1
|
Cunningham KY, Hur B, Gupta VK, Koster MJ, Weyand CM, Cuthbertson D, Khalidi NA, Koening CL, Langford CA, McAlear CA, Monach PA, Moreland LW, Pagnoux C, Rhee RL, Seo P, Merkel PA, Warrington KJ, Sung J. Plasma proteome profiling in giant cell arteritis. Ann Rheum Dis 2024:ard-2024-225868. [PMID: 39153834 DOI: 10.1136/ard-2024-225868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 07/23/2024] [Indexed: 08/19/2024]
Abstract
OBJECTIVES This study aimed to identify plasma proteomic signatures that differentiate active and inactive giant cell arteritis (GCA) from non-disease controls. By comprehensively profiling the plasma proteome of both patients with GCA and controls, we aimed to identify plasma proteins that (1) distinguish patients from controls and (2) associate with disease activity in GCA. METHODS Plasma samples were obtained from 30 patients with GCA in a multi-institutional, prospective longitudinal study: one captured during active disease and another while in clinical remission. Samples from 30 age-matched/sex-matched/race-matched non-disease controls were also collected. A high-throughput, aptamer-based proteomics assay, which examines over 7000 protein features, was used to generate plasma proteome profiles from study participants. RESULTS After adjusting for potential confounders, we identified 537 proteins differentially abundant between active GCA and controls, and 781 between inactive GCA and controls. These proteins suggest distinct immune responses, metabolic pathways and potentially novel physiological processes involved in each disease state. Additionally, we found 16 proteins associated with disease activity in patients with active GCA. Random forest models trained on the plasma proteome profiles accurately differentiated active and inactive GCA groups from controls (95.0% and 98.3% in 10-fold cross-validation, respectively). However, plasma proteins alone provided limited ability to distinguish between active and inactive disease states within the same patients. CONCLUSIONS This comprehensive analysis of the plasma proteome in GCA suggests that blood protein signatures integrated with machine learning hold promise for discovering multiplex biomarkers for GCA.
Collapse
Affiliation(s)
- Kevin Y Cunningham
- Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, Minnesota, USA
| | - Benjamin Hur
- Microbiomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Vinod K Gupta
- Microbiomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew J Koster
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Cornelia M Weyand
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Department of Immunology, Mayo Clinic, Rochester, Minnesota, USA
| | - David Cuthbertson
- Department of Biostatistics and Informatics, Department of Pediatrics, University of South Florida, Tampa, Florida, USA
| | - Nader A Khalidi
- Division of Rheumatology, St. Joseph's Healthcare Hamilton, McMaster University, Hamilton, Ontario, Canada
| | - Curry L Koening
- Division of Rheumatology, University of Utah, Salt Lake City, Utah, USA
| | - Carol A Langford
- Division of Rheumatology, Cleveland Clinic, Cleveland, Ohio, USA
| | - Carol A McAlear
- Division of Rheumatology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Paul A Monach
- Rheumatology Section, VA Boston Healthcare System, Boston, Massachusetts, USA
| | - Larry W Moreland
- Division of Rheumatology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Christian Pagnoux
- Division of Rheumatology, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Rennie L Rhee
- Division of Rheumatology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Philip Seo
- Division of Rheumatology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Peter A Merkel
- Division of Rheumatology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kenneth J Warrington
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Jaeyun Sung
- Microbiomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Rheumatology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Computational Biology, Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
2
|
Jobson ME, Tomlinson BR, Mustor EM, Felton EA, Weiss A, Caswell CC, Shaw LN. SSR42 is a Novel Regulator of Cytolytic Activity in Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603084. [PMID: 39026779 PMCID: PMC11257634 DOI: 10.1101/2024.07.11.603084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
SSR42 is the longest noncoding RNA in the S. aureus cell and the second-most abundant transcript in the stationary phase transcriptome, second only to RNAIII. It is highly conserved across strains and exhibits pronounced stability in stationary phase, however the mechanism behind its regulatory role has yet to be fully elucidated. Herein, we used transcriptomic and proteomic approaches to probe the role of SSR42, revealing that it is a powerful, novel activator of the primary leukocidin LukAB. SSR42 is required for cytotoxicity towards, and escape from within, human neutrophils, and also mediates survival within human blood. We show that SSR42 wields this role via derepression by the peroxide repressor PerR in response to the presence of human neutrophils and governs lukAB induction in this niche. Importantly, this regulation is driven by direct RNA-RNA interaction, as we show binding of the 5' UTR of the lukAB transcript with the 3' end of SSR42, which ultimately modulates transcript stability as well as translational activity. Finally, we demonstrate that this behavior is absolutely required for full virulence of S. aureus in murine models of both pneumonia and sepsis. Collectively, we present SSR42 as a pleiotropic regulatory RNA that acts as a nexus between environmental sensing and the regulation of pathogenesis, responding to environmental stimuli and host immune factors to bolster cytotoxic behavior and facilitate infection in S. aureus . Importance S. aureus is a master pathogen due to its formidable collection of virulence factors. These are tightly controlled by a diverse group of regulators that titrate their abundance to adapt to unique infectious niches. The role of regulatory RNAs in stress adaptation and pathogenesis is becoming increasingly more relevant in S. aureus . In this study, we provide the most comprehensive global analysis to date of just such a factor, SSR42. Specifically, we uncover that SSR42 is required for mediating cytotoxicity - one of the pillars of infection - in response to phagocytosis by human neutrophils. We find that SSR42 is induced by components of the host immune system and facilitates downstream activation of cytotoxic factors via RNA-RNA interactions. This illustrates that SSR42 forms a pivotal link between sensing the external environment and mediating resistance to oxidative stress while promoting virulence, solidifying it as a major global regulator in S. aureus .
Collapse
|
3
|
Miles JT, Mullins GL, Mizumori SJY. Flexible decision-making is related to strategy learning, vicarious trial and error, and medial prefrontal rhythms during spatial set-shifting. Learn Mem 2024; 31:a053911. [PMID: 39038921 DOI: 10.1101/lm.053911.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/14/2024] [Indexed: 07/24/2024]
Abstract
Flexible decision-making requires a balance between exploring features of an environment and exploiting prior knowledge. Behavioral flexibility is typically measured by how long it takes subjects to consistently make accurate choices after reward contingencies switch or task rules change. This measure, however, only allows for tracking flexibility across multiple trials, and does not assess the degree of flexibility. Plus, although increases in decision-making accuracy are strong indicators of learning, other decision-making behaviors have also been suggested as markers of flexibility, such as the on-the-fly decision reversals known as vicarious trial and error (VTE) or switches to a different, but incorrect, strategy. We sought to relate flexibility, learning, and neural activity by comparing choice history-derived evaluation of strategy use with changes in decision-making accuracy and VTE behavior while recording from the medial prefrontal cortex (mPFC) in rats. Using a set-shifting task that required rats to repeatedly switch between spatial decision-making strategies, we show that a previously developed strategy likelihood estimation procedure could identify putative learning points based on decision history. We confirm the efficacy of learning point estimation by showing increases in decision-making accuracy aligned to the learning point. Additionally, we show increases in the rate of VTE behavior surrounding identified learning points. By calculating changes in strategy likelihoods across trials, we tracked flexibility on a trial-by-trial basis and show that flexibility scores also increased around learning points. Further, we demonstrate that VTE behaviors could be separated into indecisive and deliberative subtypes depending on whether they occurred during periods of high or low flexibility and whether they led to correct or incorrect choice outcomes. Field potential recordings from the mPFC during decisions exhibited increased beta band activity on trials with VTE compared to non-VTE trials, as well as increased gamma during periods when learned strategies could be exploited compared to prelearning, exploratory periods. This study demonstrates that increased behavioral flexibility and VTE rates are often aligned to task learning. These relationships can break down, however, suggesting that VTE is not always an indicator of deliberative decision-making. Additionally, we further implicate the mPFC in decision-making and learning by showing increased beta-based activity on VTE trials and increased gamma after learning.
Collapse
Affiliation(s)
- Jesse T Miles
- Neuroscience Graduate Program, University of Washington, Seattle, Washington 98195, USA
- Psychology Department, University of Washington, Seattle, Washington 98195, USA
| | - Ginger L Mullins
- Psychology Department, University of Washington, Seattle, Washington 98195, USA
| | - Sheri J Y Mizumori
- Neuroscience Graduate Program, University of Washington, Seattle, Washington 98195, USA
- Psychology Department, University of Washington, Seattle, Washington 98195, USA
| |
Collapse
|
4
|
Strober BJ, Zhang MJ, Amariuta T, Rossen J, Price AL. Fine-mapping causal tissues and genes at disease-associated loci. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.11.01.23297909. [PMID: 37961337 PMCID: PMC10635248 DOI: 10.1101/2023.11.01.23297909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Heritable diseases often manifest in a highly tissue-specific manner, with different disease loci mediated by genes in distinct tissues or cell types. We propose Tissue-Gene Fine-Mapping (TGFM), a fine-mapping method that infers the posterior probability (PIP) for each gene-tissue pair to mediate a disease locus by analyzing GWAS summary statistics (and in-sample LD) and leveraging eQTL data from diverse tissues to build cis-predicted expression models; TGFM also assigns PIPs to causal variants that are not mediated by gene expression in assayed genes and tissues. TGFM accounts for both co-regulation across genes and tissues and LD between SNPs (generalizing existing fine-mapping methods), and incorporates genome-wide estimates of each tissue's contribution to disease as tissue-level priors. TGFM was well-calibrated and moderately well-powered in simulations; unlike previous methods, TGFM was able to attain correct calibration by modeling uncertainty in cis-predicted expression models. We applied TGFM to 45 UK Biobank diseases/traits (average N = 316K) using eQTL data from 38 GTEx tissues. TGFM identified an average of 147 PIP > 0.5 causal genetic elements per disease/trait, of which 11% were gene-tissue pairs. Implicated gene-tissue pairs were concentrated in known disease-critical tissues, and causal genes were strongly enriched in disease-relevant gene sets. Causal gene-tissue pairs identified by TGFM recapitulated known biology (e.g., TPO-thyroid for Hypothyroidism), but also included biologically plausible novel findings (e.g., SLC20A2-artery aorta for Diastolic blood pressure). Further application of TGFM to single-cell eQTL data from 9 cell types in peripheral blood mononuclear cells (PBMC), analyzed jointly with GTEx tissues, identified 30 additional causal gene-PBMC cell type pairs at PIP > 0.5-primarily for autoimmune disease and blood cell traits, including the biologically plausible example of CD52 in classical monocyte cells for Monocyte count. In conclusion, TGFM is a robust and powerful method for fine-mapping causal tissues and genes at disease-associated loci.
Collapse
Affiliation(s)
- Benjamin J. Strober
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Martin Jinye Zhang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Tiffany Amariuta
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jordan Rossen
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Alkes L. Price
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| |
Collapse
|
5
|
Torres-Simon L, Del Cerro-León A, Yus M, Bruña R, Gil-Martinez L, Marcos Dolado A, Maestú F, Arrazola-Garcia J, Cuesta P. Decoding the Best Automated Segmentation Tools for Vascular White Matter Hyperintensities in the Aging Brain: A Clinician's Guide to Precision and Purpose. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.03.30.23287946. [PMID: 38798616 PMCID: PMC11118558 DOI: 10.1101/2023.03.30.23287946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Cerebrovascular damage from small vessel disease (SVD) occurs in healthy and pathological aging. SVD markers, such as white matter hyperintensities (WMH), are commonly found in individuals over 60 and increase in prevalence with age. WMHs are detectable on standard MRI by adhering to the STRIVE criteria. Currently, visual assessment scales are used in clinical and research scenarios but is time-consuming and has rater variability, limiting its practicality. Addressing this issue, our study aimed to determine the most precise WMH segmentation software, offering insights into methodology and usability to balance clinical precision with practical application. This study employed a dataset comprising T1, FLAIR, and DWI images from 300 cognitively healthy older adults. WMHs in this cohort were evaluated using four automated neuroimaging tools: Lesion Prediction Algorithm (LPA) and Lesion Growth Algorithm (LGA) from Lesion Segmentation Tool (LST), Sequence Adaptive Multimodal Segmentation (SAMSEG), and Brain Intensity Abnormalities Classification Algorithm (BIANCA). Additionally, clinicians manually segmented WMHs in a subsample of 45 participants to establish a gold standard. The study assessed correlations with the Fazekas scale, algorithm performance, and the influence of WMH volume on reliability. Results indicated that supervised algorithms were superior, particularly in detecting small WMHs, and can improve their consistency when used in parallel with unsupervised tools. The research also proposed a biomarker for moderate vascular damage, derived from the top 95th percentile of WMH volume in healthy individuals aged 50 to 60. This biomarker effectively differentiated subgroups within the cohort, correlating with variations in brain structure and behavior.
Collapse
|
6
|
Rossi Sebastiano A, Poles K, Gualtiero S, Romeo M, Galigani M, Bruno V, Fossataro C, Garbarini F. Balancing the Senses: Electrophysiological Responses Reveal the Interplay between Somatosensory and Visual Processing During Body-Related Multisensory Conflict. J Neurosci 2024; 44:e1397232024. [PMID: 38508711 PMCID: PMC11079966 DOI: 10.1523/jneurosci.1397-23.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/27/2023] [Accepted: 01/03/2024] [Indexed: 03/22/2024] Open
Abstract
In the study of bodily awareness, the predictive coding theory has revealed that our brain continuously modulates sensory experiences to integrate them into a unitary body representation. Indeed, during multisensory illusions (e.g., the rubber hand illusion, RHI), the synchronous stroking of the participant's concealed hand and a fake visible one creates a visuotactile conflict, generating a prediction error. Within the predictive coding framework, through sensory processing modulation, prediction errors are solved, inducing participants to feel as if touches originated from the fake hand, thus ascribing the fake hand to their own body. Here, we aimed to address sensory processing modulation under multisensory conflict, by disentangling somatosensory and visual stimuli processing that are intrinsically associated during the illusion induction. To this aim, we designed two EEG experiments, in which somatosensory- (SEPs; Experiment 1; N = 18; F = 10) and visual-evoked potentials (VEPs; Experiment 2; N = 18; F = 9) were recorded in human males and females following the RHI. Our results show that, in both experiments, ERP amplitude is significantly modulated in the illusion as compared with both control and baseline conditions, with a modality-dependent diametrical pattern showing decreased SEP amplitude and increased VEP amplitude. Importantly, both somatosensory and visual modulations occur in long-latency time windows previously associated with tactile and visual awareness, thus explaining the illusion of perceiving touch at the sight location. In conclusion, we describe a diametrical modulation of somatosensory and visual processing as the neural mechanism that allows maintaining a stable body representation, by restoring visuotactile congruency under the occurrence of multisensory conflicts.
Collapse
Affiliation(s)
| | - Karol Poles
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Stefano Gualtiero
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Marcella Romeo
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
- IMT School for Advanced Studies Lucca, Lucca 55100, Italy
| | - Mattia Galigani
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Valentina Bruno
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Carlotta Fossataro
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
| | - Francesca Garbarini
- MANIBUS Lab, Psychology Department, University of Turin, Turin 10124, Italy
- Neuroscience Institute of Turin (NIT), Turin 10124, Italy
| |
Collapse
|
7
|
Zhong Y, Lan M, Chen H, Chen Y, Zhang Y. Comparative efficacy and acceptability of different exercise patterns for reducing cardiovascular events in pre-diabetes: protocol for a systematic review and network meta-analysis of randomised controlled trials. BMJ Open 2024; 14:e075783. [PMID: 38719281 PMCID: PMC11086503 DOI: 10.1136/bmjopen-2023-075783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024] Open
Abstract
INTRODUCTION Exercise has been used to reverse dysglycaemic states in patients with pre-diabetes. Systematic reviews show that exercise is an effective way to reduce the incidence of diabetes, but there is conflicting evidence for reducing the occurrence of cardiovascular events. Therefore, we present a systematic review and network meta-analysis protocol designed to compare the effectiveness of different forms of exercise in reducing cardiovascular events and their tolerability in different populations. METHODS AND ANALYSIS We will include all randomised controlled trials and compare one exercise intervention to another. We will compare the following exercise patterns: standard endurance training, strength training, high-intensity interval training, mind-body exercise, and mixed strength and aerobic training. The primary outcomes are the occurrence of major cardiovascular events and the rate of patient attrition during the intervention. We will search major English and Chinese databases as well as trial registry websites for published and unpublished studies. All reference selection and data extraction will be conducted by at least two independent reviewers. We will conduct a random effects model to combine effect sizes and use the surface under the cumulative ranking curve and the mean ranks to rank the effectiveness of interventions. All data will be fitted at WinBUGS in a Bayesian framework and correlation graphs will be plotted using StataSE 14. We will also use the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) framework to evaluate the quality of evidence for the study results. ETHICS AND DISSEMINATION This study does not involve a population-based intervention, and therefore, does not require ethical approval. We will publish the findings of this systematic review in a peer-reviewed scientific journal, and the dataset will be made available free of charge. The completed review will be disseminated electronically in print and on social media, where appropriate. PROSPERO REGISTRATION NUMBER CRD42023422737.
Collapse
Affiliation(s)
- Yumei Zhong
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Meijuan Lan
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Haotian Chen
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Yuanyuan Chen
- Neurology Department, Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, Zhejiang, China
| | - Yuping Zhang
- Zhejiang University School of Medicine Second Affiliated Hospital, Hangzhou, Zhejiang, China
| |
Collapse
|
8
|
Bertran-Cobo C, Dumont E, Noordin NR, Lai MY, Stone W, Tetteh KK, Drakeley C, Krishna S, Lau YL, Wassmer SC. Plasmodium knowlesi infection is associated with elevated circulating biomarkers of brain injury and endothelial activation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.25.24306382. [PMID: 38712121 PMCID: PMC11071568 DOI: 10.1101/2024.04.25.24306382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Introduction Malaria remains a major public health concern with substantial morbidity and mortality worldwide. In Malaysia, the emergence of Plasmodium knowlesi has led to a surge in zoonotic malaria cases and deaths in recent years. Signs of cerebral involvement have been observed in a non-comatose, fatal case of severe knowlesi infection, but the potential impact of this malaria species on the brain remains underexplored. To address this gap, we investigated circulating levels of brain injury, inflammation, and vascular biomarkers in a cohort of knowlesi-infected patients and controls. Methods Archived plasma samples from 19 patients with confirmed symptomatic knowlesi infection and 19 healthy, age-matched controls from Peninsular Malaysia were analysed. A total of 52 plasma biomarkers of brain injury, inflammation, and vascular activation were measured using Luminex and SIMOA assays. Wilcoxon tests were used to examine group differences, and biomarker profiles were explored through hierarchical clustering heatmap analysis. Results Bonferroni-corrected analyses revealed significantly elevated brain injury biomarker levels in knowlesi-infected patients, including S100B (p<0.0001), Tau (p=0.0007), UCH-L1 (p<0.0001), αSyn (p<0.0001), Park7 (p=0.0006), NRGN (p=0.0022), and TDP-43 (p=0.005). Compared to controls, levels were lower in the infected group for BDNF (p<0.0001), CaBD (p<0.0001), CNTN1 (p<0.0001), NCAM-1 (p<0.0001), GFAP (p=0.0013), and KLK6 (p=0.0126). Hierarchical clustering revealed distinct group profiles for circulating levels of brain injury and vascular activation biomarkers. Conclusions Our findings highlight for the first time the impact of Plasmodium knowlesi infection on the brain, with distinct alterations in cerebral injury and endothelial activation biomarker profiles compared to healthy controls. Further studies are warranted to investigate the pathophysiology and clinical significance of these altered surrogate markers, through both neuroimaging and long-term neurocognitive assessments.
Collapse
|
9
|
Tsantilas KA, Merrihew GE, Robbins JE, Johnson RS, Park J, Plubell DL, Huang E, Riffle M, Sharma V, MacLean BX, Eckels J, Wu CC, Bereman MS, Spencer SE, Hoofnagle AN, MacCoss MJ. A framework for quality control in quantitative proteomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589318. [PMID: 38645098 PMCID: PMC11030400 DOI: 10.1101/2024.04.12.589318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
A thorough evaluation of the quality, reproducibility, and variability of bottom-up proteomics data is necessary at every stage of a workflow from planning to analysis. We share real-world case studies applying adaptable quality control (QC) measures to assess sample preparation, system function, and quantitative analysis. System suitability samples are repeatedly measured longitudinally with targeted methods, and we share examples where they are used on three instrument platforms to identify severe system failures and track function over months to years. Internal QCs incorporated at protein and peptide-level allow our team to assess sample preparation issues and to differentiate system failures from sample-specific issues. External QC samples prepared alongside our experimental samples are used to verify the consistency and quantitative potential of our results during batch correction and normalization before assessing biological phenotypes. We combine these controls with rapid analysis using Skyline, longitudinal QC metrics using AutoQC, and server-based data deposition using PanoramaWeb. We propose that this integrated approach to QC be used as a starting point for groups to facilitate rapid quality control assessment to ensure that valuable instrument time is used to collect the best quality data possible.
Collapse
Affiliation(s)
- Kristine A. Tsantilas
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Julia E. Robbins
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Richard S. Johnson
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Jea Park
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Deanna L. Plubell
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Eric Huang
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael Riffle
- Department of Biochemistry, University of Washington, Washington 98195, United States
| | - Vagisha Sharma
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Brendan X. MacLean
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Josh Eckels
- LabKey, 500 Union St #1000, Seattle, Washington 98101, United States
| | - Christine C. Wu
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| | - Michael S. Bereman
- Department of Biological Sciences, North Carolina State University, Raleigh, North Carolina 27607
| | - Sandra E. Spencer
- Canada’s Michael Smith Genome Sciences Centre (BC Cancer Research Institute), University of British Columbia, Vancouver, British Columbia V5Z 4S6, Canada
| | - Andrew N. Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Washington 98195, United States
| |
Collapse
|
10
|
Yin R, Zhao H, Li L, Yang Q, Zeng M, Yang C, Bian J, Xie M. Gra-CRC-miRTar: The pre-trained nucleotide-to-graph neural networks to identify potential miRNA targets in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589599. [PMID: 38659732 PMCID: PMC11042274 DOI: 10.1101/2024.04.15.589599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Colorectal cancer (CRC) is the third most diagnosed cancer and the second deadliest cancer worldwide representing a major public health problem. In recent years, increasing evidence has shown that microRNA (miRNA) can control the expression of targeted human messenger RNA (mRNA) by reducing their abundance or translation, acting as oncogenes or tumor suppressors in various cancers, including CRC. Due to the significant up-regulation of oncogenic miRNAs in CRC, elucidating the underlying mechanism and identifying dysregulated miRNA targets may provide a basis for improving current therapeutic interventions. In this paper, we proposed Gra-CRC-miRTar, a pre-trained nucleotide-to-graph neural network framework, for identifying potential miRNA targets in CRC. Different from previous studies, we constructed two pre-trained models to encode RNA sequences and transformed them into de Bruijn graphs. We employed different graph neural networks to learn the latent representations. The embeddings generated from de Bruijn graphs were then fed into a Multilayer Perceptron (MLP) to perform the prediction tasks. Our extensive experiments show that Gra-CRC-miRTar achieves better performance than other deep learning algorithms and existing predictors. In addition, our analyses also successfully revealed 172 out of 201 functional interactions through experimentally validated miRNA-mRNA pairs in CRC. Collectively, our effort provides an accurate and efficient framework to identify potential miRNA targets in CRC, which can also be used to reveal miRNA target interactions in other malignancies, facilitating the development of novel therapeutics.
Collapse
Affiliation(s)
- Rui Yin
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, USA
- These authors contributed equally
| | - Hongru Zhao
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, USA
- These authors contributed equally
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Qiang Yang
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, USA
| | - Min Zeng
- School of Computer Science and Engineering, Central South University, Changsha, Hunan, China
| | - Carl Yang
- Department of Computer Science, Emory University, Atlanta, GA, USA
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, USA
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| |
Collapse
|
11
|
Patty BJ, Hainer SJ. Widespread impact of nucleosome remodelers on transcription at cis-regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.12.589208. [PMID: 38659863 PMCID: PMC11042195 DOI: 10.1101/2024.04.12.589208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Nucleosome remodeling complexes and other regulatory factors work in concert to build a chromatin environment that directs the expression of a distinct set of genes in each cell using cis-regulatory elements (CREs), such as promoters and enhancers, that drive transcription of both mRNAs and CRE-associated non-coding RNAs (ncRNAs). Two classes of CRE-associated ncRNAs include upstream antisense RNAs (uaRNAs), which are transcribed divergently from a shared mRNA promoter, and enhancer RNAs (eRNAs), which are transcribed bidirectionally from active enhancers. The complicated network of CRE regulation by nucleosome remodelers remains only partially explored, with a focus on a select, limited number of remodelers. We endeavored to elucidate a remodeler-based regulatory network governing CRE-associated transcription (mRNA, eRNA, and uaRNA) in murine embryonic stem (ES) cells to test the hypothesis that many SNF2-family nucleosome remodelers collaborate to regulate the coding and non-coding transcriptome via alteration of underlying nucleosome architecture. Using depletion followed by transient transcriptome sequencing (TT-seq), we identified thousands of misregulated mRNAs and CRE-associated ncRNAs across the remodelers examined, identifying novel contributions by understudied remodelers in the regulation of coding and noncoding transcription. Our findings suggest that mRNA and eRNA transcription are coordinately co-regulated, while mRNA and uaRNAs sharing a common promoter are independently regulated. Subsequent mechanistic studies suggest that while remodelers SRCAP and CHD8 modulate transcription through classical mechanisms such as transcription factors and histone variants, a broad set of remodelers including SMARCAL1 indirectly contribute to transcriptional regulation through maintenance of genomic stability and proper Integrator complex localization. This study systematically examines the contribution of SNF2-remodelers to the CRE-associated transcriptome, identifying at least two classes for remodeler action.
Collapse
Affiliation(s)
- Benjamin J. Patty
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
| | - Sarah J. Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA USA
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA USA
| |
Collapse
|
12
|
Takahashi K, Rensing NR, Eultgen EM, Wang SH, Nelvagal HR, Le SQ, Roberts MS, Doray B, Han EB, Dickson PI, Wong M, Sands MS, Cooper JD. GABAergic interneurons contribute to the fatal seizure phenotype of CLN2 disease mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587276. [PMID: 38585903 PMCID: PMC10996664 DOI: 10.1101/2024.03.29.587276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
GABAergic interneuron deficits have been implicated in the epileptogenesis of multiple neurological diseases. While epileptic seizures are a key clinical hallmark of CLN2 disease, a childhood-onset neurodegenerative lysosomal storage disorder caused by a deficiency of tripeptidyl peptidase 1 (TPP1), the etiology of these seizures remains elusive. Given that Cln2 R207X/R207X mice display fatal spontaneous seizures and an early loss of several cortical interneuron populations, we hypothesized that those two events might be causally related. To address this hypothesis, we first generated an inducible transgenic mouse expressing lysosomal membrane-tethered TPP1 (TPP1LAMP1) on the Cln2 R207X/R207X genetic background to study the cell-autonomous effects of cell-type-specific TPP1 deficiency. We crossed the TPP1LAMP1 mice with Vgat-Cre mice to introduce interneuron-specific TPP1 deficiency. Vgat-Cre ; TPP1LAMP1 mice displayed storage material accumulation in several interneuron populations both in cortex and striatum, and increased susceptibility to die after PTZ-induced seizures. Secondly, to test the role of GABAergic interneuron activity in seizure progression, we selectively activated these cells in Cln2 R207X/R207X mice using Designer Receptor Exclusively Activated by Designer Drugs (DREADDs) in in Vgat-Cre : Cln2 R207X/R207X mice. EEG monitoring revealed that DREADD-mediated activation of interneurons via chronic deschloroclozapine administration accelerated the onset of spontaneous seizures and seizure-associated death in Vgat-Cre : Cln2 R207X/R207X mice, suggesting that modulating interneuron activity can exert influence over epileptiform abnormalities in CLN2 disease. Taken together, these results provide new mechanistic insights into the underlying etiology of seizures and premature death that characterize CLN2 disease.
Collapse
|
13
|
McFadden SA, Peck MR, Sime LN, Cox MF, Ikiz ED, Findley CA, Quinn K, Fang Y, Bartke A, Hascup ER, Hascup KN. Thermotherapy has Sexually Dimorphic Responses in APP/PS1 Mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586836. [PMID: 38586039 PMCID: PMC10996586 DOI: 10.1101/2024.03.26.586836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
A thermoregulatory decline occurs with age due to changes in muscle mass, vasoconstriction, and metabolism that lowers core body temperature (Tc). Although lower Tc is a biomarker of successful aging, we have previously shown this worsens cognitive performance in the APP/PS1 mouse model of Alzheimer's disease (AD) [1]. We hypothesized that elevating Tc with thermotherapy would improve metabolism and cognition in APP/PS1 mice. From 6-12 months of age, male and female APP/PS1 and C57BL/6 mice were chronically housed at 23 or 30°C. At 12 months of age, mice were assayed for insulin sensitivity, glucose tolerance, and spatial cognition. Plasma, hippocampal, and peripheral (adipose, hepatic, and skeletal muscle) samples were procured postmortem and tissue-specific markers of amyloid accumulation, metabolism, and inflammation were assayed. Chronic 30°C exposure increased Tc in all groups except female APP/PS1 mice. All mice receiving thermotherapy had either improved glucose tolerance or insulin sensitivity, but the underlying processes responsible for these effects varied across sexes. In males, glucose regulation was influenced predominantly by hormonal signaling in plasma and skeletal muscle glucose transporter 4 expression, whereas in females, this was modulated at the tissue level. Thermotherapy improved spatial navigation in male C57BL/6 and APP/PS1 mice, with the later attributed to reduced hippocampal soluble amyloid-β (Aβ)42. Female APP/PS1 mice exhibited worse spatial memory recall after chronic thermotherapy. Together, the data highlights the metabolic benefits of passive thermotherapy with potential nonpharmacological management for some individuals with AD, and provides further evidence for the necessity of adopting personalized patient care.
Collapse
Affiliation(s)
- Samuel A. McFadden
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Mackenzie R. Peck
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Lindsey N. Sime
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - MaKayla F. Cox
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Erol D. Ikiz
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Caleigh A. Findley
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Kathleen Quinn
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Yimin Fang
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Andrzej Bartke
- Department of Internal Medicine, Southern Illinois University School of Medicine, Springfield, IL, USA
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Erin R. Hascup
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
| | - Kevin N. Hascup
- Department of Neurology, Dale and Deborah Smith Center for Alzheimer’s Research and Treatment, Neurosciences Institute, Southern Illinois University School of Medicine, Springfield, IL, USA
- Department of Pharmacology, Southern Illinois University School of Medicine, Springfield, IL, USA
- Department of Medical Microbiology, Immunology and Cell Biology, Southern Illinois University School of Medicine, Springfield, IL, USA
| |
Collapse
|
14
|
Siwo GH, Singal AG, Waljee AK. Pan-cancer molecular signatures connecting aspartate transaminase (AST) to cancer prognosis, metabolic and immune signatures. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.582939. [PMID: 38496547 PMCID: PMC10942358 DOI: 10.1101/2024.03.01.582939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Background Serum aspartate transaminase (sAST) level is used routinely in conjunction with other clinical assays to assess liver health and disease. Increasing evidence suggests that sAST is associated with all-cause mortality and has prognostic value in several cancers, including gastrointestinal and urothelial cancers. Here, we undertake a systems approach to unravel molecular connections between AST and cancer prognosis, metabolism, and immune signatures at the transcriptomic and proteomic levels. Methods We mined public gene expression data across multiple normal and cancerous tissues using the Genotype Tissue Expression (GTEX) resource and The Cancer Genome Atlas (TCGA) to assess the expression of genes encoding AST isoenzymes (GOT1 and GOT2) and their association with disease prognosis and immune infiltration signatures across multiple tumors. We examined the associations between AST and previously reported pan-cancer molecular subtypes characterized by distinct metabolic and immune signatures. We analyzed human protein-protein interaction networks for interactions between GOT1 and GOT2 with cancer-associated proteins. Using public databases and protein-protein interaction networks, we determined whether the subset of proteins that interact with AST (GOT1 and GOT2 interactomes) are enriched with proteins associated with specific diseases, miRNAs and transcription factors. Results We show that AST transcript isoforms (GOT1 and GOT2) are expressed across a wide range of normal tissues. AST isoforms are upregulated in tumors of the breast, lung, uterus, and thymus relative to normal tissues but downregulated in tumors of the liver, colon, brain, kidney and skeletal sarcomas. At the proteomic level, we find that the expression of AST is associated with distinct pan-cancer molecular subtypes with an enrichment of specific metabolic and immune signatures. Based on human protein-protein interaction data, AST physically interacts with multiple proteins involved in tumor initiation, suppression, progression, and treatment. We find enrichments in the AST interactomes for proteins associated with liver and lung cancer and dermatologic diseases. At the regulatory level, the GOT1 interactome is enriched with the targets of cancer-associated miRNAs, specifically mir34a - a promising cancer therapeutic, while the GOT2 interactome is enriched with proteins that interact with cancer-associated transcription factors. Conclusions Our findings suggest that perturbations in the levels of AST within specific tissues reflect pathophysiological changes beyond tissue damage and have implications for cancer metabolism, immune infiltration, prognosis, and treatment personalization.
Collapse
Affiliation(s)
| | - Amit G. Singal
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas TX
- Center for Global Health Equity, University of Michigan, Ann Arbor, MI, USA
| | - Akbar K. Waljee
- Department of Learning Health Sciences, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas TX
- Center for Global Health Equity, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
15
|
Snyder BM, Achten NB, Gebretsadik T, Wu P, Mitchel EF, Escobar G, Bont LJ, Hartert TV. Personalized Infant Risk Prediction for Severe Respiratory Syncytial Virus Lower Respiratory Tract Infection Requiring Intensive Care Unit Admission. Open Forum Infect Dis 2024; 11:ofae077. [PMID: 38481426 PMCID: PMC10932939 DOI: 10.1093/ofid/ofae077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 02/05/2024] [Indexed: 03/28/2024] Open
Abstract
Background Currently, there are no available tools to identify infants at the highest risk of significant morbidity and mortality from respiratory syncytial virus (RSV) lower respiratory tract infection (LRTI) who would benefit most from RSV prevention products. The objective was to develop and internally validate a personalized risk prediction tool for use among all newborns that uses readily available birth/postnatal data to predict RSV LRTI requiring intensive care unit (ICU) admission. Methods We conducted a population-based birth cohort study of infants born from 1995 to 2007, insured by the Tennessee Medicaid Program, and who did not receive RSV immunoprophylaxis during the first year of life. The primary outcome was severe RSV LRTI requiring ICU admission during the first year of life. We built a multivariable logistic regression model including demographic and clinical variables available at or shortly after birth to predict the primary outcome. Results In a population-based sample of 429 365 infants, 713 (0.2%) had severe RSV LRTI requiring ICU admission. The median age of admission was 66 days (interquartile range, 37-120). Our tool, including 19 variables, demonstrated good predictive accuracy (area under the curve, 0.78; 95% confidence interval, 0.77-0.80) and identified infants who did not qualify for palivizumab, based on American Academy of Pediatrics guidelines, but had higher predicted risk levels than infants who qualified (27% of noneligible infants with >0.16% predicted probabilities [lower quartile for eligible infants]). Conclusions We developed a personalized tool that identified infants at increased risk for severe RSV LRTI requiring ICU admission, expected to benefit most from immunoprophylaxis.
Collapse
Affiliation(s)
- Brittney M Snyder
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Niek B Achten
- Department of Pediatrics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tebeb Gebretsadik
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Pingsheng Wu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Edward F Mitchel
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gabriel Escobar
- Division of Research, Kaiser Permanente, Oakland, California, USA
| | - Louis J Bont
- Department of Pediatrics, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Tina V Hartert
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
16
|
Schafer M, Kamilar-Britt P, Sahani V, Bachi K, Schiller D. Neural Trajectories of Conceptually Related Events. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.04.569670. [PMID: 38187737 PMCID: PMC10769183 DOI: 10.1101/2023.12.04.569670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In a series of conceptually related episodes, meaning arises from the link between these events rather than from each event individually. How does the brain keep track of conceptually related sequences of events (i.e., conceptual trajectories)? In a particular kind of conceptual trajectory-a social relationship-meaning arises from a specific sequence of interactions. To test whether such abstract sequences are neurally tracked, we had participants complete a naturalistic narrative-based social interaction game, during functional magnetic resonance imaging. We modeled the simulated relationships as trajectories through an abstract affiliation and power space. In two independent samples, we found evidence of individual social relationships being tracked with unique sequences of hippocampal states. The neural states corresponded to the accumulated trial-to-trial affiliation and power relations between the participant and each character, such that each relationship's history was captured by its own neural trajectory. Each relationship had its own sequence of states, and all relationships were embedded within the same manifold. As such, we show that the hippocampus represents social relationships with ordered sequences of low-dimensional neural patterns. The number of distinct clusters of states on this manifold is also related to social function, as measured by the size of real-world social networks. These results suggest that our evolving relationships with others are represented in trajectory-like neural patterns.
Collapse
Affiliation(s)
- Matthew Schafer
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai; New York City, NY
| | - Philip Kamilar-Britt
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York City, NY
| | - Vyoma Sahani
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York City, NY
| | - Keren Bachi
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York City, NY
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai; New York City, NY
| | - Daniela Schiller
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai; New York City, NY
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York City, NY
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai; New York City, NY
| |
Collapse
|
17
|
Lucena R, Jasani A, Anastasia S, Kellogg D, Alcaide-Gavilan M. Casein kinase 1 controls components of a TORC2 signaling network in budding yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.30.578072. [PMID: 38352417 PMCID: PMC10862894 DOI: 10.1101/2024.01.30.578072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Tor kinases play diverse and essential roles in control of nutrient signaling and cell growth. Tor kinases are assembled into two large multiprotein complexes referred to as Tor Complex 1 and Tor Complex 2 (TORC1 and TORC2). In budding yeast, TORC2 controls a signaling network that relays signals regarding carbon source that strongly influence growth rate and cell size. However, the mechanisms that control TORC2 signaling are poorly understood. Activation of TORC2 requires Mss4, a phosphoinositol kinase that initiates assembly of a multi-protein complex at the plasma membrane that recruits and activates downstream targets of TORC2. Localization of Mss4 to the plasma membrane is controlled by phosphorylation and previous work suggested that yeast homologs of casein kinase 1γ, referred to as Yck1 and Yck2, control phosphorylation of Mss4. Here, we generated a new analog-sensitive allele of YCK2 and used it to test whether Yck1/2 influence signaling in the TORC2 network. We found that multiple components of the TORC2 network are strongly influenced by Yck1/2 signaling.
Collapse
Affiliation(s)
- Rafael Lucena
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Sawnta Cruz, CA 95064, USA
- Present address: Department of Cell Biology, School of Biology, University of Seville, 41012, Seville, Spain
| | - Akshi Jasani
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Sawnta Cruz, CA 95064, USA
| | - Steph Anastasia
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Sawnta Cruz, CA 95064, USA
- Present address: Monterey One Water, 5 Harris Ct, Monterey, CA, 93940, USA
| | - Douglas Kellogg
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Sawnta Cruz, CA 95064, USA
| | - Maria Alcaide-Gavilan
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Sawnta Cruz, CA 95064, USA
- Present address: Department of Cell Biology, School of Biology, University of Seville, 41012, Seville, Spain
| |
Collapse
|
18
|
Petersen C, Mucke L, Corces MR. CHOIR improves significance-based detection of cell types and states from single-cell data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.18.576317. [PMID: 38328105 PMCID: PMC10849522 DOI: 10.1101/2024.01.18.576317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Clustering is a critical step in the analysis of single-cell data, as it enables the discovery and characterization of putative cell types and states. However, most popular clustering tools do not subject clustering results to statistical inference testing, leading to risks of overclustering or underclustering data and often resulting in ineffective identification of cell types with widely differing prevalence. To address these challenges, we present CHOIR (clustering hierarchy optimization by iterative random forests), which applies a framework of random forest classifiers and permutation tests across a hierarchical clustering tree to statistically determine which clusters represent distinct populations. We demonstrate the enhanced performance of CHOIR through extensive benchmarking against 14 existing clustering methods across 100 simulated and 4 real single-cell RNA-seq, ATAC-seq, spatial transcriptomic, and multi-omic datasets. CHOIR can be applied to any single-cell data type and provides a flexible, scalable, and robust solution to the important challenge of identifying biologically relevant cell groupings within heterogeneous single-cell data.
Collapse
Affiliation(s)
- Cathrine Petersen
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Lennart Mucke
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - M. Ryan Corces
- Gladstone Institute of Neurological Disease, Gladstone Institutes, San Francisco, CA, USA
- Neuroscience Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Neurology and Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| |
Collapse
|
19
|
Jarratt Barnham I. Should vaccination status be a consideration during secondary triage? JOURNAL OF MEDICAL ETHICS 2024:jme-2023-109386. [PMID: 38050108 DOI: 10.1136/jme-2023-109386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023]
Abstract
The rapid development of widely available and effective vaccines has been integral to the international response to the COVID-19 pandemic. However, a significant minority of those offered vaccination have refused, often due to their adherence to 'anti-vax' beliefs. These beliefs include that vaccines are dangerous, render the recipient magnetic or contain government microchips.During the pandemic, numerous calls were made for those voluntarily refusing vaccination to be deprioritised when allocating scarce healthcare resources. While these calls were rejected, the likelihood of the same calls being made during future pandemics necessitates a thorough examination of the ethical implications entailed by such a policy.Here, I consider an intuitive argument for the use of vaccination status when allocating healthcare resources. This argument claims that, by avoiding vaccination, vaccine refusers are failing to fulfil a social obligation to protect those around them from harm by facilitating herd immunity. They are, therefore, less deserving of healthcare than their vaccinated peers.I explore three objections to this argument. While a first objection, asserting that no individual can be held responsible for a failure to develop herd immunity, fails, I find two further responses, respectively asserting the primacy of patient autonomy and highlighting the harms deprioritising vaccine refusers would cause to disadvantaged minorities, compelling. I, therefore, conclude that vaccination status should not be considered during healthcare resource allocation, as such discrimination would disproportionately harm marginalised communities.
Collapse
|
20
|
Sparling T, Iyer L, Pasquina P, Petrus E. Cortical Reorganization after Limb Loss: Bridging the Gap between Basic Science and Clinical Recovery. J Neurosci 2024; 44:e1051232024. [PMID: 38171645 PMCID: PMC10851691 DOI: 10.1523/jneurosci.1051-23.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/28/2023] [Accepted: 09/29/2023] [Indexed: 01/05/2024] Open
Abstract
Despite the increasing incidence and prevalence of amputation across the globe, individuals with acquired limb loss continue to struggle with functional recovery and chronic pain. A more complete understanding of the motor and sensory remodeling of the peripheral and central nervous system that occurs postamputation may help advance clinical interventions to improve the quality of life for individuals with acquired limb loss. The purpose of this article is to first provide background clinical context on individuals with acquired limb loss and then to provide a comprehensive review of the known motor and sensory neural adaptations from both animal models and human clinical trials. Finally, the article bridges the gap between basic science researchers and clinicians that treat individuals with limb loss by explaining how current clinical treatments may restore function and modulate phantom limb pain using the underlying neural adaptations described above. This review should encourage the further development of novel treatments with known neurological targets to improve the recovery of individuals postamputation.Significance Statement In the United States, 1.6 million people live with limb loss; this number is expected to more than double by 2050. Improved surgical procedures enhance recovery, and new prosthetics and neural interfaces can replace missing limbs with those that communicate bidirectionally with the brain. These advances have been fairly successful, but still most patients experience persistent problems like phantom limb pain, and others discontinue prostheses instead of learning to use them daily. These problematic patient outcomes may be due in part to the lack of consensus among basic and clinical researchers regarding the plasticity mechanisms that occur in the brain after amputation injuries. Here we review results from clinical and animal model studies to bridge this clinical-basic science gap.
Collapse
Affiliation(s)
- Tawnee Sparling
- Department of Physical Medicine and Rehabilitation, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Laxmi Iyer
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, Maryland 20817
| | - Paul Pasquina
- Department of Physical Medicine and Rehabilitation, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814
| | - Emily Petrus
- Department of Anatomy, Physiology and Genetics, Uniformed Services University, Bethesda, Maryland 20814
| |
Collapse
|
21
|
Yang C, Gao J, Glass L, Cross A, Sun J. Multi-faceted analysis and prediction for the outbreak of pediatric respiratory syncytial virus. J Am Med Inform Assoc 2023; 31:198-208. [PMID: 37934728 PMCID: PMC10746302 DOI: 10.1093/jamia/ocad212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/15/2023] [Accepted: 10/16/2023] [Indexed: 11/09/2023] Open
Abstract
OBJECTIVES Respiratory syncytial virus (RSV) is a significant cause of pediatric hospitalizations. This article aims to utilize multisource data and leverage the tensor methods to uncover distinct RSV geographic clusters and develop an accurate RSV prediction model for future seasons. MATERIALS AND METHODS This study utilizes 5-year RSV data from sources, including medical claims, CDC surveillance data, and Google search trends. We conduct spatiotemporal tensor analysis and prediction for pediatric RSV in the United States by designing (i) a nonnegative tensor factorization model for pediatric RSV diseases and location clustering; (ii) and a recurrent neural network tensor regression model for county-level trend prediction using the disease and location features. RESULTS We identify a clustering hierarchy of pediatric diseases: Three common geographic clusters of RSV outbreaks were identified from independent sources, showing an annual RSV trend shifting across different US regions, from the South and Southeast regions to the Central and Northeast regions and then to the West and Northwest regions, while precipitation and temperature were found as correlative factors with the coefficient of determination R2≈0.5, respectively. Our regression model accurately predicted the 2022-2023 RSV season at the county level, achieving R2≈0.3 mean absolute error MAE < 0.4 and a Pearson correlation greater than 0.75, which significantly outperforms the baselines with P-values <.05. CONCLUSION Our proposed framework provides a thorough analysis of RSV disease in the United States, which enables healthcare providers to better prepare for potential outbreaks, anticipate increased demand for services and supplies, and save more lives with timely interventions.
Collapse
Affiliation(s)
- Chaoqi Yang
- Computer Science Department, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| | - Junyi Gao
- University of Edinburgh, Edinburgh, United Kingdom
- Health Data Research UK, London, United Kingdom
| | - Lucas Glass
- IQVIA, Plymouth Meeting, PA 19462, United States
| | - Adam Cross
- Department of Pediatrics, University of Illinois College of Medicine Peoria, Peoria, IL 61605, United States
| | - Jimeng Sun
- Computer Science Department, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61801, United States
| |
Collapse
|
22
|
Self A, Van Buskirk J, Clark J, Cochrane JE, Knibbs L, Cass-Verco J, Gupta L. Respiratory syncytial virus disease morbidity in Australian infants aged 0 to 6 months: a systematic review with narrative synthesis. BMC Public Health 2023; 23:2560. [PMID: 38129854 PMCID: PMC10740277 DOI: 10.1186/s12889-023-17474-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/13/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND A significant proportion of the global respiratory syncytial virus (RSV) associated morbidity is accounted for by infants aged 0 to 6 months, who are particularly vulnerable to severe disease. In 2015, 44% of global hospitalisations in infants in this age group were secondary to RSV. The objective of this systematic review is to appraise and synthesise the local evidence of RSV infection morbidity among Australian infants aged 0 to 6 months and to assess the implications for future immunisation strategies. METHODS Electronic databases (Medline, Embase, Pubmed and Global Health) were searched for full-text articles published between 2000 and 2023 in English language. Studies that examined markers of RSV disease morbidity in infants aged 0 to 6 months in Australia who had laboratory confirmed RSV infection were eligible for inclusion. The outcomes of interest were incidence, prevalence, testing rate, positivity rate, mortality, emergency department visits, community health visits, hospitalisation, intensive care unit admission, supplementary oxygen use, mechanical ventilation, risk factors for disease severity and monoclonal antibody use. RESULTS The database search identified 469 studies. After removal of duplicates and full-text review, 17 articles were eligible for inclusion. This review was reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and Synthesis without meta-analysis guidelines. CONCLUSIONS Qualitative analysis of the included studies showed that Australian infants aged 0 to 6 months have higher rates of RSV testing, positivity and incidence; and more likely to develop severe disease that requires hospitalisation, intensive care unit admission or respiratory support, compared to children and adults of all ages. Aboriginal and Torres Strait Islander infants aged 0 to 6 months demonstrated higher rates of RSV infection and hospitalisation, compared to non-Indigenous infants. Age-related trends persisted in geographic areas with varying seasonal transmission of RSV, and during the SARS-CoV-2 pandemic. Passive immunisation strategies targeting infants in their first 6 months of life, either via vaccination of pregnant women or administration of long-acting monoclonal antibody during infancy, could effectively reduce RSV disease burden in Australia.
Collapse
Affiliation(s)
- Alice Self
- Sydney Local Health District, Sydney, NSW, Australia.
| | - Joseph Van Buskirk
- School of Public Health, The University of Sydney, Sydney, NSW, Australia
- Public Health Research Analytics and Methods for Evidence, Public Health Unit, Sydney Local Health District, Sydney, NSW, Australia
| | - Jayden Clark
- Sydney Local Health District, Sydney, NSW, Australia
| | | | - Luke Knibbs
- School of Public Health, The University of Sydney, Sydney, NSW, Australia
- Public Health Research Analytics and Methods for Evidence, Public Health Unit, Sydney Local Health District, Sydney, NSW, Australia
| | - John Cass-Verco
- Department of Paediatrics, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Leena Gupta
- Sydney Local Health District, Sydney, NSW, Australia
| |
Collapse
|
23
|
Kamp M, Achilonu O, Kisiangani I, Nderitu DM, Mpangase PT, Tadesse GA, Adetunji K, Iddi S, Speakman S, Hazelhurst S, Asiki G, Ramsay M. Multimorbidity in African ancestry populations: a scoping review. BMJ Glob Health 2023; 8:e013509. [PMID: 38084495 PMCID: PMC10711865 DOI: 10.1136/bmjgh-2023-013509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/01/2023] [Indexed: 12/18/2023] Open
Abstract
OBJECTIVES Multimorbidity (MM) is a growing concern linked to poor outcomes and higher healthcare costs. While most MM research targets European ancestry populations, the prevalence and patterns in African ancestry groups remain underexplored. This study aimed to identify and summarise the available literature on MM in populations with African ancestry, on the continent, and in the diaspora. DESIGN A scoping review was conducted in five databases (PubMed, Web of Science, Scopus, Science Direct and JSTOR) in July 2022. Studies were selected based on predefined criteria, with data extraction focusing on methodology and findings. Descriptive statistics summarised the data, and a narrative synthesis highlighted key themes. RESULTS Of the 232 publications on MM in African-ancestry groups from 2010 to June 2022-113 examined continental African populations, 100 the diaspora and 19 both. Findings revealed diverse MM patterns within and beyond continental Africa. Cardiovascular and metabolic diseases are predominant in both groups (80% continental and 70% diaspora). Infectious diseases featured more in continental studies (58% continental and 16% diaspora). Although many papers did not specifically address these features, as in previous studies, older age, being women and having a lower socioeconomic status were associated with a higher prevalence of MM, with important exceptions. Research gaps identified included limited data on African-ancestry individuals, inadequate representation, under-represented disease groups, non-standardised methodologies, the need for innovative data strategies, and insufficient translational research. CONCLUSION The growing global MM prevalence is mirrored in African-ancestry populations. Recognising the unique contexts of African-ancestry populations is essential when addressing the burden of MM. This review emphasises the need for additional research to guide and enhance healthcare approaches for African-ancestry populations, regardless of their geographic location.
Collapse
Affiliation(s)
- Michelle Kamp
- Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Okechinyere Achilonu
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Isaac Kisiangani
- African Population and Health Research Center (APHRC), APHRC Campus, Nairobi, Kenya
| | - Daniel Maina Nderitu
- African Population and Health Research Center (APHRC), APHRC Campus, Nairobi, Kenya
| | - Phelelani Thokozani Mpangase
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Kayode Adetunji
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Samuel Iddi
- African Population and Health Research Center (APHRC), APHRC Campus, Nairobi, Kenya
| | | | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical and Information Engineering, Faculty of Engineering and the Built Environment, University of the Witwatersrand, Johannesburg, South Africa
| | - Gershim Asiki
- African Population and Health Research Center (APHRC), APHRC Campus, Nairobi, Kenya
- Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Michèle Ramsay
- Division of Human Genetics, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| |
Collapse
|
24
|
Timire C, Houben RMGJ, Pedrazzoli D, Ferrand RA, Calderwood CJ, Bond V, Mbiba F, Kranzer K. Higher loss of livelihood and impoverishment in households affected by tuberculosis compared to non-tuberculosis affected households in Zimbabwe: a cross-sectional study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.05.23299470. [PMID: 38106129 PMCID: PMC10723493 DOI: 10.1101/2023.12.05.23299470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Introduction Tuberculosis (TB) disproportionally affects poor people, leading to income and non-income losses. Measures of socioeconomic impact of TB, e.g. impoverishment and patient costs are inadequate to capture non-income losses. We applied impoverishment and a multidimensional measure on TB and non-TB affected households in Zimbabwe. Methods We conducted a cross-sectional study in 270 households: 90 non-TB; 90 drug-susceptible TB (DS-TB), 90 drug-resistant TB (DR-TB) during the COVID-19 pandemic (2020-2021). Household data included ownership of assets, number of household members, income and indicators on five capital assets: financial, human, social, natural and physical. We determined proportions of impoverished households for periods 12 months prior and at the time of the interview. Households with incomes below US$1.90/day were considered to be impoverished. We used principal component analysis on five capital asset indicators to create a binary outcome variable indicating loss of livelihood. Log-binomial regression was used to determine associations between loss of livelihood and type of household. Results TB-affected households reported higher previous episodes of TB and household members requiring care than non-TB households. Households that were impoverished 12 months prior to the study were: 21 non-TB (23%); 40 DS-TB (45%); 37 DR-TB (41%). The proportions increased to 81%, 88% and 94%, respectively by the time of interview. Overall, 56% (152/270) of households sold assets: 44% (40/90) non-TB, 58% (52/90) DS-TB and 67% (60/90) DR-TB. Children's education was affected in 31% (56/180) of TB-affected compared to 13% (12/90) non-TB households. Overall, 133(50%) households experienced loss of livelihood, with TB-affected households twice as likely to experience loss of livelihood; adjusted prevalence ratio (aPR=2.02 (95%CI:1.35-3.03)). The effect of TB on livelihood was most pronounced in poorest households (aPR=2.64, (95%CI:1.29-5.41)). Conclusions TB-affected households experienced greater socioeconomic losses compared to non-TB households. Multidimensional measures of TB are crucial to inform multisectoral approaches to mitigate impacts of TB and other shocks.
Collapse
Affiliation(s)
- Collins Timire
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- AIDS & TB Department, Ministry of Health and Child Care, Harare, Zimbabwe
- The Health Research Unit, Biomedical Research & Training Institute, Harare, Zimbabwe
| | - Rein MGJ Houben
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, UK
| | - Debora Pedrazzoli
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, UK
| | - Rashida Abbas Ferrand
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- The Health Research Unit, Biomedical Research & Training Institute, Harare, Zimbabwe
| | - Claire J Calderwood
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- The Health Research Unit, Biomedical Research & Training Institute, Harare, Zimbabwe
| | - Virginia Bond
- Department of Global Health and Development, Faculty of Public Health and Policy London School of Hygiene &Tropical Medicine, London, UK
- Social Sciences Unit, Zambart, Lusaka, Zambia
| | - Fredrick Mbiba
- The Health Research Unit, Biomedical Research & Training Institute, Harare, Zimbabwe
| | - Katharina Kranzer
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK
- The Health Research Unit, Biomedical Research & Training Institute, Harare, Zimbabwe
- Division of Infectious Diseases and Tropical Medicine, University Hospital, LMU Munich
- German Center for Infection Research (DZIF), Munich
| |
Collapse
|
25
|
Rai D, Pattnaik B, Bangaru S, Tak J, Kumari J, Verma U, Vadala R, Yadav G, Dhaliwal RS, Kumar S, Kumar R, Jain D, Luthra K, Chosdol K, Palanichamy JK, Khan MA, Surendranath A, Mittal S, Tiwari P, Hadda V, Madan K, Agrawal A, Guleria R, Mohan A. microRNAs in exhaled breath condensate for diagnosis of lung cancer in a resource-limited setting: a concise review. Breathe (Sheff) 2023; 19:230125. [PMID: 38351949 PMCID: PMC10862127 DOI: 10.1183/20734735.0125-2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 11/30/2023] [Indexed: 02/16/2024] Open
Abstract
Lung cancer is one of the common cancers globally with high mortality and poor prognosis. Most cases of lung cancer are diagnosed at an advanced stage due to limited diagnostic resources. Screening modalities, such as sputum cytology and annual chest radiographs, have not proved sensitive enough to impact mortality. In recent years, annual low-dose computed tomography has emerged as a potential screening tool for early lung cancer detection, but it may not be a feasible option for developing countries. In this context, exhaled breath condensate (EBC) analysis has been evaluated recently as a noninvasive tool for lung cancer diagnosis. The breath biomarkers also have the advantage of differentiating various types and stages of lung cancer. Recent studies have focused more on microRNAs (miRNAs) as they play a key role in tumourigenesis by regulating the cell cycle, metastasis and angiogenesis. In this review, we have consolidated the current published literature suggesting the utility of miRNAs in EBC for the detection of lung cancer.
Collapse
Affiliation(s)
- Divyanjali Rai
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Bijay Pattnaik
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Sunil Bangaru
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Jaya Tak
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Jyoti Kumari
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Umashankar Verma
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Rohit Vadala
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Geetika Yadav
- Indian Council of Medical Research, New Delhi, India
| | | | - Sunil Kumar
- Department of Surgical Oncology, All India Institute of Medical Sciences, New Delhi, India
| | - Rakesh Kumar
- Department of Nuclear Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Deepali Jain
- Department of Pathology, All India Institute of Medical Sciences, New Delhi, India
| | - Kalpana Luthra
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | - Kunzang Chosdol
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | - Maroof Ahmad Khan
- Department of Biostatistics, All India Institute of Medical Sciences, New Delhi, India
| | - Addagalla Surendranath
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Saurabh Mittal
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Pawan Tiwari
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Vijay Hadda
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Karan Madan
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anurag Agrawal
- Trivedi School of Biosciences, Ashoka University, Sonipat, India
| | - Randeep Guleria
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Anant Mohan
- Breathomics in Respiratory Diseases Lab, Department of Pulmonary, Critical Care and Sleep Medicine, All India Institute of Medical Sciences, New Delhi, India
| |
Collapse
|
26
|
Mojica N, Kersten F, Montserrat-Canals M, Huhn GR, Tislevoll AM, Cordara G, Teter K, Krengel U. Using Vibrio natriegens for high-yield production of challenging expression targets and for protein deuteration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.03.565449. [PMID: 37961550 PMCID: PMC10635113 DOI: 10.1101/2023.11.03.565449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Production of soluble proteins is essential for structure/function studies, however, this usually requires milligram amounts of protein, which can be difficult to obtain with traditional expression systems. Recently, the Gram-negative bacterium Vibrio natriegens appeared as a novel and alternative host platform for production of proteins in high yields. Here, we used a commercial strain derived from V. natriegens (Vmax™ X2) to produce soluble bacterial and fungal proteins in milligram scale, which we struggled to achieve in Escherichia coli. These proteins include the cholera toxin (CT) and N-acetyl glucosamine binding protein A (GbpA) from Vibrio cholerae, the heat-labile enterotoxin (LT) from E. coli and the fungal nematotoxin CCTX2 from Coprinopsis cinerea. CT, GbpA and LT are secreted by the Type II secretion system in their natural hosts. When these three proteins were produced in Vmax, they were also secreted, and could be recovered from the growth media. This simplified the downstream purification procedure and resulted in considerably higher protein yields compared to production in E. coli (6- to 26-fold increase). We also tested Vmax for protein deuteration using deuterated minimal media with deuterium oxide as solvent, and achieved a 3-fold increase in yield compared to the equivalent protocol in E. coli. This is good news since isotopic labeling is expensive and often ineffective, but represents a necessary prerequisite for some structural techniques. Thus, Vmax represents a promising host for production of challenging expression targets and for protein deuteration in amounts suitable for structural biology studies.
Collapse
Affiliation(s)
- Natalia Mojica
- Department of Chemistry, University of Oslo, Blindern, Norway
| | - Flore Kersten
- Department of Chemistry, University of Oslo, Blindern, Norway
- Centre for Molecular Medicine Norway, University of Oslo, Blindern, Norway
| | - Mateu Montserrat-Canals
- Department of Chemistry, University of Oslo, Blindern, Norway
- Centre for Molecular Medicine Norway, University of Oslo, Blindern, Norway
| | - G. Robb Huhn
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, U.S.A
| | | | | | - Ken Teter
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, U.S.A
| | - Ute Krengel
- Department of Chemistry, University of Oslo, Blindern, Norway
| |
Collapse
|
27
|
Wildenbeest JG, Bont LJ. Targeting respiratory syncytial virus vaccination using individual prediction. Lancet Digit Health 2023; 5:e752-e753. [PMID: 37890900 DOI: 10.1016/s2589-7500(23)00200-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023]
Affiliation(s)
- Joanne G Wildenbeest
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, Netherlands
| | - Louis J Bont
- Department of Pediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht 3584 EA, Netherlands; ReSViNET Foundation, Julius Clinical, Zeist, Netherlands.
| |
Collapse
|
28
|
Brown TC, Crouse EC, Attaway CA, Oakes DK, Minton SW, Borghuis BG, McGee AW. Microglia are dispensable for experience-dependent refinement of visual circuitry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.17.562708. [PMID: 37905138 PMCID: PMC10614920 DOI: 10.1101/2023.10.17.562708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Microglia are proposed to be critical for the refinement of developing neural circuitry. However, evidence identifying specific roles for microglia has been limited and often indirect. Here we examined whether microglia are required for the experience-dependent refinement of visual circuitry and visual function during development. We ablated microglia by administering the colony-stimulating factor 1 receptor (CSF1R) inhibitor PLX5622, and then examined the consequences for retinal function, receptive field tuning of neurons in primary visual cortex (V1), visual acuity, and experience-dependent plasticity in visual circuitry. Eradicating microglia by treating mice with PLX5622 beginning at postnatal day (P) 14 did not alter visual response properties of retinal ganglion cells examined three or more weeks later. Mice treated with PLX5622 from P14 lacked more than 95% of microglia in V1 by P18, prior to the opening of the critical period. Despite the absence of microglia, the receptive field tuning properties of neurons in V1 were normal at P32. Similarly, eradicating microglia did not affect the maturation of visual acuity. Mice treated with PLX5622 displayed typical ocular dominance plasticity in response to brief monocular deprivation. Thus, none of these principal measurements of visual circuit development and function detectibly differed in the absence of microglia. We conclude that microglia are dispensable for experience-dependent refinement of visual circuitry. These findings challenge the proposed critical role of microglia in refining neural circuitry.
Collapse
Affiliation(s)
- Thomas C. Brown
- Department of Anatomical Sciences and Neurobiology, School of Medicine; University of Louisville, Louisville, KY, 40202
| | - Emily C. Crouse
- Department of Anatomical Sciences and Neurobiology, School of Medicine; University of Louisville, Louisville, KY, 40202
| | - Cecilia A. Attaway
- Department of Anatomical Sciences and Neurobiology, School of Medicine; University of Louisville, Louisville, KY, 40202
| | - Dana K. Oakes
- Department of Anatomical Sciences and Neurobiology, School of Medicine; University of Louisville, Louisville, KY, 40202
| | - Sarah W. Minton
- Department of Anatomical Sciences and Neurobiology, School of Medicine; University of Louisville, Louisville, KY, 40202
| | - Bart G. Borghuis
- Department of Anatomical Sciences and Neurobiology, School of Medicine; University of Louisville, Louisville, KY, 40202
| | - Aaron W. McGee
- Department of Anatomical Sciences and Neurobiology, School of Medicine; University of Louisville, Louisville, KY, 40202
| |
Collapse
|
29
|
Xie WJ, Liu D, Wang X, Zhang A, Wei Q, Nandi A, Dong S, Warshel A. Enhancing Luciferase Activity and Stability through Generative Modeling of Natural Enzyme Sequences. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558367. [PMID: 37786693 PMCID: PMC10541610 DOI: 10.1101/2023.09.18.558367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The availability of natural protein sequences synergized with generative artificial intelligence (AI) provides new paradigms to create enzymes. Although active enzyme variants with numerous mutations have been produced using generative models, their performance often falls short compared to their wild-type counterparts. Additionally, in practical applications, choosing fewer mutations that can rival the efficacy of extensive sequence alterations is usually more advantageous. Pinpointing beneficial single mutations continues to be a formidable task. In this study, using the generative maximum entropy model to analyze Renilla luciferase homologs, and in conjunction with biochemistry experiments, we demonstrated that natural evolutionary information could be used to predictively improve enzyme activity and stability by engineering the active center and protein scaffold, respectively. The success rate of designed single mutants is ~50% to improve either luciferase activity or stability. These finding highlights nature's ingenious approach to evolving proficient enzymes, wherein diverse evolutionary pressures are preferentially applied to distinct regions of the enzyme, ultimately culminating in an overall high performance. We also reveal an evolutionary preference in Renilla luciferase towards emitting blue light that holds advantages in terms of water penetration compared to other light spectrum. Taken together, our approach facilitates navigation through enzyme sequence space and offers effective strategies for computer-aided rational enzyme engineering.
Collapse
Affiliation(s)
- Wen Jun Xie
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
- Departmet of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development (CNPD3), Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Dangliang Liu
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Xiaoya Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Aoxuan Zhang
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Qijia Wei
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Ashim Nandi
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Suwei Dong
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
30
|
Sarna M, Gebremedhin A, Richmond PC, Glass K, Levy A, Moore HC. Factors Predicting Secondary Respiratory Morbidity Following Early-Life Respiratory Syncytial Virus Infections: Population-Based Cohort Study. Open Forum Infect Dis 2023; 10:ofad450. [PMID: 37790944 PMCID: PMC10544950 DOI: 10.1093/ofid/ofad450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/27/2023] [Indexed: 10/05/2023] Open
Abstract
Background The association between early-life respiratory syncytial virus (RSV) infections and later respiratory morbidity is well established. However, there is limited evidence on factors that influence this risk. We examined sociodemographic and perinatal factors associated with later childhood respiratory morbidity requiring secondary care following exposure to a laboratory-confirmed RSV episode in the first 2 years. Methods We used a probabilistically linked whole-of-population-based birth cohort including 252 287 children born in Western Australia between 2000 and 2009 with follow-up to the end of 2012. Cox proportional hazards models estimated adjusted hazard ratios (aHRs) of the association of various risk factors with the first respiratory episode for asthma, wheezing, and unspecified acute lower respiratory infection beyond the age of 2 years. Results The analytic cohort included 4151 children with a confirmed RSV test before age 2 years. The incidence of subsequent respiratory morbidity following early-life RSV infection decreased with child age at outcome (highest incidence in 2-<4-year-olds: 41.8 per 1000 child-years; 95% CI, 37.5-46.6), increased with age at RSV infection (6-<12-month-olds: 23.6/1000 child-years; 95% CI, 19.9-27.8; 12-<24-month-olds: 22.4/1000 child-years; 95% CI, 18.2-22.7) and decreasing gestational age (50.8/1000 child-years; 95% CI, 33.5-77.2 for children born extremely preterm, <28 weeks gestation). Risk factors included age at first RSV episode (6-<12 months: aHR, 1.42; 95% CI, 1.06-1.90), extreme prematurity (<28 weeks: aHR, 2.22; 95% CI, 1.40-3.53), maternal history of asthma (aHR, 1.33; 95% CI, 1.04-1.70), and low socioeconomic index (aHR, 1.76; 95% CI, 1.03-3.00). Conclusions Our results suggest that in addition to preterm and young infants, children aged 12-<24 months could also be potential target groups for RSV prevention to reduce the burden of later respiratory morbidities associated with RSV.
Collapse
Affiliation(s)
- Mohinder Sarna
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Curtin School of Population Health, Curtin University, Bentley, Western Australia, Australia
| | - Amanuel Gebremedhin
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Curtin School of Population Health, Curtin University, Bentley, Western Australia, Australia
| | - Peter C Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- School of Medicine, University of Western Australia, Nedlands, Western Australia, Australia
- Perth Children's Hospital, Nedlands, Western Australia, Australia
| | - Kathryn Glass
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- National Centre for Epidemiology and Population Health, ANU College of Health and Medicine, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Avram Levy
- PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Perth, Western Australia, Australia
- School of Biomedical Sciences, University of Western Australia, Nedlands, Perth, Western Australia, Australia
| | - Hannah C Moore
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, Western Australia, Australia
- Curtin School of Population Health, Curtin University, Bentley, Western Australia, Australia
| |
Collapse
|
31
|
Klune CB, Goodpaster CM, Gongwer MW, Gabriel CJ, Chen R, Jones NS, Schwarz LA, DeNardo LA. Developmentally distinct architectures in top-down circuits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.27.555010. [PMID: 37693480 PMCID: PMC10491090 DOI: 10.1101/2023.08.27.555010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
The medial prefrontal cortex (mPFC) plays a key role in learning, mood and decision making, including in how individuals respond to threats 1-6 . mPFC undergoes a uniquely protracted development, with changes in synapse density, cortical thickness, long-range connectivity, and neuronal encoding properties continuing into early adulthood 7-21 . Models suggest that before adulthood, the slow-developing mPFC cannot adequately regulate activity in faster-developing subcortical centers 22,23 . They propose that during development, the enhanced influence of subcortical systems underlies distinctive behavioural strategies of juveniles and adolescents and that increasing mPFC control over subcortical structures eventually allows adult behaviours to emerge. Yet it has remained unclear how a progressive strengthening of top-down control can lead to nonlinear changes in behaviour as individuals mature 24,25 . To address this discrepancy, here we monitored and manipulated activity in the developing brain as animals responded to threats, establishing direct causal links between frontolimbic circuit activity and the behavioural strategies of juvenile, adolescent and adult mice. Rather than a linear strengthening of mPFC synaptic connectivity progressively regulating behaviour, we uncovered multiple developmental switches in the behavioural roles of mPFC circuits targeting the basolateral amygdala (BLA) and nucleus accumbens (NAc). We show these changes are accompanied by axonal pruning coinciding with functional strengthening of synaptic connectivity in the mPFC-BLA and mPFC-NAc pathways, which mature at different rates. Our results reveal how developing mPFC circuits pass through distinct architectures that may make them optimally adapted to the demands of age-specific challenges.
Collapse
|
32
|
Fehr J, Piccininni M, Kurth T, Konigorski S. Assessing the transportability of clinical prediction models for cognitive impairment using causal models. BMC Med Res Methodol 2023; 23:187. [PMID: 37598141 PMCID: PMC10439645 DOI: 10.1186/s12874-023-02003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 07/27/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND Machine learning models promise to support diagnostic predictions, but may not perform well in new settings. Selecting the best model for a new setting without available data is challenging. We aimed to investigate the transportability by calibration and discrimination of prediction models for cognitive impairment in simulated external settings with different distributions of demographic and clinical characteristics. METHODS We mapped and quantified relationships between variables associated with cognitive impairment using causal graphs, structural equation models, and data from the ADNI study. These estimates were then used to generate datasets and evaluate prediction models with different sets of predictors. We measured transportability to external settings under guided interventions on age, APOE ε4, and tau-protein, using performance differences between internal and external settings measured by calibration metrics and area under the receiver operating curve (AUC). RESULTS Calibration differences indicated that models predicting with causes of the outcome were more transportable than those predicting with consequences. AUC differences indicated inconsistent trends of transportability between the different external settings. Models predicting with consequences tended to show higher AUC in the external settings compared to internal settings, while models predicting with parents or all variables showed similar AUC. CONCLUSIONS We demonstrated with a practical prediction task example that predicting with causes of the outcome results in better transportability compared to anti-causal predictions when considering calibration differences. We conclude that calibration performance is crucial when assessing model transportability to external settings.
Collapse
Affiliation(s)
- Jana Fehr
- Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.
- Digital Health and Machine Learning, Hasso-Plattner-Institute, Potsdam, Germany.
| | - Marco Piccininni
- Institute of Public Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Center for Stroke Research Berlin, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Tobias Kurth
- Institute of Public Health, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Konigorski
- Digital Engineering Faculty, University of Potsdam, Potsdam, Germany.
- Digital Health and Machine Learning, Hasso-Plattner-Institute, Potsdam, Germany.
- Icahn School of Medicine at Mount Sinai, Hasso Plattner Institute for Digital Health at Mount Sinai, New York, NY, USA.
| |
Collapse
|
33
|
Sarna M, Gebremedhin A, Richmond P, Levy A, Glass K, Moore HC. Determining the true incidence of seasonal respiratory syncytial virus-confirmed hospitalizations in preterm and term infants in Western Australia. Vaccine 2023; 41:5216-5220. [PMID: 37474407 DOI: 10.1016/j.vaccine.2023.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023]
Abstract
Respiratory syncytial virus contributes to significant global infant morbidity and mortality. We applied a previously developed statistical prediction model incorporating pre-pandemic RSV testing data and hospital admission data to estimate infant RSV-hospitalizations by birth month and prematurity, focused on infants aged <1 year. The overall predicted RSV-hospitalization incidence rates in infants <6 months were 32.7/1,000 child-years (95 % CI: 31.8, 33.5) and 3.1/1,000 child-years (95 % CI: 3.0, 3.1) in infants aged 6-<12 months. Predicted RSV-hospitalization rates for infants aged <6 months were highest for infants born in April/May. Predicted rates for preterm infants born 29-32 weeks gestation were highest in March-May, whereas infants born >33 weeks had peak RSV-hospitalization rates from May-June, similar to late preterm or term births. RSV-hospitalization rates in the pre-pandemic era were highly seasonal, and seasonality varied with degree of prematurity. Accurate estimates of RSV-hospitalization in high-risk sub-groups are essential to understand preventable burden of RSV especially given the current prevention landscape.
Collapse
Affiliation(s)
- Mohinder Sarna
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia; Curtin School of Population Health, Curtin University, Bentley, WA, Australia.
| | - Amanuel Gebremedhin
- Curtin School of Population Health, Curtin University, Bentley, WA, Australia
| | - Peter Richmond
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia; School of Medicine, University of Western Australia and Perth Children's Hospital, Nedlands, WA, Australia
| | - Avram Levy
- PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, Perth, WA, Australia; School of Biomedical Sciences, University of Western Australia, Nedlands, Perth, WA, Australia
| | - Kathryn Glass
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia; National Centre for Epidemiology and Population Health, ANU College of Health and Medicine, Australian National University, Canberra, ACT, Australia
| | - Hannah C Moore
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA, Australia; Curtin School of Population Health, Curtin University, Bentley, WA, Australia
| |
Collapse
|
34
|
Mansoubi M, Dawes J, Bhatia A, Vashisht H, Collett J, Greenwood DC, Ezekiel L, O'Connor D, Leveridge P, Rayner C, Read F, Sivan M, Tuckerbell I, Ward T, Delaney B, Muhlhausen W, Dawes H. Digital home monitoring for capturing daily fluctuation of symptoms; a longitudinal repeated measures study: Long Covid Multi-disciplinary Consortium to Optimise Treatments and Services across the NHS (a LOCOMOTION study). BMJ Open 2023; 13:e071428. [PMID: 37553189 PMCID: PMC10414119 DOI: 10.1136/bmjopen-2022-071428] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/28/2023] [Indexed: 08/10/2023] Open
Abstract
INTRODUCTION A substantial proportion of COVID-19 survivors continue to have symptoms more than 3 months after infection, especially of those who required medical intervention. Lasting symptoms are wide-ranging, and presentation varies between individuals and fluctuates within an individual. Improved understanding of undulation in symptoms and triggers may improve efficacy of healthcare providers and enable individuals to better self-manage their Long Covid. We present a protocol where we aim to develop and examine the feasibility and usability of digital home monitoring for capturing daily fluctuation of symptoms in individuals with Long Covid and provide data to facilitate a personalised approach to the classification and management of Long Covid symptoms. METHODS AND ANALYSIS This study is a longitudinal prospective cohort study of adults with Long Covid accessing 10 National Health Service (NHS) rehabilitation services in the UK. We aim to recruit 400 people from participating NHS sites. At referral to study, 6 weeks and 12 weeks, participants will complete demographic data (referral to study) and clinical outcome measures, including ecological momentary assessment (EMA) using personal mobile devices. EMA items are adapted from the COVID-19 Yorkshire Rehabilitation Scale items and include self-reported activities, symptoms and psychological factors. Passive activity data will be collected through wrist-worn sensors. We will use latent class growth models to identify trajectories of experience, potential phenotypes defined by co-occurrence of symptoms and inter-relationships between stressors, symptoms and participation in daily activities. We anticipate that n=300 participants provide 80% power to detect a 20% improvement in fatigue over 12 weeks in one class of patients relative to another. ETHICS AND DISSEMINATION The study was approved by the Yorkshire & The Humber-Bradford Leeds Research Ethics Committee (ref: 21/YH/0276). Findings will be disseminated in peer-reviewed publications and presented at conferences. TRIAL REGISTRATION NUMBER ISRCTN15022307.
Collapse
Affiliation(s)
- Maedeh Mansoubi
- NIHR Exeter Biomedical Research Center, Medical School, Faculty of Health and Life sciences, University of Exeter, Exeter, UK
- Medical School, University of Exeter, Exeter, UK
- Department of Public Health and Sport Sciences, University of Exeter, Exeter, UK
| | - Joanna Dawes
- Medical School, University of Exeter, Exeter, UK
| | | | | | - Johnny Collett
- Department of Sport, Health and Social Work, Oxford Brookes University, Oxford, UK
| | - Darren C Greenwood
- Academic Department of Rehabilitation Medicine, University of Leeds, Leeds, UK
| | - Leisle Ezekiel
- School of Health Sciences, University of Southampton, Southampton, UK
| | | | - Phaedra Leveridge
- Department of Public Health and Sport Sciences, University of Exeter, Exeter, UK
| | - Clare Rayner
- Patient Advisory Group (PAG) Representative, Leeds, UK
| | - Flo Read
- Department of Health and Community Sciences, University of Exeter, Exeter, UK
| | - Manoj Sivan
- Faculty of Medicine and Health, School of Medicine, University of Leeds, Leeds, UK
| | | | - Tomas Ward
- Insight SFI Research Centre for Data Analytics, Dublin City University, Dublin, Ireland
| | - Brendan Delaney
- Faculty of Medicine, Department of Surgery & Cancer, Imperial College, London, UK
| | | | - Helen Dawes
- NIHR Exeter Biomedical Research Center, Medical School, Faculty of Health and Life sciences, University of Exeter, Exeter, UK
- Medical School, University of Exeter, Exeter, UK
- Department of Public Health and Sport Sciences, University of Exeter, Exeter, UK
| |
Collapse
|
35
|
Vora N, Shekar P, Esmail M, Patra A, Georgakoudi I. Deep Learning-Enabled, Detection of Rare Circulating Tumor Cell Clusters in Whole Blood Using Label-free, Flow Cytometry. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551485. [PMID: 37577660 PMCID: PMC10418242 DOI: 10.1101/2023.08.01.551485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Metastatic tumors have poor prognoses for progression-free and overall survival for all cancer patients. Rare circulating tumor cells (CTCs) and rarer circulating tumor cell clusters (CTCCs) are potential biomarkers of metastatic growth, with CTCCs representing an increased risk factor for metastasis. Current detection platforms are optimized for ex vivo detection of CTCs only. Microfluidic chips and size exclusion methods have been proposed for CTCC detection; however, they lack in vivo utility and real-time monitoring capability. Confocal backscatter and fluorescence flow cytometry (BSFC) has been used for label-free detection of CTCCs in whole blood based on machine learning (ML) enabled peak classification. Here, we expand to a deep-learning (DL) -based, peak detection and classification model to detect CTCCs in whole blood data. We demonstrate that DL-based BSFC has a low false alarm rate of 0.78 events/min with a high Pearson correlation coefficient of 0.943 between detected events and expected events. DL-based BSFC of whole blood maintains a detection purity of 72% and a sensitivity of 35.3% for both homotypic and heterotypic CTCCs starting at a minimum size of two cells. We also demonstrate through artificial spiking studies that DL-based BSFC is sensitive to changes in the number of CTCCs present in the samples and does not add variability in detection beyond the expected variability from Poisson statistics. The performance established by DL-based BSFC motivates its use for in vivo detection of CTCCs. Further developments of label-free BSFC to enhance throughput could lead to critical applications in the clinical detection of CTCCs and ex vivo isolation of CTCC from whole blood with minimal disruption and processing steps.
Collapse
Affiliation(s)
- Nilay Vora
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| | - Prashant Shekar
- Department of Mathematics, Embry-Riddle Aeronautical University, Daytona Beach, FL, 32114, USA
| | - Michael Esmail
- Tufts Comparative Medicine Services, Tufts University, Medford, MA, 02155, USA
- # Current Affiliation: University of Massachusetts Amherst Animal Care Services, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Abani Patra
- Data Intensive Studies Center, Tufts University, Medford, MA 02155, USA
- Department of Mathematics, Tufts University, Medford, MA 02155, USA
| | - Irene Georgakoudi
- Department of Biomedical Engineering, Tufts University, Medford, MA 02155, USA
| |
Collapse
|
36
|
Ayad NM, Lakins JN, Ghagre A, Ehrlicher AJ, Weaver VM. Tissue tension permits β-catenin phosphorylation to drive mesoderm specification in human embryonic stem cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549074. [PMID: 37503095 PMCID: PMC10370032 DOI: 10.1101/2023.07.14.549074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The role of morphogenetic forces in cell fate specification is an area of intense interest. Our prior studies suggested that the development of high cell-cell tension in human embryonic stem cells (hESC) colonies permits the Src-mediated phosphorylation of junctional β-catenin that accelerates its release to potentiate Wnt-dependent signaling critical for initiating mesoderm specification. Using an ectopically expressed nonphosphorylatable mutant of β-catenin (Y654F), we now provide direct evidence that impeding tension-dependent Src-mediated β-catenin phosphorylation impedes the expression of Brachyury (T) and the epithelial-to-mesenchymal transition (EMT) necessary for mesoderm specification. Addition of exogenous Wnt3a or inhibiting GSK3β activity rescued mesoderm expression, emphasizing the importance of force dependent Wnt signaling in regulating mechanomorphogenesis. Our work provides a framework for understanding tension-dependent β-catenin/Wnt signaling in the self-organization of tissues during developmental processes including gastrulation.
Collapse
Affiliation(s)
- Nadia M.E. Ayad
- Graduate Program in Bioengineering, University of California, San Francisco and University of California Berkeley, San Francisco, CA 94143, USA; Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Johnathon N. Lakins
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Ajinkya Ghagre
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada
| | - Allen J. Ehrlicher
- Department of Bioengineering, Department of Anatomy and Cell Biology, Department of Biomedical Engineering, Department of Mechanical Engineering, Centre for Structural Biology, Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC H3A 1A3, Canada
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94143, USA; UCSF Comprehensive Cancer Center, Helen Diller Family Cancer Research Center, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA
| |
Collapse
|
37
|
Tromans-Coia C, Jamali N, Abbasi HS, Giuliano KA, Hagimoto M, Jan K, Kaneko E, Letzsch S, Schreiner A, Sexton JZ, Suzuki M, Trask OJ, Yamaguchi M, Yanagawa F, Yang M, Carpenter AE, Cimini BA. Assessing the performance of the Cell Painting assay across different imaging systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528711. [PMID: 36824835 PMCID: PMC9949001 DOI: 10.1101/2023.02.15.528711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Quantitative microscopy is a powerful method for performing phenotypic screens from which image-based profiling can extract a wealth of information, termed profiles. These profiles can be used to elucidate the changes in cellular phenotypes across cell populations from different patient samples or following genetic or chemical perturbations. One such image-based profiling method is the Cell Painting assay, which provides morphological insight through the imaging of eight cellular compartments. Here, we examine the performance of the Cell Painting assay across multiple high-throughput microscope systems and find that all are compatible with this assay. Furthermore, we determine independently for each microscope system the best performing settings, providing those who wish to adopt this assay an ideal starting point for their own assays. We also explore the impact of microscopy setting changes in the Cell Painting assay and find that few dramatically reduce the quality of a Cell Painting profile, regardless of the microscope used.
Collapse
|
38
|
Kuball K, Fernandes VFL, Takagi D, Yoshizawa M. Blind cavefish evolved food-searching behavior without changing sensory modality compared with sighted conspecies in the dark. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544672. [PMID: 37398421 PMCID: PMC10312625 DOI: 10.1101/2023.06.12.544672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
In nature, animals must navigate to forage according to their sensory inputs. Different species use different sensory modalities to locate food efficiently. For teleosts, food emits visual, mechanical, chemical, and/or possibly weak-electrical signals, which can be detected by optic, auditory/lateral line, and olfactory/taste buds sensory systems. However, how fish respond to and use different sensory inputs when locating food, as well as the evolution of these sensory modalities, remain unclear. We examined the Mexican tetra, Astyanax mexicanus, which is composed of two different morphs: a sighted riverine (surface fish) and a blind cave morph (cavefish). Compared with surface fish, cavefish have enhanced non-visual sensory systems, including the mechanosensory lateral line system, chemical sensors comprising the olfactory system and taste buds, and the auditory system to help navigate toward food sources. We tested how visual, chemical, and mechanical stimuli evoke food-seeking behavior. In contrast to our expectations, both surface fish and cavefish did not follow a gradient of chemical stimulus (food extract) but used it as a cue for the ambient existence of food. Surface fish followed visual cues (red plastic beads and food pellets), but, in the dark, were likely to rely on mechanosensors-the lateral line and/or tactile sensor-as cavefish did. Our results indicate cavefish used similar sensory modality to surface fish in the dark, while adherence levels to stimuli were higher in cavefish. In addition, cavefish evolved an extended circling strategy to capture food, which may yield a higher chance to capture food by swimming-by the food multiple times instead of once through zigzag motion. In summary, we propose ancestors of cavefish similar to surface fish may have needed little modification in food-seeking strategy to adapt to the dark.
Collapse
Affiliation(s)
- Kyleigh Kuball
- School of Life Sciences, the University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | | | - Daisuke Takagi
- Department of Math, the University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| | - Masato Yoshizawa
- School of Life Sciences, the University of Hawai'i at Mānoa, Honolulu, Hawai'i, USA
| |
Collapse
|
39
|
Kesthely CA, Rogers RR, Hafi BE, Jean-Pierre F, O’Toole GA. Transcriptional Profiling and Genetic Analysis of a Cystic Fibrosis Airway-Relevant Model Shows Asymmetric Responses to Growth in a Polymicrobial Community. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.24.542191. [PMID: 37293107 PMCID: PMC10245937 DOI: 10.1101/2023.05.24.542191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Bacterial infections in the lungs of persons with cystic fibrosis are typically composed of multispecies biofilm-like communities, which modulate clinically relevant phenotypes that cannot be explained in the context of a single species culture. Most analyses to-date provide a picture of the transcriptional responses of individual pathogens, however, there is relatively little data describing the transcriptional landscape of clinically-relevant multispecies communities. Harnessing a previously described cystic fibrosis-relevant, polymicrobial community model consisting of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis and Prevotella melaninogenica , we performed an RNA-Seq analysis to elucidate the transcriptional profiles of the community grown in artificial sputum medium (ASM) as compared to growth in monoculture, without mucin, and in fresh medium supplemented with tobramycin. We provide evidence that, although the transcriptional profile of P. aeruginosa is community agnostic, the transcriptomes of S. aureus and S. sanguinis are community aware. Furthermore, P. aeruginosa and P. melaninogenica are transcriptionally sensitive to the presence of mucin in ASM, whereas S. aureus and S. sanguinis largely do not alter their transcriptional profiles in the presence of mucin when grown in a community. Only P. aeruginosa shows a robust response to tobramycin. Genetic studies of mutants altered in community-specific growth provide complementary data regarding how these microbes adapt to a community context. Importance Polymicrobial infections constitute the majority of infections in the cystic fibrosis (CF) airway, but their study has largely been neglected in a laboratory setting. Our lab previously reported a polymicrobial community that can explain clinical outcomes in the lungs of persons with CF. Here we obtain transcriptional profiles of the community versus monocultures to provide transcriptional information about how this model community responds to CF-related growth conditions and perturbations. Genetic studies provide complementary functional outputs to assess how the microbes adapt to life in a community.
Collapse
Affiliation(s)
| | - Rendi R. Rogers
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| | - Bassam El Hafi
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| | - Fabrice Jean-Pierre
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| | - George A. O’Toole
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth
| |
Collapse
|
40
|
Chang S, Yang J, Novoseltseva A, Fu X, Li C, Chen SC, Augustinack JC, Magnain C, Fischl B, Mckee AC, Boas DA, Chen IA, Wang H. Multi-Scale Label-free Human Brain Imaging with Integrated Serial Sectioning Polarization Sensitive Optical Coherence Tomography and Two-Photon Microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.22.541785. [PMID: 37293092 PMCID: PMC10245911 DOI: 10.1101/2023.05.22.541785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The study of neurodegenerative processes in the human brain requires a comprehensive understanding of cytoarchitectonic, myeloarchitectonic, and vascular structures. Recent computational advances have enabled volumetric reconstruction of the human brain using thousands of stained slices, however, tissue distortions and loss resulting from standard histological processing have hindered deformation-free reconstruction of the human brain. The development of a multi-scale and volumetric human brain imaging technique that can measure intact brain structure would be a major technical advance. Here, we describe the development of integrated serial sectioning Polarization Sensitive Optical Coherence Tomography (PSOCT) and Two Photon Microscopy (2PM) to provide label-free multi-contrast imaging, including scattering, birefringence and autofluorescence of human brain tissue. We demonstrate that high-throughput reconstruction of 4×4×2cm3 sample blocks and simple registration of PSOCT and 2PM images enable comprehensive analysis of myelin content, vascular structure, and cellular information. We show that 2μm in-plane resolution 2PM images provide microscopic validation and enrichment of the cellular information provided by the PSOCT optical property maps on the same sample, revealing the sophisticated capillary networks and lipofuscin filled cell bodies across the cortical layers. Our method is applicable to the study of a variety of pathological processes, including demyelination, cell loss, and microvascular changes in neurodegenerative diseases such as Alzheimer's disease (AD) and Chronic Traumatic Encephalopathy (CTE).
Collapse
Affiliation(s)
- Shuaibin Chang
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston 02215, USA
| | - Jiarui Yang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston 02215, USA
| | - Anna Novoseltseva
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston 02215, USA
| | - Xinlei Fu
- The Chinese University of Hong Kong, Department of Mechanical Engineering, Hong Kong Special Administrative Region, China
| | - Chenglin Li
- The Chinese University of Hong Kong, Department of Mechanical Engineering, Hong Kong Special Administrative Region, China
| | - Shih-Chi Chen
- The Chinese University of Hong Kong, Department of Mechanical Engineering, Hong Kong Special Administrative Region, China
| | - Jean C. Augustinack
- Department of Radiology, Massachusetts General Hospital, A.A. Martinos Center for Biomedical Imaging, 13th Street, Boston 02129, USA
| | - Caroline Magnain
- Department of Radiology, Massachusetts General Hospital, A.A. Martinos Center for Biomedical Imaging, 13th Street, Boston 02129, USA
| | - Bruce Fischl
- Department of Radiology, Massachusetts General Hospital, A.A. Martinos Center for Biomedical Imaging, 13th Street, Boston 02129, USA
| | - Ann C. Mckee
- VA Boston Healthcare System, U.S. Department of Veteran Affairs
- Boston University Chobanian and Avedisian School of Medicine, Boston University Alzheimer’s Disease Research Center and CTE Center
- Department of Neurology, Boston University Chobanian and Avedisian School of Medicine
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine
- VA Bedford Healthcare System, U.S. Department of Veteran Affairs, Bedford, MA, USA
| | - David A. Boas
- Department of Electrical and Computer Engineering, Boston University, 8 St Mary’s St, Boston 02215, USA
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston 02215, USA
| | - Ichun Anderson Chen
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston 02215, USA
| | - Hui Wang
- Department of Radiology, Massachusetts General Hospital, A.A. Martinos Center for Biomedical Imaging, 13th Street, Boston 02129, USA
| |
Collapse
|
41
|
Wilkinson MGL, Moulding D, McDonnell TCR, Orford M, Wincup C, Ting JYJ, Otto GW, Restuadi R, Kelberman D, Papadopoulou C, Castellano S, Eaton S, Deakin CT, Rosser EC, Wedderburn LR. Role of CD14+ monocyte-derived oxidised mitochondrial DNA in the inflammatory interferon type 1 signature in juvenile dermatomyositis. Ann Rheum Dis 2023; 82:658-669. [PMID: 36564154 PMCID: PMC10176342 DOI: 10.1136/ard-2022-223469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/01/2022] [Indexed: 12/25/2022]
Abstract
OBJECTIVES To define the host mechanisms contributing to the pathological interferon (IFN) type 1 signature in Juvenile dermatomyositis (JDM). METHODS RNA-sequencing was performed on CD4+, CD8+, CD14+ and CD19+ cells sorted from pretreatment and on-treatment JDM (pretreatment n=10, on-treatment n=11) and age/sex-matched child healthy-control (CHC n=4) peripheral blood mononuclear cell (PBMC). Mitochondrial morphology and superoxide were assessed by fluorescence microscopy, cellular metabolism by 13C glucose uptake assays, and oxidised mitochondrial DNA (oxmtDNA) content by dot-blot. Healthy-control PBMC and JDM pretreatment PBMC were cultured with IFN-α, oxmtDNA, cGAS-inhibitor, TLR-9 antagonist and/or n-acetyl cysteine (NAC). IFN-stimulated gene (ISGs) expression was measured by qPCR. Total numbers of patient and controls for functional experiments, JDM n=82, total CHC n=35. RESULTS Dysregulated mitochondrial-associated gene expression correlated with increased ISG expression in JDM CD14+ monocytes. Altered mitochondrial-associated gene expression was paralleled by altered mitochondrial biology, including 'megamitochondria', cellular metabolism and a decrease in gene expression of superoxide dismutase (SOD)1. This was associated with enhanced production of oxidised mitochondrial (oxmt)DNA. OxmtDNA induced ISG expression in healthy PBMC, which was blocked by targeting oxidative stress and intracellular nucleic acid sensing pathways. Complementary experiments showed that, under in vitro experimental conditions, targeting these pathways via the antioxidant drug NAC, TLR9 antagonist and to a lesser extent cGAS-inhibitor, suppressed ISG expression in pretreatment JDM PBMC. CONCLUSIONS These results describe a novel pathway where altered mitochondrial biology in JDM CD14+ monocytes lead to oxmtDNA production and stimulates ISG expression. Targeting this pathway has therapeutical potential in JDM and other IFN type 1-driven autoimmune diseases.
Collapse
Affiliation(s)
- Meredyth G Ll Wilkinson
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| | - Dale Moulding
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Thomas C R McDonnell
- Centre for Rheumatology Research, Division of Medicine, University College London, London, UK
| | - Michael Orford
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Chris Wincup
- Centre for Rheumatology Research, Division of Medicine, University College London, London, UK
| | - Joanna Y J Ting
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Georg W Otto
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Experimental and Personalised Medicine, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
- Genetics and Genomic Medicine Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Restuadi Restuadi
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| | - Daniel Kelberman
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Experimental and Personalised Medicine, Genetics and Genomic Medicine, UCL Great Ormond Street Institute of Child Health, London, UK
- Genetics and Genomic Medicine Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Charalampia Papadopoulou
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Rheumatology, Great Ormond Street Hospital NHS Trust, London, UK
| | - Sergi Castellano
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Genetics and Genomic Medicine Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Simon Eaton
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
- Developmental Biology and Cancer Research & Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Claire T Deakin
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| | - Elizabeth C Rosser
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- Centre for Rheumatology Research, Division of Medicine, University College London, London, UK
| | - Lucy R Wedderburn
- Infection, Immunity and Inflammation Research and Teaching Department, UCL Great Ormond Street Institute of Child Health, London, UK
- Centre for Adolescent Rheumatology Versus Arthritis at UCL UCLH and GOSH, UCL, London, UK
- NIHR Biomedical Research Centre, Great Ormond Street Hospital, London, UK
| |
Collapse
|
42
|
Marchi E, Ramamurthy N, Ansari MA, Harrer CE, Barnes E, Klenerman P. Defining the key intrahepatic gene networks in HCV infection driven by sex. Gut 2023; 72:984-994. [PMID: 35613843 PMCID: PMC10086281 DOI: 10.1136/gutjnl-2021-326314] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/30/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE The transcriptional response in the liver during HCV infection is critical for determining clinical outcomes. This issue remains relatively unexplored as tissue access to address this at scale is usually limited. We aimed to profile the transcriptomics of HCV-infected livers to describe the expression networks involved and assess the effect on them of major predictors of clinical outcome such as IFNL4 (interferon lambda 4) host genotype and sex. DESIGN We took advantage of a large clinical study of HCV therapy accompanied by baseline liver biopsy to examine the drivers of transcription in tissue samples in 195 patients also genotyped genome-wide for host and viral single nucleotide polymorphisms. We addressed the role of host factors (disease status, sex, genotype, age) and viral factors (load, mutation) on transcriptional responses. RESULTS We observe key modules of transcription which can be impacted differentially by host and viral factors. Underlying cirrhotic state had the most substantial impact, even in a stable, compensated population. Notably, sex had a major impact on antiviral responses in concert with IL28B (interleukin 28B)/IFNL4 genotype, with stronger interferon and humoral responses in females. Males tended towards a dominant cellular immune response. In both sexes, there was a strong influence of the underlying host disease status and of specific viral mutations, and sex-specific expression quantitative trait loci were also observed. CONCLUSION These features help define the major influences on tissue responses in HCV infection, impacting on the response to treatment and with broader implications for responses in other sex-biased infections.
Collapse
Affiliation(s)
- Emanuele Marchi
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - M Azim Ansari
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Translational Gastroenterology Unit, University of Oxford, Oxford, UK
| |
Collapse
|
43
|
Brennan L, Brewster L, Lunn J, Egboko F, Pestotnik Stres D, Patel P, Isba R. How do hospitals address health inequalities experienced by children and young people: a grey literature scoping review protocol. BMJ Open 2023; 13:e071682. [PMID: 37105699 PMCID: PMC10151951 DOI: 10.1136/bmjopen-2023-071682] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
INTRODUCTION Health inequalities are unfair, systematic differences in health between people. In the UK, the Health and Social Care Act 2012 recognised health inequalities as a responsibility of the National Health Service (NHS). Health inequalities were foregrounded in the publication of 2019 NHS Long Term Plan and during the SARS-CoV-2/COVID-19 pandemic. Hospitals are well placed to address health inequalities through their role as anchor institutions. While many hospitals have begun to address inequalities, children are often overlooked or assumed to have the same needs as adult populations. This grey literature scoping review aims to identify, collate and present approaches taken by hospitals to address health inequalities in children and young people. METHODS AND ANALYSIS This scoping review will follow Joanna Briggs Institute guidance. A four-step approach to identifying grey literature will be used. Literature will be examined to identify approaches that aim to address health inequalities. Literature must describe the health inequality they aim to address and be initiated by the hospital. It will exclude literature not available in English and published before 2010. Two reviewers will independently review the results of the searches using the inclusion and exclusion criteria. Data will be extracted using a data extraction tool. Study findings will be presented in tabular form detailing the interventions identified. DISSEMINATION The review will synthesise information on worldwide hospital approaches to addressing child health inequalities. The findings will be used to inform guidelines for children's hospitals in the UK and will be disseminated through national and international professional bodies, conferences and research papers.
Collapse
Affiliation(s)
- Louise Brennan
- St Helens and Knowsley Teaching Hospitals NHS Trust, Prescot, UK
- Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Liz Brewster
- Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Judith Lunn
- Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Fiona Egboko
- Lancaster Medical School, Lancaster University, Lancaster, UK
| | | | - Pallavi Patel
- St Helens and Knowsley Teaching Hospitals NHS Trust, Prescot, UK
- Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Rachel Isba
- Lancaster Medical School, Lancaster University, Lancaster, UK
- Manchester University NHS Foundation Trust, Manchester, UK
| |
Collapse
|
44
|
Rankin DA, Peetluk LS, Deppen S, Slaughter JC, Katz S, Halasa NB, Khankari NK. Diagnostic models predicting paediatric viral acute respiratory infections: a systematic review. BMJ Open 2023; 13:e067878. [PMID: 37085296 PMCID: PMC10124282 DOI: 10.1136/bmjopen-2022-067878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/03/2023] [Indexed: 04/23/2023] Open
Abstract
OBJECTIVES To systematically review and evaluate diagnostic models used to predict viral acute respiratory infections (ARIs) in children. DESIGN Systematic review. DATA SOURCES PubMed and Embase were searched from 1 January 1975 to 3 February 2022. ELIGIBILITY CRITERIA We included diagnostic models predicting viral ARIs in children (<18 years) who sought medical attention from a healthcare setting and were written in English. Prediction model studies specific to SARS-CoV-2, COVID-19 or multisystem inflammatory syndrome in children were excluded. DATA EXTRACTION AND SYNTHESIS Study screening, data extraction and quality assessment were performed by two independent reviewers. Study characteristics, including population, methods and results, were extracted and evaluated for bias and applicability using the Checklist for Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modelling Studies and PROBAST (Prediction model Risk Of Bias Assessment Tool). RESULTS Of 7049 unique studies screened, 196 underwent full text review and 18 were included. The most common outcome was viral-specific influenza (n=7; 58%). Internal validation was performed in 8 studies (44%), 10 studies (56%) reported discrimination measures, 4 studies (22%) reported calibration measures and none performed external validation. According to PROBAST, a high risk of bias was identified in the analytic aspects in all studies. However, the existing studies had minimal bias concerns related to the study populations, inclusion and modelling of predictors, and outcome ascertainment. CONCLUSIONS Diagnostic prediction can aid clinicians in aetiological diagnoses of viral ARIs. External validation should be performed on rigorously internally validated models with populations intended for model application. PROSPERO REGISTRATION NUMBER CRD42022308917.
Collapse
Affiliation(s)
- Danielle A Rankin
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Epidemiology PhD Program, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Lauren S Peetluk
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Stephen Deppen
- Division of Epidemiology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Sophie Katz
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Natasha B Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Nikhil K Khankari
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| |
Collapse
|
45
|
Yuan J, Xu L, Chien CY, Yang Y, Yue Y, Fadera S, Stark AH, Schwetye KE, Nazeri A, Desai R, Athiraman U, Chaudhuri AA, Chen H, Leuthardt EC. First-in-human prospective trial of sonobiopsy in glioblastoma patients using neuronavigation-guided focused ultrasound. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.03.17.23287378. [PMID: 36993173 PMCID: PMC10055591 DOI: 10.1101/2023.03.17.23287378] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Sonobiopsy is an emerging technology that combines focused ultrasound (FUS) with microbubbles to enrich circulating brain disease-specific biomarkers for noninvasive molecular diagnosis of brain diseases. Here, we report the first-in-human prospective trial of sonobiopsy in glioblastoma patients to evaluate its feasibility and safety in enriching circulating tumor biomarkers. A nimble FUS device integrated with a clinical neuronavigation system was used to perform sonobiopsy following an established clinical workflow for neuronavigation. Analysis of blood samples collected before and after FUS sonication showed enhanced plasma circulating tumor biomarker levels. Histological analysis of surgically resected tumors confirmed the safety of the procedure. Transcriptome analysis of sonicated and unsonicated tumor tissues found that FUS sonication modulated cell physical structure-related genes but evoked minimal inflammatory response. These feasibility and safety data support the continued investigation of sonobiopsy for noninvasive molecular diagnosis of brain diseases.
Collapse
|
46
|
Janse van Mantgem MR, van Rheenen W, Hackeng AV, van Es MA, Veldink JH, van den Berg LH, van Eijk RPA. Association Between Serum Lipids and Survival in Patients With Amyotrophic Lateral Sclerosis: A Meta-analysis and Population-Based Study. Neurology 2023; 100:e1062-e1071. [PMID: 36460467 PMCID: PMC9990853 DOI: 10.1212/wnl.0000000000201657] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 10/20/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND AND OBJECTIVE To explore the association between lipids, polygenic profile scores (PPS) for biomarkers of lipid metabolism, markers of disease severity, and survival in patients with amyotrophic lateral sclerosis (ALS). METHODS We meta-analyzed the current literature on the prognostic value of lipids in patients with ALS. Subsequently, we evaluated the relationship between lipid levels at diagnosis, clinical disease stage, and survival in all consecutive patients diagnosed in the Netherlands. We determined the hazard ratio (HR) of each lipid for overall survival, defined as death from any cause. A subset of patients was matched to a previous genome-wide association study; data were used to calculate PPS for biomarkers of lipid metabolism and to determine the association between observed lipid levels at diagnosis and survival. RESULTS Meta-analysis of 4 studies indicated that none of the biomarkers of the lipid metabolism were statistically significantly associated with overall survival; there was, however, considerable heterogeneity between study results. Using individual patient data (N = 1,324), we found that increased high-density lipoprotein (HDL) cholesterol was associated with poorer survival (HR of 1.33 (95% CI 1.14-1.55, p < 0.001)). The correlation between BMI and HDL cholesterol (Pearson r -0.26, 95% CI -0.32 to -0.20) was negative and between BMI and triglycerides (TG) positive (Pearson r 0.18, 95% CI 0.12-0.24). Serum concentrations of total cholesterol and LDL cholesterol were lower in more advanced clinical stages (both p < 0.001). PPS for biomarkers of lipid metabolism explained 1.2%-13.1% of their variance at diagnosis. None of the PPS was significantly associated with survival (all p > 0.50). DISCUSSION Lipids may contain valuable information about disease severity and prognosis, but their main value may be driven as a consequence of disease progression. Our results underscore that gaining further insight into lipid metabolism and longitudinal data on serum concentrations of the lipid profile could improve the monitoring of patients and potentially further disentangle ALS pathogenesis.
Collapse
Affiliation(s)
- Mark R Janse van Mantgem
- From the Department of Neurology (M.R.J.M., W.R., A.V.H., M.A.E., J.H.V., L.H.B., R.P.A.E.), UMC Utrecht Brain Center, and Biostatistics & Research Support (R.P.A.E.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Wouter van Rheenen
- From the Department of Neurology (M.R.J.M., W.R., A.V.H., M.A.E., J.H.V., L.H.B., R.P.A.E.), UMC Utrecht Brain Center, and Biostatistics & Research Support (R.P.A.E.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Anemone V Hackeng
- From the Department of Neurology (M.R.J.M., W.R., A.V.H., M.A.E., J.H.V., L.H.B., R.P.A.E.), UMC Utrecht Brain Center, and Biostatistics & Research Support (R.P.A.E.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Michael A van Es
- From the Department of Neurology (M.R.J.M., W.R., A.V.H., M.A.E., J.H.V., L.H.B., R.P.A.E.), UMC Utrecht Brain Center, and Biostatistics & Research Support (R.P.A.E.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Jan H Veldink
- From the Department of Neurology (M.R.J.M., W.R., A.V.H., M.A.E., J.H.V., L.H.B., R.P.A.E.), UMC Utrecht Brain Center, and Biostatistics & Research Support (R.P.A.E.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| | - Leonard H van den Berg
- From the Department of Neurology (M.R.J.M., W.R., A.V.H., M.A.E., J.H.V., L.H.B., R.P.A.E.), UMC Utrecht Brain Center, and Biostatistics & Research Support (R.P.A.E.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands.
| | - Ruben P A van Eijk
- From the Department of Neurology (M.R.J.M., W.R., A.V.H., M.A.E., J.H.V., L.H.B., R.P.A.E.), UMC Utrecht Brain Center, and Biostatistics & Research Support (R.P.A.E.), Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, The Netherlands
| |
Collapse
|
47
|
Reddy Lekkala VK, Kang SY, Liu J, Shrestha S, Acharya P, Joshi P, Zolfaghar M, Lee M, Jamdagneya P, Pagnis S, Kundi A, Kabbur S, Kim UT, Yang Y, Lee MY. A pillar/perfusion plate enhances cell growth, reproducibility, throughput, and user friendliness in dynamic 3D cell culture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.16.528892. [PMID: 36824786 PMCID: PMC9949149 DOI: 10.1101/2023.02.16.528892] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2023]
Abstract
Static three-dimensional (3D) cell culture has been demonstrated in ultralow attachment well plates, hanging droplet plates, and microtiter well plates with hydrogels or magnetic nanoparticles. Although it is simple, reproducible, and relatively inexpensive, thus potentially used for high-throughput screening, statically cultured 3D cells often suffer from the necrotic core due to limited nutrient and oxygen diffusion and waste removal and have limited in vivo-like tissue structure. Here, we overcome these challenges by developing a pillar/perfusion plate platform and demonstrating high-throughput, dynamic 3D cell culture. Cell spheroids have been loaded on the pillar plate with hydrogel by simple sandwiching and encapsulation and cultured dynamically in the perfusion plate on a digital rocker. Unlike traditional microfluidic devices, fast flow rates were maintained within perfusion wells, and the pillar plate could be separated from the perfusion plate for cell-based assays. It was compatible with common lab equipment and allowed cell culture, testing, staining, and imaging in situ. The pillar/perfusion plate enhanced cell growth by rapid diffusion, reproducibility, assay throughput, and user friendliness in dynamic 3D cell culture.
Collapse
Affiliation(s)
| | - Soo-Yeon Kang
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Jiafeng Liu
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Sunil Shrestha
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Prabha Acharya
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | | | - Mona Zolfaghar
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Minseong Lee
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Paarth Jamdagneya
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Sohan Pagnis
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Arham Kundi
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Samarth Kabbur
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Ung Tae Kim
- Department of Civil and Environmental Engineering, Cleveland State University, Cleveland, Ohio
| | - Yong Yang
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
| | - Moo-Yeal Lee
- Department of Biomedical Engineering, University of North Texas, Denton, Texas
- Bioprinting Laboratories Inc., Denton, Texas
| |
Collapse
|
48
|
Ellis CA, Miller RL, Calhoun VD. Explainable Fuzzy Clustering Framework Reveals Divergent Default Mode Network Connectivity Dynamics in Schizophrenia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.13.528329. [PMID: 36824777 PMCID: PMC9949005 DOI: 10.1101/2023.02.13.528329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Dynamic functional network connectivity (dFNC) analysis of resting state functional magnetic resonance imaging data has yielded insights into many neurological and neuropsychiatric disorders. A common dFNC analysis approach uses hard clustering methods like k-means clustering to assign samples to states that summarize network dynamics. However, hard clustering methods obscure network dynamics by assuming (1) that all samples within a cluster are equally like their assigned centroids and (2) that samples closer to one another in the data space than to their centroids are well-represented by their centroids. In addition, it can be hard to compare subjects, as in some cases an individual may not manifest a state strongly enough to enter a hard cluster. Approaches that allow a dimensional approach to connectivity patterns (e.g., fuzzy clustering) can mitigate these issues. In this study, we present an explainable fuzzy clustering framework by combining fuzzy c-means clustering with several explainability metrics. We apply our framework for schizophrenia (SZ) default mode network analysis, identifying 5 states and characterizing those states with a new explainability approach. While also showing that features typically used in hard clustering can be extracted in our framework, we present a variety of unique features to quantify state dynamics and identify effects of SZ upon network dynamics. We further uncover relationships between symptom severity and interactions of the precuneus with the anterior and posterior cingulate cortex. Given the ease of implementing our framework and its enhanced insight into network dynamics, it has great potential for use in future dFNC studies.
Collapse
Affiliation(s)
- Charles A. Ellis
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science: Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, United States
| | - Robyn L. Miller
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science: Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, United States
- Department of Computer Science, Georgia State University, Atlanta, Georgia, United States
| | - Vince D. Calhoun
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States
- Tri-institutional Center for Translational Research in Neuroimaging and Data Science: Georgia State University, Georgia Institute of Technology, Emory University, Atlanta, Georgia, United States
- Department of Computer Science, Georgia State University, Atlanta, Georgia, United States
| |
Collapse
|
49
|
Gordon WE, Baek S, Nguyen HP, Kuo YM, Bradley R, Galazyuk A, Lee I, Ingala MR, Simmons NB, Schountz T, Cooper LN, Georgakopoulos-Soares I, Hemberg M, Ahituv N. Integrative single-cell characterization of frugivory adaptations in the bat kidney and pancreas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.12.528204. [PMID: 36824791 PMCID: PMC9949079 DOI: 10.1101/2023.02.12.528204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Frugivory evolved multiple times in mammals, including bats. However, the cellular and molecular components driving it remain largely unknown. Here, we used integrative single-cell sequencing on insectivorous and frugivorous bat kidneys and pancreases and identified key cell population, gene expression and regulatory element differences associated with frugivorous adaptation that also relate to human disease, particularly diabetes. We found an increase in collecting duct cells and differentially active genes and regulatory elements involved in fluid and electrolyte balance in the frugivore kidney. In the frugivorous pancreas, we observed an increase in endocrine and a decrease in exocrine cells and differences in genes and regulatory elements involved in insulin regulation. Combined, our work provides novel insights into frugivorous adaptation that also could be leveraged for therapeutic purposes.
Collapse
|
50
|
Andersen EB, Kristiansen M, Bernt Jørgensen SM. Barriers and facilitators to return to work following cardiovascular disease: a systematic review and meta-synthesis of qualitative research. BMJ Open 2023; 13:e069091. [PMID: 36707117 PMCID: PMC9884880 DOI: 10.1136/bmjopen-2022-069091] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVES Return to work is a key rehabilitation goal, however, people recovering from cardiovascular disease (CVD) often struggle with returning to work. The aim of this study was to conduct a systematic review and meta-synthesis of the existing qualitative evidence on barriers and facilitators to return to work experienced by people with CVD. METHODS A systematic literature search was conducted in PubMed, Embase, Web of Science, PsycINFO, Scopus and CINAHL in August 2022. The reference lists of the included articles were searched. The Critical Appraisal Skills Programme was used for quality appraisal and a meta-synthesis was employed. FINDINGS This review includes 15 studies of overall high methodological quality. Barriers covered four themes: physical limitations, psychological and relational factors, the working context and support within health and social care systems. Facilitators were related to five themes: return to normality, enhancing well-being, financial concerns, the working context and support within health and social care systems. CONCLUSION Our findings highlight that return to work following CVD is a complex process influenced by individual factors, as well as work-related factors, factors in the health and social care systems and social security policies and regulations. To improve return to work, this review illustrates a need for individualised, multidisciplinary and coordinated vocational rehabilitation programmes that accommodate potential barriers to re-employment. Similarly, this review highlights how vocational rehabilitation programmes should ensure individualised information and support early in the rehabilitation process, as well as the importance of engaging relevant stakeholders, such as employers, in making individualised return-to-work plans.
Collapse
Affiliation(s)
- Emma Borre Andersen
- Section of Cardiovascular Research, The Danish Heart Foundation, Copenhagen, Denmark
| | - Maria Kristiansen
- Department of Public Health & Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Sidsel Marie Bernt Jørgensen
- Section of Cardiovascular Research, The Danish Heart Foundation, Copenhagen, Denmark
- Department of Public Health & Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|