Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer
Abstract
:1. Introduction
2. Results
2.1. Identification of Chimeric RNAs by EricScript and ChimeraScan Algorithms
2.2. Fusion Junction Validation by Reverse Transcription-PCR (RT-PCR)
2.3. Fusion Junction Validation by Sanger Sequencing
2.4. Differential Gene Expression and Functional Enrichment Analyses
2.5. ceRNA Analysis and RNA-RNA Interactions
3. Discussion
4. Materials and Methods
4.1. Clinical Samples and RNA Extraction
4.2. Whole Transcriptome Sequencing (RNA-Seq)
4.3. Fusion Detection
4.4. Fusion Gene Validation by RT-PCR and Sanger Sequencing
4.5. Fusion Gene Validation and Functional Enrichment Analysis by Targeted RNA-Seq
4.6. Competing Endogenous RNA Analysis
4.7. Study of RNA-RNA and RNA-Protein Interactions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Fusion | Gene Name 5p | Gene Name 3p | chr 5p | Breakpoint 1 (End 5p) | Strand 5p | chr 3p | Breakpoint 2 (Start 3p) | strand 3p | Fusiozn Type | JunctionSequence | Score |
---|---|---|---|---|---|---|---|---|---|---|---|
RNF123-STAT3 | RNF123 | STAT3 | 3 | 49,728,680 | + | 17 | 49,728,680 | - | inter-chr | ccgcaagagctataggctgacctcagatgctgagaaatccagggtcacagCTACTCGGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGAGAGGCGGAGG | 0.91586235 |
PLK1-ERN2 | PLK1 | ERN2 | 16 | 23,701,614 | + | 16 | 23,702,074 | - | Cis | gtgggttctacagccttgtccccctccccctcaaccccaccatatgaattGCTGGGTGCAGTGGCTCACACCTGTAATCCCAGCATTTTGGGAGGCTGAG | 0.690112004 |
MRPS31-SUGT1 | MRPS31 | SUGT1 | 13 | 41,323,274 | - | 13 | 53,231,667 | + | intra-chr | gtggacaaaagaggggaaactatgggagttcccaattaacaatgaagcagGAGCTGACTAAGGCTTTGGAACAGAAACCAGATGATGCACAGTATTATTG | 0.734629203 |
LPHN1-SUZ12 | LPHN1 | SUZ12 | 19 | 14,316,797 | - | 17 | 30,267,305 | + | inter-chr | cgagccgcaggagagacacgctgggccgaccccagagaggcgctggacagAGCCAACACAGATCTATAGATTTCTTCGAACTCGGAATCTCATAGCACCA | 0.855475528 |
EIF5AL1-MSH3 | EIF5AL1 | MSH3 | 10 | 81,274,508 | + | 5 | 81,274,508 | + | inter-chr | aagactgtgaaaatgaatccagaggtgacccaagcattgaatttaacaatGGTGGCTCATGCCTGTAATCCCAGCACTTTGGGAGGCCAAGGTAGGCAGA | 0.532811583 |
GUCY2C-PLBD1 | GUCY2C | PLBD1 | 12 | 14,765,813 | - | 12 | 14,721,126 | - | Read- Through | accttccactctggaaccttattccagcagttgttccagggagcttctacCTGTGGAGGCCTCTCCAGAAACAGCAGAGGATCCGAGCTGCGTGTAGGCA | 0.896360711 |
HSPE1-MOB4 | HSPE1 | MOB4 | 2 | 198,367,852 | + | 2 | 198,388,348 | + | Read- Through | aagttcttctcccagaatatggaggcaccaaagtagttctagatgacaagGATTTCTATAATTGGCCTGATGAATCCTTTGATGAAATGGACAGTACACT | 0.821493951 |
PDLIM2-CCAR2 | PDLIM2 | CCAR2 | 8 | 22,455,537 | + | 8 | 22,463,248 | + | intra-chr | agagattggctgtgggcctcagtttccccattttataaagttttaaaatctGCCTTTTCCCCACGACTCTGAAAGAGGACAGCGTTCCCAATGTCCCAGTTT | 5 |
HPSE2-HSD11B2 | HPSE2 | HSD11B2 | 10 | 100,995,631 | - | 16 | 67,469,859 | + | inter-chr | tctcttcctactgggtctcgctagtgactaattgtccttatctaaagtgtgGGCCTGTGGGGCCTCGTCAACAACGCAGGCCACAATGAAGTAGTTGCTGAT | 2 |
HDAC1-MARCKSL1 | HDAC1 | MARCKSL1 | 1 | 32,799,223 | + | 1 | 32,799,429 | - | Adjacent_ Converging | agatactattttcatttttgtgagcctctttgtaataaaatggtacatttcTAAAGCACCACTAAAGGGACGACATTTATTCCTTTTCCAAATGTTACAGTA | 2 |
ARSA-TNS4 | ARSA | TNS4 | 22 | 51,066,600 | - | 17 | 38,632,079 | - | inter-chr | gccggtaccgggctgcgggcgcttccgcctcggccccgccccgtgacctgtCTTACTGTTTTGCAAAGACAAACATTTTATTTTTCATGATAGGAGCTGTAG | 4 |
ERBB2-MIEN1 | ERBB2 | MIEN1 | 17 | 37,883,255 | + | 17 | 37,885,408 | - | Adjacent_ Converging | cccgggcgctgggggcatggtccaccacaggcaccgcagctcatctaccagATTAGTGTTTGTAGCGCCACTTTACTGCCAATAGCTGACATTGCCCTGGGT | 4 |
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Panza, A.; Castellana, S.; Biscaglia, G.; Piepoli, A.; Parca, L.; Gentile, A.; Latiano, A.; Mazza, T.; Perri, F.; Andriulli, A.; et al. Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer. Int. J. Mol. Sci. 2020, 21, 7120. https://doi.org/10.3390/ijms21197120
Panza A, Castellana S, Biscaglia G, Piepoli A, Parca L, Gentile A, Latiano A, Mazza T, Perri F, Andriulli A, et al. Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer. International Journal of Molecular Sciences. 2020; 21(19):7120. https://doi.org/10.3390/ijms21197120
Chicago/Turabian StylePanza, Anna, Stefano Castellana, Giuseppe Biscaglia, Ada Piepoli, Luca Parca, Annamaria Gentile, Anna Latiano, Tommaso Mazza, Francesco Perri, Angelo Andriulli, and et al. 2020. "Transcriptome and Gene Fusion Analysis of Synchronous Lesions Reveals lncMRPS31P5 as a Novel Transcript Involved in Colorectal Cancer" International Journal of Molecular Sciences 21, no. 19: 7120. https://doi.org/10.3390/ijms21197120