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1.
Diabetologia ; 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38967666

ABSTRACT

AIMS/HYPOTHESIS: Disruption of pancreatic islet function and glucose homeostasis can lead to the development of sustained hyperglycaemia, beta cell glucotoxicity and subsequently type 2 diabetes. In this study, we explored the effects of in vitro hyperglycaemic conditions on human pancreatic islet gene expression across 24 h in six pancreatic cell types: alpha; beta; gamma; delta; ductal; and acinar. We hypothesised that genes associated with hyperglycaemic conditions may be relevant to the onset and progression of diabetes. METHODS: We exposed human pancreatic islets from two donors to low (2.8 mmol/l) and high (15.0 mmol/l) glucose concentrations over 24 h in vitro. To assess the transcriptome, we performed single-cell RNA-seq (scRNA-seq) at seven time points. We modelled time as both a discrete and continuous variable to determine momentary and longitudinal changes in transcription associated with islet time in culture or glucose exposure. Additionally, we integrated genomic features and genetic summary statistics to nominate candidate effector genes. For three of these genes, we functionally characterised the effect on insulin production and secretion using CRISPR interference to knock down gene expression in EndoC-ßH1 cells, followed by a glucose-stimulated insulin secretion assay. RESULTS: In the discrete time models, we identified 1344 genes associated with time and 668 genes associated with glucose exposure across all cell types and time points. In the continuous time models, we identified 1311 genes associated with time, 345 genes associated with glucose exposure and 418 genes associated with interaction effects between time and glucose across all cell types. By integrating these expression profiles with summary statistics from genetic association studies, we identified 2449 candidate effector genes for type 2 diabetes, HbA1c, random blood glucose and fasting blood glucose. Of these candidate effector genes, we showed that three (ERO1B, HNRNPA2B1 and RHOBTB3) exhibited an effect on glucose-stimulated insulin production and secretion in EndoC-ßH1 cells. CONCLUSIONS/INTERPRETATION: The findings of our study provide an in-depth characterisation of the 24 h transcriptomic response of human pancreatic islets to glucose exposure at a single-cell resolution. By integrating differentially expressed genes with genetic signals for type 2 diabetes and glucose-related traits, we provide insights into the molecular mechanisms underlying glucose homeostasis. Finally, we provide functional evidence to support the role of three candidate effector genes in insulin secretion and production. DATA AVAILABILITY: The scRNA-seq data from the 24 h glucose exposure experiment performed in this study are available in the database of Genotypes and Phenotypes (dbGap; https://www.ncbi.nlm.nih.gov/gap/ ) with accession no. phs001188.v3.p1. Study metadata and summary statistics for the differential expression, gene set enrichment and candidate effector gene prediction analyses are available in the Zenodo data repository ( https://zenodo.org/ ) under accession number 11123248. The code used in this study is publicly available at https://github.com/CollinsLabBioComp/publication-islet_glucose_timecourse .

2.
Article in English | MEDLINE | ID: mdl-38965873

ABSTRACT

INTRODUCTION: Atrial remodelling (AR) is the persistent change in atrial structure and/or function and contributes to the initiation, maintenance and progression of atrial fibrillation (AF) in a reciprocal self-perpetuating relationship. Left atrial (LA) size, geometry, fibrosis, wall thickness (LAWT) and ejection fraction (LAEF) have all been shown to vary with pathological atrial remodelling. The association of these global remodelling markers with each other for differentiating structural phenotypes in AF is not well investigated. METHOD: Patients referred for first-time AF ablation and controls without AF were prospectively recruited to undergo cardiac computed tomographic angiography (CCTA) and magnetic resonance imaging (MRI) with 3D atrial late-gadolinium enhanced (LGE) sequences. LAWT, atrial myocardial mass, LA volume and sphericity were calculated from CT. Biplane LA EF and LA fibrosis burden were derived from atrial MRI. Results were compared between patients with AF and controls. RESULTS: Forty two AF patients (64.3% male, age 64.6 ± 10.2 years, CHA2DS2-VASc 2.48 ± 1.5, 69.0% paroxysmal AF, 31% persistent AF, LVEF 57.9 ± 10.5%) and 37 controls (64.9% male, age 56.6 ± 7.2, CHA2DS2-VASc 1.54 ± 1.1, LVEF 60.4 ± 4.9%) were recruited. Patients with AF had a significantly higher LAWT (1.45 ± 0.52 mm vs 1.12 ± 0.42 mm, p = 0.003), tissue mass (15.81 ± 6.53 g vs. 12.18 ± 5.01 g, p = 0.011), fibrosis burden (9.33 ± 8.35% vs 2.41 ± 3.60%, p = 0.013), left atrial size/volume (95.68 ± 26.63 mL vs 81.22 ± 20.64 mL, p = 0.011) and lower LAEF (50.3 ± 15.3% vs 65.2 ± 8.6%, p < 0.001) compared to controls. There was no significant correlation between % fibrosis with LAWT (p = 0.29), mass (p = 0.89), volume (p = 0.49) or sphericity (p = 0.79). LAWT had a statistically significant weak positive correlation with LA volume (r = 0.25, p = .041), but not with sphericity (p = 0.86). LAEF had a statistically significant but weak negative correlation with fibrosis (r = -0.33, p = 0.008) and LAWT (r = -0.24, p = 0.07). CONCLUSION: AF is associated with significant quantifiable structural changes that are evident in LA size, tissue thickness, total LA tissue mass and fibrosis. These individual remodelling markers do not or only weakly correlate with each other suggesting different remodelling subtypes exist (e.g. fibrotic vs hypertrophic vs dilated). If confirmed, such a detailed understanding of the structural changes observed has the potential to inform clinical management strategies targeting individual mechanisms underlying the disease process.

3.
J Surg Res ; 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38862305

ABSTRACT

INTRODUCTION: Lung cancer is consistently the leading cause of cancer death among women in the United States, yet lung cancer screening (LCS) rates remain low. By contrast, screening mammography rates are reliably high, suggesting that screening mammography can be a "teachable moment" to increase LCS uptake among dual-eligible women. MATERIALS AND METHODS: This is a prospective survey study conducted at two academic institutions. Patients undergoing screening mammography were evaluated for LCS eligibility and offered enrollment in a pilot dual-cancer screening program. A series of surveys was administered to characterize participants' knowledge, perceptions, and attitudes about LCS before and after undergoing dual screening. Data were descriptively summarized. RESULTS: Between August 2022 and July 2023, 54 LCS-eligible patients were enrolled. The study cohort was 100% female and predominantly White (81%), with a median age of 57 y and median of 36 pack-y of smoking. Survey results showed that 98% felt they were at risk for lung cancer, with most (80%) motivated by early detection of potential cancer. Regarding screening barriers, 58% of patients lacked knowledge about LCS eligibility and 47% reported concerns about screening cost. Prior to undergoing LCS, 87% of patients expressed interest in combined breast and lung screening. Encouragingly, after LCS, 84% were likely or very likely to undergo dual screening again and 93% found the shared decision-making visit helpful or very helpful. CONCLUSIONS: Pairing breast and LCS is a feasible, acceptable intervention that, along with increasing patient and provider education about LCS, can increase LCS uptake and reduce lung cancer mortality.

4.
Bioinform Adv ; 4(1): vbae085, 2024.
Article in English | MEDLINE | ID: mdl-38911824

ABSTRACT

Motivation: Pooled designs for single-cell RNA sequencing, where many cells from distinct samples are processed jointly, offer increased throughput and reduced batch variation. This study describes expression-aware demultiplexing (EAD), a computational method that employs differential co-expression patterns between individuals to demultiplex pooled samples without any extra experimental steps. Results: We use synthetic sample pools and show that the top interindividual differentially co-expressed genes provide a distinct cluster of cells per individual, significantly enriching the regulation of metabolism. Our application of EAD to samples of six isogenic inbred mice demonstrated that controlling genetic and environmental effects can solve interindividual variations related to metabolic pathways. We utilized 30 samples from both sepsis and healthy individuals in six batches to assess the performance of classification approaches. The results indicate that combining genetic and EAD results can enhance the accuracy of assignments (Min. 0.94, Mean 0.98, Max. 1). The results were enhanced by an average of 1.4% when EAD and barcoding techniques were combined (Min. 1.25%, Median 1.33%, Max. 1.74%). Furthermore, we demonstrate that interindividual differential co-expression analysis within the same cell type can be used to identify cells from the same donor in different activation states. By analysing single-nuclei transcriptome profiles from the brain, we demonstrate that our method can be applied to nonimmune cells. Availability and implementation: EAD workflow is available at https://isarnassiri.github.io/scDIV/ as an R package called scDIV (acronym for single-cell RNA-sequencing data demultiplexing using interindividual variations).

5.
EMBO Rep ; 25(7): 3064-3089, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38866980

ABSTRACT

Type I interferons (IFN-I) are implicated in exacerbation of tuberculosis (TB), but the mechanisms are unclear. Mouse macrophages infected with Mycobacterium tuberculosis (Mtb) produce IFN-I, which contributes to their death. Here we investigate whether the same is true for human monocyte-derived macrophages (MDM). MDM prepared by a conventional method markedly upregulate interferon-stimulated genes (ISGs) upon Mtb infection, while MDM prepared to better restrict Mtb do so much less. A mixture of antibodies inhibiting IFN-I signaling prevents ISG induction. Surprisingly, secreted IFN-I are undetectable until nearly two days after ISG induction. These same antibodies do not diminish Mtb-infected MDM death. MDM induce ISGs in response to picogram/mL levels of exogenous IFN-I while depleting similar quantities from the medium. Exogenous IFN-I increase the proportion of dead MDM. We speculate that Mtb-infected MDM produce and respond to minute levels of IFN-I, and that only some of the resultant signaling is susceptible to neutralizing antibodies. Many types of cells may secrete IFN-I in patients with TB, where IFN-I is likely to promote the death of infected macrophages.


Subject(s)
Cell Death , Interferon Type I , Macrophages , Mycobacterium tuberculosis , Humans , Mycobacterium tuberculosis/immunology , Mycobacterium tuberculosis/pathogenicity , Macrophages/microbiology , Macrophages/metabolism , Macrophages/immunology , Interferon Type I/metabolism , Signal Transduction , Tuberculosis/microbiology , Tuberculosis/immunology , Tuberculosis/metabolism , Animals , Mice , Cells, Cultured
6.
Mol Genet Metab ; 142(2): 108488, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38735264

ABSTRACT

INTRODUCTION: Fucokinase deficiency-related congenital disorder of glycosylation (FCSK-CDG) is a rare autosomal recessive inborn error of metabolism characterized by a decreased flux through the salvage pathway of GDP-fucose biosynthesis due to a block in the recycling of L-fucose that exits the lysosome. FCSK-CDG has been described in 5 individuals to date in the medical literature, with a phenotype comprising global developmental delays/intellectual disability, hypotonia, abnormal myelination, posterior ocular disease, growth and feeding failure, immune deficiency, and chronic diarrhea, without clear therapeutic recommendations. PATIENT AND METHODS: In a so far unreported FCSK-CDG patient, we studied proteomics and glycoproteomics in vitro in patient-derived fibroblasts and also performed in vivo glycomics, before and after treatment with either D-Mannose or L-Fucose. RESULTS: We observed a marked increase in fucosylation after D-mannose supplementation in fibroblasts compared to treatment with L-Fucose. The patient was then treated with D-mannose at 850 mg/kg/d, with resolution of the chronic diarrhea, resolution of oral aversion, improved weight gain, and observed developmental gains. Serum N-glycan profiles showed an improvement in the abundance of fucosylated glycans after treatment. No treatment-attributed adverse effects were observed. CONCLUSION: D-mannose is a promising new treatment for FCSK-CDG.


Subject(s)
Congenital Disorders of Glycosylation , Fibroblasts , Mannose , Humans , Congenital Disorders of Glycosylation/drug therapy , Congenital Disorders of Glycosylation/genetics , Congenital Disorders of Glycosylation/pathology , Congenital Disorders of Glycosylation/metabolism , Mannose/metabolism , Fibroblasts/metabolism , Fibroblasts/drug effects , Male , Fucose/metabolism , Glycosylation/drug effects , Phosphotransferases (Alcohol Group Acceptor)/genetics , Phosphotransferases (Alcohol Group Acceptor)/metabolism , Female , Proteomics
7.
JTO Clin Res Rep ; 5(6): 100671, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38799132

ABSTRACT

Introduction: The screening mammogram could be a "teachable moment" to improve lung cancer screening (LCS) uptake. The aim of our project was to combine patient self-referral with eligibility identification by providers as a two-pronged approach to increase rates of LCS among eligible women. Methods: LCS education materials were created to stimulate patient education and encourage self-referral. Chart review of patients scheduled for screening mammography was performed to identify patients who met LCS criteria. The primary outcome was rate of acceptance of targeted interventions as measured by qualitative survey material and rate of LCS uptake. Results: Between August 2022 and August 2023, 116 patients were identified by providers for potential eligibility for LCS and 34 patients (29.3%) deemed eligible based on the U.S. Preventative Services Task Force 2021 guidelines. There were 19 patients (56%) who completed LCS with three patients (16%) with screen-detected nodules that led to further workup. Post-implementation qualitative survey results reveal that 100% of the participants rated their shared decision-making visit experience as "very helpful" and 67% responded "very likely" to seek simultaneous breast and LCS in the future. Informational materials were rated as 80% favorable among all respondents; however, the rate of self-referral alone was 0%. The combined rates of eligible patients lost to follow-up or refusal was 24%. Conclusion: The self-referral aspect of the intervention revealed that patients are unlikely to self-refer for LCS. Nevertheless, patients undergoing screening mammograms individually identified for LCS were very responsive to learning more about dual screening.

8.
Int J Pharm X ; 7: 100254, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38774112

ABSTRACT

Zileuton is a leukotriene inhibitor used to treat asthma. As a BCS class II drug it exhibits challenges with solubility which likely impact its absorption. As patient gender significantly impacts the pharmacokinetics of many drugs, this study aimed to investigate potential gender-based pharmacokinetic differences after oral zileuton administration in rats. Male and female Sprague Dawley rats received single oral gavage doses of pure zileuton as an active pharmaceutical ingredient (30 mg/kg body weight (bw)), physical mixture (PM; at 30 mg/kg bw of the formulation contains zileuton, kollidon VA64 fine, dowfax2A1 and trehalose), and nanocrystalline formulation of zileuton (NfZ; at 30 mg/kg bw of the formulation). Plasma, tissue, and urine concentrations were quantified using high performance liquid chromatography (HPLC). Noncompartmental pharmacokinetic analysis showed higher zileuton levels in the plasma of female versus male rats across all evaluated forms of zileuton (API, PM, and NfZ). Female rats demonstrated higher peak plasma concentrations (Cmax) and increased area under the plasma concentration-time curve (AUC) relative to males, regardless of formulation. These findings reveal substantial gender disparities in the pharmacokinetics of zileuton in the rat model. This study emphasizes the critical need to evaluate gender differences during preclinical drug development to enable gender-based precision dosing strategies for equivalent efficacy/safety outcomes in male and female patients. Additional studies are warranted to investigate underlying mechanisms of such pharmacokinetic gender divergences.

9.
Front Cardiovasc Med ; 11: 1359715, 2024.
Article in English | MEDLINE | ID: mdl-38596691

ABSTRACT

Background: A reduced left atrial (LA) strain correlates with the presence of atrial fibrillation (AF). Conventional atrial strain analysis uses two-dimensional (2D) imaging, which is, however, limited by atrial foreshortening and an underestimation of through-plane motion. Retrospective gated computed tomography (RGCT) produces high-fidelity three-dimensional (3D) images of the cardiac anatomy throughout the cardiac cycle that can be used for estimating 3D mechanics. Its feasibility for LA strain measurement, however, is understudied. Aim: The aim of this study is to develop and apply a novel workflow to estimate 3D LA motion and calculate the strain from RGCT imaging. The utility of global and regional strains to separate heart failure in patients with reduced ejection fraction (HFrEF) with and without AF is investigated. Methods: A cohort of 30 HFrEF patients with (n = 9) and without (n = 21) AF underwent RGCT prior to cardiac resynchronisation therapy. The temporal sparse free form deformation image registration method was optimised for LA feature tracking in RGCT images and used to estimate 3D LA endocardial motion. The area and fibre reservoir strains were calculated over the LA body. Universal atrial coordinates and a human atrial fibre atlas enabled the regional strain calculation and the fibre strain calculation along the local myofibre orientation, respectively. Results: It was found that global reservoir strains were significantly reduced in the HFrEF + AF group patients compared with the HFrEF-only group patients (area strain: 11.2 ± 4.8% vs. 25.3 ± 12.6%, P = 0.001; fibre strain: 4.5 ± 2.0% vs. 15.2 ± 8.8%, P = 0.001), with HFrEF + AF patients having a greater regional reservoir strain dyssynchrony. All regional reservoir strains were reduced in the HFrEF + AF patient group, in whom the inferior wall strains exhibited the most significant differences. The global reservoir fibre strain and LA volume + posterior wall reservoir fibre strain exceeded LA volume alone and 2D global longitudinal strain (GLS) for AF classification (area-under-the-curve: global reservoir fibre strain: 0.94 ± 0.02, LA volume + posterior wall reservoir fibre strain: 0.95 ± 0.02, LA volume: 0.89 ± 0.03, 2D GLS: 0.90 ± 0.03). Conclusion: RGCT enables 3D LA motion estimation and strain calculation that outperforms 2D strain metrics and LA enlargement for AF classification. Differences in regional LA strain could reflect regional myocardial properties such as atrial fibrosis burden.

10.
Child Dev ; 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38664925

ABSTRACT

Parental chronic pain is associated with adverse outcomes in children, but the mechanisms of transmission are largely untested. Mothers with chronic pain (N = 400, Mage = 40.3 years, 90.5% White) and their children (Mage = 10.33 years, 83.3% White, 50.2% female) were recruited in 2016-2018 to test longitudinal pathways of risk transmission from maternal chronic pain to children's psychological symptoms, examining roles of parenting, maternal depression, and child distress tolerance. Maternal pain was associated with positive (ß = .28) and pain-specific (ß = .10) parenting behaviors. Maternal depression was associated with lower child distress tolerance (ß = -.03), which was associated with greater child psychological symptoms (ß = -.62). Parenting and maternal pain were not prospectively associated with child outcomes. When considering the dual-generational impacts of chronic pain, physical and psychological functioning should be examined.

11.
J Vasc Surg ; 79(5): 1264-1265, 2024 May.
Article in English | MEDLINE | ID: mdl-38642972
12.
Cell Res ; 34(3): 245-257, 2024 03.
Article in English | MEDLINE | ID: mdl-38302740

ABSTRACT

Mutations in the orphan transporter MFSD7c (also known as Flvcr2), are linked to Fowler syndrome. Here, we used Mfsd7c knockout (Mfsd7c-/-) mice and cell-based assays to reveal that MFSD7c is a choline transporter at the blood-brain barrier (BBB). We performed comprehensive metabolomics analysis and detected differential changes of metabolites in the brains and livers of Mfsd7c-/-embryos. Particularly, we found that choline-related metabolites were altered in the brains but not in the livers of Mfsd7c-/- embryos. Thus, we hypothesized that MFSD7c regulates the level of choline in the brain. Indeed, expression of human MFSD7c in cells significantly increased choline uptake. Interestingly, we showed that choline uptake by MFSD7c is greatly increased by choline-metabolizing enzymes, leading us to demonstrate that MFSD7c is a facilitative transporter of choline. Furthermore, single-cell patch clamp analysis showed that the import of choline by MFSD7c is electrogenic. Choline transport function of MFSD7c was shown to be conserved in vertebrates, but not in yeasts. We demonstrated that human MFSD7c is a functional ortholog of HNM1, the yeast choline importer. We also showed that several missense mutations identified in patients exhibiting Fowler syndrome had abolished or reduced choline transport activity. Mice lacking Mfsd7c in endothelial cells of the central nervous system suppressed the import of exogenous choline from blood but unexpectedly had increased choline levels in the brain. Stable-isotope tracing study revealed that MFSD7c was required for exporting choline derived from lysophosphatidylcholine in the brain. Collectively, our work identifies MFSD7c as a choline exporter at the BBB and provides a foundation for future work to reveal the disease mechanisms of Fowler syndrome.


Subject(s)
Blood-Brain Barrier , Endothelial Cells , Polycystic Ovary Syndrome , Urination Disorders , Animals , Humans , Mice , Biological Transport , Brain , Choline
13.
Medicina (Kaunas) ; 60(2)2024 Feb 10.
Article in English | MEDLINE | ID: mdl-38399593

ABSTRACT

Background and Objectives: The surge in breast-related surgeries in Korea underscores the critical need for an accurate early diagnosis of silicone breast implant-related issues. Complications such as BIA-ALCL and BIA-SCC add complexity to breast health concerns, necessitating vigilant monitoring. Despite advancements, discrepancies persist between ultrasonographic and pathologic classifications of silicone implant ruptures, highlighting a need for enhanced diagnostic tools. This study explores the reliability of ultrasonography in diagnosing silicone breast implant ruptures and determining the extent of silicone migration, specifically with a focus on guiding potential capsulectomy based on pathology. Materials and Methods: A comprehensive review of medical records encompassing 5557 breast implants across 2790 patients who underwent ultrasound-assisted examinations was conducted. Among the screened implants, 8.9% (249 cases) were diagnosed with silicone breast implant rupture through ultrasonography. Subsequently, 89 women underwent revisional surgery, involving capsulectomy. The pathological analysis of 111 periprosthetic capsules from these cases aimed to assess the extent of silicone migration, and the findings were juxtaposed with the existing ultrasonographic rupture classification. Results: The diagnostic agreement between preoperative sonography and postoperative findings reached 100% for silicone breast implant ruptures. All eighty prosthetic capsules exhibiting a snowstorm sign in ultrasonography demonstrated silicone migration to capsules upon pathologic findings. Conclusions: High-resolution ultrasonography emerged as a valuable and reliable imaging modality for diagnosing silicone breast implant ruptures, with a notable ability to ascertain the extent of free silicone migration to capsules. This diagnostic precision is pivotal in informing decisions about potential capsulectomy during revisional surgery. The study advocates for an update to the current binary ultrasonographic classification, suggesting a more nuanced categorization into three types (subcapsular, intracapsular, and extracapsular) based on pathology.


Subject(s)
Breast Implants , Female , Humans , Breast Implants/adverse effects , Silicones/adverse effects , Point-of-Care Systems , Reproducibility of Results , Prosthesis Failure , Ultrasonography , Rupture , Magnetic Resonance Imaging/methods
14.
Nat Commun ; 15(1): 1394, 2024 Feb 19.
Article in English | MEDLINE | ID: mdl-38374174

ABSTRACT

Frozen shoulder is a spontaneously self-resolving chronic inflammatory fibrotic human disease, which distinguishes the condition from most fibrotic diseases that are progressive and irreversible. Using single-cell analysis, we identify pro-inflammatory MERTKlowCD48+ macrophages and MERTK + LYVE1 + MRC1+ macrophages enriched for negative regulators of inflammation which co-exist in frozen shoulder capsule tissues. Micro-cultures of patient-derived cells identify integrin-mediated cell-matrix interactions between MERTK+ macrophages and pro-resolving DKK3+ and POSTN+ fibroblasts, suggesting that matrix remodelling plays a role in frozen shoulder resolution. Cross-tissue analysis reveals a shared gene expression cassette between shoulder capsule MERTK+ macrophages and a respective population enriched in synovial tissues of rheumatoid arthritis patients in disease remission, supporting the concept that MERTK+ macrophages mediate resolution of inflammation and fibrosis. Single-cell transcriptomic profiling and spatial analysis of human foetal shoulder tissues identify MERTK + LYVE1 + MRC1+ macrophages and DKK3+ and POSTN+ fibroblast populations analogous to those in frozen shoulder, suggesting that the template to resolve fibrosis is established during shoulder development. Crosstalk between MerTK+ macrophages and pro-resolving DKK3+ and POSTN+ fibroblasts could facilitate resolution of frozen shoulder, providing a basis for potential therapeutic resolution of persistent fibrotic diseases.


Subject(s)
Bursitis , Humans , c-Mer Tyrosine Kinase/metabolism , Inflammation/metabolism , Synovial Membrane/metabolism , Fibrosis
15.
CRISPR J ; 7(1): 53-67, 2024 02.
Article in English | MEDLINE | ID: mdl-38353623

ABSTRACT

We developed an efficient CRISPR prime editing protocol and generated isogenic-induced pluripotent stem cell (iPSC) lines carrying heterozygous or homozygous alleles for putatively causal single nucleotide variants at six type 2 diabetes loci (ABCC8, MTNR1B, TCF7L2, HNF4A, CAMK1D, and GCK). Our two-step sequence-based approach to first identify transfected cell pools with the highest fraction of edited cells significantly reduced the downstream efforts to isolate single clones of edited cells. We found that prime editing can make targeted genetic changes in iPSC and optimization of system components and guide RNA designs that were critical to achieve acceptable efficiency. Systems utilizing PEmax, epegRNA modifications, and MLH1dn provided significant benefit, producing editing efficiencies of 36-73%. Editing success and pegRNA design optimization required for each variant differed depending on the sequence at the target site. With attention to design, prime editing is a promising approach to generate isogenic iPSC lines, enabling the study of specific genetic changes in a common genetic background.


Subject(s)
Diabetes Mellitus, Type 2 , Induced Pluripotent Stem Cells , Humans , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , CRISPR-Cas Systems/genetics , Gene Editing , RNA, Guide, CRISPR-Cas Systems
16.
EClinicalMedicine ; 69: 102461, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38374968

ABSTRACT

Background: The Paediatric Difficult Intubation Collaborative identified multiple attempts and persistence with direct laryngoscopy as risk factors for complications in children with difficult tracheal intubations and subsequently engaged in initiatives to reduce repeated attempts and persistence with direct laryngoscopy in children. We hypothesised these efforts would lead to fewer attempts, fewer direct laryngoscopy attempts and decrease complications. Methods: Paediatric patients less than 18 years of age with difficult direct laryngoscopy were enrolled in the Paediatric Difficult Intubation Registry. We define patients with difficult direct laryngoscopy as those in whom (1) an attending or consultant obtained a Cormack Lehane Grade 3 or 4 view on direct laryngoscopy, (2) limited mouth opening makes direct laryngoscopy impossible, (3) direct laryngoscopy failed in the preceding 6 months, and (4) direct laryngoscopy was deferred due to perceived risk of harm or poor chance of success. We used a 5:1 propensity score match to compare an early cohort from the initial Paediatric Difficult Intubation Registry analysis (August 6, 2012-January 31, 2015, 785 patients, 13 centres) and a current cohort from the Registry (March 4, 2017-March 31, 2023, 3925 patients, 43 centres). The primary outcome was first attempt success rate between cohorts. Success was defined as confirmed endotracheal intubation and assessed by the treating clinician. Secondary outcomes were eventual success rate, number of attempts at intubation, number of attempts with direct laryngoscopy, the incidence of persistence with direct laryngoscopy, use of supplemental oxygen, all complications, and severe complications. Findings: First-attempt success rate was higher in the current cohort (42% vs 32%, OR 1.5 95% CI 1.3-1.8, p < 0.001). In the current cohort, there were fewer attempts (2.2 current vs 2.7 early, regression coefficient -0.5 95% CI -0.6 to -0.4, p < 0.001), fewer attempts with direct laryngoscopy (0.6 current vs 1.0 early, regression coefficient -0.4 95% CI -0.4 to 0.3, p < 0.001), and reduced persistence with direct laryngoscopy beyond two attempts (7.3% current vs 14.1% early, OR 0.5 95% CI 0.4-0.6, p < 0.001). Overall complication rates were similar between cohorts (19% current vs 20% early). Severe complications decreased to 1.8% in the current cohort from 3.2% in the early cohort (OR 0.55 95% CI 0.35-0.87, p = 0.011). Cardiac arrests decreased to 0.8% in the current cohort from 1.8% in the early cohort. We identified persistence with direct laryngoscopy as a potentially modifiable factor associated with severe complications. Interpretation: In the current cohort, children with difficult tracheal intubations underwent fewer intubation attempts, fewer attempts with direct laryngoscopy, and had a nearly 50% reduction in severe complications. As persistence with direct laryngoscopy continues to be associated with severe complications, efforts to limit direct laryngoscopy and promote rapid transition to advanced techniques may enhance patient safety. Funding: None.

17.
J Osteopath Med ; 124(5): 219-230, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38197301

ABSTRACT

CONTEXT: The evidence for the efficacy of osteopathic manipulative treatment (OMT) in the management of low back pain (LBP) is considered weak by systematic reviews, because it is generally based on low-quality studies. Consequently, there is a need for more randomized controlled trials (RCTs) with a low risk of bias. OBJECTIVES: The objective of this study is to evaluate the efficacy of an OMT intervention for reducing pain and disability in patients with chronic LBP. METHODS: A single-blinded, crossover, RCT was conducted at a university-based health system. Participants were adults, 21-65 years old, with nonspecific LBP. Eligible participants (n=80) were randomized to two trial arms: an immediate OMT intervention group and a delayed OMT (waiting period) group. The intervention consisted of three to four OMT sessions over 4-6 weeks, after which the participants switched (crossed-over) groups. The primary clinical outcomes were average pain, current pain, Patient-Reported Outcomes Measurement Information System (PROMIS) 29 v1.0 pain interference and physical function, and modified Oswestry Disability Index (ODI). Secondary outcomes included the remaining PROMIS health domains and the Fear Avoidance Beliefs Questionnaire (FABQ). These measures were taken at baseline (T0), after one OMT session (T1), at the crossover point (T2), and at the end of the trial (T3). Due to the carryover effects of OMT intervention, only the outcomes obtained prior to T2 were evaluated utilizing mixed-effects models and after adjusting for baseline values. RESULTS: Totals of 35 and 36 participants with chronic LBP were available for the analysis at T1 in the immediate OMT and waiting period groups, respectively, whereas 31 and 33 participants were available for the analysis at T2 in the immediate OMT and waiting period groups, respectively. After one session of OMT (T1), the analysis showed a significant reduction in the secondary outcomes of sleep disturbance and anxiety compared to the waiting period group. Following the entire intervention period (T2), the immediate OMT group demonstrated a significantly better average pain outcome. The effect size was a 0.8 standard deviation (SD), rendering the reduction in pain clinically significant. Further, the improvement in anxiety remained statistically significant. No study-related serious adverse events (AEs) were reported. CONCLUSIONS: OMT intervention is safe and effective in reducing pain along with improving sleep and anxiety profiles in patients with chronic LBP.

18.
Child Neuropsychol ; : 1-13, 2024 Jan 12.
Article in English | MEDLINE | ID: mdl-38214531

ABSTRACT

Social-emotional difficulties are common sequelae of traumatic brain injury (TBI). Children who have experienced inflicted TBI (iTBI) may be at increased risk for social-emotional problems due to the risk factors associated with both early neurologic injury and with child maltreatment. We characterized the associations among injury severity, caregiver type (i.e., biological parents, non-kinship, kinship), and child social-emotional functioning in 41 infants and young children who had sustained iTBI and were seen in a large, regional children's hospital. This study was a retrospective analysis, utilizing data collected from the medical record as part of routine clinical care. Social-emotional functioning was assessed with the Bayley Scales of Infant and Toddler Development-Third Edition. Children with more severe injuries were rated as having worse social-emotional functioning. Caregiver type was associated with child social-emotional scores, above and beyond injury and demographic predictors. Biological parents were more likely to report better social-emotional skills than non-kinship caregivers, with the pattern of results suggesting that rater bias plays a role in this difference. In order to ensure that children are accurately identified for supports, these relationships should be considered when interpreting caregiver report of social-emotional skills.

19.
JMIR Ment Health ; 11: e50150, 2024 Jan 25.
Article in English | MEDLINE | ID: mdl-38271138

ABSTRACT

BACKGROUND: Health care providers and health-related researchers face significant challenges when applying sentiment analysis tools to health-related free-text survey data. Most state-of-the-art applications were developed in domains such as social media, and their performance in the health care context remains relatively unknown. Moreover, existing studies indicate that these tools often lack accuracy and produce inconsistent results. OBJECTIVE: This study aims to address the lack of comparative analysis on sentiment analysis tools applied to health-related free-text survey data in the context of COVID-19. The objective was to automatically predict sentence sentiment for 2 independent COVID-19 survey data sets from the National Institutes of Health and Stanford University. METHODS: Gold standard labels were created for a subset of each data set using a panel of human raters. We compared 8 state-of-the-art sentiment analysis tools on both data sets to evaluate variability and disagreement across tools. In addition, few-shot learning was explored by fine-tuning Open Pre-Trained Transformers (OPT; a large language model [LLM] with publicly available weights) using a small annotated subset and zero-shot learning using ChatGPT (an LLM without available weights). RESULTS: The comparison of sentiment analysis tools revealed high variability and disagreement across the evaluated tools when applied to health-related survey data. OPT and ChatGPT demonstrated superior performance, outperforming all other sentiment analysis tools. Moreover, ChatGPT outperformed OPT, exhibited higher accuracy by 6% and higher F-measure by 4% to 7%. CONCLUSIONS: This study demonstrates the effectiveness of LLMs, particularly the few-shot learning and zero-shot learning approaches, in the sentiment analysis of health-related survey data. These results have implications for saving human labor and improving efficiency in sentiment analysis tasks, contributing to advancements in the field of automated sentiment analysis.


Subject(s)
COVID-19 , Sentiment Analysis , United States/epidemiology , Humans , COVID-19/epidemiology , Health Surveys , Learning , Dissent and Disputes
20.
J Vasc Surg ; 79(3): 478-484, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37925040

ABSTRACT

OBJECTIVE: Spinal cord ischemia (SCI) with paraplegia or paraparesis is a devastating complication of complex aortic repair (CAR). Treatment includes cerebrospinal fluid drainage, maintenance of hemoglobin concentration (>10 g/L), and elevating mean arterial blood pressure. Animal and human case series have reported improvements in SCI outcomes with hyperbaric oxygen therapy (HBOT). We reviewed our center's experience with HBOT as a rescue treatment for spinal cord ischemia post-CAR in addition to standard treatment. METHODS: A retrospective review of the University Health Network's Hyperbaric Medicine Unit treatment database identified HBOT sessions for patients with SCI post-CAR between January 2013 and June 2021. Mean estimates of overall motor function scores were determined for postoperative, pre-HBOT, post-HBOT (within 4 hours of the final HBOT session), and at the final assessment (last available in-hospital evaluation) using a linear mixed model. A subgroup analysis compared the mean estimates of overall motor function scores between improvement and non-improvement groups at given timepoints. Improvement of motor function was defined as either a ≥2 point increase in overall muscle function score in patients with paraparesis or an upward change in motor deficit categorization (para/monoplegia, paraparesis, and no deficit). Subgroup analysis was performed by stratifying by improvement or non-improvement of motor function from pre-HBOT to final evaluation. RESULTS: Thirty patients were treated for SCI. Pre-HBOT, the motor deficit categorization was 10 paraplegia, three monoplegia, 16 paraparesis, and one unable to assess. At the final assessment, 14 patients demonstrated variable degrees of motor function improvement; eight patients demonstrated full motor function recovery. Seven of the 10 patients with paraplegia remained paraplegic despite HBOT. The estimated mean of overall muscle function score for pre-HBOT was 16.6 ± 2.9 (95% confidence interval [CI], 10.9-22.3) and for final assessment was 23.4 ± 2.9 (95% CI, 17.7-29.1). The estimated mean difference between pre-HBOT and final assessment overall muscle function score was 6.7 ± 3.1 (95% CI, 0.6-16.1). The estimated mean difference of the overall muscle function score between pre-HBOT and final assessment for the improved group was 16.6 ± 3.5 (95% CI, 7.5-25.7) vs -4.9 ± 4.2 (95% CI, -16.0 to 6.2) for the non-improved group. CONCLUSIONS: HBOT, in addition to standard treatment, may potentially improve recovery in spinal cord function following SCI post-CAR. However, the potential benefits of HBOT are not equally distributed among subgroups.


Subject(s)
Aortic Aneurysm, Thoracic , Hyperbaric Oxygenation , Spinal Cord Ischemia , Humans , Aortic Aneurysm, Thoracic/surgery , Hemiplegia/complications , Hemiplegia/therapy , Paraparesis/etiology , Paraplegia/diagnosis , Paraplegia/etiology , Paraplegia/therapy , Spinal Cord , Spinal Cord Ischemia/diagnosis , Spinal Cord Ischemia/etiology , Spinal Cord Ischemia/therapy , Treatment Outcome
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