R44AI179547
Project Grant
Overview
Grant Description
Rapid and Robust Assay for Measurement of In Vivo Activity of Chromatin-Interacting Proteins - Project Summary
The activity of chromatin-associating proteins (CAPs) is fundamental to regulation of gene expression. Elucidating CAP activity is central to understanding the regulatory mechanisms that drive cell biology, both in the context of health and disease, and to guide development of novel therapeutics.
However, this work is not straightforward, as CAP activity is regulated by multiple factors including post-translational modifications and subcellular localization. Thus, assays to study CAP activity must specifically detect CAPs in their active form (i.e., bound to chromatin, directly or in complex).
Genomic mapping assays can provide detailed information on CAP engagement and localization; however, these assays are inaccessible to a majority of researchers and unsuitable for large-scale, high-throughput studies due to a high barrier of entry associated with cost, complexity, equipment, and data analysis.
Other existing assays to study CAPs capture total cellular abundance (e.g., EMSAs, ELISAs, IHC) or transcript levels (e.g., qPCR, RNA-Seq), and do not specifically quantify CAPs actually associated with chromatin in vivo. Thus, there is a field need for a high-throughput, low-cost assay that is accessible to all researchers, and can inform CAP activity via quantification of in vivo engagement on chromatin.
Market availability of such an assay would be transformative for biomedical research by providing convenient access to study the role and response of CAP in gene regulatory programs, including analysis of drug mechanism of action and immune stimulus responses, as well as for high-throughput drug screening.
Here, EpicCypher will develop QuantiCAPTM, a breakthrough assay that will enable the study of in vivo activity of CAPs. The innovation of this proposal is the development of a targeted approach to directly quantify the total amount of CAP-bound chromatin in cells. Our approach leverages an in situ immunotargeting strategy to excise CAP-bound chromatin combined with highly sensitive detection by a fluorescent DNA stain.
Overall, this platform will provide the first quantitative, low-cost, and scalable approach to leverage analysis of CAPs for biomedical research.
In this Direct to Phase II research program, we are highlighting development of the platform to study transcription factors (TFs) and chromatin reader proteins, though our platform will be broadly applicable for the study of any CAP.
In Phase I, we developed an automated QuantiCAP workflow, demonstrating feasibility for the assay to quantify changes in a CAP following drug treatment, and identified assay conditions to further improve sensitivity.
In Phase II, we will extend QuantiCAP assay development to cover five (5) high value targets using both manual and automated workflows, including genomics validation. We will validate our assays across diverse primary immune cells and stimuli, then determine cell input thresholds, a robust normalization strategy, and quantitative assay parameters.
Finally, we will prepare for marketing and commercialization by developing a QuantiCAP beta kit and applying the automated assay to perform high-impact drug development studies.
The activity of chromatin-associating proteins (CAPs) is fundamental to regulation of gene expression. Elucidating CAP activity is central to understanding the regulatory mechanisms that drive cell biology, both in the context of health and disease, and to guide development of novel therapeutics.
However, this work is not straightforward, as CAP activity is regulated by multiple factors including post-translational modifications and subcellular localization. Thus, assays to study CAP activity must specifically detect CAPs in their active form (i.e., bound to chromatin, directly or in complex).
Genomic mapping assays can provide detailed information on CAP engagement and localization; however, these assays are inaccessible to a majority of researchers and unsuitable for large-scale, high-throughput studies due to a high barrier of entry associated with cost, complexity, equipment, and data analysis.
Other existing assays to study CAPs capture total cellular abundance (e.g., EMSAs, ELISAs, IHC) or transcript levels (e.g., qPCR, RNA-Seq), and do not specifically quantify CAPs actually associated with chromatin in vivo. Thus, there is a field need for a high-throughput, low-cost assay that is accessible to all researchers, and can inform CAP activity via quantification of in vivo engagement on chromatin.
Market availability of such an assay would be transformative for biomedical research by providing convenient access to study the role and response of CAP in gene regulatory programs, including analysis of drug mechanism of action and immune stimulus responses, as well as for high-throughput drug screening.
Here, EpicCypher will develop QuantiCAPTM, a breakthrough assay that will enable the study of in vivo activity of CAPs. The innovation of this proposal is the development of a targeted approach to directly quantify the total amount of CAP-bound chromatin in cells. Our approach leverages an in situ immunotargeting strategy to excise CAP-bound chromatin combined with highly sensitive detection by a fluorescent DNA stain.
Overall, this platform will provide the first quantitative, low-cost, and scalable approach to leverage analysis of CAPs for biomedical research.
In this Direct to Phase II research program, we are highlighting development of the platform to study transcription factors (TFs) and chromatin reader proteins, though our platform will be broadly applicable for the study of any CAP.
In Phase I, we developed an automated QuantiCAP workflow, demonstrating feasibility for the assay to quantify changes in a CAP following drug treatment, and identified assay conditions to further improve sensitivity.
In Phase II, we will extend QuantiCAP assay development to cover five (5) high value targets using both manual and automated workflows, including genomics validation. We will validate our assays across diverse primary immune cells and stimuli, then determine cell input thresholds, a robust normalization strategy, and quantitative assay parameters.
Finally, we will prepare for marketing and commercialization by developing a QuantiCAP beta kit and applying the automated assay to perform high-impact drug development studies.
Awardee
Funding Goals
TO ASSIST PUBLIC AND PRIVATE NONPROFIT INSTITUTIONS AND INDIVIDUALS TO ESTABLISH, EXPAND AND IMPROVE BIOMEDICAL RESEARCH AND RESEARCH TRAINING IN INFECTIOUS DISEASES AND RELATED AREAS, TO CONDUCT DEVELOPMENTAL RESEARCH, TO PRODUCE AND TEST RESEARCH MATERIALS. TO ASSIST PUBLIC, PRIVATE AND COMMERCIAL INSTITUTIONS TO CONDUCT DEVELOPMENTAL RESEARCH, TO PRODUCE AND TEST RESEARCH MATERIALS, TO PROVIDE RESEARCH SERVICES AS REQUIRED BY THE AGENCY FOR PROGRAMS IN INFECTIOUS DISEASES, AND CONTROLLING DISEASE CAUSED BY INFECTIOUS OR PARASITIC AGENTS, ALLERGIC AND IMMUNOLOGIC DISEASES AND RELATED AREAS. PROJECTS RANGE FROM STUDIES OF MICROBIAL PHYSIOLOGY AND ANTIGENIC STRUCTURE TO COLLABORATIVE TRIALS OF EXPERIMENTAL DRUGS AND VACCINES, MECHANISMS OF RESISTANCE TO ANTIBIOTICS AS WELL AS RESEARCH DEALING WITH EPIDEMIOLOGICAL OBSERVATIONS IN HOSPITALIZED PATIENTS OR COMMUNITY POPULATIONS AND PROGRESS IN ALLERGIC AND IMMUNOLOGIC DISEASES. BECAUSE OF THIS DUAL FOCUS, THE PROGRAM ENCOMPASSES BOTH BASIC RESEARCH AND CLINICAL RESEARCH. SMALL BUSINESS INNOVATION RESEARCH (SBIR) PROGRAM EXPANDS AND IMPROVES PRIVATE SECTOR PARTICIPATION IN BIOMEDICAL RESEARCH. THE SBIR PROGRAM INTENDS TO INCREASE AND FACILITATE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, TO INCREASE SMALL BUSINESS PARTICIPATION IN FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. THE SMALL BUSINESS TECHNOLOGY TRANSFER (STTR) PROGRAM STIMULATES AND FOSTERS SCIENTIFIC AND TECHNOLOGICAL INNOVATION THROUGH COOPERATIVE RESEARCH AND DEVELOPMENT CARRIED OUT BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO FOSTER TECHNOLOGY TRANSFER BETWEEN SMALL BUSINESS CONCERNS AND RESEARCH INSTITUTIONS, TO INCREASE PRIVATE SECTOR COMMERCIALIZATION OF INNOVATIONS DERIVED FROM FEDERAL RESEARCH AND DEVELOPMENT, AND TO FOSTER AND ENCOURAGE PARTICIPATION OF SOCIALLY AND ECONOMICALLY DISADVANTAGED SMALL BUSINESS CONCERNS AND WOMEN-OWNED SMALL BUSINESS CONCERNS IN TECHNOLOGICAL INNOVATION. RESEARCH CAREER DEVELOPMENT AWARDS SUPPORT THE DEVELOPMENT OF SCIENTISTS DURING THE FORMATIVE STAGES OF THEIR CAREERS. INDIVIDUAL NATIONAL RESEARCH SERVICE AWARDS (NRSAS) ARE MADE DIRECTLY TO APPROVE APPLICANTS FOR RESEARCH TRAINING IN SPECIFIED BIOMEDICAL SHORTAGE AREAS. IN ADDITION, INSTITUTIONAL NATIONAL RESEARCH SERVICE AWARDS ARE MADE TO ENABLE INSTITUTIONS TO SELECT AND MAKE AWARDS TO INDIVIDUALS TO RECEIVE TRAINING UNDER THE AEGIS OF THEIR INSTITUTIONAL PROGRAM.
Grant Program (CFDA)
Awarding / Funding Agency
Place of Performance
Research Triangle Park,
North Carolina
277090003
United States
Geographic Scope
Single Zip Code
Related Opportunity
Analysis Notes
Amendment Since initial award the total obligations have increased 200% from $1,008,869 to $3,026,607.
Epicypher was awarded
QuantiCAPTM: In Vivo CAP Activity Assay
Project Grant R44AI179547
worth $3,026,607
from the National Institute of Allergy and Infectious Diseases in July 2023 with work to be completed primarily in Research Triangle Park North Carolina United States.
The grant
has a duration of 3 years and
was awarded through assistance program 93.855 Allergy and Infectious Diseases Research.
The Project Grant was awarded through grant opportunity PHS 2022-2 Omnibus Solicitation of the NIH, CDC and FDA for Small Business Innovation Research Grant Applications (Parent SBIR [R43/R44] Clinical Trial Not Allowed).
SBIR Details
Research Type
SBIR Phase II
Title
Rapid and robust assay for measurement of in vivo activity of chromatin-interacting proteins
Abstract
PROJECT SUMMARYThe activity of chromatin-associating proteins (CAPs) is fundamental to regulation of gene expression. Elucidating CAP activity is central to understanding the regulatory mechanisms that drive cell biology, both in the context of health and disease, and to guide development of novel therapeutics. However, this work is not straightforward, as CAP activity is regulated by multiple factors including post-translational modifications and subcellular localization. Thus, assays to study CAP activity must specifically detect CAPs in their active form (i.e., bound to chromatin, directly or in complex). Genomic mapping assays can provide detailed information on CAP engagement and localization; however, these assays are inaccessible to a majority of researchers and unsuitable for large-scale, high-throughput studies due to a high barrier of entry associated with cost, complexity, equipment, and data analysis. Other existing assays to study CAPs capture total cellular abundance (e.g., EMSAs, ELISAs, IHC) or transcript levels (e.g., qPCR, RNA-seq), and do not specifically quantify CAPs actually associated with chromatin in vivo. Thus, there is a field need for a high-throughput, low-cost assay that is accessible to all researchers, and can inform CAP activity via quantification of in vivo engagement on chromatin. Market availability of such an assay would be transformative for biomedical research by providing convenient access to study the role and response of CAP in gene regulatory programs, including analysis of drug mechanism of action and immune stimulus responses, as well as for high-throughput drug screening.Here, EpiCypher will develop QuantiCAPTM, a breakthrough assay that will enable the study of in vivo activity of CAPs. The innovation of this proposal is the development of a targeted approach to directly quantify the total amount of CAP-bound chromatin in cells. Our approach leverages an in situ immunotargeting strategy to excise CAP-bound chromatin combined with highly sensitive detection by a fluorescent DNA stain. Overall, this platform will provide the first quantitative, low-cost, and scalable approach to leverage analysis of CAPs for biomedical research. In this Direct to Phase II research program, we are highlighting development of the platform to study transcription factors (TFs) and chromatin reader proteins, though our platform will be broadly applicable for the study of any CAP. In Phase I, we developed an automated QuantiCAP workflow, demonstrating feasibility for the assay to quantify changes in a CAP following drug treatment, and identified assay conditions to further improve sensitivity. In Phase II, we will extend QuantiCAP assay development to cover five (5) high value targets using both manual and automated workflows, including genomics validation. We will validate our assays across diverse primary immune cells and stimuli, then determine cell input thresholds, a robust normalization strategy, and quantitative assay parameters. Finally, we will prepare for marketing and commercialization by developing a QuantiCAP beta kit and applying the automated assay to perform high-impact drug development studies.
Topic Code
NIAID
Solicitation Number
PA22-176
Status
(Ongoing)
Last Modified 7/21/25
Period of Performance
7/19/23
Start Date
6/30/26
End Date
Funding Split
$3.0M
Federal Obligation
$0.0
Non-Federal Obligation
$3.0M
Total Obligated
Activity Timeline
Transaction History
Modifications to R44AI179547
Additional Detail
Award ID FAIN
R44AI179547
SAI Number
R44AI179547-1798389242
Award ID URI
SAI UNAVAILABLE
Awardee Classifications
Small Business
Awarding Office
75NM00 NIH National Institute of Allergy and Infectious Diseases
Funding Office
75NM00 NIH National Institute of Allergy and Infectious Diseases
Awardee UEI
UWNWSADJYYZ3
Awardee CAGE
6XLY4
Performance District
NC-04
Senators
Thom Tillis
Ted Budd
Ted Budd
Budget Funding
| Federal Account | Budget Subfunction | Object Class | Total | Percentage |
|---|---|---|---|---|
| National Institute of Allergy and Infectious Diseases, National Institutes of Health, Health and Human Services (075-0885) | Health research and training | Grants, subsidies, and contributions (41.0) | $1,008,869 | 100% |
Modified: 7/21/25