Table 3.
Genes with UTR-APA specific to the SI-NETs.
| Gene | Function | Role in cancer | APA | Functional consequence |
|---|---|---|---|---|
| PSMD8 | Subunit of the proteasome | Overexpressed in breast cancer (27) | Increased usage of a proximal polyA site in the 3′UTR | Shortening of 3′UTR by 325 nt with loss of miRNA target sites for three miRNAs present in SI-NETs: hsa-mir-22*, hsa-mir-192*, and hsa-mir-1263 |
| DACT2 | Negative regulator of the TGF-β/nodal signaling pathway | Tumor suppressor (28) | Increased usage of two proximal polyA sites in the 3′UTR | Shortening of 3′UTR by up to 12113 nt without loss of miRNA target sites |
| TM9SF3 | Transmembrane protein with unknown function | Unknown | Increased usage of two proximal polyA sites in the 3′UTR | Shortening of 3′UTR by up to 2848 nt with loss of miRNA target sites for 13 miRNAs present in SI-NETs: hsa-mir-1826, hsa-mir-338-5p, hsa-mir-552, hsa-mir-532-3p, hsa-mir-7-2*, hsa-mir-7-1*, hsa-mir-10b*, hsa-mir-140-3p, hsa-mir-193b*, hsa-mir-550*, hsa-mir-200c*, hsa-mir-17*, and hsa-mir-93* |
| CD59 | Membrane complement regulatory protein | Overexpressed and anti-apoptotic (29) | Increased usage of two proximal polyA sites in the 3′UTR | Shortening of 3′UTR by up to 4707 nt with loss of miRNA target sites for one miRNA present in SI-NETs: hsa-mir-629 |
| ANKH | Pyrophosphate transport regulator | Amplified and suggested overexpressed (30) | Increased usage of a proximal polyA site in the 3′UTR | Shortening of 3′UTR by 4879 nt with loss of miRNA target sites for eight miRNAs present in SI-NETs: hsa-mir-330-3p, hsa-mir-29b-2*, hsa-mir-1275, hsa-mir-625, hsa-mir-452, hsa-mir-628-3p, hsa-mir-30a*, and hsa-mir-30e* |
| CIAO1 | Role in iron–sulfur protein biogenesis | Interacts with tumor suppressor WT1 (31) | Increased usage of two proximal polyA sites in the 3′UTR | Shortening of 3′UTR by up to 2581 nt with loss of miRNA target sites for nine miRNAs present in SI-NETs: hsa-mir-550*, hsa-mir-200c*, hsa-mir-214*, hsa-mir-423-5p, hsa-mir-660, hsa-mir-29b-1*, hsa-mir-1246, hsa-mir-7-1*, and hsa-mir-7-2* |
| SRSF5 | Splice factor | Overexpressed in breast cancer and anti-apoptotic (32) | Increased usage of a proximal polyA site in the 3′UTR | Shortening of 3′UTR by 312 nt with loss of miRNA target sites for seven miRNAs present in SI-NETs: hsa-mir-338-5p, hsa-mir-628-3p, hsa-mir-409-3p, hsa-mir-183*, hsa-mir-330-3p, hsa-mir-7-1*, and hsa-mir-7-2* |
| MRSP16 | Mitochondrial ribosomal protein | Unknown | Increased usage of a proximal polyA site in the 3′UTR | Shortening of 3′UTR by 1888 nt with loss of miRNA target sites for 16 miRNAs present in SI-NETs: hsa-mir-671-5p, hsa-mir-193b*, hsa-mir-551b*, hsa-mir-338-5p, hsa-mir-30b*, hsa-mir-125b-2*, hsa-mir-330-3p, hsa-mir-7-1*, hsa-mir-7-2*, hsa-mir-188-5p, hsa-mir-769-5p, hsa-mir-324-3p, hsa-mir-552, hsa-mir-193a-5p, hsa-mir-501-5p, and hsa-mir-362-5p |
| NDUFA6 | NADH dehydrogenase | Unknown | Increased usage of a proximal polyA site in the 3′UTR | Shortening of 3′UTR by 563 nt with loss of miRNA target sites for six miRNAs present in SI-NETs: hsa-mir-552, hsa-mir-21*, hsa-mir-664*, hsa-mir-505*, hsa-mir-550, and hsa-mir-500* |