Dylan G Chitwood1, Qinghua Wang2, Kathryn Elliott1, Aiyana Bullock3, Dwon Jordana4, Zhigang Li5, Cathy Wu2, Sarah W Harcum1, Christopher A Saski6. 1. Department of Bioengineering, College of Engineering, Computing and Applied Sciences, Clemson University, Clemson, SC, 29634, USA. 2. Center for Bioinformatics & Computational Biology, University of Delaware, Newark, DE, 19716, USA. 3. Department of Biological Sciences, College of Agriculture, Science & Technology, Delaware State University, Dover, DE, 19901, USA. 4. Department of Biological Sciences, Grambling State University, Grambling, LA, 71245, USA. 5. Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA. 6. Department of Plant and Environmental Sciences, College of Agriculture, Forestry and Life Sciences, Clemson University, Clemson, SC, 29634, USA. saski@clemson.edu.
Abstract
BACKGROUND: As bioprocess intensification has increased over the last 30 years, yields from mammalian cell processes have increased from 10's of milligrams to over 10's of grams per liter. Most of these gains in productivity can be attributed to increasing cell densities within bioreactors. As such, strategies have been developed to minimize accumulation of metabolic wastes, such as lactate and ammonia. Unfortunately, neither cell growth nor biopharmaceutical production can occur without some waste metabolite accumulation. Inevitably, metabolic waste accumulation leads to decline and termination of the culture. While it is understood that the accumulation of these unwanted compounds imparts a suboptimal culture environment, little is known about the genotoxic properties of these compounds that may lead to global genome instability. In this study, we examined the effects of high and moderate extracellular ammonia on the physiology and genomic integrity of Chinese hamster ovary (CHO) cells. RESULTS: Through whole genome sequencing, we discovered 2394 variant sites within functional genes comprised of both single nucleotide polymorphisms and insertion/deletion mutations as a result of ammonia stress with high or moderate impact on functional genes. Furthermore, several of these de novo mutations were found in genes whose functions are to maintain genome stability, such as Tp53, Tnfsf11, Brca1, as well as Nfkb1. Furthermore, we characterized microsatellite content of the cultures using the CriGri-PICR Chinese hamster genome assembly and discovered an abundance of microsatellite loci that are not replicated faithfully in the ammonia-stressed cultures. Unfaithful replication of these loci is a signature of microsatellite instability. With rigorous filtering, we found 124 candidate microsatellite loci that may be suitable for further investigation to determine whether these loci may be reliable biomarkers to predict genome instability in CHO cultures. CONCLUSION: This study advances our knowledge with regards to the effects of ammonia accumulation on CHO cell culture performance by identifying ammonia-sensitive genes linked to genome stability and lays the foundation for the development of a new diagnostic tool for assessing genome stability.
BACKGROUND: As bioprocess intensification has increased over the last 30 years, yields from mammalian cell processes have increased from 10's of milligrams to over 10's of grams per liter. Most of these gains in productivity can be attributed to increasing cell densities within bioreactors. As such, strategies have been developed to minimize accumulation of metabolic wastes, such as lactate and ammonia. Unfortunately, neither cell growth nor biopharmaceutical production can occur without some waste metabolite accumulation. Inevitably, metabolic waste accumulation leads to decline and termination of the culture. While it is understood that the accumulation of these unwanted compounds imparts a suboptimal culture environment, little is known about the genotoxic properties of these compounds that may lead to global genome instability. In this study, we examined the effects of high and moderate extracellular ammonia on the physiology and genomic integrity of Chinese hamsterovary (CHO) cells. RESULTS: Through whole genome sequencing, we discovered 2394 variant sites within functional genes comprised of both single nucleotide polymorphisms and insertion/deletion mutations as a result of ammonia stress with high or moderate impact on functional genes. Furthermore, several of these de novo mutations were found in genes whose functions are to maintain genome stability, such as Tp53, Tnfsf11, Brca1, as well as Nfkb1. Furthermore, we characterized microsatellite content of the cultures using the CriGri-PICR Chinese hamster genome assembly and discovered an abundance of microsatellite loci that are not replicated faithfully in the ammonia-stressed cultures. Unfaithful replication of these loci is a signature of microsatellite instability. With rigorous filtering, we found 124 candidate microsatellite loci that may be suitable for further investigation to determine whether these loci may be reliable biomarkers to predict genome instability in CHO cultures. CONCLUSION: This study advances our knowledge with regards to the effects of ammonia accumulation on CHO cell culture performance by identifying ammonia-sensitive genes linked to genome stability and lays the foundation for the development of a new diagnostic tool for assessing genome stability.
Authors: C R Boland; S N Thibodeau; S R Hamilton; D Sidransky; J R Eshleman; R W Burt; S J Meltzer; M A Rodriguez-Bigas; R Fodde; G N Ranzani; S Srivastava Journal: Cancer Res Date: 1998-11-15 Impact factor: 12.701
Authors: Julia Feichtinger; Inmaculada Hernández; Christoph Fischer; Michael Hanscho; Norbert Auer; Matthias Hackl; Vaibhav Jadhav; Martina Baumann; Peter M Krempl; Christian Schmidl; Matthias Farlik; Michael Schuster; Angelika Merkel; Andreas Sommer; Simon Heath; Daniel Rico; Christoph Bock; Gerhard G Thallinger; Nicole Borth Journal: Biotechnol Bioeng Date: 2016-04-29 Impact factor: 4.530