SMART-SLE: serology monitoring and repeat testing in systemic lupus erythematosus-an analysis of anti-double-stranded DNA monitoring.

OBJECTIVE: Disease activity monitoring in SLE includes serial measurement of anti-double stranded-DNA (dsDNA) antibodies, but in patients who are persistently anti-dsDNA positive, the utility of repeated measurement is unclear. We investigated the usefulness of serial anti-dsDNA testing in predicting flare in SLE patients who are persistently anti-dsDNA positive. METHODS: Data were analysed from patients in a multinational longitudinal cohort with known anti-dsDNA results from 2013 to 2021. Patients were categorized based on their anti-dsDNA results as persistently negative, fluctuating or persistently positive. Cox regression models were used to examine longitudinal associations of anti-dsDNA results with flare. RESULTS: Data from 37 582 visits of 3484 patients were analysed. Of the patients 1029 (29.5%) had persistently positive anti-dsDNA and 1195 (34.3%) had fluctuating results. Anti-dsDNA expressed as a ratio to the normal cut-off was associated with the risk of subsequent flare, including in the persistently positive cohort (adjusted hazard ratio [HR] 1.56; 95% CI: 1.30, 1.87; P < 0.001) and fluctuating cohort (adjusted HR 1.46; 95% CI: 1.28, 1.66), both for a ratio >3. Both increases and decreases in anti-dsDNA more than 2-fold compared with the previous visit were associated with increased risk of flare in the fluctuating cohort (adjusted HR 1.33; 95% CI: 1.08, 1.65; P = 0.008) and the persistently positive cohort (adjusted HR 1.36; 95% CI: 1.08, 1.71; P = 0.009). CONCLUSION: Absolute value and change in anti-dsDNA titres predict flares, including in persistently anti-dsDNA positive patients. This indicates that repeat monitoring of dsDNA has value in routine testing.

Frequency and Clinical Utility of Antibodies to Extractable Nuclear Antigen in the Setting of a Negative Antinuclear Antibody Test.

OBJECTIVE: Simultaneous antibody testing during screening for autoimmune conditions is discouraged. The incidence of positive extractable nuclear antigen (ENA) in the setting of a negative antinuclear antibody (ANA) has been reported as low. Our objective was to characterize the frequency of diagnosis of new ANA-associated rheumatic disease (AARD) in the setting of a negative ANA with a positive ENA. METHODS: This was a 7-year retrospective study from a multicenter tertiary health network in Australia. Clinical information was sought on patients over 18 years old who had a negative ANA but positive ENA test result. Results were extracted from hospital computer systems. RESULTS: From March 19, 2011, to July 23, 2018, ENA testing was ordered simultaneously with an ANA test on 4,248 occasions in 3,484 patients. ANA was positive in 2,520 patients (59.3%) and ENA was positive in 1,980 patients (46.6%). Among positive ANA patients, ENA was positive in 1,563 patients (62.0%). Among 1,728 negative ANA tests, ENA was positive in 417 (24.1%) (P < 0.001). A total of 328 patients with discordant ANA/ENA results had data available for further analysis, of whom 279 had no pre-established rheumatologic condition. A new AARD was diagnosed in 17 of 279 patients, yielding a positive predictive value of 6.09% (95% confidence interval 3.59-9.58). CONCLUSION: Despite the higher-than-expected incidence of positive ENA in the setting of a negative ANA, the yield of newly diagnosed rheumatic diseases was low. Our findings support the stepwise addition of ENA requests when an ANA test result is positive and clinical suspicion of an AARD is high.

Utility of repeat extractable nuclear antigen antibody testing: a retrospective audit.

OBJECTIVES: Autoantibodies to ENA are frequently ordered during the workup of suspected autoimmune connective tissue diseases. There are no current guidelines for repeat test ordering. The objective of this study was to assess the utility of repeat ENA testing after an initial negative result. METHODS: A retrospective study was conducted in a single, multicentre tertiary health network in Melbourne, Australia. Results of all ENA tests were extracted from the hospital laboratory information system. For patients who had a change in ENA result from negative to positive, clinical information was obtained from the hospital records regarding new diagnosis of an ANA-associated rheumatic disease (AARD). RESULTS: A total of 23 438 ENA tests were performed in 19 603 patients from 29 July 2013 to 28 September 2020. In total, 20 918 (89.2%) were negative with 215 (0.9%) being equivocal. Of the 2305 positive tests, the most common ENA auto-antibody specificity detected was anti-Ro52 (1185, 51.4%). A total of 2636 of 19 603 patients (13.4%) had more than one ENA test performed during the study period. Of these, most (2523, 95.7%) had stable ENA results with no change compared with the first test. Only 53 patients (2.2%) had an ENA result that changed from negative to positive. Excluding patients with pre-existing rheumatic conditions and those under 18, there were five new AARDs found in the remaining 34 patients. CONCLUSION: Repeat ENA test results rarely change or result in a new diagnosis of an AARD, with repeated testing only warranted if there is a change in clinical manifestations.

Predictors of infection requiring hospitalization in patients with systemic lupus erythematosus: a time-to-event analysis.

OBJECTIVES: To evaluate the predictors of serious infection in patients with systemic lupus erythematosus (SLE). METHODS: Serious infections were identified in SLE patients in a prospectively-followed single centre cohort. Associations of serious infection with disease-related variables and medication use were analysed using Cox and related regression models. RESULTS: 346 patients were followed for a mean (SD) of 6.6 (3.7) years. 86 episodes of serious infection were observed, with an incidence rate of 3.8 episodes per 100 person-years. Patients who had serious infection had higher baseline SLE Damage Index (SDI) and Charlston Comorbidity Index (CCI); they were also more likely to have high disease activity status (HDAS), and higher disease activity in multiple clinical domains, higher flare rates, higher time-adjusted prednisolone dose exposure, and less time in lupus low disease activity state (LLDAS). Patients who have received cyclophosphamide, rituximab and mycophenolate were more likely to have experienced serious infection. After multivariable adjustment in Cox regression analysis, cyclophosphamide, higher SDI score, and higher disease activity were associated with an increased hazard of first serious infection. History of previous serious infection conferred the highest risk. Lymphopenia was also a modest but statistically significant predictor of serious infection. CONCLUSION: History of previous serious infection was the strongest predictor of serious infection in our SLE cohort. This study also suggests that clinical factors such as damage accrual, disease activity, and choice of immunosuppressant, can each have an independent risk in predicting serious infection particularly the first episode.

Impact of COVID-19 telehealth on outpatient test completion.

BACKGROUND: Pathology and imaging tests are frequently requested in the outpatient setting despite historically poor completion rates. The impact of COVID-19 telehealth on test completion rates is unknown. AIMS: To examine the impact of the COVID-19 pandemic and telehealth transition on pathology and imaging test request and completion rates in Australian outpatient clinics. METHODS: We performed a prospective cohort study with historical controls between March-May 2019 and March-May 2020. Pathology and imaging request and completion rates were collected in review consultation patients attending gastroenterology and rheumatology outpatient clinics at a tertiary healthcare system prior and during the early phases of the COVID-19 pandemic in Melbourne. RESULTS: A total of 1376 patients was included in the study. Pathology tests were requested more frequently in the COVID-19 group (n = 582/684, 85.2%) than the control group (n = 492/692, 71.1%, P < 0.001), but completion rates were lower in the COVID-19 group (n = 443/582, 76.1%) than the control group (n = 426/492 (86.6%), P < 0.001). Imaging tests were requested more frequently in the COVID-19 group (n = 345/682, 50.6%) than the control group (n = 295/692, 42.6%, P = 0.003), with lower rates of completion in the COVID-19 group (n = 229/345, 66.4%) than the control group (n = 247/295, 83.7%, P < 0.001). CONCLUSIONS: The COVID-19 pandemic and telehealth transition have resulted in more frequent pathology and imaging requests but fewer test completion in the outpatients setting. This study has identified new clinical risks associated with the abrupt transition to telehealth during COVID-19 that should be explored in future studies and appropriately mitigated.

Severe infections remain common in a real-world rheumatoid arthritis cohort: A simple clinical model to predict infection risk.

OBJECTIVE: This study aimed to investigate the incidence of severe infections in patients of a dedicated rheumatoid arthritis (RA) clinic, identify the associated risk factors, and derive an infection risk screening tool. METHODS: Between January and July 2019, 263 eligible patients with a diagnosis of RA were recruited retrospectively and consecutively from an RA clinic of an Australian tertiary hospital. The primary outcome was severe infection (requiring hospital admission) between January 2018 and July 2019. We collected data from medical records and pathology results. We used validated scores, such as the disease activity score of 28 joints (DAS28) and the Charlson comorbidity index, to assess the disease activity and comorbidity burden. Multivariable logistic regression was used for statistical analysis. RESULTS: A total of 45 severe infection episodes occurred in 34 (13%) patients, corresponding to 10.8 infections per 100 patient-years. Respiratory (53%) and urinary (13%) tract infections were the most common. In the multivariable analysis, significant risk factors included low lymphocyte count (odds ratio [OR], 4.08; 95% confidence interval [CI], 1.16-14.29), severe infection in the past 3 years (OR, 3.58; 95% CI, 1.28-9.97), Charlson comorbidity index >2 (OR, 2.69; 95% CI, 1.03-7.00), and higher DAS28 (OR, 1.35/0.5-unit increment; 95% CI, 1.10-1.67). A model incorporating these factors and age had an area under receiver operating characteristic curve of 0.82. CONCLUSION: To the best of our knowledge, this was one of the first Australian studies to evaluate severe infection rates in a real-world RA cohort. The rates remained high and comparable with those of the older studies. Lymphopenia, disease activity, comorbidity burden, and previous severe infection were the independent risk factors for infection. A model comprising easily assessable clinical and biological parameters has an excellent predictive potential for severe infection. Once validated, it may be developed into a screening tool to help clinicians rapidly identify the high-risk patients and inform the tailored clinical decision making.

Lupus Low Disease Activity State and Reduced Direct Health Care Costs in Patients With Systemic Lupus Erythematosus.

OBJECTIVE: Treat-to-target end points for systemic lupus erythematosus (SLE) have been assessed for their impact on damage accrual and flare, but whether they have an impact on the high health care utilization and costs in SLE has not been studied. The purpose of this study was to examine our hypothesis that the recently described lupus low disease activity state (LLDAS) would be associated with reduced health care cost. METHODS: Data from a single tertiary hospital longitudinal SLE cohort were assessed. Baseline demographics, disease activity (Systemic Lupus Erythematosus Disease Activity Index 2000 [SLEDAI-2K], physician global assessment [PhGA], and flare index), and medication use were evaluated, and direct health care utilization and cost data were obtained from hospital information systems. LLDAS was defined as previously published: briefly, SLEDAI-2K ≤4 with no new activity, PhGA ≤1, prednisolone ≤7.5 mg/day, and optimal standard immunosuppressive agents. Analysis was performed using multivariable linear regression. RESULTS: Two hundred SLE patients, contributing 357.8 person-years of observation, were included. A history of lupus nephritis was present in 42% of patients, and damage (Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index >0) was present at study commencement in 57.3% of patients. The mean ± SD annual direct medical cost per patient was US$7,413 ± 13,133/year. In multivariable analysis, increased cost was associated with the presence of baseline organ damage (41.7% increase; P = 0.009) and corticosteroid use (>7.5-15 mg/day: 55.7% increase; P = 0.02; and >15 mg/day: 202% increase; P < 0.001). In contrast, spending ≥50% of the observation period in LLDAS was associated with a 25.9% reduction in annual direct medical cost (P = 0.04). CONCLUSION: Greater time spent in LLDAS was associated with significantly reduced direct hospital health care costs among patients with SLE.

Utility of repeated antinuclear antibody tests: a retrospective database study.

BACKGROUND: Anti-nuclear antibody (ANA) testing is frequently used as a diagnostic or screening test in patients with inflammatory or musculoskeletal symptoms. The value of repeat testing is unclear. We sought to evaluate the frequency, utility, and cost of repeat ANA testing. The main objective was to assess the positive predictive value of a repeat ANA test for the diagnosis of rheumatological conditions associated with ANA. METHODS: In this retrospective cohort study, we analysed data from a single, multisite tertiary health network in Australia across a 7-year period. ANA and other autoimmune test results were obtained from the hospital pathology system with a positive ANA titre cutoff set at 1:160. Clinical information was sourced from clinical information systems on any patient who had a change in ANA result from negative to positive on repeat testing. The cost of repeated ANA testing was calculated using the Australian Government Medicare Benefits Schedule. FINDINGS: From March 19, 2011, to July 23, 2018, a total of 36 715 ANA tests were done in 28 840 patients at a total cost of US$675 029 (2018 equivalent). 14 058 (38·3%) of these ANA tests were positive. 7875 (21·4%) of the ordered tests were repeats in 4887 (16·9%) of the patients, among whom 2683 (54·9%) had initially negative tests, and 2204 (45·1%) had initially positive tests. 511 (19·0%) of the 2683 patients with initially negative tests had a positive result on at least one repeat test, with a median time to first positive result of 1·74 years (IQR 0·54-3·60). A change from negative to positive ANA was associated with a new diagnosis in only five (1·1%) of the 451 patients with clinical information available and no previous diagnosis of an ANA-associated rheumatological condition, yielding a positive predictive value of 1·1% (95% CI 0·4-2·7). INTERPRETATION: Repeat ANA testing after a negative result has low utility and results in high cost. FUNDING: Monash Health.

A real-life snapshot of the use and abuse of urinary catheters on general medical wards.

An observational study was performed on 2 wards in a tertiary hospital to determine staff awareness, knowledge, and documentation of catheter use and the effects these have on duration of catheterization. Overall, there was poor knowledge of the indications and date of catheterization. Doctor awareness decreases duration of catheterization.

Inferring transcription factor targets from gene expression changes and predicted promoter occupancy.

We have developed a method for inferring condition-specific targets of transcription factors based on ranking genes by gene expression change and ranking genes based on predicted transcription factor occupancy. The average of these two ranks, used as a test statistic, allows target genes to be inferred in a stringent manner. The method complements chromatin immunoprecipitation experiments by predicting targets under many conditions for which ChIP experiments have not been performed. We used the method to predict targets of 102 yeast transcription factors in approximately 1600 expression microarray experiments. The reliability of the method is suggested by the strong enrichment of genes previously shown to be bound, by the validation of binding to novel targets, by the way transcription factors with similar specificities can be functionally distinguished, and by the greater-than-expected number of regulatory network motifs, such as auto-regulatory interactions, that arise from new, predicted interactions. The combination of ChIP data and the targets inferred from this analysis results in a high-confidence regulatory network that includes many novel interactions. Interestingly, we find only a weak association between conditions in which we can infer the activity of a transcription factor and conditions in which the transcription gene itself is regulated. Thus, methods that rely on transcription factor regulation to help define regulatory interactions may miss regulatory relationships that are detected by the method reported here.

Liver X receptors regulate adrenal steroidogenesis and hypothalamic-pituitary-adrenal feedback.

The nuclear hormone receptors liver X receptor alpha (LXRalpha) (NR1H3) and LXRbeta (NR1H2) are established regulators of cholesterol, lipid, and glucose metabolism and are attractive drug targets for the treatment of diabetes and cardiovascular disease. Adrenal steroid hormones including glucocorticoids and mineralocorticoids are known to interfere with glucose metabolism, insulin signaling, and blood pressure regulation. Here we present genome-wide expression profiles of LXR-responsive genes in both the adrenal and the pituitary gland. LXR activation in cultured adrenal cells inhibited expression of multiple steroidogenic genes and consequently decreased adrenal steroid hormone production. In addition, LXR agonist treatment elevated ACTH mRNA expression and hormone secretion from pituitary cells both in vitro and in vivo. Reduced expression of the glucocortioid-activating enzyme 11beta-hydroxysteroid dehydrogenase 1 in pituitary cells upon LXR activation suggests blunting of the negative feedback of glucocorticoids by LXRs. In conclusion, LXRs independently interfere with the hypothalamic-pituitary-adrenal axis regulation at the level of the pituitary and the adrenal gland.

Multiplatform genome-wide identification and modeling of functional human estrogen receptor binding sites.

BACKGROUND: Transcription factor binding sites (TFBS) impart specificity to cellular transcriptional responses and have largely been defined by consensus motifs derived from a handful of validated sites. The low specificity of the computational predictions of TFBSs has been attributed to ubiquity of the motifs and the relaxed sequence requirements for binding. We posited that the inadequacy is due to limited input of empirically verified sites, and demonstrated a multiplatform approach to constructing a robust model. RESULTS: Using the TFBS for the estrogen receptor (ER)alpha (estrogen response element [ERE]) as a model system, we extracted EREs from multiple molecular and genomic platforms whose binding to ERalpha has been experimentally confirmed or rejected. In silico analyses revealed significant sequence information flanking the standard binding consensus, discriminating ERE-like sequences that bind ERalpha from those that are nonbinders. We extended the ERE consensus by three bases, bearing a terminal G at the third position 3' and an initiator C at the third position 5', which were further validated using surface plasmon resonance spectroscopy. Our functional human ERE prediction algorithm (h-ERE) outperformed existing predictive algorithms and produced fewer than 5% false negatives upon experimental validation. CONCLUSION: Building upon a larger experimentally validated ERE set, the h-ERE algorithm is able to demarcate better the universe of ERE-like sequences that are potential ER binders. Only 14% of the predicted optimal binding sites were utilized under the experimental conditions employed, pointing to other selective criteria not related to EREs. Other factors, in addition to primary nucleotide sequence, will ultimately determine binding site selection.

Discovery of estrogen receptor alpha target genes and response elements in breast tumor cells.

BACKGROUND: Estrogens and their receptors are important in human development, physiology and disease. In this study, we utilized an integrated genome-wide molecular and computational approach to characterize the interaction between the activated estrogen receptor (ER) and the regulatory elements of candidate target genes. RESULTS: Of around 19,000 genes surveyed in this study, we observed 137 ER-regulated genes in T-47D cells, of which only 89 were direct target genes. Meta-analysis of heterogeneous in vitro and in vivo datasets showed that the expression profiles in T-47D and MCF-7 cells are remarkably similar and overlap with genes differentially expressed between ER-positive and ER-negative tumors. Computational analysis revealed a significant enrichment of putative estrogen response elements (EREs) in the cis-regulatory regions of direct target genes. Chromatin immunoprecipitation confirmed ligand-dependent ER binding at the computationally predicted EREs in our highest ranked ER direct target genes, NRIP1, GREB1 and ABCA3. Wider examination of the cis-regulatory regions flanking the transcriptional start sites showed species conservation in mouse-human comparisons in only 6% of predicted EREs. CONCLUSIONS: Only a small core set of human genes, validated across experimental systems and closely associated with ER status in breast tumors, appear to be sufficient to induce ER effects in breast cancer cells. That cis-regulatory regions of these core ER target genes are poorly conserved suggests that different evolutionary mechanisms are operative at transcriptional control elements than at coding regions. These results predict that certain biological effects of estrogen signaling will differ between mouse and human to a larger extent than previously thought.