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Liu B, Yi D, Li S, Ramirez K, Xia X, Cao Y, Zhao H, Tripathi A, Qiu S, Kala M, Rafikov R, Gu H, Perez VDJ, Lemay SE, Glembotski CC, Knox KS, Bonnet S, Kalinichenko VV, Zhao YY, Fallon MB, Boucherat O, Dai Z. Single-cell and Spatial Transcriptomics Identified Fatty Acid-binding Proteins Controlling Endothelial Glycolytic and Arterial Programming in Pulmonary Hypertension. bioRxiv 2024:2024.02.11.579846. [PMID: 38370670 PMCID: PMC10871348 DOI: 10.1101/2024.02.11.579846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Pulmonary arterial hypertension (PAH) is a devastating disease characterized by obliterative vascular remodeling and persistent increase of vascular resistance, leading to right heart failure and premature death. Understanding the cellular and molecular mechanisms will help develop novel therapeutic approaches for PAH patients. Single-cell RNA sequencing (scRNAseq) analysis found that both FABP4 and FABP5 were highly induced in endothelial cells (ECs) of Egln1 Tie2Cre (CKO) mice, which was also observed in pulmonary arterial ECs (PAECs) from idiopathic PAH (IPAH) patients, and in whole lungs of pulmonary hypertension (PH) rats. Plasma levels of FABP4/5 were upregulated in IPAH patients and directly correlated with severity of hemodynamics and biochemical parameters using plasma proteome analysis. Genetic deletion of both Fabp4 and 5 in CKO mice ( Egln1 Tie2Cre /Fabp4-5 -/- , TKO) caused a reduction of right ventricular systolic pressure (RVSP) and RV hypertrophy, attenuated pulmonary vascular remodeling and prevented the right heart failure assessed by echocardiography, hemodynamic and histological analysis. Employing bulk RNA-seq and scRNA-seq, and spatial transcriptomic analysis, we showed that Fabp4/5 deletion also inhibited EC glycolysis and distal arterial programming, reduced ROS and HIF-2α expression in PH lungs. Thus, PH causes aberrant expression of FABP4/5 in pulmonary ECs which leads to enhanced ECs glycolysis and distal arterial programming, contributing to the accumulation of arterial ECs and vascular remodeling and exacerbating the disease.
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Bixby B, Vrba L, Lenka J, Oshiro MM, Watts GS, Hughes T, Erickson H, Chopra M, Knepler JL, Knox KS, Jarnagin L, Alalawi R, Kala M, Bernert R, Routh J, Roe DJ, Garland LL, Futscher BW, Nelson MA. Cell-free DNA methylation analysis as a marker of malignancy in pleural fluid. Sci Rep 2024; 14:2939. [PMID: 38316884 PMCID: PMC10844328 DOI: 10.1038/s41598-024-53132-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/29/2024] [Indexed: 02/07/2024] Open
Abstract
Diagnosis of malignant pleural effusion (MPE) is made by cytological examination of pleural fluid or histological examination of pleural tissue from biopsy. Unfortunately, detection of malignancy using cytology has an overall sensitivity of 50%, and is dependent upon tumor load, volume of fluid assessed, and cytopathologist experience. The diagnostic yield of pleural fluid cytology is also compromised by low abundance of tumor cells or when morphology is obscured by inflammation or reactive mesothelial cells. A reliable molecular marker that may complement fluid cytology for the diagnosis of malignant pleural effusion is needed. The purpose of this study was to establish a molecular diagnostic approach based on pleural effusion cell-free DNA methylation analysis for the differential diagnosis of malignant pleural effusion and benign pleural effusion. This was a blind, prospective case-control biomarker study. We recruited 104 patients with pleural effusion for the study. We collected pleural fluid from patients with: MPE (n = 48), indeterminate pleural effusion in subjects with known malignancy or IPE (n = 28), and benign PE (n = 28), and performed the Sentinel-MPE liquid biopsy assay. The methylation level of Sentinel-MPE was markedly higher in the MPE samples compared to BPE control samples (p < 0.0001) and the same tendency was observed relative to IPE (p = 0.004). We also noted that the methylation signal was significantly higher in IPE relative to BPE (p < 0.001). We also assessed the diagnostic efficiency of the Sentinel-MPE test by performing receiver operating characteristic analysis (ROC). For the ROC analysis we combined the malignant and indeterminate pleural effusion groups (n = 76) and compared against the benign group (n = 28). The detection sensitivity and specificity of the Sentinel-MPE test was high (AUC = 0.912). The Sentinel-MPE appears to have better performance characteristics than cytology analysis. However, combining Sentinel-MPE with cytology analysis could be an even more effective approach for the diagnosis of MPE. The Sentinel-MPE test can discriminate between BPE and MPE. The Sentinel-MPE liquid biopsy test can detect aberrant DNA in several different tumor types. The Sentinel-MPE test can be a complementary tool to cytology in the diagnosis of MPE.
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Affiliation(s)
- Billie Bixby
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | | | - Jyoti Lenka
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Marc M Oshiro
- Boyer Liver Institute, Department of Medicine, University of Arizona, Tucson, USA
| | - George S Watts
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, USA
| | - Trina Hughes
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Heidi Erickson
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Madhav Chopra
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - James L Knepler
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, USA
| | - Kenneth S Knox
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Phoenix, USA
| | - Lisa Jarnagin
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Phoenix, USA
| | - Raed Alalawi
- Pulmonary, Critical Care, Allergy and Sleep Medicine, Department of Medicine, University of Arizona, Phoenix, USA
| | - Mrinalini Kala
- Department of Internal Medicine, University of Arizona, Phoenix, USA
| | | | | | - Denise J Roe
- Mel and Enid Zuckerman College of Public Health, University of Arizona, Tucson, USA
| | - Linda L Garland
- Hematology Oncology, Department of Medicine, University of Arizona, Tucson, USA
| | - Bernard W Futscher
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, USA
| | - Mark A Nelson
- Department of Pathology, University of Arizona, Tucson, AZ, 85724, USA.
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Feng A, Caro YM, Gardner C, Grischo G, Liang Y, Wickremasinghe PD, Polmann M, Kala M, Marlowe T, Black SM, Knox KS, Wang T. PTK2-associated gene signature could predict the prognosis of IPF. Respir Res 2023; 24:304. [PMID: 38053045 PMCID: PMC10699084 DOI: 10.1186/s12931-023-02582-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 10/26/2023] [Indexed: 12/07/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal lung disease with a poor prognosis. Current/available clinical prediction tools have limited sensitivity and accuracy when evaluating clinical outcomes of IPF. Research has shown that focal adhesion kinase (FAK), produced by the protein tyrosine kinase 2 (PTK2) gene, is crucial in IPF development. FAK activation is a characteristic of lesional fibroblasts; Thus, FAK may be a valuable therapeutic target or prognostic biomarker for IPF. This study aimed to create a gene signature based on PTK2-associated genes and microarray data from blood cells to predict disease prognosis in patients with IPF. PTK2 levels were found to be higher in lung tissues of IPF patients compared to healthy controls, and PTK2 inhibitor Defactinib was found to reduce TGFβ-induced FAK activation and increase α-smooth muscle actin. Although the blood PTK2 levels were higher in IPF patients, blood PTK level alone could not predict IPF prognosis. From 196 PTK2-associated genes, 11 genes were prioritized to create a gene signature (PTK2 molecular signature) and a risk score system using univariate and multivariate Cox regression analysis. Patients were divided into high-risk and low-risk groups using PTK2 molecular signature. Patients in the high-risk group experienced decreased survival rates compared to patients in the low-risk group across all discovery and validation cohorts. Further functional enrichment and immune cell proportion analyses revealed that the PTK2 molecular signature strongly reflected the activation levels of immune pathways and immune cells. These findings suggested that PTK2 is a molecular target of IPF and the PTK2 molecular signature is an effective IPF prognostic biomarker.
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Affiliation(s)
- Anlin Feng
- Center for Translational Science, and Department of Environmental Health, Florida International University, Port St. Lucie, FL, 36987, USA
| | - Yesenia Moreno Caro
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, 85004, USA
| | - Colin Gardner
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, 85004, USA
| | - Garrett Grischo
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, 85004, USA
| | - Ying Liang
- Center for Translational Science, and Department of Environmental Health, Florida International University, Port St. Lucie, FL, 36987, USA
| | - Praveen D Wickremasinghe
- Herbert Wertheim College of Medicine, Florida International University, Port St. Lucie, FL, 33199, USA
| | - Michaela Polmann
- Herbert Wertheim College of Medicine, Florida International University, Port St. Lucie, FL, 33199, USA
| | - Mrinalini Kala
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, 85004, USA
| | - Timothy Marlowe
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, 85004, USA
| | - Stephen M Black
- Center for Translational Science, and Department of Environmental Health, Florida International University, Port St. Lucie, FL, 36987, USA
- Herbert Wertheim College of Medicine, Florida International University, Port St. Lucie, FL, 33199, USA
| | - Kenneth S Knox
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, 85004, USA
| | - Ting Wang
- Center for Translational Science, and Department of Environmental Health, Florida International University, Port St. Lucie, FL, 36987, USA.
- Department of Internal Medicine, University of Arizona, Phoenix, AZ, 85004, USA.
- Herbert Wertheim College of Medicine, Florida International University, Port St. Lucie, FL, 33199, USA.
- Center for Translational Science, Florida International University, 11350 SW Village Pkwy, Port St. Lucie, FL, 34987, USA.
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Jasbi P, Nikolich-Žugich J, Patterson J, Knox KS, Jin Y, Weinstock GM, Smith P, Twigg HL, Gu H. Targeted metabolomics reveals plasma biomarkers and metabolic alterations of the aging process in healthy young and older adults. GeroScience 2023; 45:3131-3146. [PMID: 37195387 PMCID: PMC10643785 DOI: 10.1007/s11357-023-00823-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/10/2023] [Indexed: 05/18/2023] Open
Abstract
With the exponential growth in the older population in the coming years, many studies have aimed to further investigate potential biomarkers associated with the aging process and its incumbent morbidities. Age is the largest risk factor for chronic disease, likely due to younger individuals possessing more competent adaptive metabolic networks that result in overall health and homeostasis. With aging, physiological alterations occur throughout the metabolic system that contribute to functional decline. In this cross-sectional analysis, a targeted metabolomic approach was applied to investigate the plasma metabolome of young (21-40y; n = 75) and older adults (65y + ; n = 76). A corrected general linear model (GLM) was generated, with covariates of gender, BMI, and chronic condition score (CCS), to compare the metabolome of the two populations. Among the 109 targeted metabolites, those associated with impaired fatty acid metabolism in the older population were found to be most significant: palmitic acid (p < 0.001), 3-hexenedioic acid (p < 0.001), stearic acid (p = 0.005), and decanoylcarnitine (p = 0.036). Derivatives of amino acid metabolism, 1-methlyhistidine (p = 0.035) and methylhistamine (p = 0.027), were found to be increased in the younger population and several novel metabolites were identified, such as cadaverine (p = 0.034) and 4-ethylbenzoic acid (p = 0.029). Principal component analysis was conducted and highlighted a shift in the metabolome for both groups. Receiver operating characteristic analyses of partial least squares-discriminant analysis models showed the candidate markers to be more powerful indicators of age than chronic disease. Pathway and enrichment analyses uncovered several pathways and enzymes predicted to underlie the aging process, and an integrated hypothesis describing functional characteristics of the aging process was synthesized. Compared to older participants, the young group displayed greater abundance of metabolites related to lipid and nucleotide synthesis; older participants displayed decreased fatty acid oxidation and reduced tryptophan metabolism, relative to the young group. As a result, we offer a better understanding of the aging metabolome and potentially reveal new biomarkers and predicted mechanisms for future study.
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Affiliation(s)
- Paniz Jasbi
- College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85281, USA
| | - Janko Nikolich-Žugich
- University of Arizona Center on Aging, University of Arizona, Tucson, AZ, 85724, USA
| | - Jeffrey Patterson
- College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, AZ, 85724, USA
| | - Yan Jin
- College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA
- Center for Translational Science, Florida International University, 11350 SW Village Pkwy, Port St. Lucie, FL, 34987, USA
| | | | - Patricia Smith
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Indiana University Medical Center, 1120 West Michigan Street, CL 260A, Indianapolis, IN, 46202, USA
| | - Homer L Twigg
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Indiana University Medical Center, 1120 West Michigan Street, CL 260A, Indianapolis, IN, 46202, USA.
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ, 85004, USA.
- Center for Translational Science, Florida International University, 11350 SW Village Pkwy, Port St. Lucie, FL, 34987, USA.
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Yi D, Liu B, Ding H, Li S, Li R, Pan J, Ramirez K, Xia X, Kala M, Ye Q, Lee WH, Frye RE, Wang T, Zhao Y, Knox KS, Glembotski CC, Fallon MB, Dai Z. E2F1 Mediates SOX17 Deficiency-Induced Pulmonary Hypertension. Hypertension 2023; 80:2357-2371. [PMID: 37737027 PMCID: PMC10591929 DOI: 10.1161/hypertensionaha.123.21241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Accepted: 08/17/2023] [Indexed: 09/23/2023]
Abstract
BACKGROUND Rare genetic variants and genetic variation at loci in an enhancer in SOX17 (SRY-box transcription factor 17) are identified in patients with idiopathic pulmonary arterial hypertension (PAH) and PAH with congenital heart disease. However, the exact role of genetic variants or mutations in SOX17 in PAH pathogenesis has not been reported. METHODS SOX17 expression was evaluated in the lungs and pulmonary endothelial cells (ECs) of patients with idiopathic PAH. Mice with Tie2Cre-mediated Sox17 knockdown and EC-specific Sox17 deletion were generated to determine the role of SOX17 deficiency in the pathogenesis of PAH. Human pulmonary ECs were cultured to understand the role of SOX17 deficiency. Single-cell RNA sequencing, RNA-sequencing analysis, and luciferase assay were performed to understand the underlying molecular mechanisms of SOX17 deficiency-induced PAH. E2F1 (E2F transcription factor 1) inhibitor HLM006474 was used in EC-specific Sox17 mice. RESULTS SOX17 expression was downregulated in the lung and pulmonary ECs from patients with idiopathic PAH. Mice with Tie2Cre-mediated Sox17 knockdown and EC-specific Sox17 deletion induced spontaneously mild pulmonary hypertension. Loss of endothelial Sox17 in EC exacerbated hypoxia-induced pulmonary hypertension in mice. Loss of SOX17 in lung ECs induced endothelial dysfunctions including upregulation of cell cycle programming, proliferative and antiapoptotic phenotypes, augmentation of paracrine effect on pulmonary arterial smooth muscle cells, impaired cellular junction, and BMP (bone morphogenetic protein) signaling. E2F1 signaling was shown to mediate the SOX17 deficiency-induced EC dysfunction. Pharmacological inhibition of E2F1 in Sox17 EC-deficient mice attenuated pulmonary hypertension development. CONCLUSIONS Our study demonstrated that endothelial SOX17 deficiency induces pulmonary hypertension through E2F1. Thus, targeting E2F1 signaling represents a promising approach in patients with PAH.
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Affiliation(s)
- Dan Yi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Bin Liu
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Hongxu Ding
- Department of Pharmacy Practice & Science, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Shuai Li
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Rebecca Li
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Jiakai Pan
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Karina Ramirez
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Xiaomei Xia
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Mrinalini Kala
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Qinmao Ye
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Won Hee Lee
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | | | - Ting Wang
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Environmental Health Science and Center of Translational Science, Florida International University, Port Saint Lucie, Florida, USA
| | - Yutong Zhao
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Kenneth S. Knox
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Christopher C. Glembotski
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Michael B. Fallon
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Zhiyu Dai
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Sarver Heart Center, University of Arizona, Tucson, Arizona, USA
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6
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Bixby B, Vrba L, Lenka J, Oshiro M, Watts GS, Hughes T, Erickson H, Chopra M, Knepler JL, Knox KS, Jarnagin L, Alalawi R, Kala M, Bernert R, Routh J, Roe DJ, Garland LL, Futscher BW, Nelson MA. Cell-Free DNA Methylation Analysis as a Marker of Malignancy in Pleural Fluid. Res Sq 2023:rs.3.rs-3390107. [PMID: 37886511 PMCID: PMC10602127 DOI: 10.21203/rs.3.rs-3390107/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Background Diagnosis of malignant pleural effusion (MPE) is made by cytological examination of pleural fluid or histological examination of pleural tissue from biopsy. Unfortunately, detection of malignancy using cytology has an overall sensitivity of 50%, and is dependent upon tumor load, volume of fluid assessed, and cytopathologist experience. The diagnostic yield of pleural fluid cytology is also compromised by low abundance of tumor cells or when morphology is obscured by inflammation or reactive mesothelial cells. A reliable molecular marker that may complement fluid cytology malignant pleural effusion diagnosis is needed. The purpose of this study was to establish a molecular diagnostic approach based on pleural effusion cell-free DNA methylation analysis for the differential diagnosis of malignant pleural effusion and benign pleural effusion. Results This was a blind, prospective case-control biomarker study. We recruited 104 patients with pleural effusion for the study. We collected pleural fluid from patients with: MPE (n = 48), PPE (n = 28), and benign PE (n = 28), and performed the Sentinel-MPE liquid biopsy assay. The methylation level of Sentinel-MPE was markedly higher in the MPE samples compared to BPE control samples (p < 0.0001) and the same tendency was observed relative to PPE (p = 0.004). We also noted that the methylation signal was significantly higher in PPE relative to BPE (p < 0.001). We also assessed the diagnostic efficiency of the Sentinel-MPE test by performing receiver operating characteristic analysis (ROC). For the ROC analysis we combined the malignant and paramalignant groups (n = 76) and compared against the benign group (n = 28). The detection sensitivity and specificity of the Sentinel-MPE test was high (AUC = 0.912). The Sentinel-MPE appears to have better performance characteristics than cytology analysis. However, combining Sentinel-MPE with cytology analysis could be an even more effective approach for the diagnosis of MPE. Conclusions The Sentinel-MPE test can discriminate between BPE and MPE. The Sentinel-MPE liquid biopsy test can detect aberrant DNA in several different tumor types. The Sentinel-MPE test can be a complementary tool to cytology in the diagnosis of MPE.
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7
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Horwitz LI, Thaweethai T, Brosnahan SB, Cicek MS, Fitzgerald ML, Goldman JD, Hess R, Hodder SL, Jacoby VL, Jordan MR, Krishnan JA, Laiyemo AO, Metz TD, Nichols L, Patzer RE, Sekar A, Singer NG, Stiles LE, Taylor BS, Ahmed S, Algren HA, Anglin K, Aponte-Soto L, Ashktorab H, Bassett IV, Bedi B, Bhadelia N, Bime C, Bind MAC, Black LJ, Blomkalns AL, Brim H, Castro M, Chan J, Charney AW, Chen BK, Chen LQ, Chen P, Chestek D, Chibnik LB, Chow DC, Chu HY, Clifton RG, Collins S, Costantine MM, Cribbs SK, Deeks SG, Dickinson JD, Donohue SE, Durstenfeld MS, Emery IF, Erlandson KM, Facelli JC, Farah-Abraham R, Finn AV, Fischer MS, Flaherman VJ, Fleurimont J, Fonseca V, Gallagher EJ, Gander JC, Gennaro ML, Gibson KS, Go M, Goodman SN, Granger JP, Greenway FL, Hafner JW, Han JE, Harkins MS, Hauser KSP, Heath JR, Hernandez CR, Ho O, Hoffman MK, Hoover SE, Horowitz CR, Hsu H, Hsue PY, Hughes BL, Jagannathan P, James JA, John J, Jolley S, Judd SE, Juskowich JJ, Kanjilal DG, Karlson EW, Katz SD, Kelly JD, Kelly SW, Kim AY, Kirwan JP, Knox KS, Kumar A, Lamendola-Essel MF, Lanca M, Lee-lannotti JK, Lefebvre RC, Levy BD, Lin JY, Logarbo BP, Logue JK, Longo MT, Luciano CA, Lutrick K, Malakooti SK, Mallett G, Maranga G, Marathe JG, Marconi VC, Marshall GD, Martin CF, Martin JN, May HT, McComsey GA, McDonald D, Mendez-Figueroa H, Miele L, Mittleman MA, Mohandas S, Mouchati C, Mullington JM, Nadkarni GN, Nahin ER, Neuman RB, Newman LT, Nguyen A, Nikolich JZ, Ofotokun I, Ogbogu PU, Palatnik A, Palomares KTS, Parimon T, Parry S, Parthasarathy S, Patterson TF, Pearman A, Peluso MJ, Pemu P, Pettker CM, Plunkett BA, Pogreba-Brown K, Poppas A, Porterfield JZ, Quigley JG, Quinn DK, Raissy H, Rebello CJ, Reddy UM, Reece R, Reeder HT, Rischard FP, Rosas JM, Rosen CJ, Rouphael NG, Rouse DJ, Ruff AM, Saint Jean C, Sandoval GJ, Santana JL, Schlater SM, Sciurba FC, Selvaggi C, Seshadri S, Sesso HD, Shah DP, Shemesh E, Sherif ZA, Shinnick DJ, Simhan HN, Singh U, Sowles A, Subbian V, Sun J, Suthar MS, Teunis LJ, Thorp JM, Ticotsky A, Tita ATN, Tragus R, Tuttle KR, Urdaneta AE, Utz PJ, VanWagoner TM, Vasey A, Vernon SD, Vidal C, Walker T, Ward HD, Warren DE, Weeks RM, Weiner SJ, Weyer JC, Wheeler JL, Whiteheart SW, Wiley Z, Williams NJ, Wisnivesky JP, Wood JC, Yee LM, Young NM, Zisis SN, Foulkes AS. Researching COVID to Enhance Recovery (RECOVER) adult study protocol: Rationale, objectives, and design. PLoS One 2023; 18:e0286297. [PMID: 37352211 PMCID: PMC10289397 DOI: 10.1371/journal.pone.0286297] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/12/2023] [Indexed: 06/25/2023] Open
Abstract
IMPORTANCE SARS-CoV-2 infection can result in ongoing, relapsing, or new symptoms or other health effects after the acute phase of infection; termed post-acute sequelae of SARS-CoV-2 infection (PASC), or long COVID. The characteristics, prevalence, trajectory and mechanisms of PASC are ill-defined. The objectives of the Researching COVID to Enhance Recovery (RECOVER) Multi-site Observational Study of PASC in Adults (RECOVER-Adult) are to: (1) characterize PASC prevalence; (2) characterize the symptoms, organ dysfunction, natural history, and distinct phenotypes of PASC; (3) identify demographic, social and clinical risk factors for PASC onset and recovery; and (4) define the biological mechanisms underlying PASC pathogenesis. METHODS RECOVER-Adult is a combined prospective/retrospective cohort currently planned to enroll 14,880 adults aged ≥18 years. Eligible participants either must meet WHO criteria for suspected, probable, or confirmed infection; or must have evidence of no prior infection. Recruitment occurs at 86 sites in 33 U.S. states, Washington, DC and Puerto Rico, via facility- and community-based outreach. Participants complete quarterly questionnaires about symptoms, social determinants, vaccination status, and interim SARS-CoV-2 infections. In addition, participants contribute biospecimens and undergo physical and laboratory examinations at approximately 0, 90 and 180 days from infection or negative test date, and yearly thereafter. Some participants undergo additional testing based on specific criteria or random sampling. Patient representatives provide input on all study processes. The primary study outcome is onset of PASC, measured by signs and symptoms. A paradigm for identifying PASC cases will be defined and updated using supervised and unsupervised learning approaches with cross-validation. Logistic regression and proportional hazards regression will be conducted to investigate associations between risk factors, onset, and resolution of PASC symptoms. DISCUSSION RECOVER-Adult is the first national, prospective, longitudinal cohort of PASC among US adults. Results of this study are intended to inform public health, spur clinical trials, and expand treatment options. REGISTRATION NCT05172024.
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Affiliation(s)
- Leora I. Horwitz
- Department of Population Health, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Tanayott Thaweethai
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Shari B. Brosnahan
- Division of Pulmonary Critical Care and Sleep Medicine, NYU Langone Health, New York, New York, United States of America
| | - Mine S. Cicek
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Megan L. Fitzgerald
- Patient Led Research Collaboration on COVID-19, Washington, DC, United States of America
| | - Jason D. Goldman
- Division of Infectious Diseases, Providence Swedish Medical Center, Seattle, Washington, United States of America
| | - Rachel Hess
- Department of Population Health Sciences and Internal Medicine, University of Utah School of Medicine, Salt Lake City, Utah, United States of America
| | - S. L. Hodder
- Department of Medicine, West Virginia University, Morgantown, West Virginia, United States of America
| | - Vanessa L. Jacoby
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California, United States of America
| | - Michael R. Jordan
- Division of Geographic Medicine and Infectious Diseases, Tufts Medical Center, Medford, Massachusetts, United States of America
| | - Jerry A. Krishnan
- Department of Medicine, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Adeyinka O. Laiyemo
- Department of Medicine, Howard University, Washington, DC, United States of America
| | - Torri D. Metz
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
| | - Lauren Nichols
- Body Politic COVID-19 Support Group, Boston, Massachusetts, United States of America
| | - Rachel E. Patzer
- Department of Medicine and Surgery, Health Services Research Center, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Anisha Sekar
- Patient Led Research Collaboration on COVID-19, Washington, DC, United States of America
| | - Nora G. Singer
- Department of Medicine and Rheumatology, The MetroHealth Medical Center, Cleveland, Ohio, United States of America
| | - Lauren E. Stiles
- Department of Neurology, Stony Brook University Renaissance School of Medicine, Stony Brook, New York, United States of America
| | - Barbara S. Taylor
- Department of Medicine, Division of Infectious Diseases and Infectious Diseases, Long School of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, United States of America
| | - Shifa Ahmed
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Heather A. Algren
- Swedish Center for Research and Innovation, Providence Swedish Medical Center, Seattle, Washington, United States of America
| | - Khamal Anglin
- Department of Epidemiology and Biostatistics, University of California at San Francisco Institute of Global Health Sciences, San Francisco, San Francisco, California, United States of America
| | - Lisa Aponte-Soto
- College of Science and Health, Department of Health Sciences, DePaul University, Chicago, Illinois, United States of America
| | - Hassan Ashktorab
- Department of Medicine, Howard University, Washington, DC, United States of America
| | - Ingrid V. Bassett
- Medical Practice Evaluation Center, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Brahmchetna Bedi
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Nahid Bhadelia
- Center for Emerging Infectious Diseases Policy and Research, Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Christian Bime
- Department of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Marie-Abele C. Bind
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Lora J. Black
- Department of Clinical Research, Sanford Research, Sioux Falls, South Dakota, United States of America
| | - Andra L. Blomkalns
- Department of Emergency Medicine, Stanford University, Stanford, California, United States of America
| | - Hassan Brim
- Department of Pathology, Howard University, Washington, DC, United States of America
| | - Mario Castro
- Division of Pulmonary and Critical Care, University of Kansas Medical Center, Kansas City, Kansas City, United States of America
| | - James Chan
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Alexander W. Charney
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Benjamin K. Chen
- Division of Infectious Disease, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Li Qing Chen
- Department of Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Peter Chen
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - David Chestek
- Department of Emergency Medicine, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Lori B. Chibnik
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Dominic C. Chow
- Department of Medicine, University of Hawaii at Manoa John A. Burns School of Medicine, Honolulu, Hawaii, United States of America
| | - Helen Y. Chu
- Department of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Rebecca G. Clifton
- Department of Biostatistics, George Washington University, Washington, DC, United States of America
| | - Shelby Collins
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Maged M. Costantine
- Department of Obstetrics and Gynecology, The Ohio State University Hospital, Columbus, Ohio, United States of America
| | - Sushma K. Cribbs
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - John D. Dickinson
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sarah E. Donohue
- Department of Research Services, University of Illinois College of Medicine, Peoria, Illinois, United States of America
| | - Matthew S. Durstenfeld
- Department of Medicine, Division of Cardiology at Zuckerberg San Francisco General, University of California San Francisco, San Francisco, California, United States of America
| | - Ivette F. Emery
- MaineHealth Institute for Research, MaineHealth, Scarborough, Maine, United States of America
| | - Kristine M. Erlandson
- Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Julio C. Facelli
- Department of Biomedical Informatics and Clinical and Translational Science Institute, University of Utah, Salt Lake City, Utah, United States of America
| | - Rachael Farah-Abraham
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Aloke V. Finn
- Department of Pathology, CVPath Institute, Gaithersburg, Maryland, United States of America
| | - Melinda S. Fischer
- Department of Medicine, Division of Infectious Diseases and Infectious Diseases, Long School of Medicine, University of Texas Health Science Center San Antonio, San Antonio, Texas, United States of America
| | - Valerie J. Flaherman
- Department of Pediatrics, University of California, San Francisco, San Francisco, California, United States of America
| | - Judes Fleurimont
- Mile Square Health Center, University of Illinois Chicago, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Vivian Fonseca
- Department of Medicine, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Emily J. Gallagher
- Department of Endocrinology, Diabetes and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Jennifer C. Gander
- Center for Research and Evaluation, Kaiser Permanente of Georgia, Atlanta, Georgia, United States of America
| | - Maria Laura Gennaro
- Public Health Research Institute and Department of Medicine, Rutgers New Jersey Medical School, Newark, New Jersey, United States of America
| | - Kelly S. Gibson
- Department of Obstetrics and Gynecology, MetroHealth System, Cleveland, Ohio, United States of America
| | - Minjoung Go
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Steven N. Goodman
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, California, United States of America
| | - Joey P. Granger
- Department of Physiology & Biophysics, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Frank L. Greenway
- Clinical Trials, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States of America
| | - John W. Hafner
- Department of Emergency Medicine, OSF Saint Francis Medical Center, Peoria, Illinois, United States of America
| | - Jenny E. Han
- Department of Pulmonary and Critical Care, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Michelle S. Harkins
- Department of Internal Medicine University of New Mexico, Health Science Center, Albuquerque, New Mexico, United States of America
| | - Kristine S. P. Hauser
- Clinical Research Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - James R. Heath
- Department of Bioengineering, Institute for Systems Biology, Seattle, Washington, United States of America
| | - Carla R. Hernandez
- Clinical Research Center, University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
| | - On Ho
- Seattle Children’s Therapeutics, Seattle, Washington, United States of America
| | - Matthew K. Hoffman
- Department of Obstetrics and Gynecology, Christiana Care Health Services, Newark, Delaware, United States of America
| | - Susan E. Hoover
- Department of Clinical Research, Sanford Research, Sioux Falls, South Dakota, United States of America
| | - Carol R. Horowitz
- Institute for Health Equity Research, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Harvey Hsu
- Department of Internal Medicine, University of Arizona, Phoenix, Arizona, United States of America
| | - Priscilla Y. Hsue
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Brenna L. Hughes
- Department of Obstetrics and Gynecology, Duke University, Durham, North Carolina, United States of America
| | - Prasanna Jagannathan
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | - Judith A. James
- Department of Arthritis & Clinical Immunology, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States of America
| | - Janice John
- Department of Family Medicine, Cambridge Health Alliance, Cambridge, Massachusetts, United States of America
| | - Sarah Jolley
- Department of Pulmonary and Critical Care Medicine, University of Colorado, Aurora, Colorado, United States of America
| | - S. E. Judd
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Joy J. Juskowich
- Department of Medicine, Division of Infectious Diseases, West Virginia School of Medicine, Morgantown, West Virginia, United States of America
| | - Diane G. Kanjilal
- Department of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Elizabeth W. Karlson
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Stuart D. Katz
- Department of Medicine, NYU Langone Health, New York, New York, United States of America
| | - J. Daniel Kelly
- Department of Medicine, University of California, San Francisco, San Francisco, California, United States of America
| | - Sara W. Kelly
- Department of Pediatrics & Department of Research Services, University of Illinois College of Medicine, Peoria, Illinois, United States of America
| | - Arthur Y. Kim
- Department of Infectious Diseases, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - John P. Kirwan
- Department Integrated Physiology and Molecular Medicine, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States of America
| | - Kenneth S. Knox
- Department of Internal Medicine, University of Arizona, Phoenix, Arizona, United States of America
| | - Andre Kumar
- Department of Medicine, Stanford University, Stanford, California, United States of America
| | | | - Margaret Lanca
- Department of Psychiatry, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Joyce K. Lee-lannotti
- Department of Internal Medicine and Neurology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - R. Craig Lefebvre
- Communications Practice Area, RTI International, Research Triangle Park, North Carolina, United States of America
| | - Bruce D. Levy
- Department of Internal Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Janet Y. Lin
- Department of Emergency Medicine, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Brian P. Logarbo
- Tulane Center for Clinical Research, Tulane University School of Medicine, New Orleans, Louisiana, United States of America
| | - Jennifer K. Logue
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Michele T. Longo
- Tulane Center for Clinical Neurosciences, Tulane School of Medicine, New Orleans, Louisiana, United States of America
| | - Carlos A. Luciano
- Department of Neurology, University of Puerto Rico School of Medicine, San Juan, Puerto Rico, United States of America
| | - Karen Lutrick
- Department of Family & Community Medicine, University of Arizona, College of Medicine – Tucson, Tucson, Arizona, United States of America
| | - Shahdi K. Malakooti
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Gail Mallett
- Department of Obstetrics and Gynecology, Northwestern University, Chicago, Illinois, United States of America
| | - Gabrielle Maranga
- Department of Population Health, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Jai G. Marathe
- Department of Medicine, Section of Infectious Diseases, Boston University Medical Center, Boston, Massachusetts, United States of America
| | - Vincent C. Marconi
- Department of Medicine, Infectious Diseases and Department of Global Health, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Gailen D. Marshall
- Department of Medicine, University of Mississippi Medical Center, Jackson, Mississippi, United States of America
| | - Christopher F. Martin
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Jeffrey N. Martin
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, United States of America
| | - Heidi T. May
- Department of Cardiology, Intermountain Medical Center, Salt Lake City, Utah, United States of America
| | - Grace A. McComsey
- Department of Medicine, Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Dylan McDonald
- Department of Allergy & Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Hector Mendez-Figueroa
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Texas Health Science Center at Houston, Houston, Texas, United States of America
| | - Lucio Miele
- Department of Genetics, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Murray A. Mittleman
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sindhu Mohandas
- Department of Infectious Diseases, Children’s Hospital Los Angeles, University of Southern California, Los Angeles, California, United States of America
| | - Christian Mouchati
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Janet M. Mullington
- Department of Neurology and Sleep Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
| | - Girish N. Nadkarni
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Erica R. Nahin
- Department of Medicine, NYU Langone Health, New York, New York, United States of America
| | - Robert B. Neuman
- Division of Cardiology, Kaiser Permanente of Georgia, Atlanta, Georgia, United States of America
| | - Lisa T. Newman
- Department of Social, Statistical and Environmental Sciences, RTI International, Research Triangle Park, North Carolina, United States of America
| | - Amber Nguyen
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Janko Z. Nikolich
- Department of Immunobiology, University of Arizona College of Medicine, Tucson, Arizona, United States of America
| | - Igho Ofotokun
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Princess U. Ogbogu
- Division of Pediatric Allergy, Immunology, and Rheumatology, University Hospitals Rainbow Babies and Children’s Hospital, Cleveland, Ohio, United States of America
| | - Anna Palatnik
- Department of Obstetrics and Gynecology, Medical College of Wisconsin, Milwaukee, Wisconsin, United States of America
| | - Kristy T. S. Palomares
- Department of Obstetrics and Gynecology, Division of Maternal Fetal Medicine, Saint Peter’s University Hospital, New Brunswick, New Jersey, United States of America
| | - Tanyalak Parimon
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Samuel Parry
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Sairam Parthasarathy
- Department of Medicine, University of Arizona, Tucson, Arizona, United States of America
| | - Thomas F. Patterson
- Department of Medicine, Department of Infectious Disease, University of Texas Health, San Antonio, Texas, United States of America
| | - Ann Pearman
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Michael J. Peluso
- Division of HIV, Infectious Disease, and Global Medicine, University of California, San Francisco, California, United States of America
| | - Priscilla Pemu
- Department of Medicine, Morehouse School of Medicine, Atlanta, Georgia, United States of America
| | - Christian M. Pettker
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Beth A. Plunkett
- Department of Obstetrics and Gynecology, NorthShore University Health System, Evanston, Illinois, United States of America
| | - Kristen Pogreba-Brown
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, Arizona, United States of America
| | - Athena Poppas
- Division of Cardiology, Warren Alpert Medical School of Brown University, Providence, Rhode Island, United States of America
| | - J. Zachary Porterfield
- Department of Internal Medicine, Division of Infectious Diseases, University of Kentucky, Lexington, Kentucky, United States of America
| | - John G. Quigley
- Department of Medicine, Division of Hematology/Oncology, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Davin K. Quinn
- Department of Psychiatry and Behavioral Sciences, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States of America
| | - Hengameh Raissy
- Department of Pediatrics, University of New Mexico, Health Sciences Center, Albuquerque, New Mexico, United States of America
| | - Candida J. Rebello
- Department of Nutrition and Chronic Disease, Pennington Biomedical Research Center, Baton Rouge, Louisiana, United States of America
| | - Uma M. Reddy
- Department of Obstetrics and Gynecology, Columbia University, New York, New York, United States of America
| | - Rebecca Reece
- Department of Medicine, Division of Infectious Diseases, West Virginia School of Medicine, Morgantown, West Virginia, United States of America
| | - Harrison T. Reeder
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Franz P. Rischard
- Department of Pulmonary and Critical Care, University of Arizona, Tucson, Arizona, United States of America
| | - Johana M. Rosas
- Department of Medicine, NYU Langone Health, New York, New York, United States of America
| | - Clifford J. Rosen
- MaineHealth Institute for Research, MaineHealth, Scarborough, Maine, United States of America
| | - Nadine G. Rouphael
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Dwight J. Rouse
- Department of Obstetrics and Gynecology, Brown University, Providence, Rhode Island, United States of America
| | - Adam M. Ruff
- Division of Pulmonary and Critical Care, University of Kansas Medical Center, Kansas City, Kansas City, United States of America
| | - Christina Saint Jean
- Department of Population Health, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Grecio J. Sandoval
- Department of Biostatistics, George Washington University, Washington, DC, United States of America
| | - Jorge L. Santana
- Department of Medicine, University of Puerto Rico, San Juan, Puerto Rico, United States of America
| | - Shannon M. Schlater
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, United States of America
| | - Frank C. Sciurba
- Department of Medicine, Division of Pulmonary Allergy and Critical Care Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Caitlin Selvaggi
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Sudha Seshadri
- Glenn Biggs Institute for Alzheimer’s and Neurodegenerative Diseases, University of Texas Health Sciences Center San Antonio, San Antonio, Texas, United States of America
| | - Howard D. Sesso
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston, Massachusetts, United States of America
| | - Dimpy P. Shah
- Department of Population Health Sciences, Mays Cancer Center, University of Texas Health, San Antonio, Texas, United States of America
| | - Eyal Shemesh
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Zaki A. Sherif
- Department of Biochemistry & Molecular Biology, Howard University College of Medicine, Washington, DC, United States of America
| | - Daniel J. Shinnick
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Hyagriv N. Simhan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Upinder Singh
- Department of Internal Medicine, Stanford University, Stanford, California, United States of America
| | - Amber Sowles
- Department of Obstetrics and Gynecology, University of Utah Health, Salt Lake City, Utah, United States of America
| | - Vignesh Subbian
- Department of Biomedical Engineering, Department of Systems and Industrial Engineering, University of Arizona College of Engineering, Tucson, Arizona, United States of America
| | - Jun Sun
- Department of Medicine, University of Illinois Chicago, Chicago, Illinois, United States of America
| | - Mehul S. Suthar
- Department of Pediatrics, Emory Vaccine Center, Emory University, Atlanta, Georgia, United States of America
| | - Larissa J. Teunis
- Health Services Research Center, Emory University, Atlanta, Georgia, United States of America
| | - John M. Thorp
- Department of Obstetrics and Gynecology, University of North Carolina Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Amberly Ticotsky
- Department of Family Medicine, Cambridge Health Alliance, Cambridge, Massachusetts, United States of America
| | - Alan T. N. Tita
- Department of Obstetrics and Gynecology and Center for Women’s Reproductive Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Robin Tragus
- Department of Medicine, University of Texas Health Science Center, San Antonio, Texas, United States of America
| | - Katherine R. Tuttle
- Department of Medicine, Division of Nephrology, University of Washington School of Medicine, Spokane, Washington, United States of America
| | - Alfredo E. Urdaneta
- Department of Emergency Medicine, Stanford University, Stanford, California, United States of America
| | - P. J. Utz
- Department of Internal Medicine, Stanford University, Stanford, California, United States of America
| | - Timothy M. VanWagoner
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Andrew Vasey
- Department of Internal Medicine, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Suzanne D. Vernon
- Department of Research, Bateman Horne Center, Salt Lake City, Utah, United States of America
| | - Crystal Vidal
- Department of Population Health, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Tiffany Walker
- Department of Medicine, Emory University, Atlanta, Georgia, United States of America
| | - Honorine D. Ward
- Department of Medicine, Tufts Medical Center, Boston, Massachusetts, United States of America
| | - David E. Warren
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Ryan M. Weeks
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, Kentucky, United States of America
| | - Steven J. Weiner
- Department of Biostatistics, George Washington University, Washington, DC, United States of America
| | - Jordan C. Weyer
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Jennifer L. Wheeler
- Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Sidney W. Whiteheart
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, United States of America
| | - Zanthia Wiley
- Department of Medicine, Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Natasha J. Williams
- Institute for Excellence in Health Equity, NYU Grossman School of Medicine, New York, New York, United States of America
| | - Juan P. Wisnivesky
- Division of General Internal Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - John C. Wood
- Department of Pediatrics and Radiology, Children’s Hospital of Los Angeles, Los Angeles, California, United States of America
| | - Lynn M. Yee
- Department of Obstetrics and Gynecology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
| | - Natalie M. Young
- Swedish Center for Research and Innovation, Providence Swedish Medical Center, Seattle, Washington, United States of America
| | - Sokratis N. Zisis
- Department of Medicine, Department of Pediatrics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America
| | - Andrea S. Foulkes
- Department of Biostatistics, Massachusetts General Hospital, Boston, Massachusetts, United States of America
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Thaweethai T, Jolley SE, Karlson EW, Levitan EB, Levy B, McComsey GA, McCorkell L, Nadkarni GN, Parthasarathy S, Singh U, Walker TA, Selvaggi CA, Shinnick DJ, Schulte CCM, Atchley-Challenner R, Alba GA, Alicic R, Altman N, Anglin K, Argueta U, Ashktorab H, Baslet G, Bassett IV, Bateman L, Bedi B, Bhattacharyya S, Bind MA, Blomkalns AL, Bonilla H, Bush PA, Castro M, Chan J, Charney AW, Chen P, Chibnik LB, Chu HY, Clifton RG, Costantine MM, Cribbs SK, Davila Nieves SI, Deeks SG, Duven A, Emery IF, Erdmann N, Erlandson KM, Ernst KC, Farah-Abraham R, Farner CE, Feuerriegel EM, Fleurimont J, Fonseca V, Franko N, Gainer V, Gander JC, Gardner EM, Geng LN, Gibson KS, Go M, Goldman JD, Grebe H, Greenway FL, Habli M, Hafner J, Han JE, Hanson KA, Heath J, Hernandez C, Hess R, Hodder SL, Hoffman MK, Hoover SE, Huang B, Hughes BL, Jagannathan P, John J, Jordan MR, Katz SD, Kaufman ES, Kelly JD, Kelly SW, Kemp MM, Kirwan JP, Klein JD, Knox KS, Krishnan JA, Kumar A, Laiyemo AO, Lambert AA, Lanca M, Lee-Iannotti JK, Logarbo BP, Longo MT, Luciano CA, Lutrick K, Maley JH, Marathe JG, Marconi V, Marshall GD, Martin CF, Matusov Y, Mehari A, Mendez-Figueroa H, Mermelstein R, Metz TD, Morse R, Mosier J, Mouchati C, Mullington J, Murphy SN, Neuman RB, Nikolich JZ, Ofotokun I, Ojemakinde E, Palatnik A, Palomares K, Parimon T, Parry S, Patterson JE, Patterson TF, Patzer RE, Peluso MJ, Pemu P, Pettker CM, Plunkett BA, Pogreba-Brown K, Poppas A, Quigley JG, Reddy U, Reece R, Reeder H, Reeves WB, Reiman EM, Rischard F, Rosand J, Rouse DJ, Ruff A, Saade G, Sandoval GJ, Schlater SM, Shepherd F, Sherif ZA, Simhan H, Singer NG, Skupski DW, Sowles A, Sparks JA, Sukhera FI, Taylor BS, Teunis L, Thomas RJ, Thorp JM, Thuluvath P, Ticotsky A, Tita AT, Tuttle KR, Urdaneta AE, Valdivieso D, VanWagoner TM, Vasey A, Verduzco-Gutierrez M, Wallace ZS, Ward HD, Warren DE, Weiner SJ, Welch S, Whiteheart SW, Wiley Z, Wisnivesky JP, Yee LM, Zisis S, Horwitz LI, Foulkes AS. Development of a Definition of Postacute Sequelae of SARS-CoV-2 Infection. JAMA 2023; 329:1934-1946. [PMID: 37278994 PMCID: PMC10214179 DOI: 10.1001/jama.2023.8823] [Citation(s) in RCA: 148] [Impact Index Per Article: 148.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/01/2023] [Indexed: 06/07/2023]
Abstract
Importance SARS-CoV-2 infection is associated with persistent, relapsing, or new symptoms or other health effects occurring after acute infection, termed postacute sequelae of SARS-CoV-2 infection (PASC), also known as long COVID. Characterizing PASC requires analysis of prospectively and uniformly collected data from diverse uninfected and infected individuals. Objective To develop a definition of PASC using self-reported symptoms and describe PASC frequencies across cohorts, vaccination status, and number of infections. Design, Setting, and Participants Prospective observational cohort study of adults with and without SARS-CoV-2 infection at 85 enrolling sites (hospitals, health centers, community organizations) located in 33 states plus Washington, DC, and Puerto Rico. Participants who were enrolled in the RECOVER adult cohort before April 10, 2023, completed a symptom survey 6 months or more after acute symptom onset or test date. Selection included population-based, volunteer, and convenience sampling. Exposure SARS-CoV-2 infection. Main Outcomes and Measures PASC and 44 participant-reported symptoms (with severity thresholds). Results A total of 9764 participants (89% SARS-CoV-2 infected; 71% female; 16% Hispanic/Latino; 15% non-Hispanic Black; median age, 47 years [IQR, 35-60]) met selection criteria. Adjusted odds ratios were 1.5 or greater (infected vs uninfected participants) for 37 symptoms. Symptoms contributing to PASC score included postexertional malaise, fatigue, brain fog, dizziness, gastrointestinal symptoms, palpitations, changes in sexual desire or capacity, loss of or change in smell or taste, thirst, chronic cough, chest pain, and abnormal movements. Among 2231 participants first infected on or after December 1, 2021, and enrolled within 30 days of infection, 224 (10% [95% CI, 8.8%-11%]) were PASC positive at 6 months. Conclusions and Relevance A definition of PASC was developed based on symptoms in a prospective cohort study. As a first step to providing a framework for other investigations, iterative refinement that further incorporates other clinical features is needed to support actionable definitions of PASC.
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Affiliation(s)
- Tanayott Thaweethai
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
| | | | | | | | - Bruce Levy
- Harvard Medical School, Boston, Massachusetts
- Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Lisa McCorkell
- Patient-Led Research Collaborative, Calabasas, California
| | | | | | - Upinder Singh
- Stanford University School of Medicine, Stanford, California
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mario Castro
- University of Kansas Medical Center, Kansas City
| | | | | | - Peter Chen
- Cedars-Sinai Medical Center, Los Angeles, California
| | | | - Helen Y Chu
- University of Washington School of Medicine, Seattle
| | | | | | | | | | | | | | | | | | | | | | | | - Cheryl E Farner
- The University of Texas Health Science Center at San Antonio
| | | | | | - Vivian Fonseca
- Tulane University Health Sciences Center, New Orleans, Louisiana
| | | | | | | | | | | | | | - Minjoung Go
- Stanford University School of Medicine, Stanford, California
| | | | | | | | | | - John Hafner
- University of Illinois Chicago College of Medicine
| | - Jenny E Han
- Emory University School of Medicine, Atlanta, Georgia
| | | | - James Heath
- Institute for Systems Biology, Seattle, Washington
| | | | - Rachel Hess
- University of Utah Schools of the Health Sciences, Salt Lake City
| | - Sally L Hodder
- West Virginia Clinical and Translational Science Institute, Morgantown
| | | | | | | | | | | | - Janice John
- Cambridge Health Alliance, Cambridge, Massachusetts
| | | | - Stuart D Katz
- New York University Grossman School of Medicine, New York
| | | | | | - Sara W Kelly
- University of Illinois College of Medicine at Peoria
| | | | - John P Kirwan
- Pennington Biomedical Research Center, Baton Rouge, Louisiana
| | | | | | - Jerry A Krishnan
- University of Illinois Hospital and Health Sciences System, Chicago
| | - Andre Kumar
- Stanford University School of Medicine, Stanford, California
| | | | | | | | | | | | | | | | | | - Jason H Maley
- Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | | | | | | | | | - Yuri Matusov
- Cedars-Sinai Medical Center, Los Angeles, California
| | - Alem Mehari
- Howard University College of Medicine, Washington, DC
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jan E Patterson
- The University of Texas Health Science Center at San Antonio
| | | | | | | | | | | | - Beth A Plunkett
- Harvard Medical School, Boston, Massachusetts
- NorthShore University HealthSystem, Evanston, Illinois
| | | | - Athena Poppas
- Warren Alpert Medical School, Brown University, Providence, Rhode Island
| | | | - Uma Reddy
- Columbia University Irving Medical Center, New York, New York
| | - Rebecca Reece
- West Virginia University School of Medicine, Morgantown
| | | | - W B Reeves
- Department of Medicine, The University of Texas Health Science Center at San Antonio
| | | | | | | | | | - Adam Ruff
- The University of Kansas Medical Center, Kansas City
| | | | - Grecio J Sandoval
- Milken Institute of Public Health, The George Washington University, Washington, DC
| | | | | | - Zaki A Sherif
- Howard University College of Medicine, Washington, DC
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Steven J Weiner
- The George Washington University Biostatistics Center, Rockville, Maryland
| | | | | | | | | | - Lynn M Yee
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | | | | | - Andrea S Foulkes
- Massachusetts General Hospital, Boston
- Harvard Medical School, Boston, Massachusetts
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9
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Yi D, Liu B, Ding H, Li S, Li R, Pan J, Ramirez K, Xia X, Kala M, Singh I, Ye Q, Lee WH, Frye RE, Wang T, Zhao Y, Knox KS, Glembotski CC, Fallon MB, Dai Z. E2F1 Mediates SOX17 Deficiency-Induced Pulmonary Hypertension. bioRxiv 2023:2023.02.15.528740. [PMID: 36824855 PMCID: PMC9949178 DOI: 10.1101/2023.02.15.528740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Rationale Rare genetic variants and genetic variation at loci in an enhancer in SRY-Box Transcription Factor 17 (SOX17) are identified in patients with idiopathic pulmonary arterial hypertension (PAH) and PAH with congenital heart disease. However, the exact role of genetic variants or mutation in SOX17 in PAH pathogenesis has not been reported. Objectives To investigate the role of SOX17 deficiency in pulmonary hypertension (PH) development. Methods Human lung tissue and endothelial cells (ECs) from IPAH patients were used to determine the expression of SOX17. Tie2Cre-mediated and EC-specific deletion of Sox17 mice were assessed for PH development. Single-cell RNA sequencing analysis, human lung ECs, and smooth muscle cell culture were performed to determine the role and mechanisms of SOX17 deficiency. A pharmacological approach was used in Sox17 deficiency mice for therapeutic implication. Measurement and Main Results SOX17 expression was downregulated in the lungs and pulmonary ECs of IPAH patients. Mice with Tie2Cre mediated Sox17 knockdown and EC-specific Sox17 deletion developed spontaneously mild PH. Loss of endothelial Sox17 in EC exacerbated hypoxia-induced PH in mice. Loss of SOX17 in lung ECs induced endothelial dysfunctions including upregulation of cell cycle programming, proliferative and anti-apoptotic phenotypes, augmentation of paracrine effect on pulmonary arterial smooth muscle cells, impaired cellular junction, and BMP signaling. E2F Transcription Factor 1 (E2F1) signaling was shown to mediate the SOX17 deficiency-induced EC dysfunction and PH development. Conclusions Our study demonstrated that endothelial SOX17 deficiency induces PH through E2F1 and targeting E2F1 signaling represents a promising approach in PAH patients.
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Affiliation(s)
- Dan Yi
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Bin Liu
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Hongxu Ding
- Department of Pharmacy Practice & Science, College of Pharmacy, University of Arizona, Tucson, Arizona, USA
| | - Shuai Li
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Rebecca Li
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Jiakai Pan
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Karina Ramirez
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Xiaomei Xia
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Mrinalini Kala
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Indrapal Singh
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Qinmao Ye
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Won Hee Lee
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | | | - Ting Wang
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Environmental Health Science and Center of Translational Science, Florida International University, Port Saint Lucie, Florida, USA
| | - Yutong Zhao
- Department of Physiology and Cell Biology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Kenneth S. Knox
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Christopher C. Glembotski
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Michael B. Fallon
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - Zhiyu Dai
- Division of Pulmonary, Critical Care and Sleep, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Internal Medicine, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- Translational Cardiovascular Research Center, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- BIO5 Institute, University of Arizona, Tucson, Arizona, USA
- Sarver Heart Center, University of Arizona, Tucson, Arizona, USA
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10
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Malo J, Natt B, Chaudhary S, Knox KS. Prophylaxis in Lung Transplant Recipients. Clin Infect Dis 2023; 76:368-369. [PMID: 36037080 DOI: 10.1093/cid/ciac706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/25/2022] [Indexed: 01/18/2023] Open
Affiliation(s)
- Joshua Malo
- Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Bhupinder Natt
- Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Sachin Chaudhary
- Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, Arizona, USA
| | - Kenneth S Knox
- Department of Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
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11
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Kala M, Casanova NG, Feng A, Jacobsen JR, Grischo G, Liang Y, Moreno Y, Wang T, Knox KS. Carbon nanotube stimulation of human mononuclear cells to model granulomatous inflammation. Am J Transl Res 2023; 15:1704-1714. [PMID: 37056834 PMCID: PMC10086910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/06/2023] [Indexed: 04/15/2023]
Abstract
OBJECTIVES Sarcoidosis is a multisystem inflammatory granulomatous disease of unknown etiology. The disease most often affects the lung and leads to death in 5% of patients. Patients who die often succumb due to progressive fibrotic lung disease. Translational research in sarcoidosis is significantly limited by a paucity of available experimental models. Carbon nanotubes are released into the environment during fuel combustion, manufacturing, and natural fires. Exposed individuals are at risk for cancer, lung inflammation and other chronic pulmonary disorders, including diseases resembling sarcoidosis and pulmonary fibrosis. In this study, we developed and characterized an in vitro experimental model relevant to sarcoidosis using human peripheral blood mononuclear cells (PBMCs) exposed to multiwalled carbon nanotubes (MWCNTs). METHODS MWCNT-exposed PBMCs were cultured and analyzed by Giemsa staining, immunohistochemistry (IHC) and RNA-seq analysis on days 1 and 7. Normalization and differential expression were calculated using DESeq2, Limma and edgeR methods from Bioconductor (adjP, log2Fold change and rawP). RESULTS MWCNT stimulation of PBMCs from healthy subjects leads to the formation of granuloma-like cell clusters and stereotypical inflammatory cytokine secretion. PBMC transcriptomic analysis demonstrated activation of defense- and inflammation-related pathways, including the Jak-Stat pathway and TNF signaling pathway. CONCLUSIONS This model is unique, as cell clustering is seen in the absence of specific antigenic stimulation (e.g., mycobacterial) or the addition of exogenous cytokines. Modeling with PBMCs provides a platform for precision medicine and evaluation of future therapies for granulomatous and fibrotic lung diseases.
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Affiliation(s)
- Mrinalini Kala
- Department of Internal Medicine, University of Arizona College of Medicine PhoenixPhoenix, AZ, United States
| | - Nancy G Casanova
- Department of Medicine, University of ArizonaTucson, AZ, United States
| | - Anlin Feng
- Center for Translational Science, Florida International UniversityPort Saint Lucie, FL, United States
| | - Jeffrey R Jacobsen
- Department of Pathology, University of Utah School of Medicine and ARUP LabUnited States
| | - Garrett Grischo
- Department of Internal Medicine, University of Arizona College of Medicine PhoenixPhoenix, AZ, United States
| | - Ying Liang
- Center for Translational Science, Florida International UniversityPort Saint Lucie, FL, United States
| | - Yesenia Moreno
- Department of Internal Medicine, University of Arizona College of Medicine PhoenixPhoenix, AZ, United States
| | - Ting Wang
- Department of Internal Medicine, University of Arizona College of Medicine PhoenixPhoenix, AZ, United States
- Center for Translational Science, Florida International UniversityPort Saint Lucie, FL, United States
| | - Kenneth S Knox
- Department of Internal Medicine, University of Arizona College of Medicine PhoenixPhoenix, AZ, United States
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12
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Martinez GF, Knox KS. Precepting medical students in the clinical setting: Its time, not money. Med Educ 2022; 56:698-700. [PMID: 35485371 DOI: 10.1111/medu.14815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Affiliation(s)
| | - Kenneth S Knox
- University of Arizona College of Medicine - Phoenix, Phoenix, Arizona, USA
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13
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Kato K, Papageorgiou I, Shin YJ, Kleinhenz JM, Palumbo S, Hahn S, Irish JD, Rounseville SP, Knox KS, Hecker L. Lung-Targeted Delivery of Dimethyl Fumarate Promotes the Reversal of Age-Dependent Established Lung Fibrosis. Antioxidants (Basel) 2022; 11:492. [PMID: 35326142 PMCID: PMC8944574 DOI: 10.3390/antiox11030492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 01/27/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF), a severe and deadly form of lung fibrosis, is widely regarded as a disease of aging. We previously demonstrated that aged mice with persistent lung fibrosis and IPF lung myofibroblasts exhibit deficient Nrf2-mediated antioxidant responses. Tecfidera is an orally administered FDA-approved drug for the treatment of multiple sclerosis, where the active pharmaceutical ingredient is dimethyl fumarate (DMF), an active Nrf2 activator. However, no studies have evaluated the efficacy of DMF for age-associated persistent lung fibrosis. Here, we demonstrate that in IPF lung fibroblasts, DMF treatment inhibited both TGF-β-mediated pro-fibrotic phenotypes and led to a reversal of established pro-fibrotic phenotypes. We also evaluated the pre-clinical efficacy of lung-targeted (inhaled) vs. systemic (oral) delivery of DMF in an aging murine model of bleomycin-induced persistent lung fibrosis. DMF or vehicle was administered daily to aged mice by oral gavage or intranasal delivery from 3-6 weeks post-injury when mice exhibited non-resolving lung fibrosis. In contrast to systemic (oral) delivery, only lung-targeted (inhaled) delivery of DMF restored lung Nrf2 expression levels, reduced lung oxidative stress, and promoted the resolution of age-dependent established fibrosis. This is the first study to demonstrate the efficacy of lung-targeted DMF delivery to promote the resolution of age-dependent established lung fibrosis.
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Affiliation(s)
- Kosuke Kato
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (K.K.); (I.P.); (Y.-J.S.); (J.M.K.)
| | - Ioannis Papageorgiou
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (K.K.); (I.P.); (Y.-J.S.); (J.M.K.)
| | - Yoon-Joo Shin
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (K.K.); (I.P.); (Y.-J.S.); (J.M.K.)
| | - Jennifer M. Kleinhenz
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (K.K.); (I.P.); (Y.-J.S.); (J.M.K.)
| | - Sunny Palumbo
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85721, USA; (S.P.); (S.H.); (J.D.I.); (S.P.R.)
| | - Seongmin Hahn
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85721, USA; (S.P.); (S.H.); (J.D.I.); (S.P.R.)
| | - Joseph D. Irish
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85721, USA; (S.P.); (S.H.); (J.D.I.); (S.P.R.)
| | - Skye P. Rounseville
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, AZ 85721, USA; (S.P.); (S.H.); (J.D.I.); (S.P.R.)
| | - Kenneth S. Knox
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, AZ 85004, USA;
| | - Louise Hecker
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, Department of Medicine, Emory University, Atlanta, GA 30322, USA; (K.K.); (I.P.); (Y.-J.S.); (J.M.K.)
- Atlanta VA Healthcare System, Atlanta, GA 30033, USA
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14
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Epelbaum O, Carmona EM, Evans SE, Hage CA, Jarrett B, Knox KS, Limper AH, Pennington KM. Antifungal Prophylaxis for Adult Recipients of Veno-Venous Extracorporeal Membrane Oxygenation: A Cautionary Stance During the COVID-19 Pandemic. ASAIO J 2021; 67:611-613. [PMID: 33769344 PMCID: PMC8153986 DOI: 10.1097/mat.0000000000001456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Oleg Epelbaum
- From the Division of Pulmonary, Critical Care, and Sleep Medicine, Westchester Medical Center, Valhalla, New York
| | - Eva M. Carmona
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota
| | - Scott E. Evans
- Department of Pulmonary Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Chadi A. Hage
- Division of Pulmonary, Critical Care, and Sleep Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Benjamin Jarrett
- Division of Pulmonary and Critical Care Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Kenneth S. Knox
- Division of Pulmonary and Critical Care Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Andrew H. Limper
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota
| | - Kelly M. Pennington
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, Minnesota
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15
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Chaudhary S, Natt B, Bime C, Knox KS, Glassberg MK. Corrigendum: Antifibrotics in COVID-19 Lung Disease: Let Us Stay Focused. Front Med (Lausanne) 2021; 7:604640. [PMID: 33777966 PMCID: PMC7992361 DOI: 10.3389/fmed.2020.604640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/28/2022] Open
Affiliation(s)
- Sachin Chaudhary
- Interstitial Lung Disease Program, University of Arizona Colleges of Medicine, Tucson, AZ, United States
| | - Bhupinder Natt
- Interstitial Lung Disease Program, University of Arizona Colleges of Medicine, Tucson, AZ, United States
| | - Christian Bime
- Interstitial Lung Disease Program, University of Arizona Colleges of Medicine, Tucson, AZ, United States
| | - Kenneth S Knox
- Banner-University Medicine Division, Phoenix, AZ, United States
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16
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Casanova NG, Zhou T, Gonzalez-Garay ML, Lussier YA, Sweiss N, Ma SF, Noth I, Knox KS, Garcia JGN. MicroRNA and protein-coding gene expression analysis in idiopathic pulmonary fibrosis yields novel biomarker signatures associated to survival. Transl Res 2021; 228:1-12. [PMID: 32711186 PMCID: PMC7779721 DOI: 10.1016/j.trsl.2020.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 07/09/2020] [Accepted: 07/16/2020] [Indexed: 02/04/2023]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive interstitial lung disease of unknown etiology that poses significant challenges in early diagnosis and prediction of progression. Analyses of microRNA and gene expression in IPF have yielded potentially predictive information. However, the relationship between microRNA/gene expression and quantitative phenotypic value in IPF remains controversial, as is the added value of this approach to current molecular signatures in IPF. To identify biomarkers predictive of survival in IPF via a microRNA-driven strategy. We profiled microRNA and protein-coding gene expression in peripheral blood mononuclear cells from 70 IPF subjects in a discovery cohort. We linked the microRNA/gene expression level with the quantitative phenotypic variation in IPF, including diffusing capacity of the lung for carbon monoxide and the forced vital capacity percent predicted. In silico analyses of expression profiles and quantitative phenotypic data allowed the generation of 2 sets of IPF molecular signatures (unique for microRNAs and protein-coding genes) that predict IPF survival. Each signature performed well in a validation cohort comprised of IPF patients aggregated from distinct patient populations recruited from different sites. Resampling test suggests that the protein-coding gene based signature is comparable and potentially superior to published IPF prognostic gene signatures. In conclusion, these results highlight the utility of microRNA-driven peripheral blood molecular signatures as valuable and novel biomarkers associated to individuals at high survival risk and for potentially facilitating individualized therapies in this enigmatic disorder.
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Affiliation(s)
- Nancy G Casanova
- Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada
| | | | - Yves A Lussier
- Center for Biomedical Informatics and Biostatistics, University of Arizona, Tucson, Arizona
| | - Nadera Sweiss
- Section of Rheumatology Department of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Shwu-Fan Ma
- Section of Pulmonary/Critical Care, Department of Medicine, University of Chicago, Chicago, Illinois
| | - Imre Noth
- Division of Pulmonary and Critical Care Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Kenneth S Knox
- Department of Medicine, College of Medicine-Phoenix, University of Arizona Health Sciences, Phoenix, Arizona
| | - Joe G N Garcia
- Department of Medicine, University of Arizona Health Sciences, Tucson, Arizona.
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17
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Saber M, Rice AD, Christie I, Roberts RG, Knox KS, Nakaji P, Rowe RK, Wang T, Lifshitz J. Remote Ischemic Conditioning Reduced Acute Lung Injury After Traumatic Brain Injury in the Mouse. Shock 2021; 55:256-267. [PMID: 32769821 PMCID: PMC8878575 DOI: 10.1097/shk.0000000000001618] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
ABSTRACT Traumatic brain injury (TBI) can induce acute lung injury (ALI). The exact pathomechanism of TBI-induced ALI is poorly understood, limiting treatment options. Remote ischemic conditioning (RIC) can mitigate detrimental outcomes following transplants, cardiac arrests, and neurological injuries. In this study, we hypothesized that RIC would reduce TBI-induced ALI by regulating the sphingosine-1-phosphate (S1P)-dependent pathway, a central regulator of endothelial barrier integrity, lymphocyte, and myokine trafficking. Male mice were subjected to either diffuse TBI by midline fluid percussion or control sham injury and randomly assigned among four groups: sham, TBI, sham RIC, or TBI RIC; RIC was performed 1 h prior to TBI. Mice were euthanized at 1-h postinjury or 7 days post-injury (DPI) and lung tissue, bronchoalveolar lavage (BAL) fluid, and blood were collected. Lung tissue was analyzed for histopathology, irisin myokine levels, and S1P receptor levels. BAL fluid and blood were analyzed for cellularity and myokine/S1P levels, respectively. One-hour postinjury, TBI damaged lung alveoli and increased neutrophil infiltration; RIC preserved alveoli. BAL from TBI mice had more neutrophils and higher neutrophil/monocyte ratios compared with sham, where TBI RIC mice showed no injury-induced change. Further, S1P receptor 3 and irisin-associated protein levels were significantly increased in the lungs of TBI mice compared with sham, which was prevented by RIC. However, there was no RIC-associated change in plasma irisin or S1P. At 7 DPI, ALI in TBI mice was largely resolved, with evidence for residual lung pathology. Thus, RIC may be a viable intervention for TBI-induced ALI to preserve lung function and facilitate clinical management.
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Affiliation(s)
- Maha Saber
- Child Health, University of Arizona College of Medicine – Phoenix, Phoenix, AZ
- Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, AZ
| | - Amanda D. Rice
- Internal Medicine, University of Arizona College of Medicine - Phoenix, Phoenix, AZ
| | - Immaculate Christie
- Child Health, University of Arizona College of Medicine – Phoenix, Phoenix, AZ
- Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, AZ
| | - Rebecca G. Roberts
- Internal Medicine, University of Arizona College of Medicine - Phoenix, Phoenix, AZ
| | - Kenneth S. Knox
- Internal Medicine, University of Arizona College of Medicine - Phoenix, Phoenix, AZ
| | - Peter Nakaji
- Neurosurgery, University of Arizona College of Medicine - Phoenix, Phoenix, AZ
| | - Rachel K. Rowe
- Child Health, University of Arizona College of Medicine – Phoenix, Phoenix, AZ
- Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, AZ
- Phoenix VA Health Care System, Phoenix, AZ
| | - Ting Wang
- Internal Medicine, University of Arizona College of Medicine - Phoenix, Phoenix, AZ
| | - Jonathan Lifshitz
- Child Health, University of Arizona College of Medicine – Phoenix, Phoenix, AZ
- Barrow Neurological Institute at Phoenix Children’s Hospital, Phoenix, AZ
- Phoenix VA Health Care System, Phoenix, AZ
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18
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Zhou JJ, Zhai J, Zhou H, Chen Y, Guerra S, Robey I, Weinstock GM, Weinstock E, Dong Q, Knox KS, Twigg HL. Supraglottic Lung Microbiome Taxa Are Associated with Pulmonary Abnormalities in an HIV Longitudinal Cohort. Am J Respir Crit Care Med 2021; 202:1727-1731. [PMID: 32783620 DOI: 10.1164/rccm.202004-1086le] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | - Jing Zhai
- University of Arizona Tucson, Arizona
| | - Hua Zhou
- University of California, Los Angeles Los Angeles, California
| | - Yin Chen
- University of Arizona Tucson, Arizona
| | | | - Ian Robey
- University of Arizona Tucson, Arizona
| | | | - Erica Weinstock
- Jackson Laboratory for Genomic Medicine Farmington, Connecticut
| | | | - Kenneth S Knox
- University of Arizona College of Medicine-Phoenix Phoenix, Arizona and
| | - Homer L Twigg
- Indiana University Medical Center Indianapolis, Indiana
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19
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Casanova NG, Gonzalez-Garay ML, Sun B, Bime C, Sun X, Knox KS, Crouser ED, Sammani N, Gonzales T, Natt B, Chaudhary S, Lussier Y, Garcia JGN. Differential transcriptomics in sarcoidosis lung and lymph node granulomas with comparisons to pathogen-specific granulomas. Respir Res 2020; 21:321. [PMID: 33276795 PMCID: PMC7716494 DOI: 10.1186/s12931-020-01537-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/06/2020] [Indexed: 12/15/2022] Open
Abstract
Rationale Despite the availability of multi-“omics” strategies, insights into the etiology and pathogenesis of sarcoidosis have been elusive. This is partly due to the lack of reliable preclinical models and a paucity of validated biomarkers. As granulomas are a key feature of sarcoidosis, we speculate that direct genomic interrogation of sarcoid tissues, may lead to identification of dysregulated gene pathways or biomarker signatures. Objective To facilitate the development sarcoidosis genomic biomarkers by gene expression profiling of sarcoidosis granulomas in lung and lymph node tissues (most commonly affected organs) and comparison to infectious granulomas (coccidiodomycosis and tuberculosis). Methods Transcriptomic profiles of immune-related gene from micro-dissected sarcoidosis granulomas within lung and mediastinal lymph node tissues and compared to infectious granulomas from paraffin-embedded blocks. Differentially-expressed genes (DEGs) were profiled, compared among the three granulomatous diseases and analyzed for functional enrichment pathways. Results Despite histologic similarities, DEGs and pathway enrichment markedly differed in sarcoidosis granulomas from lymph nodes and lung. Lymph nodes showed a clear immunological response, whereas a structural regenerative response was observed in lung. Sarcoidosis granuloma gene expression data corroborated previously reported genomic biomarkers (STAB1, HBEGF, and NOTCH4), excluded others and identified new genomic markers present in lung and lymph nodes, ADAMTS1, NPR1 and CXCL2. Comparisons between sarcoidosis and pathogen granulomas identified pathway divergences and commonalities at gene expression level. Conclusion These findings suggest the importance of tissue and disease-specificity evaluation when exploring sarcoidosis genomic markers. This relevant translational information in sarcoidosis and other two histopathological similar infections provides meaningful specific genomic-derived biomarkers for sarcoidosis diagnosis and prognosis.
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Affiliation(s)
- Nancy G Casanova
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Manuel L Gonzalez-Garay
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Belinda Sun
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Christian Bime
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Xiaoguang Sun
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Kenneth S Knox
- Department of Medicine, College of Medicine, University of Arizona, Phoenix, AZ, USA
| | - Elliott D Crouser
- Division of Pulmonary and Critical Care Medicine, The Ohio State University, Columbus, OH, USA
| | - Nora Sammani
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Taylor Gonzales
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Bhupinder Natt
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Sachin Chaudhary
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Yves Lussier
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA
| | - Joe G N Garcia
- Department of Medicine, College of Medicine, University of Arizona Health Sciences, Tucson, AZ, USA.
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20
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Gu W, Shi J, Liu H, Zhang X, Zhou JJ, Li M, Zhou D, Li R, Lv J, Wen G, Zhu S, Qi T, Li W, Wang X, Wang Z, Zhu H, Zhou C, Knox KS, Wang T, Chen Q, Qian Z, Zhou T. Peripheral blood non-canonical small non-coding RNAs as novel biomarkers in lung cancer. Mol Cancer 2020; 19:159. [PMID: 33176804 PMCID: PMC7659116 DOI: 10.1186/s12943-020-01280-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/03/2020] [Indexed: 01/09/2023] Open
Abstract
One unmet challenge in lung cancer diagnosis is to accurately differentiate lung cancer from other lung diseases with similar clinical symptoms and radiological features, such as pulmonary tuberculosis (TB). To identify reliable biomarkers for lung cancer screening, we leverage the recently discovered non-canonical small non-coding RNAs (i.e., tRNA-derived small RNAs [tsRNAs], rRNA-derived small RNAs [rsRNAs], and YRNA-derived small RNAs [ysRNAs]) in human peripheral blood mononuclear cells and develop a molecular signature composed of distinct ts/rs/ysRNAs (TRY-RNA). Our TRY-RNA signature precisely discriminates between control, lung cancer, and pulmonary TB subjects in both the discovery and validation cohorts and outperforms microRNA-based biomarkers, which bears the diagnostic potential for lung cancer screening.
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Affiliation(s)
- Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, Jiangsu, China.
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Hui Liu
- Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Department of Laboratory Medicine, Bengbu Medical College, 2600 Donghaidadao, Bengbu, 233003, Anhui, China
| | - Xudong Zhang
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, 85721, USA
| | - Musheng Li
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, Nevada, 89557, USA
| | - Dandan Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, Nevada, 89557, USA
| | - Rui Li
- Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Department of Laboratory Medicine, Bengbu Medical College, 2600 Donghaidadao, Bengbu, 233003, Anhui, China
| | - Jingzhu Lv
- Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Department of Laboratory Medicine, Bengbu Medical College, 2600 Donghaidadao, Bengbu, 233003, Anhui, China
| | - Guoxia Wen
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, Jiangsu, China
| | - Shanshan Zhu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, Jiangsu, China
| | - Ting Qi
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, 2 Sipailou, Nanjing, 210096, Jiangsu, China
| | - Wei Li
- Anhui Clinical and Preclinical Key Laboratory of Respiratory Disease, Department of Respiration, First Affiliated Hospital, Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Xiaojing Wang
- Anhui Clinical and Preclinical Key Laboratory of Respiratory Disease, Department of Respiration, First Affiliated Hospital, Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Zhaohua Wang
- The Infectious Disease Hospital of Bengbu City, Bengbu, 233000, Anhui, China
| | - Hua Zhu
- Department of Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Changcheng Zhou
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA
| | - Kenneth S Knox
- Department of Internal Medicine, College of Medicine Phoenix, University of Arizona, Phoenix, AZ, 85004, USA
| | - Ting Wang
- Department of Internal Medicine, College of Medicine Phoenix, University of Arizona, Phoenix, AZ, 85004, USA
| | - Qi Chen
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521, USA.
| | - Zhongqing Qian
- Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Department of Laboratory Medicine, Bengbu Medical College, 2600 Donghaidadao, Bengbu, 233003, Anhui, China.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, 1664 North Virginia Street, Reno, Nevada, 89557, USA.
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21
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Chaudhary S, Natt B, Bime C, Knox KS, Glassberg MK. Antifibrotics in COVID-19 Lung Disease: Let Us Stay Focused. Front Med (Lausanne) 2020; 7:539. [PMID: 33072773 PMCID: PMC7531602 DOI: 10.3389/fmed.2020.00539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 07/30/2020] [Indexed: 01/28/2023] Open
Abstract
After decades of research, two therapies for chronic fibrotic lung disease are now approved by the FDA, with dozens more anti-fibrotic therapies in the pipeline. A great deal of enthusiasm has been generated for the use of these drugs, which are by no means curative but clearly have a favorable impact on lung function decline over time. Amidst a flurry of newly developed and repurposed drugs to treat the coronavirus disease 2019 (COVID-19) and its accompanying acute respiratory distress syndrome (ARDS), few have emerged as effective. Historically, survivors of severe viral pneumonia and related acute lung injury with ARDS often have near full recovery of lung function. While the pathological findings of the lungs of patients with COVID-19 can be diverse, current reports have shown significant lung fibrosis predominantly in autopsy studies. There is growing enthusiasm to study anti-fibrotic therapy for inevitable lung fibrosis, and clinical trials are underway using currently FDA-approved anti-fibrotic therapies. Given the relatively favorable outcomes of survivors of virus-mediated ARDS and the low prevalence of clinically meaningful lung fibrosis in survivors, this perspective examines if there is a rationale for testing these repurposed antifibrotic agents in COVID-19-associated lung disease.
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Affiliation(s)
- Sachin Chaudhary
- Interstitial Lung Disease Program, University of Arizona Colleges of Medicine, Tucson, AZ, United States
| | - Bhupinder Natt
- Interstitial Lung Disease Program, University of Arizona Colleges of Medicine, Tucson, AZ, United States
| | - Christian Bime
- Interstitial Lung Disease Program, University of Arizona Colleges of Medicine, Tucson, AZ, United States
| | - Kenneth S Knox
- Interstitial Lung Disease Program, University of Arizona Colleges of Medicine, Tucson, AZ, United States.,Banner-University Medicine Division, Phoenix, AZ, United States
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22
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Kato K, Logsdon NJ, Shin YJ, Palumbo S, Knox A, Irish JD, Rounseville SP, Rummel SR, Mohamed M, Ahmad K, Trinh JM, Kurundkar D, Knox KS, Thannickal VJ, Hecker L. Impaired Myofibroblast Dedifferentiation Contributes to Nonresolving Fibrosis in Aging. Am J Respir Cell Mol Biol 2020; 62:633-644. [PMID: 31962055 DOI: 10.1165/rcmb.2019-0092oc] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Idiopathic pulmonary fibrosis (IPF) is a fatal age-associated disease with no cure. Although IPF is widely regarded as a disease of aging, the cellular mechanisms that contribute to this age-associated predilection remain elusive. In this study, we sought to evaluate the consequences of senescence on myofibroblast cell fate and fibrotic responses to lung injury in the context of aging. We demonstrated that nonsenescent lung myofibroblasts maintained the capacity for dedifferentiation, whereas senescent/IPF myofibroblasts exhibited an impaired capacity for dedifferentiation. We previously demonstrated that the transcription factor MyoD acts as a critical switch in the differentiation and dedifferentiation of myofibroblasts. Here, we demonstrate that decreased levels of MyoD preceded myofibroblast dedifferentiation and apoptosis susceptibility in nonsenescent cells, whereas MyoD expression remained elevated in senescent/IPF myofibroblasts, which failed to undergo dedifferentiation and demonstrated resistance to apoptosis. Genetic strategies to silence MyoD restored the susceptibility of IPF myofibroblasts to undergo apoptosis and led to a partial reversal of age-associated persistent fibrosis in vivo. The capacity for myofibroblast dedifferentiation and subsequent apoptosis may be critical for normal physiologic responses to tissue injury, whereas restricted dedifferentiation and apoptosis resistance in senescent cells may underlie the progressive nature of age-associated human fibrotic disorders. These studies support the concept that senescence may promote profibrotic effects via impaired myofibroblast dedifferentiation and apoptosis resistance, which contributes to myofibroblast accumulation and ultimately persistent fibrosis in aging.
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Affiliation(s)
- Kosuke Kato
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Naomi J Logsdon
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Yoon-Joo Shin
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Sunny Palumbo
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Adam Knox
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Joseph D Irish
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Skye P Rounseville
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Sydney R Rummel
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Mohamed Mohamed
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Kareem Ahmad
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Johnny M Trinh
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Deepali Kurundkar
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona
| | - Kenneth S Knox
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona
| | - Victor J Thannickal
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama.,Birmingham VA Medical Center, Birmingham, Alabama; and
| | - Louise Hecker
- Division of Pulmonary, Allergy and Critical Care and Sleep Medicine, University of Arizona, Tucson, Arizona.,Southern Arizona VA Health Care System, Tucson, Arizona
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23
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Malo J, Holbrook E, Zangeneh T, Strawter C, Oren E, Robey I, Erickson H, Carranza-Chahal R, Durkin M, Thompson C, Hoover SE, Ampel NM, Wheat LJ, Knox KS. Comparison of three anti-coccidioides antibody enzyme immunoassay kits for the diagnosis of coccidioidomycosis. Med Mycol 2020; 58:774-778. [DOI: 10.1093/mmy/myz125] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/03/2019] [Accepted: 12/02/2019] [Indexed: 11/14/2022] Open
Abstract
AbstractCoccidioidomycosis is a common cause of community-acquired pneumonia in endemic areas of the southwestern United States. Clinical presentations range from self-limited disease to severe, disseminated disease. As such, early and accurate diagnosis is essential to ensure appropriate treatment and monitoring. Currently available diagnostic testing has variable accuracy, particularly in certain patient populations, and new tests may offer improved accuracy for the diagnosis of coccidioidomycosis. Serum samples from patients with coccidioidomycosis and controls were tested for immunoglobulin G (IgG) and immunoglobulin M (IgM) antibodies using the MVista Coccidioides antibody detection EIA and two commonly used commercial enzyme immunoassay (EIA) kits: the IMMY Omega EIA and the Meridian Premier EIA. The sensitivity of the IgG antibody detection was 87.4% using the MVista test compared to 46.6% for IMMY and 70.9% for Meridian. The sensitivity for IgM antibody detection was 61.2% for the MVista test, 22.3% for IMMY and 29.1% for Meridian. For IgG antibody detection, specificity was 90% for the MVista EIA, 94.6% for IMMY, 96.4% for Meridian. For IgM antibody detection, specificity was 95.3% for the MVista test 98.2% for IMMY and 99.1% for Meridian. The MVista Coccidioides antibody EIA offers improved sensitivity, including among high-risk patient populations, for the detection of IgG and IgM antibodies in comparison to other currently available EIAs.
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Affiliation(s)
- Joshua Malo
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | | | - Tirdad Zangeneh
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | - Chris Strawter
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | - Eyal Oren
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | - Ian Robey
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | - Heidi Erickson
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | | | | | - Cindy Thompson
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | - Susan E Hoover
- Department of Medicine, University of South Dakota Sanford School of Medicine, Sioux Falls, South Dakota USA
| | - Neil M Ampel
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
| | | | - Kenneth S Knox
- Department of Medicine, The University of Arizona College of Medicine, Tucson, Arizona USA
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24
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Nikolich-Zugich J, Knox KS, Rios CT, Natt B, Bhattacharya D, Fain MJ. SARS-CoV-2 and COVID-19 in older adults: what we may expect regarding pathogenesis, immune responses, and outcomes. GeroScience 2020; 42:505-514. [PMID: 32274617 PMCID: PMC7145538 DOI: 10.1007/s11357-020-00186-0] [Citation(s) in RCA: 313] [Impact Index Per Article: 78.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 03/27/2020] [Indexed: 02/07/2023] Open
Abstract
SARS-CoV-2 virus, the causative agent of the coronavirus infectious disease-19 (COVID-19), is taking the globe by storm, approaching 500,000 confirmed cases and over 21,000 deaths as of March 25, 2020. While under control in some affected Asian countries (Taiwan, Singapore, Vietnam), the virus demonstrated an exponential phase of infectivity in several large countries (China in late January and February and many European countries and the USA in March), with cases exploding by 30–50,000/day in the third and fourth weeks of March, 2020. SARS-CoV-2 has proven to be particularly deadly to older adults and those with certain underlying medical conditions, many of whom are of advanced age. Here, we briefly review the virus, its structure and evolution, epidemiology and pathogenesis, immunogenicity and immune, and clinical response in older adults, using available knowledge on SARS-CoV-2 and its highly pathogenic relatives MERS-CoV and SARS-CoV-1. We conclude by discussing clinical and basic science approaches to protect older adults against this disease.
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Affiliation(s)
- Janko Nikolich-Zugich
- Department of Immunobiology, University of Arizona College of Medicine-Tucson, Tucson, AZ, 85724, USA.
- University of Arizona Center on Aging, University of Arizona College of Medicine-Tucson, P.O. Box 249221, 1501 N. Campbell Ave, Tucson, AZ, 8524, USA.
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, AZ, 85724, USA
- Department of Medicine, University of Arizona-Phoenix, Phoenix, AZ, 85004, USA
| | - Carlos Tafich Rios
- Division of Geriatrics, General and Palliative Medicine, Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, AZ, 85724, USA
| | - Bhupinder Natt
- Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, AZ, 85724, USA
| | - Deepta Bhattacharya
- Department of Immunobiology, University of Arizona College of Medicine-Tucson, Tucson, AZ, 85724, USA
| | - Mindy J Fain
- University of Arizona Center on Aging, University of Arizona College of Medicine-Tucson, P.O. Box 249221, 1501 N. Campbell Ave, Tucson, AZ, 8524, USA
- Division of Geriatrics, General and Palliative Medicine, Department of Medicine, University of Arizona College of Medicine-Tucson, Tucson, AZ, 85724, USA
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Hage CA, Carmona EM, Epelbaum O, Evans SE, Gabe LM, Haydour Q, Knox KS, Kolls JK, Murad MH, Wengenack NL, Limper AH. Microbiological Laboratory Testing in the Diagnosis of Fungal Infections in Pulmonary and Critical Care Practice. An Official American Thoracic Society Clinical Practice Guideline. Am J Respir Crit Care Med 2019; 200:535-550. [PMID: 31469325 PMCID: PMC6727169 DOI: 10.1164/rccm.201906-1185st] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Fungal infections are of increasing incidence and importance in immunocompromised and immunocompetent patients. Timely diagnosis relies on appropriate use of laboratory testing in susceptible patients.Methods: The relevant literature related to diagnosis of invasive pulmonary aspergillosis, invasive candidiasis, and the common endemic mycoses was systematically reviewed. Meta-analysis was performed when appropriate. Recommendations were developed using the Grading of Recommendations Assessment, Development, and Evaluation approach.Results: This guideline includes specific recommendations on the use of galactomannan testing in serum and BAL and for the diagnosis of invasive pulmonary aspergillosis, the role of PCR in the diagnosis of invasive pulmonary aspergillosis, the role of β-d-glucan assays in the diagnosis of invasive candidiasis, and the application of serology and antigen testing in the diagnosis of the endemic mycoses.Conclusions: Rapid, accurate diagnosis of fungal infections relies on appropriate application of laboratory testing, including antigen testing, serological testing, and PCR-based assays.
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Zhou T, Xie X, Li M, Shi J, Zhou JJ, Knox KS, Wang T, Chen Q, Gu W. Rat BodyMap transcriptomes reveal unique circular RNA features across tissue types and developmental stages. RNA 2018; 24:1443-1456. [PMID: 30093490 PMCID: PMC6191709 DOI: 10.1261/rna.067132.118] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 08/03/2018] [Indexed: 06/08/2023]
Abstract
Circular RNAs (circRNAs) are a novel class of regulatory RNAs. Here, we present a comprehensive investigation of circRNA expression profiles across 11 tissues and four developmental stages in rats, along with cross-species analyses in humans and mice. Although the expression of circRNAs is positively correlated with that of cognate mRNAs, highly expressed genes tend to splice a larger fraction of circular transcripts. Moreover, circRNAs exhibit higher tissue specificity than cognate mRNAs. Intriguingly, while we observed a monotonic increase of circRNA abundance with age in the rat brain, we further discovered a dynamic, age-dependent pattern of circRNA expression in the testes that is characterized by a dramatic increase with advancing stages of sexual maturity and a decrease with aging. The age-sensitive testicular circRNAs are highly associated with spermatogenesis, independent of cognate mRNA expression. The tissue/age implications of circRNAs suggest that they present unique physiological functions rather than simply occurring as occasional by-products of gene transcription.
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Affiliation(s)
- Tong Zhou
- Department of Physiology and Cell Biology, The University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Xueying Xie
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Musheng Li
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Junchao Shi
- Department of Physiology and Cell Biology, The University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, The University of Arizona, Tucson, Arizona 85721, USA
| | - Kenneth S Knox
- Department of Internal Medicine, College of Medicine Phoenix, The University of Arizona, Phoenix, Arizona 85004, USA
| | - Ting Wang
- Department of Internal Medicine, College of Medicine Phoenix, The University of Arizona, Phoenix, Arizona 85004, USA
| | - Qi Chen
- Department of Physiology and Cell Biology, The University of Nevada, Reno School of Medicine, Reno, Nevada 89557, USA
| | - Wanjun Gu
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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Zhai J, Kim J, Knox KS, Twigg HL, Zhou H, Zhou JJ. Variance Component Selection With Applications to Microbiome Taxonomic Data. Front Microbiol 2018; 9:509. [PMID: 29643839 PMCID: PMC5883493 DOI: 10.3389/fmicb.2018.00509] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 03/06/2018] [Indexed: 12/21/2022] Open
Abstract
High-throughput sequencing technology has enabled population-based studies of the role of the human microbiome in disease etiology and exposure response. Microbiome data are summarized as counts or composition of the bacterial taxa at different taxonomic levels. An important problem is to identify the bacterial taxa that are associated with a response. One method is to test the association of specific taxon with phenotypes in a linear mixed effect model, which incorporates phylogenetic information among bacterial communities. Another type of approaches consider all taxa in a joint model and achieves selection via penalization method, which ignores phylogenetic information. In this paper, we consider regression analysis by treating bacterial taxa at different level as multiple random effects. For each taxon, a kernel matrix is calculated based on distance measures in the phylogenetic tree and acts as one variance component in the joint model. Then taxonomic selection is achieved by the lasso (least absolute shrinkage and selection operator) penalty on variance components. Our method integrates biological information into the variable selection problem and greatly improves selection accuracies. Simulation studies demonstrate the superiority of our methods versus existing methods, for example, group-lasso. Finally, we apply our method to a longitudinal microbiome study of Human Immunodeficiency Virus (HIV) infected patients. We implement our method using the high performance computing language Julia. Software and detailed documentation are freely available at https://github.com/JingZhai63/VCselection.
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Affiliation(s)
- Jing Zhai
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, United States
| | - Juhyun Kim
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona, Tucson, AZ, United States
| | - Homer L Twigg
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Indiana University Medical Center, Indianapolis, IN, United States
| | - Hua Zhou
- Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Jin J Zhou
- Department of Epidemiology and Biostatistics, University of Arizona, Tucson, AZ, United States
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Twigg HL, Knox KS, Zhou J, Crothers KA, Nelson DE, Toh E, Day RB, Lin H, Gao X, Dong Q, Mi D, Katz BP, Sodergren E, Weinstock GM. Effect of Advanced HIV Infection on the Respiratory Microbiome. Am J Respir Crit Care Med 2017; 194:226-35. [PMID: 26835554 DOI: 10.1164/rccm.201509-1875oc] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
RATIONALE Previous work found the lung microbiome in healthy subjects infected with HIV was similar to that in uninfected subjects. We hypothesized the lung microbiome from subjects infected with HIV with more advanced disease would differ from that of an uninfected control population. OBJECTIVES To measure the lung microbiome in an HIV-infected population with advanced disease. METHODS 16s RNA gene sequencing was performed on acellular bronchoalveolar lavage (BAL) fluid from 30 subjects infected with HIV with advanced disease (baseline mean CD4 count, 262 cells/mm(3)) before and up to 3 years after starting highly active antiretroviral therapy (HAART) and compared with 22 uninfected control subjects. MEASUREMENTS AND MAIN RESULTS The lung microbiome in subjects infected with HIV with advanced disease demonstrated decreased alpha diversity (richness and diversity) and greater beta diversity compared with uninfected BAL. Differences improved with HAART, but still persisted up to 3 years after starting therapy. Population dispersion in the group infected with HIV was significantly greater than in the uninfected cohort and declined after treatment. There were differences in the relative abundance of some bacteria between the two groups at baseline and after 1 year of therapy. After 1 year on HAART, HIV BAL contained an increased abundance of Prevotella and Veillonella, bacteria previously associated with lung inflammation. CONCLUSIONS The lung microbiome in subjects infected with HIV with advanced disease is altered compared with an uninfected population both in diversity and bacterial composition. Differences remain up to 3 years after starting HAART. We speculate an altered lung microbiome in HIV infection may contribute to chronic inflammation and lung complications seen in the HAART era.
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Affiliation(s)
| | - Kenneth S Knox
- 2 Department of Medicine, University of Arizona, Tucson, Arizona
| | - Jin Zhou
- 2 Department of Medicine, University of Arizona, Tucson, Arizona
| | | | | | - Evelyn Toh
- 4 Department of Microbiology and Immunology, and
| | | | - Huaiying Lin
- 5 Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois; and
| | - Xiang Gao
- 5 Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois; and
| | - Qunfeng Dong
- 5 Center for Biomedical Informatics, Department of Public Health Sciences, Loyola University Chicago, Maywood, Illinois; and
| | - Deming Mi
- 6 Department of Biostatistics, Indiana University, Indianapolis, Indiana
| | - Barry P Katz
- 6 Department of Biostatistics, Indiana University, Indianapolis, Indiana
| | - Erica Sodergren
- 7 Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
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Zhou T, Casanova N, Pouladi N, Wang T, Lussier Y, Knox KS, Garcia JGN. Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. Sci Rep 2017; 7:4237. [PMID: 28652588 PMCID: PMC5484682 DOI: 10.1038/s41598-017-04109-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 05/10/2017] [Indexed: 11/28/2022] Open
Abstract
Sarcoidosis is a granulomatous lung disorder of unknown cause. The majority of individuals with sarcoidosis spontaneously achieve full remission (uncomplicated sarcoidosis), however, ~20% of sarcoidosis-affected individuals experience progressive lung disease or cardiac and nervous system involvement (complicated sarcoidosis). We investigated peripheral blood mononuclear cell (PBMC) microRNA and protein-coding gene expression data from healthy controls and patients with uncomplicated or complicated sarcoidosis. We identified 46 microRNAs and 1,559 genes that were differentially expressed across a continuum of sarcoidosis severity (healthy control → uncomplicated sarcoidosis → complicated sarcoidosis). A total of 19 microRNA-mRNA regulatory pairs were identified within these deregulated microRNAs and mRNAs, which consisted of 17 unique protein-coding genes yielding a 17-gene signature. Pathway analysis of the 17-gene signature revealed Jak-STAT signaling pathway as the most significantly represented pathway. A severity score was assigned to each patient based on the expression of the 17-gene signature and a significant increasing trend in the severity score was observed from healthy control, to uncomplicated sarcoidosis, and finally to complicated sarcoidosis. In addition, this microRNA-regulated gene signature differentiates sarcoidosis patients from healthy controls in independent validation cohorts. Our study suggests that PBMC gene expression is useful in diagnosis of sarcoidosis.
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Affiliation(s)
- Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, 89557, USA
| | - Nancy Casanova
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Nima Pouladi
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Ting Wang
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Yves Lussier
- Center for Bioinformatics and Biostatistics, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Kenneth S Knox
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA
| | - Joe G N Garcia
- Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Department of Medicine, University of Arizona Health Sciences, Tucson, AZ, 78721, USA.
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Chaudhary S, Meinke L, Ateeli H, Knox KS, Raz Y, Ampel NM. Coccidioidomycosis among persons undergoing lung transplantation in the coccidioidal endemic region. Transpl Infect Dis 2017; 19. [PMID: 28452423 DOI: 10.1111/tid.12713] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 01/30/2017] [Accepted: 02/05/2017] [Indexed: 12/23/2022]
Abstract
BACKGROUND Coccidioidomycosis, an endemic fungal infection, is more likely to be symptomatic and severe among those receiving allogeneic transplants. While several case series have been published for various transplanted organs, none has described the incidence and outcomes in those receiving lung transplants within the coccidioidal endemic region. METHODS Patients receiving a heart-lung, single-lung, or bilateral-lung transplantation at the University of Arizona between 1985 and 2009 were retrospectively reviewed. RESULTS Coccidioidomycosis occurred post transplantation in 11 (5.8%) of 189 patients. All but one patient was diagnosed with pulmonary coccidioidomycosis and only one had a history of prior coccidioidomycosis. Two patients received transplants from donors found to have coccidioidomycosis at the time of transplantation and one death was directly attributed to coccidioidomycosis. The risk of developing active coccidioidomycosis was significantly higher if the patient did not receive some type of antifungal therapy post transplantation (P<.001). CONCLUSION Within the coccidioidal endemic region, post-transplantation coccidioidomycosis was a definable risk among lung transplant recipients. Use of antifungals appeared to reduce this incidence of disease. Almost all cases resulted in pulmonary disease, suggesting that the lung is the primary site of infection.
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Affiliation(s)
- Sachin Chaudhary
- Pulmonary Division, Department of Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | - Laura Meinke
- Pulmonary Division, Department of Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | - Huthayfa Ateeli
- Pulmonary Division, Department of Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | - Kenneth S Knox
- Pulmonary Division, Department of Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | - Yuval Raz
- Pulmonary Division, Department of Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA
| | - Neil M Ampel
- Infectious Diseases Division of the Department of Medicine, The University of Arizona College of Medicine, Tucson, AZ, USA.,Medicine, Southern Arizona Veterans Affairs Health Care System, Tucson, AZ, USA
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Twigg HL, Weinstock GM, Knox KS. Lung microbiome in human immunodeficiency virus infection. Transl Res 2017; 179:97-107. [PMID: 27496318 PMCID: PMC5164960 DOI: 10.1016/j.trsl.2016.07.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 12/28/2022]
Abstract
The lung microbiome plays a significant role in normal lung function and disease. Because microbial colonization is likely influenced by immunodeficiency, one would speculate that infection with human immunodeficiency virus (HIV) alters the lung microbiome. Furthermore, how this alteration might impact pulmonary complications now seen in HIV-infected patients on antiretroviral therapy (ART), which has shifted from opportunistic infections to diseases associated with chronic inflammation, is not known. There have been limited publications on the lung microbiome in HIV infection, many of them emanating from the Lung HIV Microbiome Project. Current evidence suggests that the lung microbiome in healthy HIV-infected individuals with preserved CD4 counts is similar to uninfected individuals. However, in individuals with more advanced disease, there is an altered alveolar microbiome characterized by a loss of richness and evenness (alpha diversity) within individuals. Furthermore, as a group the taxa making up the HIV-infected and uninfected lung microbiome are different (differences in beta diversity), and the HIV-infected population is more spread out (greater dispersion) than the uninfected population. These differences decline with ART, but even after effective therapy the alveolar microbiome in HIV-infected individuals contains increased amounts of signature bacteria, some of which have previously been associated with chronic lung inflammation. Furthermore, more recent investigations into the lung virome in HIV infection suggest that perturbations in lung viral communities also exist in HIV infection, and that these too are associated with evidence of lung inflammation. Thus, it is likely both microbiome and virome alterations in HIV infection contribute to lung inflammation in these individuals, which has important implications on the changing spectrum of pulmonary complications in patients living with HIV.
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Affiliation(s)
- Homer L Twigg
- Department of Medicine, Indiana University, Indianapolis, Ind.
| | - George M Weinstock
- Microbial Genomics, The Jackson Laboratory for Genomic Medicine, Farmington, Conn
| | - Kenneth S Knox
- Department of Medicine, University of Arizona, Tucson, Ariz
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Holbrook ED, Zangeneh T, Malo J, Strawter C, Oren E, Robey I, Erickson H, Chahal R, Thompson C, Ampel NM, Wheat LJ, Knox KS. Development of an Improved Antibody Detection Enzyme Immunoassay for Use in Detection of Coccidioidomycosis. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abstract
This article briefly reviews conventional biomarkers used clinically to (1) support a diagnosis and (2) monitor disease progression in patients with sarcoidosis. Potential new biomarkers identified by genome-wide screening and the approaches to discover these biomarkers are described.
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Affiliation(s)
- Nancy Casanova
- University of Arizona Health Sciences Center, Arizona Respiratory Center and Department of Medicine, University of Arizona, Tucson, AZ 78721, USA
| | - Tong Zhou
- University of Arizona Health Sciences Center, Arizona Respiratory Center and Department of Medicine, University of Arizona, Tucson, AZ 78721, USA
| | - Kenneth S Knox
- University of Arizona Health Sciences Center, Arizona Respiratory Center and Department of Medicine, University of Arizona, Tucson, AZ 78721, USA
| | - Joe G N Garcia
- University of Arizona Health Sciences Center, Arizona Respiratory Center and Department of Medicine, University of Arizona, Tucson, AZ 78721, USA
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Zangeneh TT, Malo J, Luraschi-Monjagatta C, Hage CA, Wheat LJ, Strawter C, Klotz SA, Knox KS. Positive (1-3) B-d-glucan and cross reactivity of fungal assays in coccidioidomycosis. Med Mycol 2014; 53:171-3. [PMID: 25541557 DOI: 10.1093/mmy/myu077] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fungal antigen testing in immunosuppressed patients has emerged as a powerful diagnostic tool. Some assays are relatively nonspecific, and misinterpretation can have severe clinical consequences. Additionally, when new assays become commercially available it is important to evaluate the potential for cross reactivity. We recently observed several immunosuppressed patients with positive (1→3)-β-D-glucan (BG) who were eventually diagnosed with coccidioidomycosis in the endemic area of Tucson, Arizona. Although the BG assay is known to detect glucans of many fungal pathogens, reports of cross-reactivity with Coccidioides remain sparsely reported. To test the cross-reactivity of fungal antigens in detection assays, serum samples from patients with coccidioidomycosis testing positive for Coccidioides antigen were evaluated for BG. Of 12 samples positive for Coccidioides antigen (≥0.07 ng/ml), 11 (92%) were positive by BG (>80 pg/ml), and of 11 positive for Aspergillus galactomannan, 10 (91%) were positive by BG (>80 pg/ml). We conclude that the BG assay is nonspecific, detecting glucans from many fungal pathogens, including Coccidioides. In the endemic area, a positive BG warrants further specific testing.
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Affiliation(s)
- Tirdad T Zangeneh
- University of Arizona College of Medicine, Division of Infectious Diseases, Tucson, Arizona
| | - Joshua Malo
- University of Arizona College of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Tucson, Arizona
| | - Carmen Luraschi-Monjagatta
- University of Arizona College of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Tucson, Arizona
| | - Chadi A Hage
- Indiana University School of Medicine, Department of Pulmonary Medicine, Indianapolis, Indiana
| | | | - Christopher Strawter
- University of Arizona College of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Tucson, Arizona
| | - Stephen A Klotz
- University of Arizona College of Medicine, Division of Infectious Diseases, Tucson, Arizona
| | - Kenneth S Knox
- University of Arizona College of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Tucson, Arizona
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Reyes N, Onadeko OO, Luraschi-Monjagatta MDC, Knox KS, Rennels MA, Walsh TK, Ampel NM. Positron emission tomography in the evaluation of pulmonary nodules among patients living in a coccidioidal endemic region. Lung 2014; 192:589-93. [PMID: 24801058 DOI: 10.1007/s00408-014-9589-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 04/15/2014] [Indexed: 10/25/2022]
Abstract
BACKGROUND Within a coccidioidal endemic region, pulmonary nodules due to coccidioidomycosis are common. Uptake of (18)fluorodeoxyglucose ((18)FDG) by positron emission tomography with computed axial tomography (PET/CT) has been used to assess whether pulmonary nodules are malignant but inflammatory lesions can be positive. The purpose of this study was to compare by PET/CT the (18)FDG uptake in pulmonary nodules likely due to coccidioidomycosis to that of nodules shown to be malignant among patients living in a coccidioidal endemic region. METHODS We retrospectively reviewed patients who underwent a PET/CT at the Southern Arizona Veterans Affairs Health Care System between January 2008 and March 2012 who were subsequently found on biopsy to have pulmonary nodules that were coccidioidal or granulomatous or were due to malignancy. RESULTS Among 245 diagnostic biopsies where the subject had a previous PET/CT, 15 (6.1 %) were either coccidioidal (n = 12) or granulomatous without an identified organism (n = 3). The median maximum standard unit of uptake (SUV(max)) on PET/CT of coccidioidal or granulomatous lesions was 2.0 compared to 9.8 for malignant lesions (P < 0.001). The maximum diameter of the coccidioidal or granulomatous nodules was 2.1 cm compared to 3.0 cm for the malignant lesions (P = 0.009). On multivariable analysis, an elevated SUV(max) was the only distinguishing feature between the malignant and the granulomatous lesions (OR 1.28, 95 % CI 1.05-1.55; P = 0.013). CONCLUSIONS Coccidioidal pulmonary nodules take up significantly less (18)FDG than those due to malignancies, but there is considerable overlap between granulomatous and malignant lesions at lower SUV(max).
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Affiliation(s)
- Nathaniel Reyes
- Pulmonary and Critical Care Division, University of Arizona, Tucson, AZ, USA
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Lozupone C, Cota-Gomez A, Palmer BE, Linderman DJ, Charlson ES, Sodergren E, Mitreva M, Abubucker S, Martin J, Yao G, Campbell TB, Flores SC, Ackerman G, Stombaugh J, Ursell L, Beck JM, Curtis JL, Young VB, Lynch SV, Huang L, Weinstock GM, Knox KS, Twigg H, Morris A, Ghedin E, Bushman FD, Collman RG, Knight R, Fontenot AP. Widespread colonization of the lung by Tropheryma whipplei in HIV infection. Am J Respir Crit Care Med 2013; 187:1110-7. [PMID: 23392441 DOI: 10.1164/rccm.201211-2145oc] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
RATIONALE Lung infections caused by opportunistic or virulent pathogens are a principal cause of morbidity and mortality in HIV infection. It is unknown whether HIV infection leads to changes in basal lung microflora, which may contribute to chronic pulmonary complications that increasingly are being recognized in individuals infected with HIV. OBJECTIVES To determine whether the immunodeficiency associated with HIV infection resulted in alteration of the lung microbiota. METHODS We used 16S ribosomal RNA targeted pyrosequencing and shotgun metagenomic sequencing to analyze bacterial gene sequences in bronchoalveolar lavage (BAL) and mouths of 82 HIV-positive and 77 HIV-negative subjects. MEASUREMENTS AND MAIN RESULTS Sequences representing Tropheryma whipplei, the etiologic agent of Whipple's disease, were significantly more frequent in BAL of HIV-positive compared with HIV-negative individuals. T. whipplei dominated the community (>50% of sequence reads) in 11 HIV-positive subjects, but only 1 HIV-negative individual (13.4 versus 1.3%; P = 0.0018). In 30 HIV-positive individuals sampled longitudinally, antiretroviral therapy resulted in a significantly reduced relative abundance of T. whipplei in the lung. Shotgun metagenomic sequencing was performed on eight BAL samples dominated by T. whipplei 16S ribosomal RNA. Whole genome assembly of pooled reads showed that uncultured lung-derived T. whipplei had similar gene content to two isolates obtained from subjects with Whipple's disease. CONCLUSIONS Asymptomatic subjects with HIV infection have unexpected colonization of the lung by T. whipplei, which is reduced by effective antiretroviral therapy and merits further study for a potential pathogenic role in chronic pulmonary complications of HIV infection.
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Affiliation(s)
- Catherine Lozupone
- Department of Chemistry and Biochemistry and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
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Twigg HL, Morris A, Ghedin E, Curtis JL, Huffnagle GB, Crothers K, Campbell TB, Flores SC, Fontenot AP, Beck JM, Huang L, Lynch S, Knox KS, Weinstock G. Use of bronchoalveolar lavage to assess the respiratory microbiome: signal in the noise. Lancet Respir Med 2013; 1:354-6. [PMID: 24429191 DOI: 10.1016/s2213-2600(13)70117-6] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Homer L Twigg
- Indiana University Medical Center, CL 260A, Indianapolis, IN 46202, USA.
| | | | | | - Jeffrey L Curtis
- University of Michigan, MI, USA; Department of Veterans Affairs, Ann Arbor, MI, USA
| | | | | | | | | | | | - James M Beck
- Department of Veterans Affairs, Ann Arbor, MI, USA
| | - Laurence Huang
- University of California San Francisco, San Francisco, CA, USA
| | - Susan Lynch
- University of California San Francisco, San Francisco, CA, USA
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Nesbit LA, Knox KS, Nguyen CT, Roesch J, Wheat LJ, Johnson SM, Pappagianis D, Chavez S, Ampel NM. Immunological Characterization of Bronchoalveolar Lavage Fluid in Patients With Acute Pulmonary Coccidioidomycosis. J Infect Dis 2013; 208:857-63. [DOI: 10.1093/infdis/jit246] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
Human immunodeficiency virus (HIV) infection causes profound changes in the lung compartment characterized by macrophage and lymphocyte activation, secretion of proinflammatory cytokines and chemokines, and accumulation of CD8 T cells in the alveolar space, leading to lymphocytic alveolitis. Because many of the changes seen in the lung can be attributed to the direct effect of HIV on immune cells, therapy to reduce the HIV burden should have significant beneficial effects. Indeed, antiretroviral therapy rapidly reduces the viral burden in the lung, number of CD8 T cells in the alveolar space, and amount of proinflammatory cytokines and chemokines in bronchoalveolar lavage.
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Affiliation(s)
- Homer L Twigg
- Division of Pulmonary and Critical Care Medicine, Indiana University Medical Center, Indianapolis, IN 46202, USA.
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Abstract
Indoleamine 2,3 dioxygenase (IDO) plays an important role in immunoregulation as it is involved in downregulating immune responses to infections. We sought to characterize IDO activity in histoplasmosis and to do so, C57Bl6 mice were infected intranasally with Histoplasma capsulatum. After infection, lung and spleen IDO activity was assessed by HPLC and IDO expression by qRT-PCR. The distribution of IDO was determined by immunohistochemical staining. Cytokine levels were measured in lung and spleen homogenates using cytokine bead array. Fungal burden was quantified by culture. Subcutaneous pellets containing methyltryptophane (1-MT) were employed to inhibit IDO in vivo. Histoplasma infection strongly induced functional lung IDO, with activity at its highest at weeks 1 and 2 and then decreased thereafter as the mice cleared the infection. Lung IDO activity positively correlated with the fungal burden (Rho = 0.845), interferon-γ (Rho = 0.839) and tumor necrosis factor-α (Rho = 0.791) levels, P < 0.001. In contrast, spleen IDO activity was not induced despite high infection burden and cytokine levels. IDO expressing cells were predominately located at the ring edge of Histoplasma-induced granulomas. IDO inhibition prior to infection reduced fungal burdens and inflammation in lungs and spleen. Histoplasma preferentially induces lung IDO, as early as one week after infection. IDO appears to modulate the immune response to Histoplasma infection.
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Affiliation(s)
- Chadi A Hage
- Indiana University School of Medicine and Roudebush Veterans' Administration Medical Center, Pulmonary Critical Care Medicine, Indianapolis, Indiana 46202, USA. @iupui.edu
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Zhou T, Zhang W, Sweiss NJ, Chen ES, Moller DR, Knox KS, Ma SF, Wade MS, Noth I, Machado RF, Garcia JGN. Peripheral blood gene expression as a novel genomic biomarker in complicated sarcoidosis. PLoS One 2012; 7:e44818. [PMID: 22984568 PMCID: PMC3440319 DOI: 10.1371/journal.pone.0044818] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 08/14/2012] [Indexed: 12/21/2022] Open
Abstract
Sarcoidosis, a systemic granulomatous syndrome invariably affecting the lung, typically spontaneously remits but in ~20% of cases progresses with severe lung dysfunction or cardiac and neurologic involvement (complicated sarcoidosis). Unfortunately, current biomarkers fail to distinguish patients with remitting (uncomplicated) sarcoidosis from other fibrotic lung disorders, and fail to identify individuals at risk for complicated sarcoidosis. We utilized genome-wide peripheral blood gene expression analysis to identify a 20-gene sarcoidosis biomarker signature distinguishing sarcoidosis (n = 39) from healthy controls (n = 35, 86% classification accuracy) and which served as a molecular signature for complicated sarcoidosis (n = 17). As aberrancies in T cell receptor (TCR) signaling, JAK-STAT (JS) signaling, and cytokine-cytokine receptor (CCR) signaling are implicated in sarcoidosis pathogenesis, a 31-gene signature comprised of T cell signaling pathway genes associated with sarcoidosis (TCR/JS/CCR) was compared to the unbiased 20-gene biomarker signature but proved inferior in prediction accuracy in distinguishing complicated from uncomplicated sarcoidosis. Additional validation strategies included significant association of single nucleotide polymorphisms (SNPs) in signature genes with sarcoidosis susceptibility and severity (unbiased signature genes - CX3CR1, FKBP1A, NOG, RBM12B, SENS3, TSHZ2; T cell/JAK-STAT pathway genes such as AKT3, CBLB, DLG1, IFNG, IL2RA, IL7R, ITK, JUN, MALT1, NFATC2, PLCG1, SPRED1). In summary, this validated peripheral blood molecular gene signature appears to be a valuable biomarker in identifying cases with sarcoidoisis and predicting risk for complicated sarcoidosis.
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Affiliation(s)
- Tong Zhou
- Institute for Personalized Respiratory Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- Section of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Wei Zhang
- Institute of Human Genetics, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- Department of Pediatrics, The University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Nadera J. Sweiss
- Section of Rheumatology, Department of Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Edward S. Chen
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - David R. Moller
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, The Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Kenneth S. Knox
- Section of Pulmonary and Critical Care, Department of Medicine, The University of Arizona, Tuscon, Arizona, United States of America
| | - Shwu-Fan Ma
- Section of Pulmonary/Critical Care, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Michael S. Wade
- Institute for Personalized Respiratory Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- Section of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Imre Noth
- Section of Pulmonary/Critical Care, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
| | - Roberto F. Machado
- Institute for Personalized Respiratory Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- Section of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Joe G. N. Garcia
- Institute for Personalized Respiratory Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- Section of Pulmonary, Critical Care, Sleep and Allergy, Department of Medicine, The University of Illinois at Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Hage CA, Knox KS, Wheat LJ. Endemic mycoses: overlooked causes of community acquired pneumonia. Respir Med 2012; 106:769-76. [PMID: 22386326 DOI: 10.1016/j.rmed.2012.02.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Revised: 02/03/2012] [Accepted: 02/10/2012] [Indexed: 11/30/2022]
Abstract
The endemic mycoses are important but often overlooked causes for community acquired pneumonia. Delays in recognition, diagnosis and proper treatment often lead to disastrous outcomes. This topic is not usually discussed in reviews and guidelines addressing the subject of community acquired pneumonia. In this review we discuss the three major endemic mycoses in North America that present as community acquired pneumonias; Coccidioidomycosis, Histoplasmosis and Blastomycosis. We discuss their epidemiology, clinical presentations, methods of diagnosis and current treatment strategies.
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Affiliation(s)
- Chadi A Hage
- Pulmonary-Critical Care and Infectious Diseases, Indiana University and Richard L. Roudebush VA Medical Center, 1481 W. 10th St., 111P-IU, Indianapolis, IN, USA.
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Hershcovici T, Jha LK, Johnson T, Gerson L, Stave C, Malo J, Knox KS, Quan S, Fass R. Systematic review: the relationship between interstitial lung diseases and gastro-oesophageal reflux disease. Aliment Pharmacol Ther 2011; 34:1295-305. [PMID: 21999527 DOI: 10.1111/j.1365-2036.2011.04870.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND A potential relationship has been suggested between gastro-oesophageal reflux disease (GERD) and interstitial lung diseases (ILDs). AIM To evaluate whether there is a causal relationship between GERD and different ILDs. METHODS We conducted a systematic search of literature published between 1980 and 2010. After a review by two independent authors, each study was assigned an evidence-based rating according to a standard scoring system. RESULTS We identified 319 publications and 22 of them met the entry criteria. Of those, the relationship between GERD and idiopathic pulmonary fibrosis (IPF) was investigated in 14 articles, pulmonary involvement in systemic sclerosis (SSc) in six articles and pulmonary involvement in mixed connective tissue disease (MCTD) in two articles. We found the prevalence of GERD and/or oesophageal dysmotility to be higher in patients with different types of ILD as compared with those without ILD [Evidence B]. Among patients with IPF, 67-76% demonstrated abnormal oesophageal acid exposure off PPI treatment. No relationship was demonstrated between severity of GERD and severity of IPF [Evidence B]. Data are scant on outcomes of antireflux treatment in patients with IPF. There is a correlation between the severity of ILD and the degree of oesophageal motor impairment in patients with SSc and MCTD [Evidence B]. CONCLUSIONS Based on the currently available data, a causal relationship between GERD and idiopathic pulmonary fibrosis cannot be established. There is scant evidence about antireflux therapy in idiopathic pulmonary fibrosis patients. There may be an association between lung and oesophageal involvement in systemic sclerosis and mixed connective tissue disease, but a causal relationship cannot be established.
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Affiliation(s)
- T Hershcovici
- The Neuroenteric Clinical Research Group, Southern Arizona VA Health Care System, Tucson, USA
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Limper AH, Knox KS, Sarosi GA, Ampel NM, Bennett JE, Catanzaro A, Davies SF, Dismukes WE, Hage CA, Marr KA, Mody CH, Perfect JR, Stevens DA. An official American Thoracic Society statement: Treatment of fungal infections in adult pulmonary and critical care patients. Am J Respir Crit Care Med 2011; 183:96-128. [PMID: 21193785 DOI: 10.1164/rccm.2008-740st] [Citation(s) in RCA: 357] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
With increasing numbers of immune-compromised patients with malignancy, hematologic disease, and HIV, as well as those receiving immunosupressive drug regimens for the management of organ transplantation or autoimmune inflammatory conditions, the incidence of fungal infections has dramatically increased over recent years. Definitive diagnosis of pulmonary fungal infections has also been substantially assisted by the development of newer diagnostic methods and techniques, including the use of antigen detection, polymerase chain reaction, serologies, computed tomography and positron emission tomography scans, bronchoscopy, mediastinoscopy, and video-assisted thorascopic biopsy. At the same time, the introduction of new treatment modalities has significantly broadened options available to physicians who treat these conditions. While traditionally antifungal therapy was limited to the use of amphotericin B, flucytosine, and a handful of clinically available azole agents, current pharmacologic treatment options include potent new azole compounds with extended antifungal activity, lipid forms of amphotericin B, and newer antifungal drugs, including the echinocandins. In view of the changing treatment of pulmonary fungal infections, the American Thoracic Society convened a working group of experts in fungal infections to develop a concise clinical statement of current therapeutic options for those fungal infections of particular relevance to pulmonary and critical care practice. This document focuses on three primary areas of concern: the endemic mycoses, including histoplasmosis, sporotrichosis, blastomycosis, and coccidioidomycosis; fungal infections of special concern for immune-compromised and critically ill patients, including cryptococcosis, aspergillosis, candidiasis, and Pneumocystis pneumonia; and rare and emerging fungal infections.
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Onadeko OO, Nesbit L, Chavez S, Goldman M, Ampel N, Knox KS. Coccidioides Antigen Detection in Bronchoalveolar Lavage. Chest 2010. [DOI: 10.1378/chest.10822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
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Abstract
BACKGROUND The endemic region of blastomycosis historically has included the state of Indiana. However, few published reports of blastomycosis exist to substantiate this distinction. A surge of patients with blastomycosis in central Indiana (Indianapolis and surrounding counties) beginning in 2005 prompted us to review our local experience. We propose that this surge was related to major highway construction around Indianapolis. METHODS We reviewed all microbiologically confirmed cases from four hospitals serving central Indiana. Chart review was completed for adult patients, and data were collected on clinical presentations, methods of diagnosis, comorbidities, radiologic findings, treatment, and outcomes. We plotted patient residence addresses with sites of highway construction. RESULTS Fifty-nine patients were identified from laboratory results and physician referral. Interestingly, a surge of blastomycosis incidence occurred in 34 patients between 2005 and 2008 during which time major highway projects were under way around the Indianapolis metropolitan area. The majority of these patients presented acutely and with pulmonary involvement. Fungal culture and antigen testing were the most sensitive means to diagnosis. Antifungal therapy was highly effective. CONCLUSIONS This urban outbreak of blastomycosis in Indianapolis should prompt clinicians to consider blastomycosis in this highly endemic area of histoplasmosis.
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Affiliation(s)
- W Graham Carlos
- Pulmonary-Critical Care and Infectious Diseases, Roudebush VA Medical Center and Indiana University, Indianapolis, IN 46202, USA.
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Onadeko O, Knox KS. The early riser. Reassurance. J Clin Sleep Med 2010; 6:297-298. [PMID: 20572426 PMCID: PMC2883044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Affiliation(s)
- Oluwole Onadeko
- University of Arizona and Southern Arizona VA Health Care System, Tucson, AZ
| | - Kenneth S. Knox
- University of Arizona and Southern Arizona VA Health Care System, Tucson, AZ
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Onadeko O, Knox KS. The Early Riser. J Clin Sleep Med 2010. [DOI: 10.5664/jcsm.27830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Oluwole Onadeko
- University of Arizona and Southern Arizona VA Health Care System, Tucson, AZ
| | - Kenneth S. Knox
- University of Arizona and Southern Arizona VA Health Care System, Tucson, AZ
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