Proteomics of Primary Uveal Melanoma: Insights into Metastasis and Protein Biomarkers
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. Primary UM Tumor Samples
2.2. Proteomic Characterization of the Choroid Controls
2.3. pUM Quantitative Proteomics Overview
2.4. Independent Evidence Supporting the iTRAQ Protein Quantitation
2.5. Identification of Differentially Expressed Proteins
2.6. Bioinformatic Differences between Metastasizing and Non-Metastasizing pUM
2.7. Immune Protein Profiling
2.8. Prediction Modeling
3. Discussion
4. Materials and Methods
4.1. Specimens
4.2. Sample Preparation
4.3. ITRAQ Labeling and Peptide Fractionation
4.4. Protein Identification
4.5. Protein Quantitation
4.6. Statistical Analysis
4.7. Bioinformatics
4.8. Western Blot Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Metastasizing | Non-Metastasizing | |
---|---|---|
Total pUM specimens | 53 | 47 |
Total Proteins Quantified with ≥2 peptides | 3935 | 3934 |
Average number proteins quantified per tumor | 2567 | 2541 |
Proteins Elevated ≥ 1SD from Mean, adjusted p ≤ 0.05, imputation ≤ 20% | 232 | 224 |
Proteins Decreased ≥ 1SD from Mean, adjusted p ≤ 0.05, imputation ≤ 20% | 206 | 201 |
UniProt Accession | Gene Name | Protein (Sorted by Decreasing Protein Ratio) | Protein Ratio Met/NoMet | Adjusted p-Value | Frequency | |
---|---|---|---|---|---|---|
Metastasizing pUM | Non-Metastasizing pUM | |||||
DE Proteins Most Abundant in Metastasizing pUM | ||||||
P23381 | WARS1 | Tryptophan--tRNA ligase, cytoplasmic | 1.906 | 4.6 × 10−6 | 53 | 47 |
P04439 | HLA-A | HLA class I histocompatibility antigen, A alpha chain | 1.818 | 1.6 × 10−6 | 53 | 47 |
P61769 | B2M | Beta-2-microglobulin | 1.768 | 2.7 × 10−5 | 47 | 39 |
P01903 | HLA-DRA | HLA class II histocompatibility antigen, DR alpha chain | 1.727 | 9.2 × 10−5 | 53 | 47 |
Q03518 | TAP1 | Antigen peptide transporter 1 | 1.630 | 3.2 × 10−5 | 53 | 47 |
P10321 | HLA-C | HLA class I histocompatibility antigen, C alpha chain | 1.624 | 1.8 × 10−5 | 52 | 46 |
Q8IVF2 | AHNAK2 | Protein AHNAK2 | 1.616 | 8.8 × 10−4 | 44 | 36 |
O95816 | BAG2 | BAG family molecular chaperone regulator 2 | 1.595 | 2.3 × 10−7 | 42 | 39 |
P07686 | HEXB | Beta-hexosaminidase subunit beta | 1.589 | 1.9 × 10−4 | 53 | 47 |
P33121 | ACSL1 | Long-chain-fatty-acid--CoA ligase 1 | 1.562 | 1.4 × 10−5 | 53 | 47 |
P17931 | LGALS3 | Galectin-3 | 1.549 | 4.6 × 10−5 | 52 | 47 |
P19971 | TYMP | Thymidine phosphorylase | 1.534 | 9.4 × 10−4 | 53 | 47 |
P51810 | GPR143 | G-protein coupled receptor 143 | 1.530 | 4.6 × 10−4 | 53 | 47 |
Q06210 | GFPT1 | Glutamine--fructose-6-phosphate aminotransferase [isomerizing] 1 | 1.505 | 3.8 × 10−5 | 53 | 47 |
Q9H3G5 | CPVL | Probable serine carboxypeptidase CPVL | 1.486 | 7.4 × 10−4 | 53 | 47 |
DE Proteins Least Abundant in Metastasizing pUM | ||||||
P04792 | HSPB1 | Heat shock protein beta-1 | 0.726 | 1.4 × 10−5 | 53 | 47 |
Q9UBI6 | GNG12 | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-12 | 0.722 | 1.6 × 10−3 | 45 | 40 |
Q9BZQ8 | NIBAN1 | Protein Niban 1 | 0.720 | 1.2 × 10−3 | 53 | 47 |
Q8NC51 | SERBP1 | Plasminogen activator inhibitor 1 RNA-binding protein | 0.718 | 1.6 × 10−2 | 53 | 47 |
P28161 | GSTM2 | Glutathione S-transferase Mu 2 | 0.710 | 5.4 × 10−4 | 53 | 47 |
Q9P0M6 | MACROH2A2 | Core histone macro-H2A.2 | 0.708 | 1.1 × 10−5 | 47 | 39 |
Q9NUJ1 | ABHD10 | Mycophenolic acid acyl-glucuronide esterase, mitochondrial | 0.707 | 6.8 × 10−7 | 53 | 47 |
Q14240 | EIF4A2 | Eukaryotic initiation factor 4A-II | 0.697 | 2.3 × 10−7 | 53 | 47 |
P05387 | RPLP2 | 60S acidic ribosomal protein P2 | 0.697 | 4.1 × 10−5 | 53 | 47 |
P34913 | EPHX2 | Bifunctional epoxide hydrolase 2 | 0.688 | 8.4 × 10−5 | 53 | 47 |
Q02252 | ALDH6A1 | Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial | 0.681 | 1.3 × 10−6 | 53 | 47 |
P21266 | GSTM3 | Glutathione S-transferase Mu 3 | 0.676 | 2.6 × 10−3 | 53 | 47 |
P09211 | GSTP1 | Glutathione S-transferase P | 0.673 | 5.5 × 10−3 | 53 | 47 |
Q02338 | BDH1 | D-beta-hydroxybutyrate dehydrogenase, mitochondrial | 0.672 | 1.4 × 10−5 | 50 | 44 |
O75891 | ALDH1L1 | Cytosolic 10-formyltetrahydrofolate dehydrogenase | 0.604 | 4.6 × 10−6 | 46 | 42 |
Uniprot Accession | Gene Nmae | Protein | Regression Coefficients | Odds Ratio | Protein Ratio Met/NoMet | Cell Surface Localization |
---|---|---|---|---|---|---|
P04439 | HLA-A | HLA class I histocompatibility antigen, A alpha chain | 0.436 | 1.547 | 1.818 | X |
Q86UX7 | FERMT3 | Fermitin family homolog 3 | 0.028 | 1.029 | 1.419 | |
P04062 | GBA | Lysosomal acid glucosylceramidase | 0.499 | 1.647 | 1.412 | |
P67936 | TPM4 | Tropomyosin alpha-4 chain | 0.061 | 1.063 | 1.330 | |
P21796 | VDAC1 | Voltage-dependent anion-selective channel protein 1 | 0.546 | 1.727 | 1.225 | X |
A0FGR8 | ESYT2 | Extended synaptotagmin-2 | 0.497 | 1.643 | 1.216 | X |
P13674 | P4HA1 | Prolyl 4-hydroxylase subunit alpha-1 | −0.310 | 0.733 | 1.211 | |
P23368 | ME2 | NAD-dependent malic enzyme, mitochondrial | 0.050 | 1.051 | 1.201 | |
Q15056 | EIF4H | Eukaryotic translation initiation factor 4H | 0.702 | 2.017 | 1.190 | |
P50570 | DNM2 | Dynamin-2 | 0.131 | 1.140 | 1.175 | X |
Q99829 | CPNE1 | Copine-1 | 0.072 | 1.075 | 1.174 | X |
Q9HD67 | MYO10 | Unconventional myosin-X | 0.252 | 1.287 | 1.160 | X |
P49748 | ACADVL | Very long-chain specific acyl-CoA dehydrogenase, mitochondrial | 0.072 | 1.075 | 1.154 | |
Q00341 | HDLBP | Vigilin | 0.485 | 1.623 | 1.122 | X |
P48729 | CSNK1A1 | Casein kinase I isoform alpha | 0.030 | 1.031 | 1.121 | |
P53621 | COPA | Coatomer subunit alpha | 0.490 | 1.632 | 1.116 | |
P11142 | HSPA8 | Heat shock cognate 71 kDa protein | 0.018 | 1.018 | 1.096 | X |
P54920 | NAPA | Alpha-soluble NSF attachment protein | 0.050 | 1.051 | 1.095 | X |
Q13616 | CUL1 | Cullin-1 | −0.178 | 0.837 | 0.903 | X |
Q9BPX5 | ARPC5L | Actin-related protein 2/3 complex subunit 5-like protein | −0.102 | 0.903 | 0.895 | |
P38606 | ATP6V1A | V-type proton ATPase catalytic subunit A | −0.124 | 0.883 | 0.885 | X |
Q9BR76 | CORO1B | Coronin-1B | −0.110 | 0.896 | 0.874 | X |
Q96TA1 | NIBAN2 | Protein Niban 2 | −0.448 | 0.639 | 0.864 | X |
Q14344 | GNA13 | Guanine nucleotide-binding protein subunit alpha-13 | −0.213 | 0.808 | 0.844 | X |
P01024 | C3 | Complement C3 | −0.124 | 0.883 | 0.840 | X |
Q8N1G4 | LRRC47 | Leucine-rich repeat-containing protein 47 | −0.391 | 0.677 | 0.838 | |
Q14624 | ITIH4 | Inter-alpha-trypsin inhibitor heavy chain H4 | −0.380 | 0.684 | 0.836 | X |
Q9NXF1 | TEX10 | Testis-expressed protein 10 | −0.512 | 0.599 | 0.802 | |
P62899 | RPL31 | 60S ribosomal protein L31 | −0.094 | 0.911 | 0.795 | |
Q96I99 | SUCLG2 | Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial | −0.254 | 0.775 | 0.789 | X |
Q9BZQ8 | NIBAN1 | Protein Niban 1 | −0.095 | 0.910 | 0.720 | X |
P28161 | GSTM2 | Glutathione S-transferase Mu 2 | −0.171 | 0.843 | 0.710 |
TCGA Coding mRNA | Laurent Coding mRNA | TCGA Transcripts DA SCNA Cluster 3 vs. 4 | TCGA + Laurent Transcripts DA SCNA Cluster 3 vs. 4 | TCGA Transcripts Up in mRNA Cluster 3 vs. 4 | TCGA Transcripts Down in mRNA Cluster 3 vs. 4 | |
---|---|---|---|---|---|---|
Number transcripts * | 12,319 | 13,142 | 591 | 510 | 338 | 2172 |
Transcripts Identified at protein level * | 3433 | 3524 | 133 | 128 | 109 | 373 |
Fraction of transcript detected as proteins | 27.9% | 26.8% | 22.5% | 25.1% | 32.2% | 17.2% |
Total DE proteins | 378 | 364 | 20 | 19 | 18 | 28 |
DE proteins Elevated in Mets | 181 | 181 | 17 | 17 | 5 | 18 |
DE proteins Decreased in Mets | 197 | 183 | 3 | 2 | 13 | 10 |
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Jang, G.-F.; Crabb, J.S.; Hu, B.; Willard, B.; Kalirai, H.; Singh, A.D.; Coupland, S.E.; Crabb, J.W. Proteomics of Primary Uveal Melanoma: Insights into Metastasis and Protein Biomarkers. Cancers 2021, 13, 3520. https://doi.org/10.3390/cancers13143520
Jang G-F, Crabb JS, Hu B, Willard B, Kalirai H, Singh AD, Coupland SE, Crabb JW. Proteomics of Primary Uveal Melanoma: Insights into Metastasis and Protein Biomarkers. Cancers. 2021; 13(14):3520. https://doi.org/10.3390/cancers13143520
Chicago/Turabian StyleJang, Geeng-Fu, Jack S. Crabb, Bo Hu, Belinda Willard, Helen Kalirai, Arun D. Singh, Sarah E. Coupland, and John W. Crabb. 2021. "Proteomics of Primary Uveal Melanoma: Insights into Metastasis and Protein Biomarkers" Cancers 13, no. 14: 3520. https://doi.org/10.3390/cancers13143520