Theranostics 2020; 10(2):898-909. doi:10.7150/thno.30204

Research Paper

Polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) method for gene methylation level detection in plasma

Xiaozhou Li1,2✉*, Tianyue Yang1,2*, Caesar Siqi Li3*, Youtao Song2✉, Deli Wang1, Lili Jin4, Hong Lou4, Wei Li5✉

1. School of Science, Shenyang Ligong University, Shenyang 110159, China
2. College of Environmental Sciences, Liaoning University, Shenyang 110036, China
3. College of Medicine, Northeast Ohio Medical University, Rootstown 44272, USA
4. School of Life Science, Liaoning University, Shenyang 110036, China
5. School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China
*Contributed equally.

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Citation:
Li X, Yang T, Li CS, Song Y, Wang D, Jin L, Lou H, Li W. Polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) method for gene methylation level detection in plasma. Theranostics 2020; 10(2):898-909. doi:10.7150/thno.30204. Available from http://www.thno.org/v10p0898.htm

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Abstract

Gene promoter hypermethylation is a vital step in tumorigenesis. This paper set out to explore the use of polymerase chain reaction - surface-enhanced Raman spectroscopy (PCR-SERS) for the detection of gene methylation levels, with a focus on cancer diagnosis.

Methods: PCR with methylation independent primers were used on DNA samples to amplify target genes regardless of their methylation states. SERS was used on the obtained PCR products to generate spectra that contained peak changes belonging to CG and AT base pairs. Multiple linear regression (MLR) was then used to deconvolute the SERS spectra so that the CG/AT ratios of the sample could be obtained. These MLR results were used to calculate methylation levels of the target genes. For protocol verification, three sets of seven reference DNA solutions with known methylation levels (0%, 1%, 5%, 25%, 50%, 75%, and 100%) were analysed. Clinically, blood plasma samples were taken from 48 non-small-cell lung cancer (NSCLC) patients and 51 healthy controls. The methylation levels of the genes p16, MGMT, and RASSF1 were determined for each patient using this method.

Results: Verification experiment on the mixtures with known methylation levels resulted in an error of less than 6% from the actual levels. When applied to our clinical samples, the frequency of methylation in at least one of the three target genes among the NSCLC patients was 87.5%, but this percentage decreased to 11.8% for the control group. The methylation levels of p16 were found to be significantly higher in NSCLC patients with more pack-years smoked (p=0.04), later cancer stages (p=0.03), and cancer types of squamous cell and large cell versus adenocarcinoma (p=0.03). Prediction accuracy of 88% was achieved from classification and regression trees (CART) based on methylation levels and states, respectively.

Conclusion: This research showed that the PCR-SERS protocol could quantitatively measure the methylation levels of genes in plasma. The methylation levels of the genes p16, MGMT, and RASSF1 were higher in NSCLC patients than in controls.

Keywords: PCR, methylation level, plasma, surface-enhanced Raman spectroscopy, SERS