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Weir K, Vega N, Busa VF, Sajdak B, Kallestad L, Merriman D, Palczewski K, Carroll J, Blackshaw S. Identification of shared gene expression programs activated in multiple modes of torpor across vertebrate clades. Sci Rep 2024; 14:24360. [PMID: 39420030 PMCID: PMC11487170 DOI: 10.1038/s41598-024-74324-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 09/25/2024] [Indexed: 10/19/2024] Open
Abstract
Torpor encompasses diverse adaptations to extreme environmental stressors such as hibernation, aestivation, brumation, and daily torpor. Here we introduce StrokeofGenus, an analytic pipeline that identifies distinct transcriptomic states and shared gene expression patterns across studies, tissues, and species. We use StrokeofGenus to study multiple and diverse forms of torpor from publicly-available RNA-seq datasets that span eight species and two classes. We identify three transcriptionally distinct states during the cycle of heterothermia: euthermia, torpor, and interbout arousal. We also identify torpor-specific gene expression patterns that are shared both across tissues and between species with over three hundred million years of evolutionary divergence. We further demonstrate the general sharing of gene expression patterns in multiple forms of torpor, implying a common evolutionary origin for this process. Although here we apply StrokeofGenus to analysis of torpor, it can be used to interrogate any other complex physiological processes defined by transient transcriptomic states.
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Affiliation(s)
- Kurt Weir
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Genome Biology Unit, European Molecular Biology Laboratories, Heidelberg, Germany
| | - Natasha Vega
- Department of Biology, Johns Hopkins University Krieger School of Arts and Sciences, Baltimore, MD, USA
| | | | - Ben Sajdak
- Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, USA
- Fauna Bio, Emeryville, CA, USA
- Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Les Kallestad
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, 92697, USA
| | - Dana Merriman
- Biology, University of Wisconsin Oshkosh, Oshkosh, WI, USA
| | - Krzysztof Palczewski
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, 92697, USA
- Department of Chemistry, University of California Irvine, Irvine, CA, 92697, USA
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, 92697, USA
| | - Joseph Carroll
- Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, WI, USA
- Ophthalmology and Visual Sciences, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Seth Blackshaw
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Borg AM, Baker JE. Contemporary biomedical engineering perspective on volitional evolution for human radiotolerance enhancement beyond low-earth orbit. Synth Biol (Oxf) 2021; 6:ysab023. [PMID: 34522784 PMCID: PMC8434797 DOI: 10.1093/synbio/ysab023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 07/15/2021] [Accepted: 09/01/2021] [Indexed: 11/14/2022] Open
Abstract
A primary objective of the National Aeronautics and Space Administration (NASA) is expansion of humankind's presence outside low-Earth orbit, culminating in permanent interplanetary travel and habitation. Having no inherent means of physiological detection or protection against ionizing radiation, humans incur capricious risk when journeying beyond low-Earth orbit for long periods. NASA has made large investments to analyze pathologies from space radiation exposure, emphasizing the importance of characterizing radiation's physiological effects. Because natural evolution would require many generations to confer resistance against space radiation, immediately pragmatic approaches should be considered. Volitional evolution, defined as humans steering their own heredity, may inevitably retrofit the genome to mitigate resultant pathologies from space radiation exposure. Recently, uniquely radioprotective genes have been identified, conferring local or systemic radiotolerance when overexpressed in vitro and in vivo. Aiding in this process, the CRISPR/Cas9 technique is an inexpensive and reproducible instrument capable of making limited additions and deletions to the genome. Although cohorts can be identified and engineered to protect against radiation, alternative and supplemental strategies should be seriously considered. Advanced propulsion and mild synthetic torpor are perhaps the most likely to be integrated. Interfacing artificial intelligence with genetic engineering using predefined boundary conditions may enable the computational modeling of otherwise overly complex biological networks. The ethical context and boundaries of introducing genetically pioneered humans are considered.
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Affiliation(s)
- Alexander M Borg
- Departments of Biomedical Engineering and Radiation Oncology, Wake Forest University, Winston-Salem, NC, USA
| | - John E Baker
- Radiation Biosciences Laboratory, Medical College of Wisconsin, Milwaukee, WI, USA
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Hibernation as a Tool for Radiation Protection in Space Exploration. Life (Basel) 2021; 11:life11010054. [PMID: 33466717 PMCID: PMC7828799 DOI: 10.3390/life11010054] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/29/2020] [Accepted: 01/11/2021] [Indexed: 02/08/2023] Open
Abstract
With new and advanced technology, human exploration has reached outside of the Earth's boundaries. There are plans for reaching Mars and the satellites of Jupiter and Saturn, and even to build a permanent base on the Moon. However, human beings have evolved on Earth with levels of gravity and radiation that are very different from those that we have to face in space. These issues seem to pose a significant limitation on exploration. Although there are plausible solutions for problems related to the lack of gravity, it is still unclear how to address the radiation problem. Several solutions have been proposed, such as passive or active shielding or the use of specific drugs that could reduce the effects of radiation. Recently, a method that reproduces a mechanism similar to hibernation or torpor, known as synthetic torpor, has started to become possible. Several studies show that hibernators are resistant to acute high-dose-rate radiation exposure. However, the underlying mechanism of how this occurs remains unclear, and further investigation is needed. Whether synthetic hibernation will also protect from the deleterious effects of chronic low-dose-rate radiation exposure is currently unknown. Hibernators can modulate their neuronal firing, adjust their cardiovascular function, regulate their body temperature, preserve their muscles during prolonged inactivity, regulate their immune system, and most importantly, increase their radioresistance during the inactive period. According to recent studies, synthetic hibernation, just like natural hibernation, could mitigate radiation-induced toxicity. In this review, we see what artificial hibernation is and how it could help the next generation of astronauts in future interplanetary missions.
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