Integrated DNA Copy Number and Expression Profiling Identifies IGF1R as a Prognostic Biomarker in Pediatric Osteosarcoma
Abstract
:1. Introduction
2. Results
2.1. NMF Clustering of Gene Expression Data Identifies Two Distinct Clusters
2.2. mRNA Expression Predicts Clinical Outcomes
2.3. Characterization of Osteosarcoma Copy Number Aberrations
2.4. IGF1R Amplification Is Associated with Higher Expression and Worse Prognosis
3. Discussion
4. Materials and Methods
4.1. Patient Samples
4.2. Single Nucleotide Polymorphism Array Profiling
4.3. mRNA Expression Profiling
4.4. mRNA Clustering
4.5. Differential Expression and Pathway Analysis
4.6. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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# | Process Networks | In Data | Total | p-Value | FDR | Network Objects from Active Data |
---|---|---|---|---|---|---|
1 | Cell adhesion_Integrin priming | 9 | 110 | 1.05 × 10−5 | 6.71 × 10−4 | ACTA2, G-protein alpha-i family, PIB4, SDF-1, SOS, Actin, Collagen III, PLC-beta, SOS1 |
2 | Cell adhesion_Leucocyte chemotaxis | 12 | 205 | 1.09 × 10−5 | 6.71 × 10−4 | G-protein alpha-i family, VCAM1, PIB4, Galpha(i)-specific EDG GPCRs, CCL2, CCL13, SDF-1, CXCL13, Actin, LPA3 receptor, PLC-beta, Galpha(q)-specific EDG GPCRs |
3 | Development_Regulation of angiogenesis | 11 | 223 | 1.25 × 10−4 | 4.66 × 10−3 | FAP48, G-protein alpha-i1, Angiopoietin 1, Ephrin-A receptors, G-protein alpha-i family, IL-6, CCL2, PGAR, N-cadherin, SOS, PLC-beta |
4 | Development_Blood vessel morphogenesis | 11 | 228 | 1.52 × 10−4 | 4.66 × 10−3 | G-protein alpha-i1, Angiopoietin 1, G-protein alpha-i family, VCAM1, ErbB4, Galpha(i)-specific EDG GPCRs, PGAR, SDF-1, PLGF, SOS, HGF receptor (Met) |
5 | Development_Ossification and bone remodeling | 8 | 157 | 8.88 × 10−4 | 2.18 × 10−2 | AEBP1, Frizzled, SFRP4, OSF-2, DMP1, MEPE, Osteomodulin, Bone sialoprotein |
6 | Cell adhesion_Cadherins | 8 | 180 | 2.13 × 10−3 | 3.53 × 10−2 | Frizzled, SFRP4, DKK1, N-cadherin, PTPR-zeta, WIF1, Actin, HGF receptor (Met) |
7 | Development_EMT_Regulation of epithelial-to-mesenchymal transition | 9 | 225 | 2.33 × 10−3 | 3.53 × 10−2 | HGF, ACTA2, Frizzled, G-protein alpha-i family, N-cadherin, SOS, Actin, HGF receptor (Met), Collagen III |
8 | Development_Skeletal muscle development | 7 | 144 | 2.46 × 10−3 | 3.53 × 10−2 | ACTA2, ER81, Actin muscle, ITGA11, ACTG2, Actin, HGF receptor (Met) |
9 | Inflammation_Protein C signaling | 6 | 108 | 2.59 × 10−3 | 3.53 × 10−2 | G-protein alpha-i family, PIB4, Galpha(i)-specific EDG GPCRs, IL-6, Actin, PLC-beta |
10 | Inflammation_Histamine signaling | 8 | 213 | 5.95 × 10−3 | 6.28 × 10−2 | Kappa chain (Ig light chain), G-protein alpha-i family, VCAM1, PIB4, IL-6, CCL2, Actin, PLC-beta |
HuEx Discovery Set (n = 88) | |||||||||
Probeset ID | Associated Gene(s) | Event-free Survival Model | Overall Survival Model | ||||||
Hazard ratio † | p-value †,‡ | Corrected p-value * | Full-model p-value | Hazard ratio † | p-value †,‡ | Corrected p-value * | Full-model p-value | ||
3310041 | FGFR2 | 0.718 | 1.377 × 10−2 | 1.316 × 10−1 | 5.840 × 10−5 | 0.561 | 5.440 × 10−4 | 3.878 × 10−2 | 8.294 × 10−6 |
3324447 | FIBIN | 0.698 | 6.198 × 10−3 | 1.042 × 10−1 | 2.256 × 10−5 | 0.559 | 5.170 × 10−4 | 3.878 × 10−2 | 6.542 × 10−6 |
3074857 | PTN///DGKI | 0.729 | 3.402 × 10−3 | 8.746 × 10−2 | 1.018 × 10−5 | 0.618 | 6.211 × 10−4 | 3.878 × 10−2 | 3.849 × 10−6 |
3074857 | PTN///DGKI | 0.729 | 3.402 × 10−3 | 8.746 × 10−2 | 1.018 × 10−5 | 0.618 | 6.211 × 10−4 | 3.878 × 10−2 | 3.849 × 10−6 |
U133 Validation Set (n = 60) | |||||||||
Probeset ID | Associated Gene | Event-free Survival Model | Overall Survival Model | ||||||
Hazard ratio † | p-value †,‡ | Full model p-value | Hazard ratio † | p-value †,‡ | Full model p-value | ||||
211399_at | FGFR2 | 0.026 | 1.825 × 10−3 | 2.749 × 10−5 | 0.042 | 5.347 × 10−3 | 4.658 × 10−6 | ||
231001_at | FIBIN | 0.602 | 1.129 × 10−2 | 1.216 × 10−4 | 0.595 | 2.149 × 10−2 | 1.262 × 10−5 | ||
208408_at | PTN | 8.914 | 4.325 × 10−2 | 3.864 × 10−4 | 24.039 | 1.163 × 10−2 | 1.985 × 10−5 | ||
206806_at | DGKI | 0.755 | 3.288 × 10−1 | 1.197 × 10−3 | 0.502 | 4.080 × 10−2 | 1.741 × 10−5 |
Cytoband | Location(Mbs) | Width(Mbs) | Residual q Value | Frequency | High Frequency ‘ | Key Genes | |
---|---|---|---|---|---|---|---|
17p11.2 | chr17:18.123–18.237 | 0.114 | 0 | 44.9 | 30.6 | TOP3A, FLI1 | * |
8q24.21 | chr8:128.357–128.772 | 0.415 | 0 | 46.9 | 27.2 | MYC | * |
20p13 | chr20:1.52–1.529 | 0.009 | 0 | 49 | 20.4 | ||
15q26.3 | chr15:99.366–99.408 | 0.043 | 0 | 42.2 | 20.4 | IGF1R | * |
1q21.3 | chr1:149.996–151.21 | 1.214 | 0.001 | 48.3 | 19 | * | |
13q34 | chr13:105.817–114.882 | 9.065 | 0.116 | 44.2 | 19 | ||
19p13.2 | chr19:12.686–13.498 | 0.812 | 0 | 43.5 | 18.4 | * | |
6p21.1 | chr6:43.323–44.511 | 1.187 | 0 | 40.1 | 17.7 | * | |
19q12 | chr19:30.082–30.306 | 0.224 | 0 | 40.1 | 17 | CCNE1 | * |
8p11.1 | chr8:41.441–50.441 | 9 | 0.033 | 50.3 | 16.3 | ||
17p13.1 | chr17:7.305–7.329 | 0.024 | 0.001 | 58.5 | |||
19q12 | chr19:28.283–30.098 | 1.814 | 0 | 58.5 | |||
13q14.2 | chr13:48.834–49.065 | 0.231 | 0 | 56.5 | RB1 | * | |
17p13.1 | chr17:10.372–10.532 | 0.16 | 0 | 56.5 | |||
3q13.31 | chr3:116.162–118.625 | 2.463 | 0 | 55.1 | LSAMP1, LSAMP-AS1 | * | |
8q24.3 | chr8:146.066–146.28 | 0.214 | 0 | 55.1 | |||
17p13.1 | chr17:7.611–7.763 | 0.152 | 0 | 55.1 | |||
4q35.2 | chr4:190.883–191.154 | 0.271 | 0 | 53.7 | |||
16q24.3 | chr16:89.995–90.355 | 0.36 | 0 | 53.1 | |||
20q13.33 | chr20:62.735–62.89 | 0.155 | 0 | 53.1 |
Cytoband | Change | Genes | Full Model | Including Initial Metastasis | ||||||
---|---|---|---|---|---|---|---|---|---|---|
OS | EFS | OS | EFS | |||||||
HR | p-Value | HR | p-Value | HR | p-Value | HR | p-Value | |||
15q26.3 | Amp | IGF1R | 1.110 | 9.00 × 10−3 | 1.108 | 3.40 × 10−2 | 1.116 | 1.30 × 10−2 | 1.093 | 2.25 × 10−1 |
8q24.21 | Amp | MYC, POU5F1B, LOC727677 | 1.170 | 1.10 × 10−2 | 1.211 | 4.00 × 10−3 |
All Samples | HuEx Samples | U133 Samples | Copy Number Only Samples | ||||||
# | % | # | % | # | % | # | % | ||
Total | 214 | 100 | 103 | 100 | 64 | 100 | 47 | 100 | |
Gender | Male | 122 | 57 | 55 | 53 | 36 | 56 | 31 | 66 |
Female | 92 | 43 | 48 | 47 | 28 | 44 | 16 | 34 | |
Age at Diagnosis | <12 | 151 | 71 | 70 | 68 | 46 | 72 | 35 | 74 |
>12 | 63 | 29 | 33 | 32 | 18 | 28 | 12 | 26 | |
Location | Leg/Foot | 183 | 86 | 90 | 87 | 58 | 91 | 35 | 74 |
Arm/Hand | 17 | 8 | 10 | 10 | 2 | 3 | 5 | 11 | |
Other | 11 | 5 | 1 | 1 | 4 | 6 | 6 | 13 | |
No Data | 3 | 1 | 2 | 2 | 0 | 0 | 1 | 2 | |
SNP Data | Yes | 147 | 69 | 93 | 90 | 7 | 11 | 47 | 100 |
No | 67 | 31 | 10 | 10 | 57 | 89 | 0 | 0 | |
Event | Occurred | 87 | 41 | 38 | 37 | 31 | 48 | 18 | 38 |
Censored | 100 | 47 | 50 | 49 | 29 | 45 | 21 | 45 | |
No Data | 27 | 13 | 15 | 15 | 4 | 6 | 8 | 17 | |
Death | Occurred | 68 | 32 | 27 | 26 | 28 | 44 | 13 | 28 |
Censored | 119 | 56 | 61 | 59 | 32 | 50 | 26 | 55 | |
No Data | 27 | 13 | 15 | 15 | 4 | 6 | 8 | 17 | |
Metastasis at Diagnosis | No | 170 | 79 | 81 | 79 | 54 | 84 | 35 | 74 |
Yes | 44 | 21 | 22 | 21 | 10 | 16 | 12 | 26 | |
Mean | SD | Mean | SD | Mean | SD | Mean | SD | ||
Age at Diagnosis | Years | 13.89 | 3.78 | 13.36 | 3.6 | 14.4 | 3.65 | 14.37 | 4.25 |
Follow-up of Survivors | Years | 6.47 | 2.77 | 6.83 | 2.78 | 6.26 | 2.9 | 5.87 | 2.53 |
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Taylor, A.M.; Sun, J.M.; Yu, A.; Voicu, H.; Shen, J.; Barkauskas, D.A.; Triche, T.J.; Gastier-Foster, J.M.; Man, T.-K.; Lau, C.C. Integrated DNA Copy Number and Expression Profiling Identifies IGF1R as a Prognostic Biomarker in Pediatric Osteosarcoma. Int. J. Mol. Sci. 2022, 23, 8036. https://doi.org/10.3390/ijms23148036
Taylor AM, Sun JM, Yu A, Voicu H, Shen J, Barkauskas DA, Triche TJ, Gastier-Foster JM, Man T-K, Lau CC. Integrated DNA Copy Number and Expression Profiling Identifies IGF1R as a Prognostic Biomarker in Pediatric Osteosarcoma. International Journal of Molecular Sciences. 2022; 23(14):8036. https://doi.org/10.3390/ijms23148036
Chicago/Turabian StyleTaylor, Aaron M., Jiayi M. Sun, Alexander Yu, Horatiu Voicu, Jianhe Shen, Donald A. Barkauskas, Timothy J. Triche, Julie M. Gastier-Foster, Tsz-Kwong Man, and Ching C. Lau. 2022. "Integrated DNA Copy Number and Expression Profiling Identifies IGF1R as a Prognostic Biomarker in Pediatric Osteosarcoma" International Journal of Molecular Sciences 23, no. 14: 8036. https://doi.org/10.3390/ijms23148036