MiR-378a-3p Is Critical for Burkitt Lymphoma Cell Growth
Abstract
:Simple Summary
Abstract
1. Introduction
2. Results
2.1. MiRNA Expression Profiling in BL and GC-B Cells
2.2. MYC-Induced miR-378a-3p Controls BL Cell Growth
2.3. Identification of miR-378a-3p Targets
2.4. IRAK4 and MNT Are Involved in the Function of miR-378a-3p
3. Discussion
4. Materials and Methods
4.1. BL Cell Lines, Germinal Center (GC) B Cells, and BL Patient Material
4.2. RNA Isolation
4.3. Small RNA Library Preparation and Sequencing
4.4. qRT-PCR
4.5. Lentiviral Constructs, Transduction, and GFP Competition Assay
4.6. AGO2-IP Procedure
4.7. Western Blotting
4.8. Microarray Analysis
4.9. Identification of miR-378a-3p Seed Sites and Gene Ontology (GO) Terms
4.10. Cloning of miRNA Binding Sites and Luciferase Reporter Assay
4.11. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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IP/T Ratio | pCDH (n = 9233) | mZip (n = 8944) | ||||
---|---|---|---|---|---|---|
EV | 378a | 378a/EV | SCR | mZip-378a-3p | SCR/mZip-378a-3p | |
≥2 | 611 | 586 | 20 | 741 | 878 | 63 |
≥4 | 117 | 117 | 2 | 171 | 196 | 4 |
≥8 | 25 | 18 | 0 | 53 | 34 | 0 |
Gene | Transcript ID | IP/T Ratio | miR-378a-3p Binding Site | Growth-Related GO | ||||
---|---|---|---|---|---|---|---|---|
EV * | 378a | FC | 5′UTR | CDS | 3′UTR | |||
IRAK4 | ENST00000613694 | 1.0 | 4.6 | 4.6 | 8m | yes | ||
CDKN2A | ENST00000304494 | 1.0 | 4.0 | 4.0 | yes | |||
JPX | ENST00000415215 | 1.5 | 5.8 | 3.9 | 8m ** | |||
PLGRKT | ENST00000223864 | 1.0 | 3.0 | 3.0 | 8m | |||
TMEM245 | ENST00000374586 | 1.0 | 2.9 | 2.9 | 7m8/8m | |||
TOMM6 | ENST00000398884 | 1.5 | 4.1 | 2.7 | ||||
CDK1 | ENST00000395284 | 1.0 | 2.6 | 2.6 | yes | |||
FAM117A | ENST00000240364 | 1.4 | 3.6 | 2.6 | ||||
WDR83OS | ENST00000596731 | 1.3 | 3.2 | 2.5 | 7m8 | |||
CCNK | ENST00000389879 | 1.0 | 2.4 | 2.4 | 8m | yes | ||
MYCBP | ENST00000397572 | 2.3 | 5.4 | 2.3 | 7mA1 | |||
RNF34 | ENST00000392465 | 1.3 | 3.0 | 2.3 | yes | |||
UBC | ENST00000339647 | 1.0 | 2.3 | 2.3 | yes | |||
POP4 | ENST00000585603 | 1.0 | 2.3 | 2.3 | ||||
MNT | ENST00000174618 | 1.2 | 2.7 | 2.3 | 7m8 | 7mA1 | yes | |
HSPB1 | ENST00000248553 | 1.8 | 3.9 | 2.2 | 7mA1 | yes | ||
INAFM1 | ENST00000552360 | 1.3 | 2.8 | 2.2 | ||||
PCNA | ENST00000379160 | 1.0 | 2.1 | 2.1 | yes | |||
SP100 | ENST00000264052 | 1.2 | 2.5 | 2.1 | ||||
RPP25L | ENST00000297613 | 1.2 | 2.4 | 2.0 |
Gene | Transcript ID | IP/T Ratio | miR-378a-3p Binding Site | Growth-Related GO | ||||
---|---|---|---|---|---|---|---|---|
mZip-378a-3p * | SCR | FC | 5′UTR | CDS | 3′UTR | |||
DYNLRB1 | ENST00000357156 | 1.0 | 6.4 | 6.4 | ||||
VPS18 | ENST00000220509 | 8.5 | 43.4 | 5.1 | ||||
NAPA-AS1 | ENST00000594367 | 1.2 | 5.2 | 4.3 | 7mA1 ** | |||
C11orf95 | ENST00000433688 | 1.0 | 4.2 | 4.2 | ||||
HOMEZ | ENST00000357460 | 1.2 | 4.3 | 3.5 | ||||
TMEM79 | ENST00000405535 | 1.7 | 5.7 | 3.4 | ||||
FOXP1 | ENST00000493089 | 4.5 | 14.9 | 3.3 | 7m8/8m | yes | ||
PCIF1 | ENST00000372409 | 1.0 | 3.2 | 3.2 | 7m8 | |||
ATP6V0C | ENST00000330398 | 1.0 | 3.1 | 3.1 | ||||
CISH | ENST00000348721 | 2.1 | 6.6 | 3.1 | 8m | yes | ||
lnc-FOXB1-8 | lnc-FOXB1-8:1 | 1.0 | 3.3 | 3.1 | ||||
MT1B | ENST00000334346 | 1.1 | 3.5 | 3.1 | yes | |||
lnc-EGLN1-1 | lnc-EGLN1-1:6 | 1.0 | 2.9 | 2.9 | ||||
NELFA | ENST00000382882 | 1.0 | 3.0 | 2.9 | ||||
BCR | ENST00000305877 | 1.0 | 2.8 | 2.8 | 7m8 | 7m8 | yes | |
MT1L | ENST00000565768 | 1.2 | 3.2 | 2.8 | ||||
FAT3 | ENST00000409404 | 1.0 | 2.7 | 2.7 | 8m | 7mA1 | ||
TRAF3IP2-AS1 | ENST00000525151 | 1.0 | 2.7 | 2.7 | ||||
C22orf39 | ENST00000611555 | 1.0 | 2.6 | 2.6 | ||||
KRTCAP2 | ENST00000295682 | 1.6 | 4.1 | 2.6 | ||||
LINC01122 | ENST00000427421 | 11.2 | 29 | 2.6 | 7mA1 ** | |||
ACTG1P20 | ENSG00000241547 | 1.3 | 3.2 | 2.5 | ||||
lnc-KRTAP5-10-1 | lnc-KRTAP5-10-1:1 | 1.5 | 3.5 | 2.4 | 7m8 ** | |||
MT1E | ENST00000306061 | 1.1 | 2.8 | 2.4 | yes | |||
NUDT19 | ENST00000397061 | 1.0 | 2.5 | 2.4 | 7mA1 | |||
PRDX4 | ENST00000379341 | 1.0 | 2.4 | 2.4 | yes | |||
TMEM258 | ENST00000537328 | 1.1 | 2.6 | 2.4 | ||||
XLOC_l2_005952 | TCONS_l2_00011050 | 6.6 | 15.6 | 2.4 | 7m8 | |||
BTG3 | ENST00000629582 | 1.6 | 3.7 | 2.3 | yes | |||
EVI5L | ENST00000270530 | 1.3 | 3.0 | 2.3 | ||||
LINC01534 | ENST00000433232 | 1.0 | 2.3 | 2.3 | ||||
lnc-ADA-1 | lnc-ADA-1:2 | 1.0 | 2.3 | 2.3 | ||||
lnc-ZNF431-4 | lnc-ZNF431-4:1 | 1.1 | 2.6 | 2.3 | ||||
MT1A | ENST00000290705 | 2.5 | 5.6 | 2.3 | yes | |||
CSRP2 | ENST00000311083 | 2.7 | 5.9 | 2.2 | ||||
FYCO1 | ENST00000296137 | 1.0 | 2.2 | 2.2 | 7m8 | |||
HYAL3 | ENST00000336307 | 2.0 | 4.3 | 2.2 | ||||
KCNQ1 | ENST00000632153 | 1.0 | 2.2 | 2.2 | ||||
lnc-RP11-158I9.5.1-2 | TCONS_00019776 | 1.5 | 3.3 | 2.2 | ||||
PCNX | ENST00000304743 | 3.8 | 8.3 | 2.2 | 7mA1/8m | |||
PRSS36 | ENST00000268281 | 1.4 | 2.8 | 2.2 | ||||
SMARCA4 | ENST00000344626 | 1.0 | 2.2 | 2.2 | 7m8 | yes | ||
TNRC6C | ENST00000335749 | 8.5 | 18.3 | 2.2 | 7m8 | |||
TOLLIP | ENST00000317204 | 1.3 | 2.8 | 2.2 | 7mA1 | |||
ARF4 | ENST00000303436 | 1.0 | 2.1 | 2.1 | yes | |||
ATG4D | ENST00000309469 | 1.4 | 2.8 | 2.1 | yes | |||
CSE1L | ENST00000262982 | 1.2 | 2.5 | 2.1 | yes | |||
lnc-PCF11-1 | lnc-PCF11-1:12 | 1.5 | 3.2 | 2.1 | ||||
MARS | ENST00000262027 | 1.7 | 3.6 | 2.1 | ||||
NANS | ENST00000210444 | 1.0 | 2.1 | 2.1 | ||||
ORMDL2 | ENST00000243045 | 1.1 | 2.3 | 2.1 | ||||
PFKFB2 | ENST00000367080 | 1.4 | 3.0 | 2.1 | 7m8 | 7mA1 | ||
PGM2L1 | ENST00000298198 | 1.8 | 3.7 | 2.1 | ||||
PTPN23 | ENST00000265562 | 1.5 | 3.1 | 2.1 | ||||
TSACC | ENST00000368255 | 1.5 | 3.1 | 2.1 | ||||
TUBA1C | ENST00000301072 | 1.1 | 2.4 | 2.1 | 7mA1 | yes | ||
XLOC_l2_013031 | TCONS_l2_00024809 | 6.5 | 13.7 | 2.1 | ||||
C15orf61 | ENST00000342683 | 1.3 | 2.6 | 2.0 | 8m | |||
LAT | ENST00000360872 | 1.0 | 2.0 | 2.0 | ||||
LOC101929494 | N/A | 1.6 | 3.2 | 2.0 | ||||
MYCBP | ENST00000397572 | 1.5 | 3.1 | 2.0 | 7mA1 | |||
NDRG4 | ENST00000394279 | 1.1 | 2.2 | 2.0 | yes | |||
TUBE1 | ENST00000368662 | 1.1 | 2.2 | 2.0 | yes |
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Niu, F.; Dzikiewicz-Krawczyk, A.; Koerts, J.; de Jong, D.; Wijenberg, L.; Fernandez Hernandez, M.; Slezak-Prochazka, I.; Winkle, M.; Kooistra, W.; van der Sluis, T.; et al. MiR-378a-3p Is Critical for Burkitt Lymphoma Cell Growth. Cancers 2020, 12, 3546. https://doi.org/10.3390/cancers12123546
Niu F, Dzikiewicz-Krawczyk A, Koerts J, de Jong D, Wijenberg L, Fernandez Hernandez M, Slezak-Prochazka I, Winkle M, Kooistra W, van der Sluis T, et al. MiR-378a-3p Is Critical for Burkitt Lymphoma Cell Growth. Cancers. 2020; 12(12):3546. https://doi.org/10.3390/cancers12123546
Chicago/Turabian StyleNiu, Fubiao, Agnieszka Dzikiewicz-Krawczyk, Jasper Koerts, Debora de Jong, Laura Wijenberg, Margot Fernandez Hernandez, Izabella Slezak-Prochazka, Melanie Winkle, Wierd Kooistra, Tineke van der Sluis, and et al. 2020. "MiR-378a-3p Is Critical for Burkitt Lymphoma Cell Growth" Cancers 12, no. 12: 3546. https://doi.org/10.3390/cancers12123546