High resolution metabolomics to discriminate compounds in serum of male lung cancer patients in South Korea
© The Author(s). 2016
Received: 21 April 2016
Accepted: 2 August 2016
Published: 9 August 2016
The cancer death rate escalated during 20th century. In South Korea, lung cancer is expected to contribute 12,736 deaths in men, the highest amount among all cancers. Several risk factors may increase the chance to acquiring lung cancer, with mostly related to exogenous compounds found in cigarette smoke and synthetic manufacturing materials. As the mortality rate of lung cancer increases, deeper understanding is necessary to explore risk factors that may lead to this malignancy. In this regard, this study aims to apply high resolution metabolomics (HRM) using LC-MS to detect significant compounds that might contribute in inducing lung cancer and find the correlation of these compounds to the subjects’ smoking habit.
The comparison was made between healthy control and lung cancer groups for metabolic differences. Further analyses to determine if these differences are related to tobacco-induced lung cancer (past-smoker control vs. past-smoker lung cancer patients (LCPs) and non-smoker control vs. current-smoker LCPs) were selected. The univariate analysis was performed, including a false discovery rate (FDR) of q = 0.05, to determine the significant metabolites between the analyses. Hierarchical clustering analysis (HCA) was done to discriminate metabolites between the control and case subjects. Selected compounds based on significant m/z features of human serum then experienced MS/MS examination, showing that for many m/z, the patterns of ion dissociation matched with standards. Then, the significant metabolites were identified using Metlin database and features were mapped on the human metabolic pathway mapping tool of the Kyoto Encyclopedia of Genes and Genomes (KEGG).
Using metabolomics-wide association studies, metabolic changes were observed among control group and lung cancer patients. Bisphenol A (211.11, [M + H-H2O]+), retinol (287.23, [M + H]+) and L-proline (116.07, [M + H]+) were among the significant compounds found to have contributed in the discrimination between these groups, suggesting that these compounds might be related in the development of lung cancer. Retinol has been seen to have a correlation with smoking while both bisphenol A and L-proline were found to be unrelated.
Two potential biomarkers, retinol and L-proline, were identified and these findings may create opportunities for the development of new lung cancer diagnostic tools.
KeywordsHigh resolution metabolomics Lung cancer LC-MS Biomarker Bisphenol A Retinol L-proline
Cancer is a major public health problem that is currently one of the most leading causes of death in the United States. The cancer death rate escalated during the 20th century which was largely driven by rapid increases in lung cancer deaths as a consequence of tobacco epidemic. In 2015, the estimated number of cancer deaths in USA is dominated by lung cancer (27 % of all cancer deaths), surpassing prostate cancer for males (9 %) and breast cancer for females (15 %) . In South Korea, meanwhile, lung cancer is expected to contribute 12,736 deaths in men, the highest amount among all cancers . This increasing mortality rate in lung cancer patients has led physicians and scientists to seek a deeper understanding on this malignancy.
Lung cancer is a type of cancer that initially forms in lungs and can spread to nearby tissue even other organs, with the most recurrent metastatic sites were nervous system, bone, liver, respiratory system and adrenal gland . Several risk factors may increase the chance to acquiring lung cancer, with mostly related to exogenous compounds found in cigarette smoke and synthetic manufacturing materials . In fact, nine out of ten lung cancer cases are caused by smoking cigarettes . Moreover, smokers have a greater risk for lung cancer today than they did in 1964, even though they smoke fewer cigarettes.
There are several diagnostic tools that are available in detecting lung cancer such as computed tomography (CT), magnetic resonance imaging (MRI), and positron emission tomography (PET) [6–8]. However, lung cancer patients do not experience signs and symptoms at the early stages of the disease which lead to late diagnosis—often when the cancer has already progressed. Furthermore, there are no initial screening methods available to diagnose lung cancer at its early stages.
A study mentioned that early detection of lung cancer can be performed by NMR-based metabolomics method for urine samples . But the changes in metabolite levels in urine still cannot be correlated to compounds involved in lung cancer metabolism. Furthermore, metabolite levels in urine samples may vary depending on fluid intake prior to collection, and may also be affected by patients’ kidney function . Miyamoto et al. (2015) conducted plasma samples analysis using GC-MS in determining metabolic changes of endogenous compounds in lung cancer patients . However, the detection of exogenous compounds were not considered. Some other researches have dealt with respiratory diseases using NMR metabolomics like the study on electronic nose and exhaled breath , and on cystic fibrosis .
During the past decade, liquid chromatography coupled with mass spectrometry (LC-MS) has gone through huge development. The ability to determine thermolabile compounds directly without needing to undergo derivatization steps has given its advantage over gas chromatography (GC). With recently-developed configuration like quadrupole time-of-flight (Q-TOF), the range of screening has quickly expanded, enhancing both high mass resolution and mass fragmentation [14, 15].
Due to the disadvantages of urine samples mentioned earlier, this study aims to explore and identify significant compounds, exogenous and endogenous, that may induce cancer using LC-MS based high resolution metabolomics (HRM) on human serum samples from South Korean males for the purpose of providing early detection and non-invasive diagnosis of lung cancer. The significant compounds found to contribute in the discrimination between healthy and lung cancer subjects will also be confirmed and their correlation with smoking habit will be examined.
Age, Sex, Height, and Weight of Patients
Lung Cancer patients
Number of subjects
60.60 ± 10.03
60.60 ± 10.10
168.58 ± 5.51
165.94 ± 6.19
68.82 ± 8.05
64.77 ± 9.84
24.20 ± 2.46
23.41 ± 2.57
Sample preparation and LC-MS measurements
Fifty μl aliquots of samples were treated with acetonitrile (1:4, v/v), and centrifuged at 14,000 x g for 5 min at 4 °C for protein separating . Samples were analyzed using Ultra Performance Liquid Chromatography system (Agilent 1260 Infinity Quaternary, Agilent, Santa Clara, CA, USA) with iFunnel Q-TOF mass spectrometry (Agilent Q-TOF 6550, Agilent, Santa Clara, CA, USA) in duplicates. This LC-MS/MS is ideally suited for metabolic stability and profiling studies, since this system has the highest sensitivity to detect compounds at low pg/mL levels and 40 k resolving power to determine excellent mass and isotope accuracy for confident identification of metabolites.
An electrospray interface was operated in positive ion mode. The conditions for the acquisition parameters were: gas temperature 250 °C, drying gas 14 ml/min, nebulizer pressure 35 psig, sheath gas temperature 250 °C and sheath gas flow 11 ml/min . Mobile phase A consisted of 0.1 % formic acid in water (HPLC grade, Tedia, Ohio, USA) and mobile phase B was 0.1 % formic acid in acetonitrile (HPLC grade, Tedia, Ohio, USA). The gradient was programed as follows: 0–1 min: 5 % for B, 1–9 min: gradient increase to 5 % for B, 9–12 min: hold 56 % for B, 12–13.5 min: 90 % for B; 13.5–13.6 min: hold 5 % for B. The column heater was adjusted at 30 °C. The flow rate was 0.4 L/min. Three microliter of sample was injected on to a 1.9 μm, 100x2.1 mm C18 column (Thermo, Waltham, USA) . Detection of m/z of ions from 50 to 1000 with 20,000 resolution over 15 min LC runs with data extraction using apLCMS  provides a minimum of 3000 reproducible features, many with sufficient mass accuracy to allow prediction of elemental composition. Ion intensity, m/z, and retention time defined an m/z feature. Meanwhile, selected compounds based on significant m/z features of human serum then experienced MS/MS examination using LC-MS triple quad (QQQ) 6490 (Agilent, CA, USA), showing that for many m/z, the patterns of ion dissociation matched with standards.
Metabolic profiling with univariate and multivariate statistical analysis
After running high resolution, accurate mass system of Q-TOF, raw data were processed using apLCMS producing the total features from the samples for the subsequent analyses. In performing statistical analyses and bioinformatics, features from duplicate LC-MS analyses were averaged, log2 transformed and normalized using z-transformation. It included univariate analysis, Manhattan plot, and false discovery rate (FDR)  using Limma R package  to determine the significant metabolites between healthy controls and lung cancer patients. Additionally, the metabolic profiles were discriminated using two-way hierarchical cluster analysis (HCA) to separate two groups in connection with metabolites . Limma is originally a package for the analysis of gene expression data arising from microarray or RNA-Seq technologies. It provides the ability to compare between many targets simultaneously [23, 24]. Moreover, classification of samples based on significant metabolites levels was done using receiver operating characteristic (ROC) curves (MedCalc).
Data annotation and pathway analysis
The significant metabolites were then annotated using Metlin Metabolite Database . These metabolites were listed in a batch containing their m/z value, name and formula, which could be sorted based on the availability of Kyoto Encyclopedia of Genes and Genomes (KEGG) number. Using this number, the metabolites were queried into the human metabolic pathway . Detected features that matched known human intermediary metabolites are shown as black dots in the map.
Manhattan plot and two-way hierarchical cluster analysis (HCA)
Using metabolomics-wide association studies (MWAS), metabolic changes in lung cancer patients were determined. A Manhattan plot utilizes statistical tests to visually identify significant features which are differentially expressed in subjects when compared to a control group. FDR adjustment, a multiple testing correction method which adjusts p-values (q-values) to reduce the occurrences of false positives was also used for optimum statistical significance.
In control vs LCPs analysis, the significant features were 6096 out of the 9516 total detected features, as shown in Fig. 2a. On the other hand, 5727 significant features were seen from the 11,234 total features in non-smoker control vs current-smoker LCPs group (Fig. 2c) while 6289 significant features out of the 12,349 total features were detected in past-smoker control vs past-smoker LCPs analysis (Fig. 2e). Furthermore, two-way HCA was performed to identify which metabolites are the most important for sample grouping. A clear separation of the control and case groups is expected in a dataset with distinct components. As seen in Fig. 2 (b, d, and f), the control group which is represented by the red panel is grouped as one cluster while the others (green panel) are on the other side of the clustering. This apparent separation in the heatmaps suggest that the metabolites are highly differentiated from the control.
KEGG pathway analysis
Identification and verification of potential biomarkers
Main compounds contributing for the discrimination in each comparison group
(n = 70)
(n = 22)
(n = 35)
(n = 35)
(n = 19)
(n = 14)
This study explored lung cancer-specific low molecular weight compounds that may have potential roles in inducing the disease and can be used as candidate biomarkers for the early diagnosis of lung cancer. Using serum samples from all patients, three compounds: BPA, retinol, and L-proline were identified as statistically significant compounds and were correlated to the subjects’ smoking habit.
BPA is used in the production of polycarbonate plastics which is the main ingredient of many manufactured goods such as toys, drinking containers, food cans, eyeglass lenses and electronic appliances [27–29]. It was found to be significant only in past smoker control vs. past smoker LCPs analysis (as shown in Additional file 9). With this finding, it is possible that this compound may induce lung cancer but it is not related to the smoking history of the subjects. Since it was detected insignificant under non-smoker control vs. current-smoker LCPs analysis group, it can be inferred that BPA may have come from other sources (e.g. plastic products, food cans) and not from cigarettes. Previous studies have mentioned several possible roles of BPA in carcinogenesis [30–32]. Although having a BPA concentration of less than 10−4 M had not triggered the proliferation process of lung cancer cells, it had stimulated in vitro migration and invasion of the cells via up-regulation of matrix metalloproteinase-2 which could enhance the susceptibility to carcinogenesis. Another study showed that BPA could alter Peroxisome Proliferator-activated Receptors (PPARs), in this case, the PPARγ. This ligand-activated transcription factor was found to induce differentiation and apoptosis in lung cancer cells. As its antagonist, BPA promoted prevention of apoptosis, resulting the survival of cancer cells [30–32]. In addition, BPA concentration in human samples was correlated with intracranial tumor  and prostate cancer .
Vitamin A, on one hand, is also one of the selected metabolites observed to be differentially expressed in the comparison groups. This vitamin comes from carotenoid and retinoid. Basically, carotenoids are known for their antioxidant effects and are derived from plants . Retinoid are physiological regulators of embryonic development, vision, reproduction, bone formation, hematopoiesis, differentiation, proliferation and apoptosis . Retinol was found to be effective against breast, prostate, and ovarian cancers in animal treatment models. Also, the ability of retinol to induce apoptosis suggested that it is potential in prevention and treatment of lung cancer and other types of cancer . In this study, detection of retinol was significantly less in current-smoker patients as compared to non-smoker control (as shown in Additional file 9). Therefore, it is suggested that the level of retinol in the body may have been decreased in patients who smoke, thus increasing their risks in having the disease. In addition, using control and LCPs comparison, KEGG mapping displayed vitamin digestion and absorption as one of the affected human pathway. This finding was consistent with previous reports. Cigarette smoke could induce depletion of retinol serum levels in rats, as demonstrated by Li et al. . It was further investigated to be correlated with the development of emphysema. In addition, Yuan et al. revealed that low level of serum retinol is associated with the increase of lung cancer risk in China population .
Meanwhile, L-proline, a non-essential amino acid, was found to be lowered in LCPs, confirming a previously reported study . Zhao et al. reported that L-proline was one of the amino acid which its plasma concentration was found to be decreased in LCPs, compared with control group (p < 0.001). Rapid increase in the transcription of proline dehydrogenase by tumor suppressor p53 triggered the degradation of this amino acid in cancer . In addition, using control and LCPs comparison, KEGG mapping displayed biosynthesis of amino acids as one of the affected human pathway. As shown in Additional file 9, the decreasing L-proline occurred in all parameters that were analyzed, suggesting that this compound is possible to act as biomarker for lung cancer, regardless of smoking habit.
In summary, two potential biomarkers, retinol and L-proline, were identified using HRM with the combination of pathway analysis from significant metabolites that were found in serum samples of Korean male LCPs. It was also seen that one of them was correlated to smoking habit of LCPs. In addition, one exogenous compound, BPA, which has not been linked yet to lung cancer patients was demonstrated as significant feature that contributed to discriminate healthy and LCPs groups, regardless of smoking habit. These findings may create opportunities for the development of new lung cancer diagnostic tools. In the future, correlations to disease type, stage, also the applicability to female test subjects group may also be conducted. Also, further study using larger population should be conducted.
BPA, bisphenol A; FDR, false discovery rate; HCA, hierarchical cluster analysis; HRM, high resolution metabolomics; KEGG, kyoto encyclopedia of genes and genomes; LCPs, lung cancer patients; Q-TOF, quadrupole time-of-flight
The authors thank Ryan De Sotto and Carl Medriano for providing different insights and comments for the manuscript. ADP gratefully acknowledges Indonesia Endowment Fund for Education (LPDP) for the financial support of his master degree scholarship.
This study was supported by the National Research Foundation of Korea (NRF) Grant # NRF-2014R1A1A2053787 and KHIDI Grant # HI14C2686 Korea University.
Availability of data and material
The datasets during and/or analysed during the current study available from the corresponding author on reasonable request.
YHP, SL, and SHJ designed the study. YHP, ADP, and CP carried out the metabolomics experiments and comprehensive data analysis while SHJ organized the cohort study (Korean Cancer Prevention Study II). YHP, ADP, and CP prepared the manuscript. All authors read and approved the final manuscript.
The authors declare that they have no competing interests.
Consent for publication
Ethics approval and consent to participate
The study was approved by the Institutional Review Board of Yonsei University (2001-0029-011) and an informed consent was obtained from all participating patients.
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