Transcriptome and proteome profiling to understanding the biology of high productivity CHO cells

被引:98
|
作者
Nissom, Peter Morin
Sanny, Arleen
Kok, Yee Jiun
Hiang, Yeo Thong
Chuah, Song Hui
Shing, Tan Kher
Lee, Yih Yean
Wong, Kathy Tin Kam
Hu, Wei-shou
Sim, Miranda Yap Gek
Philp, Robin
机构
[1] Bioproc Technol Inst, Singapore 138668, Singapore
[2] Univ Minnesota, Dept Chem Engn & Mat Sci, Minneapolis, MN 55455 USA
[3] Natl Univ Singapore, Dept Chem & Biomol Engn, Singapore 119260, Singapore
关键词
microarray; proteomics; Chinese hamster ovary; biotherapeutic; transcriptome; proteome;
D O I
10.1385/MB:34:2:125
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 S100a 11) 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.
引用
收藏
页码:125 / 140
页数:16
相关论文
共 50 条
  • [21] Transcriptome and proteome profiling of neural stem cells in the human subventricular zone after Parkinson's disease
    Donega, V.
    Burm, S.
    van Strien, M. E.
    van Bodegraven, E. J.
    Paliukhovic, I.
    van de Berg, W.
    Geut, H.
    Li, K. W.
    Smit, A. B.
    Basak, O.
    Hol, E. M.
    GLIA, 2019, 67 : E497 - E498
  • [22] Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources
    Cillingova, Andrea
    Toth, Renata
    Mojakova, Anna
    Zeman, Igor
    Vrzonova, Romana
    Sivakova, Barbara
    Barath, Peter
    Nebohacova, Martina
    Klepcova, Zuzana
    Brazdovic, Filip
    Lichancova, Hana
    Hodorova, Viktoria
    Brejova, Brona
    Vinar, Tomas
    Mutalova, Sofia
    Vozarikova, Veronika
    Mutti, Giacomo
    Tomaska, Lubomir
    Gacser, Atilla
    Gabaldon, Toni
    Nosek, Jozef
    PLOS GENETICS, 2022, 18 (03):
  • [23] Transcriptome/proteome analysis of captopril-induced gene expression profiling in the smooth muscle cells.
    Naka, M
    Zang, L
    Nishimura, Y
    Tsunoda, H
    Tanaka, T
    JOURNAL OF PHARMACOLOGICAL SCIENCES, 2003, 91 : 79P - 79P
  • [24] Transcriptome and proteome profiling of neural stem cells from the human subventricular zone in Parkinson's disease
    Donega, Vanessa
    Burm, Saskia M.
    van Strien, Miriam E.
    van Bodegraven, Emma J.
    Paliukhovich, Iryna
    Geut, Hanneke
    van de Berg, Wilma D. J.
    Li, Ka Wan
    Smit, August B.
    Basak, Onur
    Hol, Elly M.
    ACTA NEUROPATHOLOGICA COMMUNICATIONS, 2019, 7 (1) : 84
  • [25] Profiling the ubiquitinated proteome in human cells
    Diaz, Stephanie S.
    Liu, Xing
    FASEB JOURNAL, 2022, 36
  • [26] Transcriptome and proteome analysis of steady-state in a perfusion CHO cell culture process
    Bertrand, Vania
    Karst, Daniel J.
    Bachmann, Alessia
    Cantalupo, Katia
    Soos, Miroslav
    Morbidelli, Massimo
    BIOTECHNOLOGY AND BIOENGINEERING, 2019, 116 (08) : 1959 - 1972
  • [27] Proteome Profiling in Rat Cardiomyoblasts: Understanding Diabetic Cardiomyopathy
    Stratmann, Bernd
    Eggers, Britta
    Mattern, Yvonne
    Marcus, Katrin
    Tschoepe, Diethelm
    DIABETES, 2020, 69
  • [28] Glycoengineering in CHO Cells: Advances in Systems Biology
    Tejwani, Vijay
    Andersen, Mikael R.
    Nam, Jong Hyun
    Sharfstein, Susan T.
    BIOTECHNOLOGY JOURNAL, 2018, 13 (03)
  • [29] Microbial Proteome Profiling and Systems Biology: Applications to Mycobacterium tuberculosis
    Schubert, Olga T.
    Aebersold, Ruedi
    PROKARYOTIC SYSTEMS BIOLOGY, 2015, 883 : 235 - 254
  • [30] The Kidney Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling
    Habuka, Masato
    Fagerberg, Linn
    Hallstrom, Bjorn M.
    Kampf, Caroline
    Edlund, Karolina
    Sivertsson, Asa
    Yamamoto, Tadashi
    Ponten, Fredrik
    Uhlen, Mathias
    Odeberg, Jacob
    PLOS ONE, 2014, 9 (12):