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Project Title:  Epigenetic State Modulation of Radiation-Induced DNA Damage: Nanoscale Modeling and Validation Reduce
Images: icon  Fiscal Year: FY 2024 
Division: Human Research 
Research Discipline/Element:
HRP SR:Space Radiation
Start Date: 04/01/2021  
End Date: 04/15/2024  
Task Last Updated: 02/16/2024 
Download report in PDF pdf
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 
Email: vrisca@rockefeller.edu 
Phone: 516-728-3406  
Congressional District: 12 
Web:  
Organization Type: UNIVERSITY 
Organization Name: The Rockefeller University 
Joint Agency:  
Comments:  
Co-Investigator(s)
Affiliation: 
Plante, Ianik  Ph.D. NASA Johnson Space Center 
Jeevarajan, Antony  Ph.D. NASA Johnson Space Center 
Pickering, Karen  NASA Johnson Space Center 
Key Personnel Changes / Previous PI: Dr. Antony Jeevarajan requested that Dr. Karen Pickering be added as the institutional Co-Investigator.
Project Information: Grant/Contract No. 80NSSC21K0565 
Responsible Center: NASA JSC 
Grant Monitor: Elgart, Robin  
Center Contact: 281-244-0596 (o)/832-221-4576 (m) 
shona.elgart@nasa.gov 
Unique ID: 14349 
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: Yes 
No. of Post Docs:
No. of PhD Candidates:
No. of Master's Candidates:  
No. of Bachelor's Candidates:  
No. of PhD Degrees:  
No. of Master's Degrees:  
No. of Bachelor's Degrees:  
Human Research Program Elements: (1) SR:Space Radiation
Human Research Program Risks: (1) Cancer:Risk of Radiation Carcinogenesis
Human Research Program Gaps: (1) Cancer-303:Identify early surrogate biomarkers that correlate with cancer, pre-malignancy, or the hallmarks of cancer.
Flight Assignment/Project Notes: NOTE: End date changed to 04/15/2024 per V. Lehman/JSC (Ed., 4/25/23)

NOTE: End date changed to 03/31/2023 per NSSC information (Ed., 11/14/22)

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.

HYPOTHESIS

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.

DELIVERABLES

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: Our research develops technology for mapping DNA breaks caused by radiation onto the human genome and studies how the sensitivity to radiation varies across the human genome. Our data and methods will have direct applicability to determining cell type specific sensitivity to radiation therapy used to treat many cancers. We anticipate that our results will also aid cancer prevention here on Earth in addition to helping to advance our understanding of the health risks associated with space travel.

Task Progress & Bibliography Information FY2024 
Task Progress: In the last reporting period, we have characterized how the chromatin structure ensembles we generate with a coarse-grained chromatin model and Monte Carlo simulations depend on the geometric parameters of chromatin, namely nucleosome wrapping by DNA and spacing of nucleosomes along the DNA. We found that the spacing and wrapping parameters can be determined from synthetic RICC-seq data predicted from a large number of simulated structures using a simple regression model. These parameter estimates help us match simulated structures against experimental data from different epigenetic states and can be used to build chromatin structure ensembles based on nucleosome spacing measurements from a variety of orthogonal epigenomic methods, such as MNase-seq.

Continuing to work with the version of RITRACKS described in the last reporting period, we have made an additional update to add elastic scattering cross-sections for DNA and estimate them for amino acids.

We have then run simulations with photons and several different ions of varying LET values to benchmark the code against other codes and against experimental data. These simulations were performed with single nucleosomes. Chromatin fiber simulations with multiple nucleosomes and different densities of nucleosomes will be started in the next month.

We have performed simulations with and without histones and observed that the yield of DNA breaks is approximately twice without histones as with histones, showing that our simulation recapitulates the well-known role of histones in protecting genomic DNA from radiation. Although the yield of double-strand breaks (DSBs) without histones is higher than predicted by other codes and observed in experiments, when histones are incorporated, the RITRACKS predictions for DSB yield agree with the other codes and experiments.

On the experimental side, we have adapted two protocols for use with cells irradiated with ionizing radiation: END-seq, which maps DNA DSBs, and GLOE-seq, which maps DNA single-strand breaks (SSBs), onto genomic DNA coordinates. These methods use single-ended mapping of breaks and do not depend on regions of high break density or on spatially correlated breaks to generate DNA fragments that can be sequenced, in contrast to RICC-seq, the method we were using in the prior reporting period.

In pilot experiments with X-rays, we have shown that by combining these protocols with normalization by irradiated genomic DNA controls, we can obtain estimates of DNA break density by epigenetic state that is different from that in scrambled genomic feature controls.

Our results from X-ray and preliminary ion experiments indicate that the density of both SSBs and DSBs varies between epigenetic states by approximately 10%, with less compact states, such as active promoters, exhibiting the highest break densities.

We have performed 200 Gy gamma ray and Fe ion irradiations at NASA Space Radiation Laboratory (NSRL) on four cell types: K562 leukemia cells, BJ fibroblasts, IMR90 fibroblasts, and RPE-1 retinal pigment epithelial cells. The DNA sequencing libraries resulting from these experiments are still being processed and we anticipate that sequencing data will be available for analysis in late spring 2024.

Bibliography: Description: (Last Updated: 03/15/2024) 

Show Cumulative Bibliography
 
Abstracts for Journals and Proceedings Canaj H, Scortea A, West D, Plante I, Risca VI. "Mapping DNA damage propensity by low and high LET ionizing radiation with respect to epigenetic states." 2023 American Society for Cell Biology Annual Meeting, Boston, Massachusetts, December 2-6, 2023.

Abstracts. 2023 American Society for Cell Biology Annual Meeting, Boston, Massachusetts, December 2-6, 2023. , Dec-2023

Abstracts for Journals and Proceedings Plante I, Risca VI. "Simulation of radiation-induced DNA damage show histone protection." 2024 NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 13-16, 2024.

Abstracts. 2024 NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 13-16, 2024. , Feb-2024

Abstracts for Journals and Proceedings Canaj H, Scortea A, Rendleman J, West D, Plante I, Risca VI. "Mapping DNA damage propensity by ionizing radiation with respect to epigenetic states." 2024 NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 13-16, 2024.

Abstracts. 2024 NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 13-16, 2024. , Feb-2024

Articles in Peer-reviewed Journals Soroczynski J, Risca V. "Technological advances in probing 4D genome organization." Curr Opin Cell Biol. 2023 Oct 23;84:102211. https://doi.org/10.1016/j.ceb.2023.102211 ; PMID: 37556867 PMCID: PMC10588670. , Oct-2023
Project Title:  Epigenetic State Modulation of Radiation-Induced DNA Damage: Nanoscale Modeling and Validation Reduce
Images: icon  Fiscal Year: FY 2023 
Division: Human Research 
Research Discipline/Element:
HRP SR:Space Radiation
Start Date: 04/01/2021  
End Date: 04/15/2024  
Task Last Updated: 04/03/2023 
Download report in PDF pdf
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 
Email: vrisca@rockefeller.edu 
Phone: 516-728-3406  
Congressional District: 12 
Web:  
Organization Type: UNIVERSITY 
Organization Name: The Rockefeller University 
Joint Agency:  
Comments:  
Co-Investigator(s)
Affiliation: 
Plante, Ianik  Ph.D. NASA Johnson Space Center 
Jeevarajan, Antony  Ph.D. NASA Johnson Space Center 
Pickering, Karen  NASA Johnson Space Center 
Key Personnel Changes / Previous PI: Dr. Antony Jeevarajan requested that Dr. Karen Pickering be added as the institutional Co-Investigator.
Project Information: Grant/Contract No. 80NSSC21K0565 
Responsible Center: NASA JSC 
Grant Monitor: Elgart, Robin  
Center Contact: 281-244-0596 (o)/832-221-4576 (m) 
shona.elgart@nasa.gov 
Unique ID: 14349 
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: Yes 
No. of Post Docs:  
No. of PhD Candidates:
No. of Master's Candidates:  
No. of Bachelor's Candidates:  
No. of PhD Degrees:  
No. of Master's Degrees:  
No. of Bachelor's Degrees:  
Human Research Program Elements: (1) SR:Space Radiation
Human Research Program Risks: (1) Cancer:Risk of Radiation Carcinogenesis
Human Research Program Gaps: (1) Cancer-303:Identify early surrogate biomarkers that correlate with cancer, pre-malignancy, or the hallmarks of cancer.
Flight Assignment/Project Notes: NOTE: End date changed to 04/15/2024 per V. Lehman/JSC (Ed., 4/25/23)

NOTE: End date changed to 03/31/2023 per NSSC information (Ed., 11/14/22)

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.

HYPOTHESIS

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.

DELIVERABLES

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: Our research develops technology for mapping DNA breaks caused by radiation onto the human genome and studies how the sensitivity to radiation varies across the human genome. Our data and methods will have direct applicability to determining cell type specific sensitivity to radiation therapy used to treat many cancers. We anticipate that our results will also aid cancer prevention here on Earth in addition to helping to advance our understanding of the health risks associated with space travel.

Task Progress & Bibliography Information FY2023 
Task Progress: Over the last year, we have updated computational for studying how the local structure and epigenetic state of chromatin, the packaged form of DNA found in cells, affects the density and type of DNA breaks caused by space radiation. We have also performed experiments using gamma rays and ions at NASA Space Radiation Laboratory (NSRL) to determine how break density varies as a function of epigenetic state in two cell types.

1. We have updated the radiochemistry code in RITRACKS, a NASA-designed software tool that simulates DNA damage events caused by ionizing radiation to support two new types of interactions with DNA and amino acids. We are working on ensuring that the new RITRACKS produces double-strand DNA break yield estimates that are consistent with the experiment.

2. We used RITRACKS to demonstrate that it can reproduce experimentally observed protection of DNA by histone proteins.

3. We have validated coarse-grained simulations of chromatin against experimental results from in vitro reconstituted chromatin and generated ensembles of chromatin structures with constant or variable linker DNA lengths.

4. We have performed ion irradiations in two cell lines and obtained preliminary data for calculating the relative sensitivity of different genomic loci to DNA damage by photons and ions. We have encountered several technical challenges in making this measurement that we are now addressing by changing the DNA break mapping protocol and one of the two cell lines, from an endothelial cell to a fibroblast.

Bibliography: Description: (Last Updated: 03/15/2024) 

Show Cumulative Bibliography
 
Abstracts for Journals and Proceedings Plante I, West D, Risca VI. "Simulation of radiation-induced DNA damage using the code RITRACKS: initial results show histone protection." Radiation Research Society 68th Annual Meeting, Waikoloa Village, Hawaii, October 16-19, 2022.

Abstracts. Radiation Research Society 68th Annual Meeting, Waikoloa Village, Hawaii, October 16-19, 2022. , Oct-2022

Abstracts for Journals and Proceedings Plante I, West D, Risca VI. "Simulation of radiation-induced DNA damage show histone protection." NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 7, 2023.

Abstracts. NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 7, 2023. , Feb-2023

Abstracts for Journals and Proceedings Canaj H, Scortea A, West D, Plante I, Risca VI. "Heavy ion damage on chromatin: break mapping across genomic compartments." NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 7, 2023.

Abstracts. NASA Human Research Program Investigators' Workshop, Galveston, Texas, February 7, 2023. , Feb-2023

Articles in Peer-reviewed Journals Canaj H, Scortea A, West DW, Plante I, Risca VI. "Heavy ion damage on chromatin; break mapping across genomic compartments." Mol Biol Cell. 2023 Feb 1;34(2):ab1. https://doi.org/10.1091/mbc.E22-12-0555 ; PubMed PMID: 36637911; PubMed Central PMCID: PMC9930526 , Feb-2023
Articles in Peer-reviewed Journals Mansisidor AR, Risca VI. "Chromatin accessibility: methods, mechanisms, and biological insights." Nucleus. 2022 Dec;13(1):238-78. https://doi.org/10.1080/19491034.2022.2143106 ; PubMed PMID: 36404679; PubMed Central PMCID: PMC9683059 , Dec-2022
Project Title:  Epigenetic State Modulation of Radiation-Induced DNA Damage: Nanoscale Modeling and Validation Reduce
Images: icon  Fiscal Year: FY 2022 
Division: Human Research 
Research Discipline/Element:
HRP SR:Space Radiation
Start Date: 04/01/2021  
End Date: 03/31/2023  
Task Last Updated: 01/28/2022 
Download report in PDF pdf
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 
Email: vrisca@rockefeller.edu 
Phone: 516-728-3406  
Congressional District: 12 
Web:  
Organization Type: UNIVERSITY 
Organization Name: The Rockefeller University 
Joint Agency:  
Comments:  
Co-Investigator(s)
Affiliation: 
Plante, Ianik  Ph.D. NASA Johnson Space Center 
Jeevarajan, Antony  Ph.D. NASA Johnson Space Center 
Pickering, Karen  NASA Johnson Space Center 
Key Personnel Changes / Previous PI: Dr. Antony Jeevarajan requested that Dr. Karen Pickering be added as the institutional Co-Investigator.
Project Information: Grant/Contract No. 80NSSC21K0565 
Responsible Center: NASA JSC 
Grant Monitor: Elgart, Robin  
Center Contact: 281-244-0596 (o)/832-221-4576 (m) 
shona.elgart@nasa.gov 
Unique ID: 14349 
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: Yes 
No. of Post Docs:  
No. of PhD Candidates:
No. of Master's Candidates:  
No. of Bachelor's Candidates:  
No. of PhD Degrees:  
No. of Master's Degrees:  
No. of Bachelor's Degrees:  
Human Research Program Elements: (1) SR:Space Radiation
Human Research Program Risks: (1) Cancer:Risk of Radiation Carcinogenesis
Human Research Program Gaps: (1) Cancer-303:Identify early surrogate biomarkers that correlate with cancer, pre-malignancy, or the hallmarks of cancer.
Flight Assignment/Project Notes: NOTE: End date changed to 03/31/2023 per NSSC information (Ed., 11/14/22)

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.

HYPOTHESIS

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.

DELIVERABLES

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: Our research develops technology for mapping DNA breaks caused by radiation onto the human genome and studies how the sensitivity to radiation varies across the human genome. Our data and methods will have direct applicability to determining cell type specific sensitivity to radiation therapy used to treat many cancers. We anticipate that our results will also aid cancer prevention here on Earth in addition to helping to advance our understanding of the health risks associated with space travel.

Task Progress & Bibliography Information FY2022 
Task Progress: Over the last year, we have updated and begun to integrate key tools for studying how the local structure and epigenetic state of chromatin, the packaged form of DNA found in cells, affects the density and type of DNA breaks caused by space radiation.

1. We have updated the radiochemistry code in RITRACKS, a NASA-designed software tool that simulates DNA damage events caused by ionizing radiation. RITRACKS was originally designed primarily for heavy ions, but we have now added the capability to simulate photons as well. Furthermore, we have changed the RITRACKS output to make it possible to directly compare its predictions with the results of DNA sequencing experiments that analyze DNA break patterns in cultured cells.

2. We have significantly improved the protocol for RICC-seq, a method that uses DNA sequencing to map the location of single-strand DNA breaks caused by ionizing radiation onto the human genome. We have also optimized immunofluorescence methods for quantifying DNA damage in cells in advance of our upcoming irradiation experiments at the NASA Space Radiation Laboratory planned for spring 2022.

3. We have made significant progress toward building structural inference software that allows us to use DNA contact data to simulate chromatin structures that are consistent with DNA-DNA contact data sets for particular epigenetic states.

Bibliography: Description: (Last Updated: 03/15/2024) 

Show Cumulative Bibliography
 
 None in FY 2022
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 
Download report in PDF pdf
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 
Email: vrisca@rockefeller.edu 
Phone: 516-728-3406  
Congressional District: 12 
Web:  
Organization Type: UNIVERSITY 
Organization Name: The Rockefeller University 
Joint Agency:  
Comments:  
Co-Investigator(s)
Affiliation: 
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) 
shona.elgart@nasa.gov 
Unique ID: 14349 
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: Yes 
No. of Post Docs:  
No. of PhD Candidates:  
No. of Master's Candidates:  
No. of Bachelor's Candidates:  
No. of PhD Degrees:  
No. of Master's Degrees:  
No. of Bachelor's Degrees:  
Human Research Program Elements: (1) SR:Space Radiation
Human Research Program Risks: (1) Cancer:Risk of Radiation Carcinogenesis
Human Research Program Gaps: (1) Cancer-303:Identify early surrogate biomarkers that correlate with cancer, pre-malignancy, or the hallmarks of cancer.
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.

HYPOTHESIS

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.

DELIVERABLES

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: Description: (Last Updated: 03/15/2024) 

Show Cumulative Bibliography
 
 None in FY 2021