Temporal-dependent effects of DNA degradation on frozen tissues archived at −80°C

Abstract

Abstract Frozen tissues, associated with natural history and biological collections, historically have been archived at temperatures between −20°C and −80°C. More recently, the availability of liquid nitrogen systems has enabled the storage of tissue samples (biobanking) at temperatures as low as −196°C. Currently, it is not known how the degree of coldness (e.g., −80°C or −196°C) or longevity (time in storage) impacts preservation of tissue samples. To examine the effects of long-term storage (−80°C and −196°C) on DNA degradation, tissue samples (muscle and liver) archived for 30, 20, 10, or 1 years were obtained from the Natural Science Research Laboratory at Texas Tech University. The integrity of DNA (measured as molecular weight and fragment length) extracted from samples was determined using automated DNA isolation methods followed by microfluidic distribution measurement. DNA distributions were compared using measures of central tendency, a regression-based molecular mass profile, and as a latent variable in a structural equation model. Muscle samples consistently outperformed liver samples in terms of quality of DNA yield. Also, muscle samples exhibited a significant linear relationship with time in which older samples were more degraded than were recent samples. The signal for a temporal effect on DNA was strongest when considering a latent variable of DNA quality based on mode and kurtosis; 37% of the variation in the latent variable was explained by variation in units of time. More recent time points tended to be more similar, but the temporal effect on the latent variable remained strong even when the oldest samples were removed from the analysis. In contrast, integrity of DNA from liver samples did not have a significant linear relationship with time; however, in some years they exhibited non-normally distributed DNA quality metrics that may have reflected sensitivity of liver tissue to degradation during specimen preparation, DNA extraction, or archive parameters. Results indicated that tissue type and temporal effects influenced rates of DNA degradation, with the latter emphasizing the long-term value of biobanking at the coldest temperatures possible (liquid nitrogen storage) to mitigate degradation of biological samples of ever-increasing scientific value.