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Coffey DG, Xu Y, Towlerton AMH, Kowanetz M, Hegde P, Darwish M, Yadav M, Blanchette C, Ruppert SM, Bertino S, Xu Q, Ferretti A, Weinheimer A, Hellmann M, Qin A, Thomas D, Warren EH, Ramnath N. Case report: A persistently expanded T cell response in an exceptional responder to radiation and atezolizumab for metastatic non-small cell lung cancer. Front Immunol 2022; 13:961105. [PMID: 36159875 PMCID: PMC9500393 DOI: 10.3389/fimmu.2022.961105] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Most patients with advanced non-small cell lung cancer (NSCLC) do not achieve a durable remission after treatment with immune checkpoint inhibitors. Here we report the clinical history of an exceptional responder to radiation and anti-program death-ligand 1 (PD-L1) monoclonal antibody, atezolizumab, for metastatic NSCLC who remains in a complete remission more than 8 years after treatment. Sequencing of the patient’s T cell repertoire from a metastatic lesion and the blood before and after anti-PD-L1 treatment revealed oligoclonal T cell expansion. Characterization of the dominant T cell clone, which comprised 10% of all clones and increased 10-fold in the blood post-treatment, revealed an activated CD8+ phenotype and reactivity against 4 HLA-A2 restricted neopeptides but not viral or wild-type human peptides, suggesting tumor reactivity. We hypothesize that the patient’s exceptional response to anti-PD-L1 therapy may have been achieved by increased tumor immunogenicity promoted by pre-treatment radiation therapy as well as long-term persistence of oligoclonal expanded circulating T cells.
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Affiliation(s)
- David G. Coffey
- Department of Medicine, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Medicine, Sylvester Comprehensive Cancer Center, Miami, FL, United States
| | - Yuexin Xu
- Department of Medicine, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | | | | | - Priti Hegde
- Foundation Medicine, Cambridge, MA, United States
| | | | | | | | | | | | - Qikai Xu
- TScan Therapeutics, Waltham, MA, United States
| | | | | | | | - Angel Qin
- Department of Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Dafydd Thomas
- Department of Pathology, University of Michigan, Ann Arbor, MI, United States
| | - Edus H. Warren
- Department of Medicine, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Nithya Ramnath
- Department of Medicine, University of Michigan, Ann Arbor, MI, United States
- Precision Oncology Program, Veterans Affairs, Ann Arbor Healthcare System, Ann Arbor, MI, United States
- *Correspondence: Nithya Ramnath,
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2
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Ferretti AP, Kula T, Wang Y, Nguyen DMV, Weinheimer A, Dunlap GS, Xu Q, Nabilsi N, Perullo CR, Cristofaro AW, Whitton HJ, Virbasius A, Olivier KJ, Buckner LR, Alistar AT, Whitman ED, Bertino SA, Chattopadhyay S, MacBeath G. Unbiased Screens Show CD8 + T Cells of COVID-19 Patients Recognize Shared Epitopes in SARS-CoV-2 that Largely Reside outside the Spike Protein. Immunity 2020; 53:1095-1107.e3. [PMID: 33128877 PMCID: PMC7574860 DOI: 10.1016/j.immuni.2020.10.006] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/03/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022]
Abstract
Developing effective strategies to prevent or treat coronavirus disease 2019 (COVID-19) requires understanding the natural immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We used an unbiased, genome-wide screening technology to determine the precise peptide sequences in SARS-CoV-2 that are recognized by the memory CD8+ T cells of COVID-19 patients. In total, we identified 3-8 epitopes for each of the 6 most prevalent human leukocyte antigen (HLA) types. These epitopes were broadly shared across patients and located in regions of the virus that are not subject to mutational variation. Notably, only 3 of the 29 shared epitopes were located in the spike protein, whereas most epitopes were located in ORF1ab or the nucleocapsid protein. We also found that CD8+ T cells generally do not cross-react with epitopes in the four seasonal coronaviruses that cause the common cold. Overall, these findings can inform development of next-generation vaccines that better recapitulate natural CD8+ T cell immunity to SARS-CoV-2.
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Affiliation(s)
| | | | - Yifan Wang
- TScan Therapeutics, Waltham, MA 02451, USA
| | | | | | | | - Qikai Xu
- TScan Therapeutics, Waltham, MA 02451, USA
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3
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Haskins JD, Lopez-Hilfiker FD, Lee BH, Shah V, Wolfe GM, DiGangi J, Fibiger D, McDuffie EE, Veres P, Schroder JC, Campuzano-Jost P, Day DA, Jimenez JL, Weinheimer A, Sparks T, Cohen RC, Campos T, Sullivan A, Guo H, Weber R, Dibb J, Greene J, Fiddler M, Bililign S, Jaeglé L, Brown SS, Thornton JA. Anthropogenic control over wintertime oxidation of atmospheric pollutants. Geophys Res Lett 2019; 46:14826-14835. [PMID: 33012881 PMCID: PMC7526063 DOI: 10.1029/2019gl085498] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 12/11/2019] [Indexed: 05/31/2023]
Abstract
During winter in the mid-latitudes, photochemical oxidation is significantly slower than in summer and the main radical oxidants driving formation of secondary pollutants, such as fine particulate matter and ozone, remain uncertain, owing to a lack of observations in this season. Using airborne observations, we quantify the contribution of various oxidants on a regional basis during winter, enabling improved chemical descriptions of wintertime air pollution transformations. We show that 25-60% of NOx is converted to N2O5 via multiphase reactions between gas-phase nitrogen oxide reservoirs and aerosol particles, with ~93% reacting in the marine boundary layer to form >2.5 ppbv ClNO2. This results in >70% of the oxidizing capacity of polluted air during winter being controlled, not by typical photochemical reactions, but from these multiphase reactions and emissions of volatile organic compounds, such as HCHO, highlighting the control local anthropogenic emissions have on the oxidizing capacity of the polluted wintertime atmosphere.
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Affiliation(s)
- J. D. Haskins
- Department of Atmospheric Sciences, University of Washington, Seattle, WA USA
| | | | - B. H. Lee
- Department of Atmospheric Sciences, University of Washington, Seattle, WA USA
| | - V. Shah
- Department of Atmospheric Sciences, University of Washington, Seattle, WA USA
| | - G. M. Wolfe
- Joint Center for Earth Systems Technology, University of Maryland Baltimore County, Baltimore, MD USA
- Atmospheric Chemistry and Dynamics Laboratory, NASA Goddard Space Flight Center, Greenbelt, MD USA
| | - J. DiGangi
- NASA Langley Research Center, Hampton, VA USA
| | - D. Fibiger
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Chemical Sciences Division, NOAA Earth System Research Laboratory, Boulder, CO USA
| | - E. E. McDuffie
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Chemistry, University of Colorado, Boulder, CO USA
- Chemical Sciences Division, NOAA Earth System Research Laboratory, Boulder, CO USA
| | - P. Veres
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
| | - J. C. Schroder
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Chemistry, University of Colorado, Boulder, CO USA
| | - P. Campuzano-Jost
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Chemistry, University of Colorado, Boulder, CO USA
| | - D. A. Day
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Chemistry, University of Colorado, Boulder, CO USA
| | - J. L. Jimenez
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO, USA
- Department of Chemistry, University of Colorado, Boulder, CO USA
| | - A. Weinheimer
- Earth Observing Laboratory, National Center for Atmospheric Research, Boulder, CO USA
| | - T. Sparks
- Department of Chemistry, University of California, Berkeley CA USA
| | - R. C. Cohen
- Department of Chemistry, University of California, Berkeley CA USA
| | - T. Campos
- Earth Observing Laboratory, National Center for Atmospheric Research, Boulder, CO USA
| | - A. Sullivan
- Department of Atmospheric Sciences, Colorado State University, Fort Collins, CO USA
| | - H. Guo
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
| | - R. Weber
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA USA
| | - J. Dibb
- Department of Earth Sciences, University of New Hampshire, Durham, NH USA
| | - J. Greene
- Department of Physics, North Carolina A&T State University, Greensboro, NC USA
| | - M. Fiddler
- Department of Physics, North Carolina A&T State University, Greensboro, NC USA
| | - S. Bililign
- Department of Physics, North Carolina A&T State University, Greensboro, NC USA
| | - L. Jaeglé
- Department of Atmospheric Sciences, University of Washington, Seattle, WA USA
| | - S. S. Brown
- Department of Chemistry, University of Colorado, Boulder, CO USA
- Chemical Sciences Division, NOAA Earth System Research Laboratory, Boulder, CO USA
| | - J. A. Thornton
- Department of Atmospheric Sciences, University of Washington, Seattle, WA USA
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4
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Hong D, Fritz AJ, Finstad KH, Fitzgerald MP, Weinheimer A, Viens AL, Ramsey J, Stein JL, Lian JB, Stein GS. Suppression of Breast Cancer Stem Cells and Tumor Growth by the RUNX1 Transcription Factor. Mol Cancer Res 2018; 16:1952-1964. [PMID: 30082484 PMCID: PMC6289193 DOI: 10.1158/1541-7786.mcr-18-0135] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [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: 02/12/2018] [Revised: 07/02/2018] [Accepted: 07/27/2018] [Indexed: 12/31/2022]
Abstract
Breast cancer remains the most common malignant disease in women worldwide. Despite advances in detection and therapies, studies are still needed to understand the mechanisms underlying this cancer. Cancer stem cells (CSC) play an important role in tumor formation, growth, drug resistance, and recurrence. Here, it is demonstrated that the transcription factor RUNX1, well known as essential for hematopoietic differentiation, represses the breast cancer stem cell (BCSC) phenotype and suppresses tumor growth in vivo. The current studies show that BCSCs sorted from premalignant breast cancer cells exhibit decreased RUNX1 levels, whereas ectopic expression of RUNX1 suppresses tumorsphere formation and reduces the BCSC population. RUNX1 ectopic expression in breast cancer cells reduces migration, invasion, and in vivo tumor growth (57%) in mouse mammary fat pad. Mechanistically, RUNX1 functions to suppress breast cancer tumor growth through repression of CSC activity and direct inhibition of ZEB1 expression. Consistent with these cellular and biochemical results, clinical findings using patient specimens reveal that the highest RUNX1 levels occur in normal mammary epithelial cells and that low RUNX1 expression in tumors is associated with poor patient survival. IMPLICATIONS: The key finding that RUNX1 represses stemness in several breast cancer cell lines points to the importance of RUNX1 in other solid tumors where RUNX1 may regulate CSC properties.
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Affiliation(s)
- Deli Hong
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
- Graduate Program in Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Andrew J Fritz
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Kristiaan H Finstad
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Mark P Fitzgerald
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Adam Weinheimer
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Adam L Viens
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Jon Ramsey
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Janet L Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Jane B Lian
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont
| | - Gary S Stein
- Department of Biochemistry and University of Vermont Cancer Center, University of Vermont College of Medicine, Burlington, Vermont.
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Knepp T, Pippin M, Crawford J, Chen G, Szykman J, Long R, Cowen L, Cede A, Abuhassan N, Herman J, Delgado R, Compton J, Berkoff T, Fishman J, Martins D, Stauffer R, Thompson AM, Weinheimer A, Knapp D, Montzka D, Lenschow D, Neil D. Estimating surface NO 2 and SO 2 mixing ratios from fast-response total column observations and potential application to geostationary missions. J Atmos Chem 2015; 72:261-286. [PMID: 26692593 PMCID: PMC4665805 DOI: 10.1007/s10874-013-9257-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 04/08/2013] [Indexed: 05/20/2023]
Abstract
Total-column nitrogen dioxide (NO2) data collected by a ground-based sun-tracking spectrometer system (Pandora) and an photolytic-converter-based in-situ instrument collocated at NASA's Langley Research Center in Hampton, Virginia were analyzed to study the relationship between total-column and surface NO2 measurements. The measurements span more than a year and cover all seasons. Surface mixing ratios are estimated via application of a planetary boundary-layer (PBL) height correction factor. This PBL correction factor effectively corrects for boundary-layer variability throughout the day, and accounts for up to ≈75 % of the variability between the NO2 data sets. Previous studies have made monthly and seasonal comparisons of column/surface data, which has shown generally good agreement over these long average times. In the current analysis comparisons of column densities averaged over 90 s and 1 h are made. Applicability of this technique to sulfur dioxide (SO2) is briefly explored. The SO2 correlation is improved by excluding conditions where surface levels are considered background. The analysis is extended to data from the July 2011 DISCOVER-AQ mission over the greater Baltimore, MD area to examine the method's performance in more-polluted urban conditions where NO2 concentrations are typically much higher.
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Affiliation(s)
- T. Knepp
- Science Systems and Applications, Inc., Hampton, VA 23681 USA
- NASA Langley Research Center, Hampton, VA 23681 USA
| | - M. Pippin
- NASA Langley Research Center, Hampton, VA 23681 USA
| | - J. Crawford
- NASA Langley Research Center, Hampton, VA 23681 USA
| | - G. Chen
- NASA Langley Research Center, Hampton, VA 23681 USA
| | - J. Szykman
- US EPA, Research Triangle Park, Durham, NC 27701 USA
| | - R. Long
- US EPA, Research Triangle Park, Durham, NC 27701 USA
| | - L. Cowen
- NASA Langley Research Center, Hampton, VA 23681 USA
| | - A. Cede
- LuftBlick, Kreith, 6162 Austria
- NASA Goddard Space Flight Center, Greenbelt, MD 20771 USA
| | - N. Abuhassan
- NASA Goddard Space Flight Center, Greenbelt, MD 20771 USA
- School of Engineering, Morgan State University, Baltimore, MD 21251 USA
| | - J. Herman
- Joint Center for Earth Systems Technology, University of Baltimore County, Baltimore, MD 21250 USA
| | - R. Delgado
- Joint Center for Earth Systems Technology, University of Baltimore County, Baltimore, MD 21250 USA
| | - J. Compton
- Joint Center for Earth Systems Technology, University of Baltimore County, Baltimore, MD 21250 USA
| | - T. Berkoff
- Joint Center for Earth Systems Technology, University of Baltimore County, Baltimore, MD 21250 USA
| | - J. Fishman
- Department of Earth and Atmospheric Sciences, Saint Louis University, St. Louis, MO 63103 USA
| | - D. Martins
- Department of Meteorology, Pennsylvania State University, University Park, PA 16802 USA
| | - R. Stauffer
- Department of Meteorology, Pennsylvania State University, University Park, PA 16802 USA
| | - A. M. Thompson
- Department of Meteorology, Pennsylvania State University, University Park, PA 16802 USA
| | - A. Weinheimer
- National Center for Atmospheric Research, Boulder, CO 80305 USA
| | - D. Knapp
- National Center for Atmospheric Research, Boulder, CO 80305 USA
| | - D. Montzka
- National Center for Atmospheric Research, Boulder, CO 80305 USA
| | - D. Lenschow
- National Center for Atmospheric Research, Boulder, CO 80305 USA
| | - D. Neil
- NASA Langley Research Center, Hampton, VA 23681 USA
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6
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Villena G, Wiesen P, Cantrell CA, Flocke F, Fried A, Hall SR, Hornbrook RS, Knapp D, Kosciuch E, Mauldin RL, McGrath JA, Montzka D, Richter D, Ullmann K, Walega J, Weibring P, Weinheimer A, Staebler RM, Liao J, Huey LG, Kleffmann J. Nitrous acid (HONO) during polar spring in Barrow, Alaska: A net source of OH radicals? ACTA ACUST UNITED AC 2011. [DOI: 10.1029/2011jd016643] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Vogel B, Pan LL, Konopka P, Günther G, Müller R, Hall W, Campos T, Pollack I, Weinheimer A, Wei J, Atlas EL, Bowman KP. Transport pathways and signatures of mixing in the extratropical tropopause region derived from Lagrangian model simulations. ACTA ACUST UNITED AC 2011. [DOI: 10.1029/2010jd014876] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Tilmes S, Pan LL, Hoor P, Atlas E, Avery MA, Campos T, Christensen LE, Diskin GS, Gao RS, Herman RL, Hintsa EJ, Loewenstein M, Lopez J, Paige ME, Pittman JV, Podolske JR, Proffitt MR, Sachse GW, Schiller C, Schlager H, Smith J, Spelten N, Webster C, Weinheimer A, Zondlo MA. An aircraft-based upper troposphere lower stratosphere O3, CO, and H2O climatology for the Northern Hemisphere. ACTA ACUST UNITED AC 2010. [DOI: 10.1029/2009jd012731] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Affiliation(s)
| | - I. J. Ford
- Department of Physics and Astronomy; University College London; London UK
| | - C. H. Twohy
- College of Oceanography and Atmospheric Sciences; Oregon State University; Corvallis Oregon USA
| | - A. Weinheimer
- National Center for Atmospheric Research; Boulder Colorado USA
| | - T. Campos
- National Center for Atmospheric Research; Boulder Colorado USA
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