R44AI174357

Development of Ultra-Efficient Antibodies for Single Cell Mapping Applications - Project Summary

Histone post-translational modifications (PTMs) are some of the most widely studied epigenomic factors, and alterations in histone PTM abundance/distribution have been implicated in numerous disease etiologies. Epigenomic mapping of histone PTMs in limited cell populations or single cells (SCs) would provide the opportunity to study the epigenetic landscape of rare and heterogeneous cell populations and be highly enabling for drug discovery research.

The recent development of the antibody-mediated genomic mapping approach CUT&TAG (Cleavage Under Targets and Tagmentation) permits the study of select, abundant histone PTMs using very few cells and even SCs. Despite this progress, ultra-low input and SC CUT&TAG assays still present a unique challenge and have not yet been successfully applied to many challenging targets, such as less abundant histone PTMs. Indeed, to maximize data yield per cell, ultra-low input and SC CUT&TAG assays require antibodies to exhibit high on-target epitope binding with minimal off-target binding, which most commercial antibodies do not offer.

We envision a new class of "SC-grade" antibodies that deliver ultra-efficient histone PTM binding for dramatically increased CUT&TAG assay sensitivity, improving reliability and providing access to new targets that are currently intractable. Here, EpicCypher will leverage a novel antibody development pipeline to generate ultra-efficient, "SC-grade" antibodies to unlock the potential of genomic mapping technology for next-generation ultra-low input/SC applications.

Unlike traditional antibody development pipelines that use histone peptides for screening, a central innovation of our strategy is the implementation of recombinant modified designer nucleosome technology during antibody development. In phase I equivalent studies, we used our novel approach to select and validate ultra-efficient antibodies for two key histone PTM targets (H3K4me1 and H3K4me3), generating antibodies that exhibit a >5-10x increase in nucleosome capture efficiency vs. current best-in-class antibodies. Importantly, these ultra-efficient antibodies generated significantly greater signal-to-noise in genomic mapping assays that employ low cell inputs, demonstrating strong proof-of-concept for our approach.

In phase II, we will leverage this validated antibody development pipeline to develop a suite of ultra-efficient antibodies and use these reagents to develop low input and SC CUT&TAG assays for breakthrough immunology research. Toward this goal, we will first develop and screen antibodies for high-value histone PTM targets (Aim 1). We will then scale up production and rigorously validate antibody lots in CUT&TAG assays using both low input and SC workflows (Aim 2). Finally, we will test the application of our next-generation ultra-efficient antibodies to enable cutting-edge immunological research and provide our antibodies and validated protocols to leading epigenetics laboratories for beta testing (Aim 3).

This research project will result in the development of a new class of histone PTM antibodies that will be used to increase the utility of CUT&TAG assays for breakthrough chromatin research and drug discovery.

Epicypher

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.

93.855 - Allergy and Infectious Diseases Research

National Institute of Allergy and Infectious Diseases (NIAID) [HHS - NIH]

Research Triangle Park, North Carolina 277090003 United States

Single Zip Code

PHS 2021-2 Omnibus Solicitation of the NIH, CDC and FDA for Small Business Innovation Research Grant Applications (Parent SBIR [R43/R44] Clinical Trial Not Allowed) (PA-21-259)

Amendment Since initial award the total obligations have increased 50% from $2,015,496 to $3,018,104.