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Genetic, Environmental, and Social Interactions Shaping Early Cannabis Use (GENESIS): Decoding Predictive Factors Among U.S. Youth

open

NIDA - National Institute on Drug Abuse

PROJECT SUMMARY Early initiation of cannabis use (<16 years of age) increases risk for cannabis use disorder (CUD), mental illness, cognitive impairment, later unemployment, and poor social relationships. Prevention of early initiation is critical for improving social and health outcomes. Precision prevention programs have reduced youth substance use, but no approaches have specifically targeted cannabis use. Furthermore, no studies have comprehensively considered risk factors for early cannabis initiation (genetic, social, behavioral, environmental, and cognitive) to enhance the prediction of early use and inform precision prevention approaches. Comprehensive multivariable prediction models for early cannabis initiation that include genetics and social/environmental factors are needed. Cannabis use is polygenic, influenced by multiple genetic variants with weak-to-moderate effects, and polygenicity makes it difficult to translate genetics for clinical application. One method for clinically applying genetics is through the development of polygenic risk scores (PRS) that are composite scores representative of overall genetic risk. Prior PRS have typically lacked portability to non-European populations; however, a state- of-the-art method has been developed to build PRS with significantly improved risk prediction (34% improvement) across ancestries. There is a need to apply this method to develop cross-ancestry PRS for cannabis use for inclusion of overall genetic risk in comprehensive prediction models. Furthermore, given the complex interplay between genetics and social/environmental factors, research is needed to understand gene by environment (GxE) interactions in which social/environmental factors synergistically impact the risk conferred by genetics. Research into GxE interactions is statistically and computationally challenging, and traditional single-variant and more recent polygenic approaches focus on lower order 2-way interactions. Our logic forest (LF) algorithm efficiently searches all possible interactions up to 8 variables without a priori specification. This study will apply these state-of-the-art computational methods to the Adolescent Brain Cognitive Development (ABCD) Study, which examines childhood risk factors and initiation of substance use from ages 9-10 years to early adulthood in a population demographically reflective of the U.S. Nearly all youth had not used cannabis at recruitment, enabling the prospective measurement of initiation and the development of prediction models integrating genetics with pre-substance use measurements of cognitive, social, and environmental factors. This research will 1) develop cross-ancestry PRS for inclusion in prediction models that comprehensively consider genetic, sociodemographic, behavioral, cognitive, and environmental factors, and 2) apply LF to gene-sets within known biological pathways across the whole genome to identify pathway-specific GxE interactions. Comprehensive models coupled with a more complete understanding of GxE factors influencing early cannabis initiation can identify 1) high risk youth populations for targeted prevention, 2) targetable factors present among high-risk clusters for tailored interventions, and 3) biological pathways for therapeutic development.

Up to $311K
2028-06-30
health research

Free to search & build · $99 one-time to unlock the application pack · No subscription

Genetics-based discovery of novel genes regulating follicular helper T cell function

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NIAID - National Institute of Allergy and Infectious Diseases

ABSTRACT The goal of the studies in this proposal is to establish how disease-associated genetic variation regulates antibody responses at the level of B cell help by follicular helper T cells (TFH). In Aim 1, we will use a powerful combination of state-of-the-art, variant-to-gene mapping approaches in follicular T cells ‘caught in the act’ of helping B cell antibody responses in human lymphoid tissue: 1) chromosome conformation data to reveal physical associations between regulatory variants and gene promoters in the context of the 3D structure of the genome, 2) quantitative expression-trait mapping to reveal statistical associations between disease-associated variants and gene expression in TFH cells, 3) massively-parallel reporter assays to identify expression- modulating variants, and 4) CRISPR interference screens to identify genes regulated by antibody disease variants in TFH cells. In Aim 2, ‘novel’ effector genes prioritized by the approaches in Aim 1 will be assessed for roles in TFH function in an in vitro lymphoid organoid model human humoral immunity and in in vivo mouse models of lupus and influenza vaccination. The proposed studies are supported by the extensive experience and preliminary data of the research team, and will use a confluence of evidence from orthogonal approaches to power discovery of novel mechanisms that regulate T cell-dependent humoral immunity, refine our understanding of how common genetic variation contributes to autoimmune disease susceptibility, and point to novel therapeutic interventions to modulate humoral immunity in the context of vaccines, infectious disease, and autoimmune disorders.

Up to $906K
2031-06-30
health research

Free to search & build · $99 one-time to unlock the application pack · No subscription

Genome editing therapeutics for the treatment of aortic aneurysm in Marfan Syndrome

open

NHLBI - National Heart Lung and Blood Institute

PROJECT SUMMARY Gene editing offers the prospect of directly modifying any nucleotide(s) in the genome, including correction of pathogenic variants underlying disease. These technologies could form the basis of cures for currently untreatable genetic conditions. The work proposed in this application aims to identify genome editing strategies to prevent aortic pathology in Marfan syndrome (MFS). MFS is the most prevalent hereditary connective tissue disorder and is associated with significantly increased morbidity and mortality due to life-limiting thoracic aortic aneurysm and dissection. MFS is caused by heterozygous pathogenic variants in FBN1, the gene encoding the main structural component of extracellular microfibrils, fibrillin-1. Microfibrils are essential for providing structural elasticity and resilience, in addition to having a signaling role, and defects in both features are thought to contribute to elastic lamina fragmentation and aortic wall weakness. We hypothesize that gene editing correction of FBN1 pathogenic variants or genome editing-based upregulation of the structurally related protein FBN2 within aortic vascular smooth muscle will reduce risk of aortic root dilation and dissection, thereby limiting the major cause of morbidity and mortality in this disease. In the first aim, the candidate will identify a prime editing strategy to correct the Fbn1 C1041G pathogenic variant in aortic vascular smooth muscle of a murine model of MFS and will test this therapeutic strategy by monitoring aortic aneurysm. In the second aim, a machine learning model will be used to identify promoter variants, putative enhancers, and transcription factor binding site motifs within the FBN2 promoter region that are predicted to augment FBN2 expression. These elements will be functionally evaluated in a massively parallel reporter assay (MPRA). Finally, in vivo genome editing will be used to introduce an optimized FBN2 upregulatory strategy established through these analyses in the Fbn1C1041G/+ mouse model of MFS for correction of aortic pathology. In addition to establishing potential gene editing treatment strategies for aortic aneurysm in Marfan syndrome, these studies will enable the candidate to obtain expertise in the design and application of state-of-the-art gene editing tools that can be used to generate disease models and investigate therapies for many different genetic disorders, which he plans to pursue throughout his career as a physician-scientist.

Up to $169K
2031-04-30
health research

Free to search & build · $99 one-time to unlock the application pack · No subscription

Genomics-Empowered AI for Personalized Cancer Risk Assessment, Monitoring, and Prevention

open

NHGRI - National Human Genome Research Institute

Project Summary This proposed MAGen development site aims to develop genomics and multi-modal artificial intelligence (AI) models to transform personalized cancer risk assessment, monitoring, and prevention. A substantial gap exists between the theoretical potential of genomics-based AI predictions and their practical application in clinical and population healthcare settings. The clinical classification of genetic variants is hindered by insufficient data to classify ultra-rare variants, particularly those found in non-European populations. Moreover, despite significant advances in AI across fields, we lack AI models that can combine diverse streams of health data to accurately predict disease risk across a person’s life course. Finally, the real-world effectiveness of these AI models remains untested and their ethical, legal, and social implications (ELSI) are unclear. To address these challenges, our primary goal is to develop state-of-the-art (SOTA) AI models that can accurately identify pathogenic variants affecting DNA repair genes and predict cancer risks over the life course of high-risk carriers, thereby optimizing screening and prevention strategies in an ELSI-informed manner. Our multidisciplinary team comprises experts in computational genomics, AI/ML, health informatics, statistical genetics, medical genetics, population health, oncology, and ELSI research from Icahn School of Medicine at Mount Sinai (ISMMS), Boston Children’s Hospital/Harvard, and Columbia University, and has complementary and extensive experience in consortium and team science projects. In our proposed project for MAGen, Aim 1 will develop robust genomic AI models for identifying protein-disrupting missense variants that confer high cancer risks. Aim 2 will combine other genetic factors, including common and rare variant polygenic risk scores (PRS), and non-genetic factors, including EHR, longitudinal lab markers, SDoH, and digital pathology, to predict cancer risk over the life course and optimize screening recommendations for carriers. Aim 3 will cross-validate AI models in real-world population biobanks and determine their clinical impact. Aim 4 will construct an ELSI framework and conduct ELSI projects to evaluate the multi-faceted impacts of AI-driven genetic diagnostics. Aim 5 will disseminate AI model/predictions, cross-validation data, and ELSI recommendations. The completion of these Aims will bring genomics-based and multi-modal AI closer to the advancement of personalized medicine in real-world settings by more accurately classifying pathogenic variants, optimizing the timing of screening, and identifying key lifestyle and medical prevention strategies that could ultimately save lives from cancer.

Up to $1.5M
2028-03-31
health research

Free to search & build · $99 one-time to unlock the application pack · No subscription

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