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Utilizing single-cell Massively Parallel Reporter Assays to dissect gene by environment interactions

Award Number: F31HG011007
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS
PERIOD OF PERFORMANCE START DATE: 12/01/2019
PERIOD OF PERFORMANCE END DATE: 08/29/2022

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Utilizing single-cell Massively Parallel Reporter Assays to dissect gene by environment interactions - PROJECT SUMMARY/ABSTRACT I propose to develop a novel assay, single-cell Massively Parallel Reporter Assay (scMPRA), to study gene by environment interactions (GxE) and in particular gain a greater understanding of how nucleotide variation in cis-regulatory elements interact with the variable environments of single cells to modulate gene expression. I hypothesize that the cellular environment modifies gene expression by modulating the activity of regulatory elements and these can behave differently due to nucleotide variants. Currently, there are no high-throughput methods available to functionally validate variants across different cellular environments. To address this, I will adapt a lentivirus based Massively Parallel Reporter Assay (lentiMPRA) developed in our lab and use it in combination with 10x Genomics scRNA-seq technology to allow the simultaneous quantification of the cellular environment via the transcriptome and of enhancer activity with the lentiMPRA construct. This assay will provide a novel platform to test the causality of variants driving changes in gene expression in specific environments in a high throughput manner. I will use this technology to study and validate GxE in distinct cell types (Aim1) and in different immune stimulation conditions (Aim 2) to dissect the relationship between immune activation and underlying genetic variation. We will use linear mixed models (LMMs) to quantify the interaction between SNPs and environments including, cell type, cell state, and donor. This work will map enhancers and their disease associated variants that are sensitive to the cellular environment, providing a platform to assign causality to variants that interact with specific environments.


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: 2024 ( Subtotal = -$14,462 )
2024	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94103	SAN FRANCISCO	USA	Human Genome Research	000	3	10/31/2023	NON-COMPETING CONTINUATION	-$14,462
														Subtotal = -$14,462

Issue Date FY: 2023 ( Subtotal = -$6,662 )
2023	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	000	3	9/15/2023	NON-COMPETING CONTINUATION	-$6,662
														Subtotal = -$6,662

Issue Date FY: 2022 ( Subtotal = $41,797 )
2022	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	000	3	11/16/2021	NON-COMPETING CONTINUATION	$41,081
2022	2022	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	001	3	6/28/2022	NON-COMPETING CONTINUATION	$716
														Subtotal = $41,797

Issue Date FY: 2021 ( Subtotal = $41,585 )
2021	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	002	2	2/4/2021	NON-COMPETING CONTINUATION	$516
2021	2021	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	000	2	11/18/2020	NON-COMPETING CONTINUATION	$40,565
2021	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	001	1	1/13/2021	NEW	$504
														Subtotal = $41,585

Issue Date FY: 2020 ( Subtotal = $40,061 )
2020	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	000	1	11/22/2019	NEW	$40,061
2020	2020	REGENTS OF THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO, THE	1855 FOLSOM ST STE 425	SAN FRANCISCO	CA	94143	SAN FRANCISCO	USA	Human Genome Research	001	1	11/22/2019	NEW	$0
														Subtotal = $40,061

Grand Total All Awards = $102,319

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Utilizing single-cell Massively Parallel Reporter Assays to dissect gene by environment interactions

Award Number: F31HG011007

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: FELLOWSHIP/SCHOLARSHIP/STUDENT LOANS

PERIOD OF PERFORMANCE START DATE: 12/01/2019

PERIOD OF PERFORMANCE END DATE: 08/29/2022

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