Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates

Jun Seok Kim, Youngju Lee, Min Young Lee, Jihye Shin, Jung Min Han, Eun Gyeong Yang, Myeong Hee Yu, Sunghoon Kim, Daehee Hwang, Cheolju Lee

Research output: Contribution to journalArticle

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Abstract

Lung cancer-related transcription factors (TFs) were identified by integrating previously reported genomic, transcriptomic, and proteomic data and were quantified by multiple reaction monitoring (MRM) in various cell lines. All experiments were performed without affinity depletion or subfractionation of cell lysates. Since the target proteins were expected to be present in low abundance, we experimentally optimized MRM transition parameters with chemically synthesized peptides. Quantitation was based on stable isotope-labeled standard peptides (SIS peptides). Out of 288 MRM measurements (36 peptides representing 28 TFs × 8 cell lines), 241 were successfully obtained within a quantitation limit of 15 amol, 221 measurements (91.7%) showed coefficients of variation (CVs) of ≤20%, and 149 (61.8%) showed CVs of ≤10%, quantifying as low as 19.4 amol/μg protein for STAT2 with a CV of 6.3% in an A549 cell. Comparisons between MRM measurements and levels of the corresponding mRNAs revealed linear, nonlinear, or no relationship between protein and mRNA levels, indicating the need for an MRM assay. An integrative analysis of MRM and gene expression profiles from doxorubicin-resistant H69AR and sensitive H69 cells further showed that 14 differentially expressed TFs, such as STAT1 and SMAD4, regulated genes associated with drug resistance and cell differentiation-related processes. Thus, the analytical performance of MRM for the quantitation of low abundance TFs suggests its usefulness for biological application.

Original languageEnglish
Pages (from-to)2582-2596
Number of pages15
JournalJournal of Proteome Research
Volume12
Issue number6
DOIs
Publication statusPublished - 2013 Jul 1

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Lung Neoplasms
Transcription Factors
Cells
Peptides
STAT2 Transcription Factor
Monitoring
Cell Line
Messenger RNA
Transcriptome
Drug Resistance
Isotopes
Proteomics
Doxorubicin
Cell Differentiation
Proteins
Genes
Gene expression
Assays
Pharmaceutical Preparations
Experiments

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Chemistry(all)

Cite this

Kim, Jun Seok ; Lee, Youngju ; Lee, Min Young ; Shin, Jihye ; Han, Jung Min ; Yang, Eun Gyeong ; Yu, Myeong Hee ; Kim, Sunghoon ; Hwang, Daehee ; Lee, Cheolju. / Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates. In: Journal of Proteome Research. 2013 ; Vol. 12, No. 6. pp. 2582-2596.
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abstract = "Lung cancer-related transcription factors (TFs) were identified by integrating previously reported genomic, transcriptomic, and proteomic data and were quantified by multiple reaction monitoring (MRM) in various cell lines. All experiments were performed without affinity depletion or subfractionation of cell lysates. Since the target proteins were expected to be present in low abundance, we experimentally optimized MRM transition parameters with chemically synthesized peptides. Quantitation was based on stable isotope-labeled standard peptides (SIS peptides). Out of 288 MRM measurements (36 peptides representing 28 TFs × 8 cell lines), 241 were successfully obtained within a quantitation limit of 15 amol, 221 measurements (91.7{\%}) showed coefficients of variation (CVs) of ≤20{\%}, and 149 (61.8{\%}) showed CVs of ≤10{\%}, quantifying as low as 19.4 amol/μg protein for STAT2 with a CV of 6.3{\%} in an A549 cell. Comparisons between MRM measurements and levels of the corresponding mRNAs revealed linear, nonlinear, or no relationship between protein and mRNA levels, indicating the need for an MRM assay. An integrative analysis of MRM and gene expression profiles from doxorubicin-resistant H69AR and sensitive H69 cells further showed that 14 differentially expressed TFs, such as STAT1 and SMAD4, regulated genes associated with drug resistance and cell differentiation-related processes. Thus, the analytical performance of MRM for the quantitation of low abundance TFs suggests its usefulness for biological application.",
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Kim, JS, Lee, Y, Lee, MY, Shin, J, Han, JM, Yang, EG, Yu, MH, Kim, S, Hwang, D & Lee, C 2013, 'Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates', Journal of Proteome Research, vol. 12, no. 6, pp. 2582-2596. https://doi.org/10.1021/pr3011414

Multiple reaction monitoring of multiple low-abundance transcription factors in whole lung cancer cell lysates. / Kim, Jun Seok; Lee, Youngju; Lee, Min Young; Shin, Jihye; Han, Jung Min; Yang, Eun Gyeong; Yu, Myeong Hee; Kim, Sunghoon; Hwang, Daehee; Lee, Cheolju.

In: Journal of Proteome Research, Vol. 12, No. 6, 01.07.2013, p. 2582-2596.

Research output: Contribution to journalArticle

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