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Bailey SM, Cross EM, Kinner-Bibeau L, Sebesta HC, Bedford JS, Tompkins CJ. Monitoring Genomic Structural Rearrangements Resulting from Gene Editing. J Pers Med 2024; 14:110. [PMID: 38276232 PMCID: PMC10817574 DOI: 10.3390/jpm14010110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/13/2024] [Indexed: 01/27/2024] Open
Abstract
The cytogenomics-based methodology of directional genomic hybridization (dGH) enables the detection and quantification of a more comprehensive spectrum of genomic structural variants than any other approach currently available, and importantly, does so on a single-cell basis. Thus, dGH is well-suited for testing and/or validating new advancements in CRISPR-Cas9 gene editing systems. In addition to aberrations detected by traditional cytogenetic approaches, the strand specificity of dGH facilitates detection of otherwise cryptic intra-chromosomal rearrangements, specifically small inversions. As such, dGH represents a powerful, high-resolution approach for the quantitative monitoring of potentially detrimental genomic structural rearrangements resulting from exposure to agents that induce DNA double-strand breaks (DSBs), including restriction endonucleases and ionizing radiations. For intentional genome editing strategies, it is critical that any undesired effects of DSBs induced either by the editing system itself or by mis-repair with other endogenous DSBs are recognized and minimized. In this paper, we discuss the application of dGH for assessing gene editing-associated structural variants and the potential heterogeneity of such rearrangements among cells within an edited population, highlighting its relevance to personalized medicine strategies.
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Affiliation(s)
- Susan M. Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Erin M. Cross
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | | | - Henry C. Sebesta
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
| | - Joel S. Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO 80523, USA;
- KromaTiD, Inc., Longmont, CO 80501, USA; (E.M.C.); (L.K.-B.); (H.C.S.)
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Bailey SM, Luxton JJ, McKenna MJ, Taylor LE, George KA, Jhavar SG, Swanson GP. Ad Astra - telomeres in space! Int J Radiat Biol 2021; 98:395-403. [PMID: 34270368 DOI: 10.1080/09553002.2021.1956010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE My journey to the stars began as I - along with the whole world - stood still and watched Neil Armstrong take those first small steps on the Moon. Fast forward 50 years and NASA astronauts Scott Kelly and Christina Koch each spend nearly a year in space aboard the International Space Station (ISS), a remarkable multinational collaborative project and floating U.S. National Laboratory that has supported continuous human presence in low Earth orbit for the past 20 years. Marking a new era of human space exploration, the first commercial rocket, SpaceX Falcon 9, recently launched NASA astronauts Doug Hurley and Bob Behnken in the Crew Dragon spacecraft Endeavor to the ISS and returned safely to Earth. NASA and its commercial partners are rapidly advancing innovative space technologies, and with the recently announced Artemis team of astronauts, plans to send the first woman and next man back to the moon and establish sustainable exploration by the end of the decade. Humankind will then be poised to take the next giant leap - pioneering human exploration of Mars. CONCLUSIONS Historically, fewer than 600 individuals have participated in spaceflight, the vast majority of whom have been middle aged males (35-55 years) on short duration missions (less than 20 days). Thus, as the number and diversity of space travelers increase, a better understanding of how long-duration spaceflight affects human health is essential to maintaining individual astronaut performance during, and improving disease and aging trajectories following, future exploration missions. Here, I review findings from our NASA Twins Study and Telomeres investigations, highlighting potential mechanistic roles of chronic space radiation exposure in changes in telomere length and persistent DNA damage responses associated with long-duration spaceflight. Importantly, similar trends were observed in prostate cancer patients undergoing intensity-modulated radiation therapy (IMRT), additional support specifically for the role of radiation exposure. Individual differences in response were also observed in both cohorts, underscoring the importance of developing personalized approaches for evaluating human health effects and long-term outcomes associated with radiation exposures, whether on Earth or living in the extreme environment of space.
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Affiliation(s)
- Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Jared J Luxton
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Miles J McKenna
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA.,Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Lynn E Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
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Luxton JJ, McKenna MJ, Taylor LE, George KA, Zwart SR, Crucian BE, Drel VR, Garrett-Bakelman FE, Mackay MJ, Butler D, Foox J, Grigorev K, Bezdan D, Meydan C, Smith SM, Sharma K, Mason CE, Bailey SM. Temporal Telomere and DNA Damage Responses in the Space Radiation Environment. Cell Rep 2020; 33:108435. [PMID: 33242411 DOI: 10.1016/j.celrep.2020.108435] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 11/04/2020] [Indexed: 02/08/2023] Open
Abstract
Telomeres, repetitive terminal features of chromosomes essential for maintaining genome integrity, shorten with cell division, lifestyle factors and stresses, and environmental exposures, and so they provide a robust biomarker of health, aging, and age-related diseases. We assessed telomere length dynamics (changes over time) in three unrelated astronauts before, during, and after 1-year or 6-month missions aboard the International Space Station (ISS). Similar to our results for National Aeronautics and Space Administration's (NASA's) One-Year Mission twin astronaut (Garrett-Bakelman et al., 2019), significantly longer telomeres were observed during spaceflight for two 6-month mission astronauts. Furthermore, telomere length shortened rapidly after return to Earth for all three crewmembers and, overall, telomere length tended to be shorter after spaceflight than before spaceflight. Consistent with chronic exposure to the space radiation environment, signatures of persistent DNA damage responses were also detected, including mitochondrial and oxidative stress, inflammation, and telomeric and chromosomal aberrations, which together provide potential mechanistic insight into spaceflight-specific telomere elongation.
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Affiliation(s)
- Jared J Luxton
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Miles J McKenna
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Lynn E Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | | | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | | | - Viktor R Drel
- Center for Renal Precision Medicine, UT Health, San Antonio, TX, USA
| | - Francine E Garrett-Bakelman
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA; Department of Medicine, University of Virginia, Charlottesville, VA, USA; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Matthew J Mackay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Kirill Grigorev
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | | | - Kumar Sharma
- Center for Renal Precision Medicine, UT Health, San Antonio, TX, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA.
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Luxton JJ, McKenna MJ, Lewis A, Taylor LE, George KA, Dixit SM, Moniz M, Benegas W, Mackay MJ, Mozsary C, Butler D, Bezdan D, Meydan C, Crucian BE, Zwart SR, Smith SM, Mason CE, Bailey SM. Telomere Length Dynamics and DNA Damage Responses Associated with Long-Duration Spaceflight. Cell Rep 2020; 33:108457. [PMID: 33242406 DOI: 10.1016/j.celrep.2020.108457] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/31/2020] [Accepted: 11/06/2020] [Indexed: 12/12/2022] Open
Abstract
Telomere length dynamics and DNA damage responses were assessed before, during, and after one-year or shorter duration missions aboard the International Space Station (ISS) in a comparatively large cohort of astronauts (n = 11). Although generally healthy individuals, astronauts tended to have significantly shorter telomeres and lower telomerase activity than age- and sex-matched ground controls before and after spaceflight. Although telomeres were longer during spaceflight irrespective of mission duration, telomere length shortened rapidly upon return to Earth, and overall astronauts had shorter telomeres after spaceflight than they did before; inter-individual differences were identified. During spaceflight, all crewmembers experienced oxidative stress, which positively correlated with telomere length dynamics. Significantly increased frequencies of chromosomal inversions were observed during and after spaceflight; changes in cell populations were also detected. We propose a telomeric adaptive response to chronic oxidative damage in extreme environments, whereby the telomerase-independent Alternative Lengthening of Telomeres (ALT) pathway is transiently activated in normal somatic cells.
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Affiliation(s)
- Jared J Luxton
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Miles J McKenna
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA
| | - Aidan Lewis
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Lynn E Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | | | - Sameer M Dixit
- Center for Molecular Dynamics - Nepal (CMDN), Kathmandu, Nepal
| | | | | | - Matthew J Mackay
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Daniela Bezdan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Brian E Crucian
- Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
| | - Sara R Zwart
- University of Texas Medical Branch, Galveston, TX, USA
| | - Scott M Smith
- Human Health and Performance Directorate, NASA Johnson Space Center, Houston, TX, USA
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA; The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA; Cell and Molecular Biology Program, Colorado State University, Fort Collins, CO, USA.
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McKenna MJ, Robinson E, Taylor L, Tompkins C, Cornforth MN, Simon SL, Bailey SM. Chromosome Translocations, Inversions and Telomere Length for Retrospective Biodosimetry on Exposed U.S. Atomic Veterans. Radiat Res 2019; 191:311-322. [PMID: 30714852 PMCID: PMC6492561 DOI: 10.1667/rr15240.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
It has now been over 60 years since U.S. nuclear testing was conducted in the Pacific islands and Nevada, exposing military personnel to varying levels of ionizing radiation. Actual doses are not well-established, as film badges in the 1950s had many limitations. We sought a means of independently assessing dose for comparison with historical film badge records and dose reconstruction conducted in parallel. For the purpose of quantitative retrospective biodosimetry, peripheral blood samples from 12 exposed veterans and 12 age-matched (>80 years) veteran controls were collected and evaluated for radiation-induced chromosome damage utilizing directional genomic hybridization (dGH), a cytogenomics-based methodology that facilitates simultaneous detection of translocations and inversions. Standard calibration curves were constructed from six male volunteers in their mid-20s to reflect the age range of the veterans at time of exposure. Doses were estimated for each veteran using translocation and inversion rates independently; however, combining them by a weighted-average generally improved the accuracy of dose estimations. Various confounding factors were also evaluated for potential effects on chromosome aberration frequencies. Perhaps not surprisingly, smoking and age-associated increases in background frequencies of inversions were observed. Telomere length was also measured, and inverse relationships with both age and combined weighted dose estimates were observed. Interestingly, smokers in the non-exposed control veteran cohort displayed similar telomere lengths as those in the never-smoker exposed veteran group, suggesting that chronic smoking had as much effect on telomere length as a single exposure to radioactive fallout. Taken together, we find that our approach of combined chromosome aberration-based retrospective biodosimetry provided reliable dose estimation capability, particularly on a group average basis, for exposures above statistical detection limits.
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Affiliation(s)
- Miles J. McKenna
- Cell and Molecular Biology Program Colorado State University, Fort Collins, Colorado
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado
- KromaTiD, Inc., Fort Collins, Colorado
| | | | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado
| | | | - Michael N. Cornforth
- Cell and Molecular Biology Program Colorado State University, Fort Collins, Colorado
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, Texas
| | - Steven L. Simon
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Susan M. Bailey
- Cell and Molecular Biology Program Colorado State University, Fort Collins, Colorado
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado
- KromaTiD, Inc., Fort Collins, Colorado
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McKenna MJ, Robinson E, Goodwin EH, Cornforth MN, Bailey SM. Telomeres and NextGen CO-FISH: Directional Genomic Hybridization (Telo-dGH™). Methods Mol Biol 2017; 1587:103-112. [PMID: 28324502 DOI: 10.1007/978-1-4939-6892-3_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The cytogenomics-based methodology of Directional Genomic Hybridization (dGH™) emerged from the concept of strand-specific hybridization, first made possible by Chromosome Orientation FISH (CO-FISH), the utility of which was demonstrated in a variety of early applications, often involving telomeres. Similar to standard whole chromosome painting (FISH), dGH™ is capable of identifying inter-chromosomal rearrangements (translocations between chromosomes), but its distinctive strength stems from its ability to detect intra-chromosomal rearrangements (inversions within chromosomes), and to do so at higher resolution than previously possible. dGH™ brings together the strand specificity and directionality of CO-FISH with sophisticated bioinformatics-based oligonucleotide probe design to unique sequences. dGH™ serves not only as a powerful discovery tool-capable of interrogating the entire genome at the megabase level-it can also be used for high-resolution targeted detection of known inversions, a valuable attribute in both research and clinical settings. Detection of chromosomal inversions, particularly small ones, poses a formidable challenge for more traditional cytogenetic approaches, especially when they occur near the ends or telomeric regions. Here, we describe Telo-dGH™, a strand-specific scheme that utilizes dGH™ in combination with telomere CO-FISH to differentiate between terminal exchange events, specifically terminal inversions, and an altogether different form of genetic recombination that often occurs near the telomere, namely sister chromatid exchange (SCE).
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Affiliation(s)
- Miles J McKenna
- Department of Environmental & Radiological Health Sciences, Colorado State University, 437 MRB Bldg., 1681 Campus Delivery, Fort Collins, CO, 80523, USA
- KromaTiD Inc., 320 East Vine Drive, Fort Collins, CO, 80524, USA
| | - Erin Robinson
- KromaTiD Inc., 320 East Vine Drive, Fort Collins, CO, 80524, USA
| | - Edwin H Goodwin
- KromaTiD Inc., 320 East Vine Drive, Fort Collins, CO, 80524, USA
| | - Michael N Cornforth
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Susan M Bailey
- Department of Environmental & Radiological Health Sciences, Colorado State University, 437 MRB Bldg., 1681 Campus Delivery, Fort Collins, CO, 80523, USA.
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