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Discovery of early immunologic biomarkers for risk of PTLDS through machine learning-assisted broad temporal profiling of humoral immune response

Award Number: R01AI178727
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: 07/07/2023
PERIOD OF PERFORMANCE END DATE: 06/30/2028

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Discovery of early immunologic biomarkers for risk of PTLDS through machine learning-assisted broad temporal profiling of humoral immune response - Project Summary/Abstract Lyme Disease (LD) is a tickborne illness with markedly increasing prevalence in the United States. While more than 80% of the LD cases can be effectively treated using established antibiotic treatments, 10-15% of patients develop post-treatment, long-term sequalae manifested as fatigue, cognitive impairment, joint pain, and other symptoms and termed Post Treatment Lyme Disease Syndrome (PTLDS) causing patients to experience substantial loss in quality of life and resulting in a marked financial burden on both patient and health care system. The absence of approved molecular diagnostic tests leads many physicians to dismiss the notion of PTLDS entirely, leaving patients with few or poorly defined treatment options. While currently no approved treatment for PTLDS exists, emerging evidence suggests substantially better clinical outcomes from early intervention with targeted therapies in a number of chronic and autoimmune disorders. Early risk assessment of developing PTLDS offers a window of opportunity by alerting both the patient and the physician to anticipate a long-term symptomatic result and adjust symptom-based treatment. The proposed study focuses on the urgent need to identify immunologic biomarkers for predicting the risk of a patient developing PTLDS early during the acute phase of the disease and has the potential to markedly improve clinical outcomes through early intervention. The proposed approach derives disease-specific antigen information from a comprehensive binding profile of the patient’s circulating antibody repertoire. The novelty of the approach is in representing an entire binding space of a donor’s circulating antibody repertoire, instead of simply focusing on a priori known antigenic targets. The approach relies on using machine learning models trained on the antibody binding profile to a diverse, random library of 126,050 unique peptides with an average length of 9-10 amino acids as a sparse representation of all possible combinatorial 9-mer sequences. Predictive models are then used to identify disease-associated pathogen epitopes with high predictive power that can be combined into a potential panel for PTLDS risk assessment. It is hypothesized that B. burg. antigens and/or self-antibodies from the human proteome are involved and that there is a set that can be used as biomarkers to predict progression to PTLDS early in the disease. The antibody response over time will be profiled in a set of longitudinally collected patient samples as they progress from confirmed acute LD, through treatment to disease outcome. This approach applied will enable the breadth of the antibody response, including a potential response/cross- reactivity to human proteins to be examined along with the heterogeneity of antibody responses across a cohort of patients. In silico predictions of protein antigenicity will be confirmed using solution-based immunoassays. The proposed work is expected to identify a set of B. burg. and potentially human autoimmune antigens that are associated with progression to PTLDS. Such knowledge is expected to serve as the basis for future diagnostics, therapeutics or in the generation of hypothesis that can be tested in disease models.


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: 2025 ( Subtotal = $610,933 )
2025	2025	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Allergy and Infectious Diseases Research	000	3	6/23/2025	NON-COMPETING CONTINUATION	$610,933
														Subtotal = $610,933

Issue Date FY: 2024 ( Subtotal = $624,294 )
2024	2024	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Allergy and Infectious Diseases Research	000	2	6/25/2024	NON-COMPETING CONTINUATION	$624,294
														Subtotal = $624,294

Issue Date FY: 2023 ( Subtotal = $649,935 )
2023	2023	ARIZONA STATE UNIVERSITY	660 S MILL AVENUE STE 204	TEMPE	AZ	85281	MARICOPA	USA	Allergy and Infectious Diseases Research	000	1	7/7/2023	NEW	$649,935
														Subtotal = $649,935

Grand Total All Awards = $1,885,162

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Discovery of early immunologic biomarkers for risk of PTLDS through machine learning-assisted broad temporal profiling of humoral immune response

Award Number: R01AI178727

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: 07/07/2023

PERIOD OF PERFORMANCE END DATE: 06/30/2028

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