Functional characterization of CD4+ T-cell receptors cross-reactive for SARS-CoV-2 and endemic coronaviruses

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Abstract

Background. Recent studies have reported T cell immunity to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in unexposed donors, possibly due to cross-recognition by T-cells specific for common cold coronaviruses (CCCs). True T-cell cross-reactivity, defined as the recognition by a single TCR of more than one distinct peptide-MHC ligand, has never been shown in the context of SARS-CoV-2. Methods. We used the ViraFEST platform to identify T cell responses cross-reactive for the spike (S) glycoproteins of SARS-CoV-2 and CCCs at the T cell receptor (TCR) clonotype level in convalescent COVID-19 patients (CCPs) and SARS-CoV-2-unexposed donors. Confirmation of SARS-CoV-2/CCC cross-reactivity and assessments of functional avidity were performed using a TCR cloning and transfection system. Results. Memory CD4+ T-cell clonotypes that cross-recognized the S proteins of SARS-CoV-2 and at least one other CCC were detected in 65% of CCPs and unexposed donors. Several of these TCRs were shared among multiple donors. Cross-reactive T-cells demonstrated significantly impaired SARS-CoV-2-specific proliferation in vitro relative to mono-specific CD4+ T-cells, which was consistent with lower functional avidity of their TCRs for SARS CoV-2 relative to CCC. Conclusions. For the first time, our data confirm the existence of unique memory CD4+ T cell clonotypes cross-recognizing SARS-CoV-2 and CCCs. The lower avidity of cross-reactive TCRs for SARS-CoV-2 may be the result of antigenic imprinting, such that pre-existing CCC-specific memory T cells have reduced expansive capacity upon SARS-CoV-2 infection. Further studies are needed to determine how these cross-reactive T-cell responses impact clinical outcomes in COVID-19 patients.

Authors

Arbor G. Dykema, Boyang Zhang, Bezawit A. Woldemeskel, Caroline C. Garliss, Laurene S. Cheung, Dilshad Choudhury, Jiajia Zhang, Luis Aparicio, Sadhana Bom, Rufiaat Rashid, Justina X. Caushi, Emily Han-Chung Hsiue, Katherine Cascino, Elizabeth A. Thompson, Abena K. Kwaa, Dipika Singh, Sampriti Thapa, Alvaro A. Ordonez, Andrew Pekosz, Franco R. D'Alessio, Jonathan D. Powell, Srinivasan Yegnasubramanian, Shibin Zhou, Drew M. Pardoll, Hongkai Ji, Andrea L. Cox, Joel N. Blankson, Kellie N. Smith

Parkinson disease among patients treated for benign prostatic hyperplasia with α1 adrenergic receptor antagonists

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Abstract

BACKGROUND. Recently the α1 adrenergic receptor antagonist terazosin was shown to activate PGK1, a possible target for the mitochondrial deficits in Parkinson disease related to its function as the initial enzyme in ATP synthesis during glycolysis. An epidemiologic study of terazosin users showed a lower incidence of Parkinson disease when compared to users of tamsulosin, an α1 adrenergic receptor antagonist of a different class that does not activate PGK1. However, prior research on tamsulosin has suggested that it may in fact potentiate neurodegeneration, raising the question of whether it is an appropriate control group. METHODS. To address this question, we undertook an epidemiological study on Parkinson disease occurrence rate in 113,450 individuals from the U.S.A. with > 5 years of follow-up. Patients were classified as tamsulosin users (n = 45,380), terazosin/alfuzosin/doxazosin users (n = 22,690) or controls matched on age, gender and Charlson Comorbidity Index score (n = 45,380). RESULTS. Incidence of Parkinson disease in tamsulosin users was 1.53%, which was significantly higher than that in both terazosin/alfuzosin/doxazosin users (1.10%; p<0.0001) and matched controls (1.01%; p < 0.0001). Terazosin/alfuzosin/doxazosin users did not differ in Parkinson disease risk from matched controls (p = 0.29). CONCLUSION. These results suggest that zosins may not confer a protective effect against Parkinson disease, but rather that tamsulosin may in some way potentiate Parkinson disease progression. FUNDING. This work was supported by Cerevel Therapeutics.

Authors

Rahul Sasane, Amy Bartels, Michelle Field, Maria I. Sierra, Sridhar Duvvuri, David L. Gray, Sokhom S. Pin, John J. Renger, David J. Stone

Accurate diagnosis of pulmonary nodules using a non-invasive DNA methylation test

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Abstract

BACKGROUND. Current clinical management of patients with pulmonary nodules involves either repeated LDCT/CT scans or invasive procedures yet causes significant patient misclassification. An accurate non-invasive test is needed to identify malignant nodules and reduce unnecessary invasive tests. METHOD. We developed a diagnostic model based on targeted DNA methylation sequencing of 389 pulmonary nodule patients’ plasma samples, and then validated in 140 plasma samples independently. We tested the model in different stages and subtypes of pulmonary nodules. RESULTS. A 100-feature model was developed and validated for pulmonary nodule diagnosis: the model achieved a ROC-AUC of 0.843 on 140 independent validation samples with an accuracy of 0.800. The performance was well maintained in, 1) 6-20 mm size subgroup (N=100), with a sensitivity of 1.000 and adjusted NPV of 1.000 at 10% prevalence; 2) stage I malignancy (N=90), with a sensitivity of 0.971; 3) different nodule types - solid nodules (N=78) with a sensitivity of 1.000 and adjusted NPV of 1.000, part-solid nodules (N=75) with a sensitivity of 0.947 and adjusted NPV of 0.983, and ground-glass nodules (N=67) with a sensitivity of 0.964 and adjusted NPV of 0.989 at 10% prevalence. This methylation test, called PulmoSeek, outperformed PET-CT and two clinical prediction models (Mayo and Veterans Affairs) in discriminating malignant pulmonary nodules from benign ones. CONCLUSION. This study suggests that the blood-based DNA methylation model may provide a better test for classifying pulmonary nodules, which could help facilitate the accurate diagnosis of early-stage lung cancer from pulmonary nodule patients and guide clinical decisions. FUNDING. The National Key Research and Development Program of China; Science and Technology Planning Project of Guangdong Province; The National Natural Science Foundation of China National.

Authors

Wenhua Liang, Zhiwei Chen, Caichen Li, Jun Liu, Jinsheng Tao, Xin Liu, Dezhi Zhao, Weiqiang Yin, Hanzhang Chen, Chao Cheng, Fenglei Yu, Chunfang Zhang, Lunxu Liu, Hui Tian, Kaican Cai, Xiang Liu, Zheng Wang, Ning Xu, Qing Dong, Liang Chen, Yue Yang, Xiuyi Zhi, Hui Li, Xixiang Tu, Xiangrui Cai, Zeyu Jiang, Hua Ji, Lili Mo, Jiaxuan Wang, Jian-Bing Fan, Jianxing He

Immunoregulatory and lipid presentation pathways are upregulated in human face transplant rejection

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Abstract

BACKGROUND. Rejection is the primary barrier to broader implementation of vascularized composite allografts (VCA), including face and limb transplants. The immunologic pathways activated in face transplant rejection have not been fully characterized. METHODS. Utilizing skin biopsies prospectively collected over nine years from seven face transplant patients, we studied rejection by gene expression profiling, histology, immunostaining and T cell receptor sequencing. RESULTS. Grade 1 rejection did not differ significantly from non-rejection, suggesting that it does not represent a pathologic state and that watchful waiting is warranted. In Grade 2, there was a balanced upregulation of both pro-inflammatory T cell activation pathways and anti-inflammatory checkpoint and immunomodulatory pathways, with a net result of no tissue injury. In Grade 3, IFNγ-driven inflammation, antigen presenting cell activation and infiltration of the skin by proliferative T cells bearing markers of antigen specific activation and cytotoxic effector molecules tipped the balance towards tissue injury. Rejection of VCA and solid organ transplants had both distinct and common features. VCA rejection was uniquely associated with upregulation of immunoregulatory genes, including SOCS1, induction of lipid antigen-presenting CD1 proteins, and infiltration by T cells predicted to recognize CD1b and CD1c. CONCLUSIONS. Our findings suggest that the distinct features of VCA rejection reflect the unique immunobiology of skin and that enhancing cutaneous immunoregulatory networks may be a useful strategy in combatting rejection.

Authors

Thet Su Win, William J. Crisler, Beatrice Dyring-Andersen, Rachel Lopdrup, Jessica E. Teague, Qian Zhan, Victor Barrera, Shannan J. Ho Sui, Sotirios Tasigiorgos, Naoka Murakami, Anil Chandraker, Stefan G. Tullius, Bohdan Pomahac, Leonardo V. Riella, Rachael Clark

Computerized tumor multinucleation index (MuNI) is prognostic in p16+ oropharyngeal carcinoma: A multi-site validation study

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BACKGROUND. p16 positive oropharyngeal squamous cell carcinoma (OPSCC) patients are potentially cured with definitive treatment. However, there are currently no reliable biomarkers of treatment failure in p16 positive OPSCC. Pathologist-based visual assessment of tumor cell multinucleation has been shown to be independently prognostic of disease-free survival in p16 positive OPSCC. However, its quantification is time-intensive, subjective, and at risk of interobserver variability. METHODS. We present a deep learning-based metric, the multi-nucleation index (MuNI), for prognostication in p16 positive OPSCC. This approach quantifies tumor multi-nucleation from digitally scanned hematoxylin eosin (H&E)-stained slides. Representative H&E whole slide images from 1,094 previously untreated p16 positive OPSCC patients were acquired from six institutions for optimizing and validating MuNI. RESULTS. MuNI was prognostic for disease-free (DFS), overall (OS), or distant metastasis-free (DMFS) survival in p16 positive OPSCC with HRs of 1.78(95%CI:1.37-2.30), 1.94(1.44-2.60), and 1.88(1.43-2.47), respectively, independent of age, smoking status, treatment type, and T/N-categories in multivariable analyses. It was also prognostic for DFS, OS, and DMFS in OPSCC patients at stages I and III. CONCLUSION. MuNI holds promise as a low-cost, tissue non-destructive, H&E stain based digital biomarker test for counseling, treatment, and surveillance of p16 positive OPSCC patients. These data support further confirmation of MuNI in prospective trials. FUNDING. This work was supported by the National Cancer Institute of the National Institutes of Health (under award numbers 1U24CA199374-01, R01CA202752-01A, R01CA208236-01A1, R01CA216579-01A1, R01CA220581-01A1, 1U01CA239055-01), the National Institute for Biomedical Imaging and Bioengineering (1R43EB028736-01), the National Center for Research Resources (1C06RR12463-01), the VA Merit Review Award (IBX004121A) from the United States Department of Veterans Affairs Biomedical Laboratory Research and Development Service, the DoD Breast Cancer Research Program Breakthrough Level 1 Award (W81XWH-19-1-0668), the DOD Prostate Cancer Idea Development Award (W81XWH-15-1-0558), the DOD Lung Cancer Investigator-Initiated Translational Research Award (W81XWH-18-1-0440), the DOD Peer Reviewed Cancer Research Program (W81XWH-16-1-0329), the Ohio Third Frontier Technology Validation Fund, the Wallace H. Coulter Foundation Program in the Department of Biomedical Engineering, and the Clinical and Translational Science Award Program (CTSA) at Case Western Reserve University, the Michael E. DeBakey VA Medical Center, an institutional pilot grant (1IK2CX001953) and Dan L Duncan Comprehensive Cancer Center Support Grant (NCI-CA125123). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health, the U.S. Department of Veterans Affairs, the Department of Defense, or the United States Government.

Authors

Can F. Koyuncu, Cheng Lu, Kaustav Bera, Zelin Zhang, Jun Xu, Paula Andrea Toro Castaño, Germán Corredor, Deborah Chute, Pingfu Fu, Wade L. Thorstad, Farhoud Faraji, Justin A. Bishop, Mitra Mehrad, Patricia D. Castro, Andrew G. Sikora, Lester D. R. Thompson, R. D. Chernock, Krystle A. Lang Kuhs, Jingqin Luo, Vlad C. Sandulache, David J. Adelstein, Shlomo Koyfman, James S. Lewis Jr., Anant Madabhushi

Long-term micro-structure and cerebral blood flow changes in patients recovered from COVID-19 without neurological manifestations

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Abstract

The coronavirus disease 2019 (COVID-19) rapidly progressed to a global pandemic. Although patients totally recover from COVID-19 pneumonia, long-term effects on the brain still need to be explored. Here, two subtypes (mild type-MG and severe type-SG) with no specific neurological manifestations at the acute stage and no obvious lesions on the conventional MRI three months after discharge were recruited. Changes in gray matter morphometry, cerebral blood flow (CBF) and white matter (WM) microstructure were investigated using MRI. The relationship between brain imaging measurements and inflammation markers were further analyzed. Compared with healthy controls, the decrease in cortical thickness/CBF, and the changes in WM microstructure were observed to be more severe in the SG than MG, especially in the frontal and limbic systems. Furthermore, changes in brain microstructure, CBF and tracts parameters were significantly correlated with inflammatory markers. The indirect injury related to inflammatory storm may damage the brain, that led to these interesting observations. There are also other likely potential causes, such as hypoxemia and dysfunction of vascular endothelium, et al. The abnormalities in these brain areas need to be monitored in the process of complete recovery, which could help clinicians to understand the potential neurological sequelae of COVID-19.

Authors

Yuanyuan Qin, Jinfeng Wu, Tao Chen, Jia Li, Guiling Zhang, Di Wu, Yiran Zhou, Ning Zheng, Aoling Cai, Qin Ning, Anne Manyande, Fuqiang Xu, Jie Wang, Wenzhen Zhu

CCR5-edited CD4 T cells augment HIV-specific immunity to enable post rebound control of HIV replication

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BACKGROUND. We performed a Phase I clinical trial that infused CCR5 gene edited CD4 T cells to determine how these T cells can better enable HIV cure strategies. METHODS. The trial addressed the method of zinc finger nuclease (ZFN) ex vivo delivery, whether CCR5 Δ32 heterozygotes preferentially benefit, the effect of CCR5 gene edited CD4 T cells on the HIV-specific T cell response, and the ability of infused CCR5 gene edited T cells to delay viral rebound during analytical treatment interruption. We enrolled 14 people living with HIV whose viral load was well controlled by antiretroviral therapy (ART). We measured time to viral rebound after ART withdrawal, persistence of CCR5-edited CD4 T cells, and whether infusion of 10 billion CCR5-edited CD4 T cells augmented the HIV-specific immune response. RESULTS. Infusion of the CD4 T cells was well tolerated with no serious adverse events. Modest delay to the time of viral rebound was observed relative to historical controls; however, three of 14 individuals of which two were CCR5 Δ32 heterozygotes appeared to regain control of viremia before ultimately rebounding. Interestingly, only these individuals had significant restoration of HIV-specific CD8 T cell responses. Immune escape to one of these re-invigorated responses was observed at viral recrudescence, illustrating a direct link between viral control and enhanced CD8 T cell responses. CONCLUSION. These findings demonstrate how CCR5 gene edited CD4 T cell infusion could aid HIV cure strategies by augmenting pre-existing HIV-specific immune responses. TRIAL REGISTRATION. ClinicalTrials.gov NCT02388594 FUNDING. R01AI104400 (C.H.J.), UM1AI126620 (J.L.R.) funded by NIAID, NIDA, NIMH, and NINDS; T32 grant AI007632 (C.R.M.)

Authors

Pablo Tebas, Julie K. Jadlowsky, Pamela A. Shaw, Lifeng Tian, Erin Esparza, Andrea Brennan, Sukyung Kim, Soe Yu Naing, Max W. Richardson, Ashley N. Vogel, Colby R. Maldini, Hong Kong, Xiaojun Liu, Simon F. Lacey, Anya M. Bauer, Felicity Mampe, Lee P. Richman, Gary Lee, Dale Ando, Bruce L. Levine, David L. Porter, Yangbing Zhao, Don L. Siegel, Katharine J. Bar, Carl H. June, James L. Riley

Pfs230 yields higher malaria transmission-blocking vaccine activity than Pfs25 in humans but not mice

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Background. Vaccines that block human-to-mosquito Plasmodium transmission are needed for malaria eradication and clinical trials have targeted zygote antigen Pfs25 for decades. We reported that a Pfs25 protein-protein conjugate vaccine formulated in alum adjuvant induced significant serum functional activity in both US and Malian adults. However, antibody titers declined rapidly, and transmission-reducing activity required four vaccine doses. Functional immunogenicity and durability must be improved before advancing TBV further in clinical development. We hypothesized that the pre-fertilization protein Pfs230 alone or in combination with Pfs25 would improve functional activity.Methods. Transmission-blocking vaccine candidates based on gamete antigen Pfs230 or Pfs25 were conjugated with Exoprotein A, formulated in Alhydrogel, and administered to mice, rhesus macaques, and humans. Antibody titers were measured by ELISA and transmission-reducing activity was assess by the Standard Membrane Feeding Assay. Results. Pfs25-EPA/Alhydrogel and Pfs230D1-EPA/Alhydrogel induced similar serum functional activity in mice, but Pfs230D1-EPA induced significantly greater activity in rhesus monkeys that was enhanced by complement. In U.S. adults, two vaccine doses induced complement-dependent activity in 4 of 5 Pfs230D1-EPA/Alhydrogel recipients but no significant activity in five Pfs25-EPA recipients, and combination with Pfs25-EPA did not increase activity over Pfs230D1-EPA alone.Conclusion. The complement-dependent functional immunogenicity of Pfs230D1-EPA represents a significant improvement over Pfs25-EPA in this comparative study. The rhesus model is more predictive of the functional human immune response to Pfs230D1 than is the mouse model. Trial Registration. ClinicalTrials.gov NCT02334462Funding. This work was supported by the Intramural Research Program of the National Institute of Allergy and Infectious Diseases, National Institutes of Health.

Authors

Sara A. Healy, Charles F. Anderson, Bruce J. Swihart, Agnes Mwakingwe-Omari, Erin E. Gabriel, Hope Decederfelt, Charlotte V. Hobbs, Kelly M. Rausch, Daming Zhu, Olga Muratova, Raul Herrera, Puthupparampil V. Scaria, Nicholas J. MacDonald, Lynn E. Lambert, Irfan Zaidi, Camila H. Coelho, Jonathan P. Renn, Yimin Wu, David L. Narum, Patrick E. Duffy

Sensitive tracking of circulating viral RNA through all stages of SARS-CoV-2 infection

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Background: Circulating SARS-CoV-2 RNA may represent a more reliable indicator of infection than nasal RNA, but RT-qPCR lacks diagnostic sensitivity for blood samples. Methods: A CRISPR-augmented RT-PCR assay that sensitively detects SARS-CoV-2 RNA was employed to analyze viral RNA kinetics in longitudinal plasma samples from nonhuman primates (NHP) after virus exposure; to evaluate the utility of blood SARS-CoV-2 RNA detection for COVID-19 diagnosis in adults cases confirmed by nasal/nasopharyngeal swab RT-PCR results; and to identify suspected COVID-19 cases in pediatric and at-risk adult populations with negative nasal swab RT-qPCR results. All blood samples were analyzed by RT-qPCR to allow direct comparisons. Results: CRISPR-augmented RT-PCR consistently detected SARS-CoV-2 RNA in the plasma of experimentally infected NHPs from 1 to 28 days post-infection, and these increases preceded and correlated with rectal swab viral RNA increases. In a patient cohort (n=159), this blood-based assay demonstrated 91.2% diagnostic sensitivity and 99.2% diagnostic specificity versus a comparator RT-qPCR nasal/nasopharyngeal test, while RT-qPCR exhibited 44.1% diagnostic sensitivity and 100% specificity for the same blood samples. This CRISPR-augmented RT-PCR assay also accurately identified COVID-19 patients with one or more negative nasal swab RT-qPCR result. Conclusion: Results of this study indicate that sensitive detection of SARS-CoV-2 RNA in blood by CRISPR-augmented RT-PCR permits accurate COVID-19 diagnosis, and can detect COVID-19 cases with transient or negative nasal swab RT-qPCR results, suggesting that this approach could improve COVID-19 diagnosis and the evaluation of SARS-CoV-2 infection clearance, and predict the severity of infection.

Authors

Zhen Huang, Bo Ning, He S. Yang, Brady M. Youngquist, Alex Niu, Christopher J. Lyon, Brandon J. Beddingfield, Alyssa C. Fears, Chandler H. Monk, Amelie E. Murrell, Samantha J. Bilton, Joshua P. Linhuber, Elizabeth B. Norton, Monika L. Dietrich, Jim K. Yee, Weihua Lai, John W. Scott, Xiao-Ming Yin, Jay Rappaport, James E. Robinson, Nakhle S. Saba, Chad J. Roy, Kevin J. Zwezdaryk, Zhen Zhao, Tony Y. Hu

A replication competent adenovirus-vectored influenza vaccine induces durable systemic and mucosal immunity

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BACKGROUND. Immunization with replication-competent recombinant vectors provides exposure to transgene-encoded antigens in the context of inflammation that may drive more potent and durable immunity compared to non-replicating vaccines. To understand the features of a replicating vaccine that drive such responses we tested a replication-competent adenovirus type 4 encoding influenza virus H5 hemagglutinin (Ad4-H5-Vtn) administered by an oral capsule or via a tonsillar swab or nasal spray. METHODS. Viral shedding from the nose, mouth, and rectum was measured by PCR and culture. H5-specific IgG and IgA antibodies were measured by bead array binding assays. Serum antibodies were measured by a pseudovirus entry inhibition assay (PVEI), microneutralization (MN), and hemagglutinin inhibition (HAI). RESULTS. Ad4-H5-Vtn DNA was shed from most upper respiratory tract (URT)-immunized volunteers for 2-4 weeks, but cultured from only 60% of participants with a median duration of one day. Ad4-H5-Vtn vaccination induced increases in H5-specific CD4+ and CD8+ T cells in the peripheral blood and IgG and IgA in nasal, cervical and rectal secretions. URT immunizations induced high levels of serum neutralizing antibodies (NAb) to H5 which remained stable at week 26. The duration of viral shedding correlated with the magnitude of the NAb response at week 26. Adverse events (AE) were mild, and peak NAb titer was associated with overall AE frequency or duration. Serum neutralizing antibody titers could be boosted to very high levels 2-5 years after Ad4-H5-Vtn vaccination with recombinant H5 or inactivated split H5N1 vaccine. CONCLUSION. Replicating Ad4 delivered to the URT causes prolonged exposure to antigen, drives durable systemic and mucosal immunity, and is a promising platform for the induction of immunity against viral surface glycoprotein targets. TRIAL REGISTRATION. ClinicalTrials.gov NCT01443936, NCT01806909. FUNDING. Intramural and Extramural Research Programs of the NIAID, NIH; and the Centers of Influenza Virus Research and SurveillanceFunding. Intramural and Extramural Research Programs of the NIAID, NIH; and the Centers of Influenza Virus Research and Surveillance.

Authors

Kenta Matsuda, Stephen A. Migueles, Jinghe Huang, Lyuba Bolkhovitinov, Sarah Stuccio, Trevor Griesman, Alyssa A. Pullano, Byong H. Kang, Elise Ishida, Matthew Zimmerman, Neena Kashyap, Kelly M. Martins, Daniel Stadlbauer, Jessica Pederson, Andy Patamawenu, Nathaniel E. Wright, Tulley Shofner, Sean Evans, C. Jason Liang, Julián Candia, Angelique Biancotto, Giovanna Fantoni, April Poole, Jonathan Smith, Jeff Alexander, Marc Gurwith, Florian Krammer, Mark Connors