The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning autoimmune and infectious diseases, transplantation and cancer. While coding variation in HLA genes has been ...extensively documented, regulatory genetic variation modulating HLA expression levels has not been comprehensively investigated. Here we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues. To mitigate technical confounding, we developed scHLApers, a pipeline to accurately quantify single-cell HLA expression using personalized reference genomes. We identified cell-type-specific cis-eQTLs for every classical HLA gene. Modeling eQTLs at single-cell resolution revealed that many eQTL effects are dynamic across cell states even within a cell type. HLA-DQ genes exhibit particularly cell-state-dependent effects within myeloid, B and T cells. For example, a T cell HLA-DQA1 eQTL ( rs3104371 ) is strongest in cytotoxic cells. Dynamic HLA regulation may underlie important interindividual variability in immune responses.
Objective
Recent studies have uncovered diverse cell types and states in the rheumatoid arthritis (RA) synovium; however, limited data exist correlating these findings with patient‐level clinical ...information. Using the largest cohort to date with clinical and multicell data, we determined associations between RA clinical factors with cell types and states in the RA synovium.
Methods
The Accelerated Medicines Partnership Rheumatoid Arthritis study recruited patients with active RA who were not receiving disease‐modifying antirheumatic drugs (DMARDs) or who had an inadequate response to methotrexate (MTX) or tumor necrosis factor inhibitors. RA clinical factors were systematically collected. Biopsies were performed on an inflamed joint, and tissue were disaggregated and processed with a cellular indexing of transcriptomes and epitopes sequencing pipeline from which the following cell type percentages and cell type abundance phenotypes (CTAPs) were derived: endothelial, fibroblast, and myeloid (EFM); fibroblasts; myeloid; T and B cells; T cells and fibroblasts (TF); and T and myeloid cells. Correlations were measured between RA clinical factors, cell type percentage, and CTAPs.
Results
We studied 72 patients (mean age 57 years, 75% women, 83% seropositive, mean RA duration 6.6 years, mean Disease Activity Score‐28 C‐reactive Protein 3 DAS28‐CRP3 score 4.8). Higher DAS28‐CRP3 correlated with a higher T cell percentage (P < 0.01). Those receiving MTX and not a biologic DMARD (bDMARD) had a higher percentage of B cells versus those receiving no DMARDs (P < 0.01). Most of those receiving bDMARDs were categorized as EFM (57%), whereas none were TF. No significant difference was observed across CTAPs for age, sex, RA disease duration, or DAS28‐CRP3.
Conclusion
In this comprehensive screen of clinical factors, we observed differential associations between DMARDs and cell phenotypes, suggesting that RA therapies, more than other clinical factors, may impact cell type/state in the synovium and ultimately influence response to subsequent therapies.
It has been presumed that rheumatoid arthritis (RA) joint pain is related to inflammation in the synovium; however, recent studies reveal that pain scores in patients do not correlate with synovial ...inflammation. We developed a machine-learning approach (graph-based gene expression module identification or GbGMI) to identify an 815-gene expression module associated with pain in synovial biopsy samples from patients with established RA who had limited synovial inflammation at arthroplasty. We then validated this finding in an independent cohort of synovial biopsy samples from patients who had early untreated RA with little inflammation. Single-cell RNA sequencing analyses indicated that most of these 815 genes were most robustly expressed by lining layer synovial fibroblasts. Receptor-ligand interaction analysis predicted cross-talk between human lining layer fibroblasts and human dorsal root ganglion neurons expressing calcitonin gene-related peptide (CGRP
). Both RA synovial fibroblast culture supernatant and netrin-4, which is abundantly expressed by lining fibroblasts and was within the GbGMI-identified pain-associated gene module, increased the branching of pain-sensitive murine CGRP
dorsal root ganglion neurons in vitro. Imaging of solvent-cleared synovial tissue with little inflammation from humans with RA revealed CGRP
pain-sensing neurons encasing blood vessels growing into synovial hypertrophic papilla. Together, these findings support a model whereby synovial lining fibroblasts express genes associated with pain that enhance the growth of pain-sensing neurons into regions of synovial hypertrophy in RA.
Familial hypercholesterolemia (FH), the most common and severe monogenic form of hypercholesterolemia, is an autosomal co-dominant disease characterized by an increased plasma low density lipoprotein ...(LDL)-cholesterol concentration and premature coronary heart disease (CHD). The clinical phenotype depends on the gene involved and severity of mutation (or mutations) present. Patients with homozygous or compound heterozygous FH have severe hypercholesterolemia (LDL-cholesterol >13 mmol/L) due to a gene dosing effect and without treatment have accelerated atherosclerotic CHD from birth, and frequently die of CHD before age 30. Cholesterol-lowering therapies have been shown to reduce both mortality and major adverse cardiovascular events in individuals with FH. Lipoprotein apheresis concomitant with lipid-lowering therapy is the treatment of choice for homozygous FH. This article describes the rationale and role of lipoprotein apheresis in the treatment of severe FH and outlines the recent advances in new pharmacotherapies for this condition.
Background Familial hypercholesterolemia (FH) is a dominantly inherited disorder characterized by high plasma cholesterol levels and a very high risk of early heart disease. The prevalence of FH is ...estimated to be at least 1:500, with at least 3.6 million individuals in the Asia-Pacific region. Objective To assess awareness, knowledge, and perception of FH among practicing physicians in Japan, South Korea, and Taiwan. Methods Physicians from 3 economically developed Asian countries were requested to anonymously complete a structured Internet-based survey regarding FH. This survey sought responses on the clinical description, inheritance, prevalence, cardiovascular disease risk, practices, and opinions on screening. Results Of 230 physicians surveyed, 47% were aware of the heritability, 27% of the prevalence, and 13% of the risk of cardiovascular disease relating to FH. The majority (70%) perceived themselves to have an above-moderate familiarity with FH. Primary care physicians (59%) and lipid specialists (41%) were perceived as the best providers for caring for FH, including cascade screening services, with a lesser role perceived for cardiologists, endocrinologists, and no significant role for nursing staff. Only 35% of physicians were aware of specialist clinical services for lipid disorders in their geographic area. Conclusion Extensive education and training programs are required to complement the implementation of region-specific models of care for FH in Asia. Further enhancement of existing lipid services and facilities are also warranted to optimise service models.
Background Familial hypercholesterolaemia (FH) is a common autosomal co-dominant condition that causes premature cardiovascular disease. Awareness of FH is poor and only 10–15% of the affected ...population is identified. Electronic health records provide an opportunity to increase detection and awareness in general practice Objective To determine whether a simple electronic extraction tool can increase detection of FH in general practice. Method An extraction tool applied to general practice electronic health records (EHR) to screen for FH, total cholesterol and low density lipoprotein cholesterol (LDL-c) levels in association with entered diagnostic criteria and demographic data in five general practices. Results Of 157,290 active patients examined, 0.7% (n=1081) had an LDL-c>5.0 mmol/L representing 1 in 146 of active patients. An additional 0.8% (n=1276) patients were at possible risk of FH. Of those with an LDL-c>5.0 mmol/L 43.7% of patients had no record of being prescribed statins. Twenty patients (0.013%) had a clinical diagnosis of FH entered in the EHR. Conclusions Patients at high risk of FH can be identified by a simple electronic screening method in general practice. Clinical data entry is variable in general practice. Targeted screening enables clinical assessment of patients at risk of cardiovascular disease and using the DLCNS will enable primary care to increase identification of FH. Approximately one in five patients extracted using this method, are likely to have phenotypically probable FH, making it a useful screening tool.
Background Familial hypercholesterolemia (FH) leads to premature coronary artery disease and aortic stenosis, with undertreated severe forms causing death at a young age. Lipoprotein apheresis (LA) ...is often required for lowering low-density lipoprotein cholesterol levels in severe FH. Objectives The objective of this study was to present the first experiences with LA in Malaysia, between 2004 and 2014. Methods We retrospectively collected data from patient records to assess the effectiveness, adverse effects, patient quality of life, and costs associated with an LA service for genetically confirmed homozygous and heterozygous FH. Results We treated 13 women and 2 men aged 6 to 59 years, 10 with homozygous and 5 with heterozygous FH, all on maximally tolerated cholesterol-lowering drug therapy, for a total of 65 patient-years. Acute lowering of low-density lipoprotein cholesterol post apheresis was 56.3 ± 7.2%, with time-averaged mean lowering of 34.9 ± 13.9%. No patients experienced any cardiovascular events during the period of receiving LA. Patients receiving LA experienced few side effects and enjoyed reasonable quality of life, but inability to continue treatment was frequent because of cost. Conclusion LA for severe FH can be delivered effectively in the short term in developing nations, but costs are a major barrier to sustaining this mode of treatment for this high-risk group of patients. New drug therapies for FH, such as the proprotein convertase subtilisin/kexin type 9 inhibitors, microsomal triglyceride transfer protein inhibitors, and apolipoprotein-B100 antisense oligonucleotides may allow improved care for these patients, but costs and long-term safety remain as issues to be addressed.
Fibroblasts are major contributors to and regulators of inflammation and dominant producers of interleukin-6 (IL-6) in inflammatory diseases like rheumatoid arthritis. Yet, compared to leukocytes, ...the regulation of inflammatory pathways in fibroblasts is largely unknown. Here, we report that analyses of genes coordinately upregulated with IL-6 pointed to STAT4 and leukemia inhibitory factor (LIF) as potentially linked. Gene silencing revealed that STAT4 was required for IL-6 transcription. STAT4 was recruited to the IL-6 promoter following fibroblast activation, and LIF receptor (LIFR) and STAT4 formed a molecular complex that together with JAK1 and TYK2 kinases, controlled STAT4 activation. Importantly, a positive feedback loop involving autocrine LIF, LIFR and STAT4 drove sustained IL-6 transcription. Besides IL-6, this autorine loop also drove the production of other key inflammatory factors including IL-8, granulocyte-colony stimulating factor (G-CSF), IL-33, IL-11, IL-1α and IL-1β. These findings define the transcriptional regulation of fibroblast-mediated inflammation as distinct from leukocytes.
Growing evidence implicates fibroblasts as inflammatory cells in sites of peripheral inflammation. Nguyen and colleagues demonstrate that regulation of IL-6 along with a set of other inflammatory cytokines and chemokines is regulated by a positive feedback loop involving LIF, LIF receptor, and STAT4 that selectively operates in fibroblasts.
Abstract Purpose The purpose of this review was to outline the current and emerging therapeutic options for the treatment of hypertriglyceridemia, with an emphasis on emerging therapies. Methods A ...systematic literature search was conducted with the use of PubMed and Embase for articles on hypertriglyceridemia, with a focus on therapeutics, pharmacology, and management. Abstracts from recent international meetings were also reviewed for presentations of Phase I and II data on agents with triglyceride-lowering effects. A further review of the references identified from these articles was also performed. Findings Consistent with the multifactorial cause of hypertriglyceridemia, the therapeutic options are broad and numerous. This review explores the current and potential therapeutic options for treating hypertriglyceridemia and outlines the potential mechanisms of action. However, the mechanism of triglyceride reduction is complex, multifactorial, or not fully elucidated for some of these agents. The magnitude of triglyceride reduction and findings of outcome studies are described. Implications Management of hypertriglyceridemia is about to enter an exciting phase, with multiple emerging therapies in the final stages of development. However, caution is warranted, because studies of therapeutic agents over the previous decade have often not found cardiovascular outcome benefits despite encouraging effects on triglyceride concentrations.
Background Familial hypercholesterolemia (FH) is the most common dominantly inherited cause of premature coronary artery disease (CAD). However, the diagnosis of FH in patients who have premature CAD ...in hospital settings is under-recognized, this also represents a missed opportunity for screening their close family members and implementing primary prevention. Objective To investigate the point prevalence of FH in a coronary care unit (CCU) among patients with early-onset CAD. Methods The prevalence of FH, based on modified phenotypic Dutch Lipid Clinic Network Criteria, and the spectrum of associated CAD risk factors, were investigated in a CCU setting. Data were collected on 175 coronary care patients with onset of CAD at age <60 years. Results The prevalence of probable/definite FH was 14.3% (95% confidence interval, 9.0%–19.5%); 46.3% of the patients gave a family history of premature CAD and 20.6% had an untreated low-density lipoprotein cholesterol >5.0 mmol/L. Diabetes, hypertension, obesity, and smoking were common and equally prevalent in patients with and without FH. Conclusions FH is relatively frequent among patients with a history of early-onset CAD in the CCU. Every effort should be made to detect FH in these patients and to initiate cascade testing of available family members to prevent the development of CAD in those who may be unaware that they also have the condition.
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