Recent Publications by CFE Educators

Recent Published articles, books, and other scholarship by Academy members, CFE Education Scientists, and CFE Faculty.
Single Cell Transcriptome and Surface Epitope Analysis of Ankylosing Spondylitis Facilitates Disease Classification by Machine Learning.
2022
Authors: Alber S, Kumar S, Liu J, Huang ZM, Paez D, Hong J, Chang HW, Bhutani T, Gensler LS, Liao W
Ankylosing spondylitis (AS) is an immune-mediated inflammatory disorder that primarily affects the axial skeleton, especially the sacroiliac joints and spine. This results in chronic back pain and, in extreme cases, ankylosis of the spine. Despite its debilitating effects, the pathogenesis of AS remains to be further elucidated. This study used single cell CITE-seq technology to analyze peripheral blood mononuclear cells (PBMCs) in AS and in healthy controls. We identified a number of molecular features associated with AS. CD52 was found to be overexpressed in both RNA and surface protein expression across several cell types in patients with AS. CD16 monocytes overexpressed and IL-18Rα in AS, while CD8 T cells and natural killer cells overexpressed genes linked with cytotoxicity, including , and . Tregs underexpressed CD39 in AS, suggesting reduced functionality. We identified an overrepresented NK cell subset in AS that overexpressed CD16, CD161, and CD38, as well as cytotoxic genes and pathways. Finally, we developed machine learning models derived from CITE-seq data for the classification of AS and achieved an Area Under the Receiver Operating Characteristic (AUROC) curve of > 0.95. In summary, CITE-seq identification of AS-associated genes and surface proteins in specific cell subsets informs our understanding of pathogenesis and potential new therapeutic targets, while providing new approaches for diagnosis machine learning.
View on PubMedThree-dimensional morphologic changes in the temporomandibular joint in asymptomatic patients who undergo orthodontic treatment: A systematic review.
2022
Authors: Rustia S, Lam J, Tahir P, Kharafi LA, Oberoi S, Ganguly R
OBJECTIVE
This systematic review aimed to summarize the morphologic changes in the temporomandibular joint (TMJ) in patients who underwent orthodontic treatment and were assessed by 3-dimensional (3D) imaging techniques (e.g., magnetic resonance imaging, cone beam computed tomography, and multidetector computed tomography).
STUDY DESIGN
The authors searched PubMed, Web of Science, and Embase databases to identify original articles from 2014 to 2021 containing keywords for morphologic changes in the TMJ, orthodontic treatment, and three-dimensional imaging methods. Prospective and retrospective studies, including observational, cross-sectional, randomized, and nonrandomized clinical trials, cohort studies, and case-control studies, were reviewed. The review was conducted in accordance with PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. The risk of bias was assessed in studies selected for the full-text review.
RESULTS
The search strategy yielded 294 publications. After an initial screening and the application of exclusion criteria, 13 studies were selected for the final review.
CONCLUSION
Differences were found in condylar positioning, typically in an anterior position; condylar morphology, primarily with increased diameter or head height; and articular disk position within the anterior-posterior plane post-treatment. Changes in the glenoid fossa were not consistent between the studies. The overall risk of bias among studies was moderate. The influence of orthodontic treatment on morphologic changes in the TMJ remains unclear.
View on PubMedStructural imaging studies of patients with chronic pain: an anatomic likelihood estimate meta-analysis.
2022
Authors: Henn AT, Larsen B, Frahm L, Xu A, Adebimpe A, Scott JC, Linguiti S, Sharma V, Basbaum AI, Corder G, Dworkin RH, Edwards RR, Woolf CJ, Habel U, Eickhoff SB, Eickhoff CR, Wagels L, Satterthwaite TD
ABSTRACT
Neuroimaging is a powerful tool to investigate potential associations between chronic pain and brain structure. However, the proliferation of studies across diverse chronic pain syndromes and heterogeneous results challenges data integration and interpretation. We conducted a preregistered anatomical likelihood estimate meta-analysis on structural magnetic imaging studies comparing patients with chronic pain and healthy controls. Specifically, we investigated a broad range of measures of brain structure as well as specific alterations in gray matter and cortical thickness. A total of 7849 abstracts of experiments published between January 1, 1990, and April 26, 2021, were identified from 8 databases and evaluated by 2 independent reviewers. Overall, 103 experiments with a total of 5075 participants met the preregistered inclusion criteria. After correction for multiple comparisons using the gold-standard family-wise error correction ( P 0.05), no significant differences associated with chronic pain were found. However, exploratory analyses using threshold-free cluster enhancement revealed several spatially distributed clusters showing structural alterations in chronic pain. Most of the clusters coincided with regions implicated in nociceptive processing including the amygdala, thalamus, hippocampus, insula, anterior cingulate cortex, and inferior frontal gyrus. Taken together, these results suggest that chronic pain is associated with subtle, spatially distributed alterations of brain structure.
View on PubMedDelayed Sigmoid Colon Erosion by Artificial Urinary Sphincter Tubing.
2022
Authors: Shieh C, Shaw NM, Decker H, Soriano I, Breyer BN
Meningioma DNA methylation groups identify biological drivers and therapeutic vulnerabilities.
2022
Authors: Choudhury A, Magill ST, Eaton CD, Prager BC, Chen WC, Cady MA, Seo K, Lucas CG, Casey-Clyde TJ, Vasudevan HN, Liu SJ, Villanueva-Meyer JE, Lam TC, Pu JK, Li LF, Leung GK, Swaney DL, Zhang MY, Chan JW, Qiu Z, Martin MV, Susko MS, Braunstein SE, Bush NAO, Schulte JD, Butowski N, Sneed PK, Berger MS, Krogan NJ, Perry A, Phillips JJ, Solomon DA, Costello JF, McDermott MW, Rich JN, Raleigh DR
Meningiomas are the most common primary intracranial tumors. There are no effective medical therapies for meningioma patients, and new treatments have been encumbered by limited understanding of meningioma biology. Here, we use DNA methylation profiling on 565 meningiomas integrated with genetic, transcriptomic, biochemical, proteomic and single-cell approaches to show meningiomas are composed of three DNA methylation groups with distinct clinical outcomes, biological drivers and therapeutic vulnerabilities. Merlin-intact meningiomas (34%) have the best outcomes and are distinguished by NF2/Merlin regulation of susceptibility to cytotoxic therapy. Immune-enriched meningiomas (38%) have intermediate outcomes and are distinguished by immune infiltration, HLA expression and lymphatic vessels. Hypermitotic meningiomas (28%) have the worst outcomes and are distinguished by convergent genetic and epigenetic mechanisms driving the cell cycle and resistance to cytotoxic therapy. To translate these findings into clinical practice, we show cytostatic cell cycle inhibitors attenuate meningioma growth in cell culture, organoids, xenografts and patients.
View on PubMedShould multiple-choice questions get the SAQ? Development of a short-answer question writing rubric.
2022
Authors: Nguyentan DC, Gruenberg K, Shin J
Identifying trajectories of radiographic spinal disease in ankylosing spondylitis: a 15-year follow-up study of the PSOAS cohort.
2022
Authors: Hwang MC, Lee M, Gensler LS, Brown MA, Tahanan A, Rahbar MH, Hunter T, Shan M, Ishimori ML, Reveille JD, Weisman MH, Learch TJ
OBJECTIVES
Little is known with certainty about the natural history of spinal disease progression in ankylosing spondylitis (AS). Our objective was to discover if there were distinct patterns of change in vertebral involvement over time and to study associated clinical factors.
METHODS
Data were analysed from the Prospective Study of Outcomes in Ankylosing Spondylitis (PSOAS) observational cohort. All patients met modified New York Criteria for AS and had ≥2 sets of radiographs scored by modified Stoke Ankylosing Spondylitis Spinal Score (mSASSS) by two independent readers between 2002 and 2017. Group-based trajectory modelling (GBTM) was used to classify patients into distinct groups of longitudinal mSASSS considering sociodemographic and clinical covariables. The optimal trajectory model and number of trajectories was selected using Nagin's Bayesian information criterion (BIC).
RESULTS
A total of 561 patients with 1618 radiographs were analysed. The optimum number of trajectory groups identified was four (BIC -4062). These groups were subsequently categorized as: non-progressors (204 patients), late-progressors (147 patients), early-progressors (107 patients) and rapid-progressors (103 patients). Baseline predictors associated with higher spinal disease burden groups included: baseline mSASSS, male gender, longer disease duration, elevated CRP and smoking history. In addition, time-varying anti-TNF use per year was associated with decreased mSASSS progression only in the rapid-progressor group.
CONCLUSIONS
GBTM identified four distinct patterns of spinal disease progression in the PSOAS cohort. Male gender, longer disease duration, elevated CRP and smoking were associated with higher spinal disease groups. Independent confirmation in other AS cohorts is needed to confirm these radiographic patterns.
View on PubMedSex differences in ICDs for primary prevention: Time to include women in ICD trials!
2022
Authors: Ciuffo LA, Redberg RF
REM-Sleep: Remote Monitoring for Sleep Promotion (P11-7.004).
2022
Authors: Hannah Beaman, Vanja Douglas, Sara LaHue
Detection of Neoplasms by Metagenomic Next-Generation Sequencing of Cerebrospinal Fluid (S27.004).
2022
Authors: Wei Gu, Andreas Rauschecker, Elaine Hsu, Kelsey Zorn, Yasemin Sucu, Scot Federman, Shaun Arevalo, Hannah Sample, Eric Nguyen, Eric Talevich, Bardia Nourbakhsh, Carl Gold, Bruce Cree, Vanja Douglas, Megan Richie, Maulik Shah, S. Josephson, Jeffrey Gelfand, Steve Miller, Linlin Wang, Tarik Tihan, Michael Wilson