Exploration of Deregulated Long Non-Coding RNAs in Association with Hepatocarcinogenesis and Survival
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patients and Tissue Samples
2.2. RNA Extraction and lncRNA Measurement
2.3. Statistical Analysis
3. Results
3.1. Clinical and Pathological Characteristics
Variables | No. of Cases (%) |
---|---|
Age at diagnosis (yrs), Mean ± SD | 59.5 ± 14.7 |
Age group | |
<60 years | 28 (43) |
≥60 years | 37 (57) |
Gender | |
Male | 49 (75) |
Female | 16 (25) |
Ethnicity | |
Caucasian | 33 (51) |
African-American | 6 (9) |
Hispanic | 6 (9) |
Asian | 14 (22) |
Unknown/Other | 6 (9) |
Viral infection | |
HBV (−), HCV (−) | 18 (28) |
HBV (−), HCV (+) | 19 (29) |
HBV (+), HCV (−) | 13 (20) |
HBV (+), HCV (+) | 4 (6) |
Missing | 11 (17) |
Cigarette smoking | |
No | 26 (40) |
Yes | 35 (54) |
Missing | 4 (6) |
Alcohol drinking | |
No | 27 (42) |
Yes | 35 (54) |
Missing | 3 (4) |
Cirrhosis | |
No | 17 (26) |
Yes | 47 (72) |
Missing | 1 (2) |
Tumor size (cm), Mean ± SD | 6.1 (4.8) |
Tumor grade * | |
I–II | 23 (35) |
III | 21 (32) |
IV | 18 (28) |
Missing | 3 (5) |
3.2. Differentially Expressed lncRNAs in HCC Tissues
lncRNAs | Tumor | Non-Tumor | Fold-Change | Unadjusted p-Value | FDR |
---|---|---|---|---|---|
lincRNA-VLDLR | −4.6 | −3.4 | −2.4 | 0.005 | 0.188 |
MEG9 | −5.6 | −4.2 | −2.8 | 0.010 | 0.188 |
H19 antisense | −1.3 | 0.2 | −2.7 | 0.010 | 0.188 |
ncR-uPAR | −1.3 | −0.03 | −2.6 | 0.018 | 0.188 |
NEAT1 (family) | −2.4 | −1.3 | −2.2 | 0.021 | 0.188 |
LUST | −0.5 | 0.6 | −2.1 | 0.037 | 0.287 |
UM9-5 | −8.7 | −7.6 | −2.5 | 0.042 | 0.287 |
HOTAIR | −8.8 | −7.1 | −2.6 | 0.048 | 0.287 |
3.3. Deregulated lncRNAs in HBV- or HCV-Related HCC
lncRNAs | Tumor | Non-Tumor | Fold-Change | Unadjusted p-value | FDR |
---|---|---|---|---|---|
Kcnq1ot1 | −8.9 | −5.2 | −9.1 | 0.005 | 0.215 |
TncRNA | −5.5 | −4.0 | −2.9 | 0.009 | 0.215 |
lincRNA-VLDLR | −3.8 | −1.8 | −4.2 | 0.014 | 0.215 |
Zfhx2as | −2.0 | 0.8 | −6.7 | 0.019 | 0.215 |
NRON | −6.1 | −3.7 | −5.3 | 0.020 | 0.215 |
HOTTIP | −9.8 | −7.8 | −4.2 | 0.025 | 0.231 |
lincRNA-RoR | −9.5 | −7.7 | −3.4 | 0.046 | 0.273 |
LncRNAs | Viral Negative (N = 18) | HBV Positive (N = 13) | Fold-Change | Unadjusted p-Value | FDR |
---|---|---|---|---|---|
Kcnq1ot1 | −8.9 | −5.2 | 12.6 | 0.004 | 0.193 |
NRON | −6.2 | −3.7 | 5.4 | 0.042 | 0.947 |
3.4. Aberrant Expression of lncRNAs in Tumor Tissue and Prediction for HCC Survival
4. Discussion
5. Conclusions
Supplementary Files
Supplementary File 1Acknowledgments
Author Contributions
Conflicts of Interest
References
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Shen, J.; Siegel, A.B.; Remotti, H.; Wang, Q.; Shen, Y.; Santella, R.M. Exploration of Deregulated Long Non-Coding RNAs in Association with Hepatocarcinogenesis and Survival. Cancers 2015, 7, 1847-1862. https://doi.org/10.3390/cancers7030865
Shen J, Siegel AB, Remotti H, Wang Q, Shen Y, Santella RM. Exploration of Deregulated Long Non-Coding RNAs in Association with Hepatocarcinogenesis and Survival. Cancers. 2015; 7(3):1847-1862. https://doi.org/10.3390/cancers7030865
Chicago/Turabian StyleShen, Jing, Abby B. Siegel, Helen Remotti, Qiao Wang, Yueyue Shen, and Regina M. Santella. 2015. "Exploration of Deregulated Long Non-Coding RNAs in Association with Hepatocarcinogenesis and Survival" Cancers 7, no. 3: 1847-1862. https://doi.org/10.3390/cancers7030865