Transfer-RNA-Derived Fragments Are Potential Prognostic Factors in Patients with Squamous Cell Carcinoma of the Head and Neck
Abstract
1. Introduction
2. Materials and Methods
2.1. Retrieval of tRF Data from MINTbase
2.2. Identification of Survival-Associated tRFs
2.3. Prediction of tRF Binding Proteins
2.4. Relationship between tRF Level and Clinical Features
2.5. Quantification of tRF Levels Using Reverse Transcription Quantitative PCR (RT-qPCR)
3. Results
3.1. Reported tRFs in the TCGA HNSC Cohort
3.2. Prognosis-Associated tRFs in SCCHN
3.3. tRF-Interacting Proteins
3.4. The Association between tRF-20-S998LO9D and Clinical Factors
3.5. Investigation of tRF-20 in Our Clinical Samples
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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MINTbase Unique ID (Sequence Derived) | Fragment Sequence | p-Value (Kaplan-Meier log Rank Test) | Number of Tumor | Number of Normal | Average Level in Tumor (RPM) | Average Level in Normal (RPM) | Chr | Type | Amino Acid and Anticodon | Predicted RNA Binding Protein |
---|---|---|---|---|---|---|---|---|---|---|
tRF-20-S998LO9D | GTCTCTGTGGCGCAATGGAC | 0.0003 | 443 | 16 | 20 | 2 | 1 | 5′-tRF | ArgTCT | eIF4B, SRSF1 |
tRF-16-I8W47WB | ATTGGTCGTGGTTGTA | 0.0003 | 285 | 37 | 12 | 29 | MT | i-tRF | GluTTC | |
tRF-16-884U1DD | TCCGGCTCGAAGGACC | 0.0003 | 255 | 37 | 10 | 8 | 14 | 3′-tRF | TyrGTA | SRSF9, eIF4B, SRSF1 |
tRF-22-8XF6RE98N | TCCTAAGCCAGGGATTGTGGGT | 0.0006 | 466 | 42 | 6 | 11 | 16 | i-tRF | ArgCCT | NONO, RBMX |
tRF-21-NYDRFU8U0 | CTTTGAATCCAGCGATCCGAG | 0.0011 | 340 | 30 | 3 | 3 | 6 | i-tRF | GlnTTG | YTHDC2, RBMX |
tRF-21-I8W47W1R0 | ATTGGTCGTGGTTGTAGTCCG | 0.0024 | 507 | 41 | 31 | 49 | MT | i-tRF | GluTTC | |
tRF-21-LE3JWB61B | CGAATCCGGCTCGAAGGACCA | 0.0030 | 209 | 29 | 3 | 2 | 6 | 3′-tRF | TyrGTA | SRSF9, YTHDC1, eIF4B, SRSF1 |
tRF-20-6S7P4PWJ | GGCCGGTTAGCTCAGTCGGC | 0.0031 | 303 | 14 | 7 | 2 | 6 | 5′-tRF | IleAAT | |
tRF-23-Z87HFK8SDZ | TTTGGGTGCGAGAGGTCCCGGGT | 0.0039 | 375 | 30 | 4 | 2 | 14 | i-tRF | ProTGG | FUS, RBMX, SRSF10 |
tRF-23-H3RXSINH0P | ATAGTGGTTAGTACTCTGCGTTG | 0.0050 | 177 | 8 | 5 | 5 | 1 | i-tRF | HisGTG | YBX1, YTHDC1 |
tRF-19-Z8SSFKJJ | TTTGGGTCCGAGAGGTCCC | 0.0063 | 155 | 19 | 2 | 2 | 11 | i-tRF | ProTGG | SRSF10 |
tRF-19-Q99P9PJZ | GCTTCTGTAGTGTAGTGGT | 0.0063 | 260 | 19 | 4 | 4 | 6 | 5′-tRF | ValCAC | |
tRF-20-MEF91SS2 | CGGATAGCTCAGTCGGTAGA | 0.0069 | 115 | 26 | 2 | 2 | 11 | i-tRF | LysTTT | |
tRF-30-XSXMSL73VL4Y | TGCCGTGATCGTATAGTGGTTAGTACTCTG | 0.0074 | 388 | 27 | 10 | 3 | 1 | 5′-tRF | HisGTG | YTHDC1 |
tRF-21-7OFIZ9WUD | GTTAAAGACTTTTTCTCTGAC | 0.0075 | 204 | 8 | 4 | 2 | MT | 3′-tRF | ProTGG | SRSF10, KHDRBS3 |
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Gu, X.; Wang, L.; Coates, P.J.; Boldrup, L.; Fåhraeus, R.; Wilms, T.; Sgaramella, N.; Nylander, K. Transfer-RNA-Derived Fragments Are Potential Prognostic Factors in Patients with Squamous Cell Carcinoma of the Head and Neck. Genes 2020, 11, 1344. https://doi.org/10.3390/genes11111344
Gu X, Wang L, Coates PJ, Boldrup L, Fåhraeus R, Wilms T, Sgaramella N, Nylander K. Transfer-RNA-Derived Fragments Are Potential Prognostic Factors in Patients with Squamous Cell Carcinoma of the Head and Neck. Genes. 2020; 11(11):1344. https://doi.org/10.3390/genes11111344
Chicago/Turabian StyleGu, Xiaolian, Lixiao Wang, Philip J. Coates, Linda Boldrup, Robin Fåhraeus, Torben Wilms, Nicola Sgaramella, and Karin Nylander. 2020. "Transfer-RNA-Derived Fragments Are Potential Prognostic Factors in Patients with Squamous Cell Carcinoma of the Head and Neck" Genes 11, no. 11: 1344. https://doi.org/10.3390/genes11111344
APA StyleGu, X., Wang, L., Coates, P. J., Boldrup, L., Fåhraeus, R., Wilms, T., Sgaramella, N., & Nylander, K. (2020). Transfer-RNA-Derived Fragments Are Potential Prognostic Factors in Patients with Squamous Cell Carcinoma of the Head and Neck. Genes, 11(11), 1344. https://doi.org/10.3390/genes11111344