Extraction of Reduced Infrared Biomarker Signatures for the Stratification of Patients Affected by Parkinson’s Disease: An Untargeted Metabolomic Approach
Abstract
:1. Introduction
Aim of the Study
2. Materials and Methods
2.1. Study Population
2.2. Collection and Handling of Plasma Samples
2.3. Instrument
2.4. Pre-Processing of Spectra
2.5. Data Analysis
2.5.1. PCA
2.5.2. Classification Methods
- -
- Total classification (prediction) rate (TR)
- -
- Category c rate (Rc)
3. Results
3.1. FTIR Spectral Profiles
3.2. Global Classification: 3-Class Approach for Discriminating Patients with PD, AD, and Healthy Controls
3.3. PD Stratification: 2-Class Approach for Discriminating between Patients with Early-Stage PD and PD-Related Dementia
3.4. Dementia Type Differentiation: 2-Class Approach for Discriminating between Patients with PD-Related Dementia and Alzheimer’s Dementia
4. Discussion
Limit of the Study
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
Appendix A
Spectral Regions in Literature | Peak Position (cm−1) ± 1 | Tentative Band Assignment | Contributions |
---|---|---|---|
~1155 | 1156, 1159 | sym. (CO-O-C) | Carbohydrates |
~1185–1120 | 1171, 1182 | (C-C) and (O-P-O); (C-O) ring vibrations | Nucleic acid “sugars” |
~1225 | 1215 | asym. (O-P-O) | Nucleic acids, phospholipids |
~1250–1220 | 1253 | sym. (P = O) of the PO2 groups | Nucleic acids, phospholipids |
~1360–1220 | 1266, 1271, 1284, 1286, 1288, 1289, 1294, 1302, 1312, 1316, 1319, 1335, 1336, 1377 | (C-C) and (C-O) (C-N) and C-(NO2) sym. (PO2), predominantly (C-N) with significant contributions from (CH2) of carbohydrate residues, δ (CH2) | Amide III band, proteins |
~1370 | 1377 | sym. def. CH3 and sym. def. CH2 | Proteins, amino acids (cytosine, guanine, proline) lipids, phospholipids |
~1400 | 1403 | (C = O) of (COO) group | Fatty acids and amino acids |
~1420 | 1424 | sym. (COO), δ asym. (CH2) | Polysaccharides |
~1455–1450 | 1455 | δ asym. (CH3) and (CH2) modes | Proteins, lipids |
~1490–1470 | 1474, 1477, 1489 | δ (CH2) | Lipids |
Spectral Regions in Literature | Peak Position (cm−1) ± 1 | Tentative Band Assignment | Contributions |
---|---|---|---|
~1185–1120 | 1170, 1171 | (C-C) and (O-P-O); (C-O) ring vibrations | Nucleic acid “sugars” |
~1233 ~1225 | 1214, 1224, 1226 | asym. (O-P-O) | Nucleic acids; phospholipids; uric ring vibrations |
~1360–1220 | 1292, 1294, 1297, 1342 | ); sym. (PO2) predominantly (C-N) with significant contributions from (CH2) of carbohydrate residues; δ (CH2) | Amide III band; proteins; collagen |
~1420 | 1435, 1437 | sym. (COO); δ (CH2) | Polysaccharides |
~1455–1450 | 1443, 1445 | δ asym. (CH3) and (CH2) modes | Proteins; lipids |
~1490–1470 | 1475, 1476 | δ (CH2) | Lipids |
Spectral Regions in Literature | Peak Position (cm−1 | Tentative Band Assignment | Contributions |
---|---|---|---|
~1185–1120 | 1187, 1188 | (C-C) and (O-P-O) (C-O) ring vibrations | Nucleic acid “sugars” |
~1360–1220 | 1277 1340 | (C-C) and (C-O) ) sym. (PO2) (C-N) with significant contributions from (CH2) of carbohydrate residues, δ (CH2) | Amide III band; proteins; collagen |
~1370 | 1379, 1380, 1382 | sym. def. CH3 and sym. def. CH2 | Proteins; amino acids (cytosine, guanine, proline) Lipids; phospholipids |
~1405–1400 | 1402 | (C = O) of (COO) group (C = C) | Fatty acids; amino acids; (aspartate, glutamate) Uric acid |
~1490–1470 | 1487, 1488 | δ (CH2) | Lipids |
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3-Class Approach SELECT-LDA: Global Classification with 30 Variables | |||
---|---|---|---|
Classification % | Prediction (CV 10) % | External Prediction % | |
PD (I + D) | 100.00 | 86.36 | 100.00 |
AD | 99.79 | 89.58 | 100.00 |
Control group | 100.00 | 95.24 | 100.00 |
Total rate | 99.89 | 90.11 | 100.00 |
1st Step Differentiation Approach: 30 Biomarkers | |||
---|---|---|---|
3 Global Categories (PD, AD and HC) Differentiation | |||
Selection Order | Wavenumber (cm−1) | Selection Order | Wavenumber (cm−1) |
1 | 1489.9008 | 16 | 1336.5712 |
2 | 1171.6696 | 17 | 1289.3187 |
3 | 1316.3201 | 18 | 1335.6069 |
4 | 1377.0734 | 19 | 1253.6382 |
5 | 1319.6382 | 20 | 1182.2773 |
6 | 1312.4628 | 21 | 1203.4927 |
7 | 1284.4970 | 22 | 1474.4714 |
8 | 1271.9606 | 23 | 1302.8194 |
9 | 1266.1746 | 24 | 1455.1847 |
10 | 1215.0647 | 25 | 1294.1404 |
11 | 1156.2402 | 26 | 1334.6425 |
12 | 1159.1332 | 27 | 1438.7909 |
13 | 1443.1286 | 28 | 1477.3644 |
14 | 1286.4257 | 29 | 1424.3259 |
15 | 1288.3544 | 30 | 1403.1105 |
2-Class Approach SELECT-LDA: Parkinson’s Differentiation with 15 Variables | |||
---|---|---|---|
Classification % | Prediction (LOO) % | External Prediction % | |
PDI | 100.00 | 100.00 | 100.00 |
PDD | 100.00 | 100.00 | 100.00 |
Total rate | 100.00 | 100.00 | 100.00 |
2nd Step Differentiation Approach: 15 Biomarkers | |
---|---|
2 Categories (PDI and PDD) Differentiation | |
Selection Order | Wavenumber (cm−1) |
1 | 1294.1404 |
2 | 1292.2117 |
3 | 1437.8266 |
4 | 1435.8979 |
5 | 1443.6126 |
6 | 1475.4357 |
7 | 1297.0334 |
8 | 1476.4001 |
9 | 1342.3572 |
10 | 1170.7052 |
11 | 1171.6696 |
12 | 1226.6368 |
13 | 1445.5413 |
14 | 1224.7081 |
15 | 1214.1004 |
2nd-Class Approach SELECT-LDA: Dementia’s Type Differentiation with 10 Variables | |||
---|---|---|---|
Classification % | Prediction (CV 10) % | External Prediction % | |
PDD | 100.00 | 87.50 | 100.00 |
AD | 100.00 | 100.00 | 100.00 |
Total rate | 100.00 | 96.67 | 100.00 |
3rd Step Differentiation Approach: 10 Biomarkers | |
---|---|
2 Categories (PDD and AD) Differentiation | |
Selection order | Wavenumber (cm−1) |
1 | 1340.4286 |
2 | 1487.0078 |
3 | 1488.9365 |
4 | 1187.0990 |
5 | 1277.7466 |
6 | 1380.9307 |
7 | 1188.0633 |
8 | 1379.0020 |
9 | 1382.8594 |
10 | 1402.1461 |
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Tkachenko, K.; Espinosa, M.; Esteban-Díez, I.; González-Sáiz, J.M.; Pizarro, C. Extraction of Reduced Infrared Biomarker Signatures for the Stratification of Patients Affected by Parkinson’s Disease: An Untargeted Metabolomic Approach. Chemosensors 2022, 10, 229. https://doi.org/10.3390/chemosensors10060229
Tkachenko K, Espinosa M, Esteban-Díez I, González-Sáiz JM, Pizarro C. Extraction of Reduced Infrared Biomarker Signatures for the Stratification of Patients Affected by Parkinson’s Disease: An Untargeted Metabolomic Approach. Chemosensors. 2022; 10(6):229. https://doi.org/10.3390/chemosensors10060229
Chicago/Turabian StyleTkachenko, Kateryna, María Espinosa, Isabel Esteban-Díez, José M. González-Sáiz, and Consuelo Pizarro. 2022. "Extraction of Reduced Infrared Biomarker Signatures for the Stratification of Patients Affected by Parkinson’s Disease: An Untargeted Metabolomic Approach" Chemosensors 10, no. 6: 229. https://doi.org/10.3390/chemosensors10060229