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Development of chimeric read amplification into a robust method for profiling targets of specific microRNAs and global amplification of all microRNA:mRNA pairings transcriptome-wide

Award Number: R44HG010603
ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 09/17/2019
PERIOD OF PERFORMANCE END DATE: 08/31/2023

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Development of chimeric read amplification into a robust method for profiling targets of specific microRNAs and global amplification of all microRNA:mRNA pairings transcriptome-wide - PROJECT SUMMARY Post-transcriptional regulation by microRNAs is fundamental for cellular homeostasis. MicroRNAs are small non-coding RNAs that fine tune gene expression by base pairing to complementary sequences in target messenger RNA (mRNA) molecules. A single microRNA can have multiple targets allowing for coordinated regulation of mRNA networks. The importance of microRNA regulation is evidenced not only by their evolutionary conservation but also by the involvement of microRNAs in nearly every biological process including proliferation, inflammation, development, and metabolism. Misregulation of individual microRNAs or global microRNA processing has important consequences for development, physiology, and disease. Aberrant microRNA expression has been linked to many diseases ranging from cancer to cardiac failure, and microRNAs have become attractive targets and tools for therapeutic approaches. Precise target identification of microRNAs is essential to understand their functional role. Current methods to identify microRNA targets are limited, as they have high false-positive rates, are unable to definitively distinguish direct from indirect microRNA-target interactions or are unable to profile low-abundance microRNAs. To this end we have applied our previously developed enhanced crosslinking and immunoprecipitation (eCLIP) technology to develop a specialized alternative, chimeric-eCLIP, to unambiguously identify microRNA targets in a transcriptome-wide manner. Chimeric-eCLIP is based on AGO2 eCLIP and includes a ligation step where microRNA and mRNA fragments are ligated to each other forming chimeric RNA molecules that can then be sequenced. Direct targets of individual microRNAs are easily identifiable from chimeric-eCLIP data using microRNA:mRNA chimeric reads. The work proposed here will expand the previously developed chimeric-eCLIP technology to include microRNA- and gene-specific read enrichment methods, and a user-friendly analysis package resulting in a robust and versatile chimeric-eCLIP kit for wide-spread use by academic and biotechnology industries, as outlined in the following aims: 1. Expand direct profiling of microRNA targets with probe-based chimeric-eCLIP 2. Refine software tools for analysis of chimeric-eCLIP data to strengthen key customer-facing features 3. Conduct expanded beta testing and finalize commercialization of the all-inclusive chimeric-eCLIP kit Eclipse Bio is an ideal candidate to perform the aims described above due to our expertise in genomics, RNA processing, and computational biology. The above aims will enable robust microRNA target mapping to be performed using a standard method by all biomedical researchers and will allow for rigorous validation of microRNA specificity. The ability to properly assess therapeutic microRNA-like molecules will provide significant benefit to researchers studying microRNA regulation and companies developing RNA therapies.


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 = $0 )
2024	2022	ECLIPSE BIOINNOVATIONS, INC	5770 OBERLIN DR	SAN DIEGO	CA	92121	SAN DIEGO	USA	Human Genome Research	000	3	2/6/2024	NON-COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2023 ( Subtotal = $0 )
2023	2021	ECLIPSE BIOINNOVATIONS, INC.	5770 OBERLIN DR	SAN DIEGO	CA	92121	SAN DIEGO	USA	Human Genome Research	000	2	11/18/2022	COMPETING CONTINUATION	$0
														Subtotal = $0

Issue Date FY: 2022 ( Subtotal = $861,551 )
2022	2022	ECLIPSE BIOINNOVATIONS, INC.	5770 OBERLIN DR	SAN DIEGO	CA	92121	SAN DIEGO	USA	Human Genome Research	001	3	9/20/2022	NON-COMPETING CONTINUATION	$0
2022	2022	ECLIPSE BIOINNOVATIONS, INC.	5770 OBERLIN DR	SAN DIEGO	CA	92121	SAN DIEGO	USA	Human Genome Research	000	3	9/9/2022	NON-COMPETING CONTINUATION	$861,551
														Subtotal = $861,551

Issue Date FY: 2021 ( Subtotal = $1,137,682 )
2021	2021	ECLIPSE BIOINNOVATIONS, INC.	6195 CORNERSTONE CT E STE 105	SAN DIEGO	CA	92121	SAN DIEGO	USA	Human Genome Research	000	2	9/22/2021	COMPETING CONTINUATION	$1,137,682
														Subtotal = $1,137,682

Grand Total All Awards = $1,999,233

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Development of chimeric read amplification into a robust method for profiling targets of specific microRNAs and global amplification of all microRNA:mRNA pairings transcriptome-wide

Award Number: R44HG010603

ORGANIZATION: NATIONAL HUMAN GENOME RESEARCH INSTITUTE

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 09/17/2019

PERIOD OF PERFORMANCE END DATE: 08/31/2023

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