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Principal Investigator: RICHARD H. FINNELL
Organization: WEILL MEDICAL COLL OF CORNELL UNIV
Fiscal Year: 2024
Award: $695,911
Funding agency: Eunice Kennedy Shriver National Institute of Child Health and Human Development
ABSTRACT: UNDERSTANDING GENETIC COMPLEXITY IN SPINA BIFIDA
Among neural tube defects (NTDs), myelomeningocele (spina bifida:SB), is a devastating but survivable,
human structural malformation. Up to 70% of SB cases are attributed to genetic predisposition, with intrauterine
environment precipitating SB manifestation in those at risk. Despite decades of research into genetic factors that
underlie NTDs in mouse models, translation to human risk assessment and amelioration of SB cases remain
elusive. This is largely attributable to limitations of the typical candidate gene approaches used in genetic studies
of human NTDs. Here, our comprehensive systems biology approach to mutation burden in whole genome
sequence (WGS) analyses is illuminating molecular pathways to human SB through interrogation of protein
coding and non-coding regions, and introduces machine learning to select, in an untargeted fashion, genes with
SB discriminatory potential based on gene enrichment by rare, likely deleterious protein coding variants.
The project extends our comprehensive genomic effort, generating new WGS on 200 recently collected
patient-parent trio (600 genomes) samples. Studies aim to identify specific gene drivers of human SB, illuminate
gene-gene interactions leading to SB, and improve mechanistic understanding of this complex birth defect.
Aim 1 uses family study and systems biology approaches to seek genes with transmitted or de novo rare
variants suggesting SB-association. This begins assessment of parental vs de novo, “second hit”, contributions
to SB. Analyses include protein-coding and noncoding sequence single nucleotide variants (SNVs), rare copy
number variants (rCNVs), and state-of-the art computational probes leveraging genome 3D structure.
Aim 2 tests the functional significance and interactions of these detected genes and variations to: (a) use
CRISPR edited isogenic, double heterozygous human stem cells in a novel SOSRS, 3-D in vitro method to
evaluate proliferation, self-organization, and differentiation, (b) test the transcriptional impact of these mutations
using bulk and single cell RNAseq in mutagenized cells.
Aim 3 examines double/multiple-heterozygous protein coding mutations using existing and CRISPR-
edited mice to test the histological and gene expression impact of gene interactions on NT closure.
Our computational approaches are highly innovative in the field, using machine learning to build network
models of human SB risk. We then apply advanced technology for the functional testing of these genetic risk
models, including gene editing of human stem cells, compared to isogenic controls, and mice for cellular and
systems based hypothesis testing in vitro and in vivo, along with evaluation of the cell-type gene expression
changes induced by these variants. Insights from our studies will pave the way for a precision medicine capability
to individualize NTD prevention and care for families and the hundreds of thousands of patients living with SB.
Terms: <0-11 years old><3-D><3-D structure><3-Dimensional><3-dimensional structure><3D><3D structure><Adhesions><Admixture><Affect><Antioncogene Protein p53><Apical><Basal Transcription Factor><Basal transcription factor genes><Binding Sites><Biological><Biological Function><Biological Process><Biological Testing><Birth Defects><Brain><Brain Nervous System><Breeding><CRISPR><CRISPR approach><CRISPR based approach><CRISPR method><CRISPR methodology><CRISPR technique><CRISPR technology><CRISPR tools><CRISPR-CAS-9><CRISPR-based method><CRISPR-based technique><CRISPR-based technology><CRISPR-based tool><CRISPR/CAS approach><CRISPR/Cas method><CRISPR/Cas system><CRISPR/Cas technology><CRISPR/Cas9><CRISPR/Cas9 technology><Candidate Disease Gene><Candidate Gene><Caring><Cas nuclease technology><Case-Base Studies><Case-Comparison Studies><Case-Compeer Studies><Case-Referent Studies><Case-Referrent Studies><Case/Control Studies><Causality><Cell Body><Cells><Cellular Tumor Antigen P53><Cellular biology><Child><Child Youth><Children (0-21)><Clustered Regularly Interspaced Short Palindromic Repeats><Clustered Regularly Interspaced Short Palindromic Repeats approach><Clustered Regularly Interspaced Short Palindromic Repeats method><Clustered Regularly Interspaced Short Palindromic Repeats methodology><Clustered Regularly Interspaced Short Palindromic Repeats technique><Clustered Regularly Interspaced Short Palindromic Repeats technology><Code><Coding System><Collaborations><Combining Site><Complex><Computational Biology><Computational toolkit><Computing Methodologies><Congenital Abnormality><Congenital Anatomical Abnormality><Congenital Defects><Congenital Deformity><Congenital Malformation><Copy Number Polymorphism><Couples><DNA seq><DNA sequencing><DNAseq><Data><Disease><Disorder><Embryo><Embryonic><Encephalon><Enhancers><Environmental Factor><Environmental Risk Factor><Epistasis><Epistatic Deviation><Equilibrium><Etiology><Evaluation><Event><Exons><Failure><Family><Family Study><Folate><Folic Acid><Food Supply><Fortification><Frequencies><Functional RNA><Gene Combinations><Gene Expression><Gene Transcription><Gene variant><General Transcription Factor Gene><General Transcription Factors><Genes><Genetic><Genetic Alteration><Genetic Change><Genetic Diversity><Genetic Epistasis><Genetic Predisposition><Genetic Predisposition to Disease><Genetic Risk><Genetic Susceptibility><Genetic Transcription><Genetic Variation><Genetic defect><Genetic propensity><Genetic study><Genome><Genomic Segment><Genomic approach><Genomics><Genotoxins><Gestation><Goals><Hand><Hereditary><Heterozygote><Histologic><Histologically><Human><Human Genome><Impairment><In Vitro><Individual><Inherited><Inherited Predisposition><Inherited Susceptibility><Innate Immunity><Interaction Deviation><MAX gene><MYC-Associated Factor X><MYC-Associated Factor X Gene><Machine Learning><Maps><Max protein><Meningomyelocele><Meningomyelocoele><Methods><Mice><Mice Mammals><Modeling><Modern Man><Molecular><Murine><Mus><Mutagens><Mutation><Myelomeningocele><Native Immunity><Natural Immunity><Nerve><Nervous System Injuries><Nervous System Trauma><Nervous System damage><Neural Tube Closure><Neural Tube Defects><Neural Tube Developmental Defects><Neural tube><Neurological Damage><Neurological Injury><Neurological trauma><Non-Coding><Non-Coding RNA><Non-Specific Immunity><Non-translated RNA><Noncoding RNA><Nonspecific Immunity><Nontranslated RNA><Oncoprotein p53><Organogenesis><Organoids><P53><Parents><Pathogenesis><Pathway interactions><Patients><Pattern><Phosphoprotein P53><Phosphoprotein pp53><Population><Population Control><Pregnancy><Prevention><Proliferating><Protein TP53><Proteins><Pteroylglutamic Acid><Publishing><RNA Expression><Reactive Site><Research><Risk><Risk Assessment><SEQ-AN><Sampling><Sampling Biases><Schistorrhachis><Selection Bias><Sequence Analyses><Sequence Analysis><Single Base Polymorphism><Single Nucleotide Polymorphism><Site><Spina Bifida><Spinal Column><Spinal Dysraphia><Spinal Dysraphism><Spine><Structural defect><Structural malformation><System><Systems Biology><TP53><TP53 gene><TRP53><Technology><Testing><Transcription><Transcription Factor Proto-Oncogene><Transcription factor genes><Transmission><Tumor Protein p53><Tumor Protein p53 Gene><Untranslated RNA><Validation><Variant><Variation><Vertebral column><Vitamin M><allele variant><allelic variant><backbone><balance><balance function><biologic><case control><case-controlled><case-controlled studies><causation><cell biology><cell type><cleft spine><cohesin><cohort><compare to control><comparison control><computational methodology><computational methods><computational toolbox><computational tools><computational toolset><computer based method><computer biology><computer methods><computerized tools><computing method><constriction><copy number variant><copy number variation><de novo mutation><de novo variant><disability><disease causation><disease risk><disorder risk><effective therapy><effective treatment><entire genome><environmental risk><epistatic relationship><folate supplementation><folic acid supplement><folic acid supplementation><frontier><full genome><gene function><gene interaction><gene x gene interaction><genetic epistases><genetic etiology><genetic mechanism of disease><genetic variant><genetic vulnerability><genetically predisposed><genome analysis><genome editing><genome mutation><genome segment><genomic editing><genomic effort><genomic region><genomic strategy><genomic variant><genotoxic agent><global gene expression><global transcription profile><hESC><hands><heterozygosity><human ES cell><human ESC><human embryonic stem cell><human model><human progenitor><human stem cells><human whole genome><hydrocele spinalis><iPS><iPSC><iPSCs><improved><in vitro Model><in vitro testing><in vivo><induced pluripotent cell><induced pluripotent stem cell><inducible pluripotent stem cell><innovate><innovation><innovative><insight><intra-uterine environment><intrauterine environment><intrauterine milieu><kids><learning activity><learning method><learning strategies><learning strategy><machine based learning><model of human><mouse model><multiple data sets><multiple datasets><murine model><network models><neurotrauma><new approaches><noncoding><novel><novel approaches><novel strategies><novel strategy><p53 Antigen><p53 Genes><p53 Tumor Suppressor><parent><pathway><precision medicine><precision-based medicine><prevent><preventing><progenitor cell proliferation><progenitor proliferation><protein p53><rachischisis posterior><rare allele><rare mutation><rare variant><scRNA-seq><self organization><single cell RNA-seq><single cell RNAseq><single cell expression profiling><single cell transcriptomic profiling><single nucleotide variant><single-cell RNA sequencing><stem and progenitor cell proliferation><stem cell proliferation><structural abnormalities><structural anomalies><supplementation with folate><supplementation with folic acid><three dimensional><three dimensional structure><transcription factor><transcriptome><translation to humans><transmission process><validations><vitamin Bc><whole genome><youngster>