Transcriptome and proteome profiling to understanding the biology of high productivity CHO cells.
A combined transcriptome and proteome analysis was carried out to identify key genes and proteins differentially expressed in Chinese hamster ovary (CHO) cells producing high and low levels of dhfr-GFP fusion protein. Comparison of transcript levels was performed using a proprietary 15K CHO cDNA microarray chip, whereas proteomic analysis was performed using iTRAQ quantitative protein profiling technique. Microarray analysis revealed 77 differentially expressed genes, with 53 genes upregulated and 24 genes downregulated. Proteomic analysis gave 75 and 80 proteins for the midexponential and stationary phase, respectively. Although there was a general lack of correlation between mRNA levels and quantitated protein abundance, results from both datasets concurred on groups of proteins/genes based on functional categorization. A number of genes (20%) and proteins (45 and 23%) were involved in processes related to protein biosynthesis. We also identified three genes/proteins involved in chromatin modification. Enzymes responsible for opening up chromatin, Hmgn3 and Hmgb1, were upregulated whereas enzymes that condense chromatin, histone H1.2, were downregulated. Genes and proteins that promote cell growth (Igfbp4, Ptma, S100a6, and Lgals3) were downregulated, whereas those that deter cell growth (Ccng2, Gsg2, and S100a11) were upregulated. Other main groups of genes and proteins include carbohydrate metabolism, signal transduction, and transport. Our findings show that an integrated genomic and proteomics approach can be effectively utilized to monitor transcriptional and posttranscriptional events of mammalian cells in culture.
Nissom
Peter Morin
PM
Bioprocessing Technology Institute, 20 Biopolis Way, #06-01 Centros, Singapore, 138668. peter_morin@bti.a-star.edu.sg
Sanny
Arleen
A
Kok
Yee Jiun
YJ
Hiang
Yeo Thong
YT
Chuah
Song Hui
SH
Shing
Tan Kher
TK
Lee
Yih Yean
YY
Wong
Kathy Tin Kam
KT
Hu
Wei-Shou
WS
Sim
Miranda Yap Gek
MY
Philp
Robin
R
D000818:Animals; D016466:CHO Cells / Q000378:metabolism*; D006224:Cricetinae; D003412:Cricetulus; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023281:Genomics; D049452:Green Fluorescent Proteins / Q000096:biosynthesis*; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis; D020543:Proteome / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis*; D013762:Tetrahydrofolate Dehydrogenase / Q000096:biosynthesis*; D014158:Transcription, Genetic
D020543:Proteome; D011993:Recombinant Fusion Proteins; D049452:Green Fluorescent Proteins; D013762:Tetrahydrofolate Dehydrogenase