Markers of active hiv reservoir
AssigneeMassachusetts Institute of Technology
InventorsAlexander K. Shalek, Carly Ziegler
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Abstract
Embodiments disclosed herein provide a pan-tissue cell atlas of healthy and diseased subjects obtained by single cell sequencing. The present invention discloses novel markers for cell types. Moreover, genes associated with disease, including HIV infection and tuberculosis are identified. The invention provides for diagnostic assays based on gene markers and cell composition, as well as therapeutic targets for controlling immune regulations and cell-cell communication of the cell types disclosed herein. In addition, novel cell types and methods of quantitating, detecting and isolating the cell types are disclosed.
Claims29
A method of modulating a cell or tissue comprising a viral or latent viral infection, the method comprising contacting the cell or tissue with a modulating agent in an amount sufficient to modify the viral or latent viral infection of the cell or tissue as compared to the viral or latent viral infection in the absence of the modulating agent.
A method of diagnosing a cell or tissue in a subject having a latent HIV or anti-retroviral therapy (ART)-resistant HIV infection, the method comprising detecting a gene expression profile in one or more cells or tissues associated with latent HIV or ART-resistant HIV infection.
A method of diagnosing a latent HIV or ART-resistant HIV infection in a cell or tissue, the method comprising detecting whether one or more genes from Table 1 or Table 2 is overexpressed compared to a cell that is HIV−.
A method of diagnosing a latent HIV or anti-retroviral therapy (ART)-resistant HIV infection in a cell or tissue, the method comprising detecting whether one or more genes from Table 3 is underexpressed compared to a cell that is HIV−.
A method of monitoring treatment of a latent HIV or anti-retroviral therapy (ART)-resistant HIV infection in a cell or tissue, the method comprising detecting whether one or more genes from Table 1 or Table 2 is overexpressed compared to a cell that is HIV−.
A method of monitoring treatment of a latent HIV or anti-retroviral therapy (ART)-resistant HIV infection in a cell or tissue, the method comprising detecting whether one or more genes from Table 3 is underexpressed compared to a cell that is HIV−.
A method of treating HIV in a patient comprising:
- detecting one or more genes or gene signatures from Tables 1 or 2;
- determining whether the patient has a latent HIV or ART-resistant HIV infection based on the presence of one or more genes or gene signatures from Tables 1 or 2;
- and
- administering an anti-HIV therapeutic if one or more genes or gene signatures from Tables 1 or 2 are present.
A method of monitoring HIV disease progression and/or treatment comprising detecting expression of one or more genes or gene products from Tables 1, 2 and 3 prior to administration of an anti-HIV therapy;
- administering a first round of an anti-HIV therapy;
- detecting expression of one or more genes or gene products from Tables 1, 2 and 3 after administration of the anti-HIV therapeutic;
- and
- administering an additional or alternative round of anti-HIV therapy if expression of one or more genes from Table 1 or 2 has increased or not decreased, or if expression of one or more genes in Table 3 has decreased relative to prior to administering the first anti-HIV therapy.
Dependencies are inferred from the claim text.