Table 1. A list of publications that have employed quantitative proteomics to identify miRNA targets.
| No. | miRNA | Type of perturbation | Cell line | Transcriptomics analysis | Quantitative proteomics | Total protein | Reference |
|---|---|---|---|---|---|---|---|
| 1 | let-7a | Stable lentiviral vector overexpression | SGC-7901 (human gastric carcinoma cells) | NA | 2DE | 10 | Zhu et al. [73] |
| 2 | let-7b | LNA-anti-let-7b knockdown | HeLa (ovarian cancer) | Microarray | pSILAC | 2700 | Selbach et al. [65] |
| 3 | miR-1 | Transient miRNA mimics overexpression | HeLa (ovarian cancer) | NA | SILAC | 504 | Vinther et al. [74] |
| 4 | miR-1 | Transient miRNA mimics overexpression | HeLa (ovarian cancer) | Microarray | pSILAC | 4962a) | Selbach et al. [65] |
| 5 | miR-1 | Transient miRNA mimics overexpression | Hela (ovarian cancer) | Microarray | SILAC | 2312 | Baek et al. [64] |
| 6 | miR-15a/16-1 | Transient miRNA mimics overexpression | MEG-01 (Leukemia) | Microarray | 2DE | 27 | Calin et al. [75] |
| 7 | miR-16 | Transient miRNA mimics overexpression | HeLa (ovarian cancer) | Microarray | pSILAC | 4962a) | Selbach et al. [65] |
| 8 | miR-17-92 | Conditional episomal miRNA vector overexpression | SHEP-TR-miR-17–92 (neuroblastoma) | NA | SILAC | NA | Mestdagh et al. [76] |
| 9 | miR-17-92 | Stable pre-miR overexpression | BEAS2B (bronchial epithelial cells) | NA | iTRAQ | 479 | Taguchi et al. [77] |
| 10 | miR-17-92 cluster | LNA-anti- miR-19a, miR-20a and miR-92–1 knockdown | SBC-3 (small-cell lung cancer cells) | NA | 2DE | 112 up-regulated proteins | Kanzaki et al. [78] |
| 11 | miR-21 | Transient anti-miRNA oligo overexpression | MCF-7 (breast cancer) | NA | iTRAQ | 1151 | Yang et al. [67] |
| 12 | miR-21 | Transient anti-miRNA oligo overexpression | MCF-7 (breast cancer) | NA | 2D-DIGE | NA | Zhu et al. [79] |
| 13 | miR-21 | Transient miRNA mimics overexpression | U266 (human myeloma cell line) | NA | SILAC | 1498 | Xiong et al. [80] |
| 14 | miR-29a | Transient miRNA mimics overexpression | DLKP-A cells (Lung carcinoma) | NA | 2D-DIGE | 75 | Muniyappa et al. [81] |
| 15 | miR-29a | Transient miRNA overexpression | HEK293T (human embryonic kidney) | NA | SILAC | 5074 | Bargaje et al. [82] |
| 16 | miR-30a | Transient miRNA mimics overexpression | HeLa (ovarian cancer) | Microarray | pSILAC | 4962a) | Selbach et al. [65] |
| 17 | miR-30e-3p | Transient miRNA mimics overexpression | DLD1 (colorectal cancer) | NA | Spectral counting | NA | Schepeler et al. [71] |
| 18 | miR-34a | Transient pre-miR mimics overexpression | HepG2 (hepatocellular carcinoma) | NA | 2D-DIGE | 116b) | Cheng et al. [43] |
| 19 | miR-34a | Episomal pri-miRNA vector overexpression | SW480 (colon cancer) | Microarray | pSILAC | 1206 | Kaller et al. [69] |
| 20 | miR-34a | Transient miRNA mimics overexpression | IMR32 (neuroblastoma) | Microarray | iCAT | 1495 | Chen et al. [83] |
| 21 | miR-34a | Transient miRNA mimics overexpression | HEK293T (human embryonic kidney) | NA | SILAC | 5688 | Bargaje et al. [82] |
| 22 | miR-122a | Stable lentiviral vector overexpression | HepG2 (Hepatocellular carcinoma) | NA | 2DE | 10 | Diao et al. [84] |
| 23 | miR-124 | Transient miRNA mimics overexpression | Hela (ovarian cancer) | Microarray | SILAC | 2120 | Baek et al. [64] |
| 24 | miR-143 | Transient miRNA mimics overexpression | MiaPaCa-2 (pancreatic cancer) | Microarray | SILAC | 1202 | Yang et al. [68] |
| 25 | miR-155 | Transient miRNA mimics overexpression | HeLa (ovarian cancer) | Microarray | pSILAC | 3299 | Selbach et al. [65] |
| 26 | miR-155 | Transient miRNA episomal vector overexpression | HEK293T (human embryonic kidney) | NA | SILAC | 3148 | Lossner et al. [85] |
| 27 | miR-155 | Transient miRNA mimics overexpression | DHL16 (diffuse large B-cell lymphoma) | NA | pSILAC | 2103 | Huang et al. [86] |
| 28 | miR-181 | Transient miRNA mimics overexpression | Hela (ovarian cancer) | Microarray | SILAC | 1774 | Baek et al. [64] |
| 29 | miR-193b | Transient pre-miRNA vector overexpression | MCF-7 (breast cancer) | Microarray | iTRAQ | 743 | Leivonen et al. [87] |
| 30 | miR-210 | Transient miRNA mimics overexpression | Human umbilical venous endothelium cells | NA | 2DE | 28 | Fasanaro et al. [88] |
| 31 | miR-223 | Congenital miRNA knockout | miR-223−/− mouse bone marrow primary culture | Microarray | SILAC | 5019 | Baek et al. [64] |
| 32 | miR-372 | Transient miRNA overexpression | CL 1–0 (lung adenocarcinoma cells) | NA | 2D-DIGE | 19 | Lai et al. [89] |
| 33 | miR-373 | Transient pre-miRNA mimics overexpression | MCF-7 (breast cancer) | NA | SILAC | 3666 | Yan et al. [90] |
| 34 | miR-516a-3p | Stable episomal miRNA vector overexpression | 44As3-miR516a-3p (gastric cancer) | NA | iTRAQ | NA | Takei et al. [91] |
2-DE: two-dimensional gel electrophoresis; 2-D DIGE: two-dimensional fluorescence difference gel electrophoresis; NA: not available.
a)
Total number of proteins from experiments of let-7b, miR-1, miR-16, miR-30a, and miR-155.
b)
The number of differentially expressed proteins identified by 2D gels.