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Reverse transcriptase-mediated expansion of the host innate immune system

Award Number: R21AI174130
ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 12/12/2022
PERIOD OF PERFORMANCE END DATE: 11/30/2025

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Reverse transcriptase-mediated expansion of the host innate immune system - PROJECT SUMMARY Large effect mutations in innate immunity genes can have dramatic effects on infectious disease susceptibility and outcome. In addition, the genetic determinants of more subtle and widespread variation in an individual’s susceptibility and immune response to viral infections has been studied in the context of mutations in the many known innate immunity genes. We propose that there are new polymorphic innate immune genes created by retroviruses (so called ‘retrocopies’) in the genome of many individuals which are typically overlooked, and which have the capacity to modulate an individual’s immune response. Thousands of young and old retrocopies are present in each human genome and their number and sequences differ among individuals in a population. Until now, old retrocopies have largely been ignored as pseudogenes, while young retrocopies have been understudied due to technical challenges of accurate identification inherent in the most common sequencing technologies. A pioneering study in our lab showed that human and other primate genomes contain retrocopies of the APOBEC3 family of viral restriction factors that are transcribed and capable of restricting virus replication in vitro. Our more recent preliminary data revealed extensive retrocopying of additional antiviral gene families within humans and other primate species, suggesting the recent retrocopying of viral restriction and host dependency factors may be widespread. Further, some of these retrocopies are very young – present in only some humans – and could represent an unappreciated source of individual variation in susceptibility or resistance to viral infection. With a combination of computational biology, in vitro virology and biochemistry, and high throughput functional assays, we will identify young retrocopies of virus-interacting genes that are present in only some humans and test these new genes’ ability to enhance or impede the innate immune system’s antiviral response. To test our hypothesis that retrocopy expansions modify immune system function, we will: (1) Identify young, polymorphic retrocopies of host dependency and restriction factor genes in humans. (2) Characterize transcription and antiviral functions of polymorphic host dependency and restriction factor retrocopies, either as restriction factors or dependency factors that evade viral co-option. (3) Identify retrocopies that act as dominant negative inhibitors of their parental antiviral genes thereby inhibiting the innate immune system and promoting viral replication. This research will discover new innate immune genes and found a new direction in understanding the genetic determinants of an individual's susceptibility and immune response to virus infection.


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 = $276,000 )
2024	2024	PACIFIC NW RESEARCH INSTITUTE	720 BROADWAY	SEATTLE	WA	98122	KING	USA	Allergy and Infectious Diseases Research	000	2	11/15/2023	NON-COMPETING CONTINUATION	$248,400
2024	2024	PACIFIC NORTHWEST RESEARCH INSTITUTE	720 BROADWAY	SEATTLE	WA	98122	KING	USA	Allergy and Infectious Diseases Research	001	2	5/14/2024	NON-COMPETING CONTINUATION	$27,600
														Subtotal = $276,000

Issue Date FY: 2023 ( Subtotal = $230,000 )
2023	2023	PACIFIC NW RESEARCH INSTITUTE	720 BROADWAY	SEATTLE	WA	98122	KING	USA	Allergy and Infectious Diseases Research	001	1	7/26/2023	NEW	$0
2023	2023	PACIFIC NW RESEARCH INSTITUTE	720 BROADWAY	SEATTLE	WA	98122	KING	USA	Allergy and Infectious Diseases Research	000	1	12/12/2022	NEW	$230,000
														Subtotal = $230,000

Grand Total All Awards = $506,000

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Reverse transcriptase-mediated expansion of the host innate immune system

Award Number: R21AI174130

ORGANIZATION: NATIONAL INSTITUTE OF ALLERGY & INFECTIOUS DISEASES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

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

PERIOD OF PERFORMANCE START DATE: 12/12/2022

PERIOD OF PERFORMANCE END DATE: 11/30/2025

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