Task Book: Biological & Physical Sciences Division and Human Research Program
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Project Title:  Epigenetic State Modulation of Radiation-Induced DNA Damage: Nanoscale Modeling and Validation Reduce
Images: icon  Fiscal Year: FY 2021 
Division: Human Research 
Research Discipline/Element:
HRP SR:Space Radiation
Start Date: 04/01/2021  
End Date: 03/31/2022  
Task Last Updated: 04/16/2021 
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Principal Investigator/Affiliation:   Risca, Viviana  Ph.D. / The Rockefeller University 
Address:  Laboratory of Genome Architecture and Dynamics 
1230 York Ave, Box 176 
New York , NY 10065-6307 
Phone: 516-728-3406  
Congressional District: 12 
Organization Type: UNIVERSITY 
Organization Name: The Rockefeller University 
Joint Agency:  
Plante, Ianik  Ph.D. NASA Johnson Space Center 
Jeevarajan, Antony  Ph.D. NASA Johnson Space Center 
Project Information: Grant/Contract No. 80NSSC21K0565 
Responsible Center: NASA JSC 
Grant Monitor: Elgart, Robin  
Center Contact: 281-244-0596 (o)/832-221-4576 (m) 
Solicitation / Funding Source: 2019-2020 HERO 80JSC019N0001-HHCBPSR, OMNIBUS2: Human Health Countermeasures, Behavioral Performance, and Space Radiation-Appendix C; Omnibus2-Appendix D 
Grant/Contract No.: 80NSSC21K0565 
Project Type: GROUND 
Flight Program:  
TechPort: No 
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Human Research Program Elements: (1) SR:Space Radiation
Human Research Program Risks: (1) Cancer:Risk of Radiation Carcinogenesis
Human Research Program Gaps: (1) Cancer-103:Determine the effects of radiation quality on cancer initiation, promotion, and progression (IRP Rev M)
(2) Cancer-104:Determine the effects of radiation dose and dose-rate on cancer initiation, promotion and progression (IRP Rev M)
(3) Cancer-202:Evaluate the contribution of genetic background/diversity on carcinogenesis risk (IRP Rev M)
(4) Cancer-303:Identify early surrogate biomarkers that correlate with cancer, pre-malignancy, or the hallmarks of cancer (IRP Rev M)
Task Description: BACKGROUND

The risks of cellular dysfunction associated with exposure to space radiation, including transcriptional and epigenetic perturbations and genomic instability due to DNA breaks, have been studied in cell lines, with DNA repair foci and products as the main readouts. Such genetic and cell biological readouts show that high linear energy transfer (LET) charged nuclei, such as those found in galactic cosmic rays (GCR), cause persistent cellular changes in stress response and genomic integrity. These effects are different from the effects of low-linear energy transfer (LET) radiation such as X-rays and occur in the context of the genome-wide epigenetic landscape of each cell, which includes nucleosome positions, nucleosome modifications, and variant histone substitutions in those nucleosomes. Epigenetic states differ in chromatin fiber conformations, with transcriptionally active chromatin adopting more open, extended structures. These differences can affect DNA break patterns in response to ionizing radiation, potentially creating distinct DNA repair and signaling outcomes. The epigenetic state landscape of a cell depends on its differentiation state, cell type, and responses to external stimuli. Because it is not practical to experimentally investigate every cell type, a more generalizable approach is needed to predict how the cell’s distinctive epigenetic landscape will interact with radiation to give rise to a certain pattern of DNA breaks and associated cellular response. A generalizable approach that takes local epigenetic map information into account can leverage the large and diverse epigenomic data sets available for a large number of human cell types. Previous investigations of chromatin structure’s role in regulating DNA damage by radiation assumed that chromatin adopts stable, regular structures such as 30-nm fibers. Recently emerging consensus in the field suggests this single-structure view is inaccurate and the ensemble of conformational fluctuations of the fiber must be taken into account.


We hypothesize that the pattern and lethality of DNA breaks generated at a given genomic locus depend on the combination of (1) the incoming ionizing radiation, with differences between low LET photons and high LET GCRs, and (2) the epigenetic state of that locus, which is associated with a characteristic ensemble of chromatin fiber conformations.


We propose to develop a generalizable mechanistic approach to determining how DNA breaks are generated by ionizing radiation including GCRs and photons. We will integrate realistic chromatin fiber ensembles with Monte Carlo simulations of photons or GCR nuclei interacting with those fibers, and Green’s function based calculation of radiochemistry kinetics after the particle delivers its energy. The chromatin fiber ensembles will be generated through a coarse-grained simulation based on a stretchable shearable worm-like chain model of linker DNA between nucleosomes that is constrained by pairwise DNA-DNA contact data. We will measure chromatin fiber contact distances, simulate sub-kilobase chromatin conformation ensembles consistent with those contact distances, and predict how these ensembles give rise to ensembles of DNA break patterns. These measurements and simulations will be carried out for multiple chromatin states across several cell types as well as for in vitro reconstituted chromatin fibers in order to build a general, cell type independent model of the relationship between epigenetic state and vulnerability to radiation induced DNA damage. The resulting software package will enable the simulation of user-programmable chromatin states, to produce chromatin state specific predictions of expected DNA fragmentation patterns for each type of heavy ion or photon of incoming radiation. These fragmentation patterns can then form the basis for future mechanistic studies of the cell’s differential repair and signaling responses to varied break cluster types.

Research Impact/Earth Benefits:

Task Progress & Bibliography Information FY2021 
Task Progress: New project for FY2021.

Bibliography Type: Description: (Last Updated: )  Show Cumulative Bibliography Listing
 None in FY 2021