An AI Approach to Identifying Novel Therapeutics for Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic autoimmune disorder that has a significant impact on quality of life and work capacity. Treatment of RA aims to control inflammation and alleviate pain; however, achieving remission with minimal toxicity is frequently not possible with the current suite of drugs. This review aims to summarise current treatment practices and highlight the urgent need for alternative pharmacogenomic approaches for novel drug discovery. These approaches can elucidate new relationships between drugs, genes, and diseases to identify additional effective and safe therapeutic options. This review discusses how computational approaches such as connectivity mapping offer the ability to repurpose FDA-approved drugs beyond their original treatment indication. This review also explores the concept of drug sensitisation to predict co-prescribed drugs with synergistic effects that produce enhanced anti-disease efficacy by involving multiple disease pathways. Challenges of this computational approach are discussed, including the availability of suitable high-quality datasets for comprehensive analysis and other data curation issues. The potential benefits include accelerated identification of novel drug combinations and the ability to trial and implement established treatments in a new index disease. This review underlines the huge opportunity to incorporate disease-related data and drug-related data to develop methods and algorithms that have strong potential to determine novel and effective treatment regimens

Exploring the involvement of NLRP3 and Il-1β in Osteoarthritis of the Hand: Results from a Pilot Study

Hand osteoarthritis (HOA) includes different subsets; a particular and uncommon form is erosive HOA (EHOA). Interleukin- (IL-) 1 plays a crucial role in the pathogenesis of osteoarthritis (OA); it is synthesized as an inactive precursor which requires the intervention of a cytosolic multiprotein complex, named inflammasome, for its activation. The aim of this study was to investigate the involvement of IL-1 and the NOD-like receptor pyrin domain containing 3 (NLRP3) inflammasome in patients with EHOA and nonerosive HOA (NEHOA) compared to healthy controls. In particular, we evaluated the gene expression of IL-1 and NLRP3, the serum levels of IL-1, IL-6, IL-17, and tumor necrosis factor- (TNF-) , and the protein levels of IL-1 and NLRP3. We also assessed the relationships between IL-1 and NLRP3 and clinical, laboratory, and radiological findings. Fifty-four patients with HOA (25 EHOA and 29 NEHOA) and 20 healthy subjects were included in the study. Peripheral blood mononuclear cell (PBMC) gene and protein expressions of IL-1 and NLRP3 were quantified by quantitative real-time PCR and western blot. IL-1, IL-6, IL-17, and TNF- serum levels were determined by ELISA. IL-1 gene expression was significantly reduced (p=0.0208) in EHOA compared to healthy controls. NLRP3 protein levels were significantly increased in the NEHOA group versus the control (p=0.0063) and EHOA groups (p=0.0038). IL-1 serum levels were not significantly different across the groups; IL-6, IL-17, and TNF- were not detectable in any sample. IL-1 concentrations were negatively correlated with the Kellgren-Lawrence score in the whole population (r=-0.446; p=0.0008) and in NEHOA (r=-0.608; p=0.004), while IL-1 gene expression was positively correlated with the number of joint swellings in the EHOA group (r=0.512; p=0.011). Taken together, our results, showing poorly detectable IL-1 concentrations and minimal inflammasome activity in the PBMCs of HOA patients, suggest a low grade of systemic inflammation in HOA. This evidence does not preclude a possible involvement of these factors at the local level

The compression type of coronary artery motion in patients with ST-segment elevation acute myocardial infarction and normal controls: a case-control study

<p>Abstract</p> <p>Background</p> <p>Prediction of the location of culprit lesions responsible for ST-segment elevation myocardial infarctions may allow for prevention of these events. A retrospective analysis of coronary artery motion (CAM) was performed on coronary angiograms of 20 patients who subsequently had ST-segment elevation myocardial infarction treated by primary or rescue angioplasty and an equal number of age and sex matched controls with normal angiograms.</p> <p>Findings</p> <p>There was no statistically significant difference between the frequency of CAM types of the ST-segment elevation acute myocardial infarction and control patients (p = 0.97). The compression type of CAM is more frequent in the proximal and mid segments of all three coronary arteries. No statistically significant difference was found when the frequency of the compression type of CAM was compared between the ST-segment elevation acute myocardial infarction and control patients for the individual coronary artery segments (p = 0.59).</p> <p>Conclusion</p> <p>The proportion of the compression type of coronary artery motion for individual artery segments is not different between patients who have subsequent ST-segment elevation myocardial infarctions and normal controls.</p

Genomic, Proteomic and Phenotypic Biomarkers of COVID-19 Severity::Protocol for a Retrospective Observational Study

Background:Background - Health organisations and countries around the world have found it difficult to control the spread of the coronavirus disease 2019. To minimise the impact on the NHS and improve patient care, there is a drive for rapid tests capable of detecting individuals who are at high risk of contracting severe COVID-19. Early work focused on single omic approaches, highlighting a limited amount of information.Objective:Objective - The Covid Response Study (COVRES, NCT05548829) aims to carry out an integrated multi-omic analysis of factors contributing to host susceptibility to SARS-CoV-2 among a patient cohort of 1000 people from the geographically isolated island of Ireland.Methods:Methods - The protocol below describes the study to be carried out in Northern Ireland (NI-COVRES) by Ulster University, the Republic of Ireland component will be described separately. All participants (n=519) were recruited from the Western Health and Social Care Trust, Northern Ireland, forty patients are also being followed up at 1, 3, 6 and 12 months to assess the longitudinal impact of infection on symptoms, general health, and immune response, this is ongoing. Data will be sourced from whole blood, saliva samples, and clinical data from the Northern Ireland Electronic Care Record, general health questionnaire, and the GHQ12 mental health survey. Saliva and blood samples were processed for DNA and RNA prior to whole genomic sequencing, RNA sequencing, DNA methylation, microbiome, 16S, and proteomic analysis. Multi-omics data will be combined with clinical data to produce sensitive and specific prognostic models of severity risk.Results:Results - An initial profile of the cohort has been completed: n=249 hospitalised and n=270 non-hospitalised patients were recruited, 64% were female, the mean age was 45 years. High levels of comorbidity were evident in the hospitalised cohort, with cardiovascular disease and metabolic and respiratory disorders (P&lt;0.001) being the most significant.Conclusions:Conclusion – This study will provide a comprehensive opportunity to study multi-omic mechanisms of COVID-19 severity in re-contactable participants. Clinical Trial: Trial Registration - The trial has been registered as an observational study on clinicaltrials.gov as NCT05548829. An outline of the trial protocol is included; SPIRIT checklist (Supplementary Figure 1)

Garden and landscape-scale correlates of moths of differing conservation status: significant effects of urbanization and habitat diversity

Moths are abundant and ubiquitous in vegetated terrestrial environments and are pollinators, important herbivores of wild plants, and food for birds, bats and rodents. In recent years, many once abundant and widespread species have shown sharp declines that have been cited by some as indicative of a widespread insect biodiversity crisis. Likely causes of these declines include agricultural intensification, light pollution, climate change, and urbanization; however, the real underlying cause(s) is still open to conjecture. We used data collected from the citizen science Garden Moth Scheme (GMS) to explore the spatial association between the abundance of 195 widespread British species of moth, and garden habitat and landscape features, to see if spatial habitat and landscape associations varied for species of differing conservation status. We found that associations with habitat and landscape composition were species-specific, but that there were consistent trends in species richness and total moth abundance. Gardens with more diverse and extensive microhabitats were associated with higher species richness and moth abundance; gardens near to the coast were associated with higher richness and moth abundance; and gardens in more urbanized locations were associated with lower species richness and moth abundance. The same trends were also found for species classified as increasing, declining and vulnerable under IUCN (World Conservation Union) criteria

Intra- and inter-individual genetic differences in gene expression

Genetic variation is known to influence the amount of mRNA produced by a gene. Given that the molecular machines control mRNA levels of multiple genes, we expect genetic variation in the components of these machines would influence multiple genes in a similar fashion. In this study we show that this assumption is correct by using correlation of mRNA levels measured independently in the brain, kidney or liver of multiple, genetically typed, mice strains to detect shared genetic influences. These correlating groups of genes (CGG) have collective properties that account for 40-90% of the variability of their constituent genes and in some cases, but not all, contain genes encoding functionally related proteins. Critically, we show that the genetic influences are essentially tissue specific and consequently the same genetic variations in the one animal may up-regulate a CGG in one tissue but down-regulate the same CGG in a second tissue. We further show similarly paradoxical behaviour of CGGs within the same tissues of different individuals. The implication of this study is that this class of genetic variation can result in complex inter- and intra-individual and tissue differences and that this will create substantial challenges to the investigation of phenotypic outcomes, particularly in humans where multiple tissues are not readily available.&#xd;&#xa;&#xd;&#xa

Analysis of SARS-CoV-2 antibody seroprevalence in Northern Ireland during 2020–2021

BackgroundWith the spread of SARS-CoV-2 impacting upon public health directly and socioeconomically, further information was required to inform policy decisions designed to limit virus spread during the pandemic. This study sought to contribute to serosurveillance work within Northern Ireland to track SARS-CoV-2 progression and guide health strategy.MethodsSera/plasma samples from clinical biochemistry laboratories were analysed for anti-SARS-CoV-2 antibodies. Samples were assessed using an Elecsys anti-SARS-CoV-2 or anti-SARS-CoV-2 S ECLIA (Roche) on an automated cobas e 801 analyser. Samples were also assessed via an anti-SARS-CoV-2 ELISA (Euroimmun). A subset of samples assessed via the Elecsys anti-SARS-CoV-2 ECLIA were subsequently analysed in an ACE2 pseudoneutralisation assay using a V-PLEX SARS-CoV-2 Panel 7 for IgG and ACE2 (Meso Scale Diagnostics).ResultsAcross three testing rounds (June–July 2020, November–December 2020 and June–July 2021 (rounds 1–3 respectively)), 4844 residual sera/plasma specimens were assayed for anti-SARS-CoV-2 antibodies. Seropositivity rates increased across the study, peaking at 11.6 % (95 % CI 10.4%–13.0 %) during round 3. Varying trends in SARS-CoV-2 seropositivity were noted based on demographic factors. For instance, highest rates of seropositivity shifted from older to younger demographics across the study period. In round 3, Alpha (B.1.1.7) variant neutralising antibodies were most frequently detected across age groups, with median concentration of anti-spike protein antibodies elevated in 50–69 year olds and anti-S1 RBD antibodies elevated in 70+ year olds, relative to other age groups.ConclusionsWith seropositivity rates of &lt;15 % across the assessment period, it can be concluded that the significant proportion of the Northern Ireland population had not yet naturally contracted the virus by mid-2021

Cohort study of Western Australia computed tomography utilisation patterns and their policy implications

Background: Computed tomography (CT) scanning is a relatively high radiation dose diagnostic imaging modality with increasing concerns about radiation exposure burden at the population level in scientific literature. This study examined the epidemiology of adult CT utilisation in Western Australia (WA) in both the public hospital and private practice settings, and the policy implications. Methods: Retrospective cohort design using aggregate adult CT data from WA public hospitals and Medical Benefits Schedule (MBS) (mid-2006 to mid-2012). CT scanning trends by sex, age, provider setting and anatomical areas were explored using crude CT scanning rates, age-standardised CT scanning rates and Poisson regression modelling. Results: From mid-2006 to mid-2012 the WA adult CT scanning rate was 129 scans per 1,000 person-years (PY). Females were consistently scanned at a higher rate than males. Patients over 65 years presented the highest scanning rates (over 300 scans per 1,000 PY). Private practice accounted for 73% of adult CT scans, comprising the majority in every anatomical area. In the private setting females predominately held higher age-standardised CT scanning rates than males. This trend reversed in the public hospital setting. Patients over 85 years in the public hospital setting were the most likely age group CT scanned in nine of ten anatomical areas. Patients in the private practice setting aged 85+ years were relatively less prominent across every anatomical area, and the least likely age group scanned in facial bones and multiple areas CT scans.Conclusion: In comparison to the public hospital setting, the MBS subsidised private sector tended to service females and relatively younger patients with a more diverse range of anatomical areas, constituting the majority of CT scans performed in WA. Patient risk and subsequent burden is greater for females, lower ages and some anatomical areas. In the context of a national health system, Australia has various avenues to monitor radiation exposure levels, improve physician training and modify funding mechanisms to ensure individual and population medical radiation exposure is as low as reasonably achievable

Demonstration of the Effect of Generic Anatomical Divisions versus Clinical Protocols on Computed Tomography Dose Estimates and Risk Burden

Objective: Choosing to undertake a CT scan relies on balancing risk versus benefit, however risks associated with CT scanning have generally been limited to broad anatomical locations, which do not provided adequate information to evaluate risk against benefit. Our study aimed to determine differences in radiation dose and risk estimates associated with modern CT scanning examinations when computed for clinical protocols compared with those using anatomical area. Methods: Technical data were extracted from a tertiary hospital Picture Archiving Communication System for random samples of 20–40 CT examinations per adult clinical CT protocol. Organ and whole body radiation dose were calculated using ImPACT Monte Carlo simulation software and cancer incidence and mortality estimated using BEIR VII age and gender specific lifetime attributable risk weights. Results: Thirty four unique CT protocols were identified by our study. When grouped according to anatomic area the radiation dose varied substantially, particularly for abdominal protocols. The total estimated number of incident cancers and cancer related deaths using the mean dose of anatomical area were 86 and 69 respectively. Using more specific protocol doses the estimates rose to 214 and 138 incident cancers and cancer related deaths, at least doubling the burden estimated. Conclusions: Modern CT scanning produces a greater diversity of effective doses than much of the literature describes; where a lack of focus on actual scanning protocols has produced estimates that do not reflect the range and complexity of modern CT practice. To allow clinicians, patients and policy makers to make informed risk versus benefit decisions the individual and population level risks associated with modern CT practices are essential

Genome-Wide Association Analysis of Incident Coronary Heart Disease (CHD) in African Americans: A Short Report

African Americans have the highest rate of mortality due to coronary heart disease (CHD). Although multiple loci have been identified influencing CHD risk in European-Americans using a genome-wide association (GWAS) approach, no GWAS of incident CHD has been reported for African Americans. We performed a GWAS for incident CHD events collected during 19 years of follow-up in 2,905 African Americans from the Atherosclerosis Risk in Communities (ARIC) study. We identified a genome-wide significant SNP (rs1859023, MAF = 31%) located at 7q21 near the PFTK1 gene (HR = 0.57, 95% CI 0.46 to 0.69, p = 1.86×10−08), which replicated in an independent sample of over 8,000 African American women from the Women's Health Initiative (WHI) (HR = 0.81, 95% CI 0.70 to 0.93, p = 0.005). PFTK1 encodes a serine/threonine-protein kinase, PFTAIRE-1, that acts as a cyclin-dependent kinase regulating cell cycle progression and cell proliferation. This is the first finding of incident CHD locus identified by GWAS in African Americans