Chinese hamster V79 cells’ dependence on background ionizing radiation for optimal growth

Castillo, Hugo; Winder, Jeremy; Smith, Geoffrey B.

doi:10.1007/s00411-021-00951-5

Cited by 9 publications

(11 citation statements)

References 18 publications

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“…In the E. coli study, we used four independent biological replicates from each treatment and control, but we still got different numbers of DEGs with different softwares. In our experiment with these low radiation treatments and based on our previous results [ 22 , 24 , 35 ], we expected small changes in gene expression patterns. Hence, we think the maximum fold change of 3.5 from the DNAstar-D pipeline is the most realistic result, in contrast to the other programs’ 20–25-fold differences in expression.…”

Section: Discussionmentioning

confidence: 88%

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A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Thawng

Smith

2022

BMC Genomics

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Background In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (69–114 differentially expressed genes, DEGs), and so the rest of the analyses used this KCl vs “Minus” comparison. After imposing a 30-read minimum cutoff, one of the DNAStar options shared two of the three steps (mapping, normalization, and statistic) with Partek Flow (they both used median of ratios to normalize and the DESeq2 statistical package), and these two programs identified the highest number of DEGs in common with each other (53). In contrast, when the programs used different approaches in each of the three steps, between 31 and 40 DEGs were found in common. Regarding the extent of expression differences, three of the four programs gave high fold-change results (15–178 fold), but one (DNAstar’s DESeq2) resulted in more conservative fold-changes (1.5–3.5). In a parallel study comparing three qPCR commercial validation software programs, these programs also gave variable results as to which genes were significantly regulated. Similarly, the C. elegans analysis showed exaggerated fold-changes in CLC and DNAstar’s edgeR while DNAstar-D was more conservative. Conclusions Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses.

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Section: Discussionmentioning

confidence: 88%

“…Hopefully, the analysis presented here will have application to the analyses of other subtle but biologically important gene expression projects. Our previous results have documented that mammalian cells [ 24 ], and bacteria [ 22 , 25 ] exhibit a stress response to the absence of normal levels of radiation.…”

Section: Introductionmentioning

confidence: 99%

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Thawng

Smith

2022

BMC Genomics

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“…This effect appears after 5 days of incubation and lasts, intermittently, for up to 21 days. The data suggest that the sole emission of γ-rays from K-40 in KCl-amended controls is able to only partially rescue the V79’s viability, and although there is a clear differentiation between the underground and the surface controls, the authors argue that it could depend on differences among the radiation spectrum in the two conditions, although the experimental set up doesn’t allow for the exclusion of the potential influence of other environmental factors such as air pressure or gas composition [ 5 ].…”

Section: Resultsmentioning

confidence: 99%

“…Being among the most efficient places for experimental isolation from radiation, some DULs have become multidisciplinary sites hosting important studies in fields such as geology, geophysics, the climate, environmental, and space sciences, technology/instrumentation development, and radiobiology. So far, all biological studies carried out in DULs strongly indicate that the deprivation of natural background radiation affects, although to varied degrees, the growth and transcription profiles of bacteria as well as of unicellular and multicellular eukaryotes [ 1 , 4 , 5 , 6 , 7 ]. Moreover, several experiments indicate that cell cultures kept in this strongly reduced background show higher susceptibility to subsequent radiation-induced DNA damage than parallel cultures kept in external radiation background [ 8 , 9 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

Reduced Environmental Dose Rates Are Responsible for the Increased Susceptibility to Radiation-Induced DNA Damage in Larval Neuroblasts of Drosophila Grown inside the LNGS Underground Laboratory

Porrazzo

Esposito

Grifoni

et al. 2022

IJMS

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A large amount of evidence from radiobiology studies carried out in Deep Underground Laboratories support the view that environmental radiation may trigger biological mechanisms that enable both simple and complex organisms to cope with genotoxic stress. In line with this, here we show that the reduced radiation background of the LNGS underground laboratory renders Drosophila neuroblasts more sensitive to ionizing radiation-induced (but not to spontaneous) DNA breaks compared to fruit flies kept at the external reference laboratory. Interestingly, we demonstrate that the ionizing radiation sensitivity of flies kept at the LNGS underground laboratory is rescued by increasing the underground gamma dose rate to levels comparable to the low-LET reference one. This finding provides the first direct evidence that the modulation of the DNA damage response in a complex multicellular organism is indeed dependent on the environmental dose rate.

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“…Below-natural-background-radiation radiobiological studies deep underground that used various organisms have produced results that do not support the LNT model as applied to radiation-induced stochastic effects (e.g., mutations). 6 Additionally, neoplastic transformation in cultured cells was reduced rather than increased by above-natural-background-radiation, gamma-ray doses of 1 to 100 mGy. 7 Given the information provided in this publication, vanishing by design of cancer risk uncertainty for decreasing low radiation doses is misleading and unscientific.…”

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confidence: 99%

Vanishing by Design of Cancer Risk Uncertainty for Low Radiation Doses Is Misleading and Unscientific

Scott

2022

Dose-Response

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Chinese hamster V79 cells’ dependence on background ionizing radiation for optimal growth

Cited by 9 publications

References 18 publications

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Reduced Environmental Dose Rates Are Responsible for the Increased Susceptibility to Radiation-Induced DNA Damage in Larval Neuroblasts of Drosophila Grown inside the LNGS Underground Laboratory

Vanishing by Design of Cancer Risk Uncertainty for Low Radiation Doses Is Misleading and Unscientific

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