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Principal Investigator: YUH-HWA WANG
Organization: UNIVERSITY OF VIRGINIA
Fiscal Year: 2024
Award: $329,762
Funding agency: National Institute of General Medical Sciences
Project Summary/Abstract:
Both physiological DNA breaks occurring during DNA metabolic processes and pathological DNA breaks
responding to a wide range of stresses, contribute to the outcome of human genome instability. DNA fragility
generated by alternative DNA secondary structures is a known cause of many human diseases, and also occurs
in normal DNA processes. Formation of these structures can arise from single-stranded DNA when the DNA
duplex is unwound during DNA processes such as replication and transcription, and thus can be affected by
cellular activities, nucleotide sequences, and chemical exposures. Here we will examine if DNA regions
having potential to form stable secondary structures when unwound during cell processes, can serve
as signals for topoisomerase II (TOP2) to recognize and cleave, and lead to the removal of the excessive
supercoiling. We have carried out a computational evaluation of the entire available human genome sequence
for optimal ability to fold single-stranded sequences into multiple-hairpin structures, and identified sites of highly
stable DNA secondary structures throughout the genome. We will measure TOP2-mediated DNA breaks at
these sites upon changes in DNA supercoiling from cell activities, then analyze TOP2-cleaved sites to identify
structural features, and examine if DNA secondary structures influence the removal of TOP2 cleavage
complexes. TOP2-mediated breaks are also often associated with pathological damage due to the use of TOP2
inhibitors as anticancer drugs. Many DNA secondary structure-rich and fragile regions are located within cancer-
specific translocation-participating gene regions, including acute myeloid leukemia (AML)-rearranged regions.
We will determine whether DNA fragility at these regions can serve as a biomarker for assessing the
potential development of cancer-causing rearrangements. We will first test if DNA fragility at gene regions
of AML rearrangements is sensitive to various chemotherapeutic agents, and if this sensitivity leads to the
formation of AML rearrangements in human cells. Then, to test if this sensitivity can predict the rearrangement
formation in patients, we will examine DNA breakage at these regions in normal cells of AML patients with the
AML rearrangements, compared to that of normal individuals, as a means to evaluate individual susceptibility
to AML. These experiments will facilitate the clinical application of using DNA fragility as a biomarker. With
personalized medicine in mind, we will evaluate the effect of naturally occurring sequence variants on the
fragility of the break-prone and AML translocation-participating gene regions, to further identify
structure characteristics contributing to DNA fragility, and to reveal an unexploited consequence of
non-coding variants. Our preliminary results suggest that sequence variants can influence DNA break
frequency of the region by changing the extent or the type of secondary structure forming ability. This proposal
will elucidate the mechanistic and functional features of DNA structure-driven fragility and provide a foundation
for future clinical use of fragile site breakage in disease diagnostics.
Terms: <AML - Acute Myeloid Leukemia><Abscission><Acute Myeloblastic Leukemia><Acute Myelocytic Leukemia><Acute Myelogenous Leukemia><Affect><Anti-Cancer Agents><Antineoplastic Agents><Antineoplastic Drugs><Antineoplastics><Assay><Base Sequence><Benign><Binding><Binding Proteins><Binding Sites><Bioassay><Biological Assay><Biological Markers><Blood Precursor Cell><Cancer Cause><Cancer Drug><Cancer Etiology><Cancers><Cell Body><Cell Communication and Signaling><Cell Function><Cell Physiology><Cell Process><Cell Signaling><Cells><Cellular Function><Cellular Physiology><Cellular Process><Characteristics><Chemical Agents><Chemical Exposure><Chemotherapy Protocol><Chemotherapy Regimen><Chemotherapy-Oncologic Procedure><Chromosome Fragile Sites><Chromosomes><Clinical><Closure by Ligation><Combination Chemotherapy Regimen><Combining Site><Complex><DNA><DNA Maintenance><DNA Rearrangement><DNA Stability><DNA Structure><DNA Topoisomerase II><DNA Type 2 Topoisomerase><DNA-Dependent RNA Polymerases><DNA-Directed RNA Polymerase><Data><Deoxyribonucleic Acid><Development><Diathesis><Disease susceptibility><Dose><Drugs><Environmental Exposure><Evaluation><Excision><Exposure to><Extirpation><Foundations><Fragile Site><Frequencies><Functional RNA><Future><Gene Rearrangement><Gene Transcription><Generations><Genes><Genetic Alteration><Genetic Change><Genetic Transcription><Genetic defect><Genome><Genome Instability><Genomic Instability><Genotype><Hematopoietic Progenitor Cells><Hematopoietic stem cells><Human><Human Genome><In Vitro><Individual><Intermediary Metabolism><Intracellular Communication and Signaling><Ligand Binding Protein><Ligand Binding Protein Gene><Ligation><Malignant Neoplasms><Malignant Tumor><Maps><Measures><Mediating><Medication><Metabolic Processes><Metabolism><Mind><Modeling><Modern Man><Molecular><Molecular Interaction><Monitor><Mutation><Neoplastic Disease Chemotherapeutic Agents><Non-Coding><Non-Coding RNA><Non-translated RNA><Noncoding RNA><Nontranslated RNA><Normal Cell><Nucleotide Sequence><Outcome><Pathologic><Patients><Pharmaceutical Preparations><Physiologic><Physiological><Population><Predisposition><Process><Protein Binding><Quimioterapia><RNA Expression><RNA Polymerases><Reactive Site><Removal><Residual><Residual state><Risk Assessment><Role><Signal Transduction><Signal Transduction Systems><Signaling><Single Base Polymorphism><Single Nucleotide Polymorphism><Single-Stranded DNA><Site><Stress><Structure><Subcellular Process><Supercoiled DNA><Superhelical DNA><Supertwisted DNA><Surgical Removal><Susceptibility><Testing><Therapeutic><Therapy-Related Acute Myeloid Leukemia><Time><Topo II><Topoisomerase II><Topoisomerase-II Inhibitor><Transcription><Transcription Initiation Site><Transcription Start Site><Treatment-Related AML><Treatment-Related Acute Myelocytic Leukemia><Treatment-Related Acute Myelogenous Leukemia><Treatment-related Acute Myeloid Leukemia><Tumor-Specific Treatment Agents><Type II DNA Topoisomerases><Untranslated RNA><Variant><Variation><Work><Yeasts><acute granulocytic leukemia><acute granulocytic leukemia cell><acute myeloblastic leukemia cell><acute myelocytic leukemia cell><acute myelogenous leukemia cell><acute myeloid leukemia><acute myeloid leukemia cell><acute nonlymphocytic leukemia cell><anti-cancer drug><bio-markers><biologic marker><biological signal transduction><biomarker><blood cell progenitor><blood progenitor><blood stem cell><blood-forming stem cell><bound protein><cancer biomarkers><cancer chemotherapy><cancer markers><chemotherapeutic agent><clinical applicability><clinical application><developmental><disease diagnostic><drug/agent><enzyme activity><experiment><experimental research><experimental study><experiments><genome mutation><genome scale><genome-wide><genomewide><hematopoietic progenitor><hematopoietic stem progenitor cell><hemopoietic progenitor><hemopoietic stem cell><high risk group><high risk individual><high risk people><high risk population><human disease><human whole genome><indel><insertion-deletion><insertion-deletion mutation><insertion/deletion><insertion/deletion mutation><liability to disease><malignancy><neoplasm/cancer><new diagnostics><next generation diagnostics><noncoding><novel diagnostics><nucleic acid sequence><personalization of treatment><personalized medicine><personalized therapy><personalized treatment><promoter><promotor><resection><response><screening><screenings><single nucleotide variant><social role><ssDNA><stem>