Olarerin-George Anthony O, Hogenesch John B
Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA.
Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
Nucleic Acids Res. 2015 Mar 11;43(5):2535-42. doi: 10.1093/nar/gkv136. Epub 2015 Feb 24.
Mycoplasmas are notorious contaminants of cell culture and can have profound effects on host cell biology by depriving cells of nutrients and inducing global changes in gene expression. Over the last two decades, sentinel testing has revealed wide-ranging contamination rates in mammalian culture. To obtain an unbiased assessment from hundreds of labs, we analyzed sequence data from 9395 rodent and primate samples from 884 series in the NCBI Sequence Read Archive. We found 11% of these series were contaminated (defined as ≥100 reads/million mapping to mycoplasma in one or more samples). Ninety percent of mycoplasma-mapped reads aligned to ribosomal RNA. This was unexpected given 37% of contaminated series used poly(A)-selection for mRNA enrichment. Lastly, we examined the relationship between mycoplasma contamination and host gene expression in a single cell RNA-seq dataset and found 61 host genes (P < 0.001) were significantly associated with mycoplasma-mapped read counts. In all, this study suggests mycoplasma contamination is still prevalent today and poses substantial risk to research quality.
支原体是细胞培养中臭名昭著的污染物，可通过剥夺细胞营养和诱导基因表达的整体变化对宿主细胞生物学产生深远影响。在过去二十年中，定点检测揭示了哺乳动物细胞培养中广泛的污染率。为了从数百个实验室获得无偏差的评估，我们分析了NCBI序列读取存档中884个系列的9395个啮齿动物和灵长类动物样本的序列数据。我们发现这些系列中有11%受到污染（定义为一个或多个样本中每百万映射到支原体的读数≥100）。90%的支原体映射读数与核糖体RNA对齐。考虑到37%受污染的系列使用聚腺苷酸选择来富集mRNA，这是出乎意料的。最后，我们在一个单细胞RNA测序数据集中检查了支原体污染与宿主基因表达之间的关系，发现61个宿主基因（P < 0.001）与支原体映射读数计数显著相关。总之，这项研究表明支原体污染如今仍然普遍存在，对研究质量构成重大风险。
