MSTPublications: October 2022
Single-Cell Identification of Melanoma Biomarkers in Circulating Tumor Cells
Fankhauser R, Chang M, Garrison Z, Berryman R, Lucero OM, Fuiten A, DePatie N, Seifert H, Kulkarni RP. Cancers. 2022; 14(19):4921. https://doi.org/10.3390/cancers14194921
The current standard for investigating tumors is surgical biopsy, which is costly, invasive, and difficult to perform serially. As an adjunct, circulating tumor cells (CTCs)—cells that have broken away from the primary tumor or metastatic sites—can be obtained from a blood draw and offer the potential for obtaining serial genetic information and serving as biomarkers. Here, we detail the potential for melanoma CTCs to serve as biomarkers and discuss a clinically viable methodology for single-cell CTC isolation and analysis that overcomes previous limitations. We explore the use of melanoma CTC biomarkers by isolating and performing single-cell RNA sequencing on CTCs from melanoma patients. We then compared transcriptional profiles of single melanoma CTCs against A375 cells and peripheral blood mononuclear cells to identify unique genes differentially regulated in circulating melanoma tumor cells. The information that can be obtained via analysis of these CTCs has significant potential in disease tracking.
COVID-19 vaccination program at a student-run free clinic: A descriptive study.
Fisher EL, Sack DE, González Peña T, Cooper Lloyd M, Weaver EO, Hagemann TM, Miller RF.
Prev Med Rep. 2022 Dec;30:101992. doi: 10.1016/j.pmedr.2022.101992. Epub 2022 Sep 19.
People historically excluded from receiving medical care in the United States, in addition to being at greater risk for SARS-CoV-2 infection, have had slower vaccine uptake due to structural barriers to availability. We present one student-run free clinic’s SARS-CoV-2 vaccination program from January 15 to August 1, 2021, in Nashville, Tennessee. We tracked SARS-CoV-2 vaccine primary series completion among 273 free clinic patients with the help of medical student volunteers, who scheduled appointments and answered vaccine-related questions. We worked with our academic medical center partner to host a single-dose vaccination event at our clinic. We compared vaccine series completion in our clinic to adult vaccine completion in Davidson County, Tennessee on August 1, 2021. Of the 273 free clinic participants, 144 identified as Spanish-speaking (52.7%) and 172 (63%) had at least one qualifying comorbidity per the December 30, 2020, Tennessee COVID-19 Vaccination Plan. As such, 183 (67%) were characterized as vaccine eligible in Phase 1a2, 1b, or 1c. On August 1, 2021, 63.1% of free clinic patients had completed their primary SARS-CoV-2 vaccination series compared with 58.9% of adults in Davidson County, Tennessee (RD 4.2%, 95% CI: -1.5% to 9.9%). Spanish-speaking free clinic patients were most likely to have completed their vaccination series. We describe a framework for a patient-centered vaccination effort to reach individuals traditionally missed by large vaccination campaigns. We highlight structural hurdles experienced by vulnerable populations, including language barriers, lack of technology or reliable internet access, inflexible working schedules, lack of transportation, and vaccine misinformation.
Loss of Vhl alters trabecular bone loss during S. aureus osteomyelitis in a cell-specific manner.
Ford CA, Hurford IM, Fulbright LE, Curry JM, Peek CT, Spoonmore TJ, Cruz Victorio V, Johnson JR, Peck SH, Cassat JE.
Front Cell Infect Microbiol. 2022 Sep 20;12:985467. doi: 10.3389/fcimb.2022.985467. eCollection 2022.
Osteomyelitis, or bone infection, is a major complication of accidental trauma or surgical procedures involving the musculoskeletal system. Staphylococcus aureus is the most frequently isolated pathogen in osteomyelitis and triggers significant bone loss. Hypoxia-inducible factor (HIF) signaling has been implicated in antibacterial immune responses as well as bone development and repair. In this study, the impact of bone cell HIF signaling on antibacterial responses and pathologic changes in bone architecture was explored using genetic models with knockout of either Hif1a or a negative regulator of HIF-1α, Vhl. Deletion of Hif1a in osteoblast-lineage cells via Osx-Cre (Hif1aΔOB ) had no impact on bacterial clearance or pathologic changes in bone architecture in a model of post-traumatic osteomyelitis. Knockout of Vhl in osteoblast-lineage cells via Osx-Cre (VhlΔOB ) caused expected increases in trabecular bone volume per total volume (BV/TV) at baseline and, intriguingly, did not exhibit an infection-mediated decline in trabecular BV/TV, unlike control mice. Despite this phenotype, bacterial burdens were not affected by loss of Vhl. In vitro studies demonstrated that transcriptional regulation of the osteoclastogenic cytokine receptor activator of NF-κB ligand (RANKL) and its inhibitor osteoprotegerin (OPG) is altered in osteoblast-lineage cells with knockout of Vhl. After observing no impact on bacterial clearance with osteoblast-lineage conditional knockouts, a LysM-Cre model was used to generate Hif1aΔMyeloid and VhlΔMyeloid mouse models to explore the impact of myeloid cell HIF signaling. In both Hif1aΔMyeloid and VhlΔMyeloid models, bacterial clearance was not impacted. Moreover, minimal impacts on bone architecture were observed. Thus, skeletal HIF signaling was not found to impact bacterial clearance in our mouse model of post-traumatic osteomyelitis, but Vhl deletion in the osteoblast lineage was found to limit infection-mediated trabecular bone loss, possibly via altered regulation of RANKL-OPG gene transcription.
Localizing seizure onset zones in surgical epilepsy with neurostimulation deep learning.
Johnson GW, Cai LY, Doss DJ, Jiang JW, Negi AS, Narasimhan S, Paulo DL, González HFJ, Williams Roberson S, Bick SK, Chang CE, Morgan VL, Wallace MT, Englot DJ.
J Neurosurg. 2022 Sep 23:1-6. doi: 10.3171/2022.8.JNS221321. Online ahead of print.
Objective: In drug-resistant temporal lobe epilepsy, automated tools for seizure onset zone (SOZ) localization that use brief interictal recordings could supplement presurgical evaluations and improve care. Thus, the authors sought to localize SOZs by training a multichannel convolutional neural network on stereoelectroencephalography (SEEG) cortico-cortical evoked potentials.
Methods: The authors performed single-pulse electrical stimulation in 10 drug-resistant temporal lobe epilepsy patients implanted with SEEG. Using 500,000 unique poststimulation SEEG epochs, the authors trained a multichannel 1-dimensional convolutional neural network to determine whether an SOZ had been stimulated.
Results: SOZs were classified with mean sensitivity of 78.1% and specificity of 74.6% according to leave-one-patient-out testing. To achieve maximum accuracy, the model required a 0- to 350-msec poststimulation time period. Post hoc analysis revealed that the model accurately classified unilateral versus bilateral mesial temporal lobe seizure onset, as well as neocortical SOZs.
Conclusions: This was the first demonstration, to the authors’ knowledge, that a deep learning framework can be used to accurately classify SOZs with single-pulse electrical stimulation-evoked responses. These findings suggest that accurate classification of SOZs relies on a complex temporal evolution of evoked responses within 350 msec of stimulation. Validation in a larger data set could provide a practical clinical tool for the presurgical evaluation of drug-resistant epilepsy.
Sex differences in health conditions associated with sexual assault in a large hospital population.
Lake AM, Goleva SB, Samuels LR, Carpenter LM, Davis LK. Complex Psychiatry 2022. doi: 10.1159/000527363
Introduction: Sexual assault is an urgent public health concern with both immediate and long-lasting health consequences, affecting 44% of women and 25% of men during their lifetimes. Large studies are needed to understand the unique healthcare needs of this patient population. Methods: We mined clinical notes to identify patients with a history of sexual assault in the electronic health record (EHR) at Vanderbilt University Medical Center (VUMC), a large university hospital in the Southeastern United States, from 1989 to 2021 (N=3,376,424). Using a phenome-wide case-control study, we identified diagnoses co-occurring with disclosures of sexual assault. We performed interaction tests to examine whether sex modified any of these associations. Association analyses were restricted to a subset of patients receiving regular care at VUMC (N=833,185). Results: The phenotyping approach identified 14,496 individuals (0.43%) across the VUMC-EHR with documentation of sexual assault and achieved a positive predictive value of 93.0% (95% CI=85.6%-97.0%), determined by manual patient chart review. Out of 1,703 clinical diagnoses tested across all subgroup analyses, 465 were associated with sexual assault. Sex-by-trauma interaction analysis revealed 55 sex-differential associations and demonstrated increased odds of psychiatric diagnoses in male survivors. Discussion / Conclusion: This case-control study identified associations between disclosures of sexual assault and hundreds of health conditions, many of which demonstrated sex-differential effects. The findings of this study suggest that patients who have experienced sexual assault are at risk for developing wide-ranging medical and psychiatric comorbidities and that male survivors may be particularly vulnerable to developing mental illness.
Functional Assays Reclassify Suspected Splice-Altering Variants of Uncertain Significance in Mendelian Channelopathies.
O’Neill MJ, Wada Y, Hall LD, Mitchell DW, Glazer A, Roden DM.
Circ Genom Precis Med. 2022 Oct 5:101161CIRCGEN122003782. doi: 10.1161/CIRCGEN.122.003782. Online ahead of print.
Background: Rare protein-altering variants in SCN5A, KCNQ1, and KCNH2 are major causes of Brugada syndrome and the congenital long QT syndrome. While splice-altering variants lying outside 2-bp canonical splice sites can cause these diseases, their role remains poorly described. We implemented 2 functional assays to assess 12 recently reported putative splice-altering variants of uncertain significance and 1 likely pathogenic variant without functional data observed in Brugada syndrome and long QT syndrome probands.
Methods: We deployed minigene assays to assess the splicing consequences of 10 variants. Three variants incompatible with the minigene approach were introduced into control induced pluripotent stem cells by CRISPR genome editing. We differentiated cells into induced pluripotent stem cell-derived cardiomyocytes and studied splicing outcomes by reverse transcription-polymerase chain reaction. We used the American College of Medical Genetics and Genomics functional assay criteria (PS3/BS3) to reclassify variants.
Results: We identified aberrant splicing, with presumed disruption of protein sequence, in 8/10 variants studied using the minigene assay and 1/3 studied in induced pluripotent stem cell-derived cardiomyocytes. We reclassified 8 variants of uncertain significance to likely pathogenic, 1 variants of uncertain significance to likely benign, and 1 likely pathogenic variant to pathogenic.
Conclusions: Functional assays reclassified splice-altering variants outside canonical splice sites in Brugada Syndrome- and long QT syndrome-associated genes.
Fundamental roles for inter-organelle communication in aging.
Donahue EKF, Ruark EM, Burkewitz K.
Biochem Soc Trans. 2022 Oct 28:BST20220519. doi: 10.1042/BST20220519. Online ahead of print.
Advances in public health have nearly doubled life expectancy over the last century, but this demographic shift has also changed the landscape of human illness. Today, chronic and age-dependent diseases dominate the leading causes of morbidity and mortality worldwide. Targeting the underlying molecular, genetic and cell biological drivers of the aging process itself appears to be an increasingly viable strategy for developing therapeutics against these diseases of aging. Towards this end, one of the most exciting developments in cell biology over the last decade is the explosion of research into organelle contact sites and related mechanisms of inter-organelle communication. Identification of the molecular mediators of inter-organelle tethering and signaling is now allowing the field to investigate the consequences of aberrant organelle interactions, which frequently seem to correlate with age-onset pathophysiology. This review introduces the major cellular roles for inter-organelle interactions, including the regulation of organelle morphology, the transfer of ions, lipids and other metabolites, and the formation of hubs for nutrient and stress signaling. We explore how these interactions are disrupted in aging and present findings that modulation of inter-organelle communication is a promising avenue for promoting longevity. Through this review, we propose that the maintenance of inter-organelle interactions is a pillar of healthy aging. Learning how to target the cellular mechanisms for sensing and controlling inter-organelle communication is a key next hurdle for geroscience.
Wnt signaling in the phenotype and function of tumor-associated macrophages.
Tigue ML, Loberg MA, Goettel JA, Weiss WA, Lee E, Weiss VL.
Cancer Res. 2022 Oct 10:CAN-22-1403. doi: 10.1158/0008-5472.CAN-22-1403. Online ahead of print.
Tumor-associated macrophages (TAM) play an important role in supporting tumor growth and suppressing anti-tumor immune responses, and TAM infiltration has been associated with poor patient prognosis in various cancers. TAMs can be classified as pro-inflammatory, M1-like, or anti-inflammatory, M2-like. While multiple factors within the tumor microenvironment affect the recruitment, polarization, and functions of TAMs, accumulating evidence suggests that Wnt signaling represents an important, targetable driver of an immunosuppressive, M2-like TAM phenotype. TAM production of Wnt ligands mediates TAM-tumor crosstalk to support cancer cell proliferation, invasion, and metastasis. Targeting TAM polarization and the pro-tumorigenic functions of TAMs through inhibitors of Wnt signaling may prove a beneficial treatment strategy in cancers where macrophages are prevalent in the microenvironment.
Axon hyperexcitability in the contralateral projection following unilateral optic nerve crush in mice.
McGrady NR, Holden JM, Ribeiro M, Boal AM, Risner ML, Calkins DJ.
Brain Commun. 2022 Oct 3;4(5):fcac251. doi: 10.1093/braincomms/fcac251. eCollection 2022.
Integrating Network Neuroscience Into Epilepsy Care: Progress, Barriers, and Next Steps.
Sinha N, Johnson GW, Davis KA, Englot DJ.
Epilepsy Curr. 2022 May 13;22(5):272-278. doi: 10.1177/15357597221101271. eCollection 2022 Sep-Oct.
Context-Dependent Roles for Toll-Like Receptors 2 and 9 in the Pathogenesis of Staphylococcus aureus Osteomyelitis.
Petronglo JR, Putnam NE, Ford CA, Cruz-Victorio V, Curry JM, Butrico CE, Fulbright LE, Johnson JR, Peck SH, Fatah SR, Cassat JE.
Infect Immun. 2022 Oct 13:e0041722. doi: 10.1128/iai.00417-22. Online ahead of print.
Reducing uncertainty in cancer risk estimation for patients with indeterminate pulmonary nodules using an integrated deep learning model.
Gao R, Li T, Tang Y, Xu K, Khan M, Kammer M, Antic SL, Deppen S, Huo Y, Lasko TA, Sandler KL, Maldonado F, Landman BA.
Comput Biol Med. 2022 Sep 29;150:106113. doi: 10.1016/j.compbiomed.2022.106113. Online ahead of print.
Distinct Tumor Necrosis Factor Alpha Receptors Dictate Stem Cell Fitness Versus Lineage Output in Dnmt3a-Mutant Clonal Hematopoiesis.
SanMiguel JM, Eudy E, Loberg MA, Young KA, Mistry JJ, Mujica KD, Schwartz LS, Stearns TM, Challen GA, Trowbridge JJ.
Cancer Discov. 2022 Sep 28:CD-22-0086. doi: 10.1158/2159-8290.CD-22-0086. Online ahead of print.
Engaging the next generation of physician-informaticians through early exposure to the field: successes and challenges associated with starting a novel clinical informatics interest group.
Quach WT, Le CH, Clark MG, McArthur E, Ancker JS, Gadd CS, Johnson KB.\
J Am Med Inform Assoc. 2022 Oct 13:ocac189. doi: 10.1093/jamia/ocac189. Online ahead of print.
A Single Nucleotide Polymorphism in SH2B3/LNK Promotes Hypertension Development and Renal Damage.
Alexander MR, Hank S, Dale BL, Himmel L, Zhong X, Smart CD, Fehrenbach DJ, Chen Y, Prabakaran N, Tirado B, Centrella M, Ao M, Du L, Shyr Y, Levy D, Madhur MS.
Circ Res. 2022 Sep 28:101161CIRCRESAHA121320625. doi: 10.1161/CIRCRESAHA.121.320625. Online ahead of print.