Showing papers by "Lewis L. Lanier published in 2020"

ImmGen at 15

Abstract: 700 comment | SERIES ImmGen at 15 Nature Immunology's 20 th anniversary is a good opportunity to reminisce about the ImmGen collective endeavor-its goals, successes and horror stories-and the group's exploration of various modes of scientific publishing The Immunological Genome Project T he Immunological Genome Project (ImmGen) is a collaborative group of immunology and computational biology laboratories that perform a thorough dissection of gene expression and its regulation in the immune system of the mouse This activity first centered on mRNA expression and then expanded to microRNA (miRNA), chromatin structure, nuclear organization and protein-RNA relationships Shared protocols, data generation and QC pipelines have yielded data that can be directly compared from >250 stem, lymphoid and myeloid cell types, at baseline or under challenge The group develops and applies computational tools to decipher regulatory connections and transcriptional control From its inception, data generated by ImmGen were meant to be a public resource, and they can be accessed through dedicated web and smartphone platforms that use interactive graphic displays that make the results intuitive to users

Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories.

Abstract: Author(s): Su, Yapeng; Chen, Daniel; Lausted, Christopher; Yuan, Dan; Choi, Jongchan; Dai, Cheng; Voillet, Valentin; Scherler, Kelsey; Troisch, Pamela; Duvvuri, Venkata R; Baloni, Priyanka; Qin, Guangrong; Smith, Brett; Kornilov, Sergey; Rostomily, Clifford; Xu, Alex; Li, Jing; Dong, Shen; Rothchild, Alissa; Zhou, Jing; Murray, Kim; Edmark, Rick; Hong, Sunga; Jones, Lesley; Zhou, Yong; Roper, Ryan; Mackay, Sean; O'Mahony, D Shane; Dale, Christopher R; Wallick, Julie A; Algren, Heather A; Michael, Zager A; Magis, Andrew; Wei, Wei; Price, Nathan D; Huang, Sui; Subramanian, Naeha; Wang, Kai; Hadlock, Jennifer; Hood, Leroy; Aderem, Alan; Bluestone, Jeffrey A; Lanier, Lewis L; Greenberg, Phil; Gottardo, Raphael; Davis, Mark M; Goldman, Jason D; Heath, James R | Abstract: Host immune responses play central roles in controlling SARS-CoV2 infection, yet remain incompletely characterized and understood. Here, we present a comprehensive immune response map spanning 454 proteins and 847 metabolites in plasma integrated with single-cell multi-omic assays of PBMCs in which whole transcriptome, 192 surface proteins, and T and B cell receptor sequence were co-analyzed within the context of clinical measures from 50 COVID19 patient samples. Our study reveals novel cellular subpopulations, such as proliferative exhausted CD8 + and CD4 + T cells, and cytotoxic CD4 + T cells, that may be features of severe COVID-19 infection. We condensed over 1 million immune features into a single immune response axis that independently aligns with many clinical features and is also strongly associated with disease severity. Our study represents an important resource towards understanding the heterogeneous immune responses of COVID-19 patients and may provide key information for informing therapeutic development.

Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories

Abstract: Host immune responses play central roles in controlling SARS-CoV2 infection, yet remain incompletely characterized and understood. Here, we present a comprehensive immune response map spanning 454 proteins and 847 metabolites in plasma integrated with single-cell multi-omic assays of 221,748 PBMCs in which whole transcriptome, 192 surface proteins, and T and B cell receptor sequence were analyzed within the context of clinical measures from 50 COVID19 patient samples. Our study reveals novel cellular subpopulations, such as proliferative exhausted CD8+ and CD4+ T cells, and cytotoxic CD4+ T cells, that may be features of severe COVID-19 infection. We condensed over 1 million immune features into a single immune response axis that independently aligns with many clinical features and is also strongly associated with disease severity. Our study represents an important resource towards understanding the heterogeneous immune responses of COVID-19 patients and may provide key information for informing therapeutic development.

Combined protein and transcript single cell RNA sequencing reveals cardiovascular disease and HIV signatures

Abstract: Background HIV-infected people have an increased risk of atherosclerosis-based cardiovascular disease (CVD), even when the HIV virus is fully controlled. Both chronic HIV infection and CVD are chronic inflammatory diseases. The interaction between these two diseases is not well understood. Methods The Women’s Interagency HIV Study (WIHS) collected peripheral blood mononuclear cells (PBMCs) and data on subclinical CVD defined by carotid artery ultrasound from HIV-infected women. We interrogated 32 PBMC samples using combined protein and transcript panel single cell (sc) RNA sequencing of women without HIV or CVD, with HIV only, with HIV and CVD, and with HIV and CVD treated with cholesterol-lowering drugs. Expression of 40 surface markers enabled detailed analysis of all major cell types, resolving 58 clusters in almost 42,000 single cells. Results Many clusters including 5 of 8 classical monocyte clusters showed significantly different gene expression between the groups of participants, revealing the inflammatory signatures of HIV, CVD and their interactions. Genes highly upregulated by CVD included CCL3, CCL4 and IL-32, whereas CXCL2 and 3 were more highly upregulated by HIV. Many genes were synergistically upregulated by HIV and CVD, but others were antagonistically regulated, revealing that the gene signature in people with HIV and CVD is not simply the sum of the HIV and CVD signatures. Elevated expression of most inflammatory genes was reversed by cholesterol control (statin treatment). The cell numbers in 3 of 5 intermediate monocyte subsets, 1 of 14 CD8 T cell subsets, 1 of 6 B cell subsets and 1 of 6 NK cell subsets showed significant changes with HIV or CVD. Conclusions We conclude that HIV and CVD show interactive inflammatory signatures including chemokines and cytokines that are improved by cholesterol-lowering drugs.

Tetramer immunization and selection followed by CELLISA Screening to Generate Monoclonal Antibodies against the Mouse Cytomegalovirus m12 Immunoevasin

Abstract: The generation of reliable mAb of unique and desired specificities serves as a valuable technology to study protein expression and function However, standard approaches to mAb generation usually involve large-scale protein purification and intensive screening In this study, we describe an optimized high-throughput proof-of-principle method for the expanded generation, enrichment, and screening of mouse hybridomas secreting mAb specific for a protein of interest Briefly, we demonstrate that small amounts of a biotinylated protein of interest can be used to generate tetramers for use as prime-boost immunogens, followed by selective enrichment of Ag-specific B cells by magnetic sorting using the same tetramers prior to hybridoma generation This serves two purposes: 1) to effectively expand both low- and high-affinity B cells specific for the antigenic bait during immunization and 2) to minimize subsequent laborious hybridoma efforts by positive selection of Ag-specific, Ab-secreting cells prior to hybridoma fusion and validation screening Finally, we employ a rapid and inexpensive screening technology, CELLISA, a high-throughput validation method that uses a chimeric Ag fused to the CD3ζ signaling domain expressed on enzyme-generating reporter cells; these reporters can detect specific mAb in hybridoma supernatants via plate-bound Ab-capture arrays, thereby easing screening Using this strategy, we generated and characterized novel mouse mAb specific for a viral immunoevasin, the mouse CMV m12 protein, and suggest that these mAb may protect mice from CMV infection via passive immunity