Interrogating CD8+ T cell reactivity on a genome-wide scale

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Science Translational Medicine  21 Aug 2019:
Vol. 11, Issue 506, eaaz0302
DOI: 10.1126/scitranslmed.aaz0302


A new method enables large-scale identification of human T cell antigens.

CD8+ cytotoxic T cells play an important role in the genesis and progression of many common diseases. Cytotoxic T cells police antigens presented on the surface of other cells. If their T cell receptor recognizes one of these antigens, they kill by secreting cytolytic molecules, including a protease called granzyme B, into the cytoplasm of target cells. Dysregulation of this process in either direction is bad: if T cells recognize antigens commonly presented by normal, well-behaved cells, autoimmune disease can ensue. Conversely, if T cells fail to adequately respond to antigens presented by virally infected or cancer cells, progressive infection and tumor growth are the result. Systematically identifying antigens that are the targets of undesired T cell responses (or non-responses) could therefore revolutionize the development of vaccines and enable a deeper mechanistic understanding of autoimmune disease. However, technologies that can effectively interrogate on a large scale which antigens produce effective responses in a given set of T cells have so far been lacking.

Now Kula et al. have developed such a technology. At the core of their approach is a reporter of granzyme B activity. The reporter consists of two infrared fluorescent protein domains, separated by a linker sequence that can be cleaved by granzyme B. Therefore, when a cell is targeted by a cytotoxic T cell, it lights up and can be isolated by fluorescence activated cell sorting. This powerful design enables enrichment screens in which primary memory T cells from donors are mixed with cells expressing the reporter, a matching human leukocyte antigen (HLA), and a library of possible antigens. Fluorescent cells which have been targeted by CD8+ T cells are sorted from the population and the antigens they contain are identified by next generation sequencing. The authors show that this method not only works in the relatively simple case of homogenous T cell populations that all express the same T cell receptor, but even in the more complex scenario in which heterogeneous T cells with different specificities (as might be recovered from a tumor) are screened against genome-wide antigen libraries.

The technology opens up a large number of exciting applications for profiling memory T cells. For example, it is conceivable that in the future T cells will routinely be isolated from tumor specimens at the time of surgery and their specificities determined with the new method. Antigens that are recognized by reactive but exhausted T cells could then be used in the design of a personalized vaccine.

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