Abstract
Non-small-cell lung cancer (NSCLC) constitutes approximately 80% of all diagnosed lung cancers, and diagnostic markers detectable in the plasma/serum of NSCLC patients are greatly needed. In this study, we established a pipeline for the discovery of markers using 9 transcriptome datasets from publicly available databases and profiling of six lung cancer cell secretomes. Thirty-one out of 312 proteins that overlapped between two-fold differentially expressed genes and identified cell secretome proteins were detected in the pooled plasma of lung cancer patients. To quantify the candidates in the serum of NSCLC patients, multiple-reaction-monitoring mass spectrometry (MRM-MS) was performed for five candidate biomarkers. Finally, two potential biomarkers (BCHE and GPx3; AUC = 0.713 and 0.673, respectively) and one two-marker panel generated by logistic regression (BCHE/GPx3; AUC = 0.773) were identified. A validation test was performed by ELISA to evaluate the reproducibility of GPx3 and BCHE expression in an independent set of samples (BCHE and GPx3; AUC = 0.630 and 0.759, respectively, BCHE/GPx3 panel; AUC = 0.788). Collectively, these results demonstrate the feasibility of using our pipeline for marker discovery and our MRM-MS platform for verifying potential biomarkers of human diseases.
| Original language | English |
|---|---|
| Article number | e0183896 |
| Journal | PloS one |
| Volume | 12 |
| Issue number | 8 |
| DOIs | |
| Publication status | Published - 2017 Aug |
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All Science Journal Classification (ASJC) codes
- Biochemistry, Genetics and Molecular Biology(all)
- Agricultural and Biological Sciences(all)
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Integrative analysis for the discovery of lung cancer serological markers and validation by MRM-MS. / Shin, Jihye; Song, Sang Yun; Ahn, Hee Sung; An, Byung Chull; Choi, Yoo Duk; Yang, Eun Gyeong; Na, Kook Joo; Lee, Seung Taek; Park, Jae Il; Kim, Seon Young; Lee, Cheolju; Lee, Seung won.
In: PloS one, Vol. 12, No. 8, e0183896, 08.2017.Research output: Contribution to journal › Article
TY - JOUR
T1 - Integrative analysis for the discovery of lung cancer serological markers and validation by MRM-MS
AU - Shin, Jihye
AU - Song, Sang Yun
AU - Ahn, Hee Sung
AU - An, Byung Chull
AU - Choi, Yoo Duk
AU - Yang, Eun Gyeong
AU - Na, Kook Joo
AU - Lee, Seung Taek
AU - Park, Jae Il
AU - Kim, Seon Young
AU - Lee, Cheolju
AU - Lee, Seung won
PY - 2017/8
Y1 - 2017/8
N2 - Non-small-cell lung cancer (NSCLC) constitutes approximately 80% of all diagnosed lung cancers, and diagnostic markers detectable in the plasma/serum of NSCLC patients are greatly needed. In this study, we established a pipeline for the discovery of markers using 9 transcriptome datasets from publicly available databases and profiling of six lung cancer cell secretomes. Thirty-one out of 312 proteins that overlapped between two-fold differentially expressed genes and identified cell secretome proteins were detected in the pooled plasma of lung cancer patients. To quantify the candidates in the serum of NSCLC patients, multiple-reaction-monitoring mass spectrometry (MRM-MS) was performed for five candidate biomarkers. Finally, two potential biomarkers (BCHE and GPx3; AUC = 0.713 and 0.673, respectively) and one two-marker panel generated by logistic regression (BCHE/GPx3; AUC = 0.773) were identified. A validation test was performed by ELISA to evaluate the reproducibility of GPx3 and BCHE expression in an independent set of samples (BCHE and GPx3; AUC = 0.630 and 0.759, respectively, BCHE/GPx3 panel; AUC = 0.788). Collectively, these results demonstrate the feasibility of using our pipeline for marker discovery and our MRM-MS platform for verifying potential biomarkers of human diseases.
AB - Non-small-cell lung cancer (NSCLC) constitutes approximately 80% of all diagnosed lung cancers, and diagnostic markers detectable in the plasma/serum of NSCLC patients are greatly needed. In this study, we established a pipeline for the discovery of markers using 9 transcriptome datasets from publicly available databases and profiling of six lung cancer cell secretomes. Thirty-one out of 312 proteins that overlapped between two-fold differentially expressed genes and identified cell secretome proteins were detected in the pooled plasma of lung cancer patients. To quantify the candidates in the serum of NSCLC patients, multiple-reaction-monitoring mass spectrometry (MRM-MS) was performed for five candidate biomarkers. Finally, two potential biomarkers (BCHE and GPx3; AUC = 0.713 and 0.673, respectively) and one two-marker panel generated by logistic regression (BCHE/GPx3; AUC = 0.773) were identified. A validation test was performed by ELISA to evaluate the reproducibility of GPx3 and BCHE expression in an independent set of samples (BCHE and GPx3; AUC = 0.630 and 0.759, respectively, BCHE/GPx3 panel; AUC = 0.788). Collectively, these results demonstrate the feasibility of using our pipeline for marker discovery and our MRM-MS platform for verifying potential biomarkers of human diseases.
UR - http://www.scopus.com/inward/record.url?scp=85028370400&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85028370400&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0183896
DO - 10.1371/journal.pone.0183896
M3 - Article
C2 - 28837649
AN - SCOPUS:85028370400
VL - 12
JO - PLoS One
JF - PLoS One
SN - 1932-6203
IS - 8
M1 - e0183896
ER -