James L Knepler

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Journals/Publications

• Bixby, B., Vrba, L., Lenka, J., Oshiro, M., Watts, G. S., Hughes, T., Erickson, H., Chopra, M., Knepler, J. L., Knox, K. S., Jarnagin, L., Alalawi, R., Kala, M., Bernert, R., Routh, J., Roe, D. J., Garland, L. L., Futscher, B. W., & Nelson, M. A. (2023). Cell-Free DNA Methylation Analysis as a Marker of Malignancy in Pleural Fluid. Research square.
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  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.
• Weinkauf, C. C., Sprissler, R., Spier, C. M., Sam, A., Rischard, F., Paul, S., Parthasarathy, S., Natt, B., Mosier, J., Merchant, N., Knox, K. S., Knepler, J. L., Jernigan, B., Insel, M., Harris, D. T., Erickson, H. E., Edwards, T., Dake, M. D., Cristan, E., , Cohen, R., et al. (2021). SARS-CoV-2 Rapid Antigen Testing of Symptomatic and Asymptomatic Individuals on the University of Arizona Campus.. Biomedicines, 9(5). doi:10.3390/biomedicines9050539
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  SARS-CoV-2, the cause of COVID19, has caused a pandemic that has infected more than 80 M and killed more than 1.6 M persons worldwide. In the US as of December 2020, it has infected more than 32 M people while causing more than 570,000 deaths. As the pandemic persists, there has been a public demand to reopen schools and university campuses. To consider these demands, it is necessary to rapidly identify those individuals infected with the virus and isolate them so that disease transmission can be stopped. In the present study, we examined the sensitivity of the Quidel Rapid Antigen test for use in screening both symptomatic and asymptomatic individuals at the University of Arizona from June to August 2020. A total of 885 symptomatic and 1551 asymptomatic subjects were assessed by antigen testing and real-time PCR testing. The sensitivity of the test for both symptomatic and asymptomatic persons was between 82 and 90%, with some caveats.
• Ripperger, T. J., Uhrlaub, J. L., Watanabe, M., Wong, R., Castaneda, Y., Pizzato, H. A., Thompson, M. R., Bradshaw, C., Weinkauf, C. C., Bime, C., Erickson, H. L., Knox, K., Bixby, B., Parthasarathy, S., Chaudhary, S., Natt, B., Cristan, E., El Aini, T., Rischard, F., , Campion, J., et al. (2020). Orthogonal SARS-CoV-2 Serological Assays Enable Surveillance of Low-Prevalence Communities and Reveal Durable Humoral Immunity. Immunity, 53(5), 925-933.e4.
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  We conducted a serological study to define correlates of immunity against SARS-CoV-2. Compared to those with mild coronavirus disease 2019 (COVID-19) cases, individuals with severe disease exhibited elevated virus-neutralizing titers and antibodies against the nucleocapsid (N) and the receptor binding domain (RBD) of the spike protein. Age and sex played lesser roles. All cases, including asymptomatic individuals, seroconverted by 2 weeks after PCR confirmation. Spike RBD and S2 and neutralizing antibodies remained detectable through 5-7 months after onset, whereas α-N titers diminished. Testing 5,882 members of the local community revealed only 1 sample with seroreactivity to both RBD and S2 that lacked neutralizing antibodies. This fidelity could not be achieved with either RBD or S2 alone. Thus, inclusion of multiple independent assays improved the accuracy of antibody tests in low-seroprevalence communities and revealed differences in antibody kinetics depending on the antigen. We conclude that neutralizing antibodies are stably produced for at least 5-7 months after SARS-CoV-2 infection.
• Scott, S. J., Nikolich-zugich, J., Knepler, J. L., Wong, R., Weinkauf, C. C., Watanabe, M., Uhrlaub, J. L., Thompson, M. R., Sprissler, R., Spier, C. M., Scott, S. J., Sam, A., Rischard, F., Ripperger, T. J., Pizzato, H. A., Parthasarathy, S., Nikolich-zugich, J., Natt, B., Mosier, J., , Lafleur, B. J., et al. (2020). Detection, prevalence, and duration of humoral responses to SARS-CoV-2 under conditions of limited population exposure.. medRxiv : the preprint server for health sciences. doi:10.1101/2020.08.14.20174490
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  We conducted an extensive serological study to quantify population-level exposure and define correlates of immunity against SARS-CoV-2. We found that relative to mild COVID-19 cases, individuals with severe disease exhibited elevated authentic virus-neutralizing titers and antibody levels against nucleocapsid (N) and the receptor binding domain (RBD) and the S2 region of spike protein. Unlike disease severity, age and sex played lesser roles in serological responses. All cases, including asymptomatic individuals, seroconverted by 2 weeks post-PCR confirmation. RBD- and S2-specific and neutralizing antibody titers remained elevated and stable for at least 2-3 months post-onset, whereas those against N were more variable with rapid declines in many samples. Testing of 5882 self-recruited members of the local community demonstrated that 1.24% of individuals showed antibody reactivity to RBD. However, 18% (13/73) of these putative seropositive samples failed to neutralize authentic SARS-CoV-2 virus. Each of the neutralizing, but only 1 of the non-neutralizing samples, also displayed potent reactivity to S2. Thus, inclusion of multiple independent assays markedly improved the accuracy of antibody tests in low seroprevalence communities and revealed differences in antibody kinetics depending on the viral antigen. In contrast to other reports, we conclude that immunity is durable for at least several months after SARS-CoV-2 infection.
• Low, S., Sam, A. R., & Knepler, J. L. (2018). ENDOBRONCHIAL VALVES THERAPY FOR ADVANCED EMPHYSEMA: A META-ANALYSIS. JOURNAL OF BRONCHOLOGY AND INTERVENTIONAL PULMONOLGY.
• Sam, A. R., Knepler, J. L., Sam, A. R., Low, S. W., Lee, J. Z., Knepler, J. L., Hsu, C. H., & Desai, H. (2019). Endobronchial Valves Therapy for Advanced Emphysema: A Meta-Analysis of Randomized Trials.. Journal of bronchology & interventional pulmonology, 26(2), 81-89. doi:10.1097/lbr.0000000000000527
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  Trials suggest that bronchoscopic lung volume reduction (BLVR) with endobronchial valve (EBV) implantation may produce similar effects as lung volume reduction surgery, by inducing atelectasis and reducing hyperinflation through a minimally invasive procedure. This study sought to investigate the efficacy and safety of BLVR with EBV for advanced emphysema..We searched PubMed, EMBASE, Web of Science, CINAHL, ClinicalTrials.gov, and Cochrane Library databases for randomized controlled trials comparing EBV implantation versus standard medical treatment or sham bronchoscopy. The main outcome of interest was the percentage change of forced expiratory volume in 1 second..Data analyzed from 5 randomized controlled trials with 703 patients revealed improvement in percentage change of forced expiratory volume in 1 second in EBV group compared with control group [weighted mean difference (WMD)=11.43; 95% confidence interval (CI), 6.05-16.80; P
• Bixby, B., & Knepler, J. (2018). Medical image of the week: post pneumonectomy syndrome. Southwest Journal of Pulmonary and Critical Care, 16(6), 332-333. doi:10.13175/swjpcc071-18
• Borg, B., & Knepler, J. (2018). Medical image of the week: mediastinal lipomasosis. Southwest Journal of Pulmonary and Critical Care, 16(4), 228-229. doi:10.13175/swjpcc046-18
• Chopra, M., Kumar, S., Ojo, T., Knepler, J., & Power, E. P. (2018). Ultrasound for critical care physicians: characteristic findings in a complicated effusion. Southwest Journal of Pulmonary and Critical Care, 17(6), 150-152. doi:10.13175/swjpcc122-18
• Knepler, J. L. (2018). Endobronchial Valves Therapy for Advanced Emphysema: A Meta-Analysis of Randomized Trial. Journal of Bronchology & Interventional Pulmonology.
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  AbstractBACKGROUND:Trials suggest that bronchoscopic lung volume reduction (BLVR) with endobronchial valve (EBV) implantation may produce similar effects as lung volume reduction surgery, by inducing atelectasis and reducing hyperinflation through a minimally invasive procedure. This study sought to investigate the efficacy and safety of BLVR with EBV for advanced emphysema.METHODS:We searched PubMed, EMBASE, Web of Science, CINAHL, ClinicalTrials.gov, and Cochrane Library databases for randomized controlled trials comparing EBV implantation versus standard medical treatment or sham bronchoscopy. The main outcome of interest was the percentage change of forced expiratory volume in 1 second.RESULTS:Data analyzed from 5 randomized controlled trials with 703 patients revealed improvement in percentage change of forced expiratory volume in 1 second in EBV group compared with control group [weighted mean difference (WMD)=11.43; 95% confidence interval (CI), 6.05-16.80; P
• Low, S., Ateeli, H., & Knepler, J. (2017). Medical image of the week: saber sheath trachea. Southwest Journal of Pulmonary and Critical Care, 14(6), 283-284. doi:10.13175/swjpcc056-17
• Natt, B., Knepler, J. L., Kazui, T., & Mosier, J. M. (2017). The use of extracorporeal membrane oxygenation in the bronchoscopic management of critical upper airway obstruction. J Bronchology Interv Pulmonol, 24(1), e12-e14.
• Natt, B., & Knepler, J. L. (2016). Medical image of the week: endobronchial valves. Southwest Journal of Pulmonary and Critical Care, 13(1), 34-35.
• Natt, B., & Knepler, J. L. (2016). Medical image of the week: lung entrapment. Southwest Journal of Pulmonary and Critical Care, 13(1), 36-37.
• Baalachandran, R., & Knepler, J. (2015). Neutropenia With Respiratory Syncytial Virus Infection in Large Granular Lymphocyte (LGL) Leukemia. Chest, 148(4), 95A. doi:10.1378/chest.2259704
• Dill, J., Gerald, J. K., Bime, C., & Knepler, J. L. (2015). September 2015 Tucson pulmonary journal club: genomic classifier for lung cancer. .. Southwest J Pulm Crit Care. doi:doi: http://dx.doi.org/10.13175/swjpcc125-15 PDF
• Dill, J., Gerald, J. K., Bime, C., & Knepler, J. L. (2015). Tucson pulmonary journal club: genomic classifier for lung cancer.. Southwest J Pulm Crit Care.
• Ganesh, A., Omar, M., Knepler, J. L., & Snyder, L. S. (2015). Medical image of the week: nocardiosis. Southwest J Pulm Crit Care.
• Knepler, J. L. (2015). Medical Image of the Week: Carcinoid at the Carina. Southwest Journal of Pulmonary and Critical Care Medicine. doi:http://dx.doi.org/10.13175/swjpcc052-15
• Moller, D. R., Koth, L. L., Maier, L. A., Morris, A., Drake, W., Rossman, M., Leader, J. K., Collman, R. G., Hamzeh, N., Sweiss, N. J., Zhang, Y., O'Neal, S., Senior, R. M., Becich, M., Hochheiser, H. S., Kaminski, N., Wisniewski, S. R., & Gibson, K. F. (2015). Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) Study. Sarcoidosis Protocol. Annals of the American Thoracic Society, 12(10), 1561-71.
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  Sarcoidosis is a systemic disease characterized by noncaseating granulomatous inflammation with tremendous clinical heterogeneity and uncertain pathobiology and lacking in clinically useful biomarkers. The Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis (GRADS) study is an observational cohort study designed to explore the role of the lung microbiome and genome in these two diseases. This article describes the design and rationale for the GRADS study sarcoidosis protocol. The study addresses the hypothesis that distinct patterns in the lung microbiome are characteristic of sarcoidosis phenotypes and are reflected in changes in systemic inflammatory responses as measured by peripheral blood changes in gene transcription. The goal is to enroll 400 participants, with a minimum of 35 in each of 9 clinical phenotype subgroups prioritized by their clinical relevance to understanding of the pathobiology and clinical heterogeneity of sarcoidosis. Participants with a confirmed diagnosis of sarcoidosis undergo a baseline visit with self-administered questionnaires, chest computed tomography, pulmonary function tests, and blood and urine testing. A research or clinical bronchoscopy with a research bronchoalveolar lavage will be performed to obtain samples for genomic and microbiome analyses. Comparisons will be made by blood genomic analysis and with clinical phenotypic variables. A 6-month follow-up visit is planned to assess each participant's clinical course. By the use of an integrative approach to the analysis of the microbiome and genome in selected clinical phenotypes, the GRADS study is powerfully positioned to inform and direct studies on the pathobiology of sarcoidosis, identify diagnostic or prognostic biomarkers, and provide novel molecular phenotypes that could lead to improved personalized approaches to therapy for sarcoidosis.
• Mosier, J. M., Malo, J., Sakles, J. C., Hypes, C. D., Natt, B., Snyder, L., Knepler, J., Bloom, J. W., Joshi, R., & Knox, K. (2015). The impact of a comprehensive airway management training program for pulmonary and critical care medicine fellows. A three-year experience. Annals of the American Thoracic Society, 12(4), 539-48.
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  Airway management in the intensive care unit (ICU) is challenging, as many patients have limited physiologic reserve and are at risk for clinical deterioration if the airway is not quickly secured. In academic medical centers, ICU intubations are often performed by trainees, making airway management education paramount for pulmonary and critical care trainees.
• Strange, C., Senior, R. M., Sciurba, F., O'Neal, S., Morris, A., Wisniewski, S. R., Bowler, R., Hochheiser, H. S., Becich, M. J., Zhang, Y., Leader, J. K., Methé, B. A., Kaminski, N., & Sandhaus, R. A. (2015). Rationale and Design of the Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis Study. Alpha-1 Protocol. Annals of the American Thoracic Society, 12(10), 1551-60.
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  Severe deficiency of alpha-1 antitrypsin has a highly variable clinical presentation. The Genomic Research in Alpha-1 Antitrypsin Deficiency and Sarcoidosis α1 Study is a prospective, multicenter, cross-sectional study of adults older than age 35 years with PiZZ or PiMZ alpha-1 antitrypsin genotypes. It is designed to better understand if microbial factors influence this heterogeneity. Clinical symptoms, pulmonary function testing, computed chest tomography, exercise capacity, and bronchoalveolar lavage (BAL) will be used to define chronic obstructive pulmonary disease (COPD) phenotypes that can be studied with an integrated systems biology approach that includes plasma proteomics; mouth, BAL, and stool microbiome and virome analysis; and blood microRNA and blood mononuclear cell RNA and DNA profiling. We will rely on global genome, transcriptome, proteome, and metabolome datasets. Matched cohorts of PiZZ participants on or off alpha-1 antitrypsin augmentation therapy, PiMZ participants not on augmentation therapy, and control participants from the Subpopulations and Intermediate Outcome Measures in COPD Study who match on FEV1 and age will be compared. In the primary analysis, we will determine if the PiZZ individuals on augmentation therapy have a difference in lower respiratory tract microbes identified compared with matched PiZZ individuals who are not on augmentation therapy. By characterizing the microbiome in alpha-1 antitrypsin deficiency (AATD), we hope to define new phenotypes of COPD that explain some of the diversity of clinical presentations. As a unique genetic cause of COPD, AATD may inform typical COPD pathogenesis, and better understanding of it may illuminate the complex interplay between environment and genetics. Although the biologic approaches are hypothesis generating, the results may lead to development of novel biomarkers, better understanding of COPD phenotypes, and development of novel diagnostic and therapeutic trials in AATD and COPD. Clinical trial registered with www.clinicaltrials.gov (NCT01832220).
• Siddiqi, T., Assar, S., Lougee, K., & Knepler, J. (2014). Malignant Transformation of Recurrent Respiratory Papillomatosis: Atypical Presentation as Right Mainstem Bronchus Occlusion. Chest, 145(3), 478A. doi:10.1378/chest.1836553
• Baumann, J., Knepler, J., Kim, S., & Sobonya, R. E. (2013). Medical image of the week: solitary fibrous tumor. Southwest Journal of Pulmonary and Critical Care, 7(3), 179-180. doi:10.13175/swjpcc120-13
• Hsu, W., & Knepler, J. (2013). Medical image of the week: tracheal stenosis. Southwest Journal of Pulmonary and Critical Care, 7(1), 53-54. doi:10.13175/swjpcc099-13
• Knepler, J., Snyder, L., Snyder, L., Siddiqi, T., Rios, C., Knepler, J., & Cantu, C. (2013). Medical image of the week: hemophagoctyic lymphohistiocytosis (HLH). Southwest Journal of Pulmonary and Critical Care, 7(6), 351-352. doi:10.13175/swjpcc157-13
• Natt, B., Knepler, J., Natt, B., Knepler, J., & Hamid, N. (2013). Medical image of the week: right main bronchus obstruction in a young man. Southwest Journal of Pulmonary and Critical Care, 7(2), 100-102. doi:10.13175/swjpcc107-13
• Samson, P., Casey, K. R., Knepler, J., & Panos, R. J. (2012). Clinical characteristics, comorbidities, and response to treatment of veterans with obstructive sleep apnea, Cincinnati Veterans Affairs Medical Center, 2005-2007.. Preventing chronic disease, 9(1), E46. doi:10.5888/pcd9.110117
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  Obstructive sleep apnea (OSA) is a common disorder that is associated with significant morbidity. Veterans may be at an elevated risk for OSA because of increased prevalence of factors associated with the development and progression of OSA. The objective of this study was to determine the clinical characteristics, comorbidities, polysomnographic findings, and response to treatment of veterans with OSA..We performed a retrospective chart review of 596 patients undergoing polysomnography at the Cincinnati Veterans Affairs Medical Center from February 2005 through December 2007. We assessed potential correlations of clinical data with polysomnography findings and response to treatment..Polysomnography demonstrated OSA in 76% of patients; 30% had mild OSA, 23% moderate OSA, and 47% severe OSA. Increasing body mass index, neck circumference, Epworth Sleepiness Scale score, hypertension, congestive heart failure, and type 2 diabetes correlated with increasing OSA severity. Positive airway pressure treatment was initiated in 81% of veterans with OSA, but only 59% reported good adherence to this treatment method. Of the patients reporting good adherence, a greater proportion of those with severe OSA (27%) than with mild or moderate disease (0%-12%) reported an excellent response to treatment..The prevalence of metabolic and cardiovascular comorbidities increased with increasing OSA severity. Only 59% of treated patients reported good adherence to treatment with positive airway pressure, and response to treatment correlated with OSA severity.

Presentations

• Afshar, S., & Knepler, J. L. (2018, Summer). Anesthetic Management of Lower Tracheal/Carinal Airway Stenosis from Tumor Encroachment. WARC. San Diego, CA: Western Anesthesia Residents' Conference.

Poster Presentations

• Natt, B., Malo, J., Snyder, L. S., Knepler, J. L., Knox, K. S., & Mosier, J. M. (2015, May/Spring). Advanced Airway Management in Critical Care Fellowship Training. ATS International Conference. Denver, CO.