effects on the index gene to several genes on each locus. Interestingly, we observed minor salivary gland eQTLs for several BTN family genes, which act as cell-surface binding partners to regulate cell-cell interactions, including interactions between epithelial cells and activated T cells [3]. Future work will assess chromatin-chromatin-interactions within the 10 SjD risk loci in salivary gland cells and tissues to map local chromatin regulatory networks that regulate gene expression. Additional transcriptional studies of SjD minor salivary gland tissues will provide further insights into how altered gene expression in the salivary gland influences SjD pathology.

References

[1]Verstappen. Nat Rev Rheumatol 2021;17(6):333-348.

[2]Khatri, et al. Annals of Rheumatic Diseases 2020;79:30-31.

[3]Arnett HA, Viney JL. Nature Reviews Immunology 2014;14:559-569.

Disclosure of Interests

Farhang Aghakhanian: None declared, Mandi M Wiley: None declared, Bhuwan Khatri: None declared, Kandice L Tessneer: None declared, Astrid Rasmussen: None declared, Simon J. Bowman Consultant of: Abbvie, Galapagos, and Novartis in 2020-2021., Lida Radfar: None declared, Roald Omdal: None declared, Marie Wahren-Herlenius: None declared, Blake M Warner: None declared, Torsten Witte: None declared, Roland Jonsson: None declared, Maureen Rischmueller: None declared, Patrick M Gaffney: None declared, Judith A. James: None declared, Lars Ronnblom: None declared, R Hal Scofield: None declared, Xavier Mariette: None declared, Marta Alarcon-Riquelme: None declared, Wan Fai Ng: None declared, Kathy Sivils Employee of: Current employee of Janssen, Gunnel Nordmark: None declared, Umesh Deshmukh: None declared, A Darise Farris: None declared, Christopher Lessard: None declared

POS0098 LINC01871, IMPLICATED IN SJÖGREN’S DISEASE PATHOGENESIS, IS REGULATED BY INTERFERON-G AND CALCINEURIN SIGNALING

Background

Sjögren’s disease (SjD) is an autoimmune disease characterized by exocrine gland dysfunction. Long non-coding RNAs (lncRNAs) are a functionally diverse class of non-protein coding RNAs that are longer than 200 nucleotides. Our previous study using whole blood RNA-seq found that lncRNA, LINC01871, is overexpressed in SjD relative to controls [1]. CRISPR-Cas9 targeting in HSB2 T cells yielded a LINC01871-/- clone with altered expression of many genes implicated in immune regulation [1].

Objectives

The goal of this study was to analyze the gene expression perturbations resulting from the loss of LINC01871 and to characterize the regulation of LINC01871 in both the LINC01871-/- clone and primary human T cells in response to immune stimuli.

Methods

Flow cytometry and LegendPlex bead assays were used to compare surface and secreted protein expression changes, respectively, in LINC01871-/- cells and the parental HSB2 cells. Parental HSB2 T cells, LINC01871-/- cells, Kasumi-3 myeloid cells, and primary human T cells were stimulated in vitro and changes in gene expression were measured over time using qRT-PCR. Responses to interferons (IFN) were assessed using universal type I IFN (IFNα) or IFNγ. TCR signaling responses were assessed using PMA/Ionomycin (PMA/I) or anti-CD3/CD28 stimulations in the presence or absence of the calcineurin inhibitor, FK506.

Results

Previous RNA-seq analysis found 1166 differentially expressed (DE) transcripts (log2FC ≥1 or ≤-1; padj ≤0.05) in LINC01871-/- cells compared to parental HSB2 cells, including many prominent immune regulatory genes. Changes in the basal expression of 7 proteins in LINC01871-/- cells were confirmed using flow cytometry (significantly decreased: CD8a (p=0.0004), CD30 (p=0.0008), CXCR3 (p=0.037), T-Bet (p=0.0002), and Aiolos (p=0.02); significantly increased: CD226 (p=0.0059) and CD44 (p=0.024)). Analysis of LINC01871-/- cells revealed a growth inhibition in LINC01871-/- cells (p=0.0014 at 72h), in which multiple secreted growth and adhesion factors were significantly reduced: GM-CSF (p=2.0e-06), M-CSF (p=2.7e-09), IGBPF4 (p=1.2e-07), s-ICAM1 (p=0.015), MMP9 (p=3.0e-14), and MMP2 (p=6e-08). In contrast, the IL-6 cytokine family member, LIF, was significantly increased in LINC01871-/- cells (p=1.2e-07). Because HSB2 cells were not responsive to all IFNs, IFN-mediated regulation of LINC01871 expression was examined in the Kasumi-3 myeloid cell line. While LINC01871 expression was not modulated by type I IFN stimulation, it was robustly responsive to IFNγ treatment. Since LINC01871 was expressed in T cells and implicated in T cell pathways, responses to TCR signaling pathways were characterized in HSB2 cells or purified primary human T cells treated with PMA/I. In both cell types, LINC01871 exhibited a prolonged decrease in expression that was abrogated by concurrent treatment with FK506, indicating that LINC01871 is regulated by calcineurin signaling. Treatment of primary human T cells with anti-CD3/CD28 to mimic true TCR engagement resulted in a modest decrease of LINC01871 expression at early time points, followed by an increase in expression with longer stimulation (2d).

Conclusion

Our findings suggest that LINC01871 is a potential mediator of the dysregulated T cell inflammatory response pathways implicated in SjD pathogenesis. LINC01871 influences the expression of many important immune cell genes and growth factors, is inducible by IFNγ, and is regulated directly by calcineurin signaling and TCR ligand engagement. Although LINC01871 functions are still unknown, observed LINC01871 overexpression in whole blood of SjD cases and after prolonged TCR stimulation in primary human T cells suggests that it could be a biomarker of SjD.

References

[1]Joachims, et al. Annals of the Rheumatic Diseases 2020;79:90.

Disclosure of Interests

Michelle L Joachims: None declared, Bhuwan Khatri: None declared, Chuang Li: None declared, Kandice L Tessneer: None declared, John Ice: None declared, Anna M Stolarczyk: None declared, Nicolas Means: None declared, Kiely Grundahl: None declared, Stuart Glenn: None declared, Jennifer Kelly: None declared, David Lewis: None declared, Lida Radfar: None declared, Donald Stone: None declared, Joel Guthridge: None declared, Judith A. James: None declared, R Hal Scofield: None declared, Graham B Wiley: None declared, Jonathan Wren: None declared, Patrick M Gaffney: None declared, Courtney Montgomery: None declared, Kathy Sivils Employee of: Current employee of Janssen., Astrid Rasmussen: None declared, A Darise Farris: None declared, Indra Adrianto: None declared, Christopher Lessard: None declared

AB0026 CELL TYPE-SPECIFIC DYSREGULATION FOUND TO DIFFERENTIATE PATIENT SUBSETS OF SJÖGREN’S DISEASE

Background

Sjögren’s disease (SjD) is a chronic, heterogenous autoimmune disorder characterized by inflammatory destruction of the exocrine glands and Ro autoantibodies. Previous studies, most in whole blood, reported transcriptional and cell type differences between SjD subphenotypes.

Objectives

Evaluate the role of cell type-specific dysregulation in subpopulations of SjD patients having focal lymphocytic sialadenitis and/or anti-Ro/SSA and/or ANA positivity using single-cell RNA-seq (scRNA-seq).

Methods

Peripherical blood mononuclear cells (PBMCs) stored at -120°C from 30 SjD patients and 10 healthy controls (HCs) were selected from our OMRF Sjögren’s Research Cohort based on ACR/EULAR 2016 criteria. PBMCs were captured, libraries processed using 10X Genomics Chromium v3.1 and sequenced to a depth of ~45,000 reads/cell. 10X Genomics Cell Ranger (v 6.1.2) cell multiplexing pipeline was used to align reads to the GRCh38 human genome and separate combined data to per-sample output files. Seurat R package was used for quality control (QC), integration, clustering, and cell type assignment. Differential expression (DE) analysis was done using Seurat for genes with 10% or more of the cells showing expression. DE transcripts (defined as padj<0.05) were evaluated using Ingenuity Pathway Analysis (IPA).

Results

After removing cells with low feature counts, high mitochondrial gene counts, and/or other QC criteria, a total of 331,981 cells were captured. Cells were mapped to 28 clusters using Seurat, then cell types were predicted using marker genes developed from an in-house reference panel of publicly available scRNA-seq datasets. Mapping condensed the 28 observed cell clusters to 19 clusters of specific cell types; 4 clusters remained unidentified. Percentages of each cell type were compared across various subsets of SjD (Ro+; Ro-; Ro-/ANA+; Ro-/ANA-) and HCs. CD14 monocytes were decreased in Ro-/ANA- vs. Ro+ or Ro-/ANA+ cases (p<0.05) and trended downward when compared to HCs (p=0.057). CD8 central memory T cells (TCM) were decreased in Ro+ vs. Ro- or Ro-/ANA- cases (p<0.02) and trended downward when vs. HCs (p=0.076). Conventional dendric cells (DCs) were increased in Ro+ vs. Ro-/ANA- SjD cases (p=0.036) and trended upward in Ro+ vs. Ro- cases (p=0.08) but were not significantly different from HCs. Natural killer (NK) cells were increased in both Ro-/ANA- and Ro- vs. Ro+ (p<0.05).

DE analysis between immune cell subsets revealed potential subphenotype-specific differences in pathophysiology. Interferon signaling was upregulated in CD14 monocytes, naïve B, and CD4 central memory (TCM) cells from the Ro+ subset. Ro+ subset also showed upregulation of genes involved in T cell receptor signaling in CD4 cytotoxic T (CTL), CD4 TCM, and CD4 effector memory T (TEM) cells, but downregulation of this pathway in CD8 TCM cells. Ro+ subset also exhibited increased B cell receptor signaling pathway in naïve and memory B cells. Ro+ subset showed downregulation of autophagy in naïve B, CD4 CTL, CD4 TCM, and CD4 TEM cells. Several cell types in Ro+ and Ro-(ANA+/-) subsets showed decreased DE of genes involved in nitric oxide production and NRF2 oxidative stress pathways. Ro- (ANA+/-) vs. HCs showed increased IL6 and TREM1 signaling pathways in CD14 and CD16 monocytes. While Ro+ subsets showed upregulation of B and T cell pathways (shown previously in lupus), Ro- (ANA+/-) showed dysregulation of osteoarthritis and neuroinflammatory pathways. Interestingly, among the DE long intergenic non-coding (linc)RNAs found herein, we observed that LINC01871, which we previously reported as DE in all subsets of SjD, was overexpressed in CD4 CTL and NK cells in both Ro+ and Ro- (ANA-) vs. HCs.

Conclusion

This interim analysis shows similarities and differences in the dysregulation of genes and pathways for specific cell subsets from our Ro+ and Ro- (ANA+/-) subsets of SjD, potentially allowing for more tailored diagnostics and interventions for the disease in the future.

Disclosure of Interests

Chuang Li: None declared, Bhuwan Khatri: None declared, Anna M Stolarczyk: None declared, Kandice L Tessneer: None declared, Astrid Rasmussen: None declared, Joel Guthridge: None declared, Judith A. James: None declared, R Hal Scofield: None declared, He Li Employee of: Current employee of Janssen, A Darise Farris Grant/research support from: Active collaborative research agreement with Janssen, Kathy Sivils Employee of: Current employee of Janssen, Christopher Lessard Grant/research support from: Active collaborative research agreement with Janssen

Anxiety, Depression and Functional Impairment among Health Care Workers during COVID-19 Pandemic: A Crosssectional Online Survey

Background COVID-19 is an infectious disease caused by a newly discovered coronavirus. The number of cases and dramatic loss of human life worldwide created psychological problems among general public, including health care workers. Objective To determine the burden of anxiety, depression, and functional impairment among health care workers in the early days of lockdown during the first wave of COVID-19 outbreak in Nepal. Method A hospital-based cross-sectional study was carried out among all the employees of Hospital for Children Eye ENT and Rehabilitation Services, Bhaktapur during the COVID-19 pandemic lockdown from April 3, 2020 to May 2, 2020 using an online questionnaire. The tools used were adopted from Nepali version of Hospital Anxiety and Depression scale (HADS) and Nepali version of WHO Disability Assessment Schedule (WHODAS 2.0). Result The mean age (SD) of the participants (n=86) was 32.53 (7.92) years. Male and female participants were equal in number. The point prevalence of anxiety and depression was 25.6% and 14.0%, respectively. Females had a higher prevalence of both anxiety (39.5% vs 11.6%, p < 0.01) and depression (18.6% vs 9.3%, p=0.351). Clinical and nonclinical staff both had a higher prevalence of both anxiety (31.0% and 20.5%, p=0.265) and depression (16.7% and 11.4%, p=0.478). The mean functional impairment score (WHODAS 2.0) among all participants and participants with anxiety and depression was 19.47 (95% CI: 18.13-20.80), 21.27 (95% CI: 18.08-24.46), and 19.92 (95% CI: 15.28- 24.56), respectively. Conclusion Anxiety and depression during the first lockdown due to COVID-19 pandemic were highly prevalent in clinical and non-clinical employees. Besides controlling the outbreak, special consideration should be given to mental health.

OP0140 DYSREGULATED EXPRESSION OF THE LONG NON-CODING RNA, LINC01871, IMPLICATED IN SJÖGREN’S SYNDROME PATHOGENESIS

Background:

Sjögren’s syndrome (SS) is a chronic, heterogenous autoimmune disease characterized by inflammatory destruction of the exocrine glands. Long non-coding RNAs (lncRNAs) have emerged as a functionally diverse class of non-protein coding RNA (ncRNA) with increasing implications in interferon signaling, immune cell regulation, and autoimmune disease pathology. The potential role of lncRNAs in SS pathogenesis is unknown.

Objectives:

To identify and characterize candidate lncRNAs with potential relevance to SS pathology.

Methods:

RNA-seq was used on whole blood from SS patients (n=30 antibody negative (Ro-); n=27 antibody positive (Ro+)) and healthy controls (HC, n=27) to identify differentially expressed (DE) lncRNAs (log2 fold change (FC) ≥ 2 or ≤ 0.5; padj<0.05). Bioinformatic and pathway analyses were used to predict lncRNA function.In vitrotime course experiments in HSB2 T cell lymphoblasts stimulated with PMA/Ionomycin (PMA/I) or type I interferon (IFN) were used to assess biological relevance.LINC01871function was further investigated by RNA-seq on a single cell clone of HSB2 with confirmed CRISPR-targetedLINC01871deletion (LINC01871-/-).

Results:

We identified a total of 1054 unique DE ncRNAs between Ro+, Ro-and/or a combined analysis relative to HC; of these, 45 (1 long intergenic ncRNA (lincRNA), 1 antisense, 43 pseudogenes) were overexpressed in all 3 SS subsets. To begin investigating the function of the previously undescribed lincRNA,LINC01871(SSRo-: FC=2.85; padj=1.1x10-4), we performed a correlation analysis of the SSRo-transcriptome, which found several co-expressed protein coding RNAs involved in immune regulation (THEMIS,TBX21,IL10RA,IL2RB,among many others). Similarly, Ingenuity Pathway Analysis of the SS transcriptome compared to HC, as well as several gene ontology enrichment analyses of publicly available RNA expression correlation databases, identified shared immune-related pathways including cytotoxic T cell, natural killer cell, and T cell regulation. To further study the role ofLINC01871in cytotoxic T cells, we used qRT-PCR to resolve the effects of PMA/I or type I IFN stimulation onLINC01871expression in the T lymphoblastoid HSB2 cells.LINC01871expression was downregulated after PMA/I stimulation, but unchanged with type I IFN stimulation. To explore the regulatory function ofLINC01871in T cells, we targetedLINC01871in HSB2 cells using CRISPR. To this end, we generated a single cellLINC01871-/-clone with no RNA expression by qPCR and confirmed homozygous deletion using DNA sequencing. RNA-seq analysis ofLINC01871-/-compared to unmodified HSB2 cells identified 1166 DE transcripts. Pathway analyses clustered the DE transcripts into similar immune regulatory, cytotoxic and T cell pathways identified in SSRo-whole blood RNA-seq and publicly available RNA-seq databases. Further, several prominent T cell regulatory transcripts that exhibited correlated upregulation withLINC01871in SSRo-whole blood RNA-seq also demonstrated downregulation afterLINC01871deletion:CD109(FC=-9.7; padj=5.3x10-16),IL22(FC=-8.1; padj=7.6x10-11),PDCD1(FC=-6.2; padj=1.1x10-6),THEMIS(FC=-3.8; padj=2.7x10-165) andTBX21(FC=-2.1; padj=3.3x10-25).

Conclusion:

LncRNAs are emerging as important regulators of immune function with increasing evidence of autoimmune disease relevance. Here, we leveraged RNA-seq, extensive bioinformatic data, and CRISPR technology to identify and functionally characterizeLINC01871as a potential mediator of the dysregulated T cell inflammatory response pathways implicated in SS pathogenesis.

Disclosure of Interests:

Michelle L Joachims: None declared, Bhuwan Khatri: None declared, Kandice L Tessneer: None declared, Anna M Stolarczyk: None declared, Graham B Wiley: None declared, Astrid Rasmussen Speakers bureau: Novartis, ThermoFischer, Joel Guthridge Grant/research support from: Xencor, Bristol Myers Squibb, DXterity, Judith A. James Grant/research support from: Progentec Diagnostics, Inc, Consultant of: Abbvie, Novartis, Jannsen, R Hal Scofield Grant/research support from: Pfizer, Kathy L Sivils: None declared, Indra Adrianto: None declared, Christopher Lessard: None declared

OP0139 FUNCTIONAL EVALUATION OF THE SJÖGREN’S SYNDROME AND SYSTEMIC LUPUS ERYTHEMATOSUS DDX6-CXCR5 RISK INTERVAL

Background:

Sjögren’s Syndrome (SS) and Systemic Lupus Erythematosus (SLE) are distinct chronic, complex autoimmune diseases with shared characteristics such as autoantibodies, heightened interferons, and polyarthritis. SS and SLE genome-wide association studies (GWAS) report strong associations with theDDX6-CXCR5risk interval. DDX6 suppresses interferon stimulated gene expression and CXCR5 regulates T cell functions implicated in autoimmunity.

Objectives:

To identify functional variants that impact regulation in theDDX6-CXCR5interval.

Methods:

Fine-mapping was done using ImmunoChip data from 3785 SLE, 1916 SS cases and 6893 population controls of European ancestry that were imputed and tested for SNP-trait association. Bayesian statistics assigned posterior probabilities to SNPs and defined a credible set of risk variants. Bioinformatic analyses further prioritized variants with predicted functionality. Electrophoretic mobility shift assays (EMSAs) and luciferase expression were used to validate predicted SNPs in EBV transformed B (EBV B) cells.

Results:

While some differences were observed, the overall SS and SLE association signals were similar. SNP-SS rs9736016 nearCXCR5and SNP-SLE rs76409436 nearDDX6were the most significant but did not show evidence of functionality. Bayesian statistics defined credible sets of variants in strong D’ in common between both SS and SLE. Bioinformatics analyses (Haploreg, RegulomeDB, ENCODE data, etc) further refined the credible set and identified 5 common SNPs with strong evidence of functionality in immune cell types: rs4938572, rs4936443, rs57494551, rs7117261 and rs4938573. EMSAs showed a significant increase in protein binding to the risk allele of rs57494551 (p=0.0001), rs7117261 (p=0.0001) and rs4938573 (p=0.0003), but not the others, using nuclear lysates from EBV B cells. Luciferase vectors with a minimal promoter or no promoter were used to test for enhancer or promoter activity, respectively. To this end, the rs57494551 risk allele exhibited a significant increase in enhancer activity (p=0.0001). In contrast, the rs7117261 risk allele decreased enhancer activity (p=0.018). The rs4938573 risk allele decreased enhancer (p=0.043) and promoter (p=0.024) activity. While rs7117261 or rs4938573 were not reported in eQTL databases, GTex data reported rs57494551 as an eQTL that altersDDX6expression in whole blood (p=1.8E-7). Additionally, these functional SNPs have been associated with looping events to several proximal promoters in nearby genes in immune cells.

Conclusion:

SS and SLE have similar genomic architecture across theDDX6-CXCR5risk interval. Multiple variants in the credible set exhibited allele specific changes in protein binding, as well as modified enhancer activity, promoter activity or both. Ongoing studies will use Cas9 in EBV B cells to determine which other loci are within the local regulatory network.

Disclosure of Interests:

Mandi M Wiley: None declared, Bhuwan Khatri: None declared, Kandice L Tessneer: None declared, Michelle L Joachims: None declared, Anna M Stolarczyk: None declared, Astrid Rasmussen Speakers bureau: Novartis, ThermoFischer, Simon J. Bowman Consultant of: Astrazeneca, Biogen, BMS, Celgene, Medimmune, MTPharma, Novartis, Ono, UCB, xtlbio, Glapagos, Speakers bureau: Novartis, Lida Radfar: None declared, Roald Omdal: None declared, Marie Wahren-Herlenius: None declared, Blake M Warner: None declared, Torsten Witte: None declared, Roland Jonsson: None declared, Maureen Rischmueller: None declared, Patrick M Gaffney: None declared, Judith A. James Grant/research support from: Progentec Diagnostics, Inc, Consultant of: Abbvie, Novartis, Jannsen, Lars Ronnblom Grant/research support from: AZ, Speakers bureau: AZ, R Hal Scofield Grant/research support from: Pfizer, Xavier Mariette: None declared, Wan-fai Ng: None declared, Kathy L Sivils: None declared, Gunnel Nordmark: None declared, Betty Tsao: None declared, Christopher Lessard: None declared

OP0047 GENOME-WIDE ASSOCIATION STUDY OF SJÖGREN’S SYNDROME IDENTIFIES TEN NEW RISK LOCI

Background:

Sjögren’s syndrome (SS) is a complex autoimmune disease with exocrine gland dysfunction leading to substantial morbidity. There are 10 published genetic susceptibility loci.

Objectives:

Our genome-wide association study (GWAS) aimed to identify additional risk loci of genome-wide significance (GWS; p<5E-08) in European-derived primary SS.

Methods:

A total of 3232 cases and 17481 controls genotyped on GWAS arrays and 619 cases and 6171 controls genotyped on ImmunoChip (IC) arrays were imputed after quality control. Logistic regression was calculated adjusting for ancestry using the first 4 principal components to identify SS-associated SNPs. GWAS and IC results were meta-analyzed using weighted Z-scores. Bayesian statistics were used to assign posterior probabilities and define credible SNP sets for each locus. Bioinformatic analyses were used to predict functionality.

Results:

Seven novel loci exceeded GWS in the GWAS analysis:NAB1,MIR146A-PTTG1,XKR6,MAPT-CRHR1,RPTOR-CHMP6-BAIAP2,TYK2andSYNGR1. Meta-analysis with IC data identified three more novel loci exceeding GWS:CD247,PRDM1-ATG5andTNFAIP3. Several additional loci with suggestive association (p<1E-05) were also identified:ADAMTSL2,CGNL1andPHRF1.

Several identified loci have reported functional implications in immune regulation and autoimmune disease. In lupus, rs2431697 correlated with rs2431098, which was shown to alterMIR146Aexpression, resulting in type I interferon pathway imbalance. Similarly,TYK2risk association reportedly drives interferon, IL10 and RET signaling pathways.PRDM1encodes Blimp-1, a master regulator of immune cell differentiation.CD247encodes the zeta subunit of the T cell receptor complex.XKR6is implicated in apoptotic cell ingestion.ATG5is also involved in apoptosis, as well as autophagy and antigen presentation.

Additional bioinformatics analyses (Haploreg, Regulome DB, ENCODE, etc.) revealed immune-relevant functional implications for each risk locus. The SS-associated credible set included variants downstream ofTNFAIP3in a region reported to abolish looping between an enhancer and theTNFAIP3promoter in lupus and a coding variant that has been shown to alter NF-kB activity and neutrophil extra-cellular traps. The rs2293765 in the 5’ UTR ofNAB1showed evidence of enhancer/promoter activities. The rs2069235 in theSYNGR1locus showed enhancer and transcription start site activities in B and T cells. The rs7210219 in theMAPT-CRHR1locus showed enhancer/promotor activities in various tissues.

Conclusion:

We have identified ten novel genetic susceptibility loci associated with SS pathology. Our finding increases the current number of GWS regions in SS patients of European origin, from 10 to 20. Future work is needed to identify and characterize the functional variants in each region.

Disclosure of Interests:

Bhuwan Khatri: None declared, Tove Ragna Reksten: None declared, Kandice L Tessneer: None declared, Astrid Rasmussen Speakers bureau: Novartis, ThermoFischer, R Hal Scofield Grant/research support from: Pfizer, Simon J. Bowman Consultant of: Astrazeneca, Biogen, BMS, Celgene, Medimmune, MTPharma, Novartis, Ono, UCB, xtlbio, Glapagos, Speakers bureau: Novartis, Joel Guthridge Grant/research support from: Xencor, Bristol Myers Squibb, DXterity, Judith A. James Grant/research support from: Progentec Diagnostics, Inc, Consultant of: Abbvie, Novartis, Jannsen, Lars Ronnblom Grant/research support from: AZ, Speakers bureau: AZ, Blake M Warner: None declared, Xavier Mariette: None declared, Roald Omdal: None declared, Javier Martin Ibanez: None declared, Maria Teruel: None declared, Janicke Liaaen Jensen: None declared, Lara A Aqrawi: None declared, Øyvind Palm: None declared, Marie Wahren-Herlenius: None declared, Torsten Witte: None declared, Roland Jonsson: None declared, Maureen Rischmueller: None declared, A Darise Farris Speakers bureau: Biogen, Marta Alarcon-Riquelme: None declared, Wan-fai Ng: None declared, Kathy L Sivils: None declared, Gunnel Nordmark: None declared, Christopher Lessard: None declared

Genome re-sequencing to identify single nucleotide polymorphism markers for muscle color traits in broiler chickens

OBJECTIVE

Meat quality including muscle color in chickens is an important trait and continuous selective pressures for fast growth and high yield have negatively impacted this trait. This study was conducted to investigate genetic variations responsible for regulating muscle color.

METHODS

Whole genome re-sequencing analysis using Illumina HiSeq paired end read method was performed with pooled DNA samples isolated from two broiler chicken lines divergently selected for muscle color (high muscle color [HMC] and low muscle color [LMC]) along with their random bred control line (RAN). Sequencing read data was aligned to the chicken reference genome sequence for Red Jungle Fowl (Galgal4) using reference based genome alignment with NGen program of the Lasergene software package. The potential causal single nucleotide polymorphisms (SNPs) showing non-synonymous changes in coding DNA sequence regions were chosen in each line. Bioinformatic analyses to interpret functions of genes retaining SNPs were performed using the ingenuity pathways analysis (IPA).

RESULTS

Millions of SNPs were identified and totally 2,884 SNPs (1,307 for HMC and 1,577 for LMC) showing >75% SNP rates could induce non-synonymous mutations in amino acid sequences. Of those, SNPs showing over 10 read depths yielded 15 more reliable SNPs including 1 for HMC and 14 for LMC. The IPA analyses suggested that meat color in chickens appeared to be associated with chromosomal DNA stability, the functions of ubiquitylation (UBC) and quality and quantity of various subtypes of collagens.

CONCLUSION

In this study, various potential genetic markers showing amino acid changes were identified in differential meat color lines, that can be used for further animal selection strategy.

EFFECT OF FINGOLIMOD VS. IFN-BETA1A ON NO EVIDENCE OF DISEASE ACTIVITY

Introduction

To compare effects of fingolimod vs. interferon beta-1a (IFN) in achieving no evidence of disease activity (NEDA-4) in patients with relapsing-remitting multiple sclerosis (RRMS) in the TRANSFORMS study. Adding Brain Volume Loss (BVL) to NEDA results in a more comprehensive and balanced measure of focal and diffuse damage.

Methods

In this post-hoc analysis, we used data from the fingolimod 0.5 mg daily (n=431) and IFN 30 µg weekly (n=435) groups. NEDA-4 was defined as absence of confirmed relapses, new/enlarging T2 lesions, 6-month confirmed disability progression (CDP) and BVL (annual percent brain volume change [PBVC] of >−0.4%). 3-month CDP and additional PBVC cut-offs representing mean BVL rates in healthy adults (0.2%), MS patients (0.6%), or accelerated BVL (1.2%) were also tested. Odds ratios (OR) were calculated for differences between fingolimod- and IFN-treated groups.

Results

Significantly more fingolimod (n=425) than IFN-treated patients (n=418) achieved NEDA-4 status: 27.9% vs. 16.7% (OR:1.93; 95% CI: 1.36–2.73; p=0.0002). Results were similar for other PBVC cut-offs: (>–0.2%): 20.2% vs 11.5%; 1.94; 1.30–2.90, p=0.0011; (>–0.6%): 34.6% vs 20.4%; 2.06; 1.49–2.86, p<0.0001; (>–1.2%): 40.8% vs 26.4%; 1.92; 1.42–2.60; p<0.0001.

Conclusion

Fingolimod-treated patients had twice the odds of achieving NEDA-4 status over 1 year as patients treated with IFN.

Maximizing productivity and improving nutrition through intercropping quality protein maize and potato

Intercropping potato with quality protein maize (QPM) could improve the livelihood and nutritional status of the resource-poor farmers who produce and consume them. A study was conducted from 2008 to 2010 to assess the performance of three improved potato varieties in an intercropping system with an improved QPM in the high hills of Nepal. The QPM was sown for four consecutive weeks following potato planting. The commercial potato varieties Janak Dev, Kufri Jyoti and Khumal Seto-1 were used, while the improved QPM was Poshilo Makai-1. Delayed intercropping caused a reduction in the maize yield, but an increase in the potato yield. The highest potato yield was obtained from maize intercropping after four weeks. The grain yield of maize was significantly reduced by late planting beyond the second week. The average weekly rate of increase due to maize intercropping was better for Janak Dev and Kufri Jyoti, while Khumal Seto-1 was less suitable for intercropping. The land equivalent ratio for potato-maize intercropping was 2.23. The results suggest that Poshilo Makai-1 could be incorporated in potato-maize intercropping, leading to higher returns and nutritional benefits. The findings underline the importance of variety and date of intercropping to maximize production. The findings have implications for harnessing higher productivity on resource-poor farms, and could contribute to food and nutritional security for resource-poor farmers.

The burden of dengue infection in some vulnerable regions of Nepal

Dengue is an emerging mosquito borne disease of public health importance in Nepal. A descriptive cross sectional study was carried out to estimate sero-prevalence and distribution pattern of dengue in certain vulnerable regions of Nepal from June to September 2009. A total of 460 venous blood samples were collected from individuals experiencing a febrile illness clinically consistent with dengue infection visiting nearby hospitals of Kanchanpur, Kailali, Banke, Dang and Chitwan districts. The sero-prevalence of dengue virus specific IgM was determined by enzyme linked immunosorbent assay (ELISA) kit. The anti-dengue IgM positivity was found to be 12.17%. The higher frequency of positive cases (16.4%) were from age group 20-40 years followed by < 20 years age group with 9.7% and 5.3% from > 40 years age group. The association between dengue infection and age is found to be statistically significant (p < 0.05). The male:female ratio was determined as 1.3:1 in IgM positive population. Among sampling areas, Kanchanpur showed highest prevalence of dengue infection (15.5%) followed by Chitwan (11.7%), Kailai (11.1%), Banke (10.7%) and Dang (8.3%). Similarly, 94.6% of the positive cases were indigeneous and had no history of travel to other countries. Dengue is firmly established in terai region with increasing trends of infection and expansion into newer areas raising a public health threat. Regular epidemiological studies are suggested which could further reveal the contributing factors associated with dengue virus infection and help in formulating strategies in reducing the transmission rate and control of the infection.

Etiology and antimicrobial susceptibility pattern of bacterial pathogens from urinary tract infection

Urinary tract infection (UTI) is the most common infection in both community and hospital patients. In majority of the cases, empirical antimicrobial treatment is practiced before the laboratory results of urine culture. Thus, antibiotic resistance may increase in urinary bacterial pathogens due to improper use of drugs. This study was designed to find out the etiological agents of UTI and their prevalence, and to determine the antimicrobial susceptibility pattern of the bacterial pathogens isolated from urine culture. This study was conducted in Kathmandu Model Hospital, Kathmandu, Nepal from April to October, 2009. Midstream Urine samples from 1323 patients suspected of UTI were analyzed by microscopy, and conventional semi-quantitative culture technique for the significant growth. Antimicrobial susceptibility test was performed for the isolates by Modified Kirby-Bauer disk diffusion method. Data were analyzed using SPSS software window version 16. The overall prevalence of UTI was found to be 18.89%. The most frequent causative organisms isolated were Escherichia coli (82.30%), Enterococcus faecalis (5.60%), Citrobacter freundii (3.60%), Enterobacter aerogenes (2.40%), Coagulase Negative Staphylococci (2.40%), Pseudomonas aeruginosa (1.20%), Proteus mirabilis (0.8%), Klebsiella pneumoniae (0.4%), and Staphylococcus aureus (0.4%). Nitrofurantoin and Amoxycillin were found to be the most effective antibiotic against gram negative and gram positive isolates respectively. E. coli was found to be the most common etiological agent of UTI and Nitrofurantoin was the most effective drug among the isolates.

Leprosy affects the tibial nerves diffusely from the middle of the thigh to the sole of the foot, including skip lesions

This study investigated where leprosy affects the posterior tibial nerve and whether neurolysis is beneficial. Nine patients with bilateral posterior tibial leprous neuropathy with no sensorimotor recovery were studied. Preoperative sensory-muscle and nerve conduction velocity testing revealed the tarsal tunnel to be the site of a severe lesion in all cases. During surgery, the most proximal site of the nerve lesion was detected by electrically stimulating the spinal roots from the second lumbar nerve to the fourth sacral nerve, evoking efferent mixed nerve compound action potentials that were recorded from the exposed tibial nerve. In all patients, the nerve compound action potentials became normal only proximal to the sciatic nerve bifurcation. Epineuriotomy within these seemingly unaffected segments revealed fibrosis of the interfascicular epineurium. Interfascicular neurolysis was performed on all affected segments. A 2-year follow-up showed an increase in girth of the proximal calf musculature in six of eight patients (the ninth patient had no recordable nerve conduction velocity). It was concluded that (1) leprosy affects the tibial nerves in a scattered way from the sciatic nerve main trunk distally to the exit of the tarsal tunnel; and (2) interfascicular, microsurgical neurolysis is beneficial provided that it is performed on all affected nerve segments.

Use of Van Nes rotationplasty to manage a burnt knee

An 11 month old child sustained a deep burn injury to the left knee causing total destruction and sequestration of the knee epiphyses. The ensuing leg length discrepancy with growth was managed by a Van Nes rotationplasty at age four with a good immediate functional result using a below 'knee' prosthesis and the prospect of continuing ambulation as he grows. The surgical options for managing this problem are discussed.

A 3 year prospective audit of burns patients treated at the Western Regional Hospital of Nepal

Burns in Nepal cause an estimated 1700 deaths per year and much suffering. We carried out a prospective 3 year audit of 237 burns patients admitted to the Western Regional Hospital in Pokhara. The aims were to assess the profile of burns injuries and what could be achieved in local conditions to guide colleagues in developing countries with limited medical facilities. The majority of burns occurred at home and were largely preventable. 61 per cent of patients were children under 15 years of age. There were more female patients and females had more severe burns. No patients with greater than 40 per cent body surface area burns of any age group survived. Public education on burns prevention is needed but poverty, ignorance and a fatalistic attitude are difficult underlying causes to change.

Immune reactivity against membranes containing ganglioside GM1 in chronic-progressive multiple sclerosis: observation by spin-membrane immunoassay

A spin-membrane immunoassay has been employed to examine the immune reactivity of whole serum from patients with chronic-progressive multiple sclerosis (CPMS) against liposomes containing ganglioside GM1. Exposure to serum resulted in complement-mediated lysis of the GM1-liposomes. No lysis occurred with liposomes devoid of ganglioside. The mean (+/- S.E.M.) lysis values were 52.6 (+/- 9.8)% for fifteen CPMS patients and 32.9 (+/- 7.2)% for nine controls. The difference between the means was highly significant (student's t-test, P less than 0.0001), indicating increased anti-ganglioside immunity in patients with CPMS.

Detection of demyelinated plaques with xenon-enhanced computed tomography

Studies of xenon-enhanced CT for detecting cerebral demyelination have produced conflicting results. Therefore, we studied the effect of xenon inhalation on the CT appearance of five demyelinated plaques. The plaques and the surrounding white matter increased commensurately in attenuation during xenon inhalation. Therefore, xenon enhancement does not generally increase the sensitivity of CT for detecting cerebral demyelination.