Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica
Abstract
:1. Introduction
2. Materials and Methods
2.1. Participant
2.2. 28-Week Data Collection
2.3. Proteomics Procedures
2.4. Data Processing
2.5. Statistics
2.6. Protein–Protein Interaction Network Analysis
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
ACN | Acetonitrile |
AGC | Automatic gain control |
AmBiC | Ammonium bicarbonate |
APO | Apolipoprotein |
C5a | Complement 5a |
C8G | Complement C8 gamma |
CBG | Cortisol-binding globulin |
CRP | C-reactive protein |
DAMP | Danger-associated molecular pattern |
desARG | Des arginine |
DIA | Data independent acquisition |
DIA-NN | Data independent acquisition-neural networks |
DBS | Dried blood spot |
FA | Formic acid |
FDR | False discovery rate |
GEE | Generalized estimating equation |
GLMM | Generalized linear mixed models |
GO | Gene ontology |
HDL | High density lipoprotein |
IL-10 | Interleukin-10 |
LASSO | Least absolute shrinkage and selection operation |
LDLR | Low density lipoprotein receptor |
LIMMA | Linear models for microarray data |
MAC | Membrane attack complex |
NanoLC-MS/MS | Nano-electrospray ionization liquid chromatography tandem mass spectrometry |
NFOR | Nonfunctional overreaching |
OTS | Overtraining syndrome |
PPI | Protein–protein interaction |
RAAM | Race Across America |
sPLSda | Sparse partial least squares discriminant analysis |
STAT3 | Signal transducer and activator of transcription 3 |
STRING | Search tool for the retrieval of interacting genes/proteins |
TDS | Training distress scale |
TNF-α | Tumor necrosis factor alpha |
UPLC | Ultraperformance liquid chromatography |
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Gene | UniProt Identifier | Protein Description | Log-Fold Change | p-Value | Adjusted p-Value |
---|---|---|---|---|---|
APOE | P02649 | apolipoprotein E† | 1.856 | 0.000 | 0.000 |
GPX3 | P22352 | glutathione peroxidase 3† | 1.590 | 0.000 | 0.000 |
APOC3 | P02656 | apolipoprotein C3† | 1.574 | 0.000 | 0.001 |
APOD | P05090 | apolipoprotein D† | 1.559 | 0.000 | 0.000 |
HGFAC | Q04756 | HGF activator† | 1.467 | 0.000 | 0.006 |
APOC2 | P02655 | apolipoprotein C2† | 1.463 | 0.000 | 0.003 |
RBP4 | P02753 | retinol binding protein 4† | 1.412 | 0.000 | 0.001 |
APOM | O95445 | apolipoprotein M† | 0.984 | 0.000 | 0.007 |
HDHD2 | Q9H0R4 | haloacid dehalogenase like hydrolase domain containing 2† | 0.976 | 0.001 | 0.038 |
SERPINA4 | P29622 | serpin family A member 4; kallistatin† | 0.971 | 0.002 | 0.038 |
APOC1 | P02654 | apolipoprotein C1† | 0.970 | 0.000 | 0.003 |
SERPING1 | P05155 | serpin family G member 1; plasma protease C1 inhibitor† | 0.947 | 0.002 | 0.041 |
CLNS1A | P54105 | chloride nucleotide-sensitive channel 1A‡ | 0.898 | 0.007 | 0.076 |
HIST1H3A–J; H3F3A; H3F3B; HIST3H3; HIST2H3A,C,D | P68431; P84243; Q16695; Q71DI3 | histone cluster 1 H3 family member a–j;‡ H3 histone family members 3A,3B; ‡ histone cluster 3 H3; ‡ histone cluster 2 H3 family member a,c,d‡ | 0.897 | 0.006 | 0.074 |
C8G | P07360 | complement C8 gamma chain† | 0.864 | 0.008 | 0.086 |
C1R | P00736 | complement C1r† | 0.810 | 0.001 | 0.028 |
APOA1 | P02647 | apolipoprotein A1† | 0.797 | 0.000 | 0.001 |
CPN2 | P22792 | carboxypeptidase N subunit 2† | 0.793 | 0.002 | 0.038 |
CPN1 | P15169 | carboxypeptidase N subunit 1† | 0.763 | 0.002 | 0.041 |
AGT | P01019 | angiotensinogen† | 0.680 | 0.002 | 0.041 |
ITIH4 | Q14624 | inter-alpha-trypsin inhibitor heavy chain 4† | 0.648 | 0.001 | 0.033 |
PLG | P00747 | plasminogen† | 0.621 | 0.000 | 0.017 |
APOA2 | P02652 | apolipoprotein A2† | 0.603 | 0.000 | 0.019 |
AFM | P43652 | afamin† | 0.602 | 0.004 | 0.064 |
PON1 | P27169 | paraoxonase 1† | 0.590 | 0.002 | 0.042 |
SERPINA6 | P08185 | serpin family A member 6 (cortisol binding globulin) † | 0.585 | 0.001 | 0.034 |
A1BG | P04217 | alpha-1-B glycoprotein† | 0.577 | 0.001 | 0.038 |
C5 | P01031 | complement C5† | 0.547 | 0.003 | 0.054 |
TTR | P02766 | transthyretin† | 0.498 | 0.004 | 0.064 |
AZGP1 | P25311 | alpha-2-glycoprotein 1, zinc-binding† | 0.468 | 0.006 | 0.075 |
CLU | P10909 | clusterin† ‡ | 0.439 | 0.002 | 0.038 |
Gene | UniProt Identifier | Protein Description | Log-Fold Change | p-Value | Adjusted p-Value |
---|---|---|---|---|---|
ACLY | P53396 | ATP citrate lyase‡ | −0.274 | 0.008 | 0.088 |
YWHAE | P62258 | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon‡ | −0.287 | 0.004 | 0.065 |
ARF1; ARF3 | P61204; P84077 | ADP ribosylation factors 1,3‡ | −0.300 | 0.005 | 0.065 |
PSMC6 | P62333 | proteasome 26S subunit, ATPase 6‡ | −0.319 | 0.006 | 0.074 |
PSMD9 | O00233 | proteasome 26S subunit, non-ATPase 9‡ | −0.356 | 0.008 | 0.089 |
PSMC5 | P62195 | proteasome 26S subunit, ATPase 5‡ | −0.358 | 0.009 | 0.095 |
PA2G4 | Q9UQ80 | proliferation-associated 2G4‡ | −0.383 | 0.002 | 0.041 |
HSPA1A; HSPA1B | P08107 | heat shock protein family A (Hsp70) members 1A, 1B‡ | −0.386 | 0.003 | 0.045 |
XPO7 | Q9UIA9 | exportin 7‡ | −0.392 | 0.006 | 0.076 |
IL10 | P22301 | interleukin 10† | −0.408 | 0.006 | 0.074 |
CAPZA1 | P52907 | capping actin protein of muscle Z-line subunit alpha 1† | −0.432 | 0.000 | 0.017 |
IGLV1-47 | P01700 | immunoglobulin lambda variable 1-47† | −0.447 | 0.005 | 0.065 |
IGKC | P01834 | immunoglobulin kappa constant† | −0.472 | 0.002 | 0.044 |
LGALS3 | P17931 | galectin 3†‡ | −0.479 | 0.007 | 0.078 |
LCP1 | P13796 | lymphocyte cytosolic protein 1‡ | −0.480 | 0.002 | 0.043 |
CALM1,2,3 | P62158 | calmodulin 1,2,3‡ | −0.484 | 0.002 | 0.038 |
PCBP1 | Q15365 | poly(rC) binding protein 1‡ | −0.544 | 0.006 | 0.074 |
AHSP | Q9NZD4 | alpha hemoglobin stabilizing protein†‡ | −0.607 | 0.001 | 0.033 |
RGS10 | O43665-3 | regulator of G protein signaling 10‡ | −0.744 | 0.003 | 0.051 |
CPPED1 | Q9BRF8 | calcineurin like phosphoesterase domain containing 1†‡ | −0.773 | 0.003 | 0.052 |
DHRS11 | Q6UWP2 | dehydrogenase/reductase 11† ‡ | −0.794 | 0.005 | 0.071 |
ADK | P55263 | adenosine kinase‡ | −0.837 | 0.002 | 0.043 |
STMN2 | Q93045 | stathmin 2‡ | −0.860 | 0.001 | 0.024 |
FSCB | Q5H9T9 | fibrous sheath CABYR binding protein†‡ | −0.891 | 0.004 | 0.063 |
EEF2 | P13639 | eukaryotic translation elongation factor 2‡ | −0.897 | 0.000 | 0.006 |
YWHAB; YWHAG; YWHAQ | P31946; P61981; P27348 | tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein beta; gamma; theta‡ | −0.897 | 0.006 | 0.074 |
ITGB3 | P05106 | integrin subunit beta 3‡ | −1.081 | 0.004 | 0.059 |
RAB6A | P20340-2 | RAB6A, member RAS oncogene family‡ | −1.090 | 0.003 | 0.053 |
EEF1A1 | P68104; Q5VTE0 | eukaryotic translation elongation factor 1 alpha 1‡ | −1.190 | 0.001 | 0.033 |
HBM | Q6B0K9 | hemoglobin subunit mu‡ | −1.196 | 0.000 | 0.001 |
HIST1H2BB-K, M–O | P33778;P62807; P58876;Q93079; P06899;O60814; Q99879;Q99877; P23527;Q16778; Q5QNW6 | histone cluster 1 H2B family members b–k, m–o; ‡ cluster 2 H2B family members e,f‡ | −1.301 | 0.000 | 0.020 |
CLLU1OS | Q5K130 | chronic lymphocytic leukemia upregulated 1 opposite strand†‡ | −1.303 | 0.002 | 0.040 |
DYNC1H1 | Q14204 | dynein cytoplasmic 1 heavy chain 1‡ | −1.325 | 0.000 | 0.018 |
S100A9 | P06702 | S100 calcium binding protein A9† | −1.357 | 0.006 | 0.075 |
S100A8 | P05109 | S100 calcium binding protein A8† | −1.680 | 0.001 | 0.032 |
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Nieman, D.C.; Groen, A.J.; Pugachev, A.; Simonson, A.J.; Polley, K.; James, K.; El-Khodor, B.F.; Varadharaj, S.; Hernández-Armenta, C. Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica. Proteomes 2020, 8, 4. https://doi.org/10.3390/proteomes8010004
Nieman DC, Groen AJ, Pugachev A, Simonson AJ, Polley K, James K, El-Khodor BF, Varadharaj S, Hernández-Armenta C. Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica. Proteomes. 2020; 8(1):4. https://doi.org/10.3390/proteomes8010004
Chicago/Turabian StyleNieman, David C., Arnoud J. Groen, Artyom Pugachev, Andrew J. Simonson, Kristine Polley, Karma James, Bassem F. El-Khodor, Saradhadevi Varadharaj, and Claudia Hernández-Armenta. 2020. "Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica" Proteomes 8, no. 1: 4. https://doi.org/10.3390/proteomes8010004
APA StyleNieman, D. C., Groen, A. J., Pugachev, A., Simonson, A. J., Polley, K., James, K., El-Khodor, B. F., Varadharaj, S., & Hernández-Armenta, C. (2020). Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica. Proteomes, 8(1), 4. https://doi.org/10.3390/proteomes8010004