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Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration

Award Number: U01DA056003
ORGANIZATION: NATIONAL INSTITUTE ON DRUG ABUSE
OPDIV: NIH
AWARD CLASS: COOPERATIVE AGREEMENT
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 06/01/2022
PERIOD OF PERFORMANCE END DATE: 03/31/2027

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Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration - PROJECT SUMMARY This application is submitted in response to RFA-D-21-019: Single Cell Opioid Responses in the Context of HIV (SCORCH) Program Expansion: CNS Data Generation for Chronic Opioid, Methamphetamine, and/or Cocaine Exposures. We have assembled an outstanding team of investigators with world-class expertise in HIV virology, addiction neurobiology, and single cell transcriptomics. We will leverage state-of-the-art single-nuclei RNA sequencing (snRNA-seq) coupled to single-nuclei epigenetics (snATAC-seq) to define the transcriptional and epigenetic landscape of neuronal and nonneuronal cells in addiction-relevant brain cells of HIV-infected mice that compulsively self-administer cocaine. In this manner we will identify cell types and brain sites in which HIV and cocaine interact to exacerbate the negative impact of HIV infection on the brain and contribute to the persistence of cocaine use disorder in infected individuals. To facilitate this goal, we have developed an extended access intravenous cocaine self-administration procedure for mice that precipitates compulsive-like response for cocaine that is resistant to negative outcome (contingently delivered noxious foot shocks). We will utilize EcoHIV, which is a modified HIV strain that can infect conventional immunocompetent mice. The Chromium Single Cell Multiome ATAC and Gene Expression assay and Multiplexed error-robust fluorescence in situ hybridization (MERFISH) will be used to identify cocaine and/or HIV-responsive cells in the brain with unprecedented cellular and spatial resolution. We will confirm our major findings using postmortem brain tissues from cocaine- experienced HIV-infected individuals. Our goals will be accomplished through the following four specific aims. In Aim 1, we will characterize compulsive-like cocaine intake in control and HIV-infected mice and determine the impact of antiretroviral treatment (ART) on cocaine response in these mice. In Aim 2, we will use snRNA-seq and Mulitome assays to identify those cells that show the most robust transcriptional and epigenetic plasticity to cocaine consumption and HIV infection. In Aim 3, we will use MERFISH to confirm and validate our major snRNA- seq and Multiome assay findings, and generate more refined spatially resolved maps of those cells most impacted by cocaine and/or HIV. In Aim 4, we will confirm our major findings using post-mortem human brain tissues. This highly innovative, collaborative and multidisciplinary program of research promises to yield fundamental new insights into disease-related interactions between HIV infection and cocaine use.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2026 ( Subtotal = $3,662,329 )
2026	2026	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Drug Use and Addiction Research Programs	000	5	3/31/2026	NON-COMPETING CONTINUATION	$3,662,329
														Subtotal = $3,662,329

Issue Date FY: 2025 ( Subtotal = $3,657,715 )
2025	2025	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Drug Use and Addiction Research Programs	001	4	9/22/2025	NON-COMPETING CONTINUATION	$0
2025	2025	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Drug Use and Addiction Research Programs	000	4	4/3/2025	NON-COMPETING CONTINUATION	$3,657,715
														Subtotal = $3,657,715

Issue Date FY: 2024 ( Subtotal = $3,653,101 )
2024	2024	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Drug Use and Addiction Research Programs	000	3	5/1/2024	NON-COMPETING CONTINUATION	$3,653,101
														Subtotal = $3,653,101

Issue Date FY: 2023 ( Subtotal = $3,648,488 )
2023	2023	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Drug Use and Addiction Research Programs	000	2	4/3/2023	NON-COMPETING CONTINUATION	$3,648,488
														Subtotal = $3,648,488

Issue Date FY: 2022 ( Subtotal = $3,557,665 )
2022	2022	ALLEN INSTITUTE	615 WESTLAKE AVE N	SEATTLE	WA	98109	KING	USA	Drug Use and Addiction Research Programs	000	1	5/26/2022	NEW	$3,557,665
														Subtotal = $3,557,665

Grand Total All Awards = $18,179,298

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Single cell transcriptomic and epigenomic changes during chronic HIV infection and cocaine self-administration

Award Number: U01DA056003

ORGANIZATION: NATIONAL INSTITUTE ON DRUG ABUSE

OPDIV: NIH

AWARD CLASS: COOPERATIVE AGREEMENT

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 06/01/2022

PERIOD OF PERFORMANCE END DATE: 03/31/2027

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