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Principal Investigator: John Tsang
Organization: NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Fiscal Year: 2021
Award: $3,754,469
Funding agency: National Institute of Allergy and Infectious Diseases
In response to the SARS-CoV-2 pandemic we have made the technologies and platforms at CHI available for characterization of COVID-19 patient samples, as a priority ahead of our ongoing collaborative studies. Initially, acutely infected patients from northern Italy were characterized by multimodal high-dimensional phenotyping, in close collaboration with the Tsang lab. This led to a study published in Cell early this year which identified a critical juncture in the disease course, around 20 days after symptom onset, characterized by a heightened wave of inflammatory responses in patients with fatal outcomes (Liu et al., 2021). For this analysis CHI contributed to CITE-seq, BCR sequencing, scATAC-seq, SomaLogic, and 27 color flow cytometry phenotyping; and several of these platforms have now been further developed and adapted for subsequent Covid studies. In the context of therapeutic intervention in acute infection, using samples from the ACTT3 trial led by John Beigel, CHI has begun phenotyping aiming to address how disease severity impacts outcomes. To analyse infection in children and lymph nodes, in collaboration with Kalpana Manthiparam, CHI has helped to generate CITE-seq and analyse cytometry from tonsil samples. To investigate longer term consequences of Covid infection, using a Tsang lab cohort, high-dimensional cytometry has characterized responses with panels including staining for antigen-specific cells. CHI has also contributed technical help to other groups, for example in an analysis of MISC published in Immunity (Ramaswamy et al., 2021), and we hope that these various platforms can be applied to new cohorts becoming available to further address questions such as variation in the outcomes of infection.
In addition to this COVID work CHI has continued to advance its previous studies that comprise 21 open collaborations across 6 Institutes (NIAID, NHGRI, NIAMS, NCI, NIDDK, NIDCR) and with the Clinical Center. Half of these studies are currently at points which are the responsibility of our collaborators, with the remainder involving active work at CHI spanning 3 stages of: initiation/sample collection (3 studies), assay/analysis (5 studies), and manuscript write up (2 studies). The studies all comprise multi-modal high-dimensional immune phenotyping of primary human samples, and the studies actively being worked on include characterizing immune changes in vaccine trials (influenza, HSV, malaria), clinical intervention studies (diet, antibiotics, hypertension), and cohort studies of rare genetic diseases (mitochondrial or immune signaling dysfunction). The influenza vaccination study is an example of an integrated design involving a clinical trial and also parallel analysis for cross-validation at Stanford University. This began with broad phenotyping which was then further developed with CITE-seq to reveal acute and persistent impacts of vaccination, and has resulted in a manuscript that is now under review at Cell. The HSV vaccine candidate study is an example where CHI was able to drive a systems level analysis using uniquely positioned samples from an NIH clinical trial, which enabled assessment of how effects of gender and prior exposure interact in vivo to shape an immune response. Another study of note is a collaboration with Kevin Hall at NIDDK to characterize immune differences after periods of highly controlled diet changes, an example of exploratory unbiased analyses where peripheral blood transcriptomic, cytometry, and proteomic phenotypes have all shown differences as a result of the diet changes. Publications arising this year from CHIs collaborative studies have included analyses of how therapeutic antibody was broadly effective in immune recovery for CHAPLE disease patients (Ozen et al., Nat Immunol.), immune profiling during Ebola infection (Kotliar et al., Cell), activation of complement pathways in HIV infection (Vujkovic-Cvijin et al., J Infect Dis.), results of a JAK inhibitor trial for lupus (Hasni et al., Nat Commun.), and analysis of effects of fasting on T cell responsiveness (Han et al., Nat Metab.).
To support CHIs mission we continue to develop wet-lab and computational infrastructure. For single cell sequencing technologies using the 10x platform, we have expanded the number of protein antigens measured in CITE-Seq, and developed scATAC-seq approaches with greater throughput and lower cost. CITE-Seq, in particular, led to a high-profile finding characterizing variation in baseline immune states that predicts immune responses (see section Scientific Advances). For flow cytometry, on the Cytek Aurora we have continued to validate >30 color cytometry panels including for markers of cell types and responses of interest for our collaborators, such as neutrophils in the case of oral tissues. For flow cytometry analysis we are applying methods to enable conventionally gated populations to be recognized and interrogated using high dimensional parameters, to help overcome the difficulties of interpreting unbiased clustering of high dimensional data. For mass cytometry analysis we are finalising a package that uses high dimensional observations to discriminate only the subset of cells that respond in ex vivo stimulation assays. This will become increasingly important as high-dimensional assays expand, such as our mass cytometry assay that quantifies phosphorylation of 10 intracellular proteins in addition to 20 cell phenotype markers, in response to 12 in vitro stimulation conditions. CHI also provides fee-for-service access to assays not otherwise accessible to NIH researchers. In the last year the SomaLogic proteomic assay has been run for over 1700 samples for 16 investigators. We continue to monitor alternative platforms and have run tests on O-Link that is offering increasingly high parameter antibody based analysis, although currently plan to transition our SomaLogic platform from the current 1.3k antigen panel to an analysis of 7k antigens.
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