Integration of genetic fine-mapping and multi-omics data reveals candidate effector genes for hypertension.

Genome-wide association studies of blood pressure (BP) have identified >1,000 loci, but the effector genes and biological pathways at these loci are mostly unknown. Using published association summary statistics, we conducted annotation-informed fine-mapping incorporating tissue-specific chromatin segmentation and colocalization to identify causal variants and candidate effector genes for systolic BP, diastolic BP, and pulse pressure. We observed 532 distinct signals associated with ≥2 BP traits and 84 with all three. For >20% of signals, a single variant accounted for >75% posterior probability, 65 were missense variants in known (SLC39A8, ADRB2, and DBH) and previously unreported BP candidate genes (NRIP1 and MMP14). In disease-relevant tissues, we colocalized >80 and >400 distinct signals for each BP trait with cis-eQTLs and regulatory regions from promoter capture Hi-C, respectively. Integrating mouse, human disorder, gene expression and tissue abundance data, and literature review, we provide consolidated evidence for 436 BP candidate genes for future functional validation and discover several potential drug targets.

CRISPR/dCas9 DNA methylation editing is heritable during human hematopoiesis and shapes immune progeny.

Aging is associated with an abnormal increase in DNA methylation (DNAm) in human gene promoters, including in bone marrow stem cells. DNAm patterns are further perturbed in hematological malignancies such as acute myeloid leukemia but the physiological significance of such epigenetic changes is unknown. Using epigenetic editing of human stem/progenitor cells (HSPCs), we show that p15 methylation affects hematopoiesis in vivo. We edited the CDKN2B (p15) promoter and ARF (p14) using dCas9-3A3L and observed DNAm spreading beyond the gRNA location. We find that despite a transient delivery system, DNAm is maintained during myeloid differentiation in vitro, and hypermethylation of the p15 promoter reduces gene expression. In vivo, edited human HSPCs can engraft the bone marrow of mice and targeted DNAm is maintained in HSPCs long term. Moreover, epigenetic changes are conserved and inherited in both myeloid and lymphoid lineages. Although the proportion of myeloid (CD33+) and lymphoid (CD19+) cells is unaffected, monocyte (CD14+) populations decreased and granulocytes (CD66b+) increased in mice engrafted with p15 hypermethylated HSPCs. Monocytes derived from p15 hypermethylated HSPCs appear to be activated and show increased inflammatory transcriptional programs. We believe these findings have clinical relevance since we found p15 promoter methylation in the peripheral blood of patients with clonal hematopoiesis. Our study shows DNAm can be targeted and maintained in human HSPCs and demonstrated functional relevance of aberrant DNAm on the p15 locus. As such, other aging-associated aberrant DNAm may impact hematopoiesis in vivo.

Epigenomic insights into common human disease pathology.

The epigenome-the chemical modifications and chromatin-related packaging of the genome-enables the same genetic template to be activated or repressed in different cellular settings. This multi-layered mechanism facilitates cell-type specific function by setting the local sequence and 3D interactive activity level. Gene transcription is further modulated through the interplay with transcription factors and co-regulators. The human body requires this epigenomic apparatus to be precisely installed throughout development and then adequately maintained during the lifespan. The causal role of the epigenome in human pathology, beyond imprinting disorders and specific tumour suppressor genes, was further brought into the spotlight by large-scale sequencing projects identifying that mutations in epigenomic machinery genes could be critical drivers in both cancer and developmental disorders. Abrogation of this cellular mechanism is providing new molecular insights into pathogenesis. However, deciphering the full breadth and implications of these epigenomic changes remains challenging. Knowledge is accruing regarding disease mechanisms and clinical biomarkers, through pathogenically relevant and surrogate tissue analyses, respectively. Advances include consortia generated cell-type specific reference epigenomes, high-throughput DNA methylome association studies, as well as insights into ageing-related diseases from biological 'clocks' constructed by machine learning algorithms. Also, 3rd-generation sequencing is beginning to disentangle the complexity of genetic and DNA modification haplotypes. Cell-free DNA methylation as a cancer biomarker has clear clinical utility and further potential to assess organ damage across many disorders. Finally, molecular understanding of disease aetiology brings with it the opportunity for exact therapeutic alteration of the epigenome through CRISPR-activation or inhibition.

Fine mapping of candidate effector genes for heart rate.

An elevated resting heart rate (RHR) is associated with increased cardiovascular mortality. Genome-wide association studies (GWAS) have identified > 350 loci. Uniquely, in this study we applied genetic fine-mapping leveraging tissue specific chromatin segmentation and colocalization analyses to identify causal variants and candidate effector genes for RHR. We used RHR GWAS summary statistics from 388,237 individuals of European ancestry from UK Biobank and performed fine mapping using publicly available genomic annotation datasets. High-confidence causal variants (accounting for > 75% posterior probability) were identified, and we collated candidate effector genes using a multi-omics approach that combined evidence from colocalisation with molecular quantitative trait loci (QTLs), and long-range chromatin interaction analyses. Finally, we performed druggability analyses to investigate drug repurposing opportunities. The fine mapping pipeline indicated 442 distinct RHR signals. For 90 signals, a single variant was identified as a high-confidence causal variant, of which 22 were annotated as missense. In trait-relevant tissues, 39 signals colocalised with cis-expression QTLs (eQTLs), 3 with cis-protein QTLs (pQTLs), and 75 had promoter interactions via Hi-C. In total, 262 candidate genes were highlighted (79% had promoter interactions, 15% had a colocalised eQTL, 8% had a missense variant and 1% had a colocalised pQTL), and, for the first time, enrichment in nervous system pathways. Druggability analyses highlighted ACHE, CALCRL, MYT1 and TDP1 as potential targets. Our genetic fine-mapping pipeline prioritised 262 candidate genes for RHR that warrant further investigation in functional studies, and we provide potential therapeutic targets to reduce RHR and cardiovascular mortality.

Applying models of care for total hip and knee arthroplasty: External validation of a published predictive model to identify extended stay risk prior to lower-limb arthroplasty.

OBJECTIVE: This study aimed to externally validate a reported model for identifying patients requiring extended stay following lower limb arthroplasty in a new setting. DESIGN: External validation of a previously reported prognostic model, using retrospective data. SETTING: Medium-sized hospital orthopaedic department, Australia. PARTICIPANTS: Electronic medical records were accessed for data collection between Sep-2019 and Feb-2020 and retrospective data extracted from 200 randomly selected total hip or knee arthroplasty patients. INTERVENTION: Participants received total hip or knee replacement between 2-Feb-16 and 4-Apr-19. This study was a non-interventional retrospective study. MAIN MEASURES: Model validation was assessed with discrimination, calibration on both original and adjusted forms of the candidate model. Decision curve analysis was conducted on the outputs of the adjusted model to determine net benefit at a predetermined decision threshold (0.5). RESULTS: The original model performed poorly, grossly overestimating length of stay with mean calibration of -3.6 (95% confidence interval -3.9 to -3.2) and calibration slope of 0.52. Performance improved following adjustment of the model intercept and model coefficients (mean calibration 0.48, 95% confidence interval 0.16 to 0.80 and slope of 1.0), but remained poorly calibrated at low and medium risk threshold and net benefit was modest (three additional patients per hundred identified as at-risk) at the a-priori risk threshold. CONCLUSIONS: External validation demonstrated poor performance when applied to a new patient population and would provide limited benefit for our institution. Implementation of predictive models for arthroplasty should include practical assessment of discrimination, calibration and net benefit at a clinically acceptable threshold.

Healthcare resource utilization and costs in patients with a newly confirmed diagnosis of lupus nephritis in the United States over a 5-year follow-up period.

BACKGROUND: We aimed to describe healthcare resource utilization (HCRU) and healthcare costs in patients with newly confirmed lupus nephritis (LN) in the United States over a 5-year follow-up period. METHODS: This retrospective, longitudinal cohort study (GSK Study 214102) utilized administrative claims data to identify individuals with a newly confirmed diagnosis of LN between August 01, 2011, and July 31, 2018, based on LN-specific International Classification of Diseases diagnosis codes. Index was the date of first LN-related diagnosis code claim. HCRU, healthcare costs, and incidence of systemic lupus erythematosus (SLE) flares were reported annually among eligible patients with at least 5 years continuous enrollment post-index. RESULTS: Of 2,159 patients with a newly confirmed diagnosis of LN meeting inclusion and exclusion criteria, 335 had at least 5 years continuous enrollment post-index. HCRU was greatest in the first year post-LN diagnosis across all categories (inpatient admission, emergency room [ER] visits, ambulatory visits, and pharmacy use), and trended lower, though remained substantial, in the 5-year follow-up period. Among patients with LN and HCRU, the mean (standard deviation [SD]) number of ER visits and inpatient admissions were 3.7 (4.6) and 1.8 (1.5), respectively, in Year 1, which generally remained stable in Years 2-5; the mean (SD) number of ambulatory visits and pharmacy fills were 35.8 (25.1) and 62.9 (43.8), respectively, in Year 1, and remained similar for Years 2-5. Most patients (≥ 91.6%) had ≥ 1 SLE flare in each of the 5 years of follow-up. The proportion of patients who experienced a severe SLE flare was higher in Year 1 (31.6%) than subsequent years (14.3-18.5%). Total costs (medical and pharmacy; mean [SD]) were higher in Year 1 ($44,205 [71,532]) than subsequent years ($29,444 [52,310]-$32,222 [58,216]), driven mainly by inpatient admissions (Year 1: $21,181 [58,886]; subsequent years: $7,406 [23,331]-$9,389 [29,283]). CONCLUSIONS: Patients with a newly confirmed diagnosis of LN have substantial HCRU and healthcare costs, particularly in the year post-diagnosis, largely driven by inpatient costs. This highlights the need for improved disease management to prevent renal damage, improve patient outcomes, and reduce costs among patients with renal involvement.

Direct nitrogen, phosphorus and carbon exchanges between Mucoromycotina 'fine root endophyte' fungi and a flowering plant in novel monoxenic cultures.

Most plants form mycorrhizal associations with mutualistic soil fungi. Through these partnerships, resources are exchanged including photosynthetically fixed carbon for fungal-acquired nutrients. Recently, it was shown that the diversity of associated fungi is greater than previously assumed, extending to Mucoromycotina fungi. These Mucoromycotina 'fine root endophytes' (MFRE) are widespread and generally co-colonise plant roots together with Glomeromycotina 'coarse' arbuscular mycorrhizal fungi (AMF). Until now, this co-occurrence has hindered the determination of the direct function of MFRE symbiosis. To overcome this major barrier, we developed new techniques for fungal isolation and culture and established the first monoxenic in vitro cultures of MFRE colonising a flowering plant, clover. Using radio- and stable-isotope tracers in these in vitro systems, we measured the transfer of 33 P, 15 N and 14 C between MFRE hyphae and the host plant. Our results provide the first unequivocal evidence that MFRE fungi are nutritional mutualists with a flowering plant by showing that clover gained both 15 N and 33 P tracers directly from fungus in exchange for plant-fixed C in the absence of other micro-organisms. Our findings and methods pave the way for a new era in mycorrhizal research, firmly establishing MFRE as both mycorrhizal and functionally important in terrestrial ecosystems.

The cost of flares among patients with systemic lupus erythematosus with and without lupus nephritis in the United States.

OBJECTIVE: Assess healthcare costs associated with systemic lupus erythematosus (SLE) flares among patients with and without lupus nephritis (LN). METHODS: This retrospective cohort study used medical and pharmacy claims data from the United States-based Optum Clinformatics database to identify adults with SLE between 1 January 2016, and 31 December 2018. Index was the date of a patient's earliest SLE diagnosis claim during the identification period. Patients were categorized based on ICD-9/-10 diagnosis codes into one of two cohorts: SLE with LN (LN) and SLE without LN (non-LN). Baseline characteristics were assessed in the 12 months preceding index (baseline period). The presence, severity, and healthcare costs (in 2019 US dollars) of flares were determined in the 12 months following index (follow-up period). RESULTS: Overall, 11,663 patients with SLE were included (LN, n = 2916; non-LN, n = 8747). During the baseline period, a greater proportion of patients in the LN cohort versus non-LN cohort had a Charlson Comorbidity Index score ≥4 (72.5% vs 13.7%) and inpatient stays (41.0% vs 17.0%). A total of 12,190 flares were identified during the follow-up period (LN, 3494; non-LN, 8696). A greater proportion of flares experienced by patients with LN versus those without LN were moderate (61.2% vs 53.6%) and severe (10.6% vs 5.4%). The mean (standard deviation [SD]) number of moderate and severe flares per patient was greater among the LN cohort than the non-LN cohort (moderate: LN, 1.8 [1.2] and non-LN, 1.4 [1.2]; severe: LN, 0.2 [0.6] and non-LN, 0.1 [0.3]). The mean (SD) total healthcare costs associated with SLE flares of any severity were greater for patients with LN (LN, $5842 [9604]; non-LN, $2600 [4249]). The mean (SD) cost per flare increased with severity (mild: LN, $2753 [4640] and non-LN, $1606 [2710]; moderate: LN, $4561 [7156] and non-LN, $2587 [3720]; severe: LN, $29,148 [27,273] and non-LN, $14,829 [19,533]). CONCLUSIONS: Patients with SLE with LN have greater healthcare costs than those without LN. Flares among patients with LN were more frequent, severe, and costly than among patients without LN. This highlights the need for treatments that prevent or reduce flares among patients with SLE, both with and without LN.

Daily mindfulness, negative affect, and eating behaviors in adolescents at risk for excess weight gain.

OBJECTIVE: Loss-of-control and overeating are common in adolescents with high body mass index (BMI). Mindfulness may affect negative affect, and both may relate to loss-of-control and overeating. Yet, there is limited understanding of these associations in adolescents' daily lives. METHODS: Forty-five adolescents (77% female; Mage = 14.4 years, SDage = 1.7 years) with high weight (92% with BMI [kg/m2 ] ≥85th percentile for age/sex) provided daily, repeated measurements of mindfulness, negative affect, loss-of-control, and overeating for ~7 days (M = 5.6 days; range = 1-13). Multilevel mixed modeling was conducted to test within-person (intraindividual) and between-person (interindividual) associations for the same-day (concurrent) and next-day (time-ordered/prospective). RESULTS: There were within-person and between-person associations of higher mindfulness with lower negative affect on the same-day and next-day. Greater between-person mindfulness related to lower odds of adolescents' loss-of-control occurrence (same-day) and conversely, more perceived control over eating (same-day and next-day). Greater within-person mindfulness related to less odds of next-day overeating. DISCUSSION: Dynamic relations exist among mindfulness, negative affect, and eating in adolescents at-risk for excess weight gain. Mindfulness may be an important element to consider in loss-of-control and overeating. Future work using momentary-data within an experimental design would help disentangle the intraindividual effects of increasing mindfulness/decreasing negative affect on disordered eating. PUBLIC SIGNIFICANCE: Loss-of-control and overeating are common in teenagers with high weight. Greater mindfulness-present-moment, non-judgmental attention-and less negative emotions may relate to healthier eating, but we do not know how these processes play out in teenagers' daily lives. Addressing this knowledge gap, the current findings showed that greater daily mindfulness, but not negative affect, related to less loss-of-control/overeating, suggesting the importance of mindfulness for eating patterns in teenagers' daily lives.

Anxiety exacerbation in a patient with chronic myeloid leukemia receiving dasatinib and venlafaxine.

INTRODUCTION: Tyrosine kinase inhibitor (TKI) use leads to near-normal life expectancy in patients with chronic myeloid leukemia (CML); unfortunately for some patients, adverse drug effects (ADEs) and medication burden associated with TKI therapy can lead to decreased quality of life. Additionally, TKIs have drug interactions that may negatively impact patients' management of co-morbidities or lead to increased ADEs. CASE REPORT: A 65-year-old female with a history of anxiety treated and controlled with venlafaxine experienced increased and resistant anxiety and insomnia after starting dasatinib for CML. MANAGEMENT AND OUTCOME: On dasatinib, the patient experienced worsening anxiety and insomnia. The stress of a new leukemia diagnosis, drug interactions, and ADEs from dasatinib were considered possible causes. Dose adjustments to dasatinib and venlafaxine were made to control the patient's symptoms. However, the patient's symptoms did not resolve. After being on dasatinib for 2.5 years, the patient discontinued TKI therapy due to being in a deep molecular remission and given ongoing challenges managing anxiety. Within 4 months of stopping dasatinib, the patient reported an improvement in anxiety and overall emotional wellbeing. She continues to feel better and remains in a complete molecular remission 20 months off treatment. DISCUSSION: This case demonstrates a possible previously unknown drug interaction with dasatinib as well as a possible rarely reported ADE of dasatinib. Additionally, it highlights the difficulties patients with psychiatric disorders may face on TKI therapy and challenges providers may have in identifying rare psychiatric ADEs, thus emphasizing the need for documentation of these types of cases.

Persistent knee extension deficits are common after anterior cruciate ligament reconstruction: a systematic review and meta-analysis of randomised controlled trials.

PURPOSE: Knee extension deficits complicate recovery from ACL injury and reconstruction; however, the incidence of knee extension loss is not well defined. The aim of this review was to identify the incidence of loss of extension (LOE) following ACL rupture and reconstruction, explore the definitions of knee extension deficits reported and identify prognostic factors affecting LOE incidence. METHODS: A systematic search was conducted in Medline, Cochrane Library and PEDro for studies in publication up to November 2021, with no restrictions on publication year. References were screened and assessed for inclusion using predetermined eligibility criteria. Randomised controlled trials (RCTs) that quantified knee angle, loss of extension or incidence of extension deficit were included for quality assessment and data extraction. Statistical summaries were generated and meta-analyses performed in two parts to examine: (i) the probability of a datapoint being zero incidence compared to a nonzero incidence and (ii) the relationship between the predictors and nonzero LOE incidence. RESULTS: A sample of 15,494 studies were retrieved using the search criteria, with 53 studies meeting eligibility criteria. The pooled results from 4991 participants were included for analysis, with 4891 participants who had undergone ACLR. The proportion of included studies judged at an overall low risk of bias was small (7.8%). The observed group and study were the most important predictors for whether a datapoint reported an incidence of extension deficit. Time to follow-up (P < 0.001) and graft type (P = 0.02) were found to have a significant influence on nonzero LOE incidence (%). Covariate adjusted estimates of average LOE indicated 1 in 3 patients presenting with LOE at 12 month follow-up, reducing to 1 in 4 at 2 years. CONCLUSIONS: This review examined the definitions for the measurement and interpretation of postoperative knee extension and established the trajectory of knee extension deficit after ACL injury and reconstruction. While factors associated with loss of extension were identified, the exact trajectory of knee extension deficits was difficult to infer due to discrepancies in measurement techniques and patient variation. On average, 1 in 3 patients may present with loss of extension of at least 3 degrees at 12-month follow-up, decreasing to 1 in 4 at 2 years. These results may be used by clinicians as an upper threshold for acceptable complication rates following ACLR. Future work should focus on LOE as a clinically relevant complication of ACL injury and treatment with appropriate attention to standardisation of definitions, measurements and better understanding of natural history. PROSPERO REGISTRATION NUMBER: CRD42018092295. LEVEL OF EVIDENCE: Level I.

Disruption of carbon for nutrient exchange between potato and arbuscular mycorrhizal fungi enhanced cyst nematode fitness and host pest tolerance.

Plants simultaneously interact with a range of biotrophic symbionts, ranging from mutualists such as arbuscular mycorrhizal fungi (AMF), to parasites such as the potato cyst nematode (PCN). The exchange of mycorrhizal-acquired nutrients for plant-fixed carbon (C) is well studied; however, the impact of competing symbionts remains underexplored. In this study, we examined mycorrhizal nutrient and host resource allocation in potato with and without AMF and PCN using radioisotope tracing, whilst determining the consequences of such allocation. The presence of PCN disrupted C for nutrient exchange between plants and AMF, with plant C overwhelmingly obtained by the nematodes. Despite this, AMF maintained transfer of nutrients on PCN-infected potato, ultimately losing out in their C for nutrient exchange with the host. Whilst PCN exploited the greater nutrient reserves to drive population growth on AMF-potato, the fungus imparted tolerance to allow the host to bear the parasitic burden. Our findings provide important insights into the belowground dynamics of plant-AMF symbioses, where simultaneous nutritional and nonnutritional benefits conferred by AMF to hosts and their parasites are seldom considered in plant community dynamics. Our findings suggest this may be a critical oversight, particularly in the consideration of C and nutrient flows in plant and soil communities.

An evaluation of costs associated with overall organ damage in patients with systemic lupus erythematosus in the United States.

INTRODUCTION: Approximately 33-50% of patients with systemic lupus erythematosus (SLE) develop organ damage within 5 years of diagnosis. Real-world studies that capture the healthcare resource utilization (HCRU) and costs associated with SLE-related organ damage are limited. The aim of this study was to evaluate HCRU and costs associated with organ damage in patients with SLE in the USA. METHODS: This retrospective study (GSK study 208380) used the PharMetrics Plus administrative claims database from 1 January 2008 to 30 June 2019. Patients with SLE and organ damage were identified using International Classification of Diseases (ICD)-9/10 codes derived from the Systemic Lupus International Collaborating Clinics/American College of Rheumatology Damage Index. The first observed diagnosis of organ damage was designated as the index date. Selection criteria included: ≥18 years of age; ≥1 inpatient or ≥2 outpatient claims for SLE (≥30 days apart before the index date; ICD-9: 710.0 or ICD-10: M32, excluding M32.0); ≥1 inpatient or ≥3 outpatient claims for organ damage within 6 months for the same organ system code; continuous enrollment of 12 months both pre- and post-index date. The proportion of patients with new organ damage, disease severity, SLE flares, SLE-related medication patterns, HCRU and all-cause costs (2018 US$) were assessed 12 months pre- and post-index date. RESULTS: Of the 360,803 patients with a diagnosis of SLE, 8952 patients met the inclusion criteria for the presence of new organ damage. Mean (standard deviation (SD)) age was 46.4 (12.2) years and 92% of patients were female. The most common sites of organ damage were neuropsychiatric (22.0%), ocular (12.9%), and cardiovascular (11.4%). Disease severity and proportion of moderate/severe flare episodes significantly increased from pre- to post-index date (p < 0.0001). Overall, SLE-related medication patterns were similar pre- versus post-index date. Inpatient, emergency department and outpatient claims increased from pre- to post-index date and mean (SD) all-cause costs were 71% higher post- versus pre-index date ($26,998 [57,982] vs $15,746 [29,637], respectively). CONCLUSIONS: The economic impact associated with organ damage in patients with SLE is profound and reducing or preventing organ damage will be pivotal in alleviating the burden for patients and healthcare providers.

Pre- and peri-operative clinical information, physiological observations and outcome measures following flexible ureterorenoscopy (FURS), for the treatment of kidney stones. A single-centre observational clinical pilot-study in 51 patients.

BACKGROUND: Kidney stone disease contributes to a significant proportion of routine urological practice and remains a common cause of worldwide morbidity. The main aim of this clinical-pilot study was to investigate the effect of flexible ureterorenoscopy (FURS) on pre- and peri-operative clinical information, physiological observations and outcome measures. METHODS: Included were 51 patients (31 males, 20 females), who underwent elective FURS, for the treatment of kidney stones. Pre-operative and peri-operative clinical information, and post-operative physiological observations and outcome measures were collected using a standard case report form. Pre-operative clinical information included age, gender, BMI, previous history of stone formation and hypertension. Pre-operative stone information included the size (mm), Hounsfield units (HU), laterality and intra-renal anatomical location. Peri-operative surgical details included surgical time in minutes; Laser use; Duration and energy of laser; and post-operative stenting. The physiological outcomes measured included systolic and diastolic blood pressure (mmHg), Likert pain score, temperature, heart rate (bpm) and respiration rate (bpm). Following initial descriptive analysis, a series of Pearson's correlation coefficient tests were performed to investigate the relationship between surgical factors other variable factors. RESULTS: A series of significant, positive correlations were observed between; age and surgical time (p = 0.014, r = 0.373); stone size and Hounsfield unit (p = 0.029, r = 0.406); surgical time and duration of laser (p < 0.001, r = 0.702); surgical time and BMI (p = 0.035, r = 0.322); baseline heart rate and Hounsfield unit (p = 0.026, r = - 0.414); base line heart rate and BMI (p = 0.030, r = 0.307).; heart rate at 120-min post FURS and age (p = 0.038, r = - 0.308); baseline pain score and BMI (p = 0.010, r = 0.361); baseline respiration rate and BMI (p = 0.037, r = 0.296); respiration rate at 240-min post FURS and BMI (p = 0.038, r = 0.329); respiration rate at 120 min post FURS and age (p = 0.022, r = - 0.330). Four patients developed post-operative complications (3-UTIs with urinary retention, 1-urosepsis). CONCLUSIONS: We report that following FURS there is an association between various physiological, clinical and surgical parameters. Although these correlations are weak, they warrant further investigation as these may be linked with untoward complications, such as infection that can occur following FURS. This data, however, will need to be validated and reproduced in larger multi-centre studies.

DNA Methylome Alterations Are Associated with Airway Macrophage Differentiation and Phenotype during Lung Fibrosis.

Rationale: Airway macrophages (AMs) are key regulators of the lung environment and are implicated in the pathogenesis of idiopathic pulmonary fibrosis (IPF), a fatal respiratory disease with no cure. However, knowledge about the epigenetics of AMs in IPF is limited. Objectives: To assess the role of epigenetic regulation of AMs during lung fibrosis. Methods: We undertook DNA methylation (DNAm) profiling by using Illumina EPIC (850k) arrays in sorted AMs from healthy donors (n = 14) and donors with IPF (n = 30). Cell-type deconvolution was performed by using reference myeloid-cell DNA methylomes. Measurements and Main Results: Our analysis revealed that epigenetic heterogeneity was a key characteristic of IPF AMs. DNAm "clock" analysis indicated that epigenetic alterations in IPF AMs were not associated with accelerated aging. In differential DNAm analysis, we identified numerous differentially methylated positions (n = 11) and differentially methylated regions (n = 49) between healthy and IPF AMs, respectively. Differentially methylated positions and differentially methylated regions encompassed genes involved in lipid (LPCAT1 [lysophosphatidylcholine acyltransferase 1]) and glucose (PFKFB3 [6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3]) metabolism, and importantly, the DNAm status was associated with disease severity in IPF. Conclusions: Collectively, our data identify that changes in the epigenome are associated with the development and function of AMs in the IPF lung.

Oral oncolytic monitoring pilot with patient-reported outcomes and adherence assessments.

INTRODUCTION: Patients on oral oncolytics are responsible for self-monitoring adherence and adverse drug reactions (ADRs). Oncology pharmacists are in position to focus on quality and safety of care for patients on oncolytics while providing communication between the patient, physician, and specialty pharmacies. This pilot aimed to monitor patients treated by our leukemia team initiated on oral oncolytics. METHODS: From July 2020 to February 2021, patients treated by our leukemia team newly started on oncolytics were included. Pharmacists performed medication reconciliation and drug interaction screening on initiation of oral oncolytic. Pharmacists followed up at predefined intervals. On follow up adherence was assessed using the Morisky Medication Adherence Scale-8 (MMAS-8) and patient reported outcomes (PROs) were assessed using the revised Edmonton Symptom Assessment Scale (ESAS-r). After each follow-up, a note was placed in the chart with assessment scores and recommendations. RESULTS: A total of 32 patients were screened with 19 patients included. Oral oncolytics included: imatinib (4), dasatinib (5), ponatinib (1), gilteritinib (2), enasidenib (1), and venetoclax (6). Fourteen drug interactions were identified, 11 medications discontinued, nine medications added, and two medications doses were changed. Twenty-six adherence assessments were performed with 21, 4, and 1 assessment demonstrating adherence, medium adherence, and low adherence, respectively. 62 ESAS-r assessments were performed with 64% reported as no symptoms, 17% as mild, 13% as moderate, and 5% as severe symptoms. Twenty laboratory tests were ordered from pharmacist recommendation on initiation and follow-up. CONCLUSION: This pilot demonstrated the role pharmacists play in oral oncolytic monitoring and symptom management.

A Call for Caution in Use of Pertussis Vaccine Effectiveness Studies to Estimate Waning Immunity: A Canadian Immunization Research Network Study.

BACKGROUND: Vaccine effectiveness (VE) studies provide essential evidence on waning vaccine-derived immunity, a major threat to pertussis control. We evaluated how study design affects estimates by comparing 2 case-control studies conducted in Ontario, Canada. METHODS: We compared results from a test-negative design (TND) with a frequency-matched design (FMD) case-control study using pertussis cases from 2005-2015. In the first study, we identified test-negative controls from the public health laboratory that diagnosed cases and, in the second, randomly selected controls from patients attending the same physicians that reported cases, frequency matched on age and year. We compared characteristics of cases and controls using standardized differences. RESULTS: In both designs, VE estimates for the early years postimmunization were consistent with clinical trials (TND, 84%; FMD, 89% at 1-3 years postvaccination) but diverged as time since last vaccination increased (TND, 41%; FMD, 74% by 8 years postvaccination). Overall, we observed lower VE and faster waning in the TND than the FMD. In the TND but not FMD, controls differed from cases in important confounders, being younger, having more comorbidities, and higher healthcare use. Differences between the controls of each design were greater than differences between cases. TND controls were more likely to be unvaccinated or incompletely vaccinated than FMD controls (P < .001). CONCLUSIONS: The FMD adjusted better for healthcare-seeking behavior than the TND. Duration of protection from pertussis vaccines is unclear because estimates vary by study design. Caution should be exercised by experts, researchers, and decision makers when evaluating evidence on optimal timing of boosters.

Increasing Incidence of Invasive Group A Streptococcus Disease in First Nations Population, Alberta, Canada, 2003-2017.

The incidence of invasive group A Streptococcus (iGAS) disease in the general population in Alberta, Canada, has been steadily increasing. To determine whether rates for specific populations such as First Nations are also increasing, we investigated iGAS cases among First Nations persons in Alberta during 2003-2017. We identified cases by isolating GAS from a sterile site and performing emm typing. We collected demographic, social, behavioral, and clinical data for patients. During the study period, 669 cases of iGAS in First Nations persons were reported. Incidence increased from 10.0 cases/100,000 persons in 2003 to 52.2 cases/100,000 persons in 2017. The 2017 rate was 6 times higher for the First Nations population than for non-First Nations populations (8.7 cases/100,000 persons). The 5 most common emm types from First Nations patients were 59, 101, 82, 41, and 11. These data indicate that iGAS is severely affecting the First Nations population in Alberta, Canada.

Plant-parasitic nematodes respond to root exudate signals with host-specific gene expression patterns.

Plant parasitic nematodes must be able to locate and feed from their host in order to survive. Here we show that Pratylenchus coffeae regulates the expression of selected cell-wall degrading enzyme genes relative to the abundance of substrate in root exudates, thereby tailoring gene expression for root entry of the immediate host. The concentration of cellulose or xylan within the exudate determined the level of ß-1,4-endoglucanase (Pc-eng-1) and ß-1,4-endoxylanase (Pc-xyl) upregulation respectively. Treatment of P. coffeae with cellulose or xylan or with root exudates deficient in cellulose or xylan conferred a specific gene expression response of Pc-eng-1 or Pc-xyl respectively with no effect on expression of another cell wall degrading enzyme gene, a pectate lyase (Pc-pel). RNA interference confirmed the importance of regulating these genes as lowered transcript levels reduced root penetration by the nematode. Gene expression in this plant parasitic nematode is therefore influenced, in a host-specific manner, by cell wall components that are either secreted by the plant or released by degradation of root tissue. Transcriptional plasticity may have evolved as an adaptation for host recognition and increased root invasion by this polyphagous species.

Universal Bound to the Amplitude of the Vortex Nernst Signal in Superconductors.

A liquid of superconducting vortices generates a transverse thermoelectric response. This Nernst signal has a tail deep in the normal state due to superconducting fluctuations. Here, we present a study of the Nernst effect in two-dimensional heterostructures of Nb-doped strontium titanate (STO) and in amorphous MoGe. The Nernst signal generated by ephemeral Cooper pairs above the critical temperature has the magnitude expected by theory in STO. On the other hand, the peak amplitude of the vortex Nernst signal below T_{c} is comparable in both and in numerous other superconductors despite the large distribution of the critical temperature and the critical magnetic fields. In four superconductors belonging to different families, the maximum Nernst signal corresponds to an entropy per vortex per layer of ≈k_{B}ln2.