Method for high-throughput screening of non-target biomarkers based on metabolic perturbation caused by pollutants

Patent metadata

Field	Value
Publication number	US-11226318-B2
Application number	US-202017050455-A
Country	US
Kind code	B2
Filing date	May 18, 2020
Priority date	Apr 26, 2020
Publication date	Jan 18, 2022
Grant date	Jan 18, 2022

Abstract

Disclosed is a method for high-throughput screening of non-target biomarkers based on metabolic disturbance caused by pollutants, belonging to the field of environmental exposure and health. The method includes the following steps: (1) extracting to obtain extracts to be tested; (2) performing chromatographic analysis to obtain a spectrum containing chromatographic peaks; (3) identifying and labeling features of pollutants, taking chromatographic peaks other than the features of the pollutants as features of potential metabolites, and performing non-target labeling of the features of the potential metabolites; (4) establishing a linear regression model by taking the peak areas of the features of the potential metabolites as dependent variables and the peak areas of the features of the pollutants as independent variables; (5) operating the model, and performing non-target screening of the biomarkers to preliminarily obtain related biomarkers; (6) identifying the MS spectra and MS/MS spectra of the preliminarily obtained biomarkers, and identifying biomarkers related to pollutant exposure. The disclosed method improves the accuracy of biomarker screening and the throughput of biomarker screening.

First claim

What is claimed is:

1. A method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants, comprising the following steps:
(1) performing sample treatment, and extracting pollutants and metabolites from biological samples to obtain extracts to be tested;
(2) performing scan analysis and detection of the extracts to be tested through a high performance liquid chromatography—time-of-flight mass spectrometer to obtain a spectrum containing chromatographic peaks;
(3) identifying and labeling features of pollutants according to the spectrum, taking chromatographic peaks other than the features of the pollutants as features of the potential metabolites, and performing non-target labeling of the features of the potential metabolites;
(4) establishing a linear regression model by taking the peak areas of the features of the potential metabolites as dependent variables and the peak areas of the features of the pollutants as independent variables;
(5) operating the model to perform non-target screening of the biomarkers, obtaining related biomarkers by preliminary screening; and
(6) identifying the mass spectrometry (MS) spectra and Tandem mass spectrometry (MS/MS) spectra of the biomarkers obtained in step (5), and identifying biomarkers related to pollutant exposure.

2. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 1 , wherein the method further comprises step (7): using a correction method to correct the model, operating the corrected model, and repeating steps (5)-(6).

3. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 2 , wherein the correction method comprises false discovery rate (FDR) correction and interference factor correction; in the process of the FDR correction, threshold p<0.05 is corrected to be FDR<20%; and in the process of the interference factor correction, interference factors existing in samples are added to the model as covariates for correction.

4. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 2 , wherein when the extracts to-be-tested contain multiple pollutants, the correction method comprises a co-exposure correction method comprised of taking multiple pollutants as potential independent variables to perform multiple stepwise regression and model correction.

5. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 4 , wherein in the process of identifying the features of the pollutants, the spectrum is converted into a data file, and the peaks in the data file are imported into a Mass Spec data interrogation software and aligned for analysis to identify the pollutants.

6. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 5 , wherein in the process of non-target labeling of the features of the potential metabolites, the spectrum is converted into a backup file, the peaks in the backup file are imported into a software program for untargeted metabolomics and aligned, and the features with detection rate greater than 80% are retained as the features of the potential metabolites.

7. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 4 , wherein in step (4), the model with significance p<0.05 after operation is taken as an effective model to implement the operation process of step (5).

8. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 7 , wherein in step (6), a software program for untargeted metabolomics and an internet-based metabolite identification platform are combined to identify the biomarkers.

9. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 8 , wherein in step (2), the adopted detection conditions are as follows:
high performance liquid chromatographic instrument: Infinity1260;
chromatographic column: C18 column: 2.1 mm×50 mm, 2.5 μm;
column temperature: 40° C.;
flow rate: 0.4 mL/min;
mobile phase: phase A in positive ion mode: 0.1% formic acid-aqueous solution; phase A in negative ion mode: 2 mM ammonium acetate aqueous solution; and phase B: methanol;
the gradient elution conditions are as follows:

Time (min)
A %
B %

1.00
95
5

11.00
75
25

19.00
50
50

25.00
25
75

29.00
0
100

32.00
0
100

32.01
95
5

36.00
100
0

full scan mode: data dependence mode;
ion source: positive and negative electrospray ionization source;
full scan mass range: MS 50-1250 Da, MS/MS 30-1000 Da;
collision energy: ±40 eV;
collision energy spread: 20 eV;
ion source temperature: 550° C.

10. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 2 , wherein the method further comprises the step of metabolic pathway enrichment of the biomarkers, and in this step, the identified biomarkers are enriched into metabolic pathways to obtain metabolic pathways disturbed by pollutants.

11. The method for screening of non-target biomarkers based on a metabolic disturbance caused by pollutants according to claim 1 , wherein the method further comprises the step of metabolic pathway enrichment of the biomarkers, and in this step, the identified biomarkers are enriched into metabolic pathways to obtain metabolic pathways disturbed by pollutants.

Assignees

• Nanjing University Of Technology

Inventors

• Wei Si
• Li Yuqian
• Yu Hongxia
• Yu Nanyang

Classifications

• G01N33/6848

  Methods of protein analysis involving mass spectrometry · CPC title

• G01N30/06

  Preparation · CPC title

• G16B40/10 Primary

  Signal processing, e.g. from mass spectrometry [MS] or from PCR · CPC title

• G16B35/20

  Screening of libraries · CPC title

• G01N30/7233

  interfaced to liquid or supercritical fluid chromatograph (interfaces in general for introducing or extracting samples to be analysed with specially adapted mass spectrometer, see H01J49/04) · CPC title