Multi-Omics Approaches to Study Long Non-coding RNA Function in Atherosclerosis

Atherosclerosis is a complex inflammatory disease of the vessel wall involving the interplay of multiple cell types including vascular smooth muscle cells, endothelial cells, and macrophages. Large-scale genome-wide association studies (GWAS) and the advancement of next generation sequencing technologies have rapidly expanded the number of long non-coding RNA (lncRNA) transcripts predicted to play critical roles in the pathogenesis of the disease. In this review, we highlight several lncRNAs whose functional role in atherosclerosis is well-documented through traditional biochemical approaches as well as those identified through RNA-sequencing and other high-throughput assays. We describe novel genomics approaches to study both evolutionarily conserved and divergent lncRNA functions and interactions with DNA, RNA, and proteins. We also highlight assays to resolve the complex spatial and temporal regulation of lncRNAs. Finally, we summarize the latest suite of computational tools designed to improve genomic and functional annotation of these transcripts in the human genome. Deep characterization of lncRNAs is fundamental to unravel coronary atherosclerosis and other cardiovascular diseases, as these regulatory molecules represent a new class of potential therapeutic targets and/or diagnostic markers to mitigate both genetic and environmental risk factors

Evaluating the typical day-to-day variability of WHOOP-derived heart rate variability in Olympic water polo athletes

Heart rate (HR) and HR variability (HRV) can be used to infer readiness to perform exercise in athletic populations. Advancements in the photoplethysmography technology of wearable devices such as WHOOP allow for the frequent and convenient measurement of HR and HRV, and therefore enhanced application in athletes. However, it is important that the reliability of such technology is acceptable prior to its application in practical settings. Eleven elite male water polo players (age 28.8 ± 5.3 years [mean ± standard deviation]; height 190.3 ± 3.8 cm; body mass 95.0 ± 6.9 kg; international matches 117.9 ± 92.1) collected their HR and HRV daily via a WHOOP strap (WHOOP 3.0, CB Rank, Boston, MA, USA) over 16 weeks ahead of the 2021 Tokyo Olympic Games. The WHOOP strap quantified HR and HRV via wrist-based photoplethysmography during overnight sleep periods. The weekly (i.e., 7-day) coefficient of variation in lnRMSSD (lnRMSSDCV) and HR (HRCV) was calculated as a measure of day-to-day variability in lnRMSSD and HR, and presented as a mean of the entire recording period. The mean weekly lnRMSSDCV and HRCV over the 16-week period was 5.4 ± 0.7% (mean ± 95% confidence intervals) and 7.6 ± 1.3%, respectively. The day-to-day variability in WHOOP-derived lnRMSSD and HR is within or below the range of day-to-day variability in alternative lnRMSSD (~3–13%) and HR (~10–11%) assessment protocols, indicating that the assessment of HR and HRV by WHOOP does not introduce any more variability than that which is naturally present in these variables

A validation study of a commercial wearable device to automatically detect and estimate sleep

The aims of this study were to: (1) compare actigraphy (ACTICAL) and a commercially available sleep wearable (i.e., WHOOP) under two functionalities (i.e., sleep auto-detection (WHOOP-AUTO) and manual adjustment of sleep (WHOOP-MANUAL)) for two-stage categorisation of sleep (sleep or wake) against polysomnography, and; (2) compare WHOOP-AUTO and WHOOP-MANUAL for four-stage categorisation of sleep (wake, light sleep, slow wave sleep (SWS), or rapid eye movement sleep (REM)) against polysomnography. Six healthy adults (male: n = 3; female: n = 3; age: 23.0 ± 2.2 yr) participated in the nine-night protocol. Fifty-four sleeps assessed by ACTICAL, WHOOP-AUTO and WHOOP-MANUAL were compared to polysomnography using difference testing, Bland–Altman comparisons, and 30-s epoch-by-epoch comparisons. Compared to polysomnography, ACTICAL overestimated total sleep time (37.6 min) and underestimated wake (−37.6 min); WHOOP-AUTO underestimated SWS (−15.5 min); and WHOOP-MANUAL underestimated wake (−16.7 min). For ACTICAL, sensitivity for sleep, specificity for wake and overall agreement were 98%, 60% and 89%, respectively. For WHOOP-AUTO, sensitivity for sleep, wake, and agreement for two-stage and four-stage categorisation of sleep were 90%, 60%, 86% and 63%, respectively. For WHOOP-MANUAL, sensitivity for sleep, wake, and agreement for two-stage and four-stage categorisation of sleep were 97%, 45%, 90% and 62%, respectively. WHOOP-AUTO and WHOOP-MANUAL have a similar sensitivity and specificity to actigraphy for two-stage categorisation of sleep and can be used as a practical alternative to polysomnography for two-stage categorisation of sleep and four-stage categorisation of sleep

Integrative single-cell meta-analysis reveals disease-relevant vascular cell states and markers in human atherosclerosis

Coronary artery disease (CAD) is characterized by atherosclerotic plaque formation in the arterial wall. CAD progression involves complex interactions and phenotypic plasticity among vascular and immune cell lineages. Single-cell RNA-seq (scRNA-seq) studies have highlighted lineage-specific transcriptomic signatures, but human cell phenotypes remain controversial. Here, we perform an integrated meta-analysis of 22 scRNA-seq libraries to generate a comprehensive map of human atherosclerosis with 118,578 cells. Besides characterizing granular cell-type diversity and communication, we leverage this atlas to provide insights into smooth muscle cell (SMC) modulation. We integrate genome-wide association study data and uncover a critical role for modulated SMC phenotypes in CAD, myocardial infarction, and coronary calcification. Finally, we identify fibromyocyte/fibrochondrogenic SMC markers (LTBP1 and CRTAC1) as proxies of atherosclerosis progression and validate these through omics and spatial imaging analyses. Altogether, we create a unified atlas of human atherosclerosis informing cell state-specific mechanistic and translational studies of cardiovascular diseases.</p

Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.</p

Multi-ancestry genetic analysis of gene regulation in coronary arteries prioritizes disease risk loci

Genome-wide association studies (GWASs) have identified hundreds of risk loci for coronary artery disease (CAD). However, non-European populations are underrepresented in GWASs, and the causal gene-regulatory mechanisms of these risk loci during atherosclerosis remain unclear. We incorporated local ancestry and haplotypes to identify quantitative trait loci for expression (eQTLs) and splicing (sQTLs) in coronary arteries from 138 ancestrally diverse Americans. Of 2,132 eQTL-associated genes (eGenes), 47% were previously unreported in coronary artery; 19% exhibited cell-type-specific expression. Colocalization revealed subgroups of eGenes unique to CAD and blood pressure GWAS. Fine-mapping highlighted additional eGenes, including TBX20 and IL5. We also identified sQTLs for 1,690 genes, among which TOR1AIP1 and ULK3 sQTLs demonstrated the importance of evaluating splicing to accurately identify disease-relevant isoform expression. Our work provides a patient-derived coronary artery eQTL resource and exemplifies the need for diverse study populations and multifaceted approaches to characterize gene regulation in disease processes.</p

An automatic entropy method to efficiently mask histology whole-slide images

Tissue segmentation of histology whole-slide images (WSI) remains a critical task in automated digital pathology workflows for both accurate disease diagnosis and deep phenotyping for research purposes. This is especially challenging when the tissue structure of biospecimens is relatively porous and heterogeneous, such as for atherosclerotic plaques. In this study, we developed a unique approach called 'EntropyMasker' based on image entropy to tackle the fore- and background segmentation (masking) task in histology WSI. We evaluated our method on 97 high-resolution WSI of human carotid atherosclerotic plaques in the Athero-Express Biobank Study, constituting hematoxylin and eosin and 8 other staining types. Using multiple benchmarking metrics, we compared our method with four widely used segmentation methods: Otsu's method, Adaptive mean, Adaptive Gaussian and slideMask and observed that our method had the highest sensitivity and Jaccard similarity index. We envision EntropyMasker to fill an important gap in WSI preprocessing, machine learning image analysis pipelines, and enable disease phenotyping beyond the field of atherosclerosis

Optimising conservative management of chronic low back pain: study protocol for a randomised controlled trial

BackgroundLower back pain is a global health issue affecting approximately 80% of people at some stage in their life. The current literature suggests that any exercise is beneficial for reducing back pain. However, as pain is a subjective evaluation and physical deficits are evident in low back pain, using it as the sole outcome measure to evaluate superiority of an exercise protocol for low back pain treatment is insufficient. The overarching goal of the current clinical trial is to implement two common, conservative intervention approaches and examine their impact on deficits in chronic low back pain.Methods/designForty participants, 25&ndash;45 years old with chronic (&gt;3 months), non-specific low back pain will be recruited. Participants will be randomised to receive either motor control and manual therapy (n&thinsp;=&thinsp;20) or general strength and conditioning (n&thinsp;=&thinsp;20) exercise treatments for 6 months. The motor control/manual therapy group will receive twelve 30-min sessions, ten in the first 3 months (one or two per week) and two in the last 3 months. The general exercise group will attend two 1-hour sessions weekly for 3 months, and one or two a week for the following 3 months. Primary outcome measures are average lumbar spine intervertebral disc T2 relaxation time and changes in thickness of the transversus abdominis muscle on a leg lift using magnetic resonance imaging (MRI). Secondary outcomes include muscle size and fat content, vertebral body fat content, intervertebral disc morphology and water diffusion measured by MRI, body composition using dual energy X-ray absorptiometry, physical function through functional tests, changes in corticospinal excitability and cortical motor representation of the spinal muscles using transcranial magnetic stimulation and self-reported measure of pain symptoms, health and disability. Outcome measures will be conducted at baseline, at the 3-month follow-up and at 6 months at the end of intervention. Pain, depressive symptomology and emotions will be captured fortnightly by questionnaires.DiscussionChronic low back pain is ranked the highest disabling disorder in Australia. The findings of this study will inform clinical practice guidelines to assist with decision-making approaches where outcomes beyond pain are sought for adults with chronic low back pain.<br /