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ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential

Award Number: R01EB027793
ORGANIZATION: NATIONAL INSTITUTE Of BIOMEDICAL IMAGING & BIOENGINEERING
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/24/2026
PERIOD OF PERFORMANCE END DATE: 06/30/2027

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ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential - PROJECT SUMMARY The recent development of continuous directed evolution (CDE) methods has made it increasingly possible to generate biomolecules with radically altered or even new functions capable of addressing unmet needs in medicine, biotechnology, and synthetic biology. By transforming the traditional stepwise process of classical directed evolution into one that operates continuously in cells, these CDE methods, such as Phage-Assisted Continuous Evolution (PACE), can theoretically enable extensive speed, scale, and depth in an evolutionary search. However, the technical limitations of implementing PACE (and other CDE techniques) have restricted what can be practically achieved with these approaches alone. To overcome these limitations, our collaborative team recently established ePACE, a new technology that combines PACE with an automated, scalable, and customizable continuous culture platform, called eVOLVER. By on-boarding the infrastructural and fluidic requirements of PACE onto eVOLVER, we overcame many of the limitations of traditional PACE and unlocked pathways for automated, parallel, and continuous evolution of biomolecules. Using ePACE, we already succeeded in generating biomedically-relevant molecules, including the multiplexed evolution of Cas9 for precision gene editing at previously-inaccessible genomic target sites. In this project, we will advance the capabilities of ePACE in two critical dimensions – scale and accessibility – through new hardware and fluidic technology developments. These developments will enable novel CDE schemes necessary to tackle new challenges in biomolecular engineering. The first challenge we will tackle is engineering systems for targeted integration of large, gene-sized DNA payloads in mammalian cells, which would enable diverse biomedical applications, including therapeutic treatments for virtually any loss-of-function disease. We will apply ePACE for highly parallelized evolution of CRISPR-associated transposases (CASTs) — recently discovered, multi- component systems that enable programmable integration of large DNA in bacteria — to generate variants with robust mammalian genomic integration activity. To effectively explore the combinatorial space of CAST components, we will develop an ultra-high-throughput eVOLVER variant that facilitates ePACE evolutions at unprecedented scale and dramatically increases the number of evolutionary trajectories explored. The second challenge is establishing generalizable methods to evolve proteins for tight and selective binding of small- molecule ligands, which would enable diverse biomedical applications, including biosensing and detection, metabolic engineering, and drug and toxin sequestration. As part of this goal, we will deliver on the broader mission of democratizing CDE by developing a miniaturized, ultra-low-cost eVOLVER variant that facilitates PACE functionality, and use it to establish general pipelines that can be easily adopted by labs with minimal financial and technical overhead. Together, this work will substantially expand the capabilities of CDE while producing bespoke biomolecules for unmet biomedical needs.


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 = $1,056,155 )
2026	2026	THE BROAD INSTITUTE, INC	415 MAIN ST	CAMBRIDGE	MA	02142	MIDDLESEX	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	002	8	8/24/2026	CHANGE OF GRANTEE / TRAINING INSTITUTION / AWARDING INSTITUTION	$1,056,155
2026	2025	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	7	8/14/2026	NON-COMPETING CONTINUATION	$0
2026	2025	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	001	7	8/19/2026	NON-COMPETING CONTINUATION	$0
														Subtotal = $1,056,155

Issue Date FY: 2025 ( Subtotal = $815,764 )
2025	2025	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	001	7	6/24/2025	NON-COMPETING CONTINUATION	$81,576
2025	2025	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	7	3/24/2025	NON-COMPETING CONTINUATION	$734,188
														Subtotal = $815,764

Issue Date FY: 2024 ( Subtotal = $804,366 )
2024	2024	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	002	6	5/2/2024	NON-COMPETING CONTINUATION	$804,366
2024	2023	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	001	5	4/3/2024	COMPETING CONTINUATION	$72,122
2024	2022	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	4	4/3/2024	NON-COMPETING CONTINUATION	-$72,122
														Subtotal = $804,366

Issue Date FY: 2023 ( Subtotal = $871,502 )
2023	2023	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	001	5	6/22/2023	COMPETING CONTINUATION	$871,502
2023	2022	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	4	6/14/2023	NON-COMPETING CONTINUATION	$0
														Subtotal = $871,502

Issue Date FY: 2022 ( Subtotal = $612,043 )
2022	2022	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	4	3/2/2022	NON-COMPETING CONTINUATION	$550,837
2022	2022	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	001	4	6/27/2022	NON-COMPETING CONTINUATION	$61,206
														Subtotal = $612,043

Issue Date FY: 2021 ( Subtotal = $608,022 )
2021	2021	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	3	4/9/2021	NON-COMPETING CONTINUATION	$608,022
2021	2021	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	001	3	5/28/2021	NON-COMPETING CONTINUATION	$0
														Subtotal = $608,022

Issue Date FY: 2020 ( Subtotal = $628,580 )
2020	2020	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	2	2/21/2020	NON-COMPETING CONTINUATION	$628,580
														Subtotal = $628,580

Issue Date FY: 2019 ( Subtotal = $687,081 )
2019	2019	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	001	1	8/8/2019	NEW	$0
2019	2019	TRUSTEES OF BOSTON UNIVERSITY	1 SILBER WAY	BOSTON	MA	02215	SUFFOLK	USA	Discovery and Applied Research for Technological Innovations to Improve Human Health	000	1	5/3/2019	NEW	$687,081
														Subtotal = $687,081

Grand Total All Awards = $6,083,513

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ePACE: automation platforms for adaptable and scalable continuous evolution of biomolecules with therapeutic potential

Award Number: R01EB027793

ORGANIZATION: NATIONAL INSTITUTE Of BIOMEDICAL IMAGING & BIOENGINEERING

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 08/24/2026

PERIOD OF PERFORMANCE END DATE: 06/30/2027

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