Systematic Investigation of the Diagnostic and Prognostic Impact of LINC01087 in Human Cancers
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Transcriptomics Data Analysis
2.2. Survival Curve Analysis
2.3. ROC Curve Analysis
2.4. Network and Pathway Enrichment Analyses of LINC01087
3. Results
3.1. Diagnostic Value of LINC01087
3.2. Prognostic Value of LINC01087 in Cancer
3.3. Impact of LINC01087 on Cancer-Related Pathways
3.4. LINC01087 Functions as Competing Endogenous RNA
4. Discussion
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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Diagnosis | Prognosis | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
TCGA and GTEx | TCGA | KM Plotter | ||||||||
Expression | Clinical Interest (ROC) | OS | ||||||||
Type of Tumor | Abbreviation | N. of Samples (N, T) | p-Value | log2FC | p-Value | AUC | p-Value | HR (95%CI) | p-Value | HR (95%CI) |
Adrenocortical carcinoma | ACC | 337 (258, 79) | NS | −0.17 | 0.03 | 0.6 | NS | 1.15 (0.53–2.5) | NA | NA |
Bladder cancer | BLCA | 452 (40, 412) | NS | 2.5 | 0.03 | 0.6 | NS | 1.01 (0.75–1.36) | NS | 1 (0.74–1.37) |
Breast cancer | BC | 1685 (572, 1113) | 2.32E-35 | 2.2 | 1.16E-35 | 0.7 | 0.01 | 0.65 (0.47–0.9) | 0.0063 | 0.64 (0.46–0.88) |
Cervical squamous cell carcinoma and endocervical adenocarcinoma | CESC | 328 (22, 306) | NS | 0.2 | NS | 0.5 | NS | 0.91 (0.57–1.44) | NS | 0.92 (0.56–1.51) |
Cholangiocarcinoma | CHOL | 270 (235, 35) | NS | 2.5 | NS | 0.5 | NS | 1.24 (0.46–3.38) | NA | NA |
Colon adenocarcinoma | COAD | 1300 (820, 480) | NS | 0.8 | 0.05 | 0.5 | NS | 0.97 (0.61–1.52) | NA | NA |
Esophageal carcinoma | ESCA | 1619 (1456, 163) | 4.08E-35 | 3.7 | 2.04E-35 | 0.8 | NS | 1.50 (0.92–2.45) | NS | 1.7 (0.89–3.23) |
Glioblastoma multiforme | GBM | 2816 (2647, 169) | NS | −0.1 | NS | 0.5 | NS | 1.09 (0.76–1.57) | NA | NA |
Lower grade glioma | LGG | 3174 (2642, 532) | 2.43E-04 | −0.3 | 0.0001 | 0.5 | NS | 0.98 (0.63–1.52) | NA | NA |
Head-neck squamous cell carcinoma | HNSC | 710 (206, 504) | 1.55E-11 | 0.1 | 7.77E-12 | 0.6 | NS | 0.92 (0.69–1.21) | NS | 0.8 (0.59–1.09) |
Hepatocellular carcinoma | HCC | 650 (276, 374) | 4.28E-07 | 0.8 | 2.14E-07 | 0.6 | NS | 1.38 (0.96–1.98) | 0.037 | 1.47 (1.02–2.13) |
Acute myeloid leukemia | AML | 1079 (929, 150) | 9.46E-08 | −1 | 4.73E-08 | 0.6 | NS | 1.26 (0.82–1.93) | NA | NA |
Lung adenocarcinoma | LUAD | 1176 (637, 539) | 0.002 | 1.3 | 0.001 | 0.5 | NS | 0.99 (0.73–1.35) | NS | 1.05 (0.77–1.44) |
squamous cell carcinoma | LUSC | 551 (49, 502) | 0.003 | 2.7 | 0.001 | 0.6 | NS | 0.98 (0.75–1.29) | NS | 124 (0.94–1.63) |
Skin cutaneous melanoma | SKCM | 2282 (1810, 472) | 7.99E-23 | 0.5 | 3.99E-23 | 0.6 | NS | 0.84 (0.64–1.12) | NA | NA |
Ovarian cancer | OV | 561 (180, 381) | 1.11E-14 | 1.5 | 5.56E-15 | 0.7 | NS | 0.97 (0.74–1.26) | NS | 0.95 (0.73–1.24) |
Pancreatic adenocarcinoma | PAAD | 511 (332, 179) | 6.86E-20 | −1.1 | 3.43E-20 | 0.7 | NS | 0.69 (0.45–1.06) | NS | 0.84 (0.53–1.34) |
Pheochromocytoma and Paraganglioma | PCPG | 445 (261,184) | 3.87E-07 | −0.7 | 1.93E-07 | 0.6 | NS | 3.3e-09 (0–Inf) | NS | 0 (0–Inf) |
Prostate adenocarcinoma | PRAD | 798 (297, 501) | NS | 1.6 | NS | 0.5 | NS | 0.94 (0.25–3.50) | NA | NA |
Rectum adenocarcinoma | READ | 956 (789,167) | 0.001 | 0.7 | 4.73E-04 | 0.6 | NS | 0.82 (0.37–1.82) | NS | 0.67 (0.29–1.53) |
Chromophobe renal cell carcinoma | chRCC | 179 (114, 65) | NS | 0.1 | NS | 0.5 | NS | 0.45 (0.05–3.56) | NA | NA |
Clear cell renal cell carcinoma | ccRCC | 702 (161, 541) | 1.25E-15 | 0.8 | 6.24E-16 | 0.7 | NS | 1.20 (0.89–1.63) | NS | 1.19 (0.88–1.61) |
Papillary renal cell carcinoma | pRCC | 412 (121, 291) | 0.005 | 0.9 | 0.002 | 0.6 | 2.86E-04 | 2.85 (1.58–5.17) | 0.0025 | 2.46 (1.35–4.49) |
Sarcoma | SARC | 265 (2, 263) | NS | 0.6 | NS | 0.6 | NS | 0.66 (0.43–1.02) | NS | 0.71 (0.46–1.12) |
Stomach adenocarcinoma | STAD | 766 (391, 375) | 2.49E-50 | 4 | 1.25E-50 | 0.8 | NS | 1.02 (0.73–1.41) | NS | 1.05 (0.76–1.47) |
Testicular germ cell tumors | TGCT | 517 (361, 156) | 6.59E-73 | −6.1 | 3.30E-73 | 1.0 | NS | 0.76 (0.07–8.38) | NS | 0.85 (0.08–9.44) |
Thymoma | THYM | 121 (2, 119) | NS | 5.2 | 0.047 | 0.8 | NS | 0.91 (0.24–3.40) | NS | 1.1 (0.3–4.4) |
Thyroid carcinoma | THCA | 1224 (712, 512) | 3.13E-10 | −0.6 | 1.56E-10 | 0.6 | NS | 1.84 (0.67–5.08) | NS | 1.05 (0.36–3.02) |
Uterine corpus endometrial carcinoma | UCEC | 731 (177, 554) | NS | 1.1 | NS | 0.5 | NS | 1.48 (0.97–2.24) | 0.0088 | 1.73 (1.14–2.62) |
Uterine carcinosarcoma | UCS | 199 (142, 57) | 0.0001 | 3.2 | 6.69E-05 | 0.6 | NS | 1.57 (0.80–3.08) | NA | NA |
BC | |||||
---|---|---|---|---|---|
Clinicopathological Features | n. of Total Cases | LINC01087 Expression | p-Value | ||
Low | High | ||||
pT | T1-T2 | 929 | 453 | 476 | 0.04 |
T3-T4 | 180 | 103 | 77 | ||
Tumor size | ≤2 cm | 282 | 123 | 159 | 0.01 |
>2 cm | 827 | 433 | 394 | ||
TGCT | |||||
Clinicopathological Features | n. of Total Cases | LINC01087 Expression | p-Value | ||
Tumor size | ≤2 cm | 80 | 41 | 39 | 0.05 |
>2 cm | 58 | 40 | 18 |
lncRNA | 10 miRNA Targets Extracted from Analysis 2 | 18 miRNA Targets Extracted from Analysis 3 | 10 mRNA Targets Shared between Analyses 1, 2, and 3 |
---|---|---|---|
LINC01087 | hsa-miR-644a | hsa-miR-7-5p | C8orf37 |
hsa-miR-1305 | hsa-miR-92a-3p | EFNA5 | |
hsa-miR-4505 | hsa-miR-181a-5p | HOOK3 | |
hsa-miR-3671 | hsa-miR-181a-5p, hsa-miR-181b-5p, hsa-miR-181d-5p | IQCG | |
hsa-miR-7975 | hsa-miR-197-3p | MYOZ3 | |
hsa-miR-4505 | hsa-miR-423-5p | PCP4L1 | |
hsa-miR-569 | hsa-miR-181a-5p, hsa-miR-181b-5p, hsa-miR-98-5p | PLAG1 | |
hsa-miR-4255 | hsa-miR-19a-3p, hsa-miR-19b-3p, hsa-miR-92a-3p | POLI | |
hsa-miR-606 | hsa-miR-34a-5p, hsa-miR-98-5p | SLC2A3 | |
hsa-miR-3174 | hsa-miR-34a-5p, hsa-miR-98-5p | SNRPA1 |
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De Palma, F.D.E.; Carbonnier, V.; Salvatore, F.; Kroemer, G.; Pol, J.G.; Maiuri, M.C. Systematic Investigation of the Diagnostic and Prognostic Impact of LINC01087 in Human Cancers. Cancers 2022, 14, 5980. https://doi.org/10.3390/cancers14235980
De Palma FDE, Carbonnier V, Salvatore F, Kroemer G, Pol JG, Maiuri MC. Systematic Investigation of the Diagnostic and Prognostic Impact of LINC01087 in Human Cancers. Cancers. 2022; 14(23):5980. https://doi.org/10.3390/cancers14235980
Chicago/Turabian StyleDe Palma, Fatima Domenica Elisa, Vincent Carbonnier, Francesco Salvatore, Guido Kroemer, Jonathan G. Pol, and Maria Chiara Maiuri. 2022. "Systematic Investigation of the Diagnostic and Prognostic Impact of LINC01087 in Human Cancers" Cancers 14, no. 23: 5980. https://doi.org/10.3390/cancers14235980