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1.
Nature ; 584(7822): 589-594, 2020 08.
Article in English | MEDLINE | ID: mdl-32814899

ABSTRACT

The inner surfaces of the human heart are covered by a complex network of muscular strands that is thought to be a remnant of embryonic development1,2. The function of these trabeculae in adults and their genetic architecture are unknown. Here we performed a genome-wide association study to investigate image-derived phenotypes of trabeculae using the fractal analysis of trabecular morphology in 18,096 participants of the UK Biobank. We identified 16 significant loci that contain genes associated with haemodynamic phenotypes and regulation of cytoskeletal arborization3,4. Using biomechanical simulations and observational data from human participants, we demonstrate that trabecular morphology is an important determinant of cardiac performance. Through genetic association studies with cardiac disease phenotypes and Mendelian randomization, we find a causal relationship between trabecular morphology and risk of cardiovascular disease. These findings suggest a previously unknown role for myocardial trabeculae in the function of the adult heart, identify conserved pathways that regulate structural complexity and reveal the influence of the myocardial trabeculae on susceptibility to cardiovascular disease.


Subject(s)
Cardiovascular Diseases/genetics , Fractals , Genetic Predisposition to Disease , Heart/anatomy & histology , Heart/physiology , Myocardium/metabolism , Adult , Aged , Animals , Cardiovascular Diseases/physiopathology , Cytoskeleton/genetics , Cytoskeleton/physiology , Gene Knockout Techniques , Genetic Loci/genetics , Genome-Wide Association Study , Heart/embryology , Hemodynamics , Humans , Middle Aged , Myocardium/cytology , Oryzias/embryology , Oryzias/genetics , Phenotype
2.
Curr Issues Mol Biol ; 46(7): 6315-6327, 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-39057019

ABSTRACT

Worldwide, hypertension is the leading risk factor for cardiovascular disease and death. An estimated 122 million people, per the American Heart Association in 2023, have been diagnosed with this common condition. It is generally agreed that the primary goal in the treatment of hypertension is to reduce overall blood pressure to below 140/90 mmHg, with a more optimal goal of 130/80 mmHg. Common medications for treating hypertension include calcium channel blockers (CCBs), angiotensin-converting enzyme inhibitors, angiotensin receptor blockers, beta-blockers, and diuretics. CCBs are one of the most widely studied agents and are generally recommended as first-line therapy alone and in combination therapies. This is largely based on the vast knowledge of CCB mechanisms and their minimal side effect profile. CCBs can be separated into two classes: dihydropyridine and non-dihydropyridine. Non-dihydropyridine CCBs act on voltage-dependent L-type calcium channels of cardiac and smooth muscle to decrease muscle contractility. Dihydropyridine CCBs act by vasodilating the peripheral vasculature. For many patients with only mild increases in systolic and diastolic blood pressure (e.g., stage 1 hypertension), the medical literature indicates that CCB monotherapy can be sufficient to control hypertension. In this regard, CCB monotherapy in those with stage 1 hypertension reduced renal and cardiovascular complications compared to other drug classes. Combination therapy with CCBs and angiotensin receptor blockers or angiotensin-converting enzyme inhibitors has been shown to be an effective dual therapy based on recent meta-analyses. This article is a review of calcium channel blockers and their use in treating hypertension with some updated and recent information on studies that have re-examined their use. As for new information, we tried to include some information from recent studies on hypertensive treatment involving calcium channel blockers.

3.
J Pathol ; 259(4): 415-427, 2023 04.
Article in English | MEDLINE | ID: mdl-36641763

ABSTRACT

CRISPR/Cas9-driven cancer modeling studies are based on the disruption of tumor suppressor genes by small insertions or deletions (indels) that lead to frame-shift mutations. In addition, CRISPR/Cas9 is widely used to define the significance of cancer oncogenes and genetic dependencies in loss-of-function studies. However, how CRISPR/Cas9 influences gain-of-function oncogenic mutations is elusive. Here, we demonstrate that single guide RNA targeting exon 3 of Ctnnb1 (encoding ß-catenin) results in exon skipping and generates gain-of-function isoforms in vivo. CRISPR/Cas9-mediated exon skipping of Ctnnb1 induces liver tumor formation in synergy with YAPS127A in mice. We define two distinct exon skipping-induced tumor subtypes with different histological and transcriptional features. Notably, ectopic expression of two exon-skipped ß-catenin transcript isoforms together with YAPS127A phenocopies the two distinct subtypes of liver cancer. Moreover, we identify similar CTNNB1 exon-skipping events in patients with hepatocellular carcinoma. Collectively, our findings advance our understanding of ß-catenin-related tumorigenesis and reveal that CRISPR/Cas9 can be repurposed, in vivo, to study gain-of-function mutations of oncogenes in cancer. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.


Subject(s)
Carcinoma, Hepatocellular , Liver Neoplasms , Animals , Mice , beta Catenin/genetics , Carcinogenesis/genetics , Carcinoma, Hepatocellular/genetics , Exons/genetics , Liver Neoplasms/genetics
4.
J Emerg Med ; 63(6): 772-776, 2022 12.
Article in English | MEDLINE | ID: mdl-36369120

ABSTRACT

BACKGROUND: Clinicians trained in point-of-care ultrasound (POCUS) use the tool to enhance diagnostic capabilities at the bedside, often excluding or diagnosing conditions that are suspected based on the history and physical examination. Thoracic outlet syndrome (TOS) involves compression of arteries and nerves between the clavicle and first rib causing pain and paresthesia in the affected limbs. To our knowledge, use of POCUS to diagnose TOS in the literature has not been described. CASE REPORT: A 46-year-old man presented with left upper extremity (LUE) edema, pain, and paresthesia, which was progressive over 3 weeks. Examination of the LUE revealed diffuse swelling without erythema and a left radial pulse present on Doppler only. A subsequent POCUS examination of the LUE was performed to exclude a deep vein thrombosis, and enlarged and turbulent veins distal to the internal jugular vein were found, which suggested venous compression external to the veins. Additional imaging confirmed narrowing of the subclavian vein and a diagnosis of venous thoracic outlet syndrome (vTOS) was made. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: Failure to promptly diagnose and treat TOS can lead to long-term chronic upper extremity pain and even permanent disability. Diagnosis of vascular TOS is often made using computed tomography to identify impinged vessels, although color Doppler sonography can be an excellent choice for initial imaging in patients with suspected vTOS. Although POCUS is being used increasingly as a diagnostic tool and for procedural guidance, our case represents a novel application of POCUS in the diagnosis of vTOS.


Subject(s)
Point-of-Care Systems , Thoracic Outlet Syndrome , Male , Humans , Middle Aged , Paresthesia/complications , Thoracic Outlet Syndrome/diagnostic imaging , Thoracic Outlet Syndrome/etiology , Ribs , Chest Pain
5.
Bioinformatics ; 34(17): 2951-2956, 2018 09 01.
Article in English | MEDLINE | ID: mdl-29617944

ABSTRACT

Motivation: Simulation is a critical part of method development and assessment. With the increasing sophistication of multi-trait and multi-locus genetic analysis techniques, it is important that the community has flexible simulation tools to challenge and explore the properties of these methods. Results: We have developed PhenotypeSimulator, a comprehensive phenotype simulation scheme that can model multiple traits with multiple underlying genetic loci as well as complex covariate and observational noise structure. This package has been designed to work with many common genetic tools both for input and output. We describe the underlying components of this simulation tool and illustrate its use on an example dataset. Availability and implementation: PhenotypeSimulator is available as a well documented R/CRAN package and the code is available on github: https://github.com/HannahVMeyer/PhenotypeSimulator. Supplementary information: Supplementary data are available at Bioinformatics online.


Subject(s)
Genotype , Phenotype , Genetic Loci , Software
6.
Bioinformatics ; 34(1): 97-103, 2018 01 01.
Article in English | MEDLINE | ID: mdl-28968671

ABSTRACT

Motivation: Left ventricular (LV) hypertrophy is a strong predictor of cardiovascular outcomes, but its genetic regulation remains largely unexplained. Conventional phenotyping relies on manual calculation of LV mass and wall thickness, but advanced cardiac image analysis presents an opportunity for high-throughput mapping of genotype-phenotype associations in three dimensions (3D). Results: High-resolution cardiac magnetic resonance images were automatically segmented in 1124 healthy volunteers to create a 3D shape model of the heart. Mass univariate regression was used to plot a 3D effect-size map for the association between wall thickness and a set of predictors at each vertex in the mesh. The vertices where a significant effect exists were determined by applying threshold-free cluster enhancement to boost areas of signal with spatial contiguity. Experiments on simulated phenotypic signals and SNP replication show that this approach offers a substantial gain in statistical power for cardiac genotype-phenotype associations while providing good control of the false discovery rate. This framework models the effects of genetic variation throughout the heart and can be automatically applied to large population cohorts. Availability and implementation: The proposed approach has been coded in an R package freely available at https://doi.org/10.5281/zenodo.834610 together with the clinical data used in this work. Contact: declan.oregan@imperial.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.


Subject(s)
Genetic Association Studies/methods , Hypertrophy, Left Ventricular/diagnostic imaging , Imaging, Three-Dimensional/methods , Polymorphism, Single Nucleotide , Software , Female , Genetic Predisposition to Disease , Heart/diagnostic imaging , Humans , Hypertrophy, Left Ventricular/genetics , Male , Phenotype
7.
J Autoimmun ; 67: 65-75, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26481130

ABSTRACT

Promiscuous expression of a plethora of tissue-restricted antigens (TRAs) in medullary thymic epithelial cells (mTECs) is essential for central tolerance. This promiscuous gene expression (pGE) is characterized by inclusion of a broad range of TRAs and by its mosaic expression patterns, i.e. each antigen is only expressed in 1-3% of mTECs. It is currently unclear to which extent random and/or deterministic mechanisms are involved in the regulation of pGE. In order to address this issue, we deconstructed the transcriptional heterogeneity in mTEC to minor subsets expressing a particular TRA. We identified six delineable co-expression groups in mouse mTECs. These co-expression groups displayed a variable degree of mutual overlap and mapped to different stages of mTEC development. Co-expressed genes showed chromosomal preference and clustered within delimited genomic regions. Moreover, co-expression groups in mice and humans selected by a pair of orthologous genes preferentially co-expressed sets of orthologous genes attesting to the species conservation of pGE between mouse and human. Furthermore, co-expressed genes were enriched for specific transcription factor binding motifs concomitant with up-regulation of the corresponding transcription factors, implicating additional factors in the regulation of pGE besides the Autoimmune Regulator (Aire). Thus promiscuous transcription of self-antigens in mTECs entails a highly coordinated process, which is evolutionary strictly conserved between species.


Subject(s)
Autoantigens/genetics , Autoantigens/immunology , Epithelial Cells/immunology , Epithelial Cells/metabolism , Gene Expression Regulation , Genetic Variation , Thymus Gland/immunology , Thymus Gland/metabolism , Animals , Binding Sites , Cell Differentiation/genetics , Cell Differentiation/immunology , Cluster Analysis , Epithelial Cells/cytology , Evolution, Molecular , Gene Expression Profiling , Humans , Mice , Mice, Transgenic , Nucleotide Motifs , Organ Specificity/genetics , Organ Specificity/immunology , Promoter Regions, Genetic , Protein Binding , Thymus Gland/cytology , Transcription Factors/metabolism , Transcriptional Activation
8.
Healthcare (Basel) ; 12(6)2024 Mar 08.
Article in English | MEDLINE | ID: mdl-38540576

ABSTRACT

Few studies explore emergency medicine (EM) residency shift scheduling software as a mechanism to reduce administrative demands and broader resident burnout. A local needs assessment demonstrated a learning curve for chief resident schedulers and several areas for improvement. In an institutional quality improvement project, we utilized an external online cross-sectional convenience sampling pilot survey of United States EM residency programs to collect information on manual versus software-based resident shift scheduling practices and associated scheduler and scheduler-perceived resident satisfaction. Our external survey response rate was 19/253 (8%), with all United States regions (i.e., northeast, southeast, midwest, west, and southwest) represented. Two programs (11%) reported manual scheduling without any software. ShiftAdmin was the most popularly reported scheduling software (53%). Although not statistically significant, manual scheduling had the lowest satisfaction score and programs with ≤30 residents reported the highest levels of satisfaction. Our data suggest that improvements in existing software-based technologies are needed. Artificial intelligence technologies may prove useful for reducing administrative scheduling demands and optimizing resident scheduling satisfaction.

9.
bioRxiv ; 2024 Feb 08.
Article in English | MEDLINE | ID: mdl-38370810

ABSTRACT

Predicting T cell receptor (TCR) activation is challenging due to the lack of both unbiased benchmarking datasets and computational methods that are sensitive to small mutations to a peptide. To address these challenges, we curated a comprehensive database encompassing complete single amino acid mutational assays of 10,750 TCR-peptide pairs, centered around 14 immunogenic peptides against 66 TCRs. We then present an interpretable Bayesian model, called BATMAN, that can predict the set of peptides that activates a TCR. When validated on our database, BATMAN outperforms existing methods by 20% and reveals important biochemical predictors of TCR-peptide interactions.

10.
bioRxiv ; 2024 Feb 08.
Article in English | MEDLINE | ID: mdl-38077028

ABSTRACT

T cell receptor (TCR) repertoire diversity enables the orchestration of antigen-specific immune responses against the vast space of possible pathogens. Identifying TCR/antigen binding pairs from the large TCR repertoire and antigen space is crucial for biomedical research. Here, we introduce copepodTCR, an open-access tool for the design and interpretation of high-throughput experimental assays to determine TCR specificity. copepodTCR implements a combinatorial peptide pooling scheme for efficient experimental testing of T cell responses against large overlapping peptide libraries, useful for "deorphaning" TCRs of unknown specificity. The scheme detects experimental errors and, coupled with a hierarchical Bayesian model for unbiased results interpretation, identifies the response-eliciting peptide for a TCR of interest out of hundreds of peptides tested using a simple experimental set-up. We experimentally validated our approach on a library of 253 overlapping peptides covering the SARS-CoV-2 spike protein. We provide experimental guides for efficient design of larger screens covering thousands of peptides which will be crucial for the identification of antigen-specific T cells and their targets from limited clinical material.

11.
Pathophysiology ; 31(3): 388-397, 2024 Jul 30.
Article in English | MEDLINE | ID: mdl-39189165

ABSTRACT

BACKGROUND: Surgeons often encounter patients with intestinal failure due to inadequate intestinal length ("short bowel syndrome"/SBS). Treatment in these patients remains challenging and the process of physiologic adaptation may take years to complete, which frequently requires parenteral nutrition. We propose a proof-of-concept mechanical bowel elongation approach using a self-expanding prototype of an intestinal expansion sleeve (IES) for use in SBS to accelerate the adaptation process. METHODS: IESs were deployed in the small intestines of Sprague Dawley rats. Mechanical characterization of these prototypes was performed. IES length-tension relationships and post-implant bowel expansion were measured ex vivo. Bowel histology before and after implantation was evaluated. RESULTS: IES mechanical studies demonstrated decreasing expansive force with elongation. The deployment of IES devices produced an immediate 21 ± 8% increase in bowel length (p < 0.001, n = 11). Mechanical load testing data showed that the IESs expressed maximum expansive forces at 50% compression of the initial pre-contracted length. The small-intestine failure load in the rats was 1.88 ± 21 N. Intestinal histology post deployment of the IES showed significant expansive changes compared to unstretched bowel tissue. CONCLUSIONS: IES devices were scalable to the rat intestinal model in our study. The failure load of the rat small intestine was many times higher than the force exerted by the contraction of the IES. Histology demonstrated preservation of intestinal structure with some mucosal erosion. Future in vivo rat studies on distraction enterogenesis with this IES should help to define this organogenesis phenomenon.

12.
Pathophysiology ; 31(2): 298-308, 2024 Jun 08.
Article in English | MEDLINE | ID: mdl-38921727

ABSTRACT

Vaginal agenesis (VA) is frequently associated with mullerian agenesis. VA treatments include mechanical dilation and surgical vaginoplasty. We created a vaginal expansion sleeve (VES) as a novel device to progressively lengthen the vaginal canal. This study evaluated the histologic effects of the VES on rat vaginal tissue. The VES is a spring-like device made of proprietary woven cylindrical material and flat resin caps. The VESs were constructed as 25-30 mm, pre-contracted springs, which were secured into the vaginas of six Sprague Dawley rats and allowed to re-expand post-surgically. After one week, the VESs were removed, and the vaginas were harvested and measured in length. Test (n = 6) and control (n = 4) formalin-fixed paraffin-embedded tissues were stained with hematoxylin and eosin (H&E), Masson's trichrome, and anti-Desmin antibodies. The VESs achieved significant vaginal lengthening. The mean vaginal canal length increased from 20.0 ± 2.4 mm to 23.8 ± 1.2 mm after removal of the VESs (n = 6, p < 0.001), a 19% increase. There was a positive correlation between the expander/tension generated in the vagina and the amount of acute and chronic inflammation. H&E staining revealed increased submucosal eosinophilia in five of the six test tissues. One VES sample that was lengthened to 30 mm long showed evidence of lymphocytic and neutrophilic inflammation. Desmin immunostaining and Masson's trichrome stain revealed a thinner muscularis with more infiltrative fibrous tissue between muscle fibers in the test tissue compared to the control tissue. Although effective, the VES may provoke at least a transient increase in eosinophils consistent with a localized immune reaction during muscularis remodeling.

13.
Telemed Rep ; 4(1): 366-386, 2023.
Article in English | MEDLINE | ID: mdl-38143795

ABSTRACT

Background: Asynchronous telemedicine (ATM), which describes telemedical interaction between a patient and provider where neither party communicates simultaneously, is an important telemedicine modality that is seeing increased use. In this article, we summarize the published peer-reviewed literature specifically related to ATM to (1) identify terms or phrases that are used to describe ATM, (2) ascertain how this research has thus far addressed the various aspects of the quadruple aim of medicine, and (3) assess the methodological rigor of research on ATM. We also divided the literature into pre- and post-COVID-19 onset periods to identify potential variations in the literature between these two periods. Methods: This systematic literature review follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The literature search, utilizing multiple databases and applying inclusion and exclusion criteria, initially produced 2624 abstracts for review. De-duplication and screening ultimately yielded 104 articles for data extraction. Results: "Store-and-forward" and variations of "e-visit" were the most frequently used alternative terms for ATM. Care quality was the most frequently addressed aspect of the Quadruple Aim of Medicine-more than double any other category-followed by patient satisfaction. We separated cost of care into two categories: patients' cost of care and providers' cost to provide care. Patient cost of care was the third most addressed aspect of the Quadruple Aim of Medicine followed by provider well-being and provider's cost to provide care. Methodological rigor of the studies was also addressed, with only 2 quantitative studies ranked "Strong," 5 ranked "Moderate," and 97 ranked "Weak." Qualitative studies were generally acceptable but struggled methodologically with accounting for all participants and articulation of results. Conclusions: Although "store-and-forward" is somewhat more frequently used in the studies included in this review, variants of "e-visit," are growing in recent usage. Given the relative newness of modality, it is not surprising that quality of care is the most researched aspect of the Quadruple Aim of Medicine in ATM research. We anticipate more balance between these areas as research in this field matures. Primary areas of research need currently relate to practitioners-specifically their costs of providing care and well-being. Finally, future ATM research needs to address research challenges of selection bias and blinding in quantitative studies and improved participant tracking and articulation of both study design and results in qualitative studies.

14.
bioRxiv ; 2023 Dec 08.
Article in English | MEDLINE | ID: mdl-38105962

ABSTRACT

The "innate-like" T cell compartment, known as Tinn, represents a diverse group of T cells that straddle the boundary between innate and adaptive immunity, having the ability to mount rapid responses following activation. In mice, this ability is acquired during thymic development. We explored the transcriptional landscape of Tinn compared to conventional T cells (Tconv) in the human thymus and blood using single cell RNA sequencing and flow cytometry. We reveal that in human blood, the majority of Tinn cells, including iNKT, MAIT, and Vδ2+Vγ9+ T cells, share an effector program characterized by the expression of unique chemokine and cytokine receptors, and cytotoxic molecules. This program is driven by specific transcription factors, distinct from those governing Tconv cells. Conversely, only a fraction of thymic Tinn cells displays an effector phenotype, while others share transcriptional features with developing Tconv cells, indicating potential divergent developmental pathways. Unlike the mouse, human Tinn cells do not differentiate into multiple effector subsets but develop a mixed type I/type III effector potential. To conduct a comprehensive cross-species analysis, we constructed a murine Tinn developmental atlas and uncovered additional species-specific distinctions, including the absence of type II Tinn cells in humans, which implies distinct immune regulatory mechanisms across species. The study provides insights into the development and functionality of Tinn cells, emphasizing their role in immune responses and their potential as targets for therapeutic interventions.

15.
Bioengineering (Basel) ; 10(3)2023 Mar 12.
Article in English | MEDLINE | ID: mdl-36978742

ABSTRACT

Vaginal atresia is seen in genetic disorders such as Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome, which can cause significant sexual dysfunction. Current treatments include surgical reconstruction or mechanical dilation of the vaginal canal. Mechanical dilation requires patients to be highly motivated and compliant while surgical reconstruction has high rates of complications. This study evaluated a novel vaginal expansion sleeve (VES) method as an alternative treatment for vaginal atresia. The proprietary cylindrical VES is a spring-like device consisting of polyethylene terephthalate helicoid trusses capped at each end with a fixed diameter resin cap for fixation within tissues. Following the development of the VES and mechanical characterization of the force-length relationships within the device, we deployed the VES in Sprague Dawley rat vaginas anchored with nonabsorbable sutures. We measured the VES length-tension relationships and post-implant vaginal canal expansion ex vivo. Vaginal histology was examined before and after implantation of the VES devices. Testing of 30 mm sleeves without caps resulted in an expansion force of 11.7 ± 3.4 N and 2.0 ± 0.1 N at 50% and 40%, respectively. The implanted 20 mm VES resulted in 5.36 mm ± 1.18 expansion of the vaginal canal, a 32.5 ± 23.6% increase (p = 0.004, Student t test). Histological evaluation of the VES implanted tissue showed a significant thinning of the vaginal wall when the VES was implanted. The novel VES device resulted in a significant expansion of the vaginal canal ex vivo. The VES device represents a unique alternative to traditional mechanical dilation therapy in the treatment of vaginal atresia and represents a useful platform for the mechanical distension of hollow compartments, which avoids reconstructive surgeries and progressive dilator approaches.

16.
Cell Genom ; 3(8): 100347, 2023 Aug 09.
Article in English | MEDLINE | ID: mdl-37601967

ABSTRACT

Cystatin C (CyC), a secreted cysteine protease inhibitor, has unclear biological functions. Many patients exhibit elevated plasma CyC levels, particularly during glucocorticoid (GC) treatment. This study links GCs with CyC's systemic regulation by utilizing genome-wide association and structural equation modeling to determine CyC production genetics in the UK Biobank. Both CyC production and a polygenic score (PGS) capturing predisposition to CyC production were associated with increased all-cause and cancer-specific mortality. We found that the GC receptor directly targets CyC, leading to GC-responsive CyC secretion in macrophages and cancer cells. CyC-knockout tumors displayed significantly reduced growth and diminished recruitment of TREM2+ macrophages, which have been connected to cancer immunotherapy failure. Furthermore, the CyC-production PGS predicted checkpoint immunotherapy failure in 685 patients with metastatic cancer from combined clinical trial cohorts. In conclusion, CyC may act as a GC effector pathway via TREM2+ macrophage recruitment and may be a potential target for combination cancer immunotherapy.

17.
Nat Commun ; 13(1): 4296, 2022 08 02.
Article in English | MEDLINE | ID: mdl-35918316

ABSTRACT

The induction of central T cell tolerance in the thymus depends on the presentation of peripheral self-epitopes by medullary thymic epithelial cells (mTECs). This promiscuous gene expression (pGE) drives mTEC transcriptomic diversity, with non-canonical transcript initiation, alternative splicing, and expression of endogenous retroelements (EREs) representing important but incompletely understood contributors. Here we map the expression of genome-wide transcripts in immature and mature human mTECs using high-throughput 5' cap and RNA sequencing. Both mTEC populations show high splicing entropy, potentially driven by the expression of peripheral splicing factors. During mTEC maturation, rates of global transcript mis-initiation increase and EREs enriched in long terminal repeat retrotransposons are up-regulated, the latter often found in proximity to differentially expressed genes. As a resource, we provide an interactive public interface for exploring mTEC transcriptomic diversity. Our findings therefore help construct a map of transcriptomic diversity in the healthy human thymus and may ultimately facilitate the identification of those epitopes which contribute to autoimmunity and immune recognition of tumor antigens.


Subject(s)
Epithelial Cells , Transcriptome , Cell Differentiation/genetics , Central Tolerance , Epithelial Cells/metabolism , Epitopes/metabolism , Humans , Thymus Gland
18.
iScience ; 25(10): 105040, 2022 Oct 21.
Article in English | MEDLINE | ID: mdl-36062073

ABSTRACT

COVID-19 has highly variable clinical courses. The search for prognostic host factors for COVID-19 outcome is a priority. We performed logistic regression for ICU admission against a polygenic score (PGS) for Cystatin C (CyC) production in patients with COVID-19. We analyzed the predictive value of longitudinal plasma CyC levels in an independent cohort of patients hospitalized with COVID-19. In four cohorts spanning European and African ancestry populations, we identified a significant association between CyC-production PGS and odds of critical illness (n cases=2,319), with the strongest association captured in the UKB cohort (OR 2.13, 95% CI 1.58-2.87, p=7.12e-7). Plasma proteomics from an independent cohort of hospitalized COVID-19 patients (n cases = 131) demonstrated that CyC production was associated with COVID-specific mortality (p=0.0007). Our findings suggest that CyC may be useful for stratification of patients and it has functional role in the host response to COVID-19.

19.
Int J Sports Physiol Perform ; 17(5): 687-693, 2022 05 01.
Article in English | MEDLINE | ID: mdl-35158324

ABSTRACT

INTRODUCTION: The relationship between the percentage of a fatiguing ambulatory task completed and rating of perceived exertion (RPE) appears to be linear and scalar, with a relatively narrow "window." Recent evidence has suggested that a similar relationship may exist for muscularly demanding tasks. METHODS: To determine whether muscularly demanding tasks fit within this "ambulatory window," we tested resistance-trained athletes performing bench press and leg press with different loadings predicted to allow 5, 10, 20, and 30 repetitions and measured RPE (category ratio scale) at the end of the concentric action for each repetition. RESULTS: There was a regular, and strongly linear, pattern of growth of RPE for both bench press (r = .89) and leg press (r = .90) during the tasks that allowed 5.2 (1.2), 11.6 (1.9), 22.7 (2.0), and 30.8 (3.2) repetitions for bench press and 5.5 (1.5), 11.4 (1.6), 20.2 (3.0), and 32.4 (4.2) repetitions for leg press, respectively. CONCLUSIONS: The path of the RPE growth versus percentage task fit within the window evident for ambulatory tasks. The results suggest that the RPE versus percentage task completed relationship is scalar, relatively linear, and apparently independent of exercise mode.


Subject(s)
Physical Exertion , Resistance Training , Athletes , Exercise , Humans , Muscle Fatigue , Resistance Training/methods , Weight Lifting
20.
Nat Cardiovasc Res ; 1(4): 361-371, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35479509

ABSTRACT

Diastole is the sequence of physiological events that occur in the heart during ventricular filling and principally depends on myocardial relaxation and chamber stiffness. Abnormal diastolic function is related to many cardiovascular disease processes and is predictive of health outcomes, but its genetic architecture is largely unknown. Here, we use machine learning cardiac motion analysis to measure diastolic functional traits in 39,559 participants of the UK Biobank and perform a genome-wide association study. We identified 9 significant, independent loci near genes that are associated with maintaining sarcomeric function under biomechanical stress and genes implicated in the development of cardiomyopathy. Age, sex and diabetes were independent predictors of diastolic function and we found a causal relationship between genetically-determined ventricular stiffness and incident heart failure. Our results provide insights into the genetic and environmental factors influencing diastolic function that are relevant for identifying causal relationships and potential tractable targets.

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