Multi-omic measurements of heterogeneity in HeLa cells across laboratories

Abstract

Reproducibility in research can be compromised by both biological and technical variation, but most of the focus is on removing the latter. Here we investigate the effects of biological variation in HeLa cell lines using a systems-wide approach. We determine the degree of molecular and phenotypic variability across 14 stock HeLa samples from 13 international laboratories. We cultured cells in uniform conditions and profiled genome-wide copy numbers, mRNAs, proteins and protein turnover rates in each cell line. We discovered substantial heterogeneity between HeLa variants, especially between lines of the CCL2 and Kyoto varieties, and observed progressive divergence within a specific cell line over 50 successive passages. Genomic variability has a complex, nonlinear effect on transcriptome, proteome and protein turnover profiles, and proteotype patterns explain the varying phenotypic response of different cell lines to Salmonella infection. These findings have implications for the interpretation and reproducibility of research results obtained from human cultured cells.

The fidelity of cancer cells in PDX models: Characteristics, mechanism and clinical significance

“…ITH in preclinical models affects experimental results and conclusions . Currently, PDX models are used extensively for drug testing and personalized medicine screening .…”

Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation

“…Furthermore, others and we have shown that the relationship between k loss and mRNA concentration is informative in understanding the protein turnover regulation between conditions (Schwanhausser et al , ; McShane et al , ; Liu et al , 2017a, ). By per‐gene relative analysis, we revealed that the protein degradation for subunits of heteromeric protein complexes was preferably regulated to buffer against the chromosomal aneuploidy impact due to trisomy 21 or high‐grade genomic instability between different HeLa cell strains (Liu et al , 2017a, ). However, to date, a detailed, systematic investigation of mRNA– k loss correlation has been still lacking.…”

“…For example, the protein‐specific degradation rates ( k loss as a proxy in steady state cells in this report, Materials and Methods) can now be quantified by “pulse labeling” with stable isotope‐labeled amino acids in cells, i.e., pulse SILAC (or pSILAC) technique (Pratt et al , ; Schwanhausser et al , , ; Eichelbaum & Krijgsveld, ; Jovanovic et al , ). At the absolute scale, previous pSILAC studies have repeatedly discovered that the protein turnover rate can be influenced by protein abundance, because higher abundant proteins normally tend to be less degraded (Claydon & Beynon, ; Liu et al , 2017a, ). Furthermore, others and we have shown that the relationship between k loss and mRNA concentration is informative in understanding the protein turnover regulation between conditions (Schwanhausser et al , ; McShane et al , ; Liu et al , 2017a, ).…”

“…At the absolute scale, previous pSILAC studies have repeatedly discovered that the protein turnover rate can be influenced by protein abundance, because higher abundant proteins normally tend to be less degraded (Claydon & Beynon, ; Liu et al , 2017a, ). Furthermore, others and we have shown that the relationship between k loss and mRNA concentration is informative in understanding the protein turnover regulation between conditions (Schwanhausser et al , ; McShane et al , ; Liu et al , 2017a, ). By per‐gene relative analysis, we revealed that the protein degradation for subunits of heteromeric protein complexes was preferably regulated to buffer against the chromosomal aneuploidy impact due to trisomy 21 or high‐grade genomic instability between different HeLa cell strains (Liu et al , 2017a, ).…”

“…Herein, we present an integrative analysis comprising of (i) a sensitive and reproducible data‐independent acquisition mass spectrometry (DIA‐MS) measurement (Gillet et al , ; Bruderer et al , ; Amon et al , ; Mehnert et al , ), (ii) an optimized pSILAC‐DIA workflow, (iii) a sample‐specific RNA‐Seq‐derived protein sequence database, and (iv) a novel transcript abundance directed strategy for calling and quantifying AS proteoforms. We then analyzed the protein turnover of differential AS groups across multiple HeLa cell lines collected from different laboratories (Liu et al , ). Our results at the isoform resolution demonstrate that the mRNA–protein degradation correlation has profound biological implications.…”