All Publications

  • Multi-Omics Resolves a Sharp Disease-State Shift between Mild and Moderate COVID-19. Cell Su, Y., Chen, D., Yuan, D., Lausted, C., Choi, J., Dai, C. L., Voillet, V., Duvvuri, V. R., Scherler, K., Troisch, P., Baloni, P., Qin, G., Smith, B., Kornilov, S. A., Rostomily, C., Xu, A., Li, J., Dong, S., Rothchild, A., Zhou, J., Murray, K., Edmark, R., Hong, S., Heath, J. E., Earls, J., Zhang, R., Xie, J., Li, S., Roper, R., Jones, L., Zhou, Y., Rowen, L., Liu, R., Mackay, S., O'Mahony, D. S., Dale, C. R., Wallick, J. A., Algren, H. A., Zager, M. A., ISB-Swedish COVID19 Biobanking Unit, Wei, W., Price, N. D., Huang, S., Subramanian, N., Wang, K., Magis, A. T., Hadlock, J. J., Hood, L., Aderem, A., Bluestone, J. A., Lanier, L. L., Greenberg, P. D., Gottardo, R., Davis, M. M., Goldman, J. D., Heath, J. R. 2020


    We present an integrated analysis of the clinical measurements, immune cells, and plasma multi-omics of 139 COVID-19 patients representing all levels of disease severity, from serial blood draws collected during the first week of infection following diagnosis. We identify a major shift between mild and moderate disease, at which point elevated inflammatory signaling is accompanied by the loss of specific classes of metabolites and metabolic processes. Within this stressed plasma environment at moderate disease, multiple unusual immune cell phenotypes emerge and amplify with increasing disease severity. We condensed over 120,000 immune features into a single axis to capture how different immune cell classes coordinate in response to SARS-CoV-2. This immune-response axis independently aligns with the major plasma composition changes, with clinical metrics of blood clotting, and with the sharp transition between mild and moderate disease. This study suggests that moderate disease may provide the most effective setting for therapeutic intervention.

    View details for DOI 10.1016/j.cell.2020.10.037

    View details for PubMedID 33171100

  • Sensitive Detection and Analysis of Neoantigen-Specific T Cell Populations from Tumors and Blood CELL REPORTS Peng, S., Zaretsky, J. M., Ng, A. C., Chour, W., Bethune, M. T., Choi, J., Hsu, A., Holman, E., Ding, X., Guo, K., Kim, J., Xu, A. M., Heath, J. E., Noh, W., Zhou, J., Su, Y., Lu, Y., McLaughlin, J., Cheng, D., Witte, O. N., Baltimore, D., Ribas, A., Heath, J. R. 2019; 28 (10): 2728-+


    Neoantigen-specific T cells are increasingly viewed as important immunotherapy effectors, but physically isolating these rare cell populations is challenging. Here, we describe a sensitive method for the enumeration and isolation of neoantigen-specific CD8+ T cells from small samples of patient tumor or blood. The method relies on magnetic nanoparticles that present neoantigen-loaded major histocompatibility complex (MHC) tetramers at high avidity by barcoded DNA linkers. The magnetic particles provide a convenient handle to isolate the desired cell populations, and the barcoded DNA enables multiplexed analysis. The method exhibits superior recovery of antigen-specific T cell populations relative to literature approaches. We applied the method to profile neoantigen-specific T cell populations in the tumor and blood of patients with metastatic melanoma over the course of anti-PD1 checkpoint inhibitor therapy. We show that the method has value for monitoring clinical responses to cancer immunotherapy and might help guide the development of personalized mutational neoantigen-specific T cell therapies and cancer vaccines.

    View details for DOI 10.1016/j.celrep.2019.07.106

    View details for Web of Science ID 000484377200022

    View details for PubMedID 31484081

  • Allosteric Inhibitor of KRas Identified Using a Barcoded Assay Microchip Platform ANALYTICAL CHEMISTRY McCarthy, A. M., Kim, J., Museth, A., Henning, R. K., Heath, J. E., Winson, E., Oh, J. J., Liang, J., Hong, S., Heath, J. R. 2018; 90 (15): 8824-8830


    Protein catalyzed capture agents (PCCs) are synthetic antibody surrogates that can target a wide variety of biologically relevant proteins. As a step toward developing a high-throughput PCC pipeline, we report on the preparation of a barcoded rapid assay platform for the analysis of hits from PCC library screens. The platform is constructed by first surface patterning a micrometer scale barcode composed of orthogonal ssDNA strands onto a glass slide. The slide is then partitioned into microwells, each of which contains multiple copies of the full barcode. Biotinylated candidate PCCs from a click screen are assembled onto the barcode stripes using a complementary ssDNA-encoded cysteine-modified streptavidin library. This platform was employed to evaluate candidate PCC ligands identified from an epitope targeted in situ click screen against the two conserved allosteric switch regions of the Kirsten rat sarcoma (KRas) protein. A single microchip was utilized for the simultaneous evaluation of 15 PCC candidate fractions under more than a dozen different assay conditions. The platform also permitted more than a 10-fold savings in time and a more than 100-fold reduction in biological and chemical reagents relative to traditional multiwell plate assays. The best ligand was shown to exhibit an in vitro inhibition constant (IC50) of ∼24 μM.

    View details for DOI 10.1021/acs.analchem.8b00706

    View details for Web of Science ID 000441476600017

    View details for PubMedID 29979578

    View details for PubMedCentralID PMC6734936

  • A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Das, S., Nag, A., Liang, J., Bunck, D. N., Umeda, A., Farrow, B., Coppock, M. B., Sarkes, D. A., Finch, A. S., Agnew, H. D., Pitram, S., Lai, B., Yu, M., Museth, A., Deyle, K. M., Lepe, B., Rodriguez-Rivera, F. P., McCarthy, A., Alvarez-Villalonga, B., Chen, A., Heath, J., Stratis-Cullum, D. N., Heath, J. R. 2015; 54 (45): 13219-13224


    We describe a general synthetic strategy for developing high-affinity peptide binders against specific epitopes of challenging protein biomarkers. The epitope of interest is synthesized as a polypeptide, with a detection biotin tag and a strategically placed azide (or alkyne) presenting amino acid. This synthetic epitope (SynEp) is incubated with a library of complementary alkyne or azide presenting peptides. Library elements that bind the SynEp in the correct orientation undergo the Huisgen cycloaddition, and are covalently linked to the SynEp. Hit peptides are tested against the full-length protein to identify the best binder. We describe development of epitope-targeted linear or macrocycle peptide ligands against 12 different diagnostic or therapeutic analytes. The general epitope targeting capability for these low molecular weight synthetic ligands enables a range of therapeutic and diagnostic applications, similar to those of monoclonal antibodies.

    View details for DOI 10.1002/anie.201505243

    View details for Web of Science ID 000363691500008

    View details for PubMedID 26377818

    View details for PubMedCentralID PMC4890538