SUPPLEMENTAL MATERIAL

online only Supplemental material

miRNA expression profiling of cerebrospinal fluid in patients with cerebral aneurysmal subarachnoid hemorrhage S. S. Stylli et al. http://thejns.org/doi/abs/10.3171/2016.1.JNS151454

Disclaimer The Journal of Neurosurgery acknowledges that the following section is published verbatim as submitted by the authors and did not go through either the Journal’s peer-review or editing process.

©AANS, 2016 J Neurosurg Supplementary Table 1 nSolver Differential Expression Analysis Comparison Groups

Comparison 1

No SAH SAH / No vasospasm (combined)

CSF0012, CSF0018, CSF0030, CSF0034 CSF0020, CSF0023, CSF0024, CSF0025, CSF0038, CSF0039, CSF0040, CSF0041, CSF0042

Comparison 2

No SAH SAH / No vasospasm (Sample Day 1)

CSF0012, CSF0018, CSF0030, CSF0034 CSF0020, CSF0023, CSF0024, CSF0027, CSF0041, CSF0038

Comparison 3

No SAH SAH / Vasospasm (combined)

CSF0012, CSF0018, CSF0030, CSF0034 CSF0 022, CSF0027, CSF0032, CSF0033, CSF0036, CSF0044, CSF0045, CSF0048, CSF0052, CSF0053

Comparison 4

No SAH SAH / Vasospasm (Sample Day 1)

CSF0012, CSF0018, CSF0030, CSF0034 CSF0027, CSF0032, CSF0036, CSF0044, CSF0052

Comparison 5

No SAH SAH / Vasospasm (post Sample Day 1) CSF0012, CSF0018, CSF0030, CSF0034 CSF0022, CSF0033, CSF0045, CSF0048, CSF0053

Comparison 6

SAH / No vasospasm (combined) SAH / Vasospasm (combined)

CSF0020, CSF0023, CSF0024, CSF0025, CSF0022, CSF0027, CSF0032, CSF0033, CSF0036, CSF0038, CSF0039, CSF0040, CSF0041, CSF0044, CSF0045, CSF0048, CSF0052, CSF0053 CSF0042

Comparison 7

SAH / No vasospasm (Sample Day 1) SAH / Vasospasm (Sample Day 1)

CSF0020, CSF0023, CSF0024, CSF0038, CSF0027, CSF0032, CSF0036, CSF0044, CSF0052 CSF0041

Comparison 8

SAH / No vasospasm (post Sample Day 1) SAH / vasospasm (post Sample Day 1)

CSF0025, CSF0038, CSF0039, CSF0040, CSF0022, CSF0033, CSF0045, CSF0048, CSF0053 CSF0042

Supplementary Table 2 miRNA showing statistically significant fold level changes as determined by nSolver Analysis Software v2.6

Comparison 1 No SAH versus SAH / No vasospasm (combined)

p-value Control Mean Case Mean Fold Change hsa-miR-451a* 0.0002 17.53 1262.2 72.01 hsa-miR-152* 0.0008 22.1 12.32 -1.79 hsa-miR-223-3p* 0.0009 9.81 28.94 2.95 hsa-miR-599* 0.0014 13.37 8.75 -1.53 hsa-miR-1224-3p* 0.0023 18.37 11.67 -1.57 hsa-miR-1301* 0.0036 13.73 8.24 -1.67 hsa-miR-548m* 0.0038 21.35 15.01 -1.42 hsa-miR-204-5p* 0.0045 13.43 42.28 3.15 hsa-miR-626* 0.0046 29.37 15.64 -1.88 hsa-miR-3180-5p* 0.0073 14.34 9.46 -1.52 hsa-miR-421* 0.0074 17.2 11.71 -1.47 hsa-miR-606* 0.0091 18.57 13 -1.43 hsa-miR-26a-5p* 0.0092 20.67 13.47 -1.53 hsa-miR-376c* 0.0097 17.1 11.62 -1.47 hsa-miR-3127-5p 0.0113 13.58 8.51 -1.6 hsa-miR-215 0.0179 30.85 19.23 -1.6 hsa-miR-1244 0.0254 34.11 23.91 -1.43 hsa-miR-580 0.0268 18.78 12.49 -1.5 hsa-miR-652-3p 0.027 12.13 8.24 -1.47 hsa-miR-452-5p 0.0291 12.7 6.85 -1.85 hsa-miR-521 0.0302 12.65 8.63 -1.47 hsa-miR-346 0.0359 20.2 11.63 -1.74 hsa-miR-510 0.0396 13.21 8.86 -1.49 hsa-miR-615-3p 0.0431 14.81 7.51 -1.97 hsa-miR-210 0.0432 16.03 10.56 -1.52 hsa-miR-485-5p 0.0454 18.94 12.16 -1.56 hsa-miR-144-3p 0.0465 25.77 66.32 2.57

Comparison 2 No SAH versus SAH / No vasospasm (Sample Day 1)

p-value Control Mean Case Mean Fold Change hsa-miR-301a-3p* 0.0024 23.15 13.44 -1.72 hsa-miR-378d* 0.0087 18.44 7.94 -2.32 hsa-miR-596 0.0105 18.09 12.11 -1.49 hsa-miR-197-3p 0.0178 17.24 9.98 -1.73 hsa-miR-326 0.0207 10.29 4.43 -2.32 hsa-miR-576-3p 0.0258 15.07 24.64 1.64 hsa-miR-301b 0.0294 18.47 11 -1.68 hsa-miR-548y 0.0296 20.17 10.28 -1.96 hsa-miR-148b-3p 0.0324 18.65 12.2 -1.53 hsa-miR-890 0.0344 21.24 28.93 1.36 hsa-miR-370 0.0367 13.18 19.06 1.45 hsa-miR-486-3p 0.0369 20.56 12.88 -1.6 hsa-miR-4647 0.0405 19.59 12.51 -1.57 hsa-miR-3690 0.0443 21.96 13.52 -1.62 hsa-miR-1291 0.049 14.67 9.46 -1.55 hsa-miR-491-5p 0.0496 20.52 11.24 -1.83

Comparison 3 No SAH versus SAH / vasospasm (combined)

p-value Control Mean Case Mean Fold Change hsa-miR-451a* 0.0005 19.26 1145.97 59.5 hsa-miR-937* 0.0006 20.27 11.19 -1.81 hsa-miR-519b-3p* 0.001 14.66 8.68 -1.69 hsa-miR-1224-3p* 0.0013 20.18 9.69 -2.08 hsa-miR-548m* 0.0014 23.46 14.3 -1.64 hsa-miR-1244* 0.0015 37.48 20.01 -1.87 hsa-miR-1301* 0.0018 15.08 8.78 -1.72 hsa-miR-2117* 0.0021 20.8 15.98 -1.3 hsa-miR-489* 0.0024 34.45 21.69 -1.59 hsa-miR-204-5p* 0.0034 14.75 41.16 2.79 hsa-miR-514b-3p* 0.0034 16.87 8.49 -1.99 hsa-miR-223-3p* 0.004 10.77 59.75 5.55 hsa-miR-521* 0.0044 13.9 7.99 -1.74 hsa-miR-624-3p* 0.0048 17.53 11.74 -1.49 hsa-miR-708-5p* 0.0052 11.86 6.75 -1.76 hsa-miR-508-3p* 0.0062 16.86 9.12 -1.85 hsa-miR-345-5p* 0.0073 17.63 9.39 -1.88 hsa-miR-137* 0.0077 18.83 10.74 -1.75 hsa-miR-599* 0.0077 14.69 7.71 -1.9 hsa-miR-4521* 0.0079 15.26 7.96 -1.92 hsa-miR-337-5p* 0.0089 21.18 17.09 -1.24 hsa-miR-320e* 0.0094 20.34 63.34 3.11 hsa-miR-346* 0.0095 22.19 13.43 -1.65 hsa-miR-152 0.0102 24.28 15.27 -1.59 hsa-miR-376c 0.011 18.79 14.85 -1.27 hsa-miR-198 0.0116 22.96 12.99 -1.77 hsa-miR-655 0.0118 18.89 8.15 -2.32 hsa-miR-580 0.0123 20.64 12.04 -1.71 hsa-miR-764 0.013 17.37 10.66 -1.63 hsa-miR-744-5p 0.0141 19.2 11.35 -1.69 hsa-miR-302a-3p 0.0177 13.69 10.37 -1.32 hsa-miR-548z 0.0189 29.2 19.87 -1.47 hsa-miR-485-5p 0.0196 20.81 11.99 -1.74 hsa-miR-548l 0.0201 15.28 11 -1.39 hsa-miR-548k 0.0202 24.2 15.79 -1.53 hsa-miR-328 0.0224 11.96 8.28 -1.44 hsa-miR-891a 0.0249 31.24 22.79 -1.37 hsa-miR-215 0.0262 33.89 24.02 -1.41 hsa-miR-4458 0.027 23.38 13.61 -1.72 hsa-miR-3147 0.0281 19.65 10.18 -1.93 hsa-miR-1277-3p 0.0284 21.41 13.34 -1.6 hsa-miR-26a-5p 0.0289 22.71 14.74 -1.54 hsa-miR-525-3p 0.0305 12.1 5.78 -2.1 hsa-miR-452-5p 0.0317 13.95 8.13 -1.72 hsa-miR-548c-5p 0.0324 21.73 14.63 -1.49 hsa-miR-765 0.0325 13.19 7.87 -1.68 hsa-miR-652-3p 0.0326 13.32 8.2 -1.62 hsa-miR-648 0.0332 15.93 8.43 -1.89 hsa-miR-615-3p 0.0339 16.27 9.39 -1.73 hsa-miR-649 0.0351 16.92 7.96 -2.13 hsa-miR-518e-3p 0.0356 9.78 6.06 -1.61 hsa-miR-519c-3p 0.0357 23.89 16.61 -1.44 hsa-miR-510 0.0365 14.51 9.28 -1.56 hsa-miR-516a-5p 0.0387 10.85 8.18 -1.33 hsa-miR-520h 0.0392 19.99 13.05 -1.53 hsa-miR-15a-5p 0.0398 19.36 27.22 1.41 hsa-miR-1281 0.0399 16.19 11.78 -1.37 hsa-miR-607 0.0402 16.82 8.06 -2.09 hsa-miR-133b 0.0418 15.77 12.3 -1.28 hsa-miR-146b-3p 0.042 12.5 8.43 -1.48 hsa-miR-421 0.0436 18.9 13.97 -1.35 hsa-miR-1303 0.0443 13.7 8.16 -1.68 hsa-miR-369-3p 0.0469 25.35 18.74 -1.35 hsa-miR-552 0.0469 15.84 10.83 -1.46 hsa-miR-596 0.0474 19.28 12.48 -1.55 hsa-miR-924 0.0475 13.91 10.51 -1.32 hsa-miR-1224-5p 0.0482 11.98 8.02 -1.49 hsa-miR-217 0.0488 39.9 26.6 -1.5 hsa-miR-320d 0.0492 12.6 8.43 -1.49 hsa-miR-626 0.0498 32.27 20.93 -1.54 hsa-miR-409-3p 0.0499 16.33 11.74 -1.39

Comparison 4 No SAH versus SAH / vasospasm (Sample Day 1)

p-value Control Mean Case Mean Fold Change hsa-miR-548m* 0.0028 22.34 13.15 -1.7 hsa-miR-337-5p* 0.0056 20.17 16.68 -1.21 hsa-miR-519b-3p* 0.0078 13.96 8.06 -1.73 hsa-miR-764 0.0102 16.54 10.46 -1.58 hsa-miR-514b-3p 0.012 16.07 8.07 -1.99 hsa-miR-1301 0.019 14.36 8.91 -1.61 hsa-miR-204-5p 0.0195 14.05 45.58 3.24 hsa-miR-545-3p 0.0202 10.55 6.43 -1.64 hsa-miR-26a-5p 0.0226 21.63 15.02 -1.44 hsa-miR-3180-5p 0.0249 15.01 9.25 -1.62 hsa-miR-521 0.0272 13.24 7.02 -1.89 hsa-miR-599 0.0281 13.99 8.4 -1.67 hsa-miR-4448 0.0297 13.99 8.56 -1.63 hsa-miR-508-3p 0.0311 16.06 8.27 -1.94 hsa-miR-137 0.0346 17.93 12.2 -1.47 hsa-miR-525-3p 0.035 11.53 6.17 -1.87 hsa-miR-708-5p 0.035 11.3 5.93 -1.91 hsa-miR-23c 0.037 31.77 21.64 -1.47 hsa-miR-937 0.0408 19.31 12.05 -1.6 hsa-miR-1246 0.0442 1.12 1.03 -1.09 hsa-miR-1253 0.0442 1.12 1.03 -1.09 hsa-miR-1283 0.0442 1.12 1.03 -1.09 hsa-miR-143-3p 0.0442 1.12 1.03 -1.09 hsa-miR-1244 0.0457 35.69 23.56 -1.52 hsa-miR-451a 0.0463 18.34 722.04 39.37 hsa-miR-10b-5p 0.0483 13 6.74 -1.93 hsa-miR-146b-3p 0.0485 11.91 7.93 -1.5 hsa-miR-548q 0.0493 10.53 5.28 -1.99 hsa-miR-323a-5p 0.0498 12.9 8.27 -1.56

Comparison 5 No SAH versus SAH / vasospasm (post Sample Day 1)

p-value Control Mean Case Mean Fold Change hsa-miR-489* 0.0007 33.41 17.31 -1.93 hsa-miR-548l* 0.0013 14.82 9.09 -1.63 hsa-miR-937* 0.003 19.66 9.81 -2 hsa-miR-302a-3p* 0.0038 13.28 8.22 -1.61 hsa-miR-1224-3p* 0.008 19.57 7.5 -2.61 hsa-miR-451a* 0.0093 18.68 2029.1 108.64 hsa-miR-345-5p* 0.0096 17.09 8.78 -1.95 hsa-miR-520h 0.0119 19.39 10.45 -1.86 hsa-miR-580 0.0165 20.01 10.74 -1.86 hsa-miR-320e 0.0172 19.72 82.09 4.16 hsa-miR-383 0.0177 16.03 11.4 -1.41 hsa-miR-548c-5p 0.018 21.08 12.23 -1.72 hsa-miR-1244 0.0184 36.35 16.03 -2.27 hsa-miR-1277-3p 0.0221 20.76 11 -1.89 hsa-miR-152 0.0229 23.55 13.58 -1.73 hsa-miR-1224-5p 0.0246 11.62 6.51 -1.78 hsa-miR-649 0.025 16.41 6.64 -2.47 hsa-miR-328 0.0254 11.6 7.21 -1.61 hsa-miR-2117 0.027 20.17 15.01 -1.34 hsa-miR-566 0.0275 21.66 13.9 -1.56 hsa-miR-409-3p 0.0278 15.84 9.38 -1.69 hsa-miR-4521 0.0292 14.8 5.69 -2.6 hsa-miR-378b 0.0302 21.54 13.24 -1.63 hsa-miR-508-3p 0.0318 16.36 9.49 -1.72 hsa-miR-1270 0.0322 16.51 10.81 -1.53 hsa-miR-624-3p 0.0338 17.01 9.61 -1.77 hsa-miR-496 0.0342 13.65 7.54 -1.81 hsa-miR-320d 0.0369 12.22 7.46 -1.64 hsa-miR-516a-5p 0.0381 10.52 7.03 -1.5 hsa-miR-655 0.0405 18.32 6.73 -2.72 hsa-miR-3147 0.0406 19.05 7.03 -2.71 hsa-miR-337-5p 0.0427 20.54 16.52 -1.24 hsa-miR-1301 0.0428 14.63 8.17 -1.79 hsa-miR-548m 0.0435 22.75 14.68 -1.55 hsa-miR-548k 0.0446 23.47 13.41 -1.75 hsa-miR-217 0.0447 38.7 23.66 -1.64 hsa-miR-215 0.0456 32.87 21.47 -1.53 hsa-miR-196b-5p 0.0462 16.51 8.54 -1.93 hsa-miR-708-5p 0.0462 11.51 7.25 -1.59 hsa-miR-421 0.0475 18.33 12.82 -1.43 hsa-miR-876-5p 0.0489 12.82 7.25 -1.77 hsa-miR-891a 0.0489 30.3 19.59 -1.55 hsa-miR-346 0.0492 21.52 13.28 -1.62 hsa-miR-133b 0.0493 15.3 10.44 -1.47 hsa-miR-376c 0.0494 18.22 13.75 -1.33 hsa-miR-4516 0.0499 16.86 10.73 -1.57

Comparison 6 SAH / No vasospasm (combined) versus SAH / vasospasm (combined)

p-value Control Mean Case Mean Fold Change

hsa-miR-566* 0.0052 21.53 15.85 -1.36 hsa-miR-508-3p* 0.0055 15.04 9.36 -1.61 hsa-miR-519b-3p* 0.0076 13.6 8.91 -1.53 hsa-miR-200b-3p 0.0107 17.68 12.8 -1.38 hsa-miR-671-5p 0.0134 24.77 17.02 -1.46 hsa-miR-876-5p 0.0136 13.04 9.13 -1.43 hsa-miR-525-3p 0.0175 10.56 5.93 -1.78 hsa-miR-937 0.0206 16.27 11.48 -1.42 hsa-miR-328 0.0212 11.24 8.5 -1.32 hsa-miR-154-5p 0.0267 17.71 12.27 -1.44 hsa-miR-1260a 0.0324 11.87 7.57 -1.57 hsa-miR-345-5p 0.035 14 9.64 -1.45 hsa-miR-561-3p 0.0373 12.53 8.11 -1.54 hsa-miR-1269b 0.0441 6.73 9.91 1.47 hsa-miR-409-3p 0.0452 15.9 12.05 -1.32 hsa-miR-1249 0.0462 12.39 8.71 -1.42 hsa-miR-606 0.0466 13.97 17.8 1.27 hsa-miR-433 0.0469 12.95 9.4 -1.38

Comparison 7 SAH / No vasospasm (Sample Day 1) versus SAH / vasospasm (Sample Day 1)

p-value Control Mean Case Mean Fold Change

hsa-miR-337-5p* 0.002 24.65 17.49 -1.41

hsa-miR-27a-3p* 0.0073 12.18 16.26 1.34

hsa-miR-1254 0.0152 13.16 7.14 -1.84

hsa-miR-22-3p 0.0183 12.46 15.32 1.23

hsa-miR-606 0.0236 14.4 20.71 1.44

hsa-miR-3127-5p 0.0245 7.43 12.63 1.7

hsa-miR-146b-3p 0.0281 5.91 8.32 1.41

hsa-miR-15a-5p 0.0305 17.11 25.86 1.51

hsa-miR-186-5p 0.034 12.09 18.63 1.54

hsa-miR-378c 0.0368 11.02 13.8 1.25

hsa-miR-210 0.0395 9.16 14.68 1.6 hsa-miR-219-2-3p 0.0417 14.48 9.38 -1.54

hsa-miR-764 0.0435 15.7 10.97 -1.43

Comparison 8

SAH / No vasospasm (post Sample Day 1) versus SAH / vasospasm (post Sample Day 1)

p-value Control Mean Case Mean Fold Change hsa-miR-1197* 0.0032 19.93 13.42 -1.48 hsa-miR-516a-5p* 0.0077 12.55 7.41 -1.69 hsa-miR-509-5p 0.01 17.87 7.73 -2.31 hsa-miR-1302 0.0108 16.15 7.23 -2.23 hsa-miR-548a-3p 0.011 12.89 4.77 -2.7 hsa-miR-345-5p 0.0112 15.17 9.24 -1.64 hsa-miR-1264 0.012 21.34 11.18 -1.91 hsa-miR-551a 0.0136 37.76 22.92 -1.65 hsa-miR-548e 0.0146 15.39 10.07 -1.53 hsa-miR-516a-3p 0.0171 35 21.83 -1.6 hsa-miR-323a-3p 0.0189 16.2 7.82 -2.07 hsa-miR-127-5p 0.0215 18.58 12.14 -1.53 hsa-miR-409-3p 0.0217 15.89 9.88 -1.61 hsa-miR-486-3p 0.0223 19.55 13.96 -1.4 hsa-miR-136-5p 0.0235 13.93 6.07 -2.29 hsa-miR-769-3p 0.0236 21.95 11.8 -1.86 hsa-miR-217 0.0245 35.32 24.91 -1.42 hsa-miR-296-5p 0.0247 14.11 10.5 -1.34 hsa-miR-576-5p 0.0256 22.22 17.3 -1.28 hsa-miR-377-3p 0.0259 15.49 10.37 -1.49 hsa-miR-1228-3p 0.0263 26.45 16.27 -1.63 hsa-miR-519b-3p 0.0279 16.44 9.28 -1.77 hsa-miR-135b-5p 0.0286 23.63 16.52 -1.43 hsa-miR-103a-3p 0.0312 21.43 8.1 -2.65 hsa-miR-4521 0.0315 14.5 5.99 -2.42 hsa-miR-548v 0.0315 20.71 14.99 -1.38 hsa-miR-671-5p 0.0338 25.86 16.79 -1.54 hsa-miR-139-5p 0.0341 19.49 10.63 -1.83 hsa-miR-302a-3p 0.0343 13.58 8.66 -1.57 hsa-miR-561-3p 0.0347 14.2 7.62 -1.86 hsa-miR-328 0.0356 12.23 7.59 -1.61 hsa-miR-200b-3p 0.0385 20.16 12.34 -1.63 hsa-miR-573 0.0402 12.62 7.09 -1.78 hsa-miR-296-3p 0.0407 18.32 8.84 -2.07 hsa-miR-1224-3p 0.0409 14.18 7.9 -1.79 hsa-miR-30a-5p 0.0422 10.78 15.7 1.46 hsa-miR-607 0.0433 15.33 7.33 -2.09 hsa-miR-1277-3p 0.0436 19.89 11.58 -1.72 hsa-miR-181c-5p 0.0444 14.23 7.87 -1.81 hsa-miR-367-3p 0.0448 22.95 15.16 -1.51 hsa-miR-649 0.0462 12.09 7 -1.73 hsa-miR-875-3p 0.047 15.18 6.07 -2.5 hsa-miR-766-3p 0.0475 32.44 20.27 -1.6 hsa-miR-193a-3p 0.0485 27.5 17.9 -1.54 hsa-miR-342-5p 0.049 17.02 10.56 -1.61

Control Mean – refers to the first named group in the comparison; Case Mean – refers to the second named group in the comparison. The miRNA listed are the ones which were differentially expressed at a statistically significant level (p<0.05) within each comparison.

*- miRNA differentially expressed within each comparison (p<0.01) Supplementary Table 3

Statistics of miRTarBase v6.0 miRNA-target interaction (MTI) Entries – Human species

Species Number of Number of Number of Number of Number of miRNA-target interactions experimentally validated by miRNA- miRNAs target articles target collected Strong evidence Less strong evidence interactions Western Reporter pSILAC Microarray NGS Blot Assay

Human 324219 2619 12738 4264 3527 5081 500 12592 304988

Supplementary Table 4 miRNA predicted target genes (mirTarBase v6.0) miRNA Strong Evidence Target Genes Comparisons where significant hsa-miR-26a-5p HMGA2, HMGA1, CCNE2, CCND2, PTEN, EZH2, PLAG1, SERBP1, SMAD1, MAP3K2, RB1, 1 SMAD4, IFNB1, GSK3B, CPEB2, CPEB3, CPEB4, GDAP1, MTDH, CDK6, CCNE1, ESR1, ABCA1, ARL4C, NOS2, IL6, MCL1, CHD1, CKS2, PRKCD, BAG4, FGF9, ACVR1, AMACR, ATM, RCBTB1, HGF, LIN28B, ZCCHC11, DNMT3B, WEE1, TET2, ADAM17, PIK3C2A, CHEK1, TDG, PHB, CDK8, CDC6,, CTGF, STRADB hsa-miR-27a-3p FOXO1, PHB, ZBTB10, MYT1, SP4, SP3, SP1, HIPK2, THRB, SPRY2, WEE1, APC, FBXW7, 7 IGF1, PAX3, WDR77, ABCA1, PDS5B, NFE2L2, EGFR, SEMA6A, MET, CCND1, YWHAZ, SLC7A11, MAP2K4, PPARG, HOXA10, LDLR, PSAP, GATA2, PIK3CG, IFNG, GRB2, SEMA7A, DPYD, KRAS,

IFNR, TP53 hsa-miR-137 CDK6, KDM1A, CDC42, CTBP1, MITF, PTGS2, ESRRA, ZNF804A, YBX1, CSE1L, PXN, 3 GLIPR1, MET, FUNDC1, BNIP3L, FMNL2, RORA, KIT, AKT2, TGFB2, SERPINA3, COX2, TRIM13, TBX3, , MTDH, Nr1i3, E2F6 hsa-miR-152 HLA-G, DNMT1, IRS1, IGF1R, TGFA, ITGA5, CSF1, CCKBR, KRAS, CD151, WNT1, ADAM17, 1 KLF4, FGF2, FGFR3, TACC3, MAFB, CCND1 hsa-miR-204-5p MEIS1, HOXA10, BCL2, TGFBR2, SNAI2, MEIS2, SPDEF, THRB, AP1S2, BCL2L2, BIRC2, 1,3 EDEM1, EZR, FZD1, IL11, M6PR, RAB22A, RAB40B, SERINC3, SERP1, TCF12, TCF4, FOXC1, MAP1LC3B, CREB5, ELOVL6, RUNX2, SOX4, EFNB2, ALPL, SOST, SMAD4, SIRT1, NTRK2, USP47, ANKRD13A, CDC42, TMPRSS3, CDH1, VIM, ITPR1, BDNF, TRPM3, SIX1, HMX1, MAP2K1, TGFBR1, SNAI1, CDX2 hsa-miR-223-3p MEF2C, STMN1, LMO2, , RHOB, NFIX, NFIA, CHUK, FBXW7, IGF1R, LIF, SP3, EPB41L3, 1,3 SLC2A4, ARTN, FOXO1, HSP90B1, SCARB1, PARP1, CDK2, ECT2, PTBP2, TAL1, ATM, CYB5A, TOX, PRDM1, STAT5A, CARM1, POLR3G, FOXO3, CDC27, SP1, CCL3, IL6, CXCL2, ABCB1, CAPRIN1, PAX6, CFTR, MEF2C hsa-miR-301a-3p MEOX2, NKRF, SERPINE1, SMAD4, RUNX3, BCL2L11, PTEN 2 hsa-miR-302a-3p CDK4, CCND1, CDKN1A, LEFTY1, LEFTY2, DAZAP2, SLAIN1, TOB2, NR2F2, AKT1, CDK2, 5 BMI1,MBD2, NANOG, CDK1 hsa-miR-320e - 3 hsa-miR-337-5p - 3,4,7 hsa-miR-345-5p CDKN1A, ABCC1, NTRK3 3,5 hsa-miR-346 EFEMP2, LIF, BTK, TAP1, ZFP36, GSK3B 3 hsa-miR-376c ACVR1C, IGF1R, GRB2, TGFBR1, TGFA 1 hsa-miR-378d - 2 hsa-miR-421 RBMXL1, CBX7, ATM, SMAD4, CASP3, FOXO4 1 hsa-miR-451a MIF, CAB39, ABCB1, AKT1, MMP2, MMP9, BCL2, MYC, RAB14, TMED7, CPNE3, RAB5A, 1,3,5 DCBLD2, IL6R, IKBKB hsa-miR-489 PTPN11 3,5 hsa-miR-508-3p - 3 hsa-miR-514b-3p - 3 hsa-miR-516-5p - 8 hsa-miR-519b-3p CDKN1A, ELAVL1 3,4,6 hsa-miR-521 ERCC8 3 hsa-miR-548m HDAC6 1,3,4 hsa-miR-566 - 6 hsa-miR-599 - 1 hsa-miR-606 - 1 hsa-miR-624-3p FXN 3 hsa-miR-626 - 1 hsa-miR-708-5p BMI1, ZEB2, BIRC5, AKT2, CD44, TMEM88, EYA3, NNAT, AKT1, CCND1, MMP2, EZH2, 3 PARP1, BCL2, CASP2, CD274, CNTFR hsa-miR-937 - 5 hsa-miR-1197 - 8 hsa-miR-1224-3p - 5 hsa-miR-1301 - 3 hsa-miR-2117 - 3 hsa-miR-3180-5p - 1 hsa-miR-4521 - 3

Supplementary Table 5

miRNA Target Functions miRNA Target Gene Description Function (www..org) hsa-miR-27a-3p

ABCA1 ATP-Binding Cassette ABC transport various molecules across extra- and intracellular membranes. With Transporter 1 cholesterol as its substrate, this functions as a cholesterol efflux pump in the cellular lipid removal pathway.

APC Adenomatous Polyposis This gene encodes a tumor suppressor protein that acts as an antagonist of the Wnt Coli signalling pathway. It is also involved in other processes including cell migration and adhesion, transcriptional activation, and apoptosis. Defects in this gene cause familial adenomatous polyposis (FAP), an autosomal dominant pre-malignant disease that usually progresses to malignancy.

CCND1 Cyclin D1 Regulatory component of the cyclin D1-CDK4 (DC) complex that phosphorylates and inhibits members of the retinoblastoma (RB) protein family including RB1 and regulates the cell-cycle during G(1)/S transition.

DPYD Dihydropyrimidine The protein encoded by this gene is a pyrimidine catabolic and the initial and rate- Dehydrogenase limiting factor in the pathway of uracil and thymidine catabolism.

EGFR Epidermal Growth Factor The protein encoded by this gene is a transmembrane glycoprotein that is a member of the protein kinase superfamily. This protein is a receptor for members of the epidermal growth factor family. EGFR is a cell surface protein that binds to epidermal growth factor. Binding of the protein to a ligand induces receptor dimerization and tyrosine autophosphorylation and leads to cell proliferation.

FBXW7 F-box and WD repeat Substrate recognition component of a SCF (SKP1-CUL1-F-box protein) E3 ubiquitin- domain containing 7, E3 protein ligase complex which mediates the ubiquitination and subsequent proteasomal ubiquitin protein ligase degradation of target proteins.

FOXO1 forkhead box O1 that is the main target of signalling and regulates metabolic homeostasis in response to oxidative stress.

GATA2 GATA Binding Protein 2 This gene encodes a member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes. The encoded protein plays an essential role in regulating transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages.

GRB2 Growth Factor Receptor- The protein encoded by this gene binds the epidermal growth factor receptor and contains Bound Protein 2 one SH2 domain and two SH3 domains. Its two SH3 domains direct complex formation with proline-rich regions of other proteins, and its SH2 domain binds tyrosine phosphorylated sequences.

HIPK2 Homeodomain Interacting This gene encodes a conserved serine/threonine kinase that is a member of the Protein Kinase 2 homeodomain-interacting protein kinase family. The encoded protein interacts with homeodomain transcription factors and many other transcription factors such as , and can function as both a co-repressor and a co-activator depending on the transcription factor and its subcellular localization.

HOXA10 A10 Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

IFNG interferon, gamma Produced by lymphocytes activated by specific antigens or mitogens. IFN-gamma, in addition to having antiviral activity, has important immunoregulatory functions. It is a potent activator of macrophages, it has anti-proliferative effects on transformed cells and it can potentiate the antiviral and antitumor effects of the type I interferons

IFNR Interferon Production IFNR (Interferon Production Regulator) is an uncategorized gene. Regulator

IGF1 Insulin-Like Growth Factor The protein encoded by this gene is similar to insulin in function and structure and is a 1 member of a family of proteins involved in mediating growth and development. The encoded protein is processed from a precursor, bound by a specific receptor, and secreted. Defects in this gene are a cause of insulin-like growth factor I deficiency.

KRAS Kirsten Rat Sarcoma Viral This gene, a Kirsten ras oncogene homolog from the mammalian ras gene family, encodes Oncogene Homolog a protein that is a member of the small GTPase superfamily. A single amino acid substitution is responsible for an activating mutation. The transforming protein that results is implicated in various malignancies, including lung adenocarcinoma, mucinous adenoma, ductal carcinoma of the pancreas and colorectal carcinoma.

LDLR Low Density Lipoprotein The low density lipoprotein receptor (LDLR) gene family consists of cell surface proteins Receptor involved in receptor-mediated endocytosis of specific ligands. Low density lipoprotein (LDL) is normally bound at the cell membrane and taken into the cell ending up in lysosomes where the protein is degraded and the cholesterol is made available for repression of microsomal enzyme 3-hydroxy-3-methylglutaryl coenzyme A (HMG CoA) reductase, the rate-limiting step in cholesterol synthesis.

MAP2K4 Mitogen-Activated Protein This gene encodes a member of the mitogen-activated protein kinase (MAPK) family. Kinase Kinase 4 Members of this family act as an integration point for multiple biochemical signals and are involved in a wide variety of cellular processes such as proliferation, differentiation, transcription regulation, and development.

MET MET Proto-Oncogene, The proto-oncogene MET product is the hepatocyte growth factor receptor and encodes Receptor Tyrosine Kinase tyrosine-kinase activity. The primary single chain precursor protein is post-translationally cleaved to produce the alpha and beta subunits, which are disulfide linked to form the mature receptor.

MYT1 Myelin Transcription Factor The protein encoded by this gene is a member of a family of neural specific, - 1 containing DNA-binding proteins. The protein binds to the promoter regions of proteolipid proteins of the central nervous system and plays a role in the developing nervous system.

NFE2L2 Nuclear Factor, Erythroid 2- This gene encodes a transcription factor which is a member of a small family of basic Like 2 (bZIP) proteins. The encoded transcription factor regulates genes which contain antioxidant response elements (ARE) in their promoters; many of these genes encode proteins involved in response to injury and inflammation which includes the production of free radicals.

PAX3 Paired Box 3 This gene is a member of the paired box (PAX) family of transcription factors. Members of the PAX family typically contain a paired box domain and a paired-type homeodomain. These genes play critical roles during fetal development. Mutations in paired box gene 3 are associated with Waardenburg syndrome, craniofacial-deafness-hand syndrome, and alveolar rhabdomyosarcoma.

PDS5B PDS5 Cohesin Associated This gene encodes a protein that interacts with the conserved protein complex termed Factor B cohesion. The cohesion complex holds together sister chromatids and facilitates accurate segregation during mitosis and meiosis. This protein is also a negative regulator of cell proliferation and may be a tumor-suppressor gene.

PHB Prohibitin This gene is evolutionarily conserved, and its product is proposed to play a role in human cellular senescence and tumor suppression. Antiproliferative activity is reported to be localized to the 3' UTR, which is proposed to function as a trans-acting regulatory RNA.

PIK3CG Phosphatidylinositol-4,5- This gene encodes a protein that belongs to the pi3/pi4-kinase family of proteins. The gene Bisphosphate 3-Kinase, product is an enzyme that phosphorylates phosphoinositides on the 3-hydroxyl group of Catalytic Subunit Gamma the inositol ring. It is an important modulator of extracellular signals, including those elicited by E-cadherin-mediated cell-cell adhesion, which plays an important role in maintenance of the structural and functional integrity of epithelia. In addition to its role in promoting assembly of adherens junctions, the protein is thought to play a pivotal role in the regulation of cytotoxicity in NK cells.

PPARG Peroxisome Proliferator- This gene encodes a member of the peroxisome proliferator-activated receptor (PPAR) Activated Receptor Gamma subfamily of nuclear receptors. PPARs form heterodimers with retinoid X receptors (RXRs) and these heterodimers regulate transcription of various genes. Three subtypes of PPARs are known: PPAR-alpha, PPAR-delta, and PPAR-gamma. The protein encoded by this gene is PPAR-gamma and is a regulator of adipocyte differentiation. Additionally, PPAR-gamma has been implicated in the pathology of numerous diseases including obesity, diabetes, atherosclerosis and .

PSAP Prosaposin This gene encodes a highly conserved glycoprotein which is a precursor for 4 cleavage products: saposins A, B, C, and D. Each domain of the precursor protein is approximately 80 amino acid residues long with nearly identical placement of cysteine residues and glycosylation sites. Saposins A-D localize primarily to the lysosomal compartment where they facilitate the catabolism of glycosphingolipids with short oligosaccharide groups. The precursor protein exists both as a secretory protein and as an integral membrane protein and has neurotrophic activities. Mutations in this gene have been associated with Gaucher disease, Tay-Sachs disease, and metachromatic leukodystrophy.

SEMA6A Sema Domain, SEMA6A (Sema Domain, Transmembrane Domain (TM), And Cytoplasmic Domain, Transmembrane Domain (Semaphorin) 6A) is a Protein Coding gene. Among its related pathways are L1CAM (TM), And Cytoplasmic interactions and L1CAM interactions. GO annotations related to this gene include Domain, (Semaphorin) 6A transmembrane signalling receptor activity and semaphorin receptor binding. The transmembrane semaphorin SEMA6A is expressed in developing neural tissue and is required for proper development of the thalamocortical projection.

SEMA7A Semaphorin 7A, GPI The protein encoded by this gene binds to cell surfaces through a Membrane Anchor (John glycosylphosphatidylinositol (GPI) linkage. The encoded glycoprotein is found on Milton Hagen Blood Group) activated lymphocytes and erythrocytes. This protein may be involved in immunomodulatory and neuronal processes. Defects in this gene can result in loss of bone mineral density (BMD).

SLC7A11 Solute Carrier Family 7 This gene encodes a member of a heteromeric, sodium-independent, anionic amino acid (Anionic Amino Acid transport system that is highly specific for cysteine and glutamate. In this system, Transporter Light Chain, designated Xc(-), the anionic form of cysteine is transported in exchange for glutamate. Xc- System), Member 11 This protein has been identified as the predominant mediator of Kaposi sarcoma-associated herpesvirus fusion and entry permissiveness into cells. Also, increased expression of this gene in primary gliomas (compared to normal brain tissue) was associated with increased glutamate secretion via the XCT channels, resulting in neuronal cell death.

SP1 The protein encoded by this gene is a zinc finger transcription factor that binds to GC-rich motifs of many promoters. The encoded protein is involved in many cellular processes, including cell differentiation, cell growth, apoptosis, immune responses, response to DNA damage, and chromatin remodeling.

SP3 Transcriptional factor that can act as an activator or repressor depending on isoform and/or post-translational modifications. Weak activator of transcription but can activate a number of genes involved in different processes such as cell-cycle regulation, hormone-induction and house-keeping

SP4 SP4 (Sp4 Transcription Factor) is a Protein Coding gene. GO annotations related to this gene include sequence-specific DNA binding transcription factor activity and transcription co-activator activity. Binds to GT and GC boxes promoters elements. Probable transcriptional activator.

SPRY2 Sprouty 2 This gene encodes a protein belonging to the sprouty family. The encoded protein contains a carboxyl-terminal cysteine-rich domain essential for the inhibitory activity on receptor tyrosine kinase signalling proteins and is required for growth factor stimulated translocation of the protein to membrane ruffles. In primary dermal endothelial cells this gene is transiently upregulated in response to fibroblast growth factor two. This protein is indirectly involved in the non-cell autonomous inhibitory effect on fibroblast growth factor two signalling. The protein interacts with Cas-Br-M (murine) ectropic retroviral transforming sequence, and can function as a bimodal regulator of epidermal growth factor receptor/mitogen-activated protein kinase signalling.

THRB thyroid , Nuclear hormone receptor that can act as a repressor or activator of transcription. It is one beta of the several receptors for thyroid hormone, and has been shown to mediate the biological activities of thyroid hormone.

TP53 tumor protein p53 Acts as a tumor suppressor in many tumor types. Induces growth arrest or apoptosis depending on the physiological circumstances and cell type.

WDR77 WD Repeat Domain 77 WDR77 is a component of the 20S PRMT5 (MIM 604045)-containing methyltransferase complex, which modifies specific arginines to dimethylarginines in several spliceosomal Sm proteins. This modification targets Sm proteins to the survival of motor neurons (SMN) complex for assembly into small nuclear ribonucleoprotein core particles.

WEE1 WEE1 G2 Checkpoint This gene encodes a nuclear protein, which is a tyrosine kinase belonging to the Ser/Thr Kinase family of protein kinases. This protein catalyzes the inhibitory tyrosine phosphorylation of CDC2/cyclin B kinase, and appears to coordinate the transition between DNA replication and mitosis by protecting the nucleus from cytoplasmically activated CDC2 kinase.

YWHAZ Tyrosine 3- This gene product belongs to the 14-3-3 family of proteins which mediate signal Monooxygenase/Tryptophan transduction by binding to phosphoserine-containing proteins. This highly conserved 5-Monooxygenase protein family is found in both plants and mammals, and this protein is 99% identical to Activation Protein, Zeta the mouse, rat and sheep orthologs. The encoded protein interacts with IRS1 protein, suggesting a role in regulating insulin sensitivity. Adapter protein implicated in the regulation of a large spectrum of both general and specialized signalling pathways.

ZBTB10 Zinc Finger And BTB ZBTB10 (Zinc Finger And BTB Domain Containing 10) is a Protein Coding gene. May be Domain Containing 10 involved in transcriptional regulation. hsa-miR-451a ABCB1 ATP-binding cassette, sub- Energy-dependent efflux pump responsible for decreased drug accumulation in multidrug- family B (MDR/TAP), resistant cells member 1

AKT1 v-akt murine thymoma viral AKT1 is one of 3 closely related serine/threonine-protein kinases (AKT1, AKT2 and oncogene homolog 1 AKT3) called the AKT kinase, and which regulate many processes including metabolism, proliferation, cell survival, growth and angiogenesis.

BCL2 B-Cell CLL/Lymphoma 2 Suppresses apoptosis in a variety of cell systems. Regulates cell death by controlling the mitochondrial membrane permeability.

CAB39 calcium binding protein 39 Component of a complex that binds and activates STK11/LKB1. In the complex, required to stabilize the interaction between CAB39/MO25 (CAB39/MO25alpha or CAB39L/MO25beta) and STK11/LKB1

CPNE3 Copine III Calcium-dependent membrane-binding proteins may regulate molecular events at the interface of the cell membrane and cytoplasm. This gene encodes a protein which contains two type II C2 domains in the amino-terminus and an A domain-like sequence in the carboxy-terminus.

DCBLD2 Discoidin, CUB And LCCL DCBLD2 (Discoidin, CUB And LCCL Domain Containing 2) is a Protein Coding gene. Domain Containing 2 Among its related pathways are Neuroscience related pathways

IKBKB Inhibitor Of Kappa Light The protein encoded by this gene phosphorylates the inhibitor in the inhibitor/NF-kappa-B Polypeptide Gene Enhancer complex, causing dissociation of the inhibitor and activation of NF-kappa-B. The encoded In B-Cells, Kinase Beta protein itself is found in a complex of proteins.

IL6R interleukin 6 receptor Part of the receptor for interleukin 6. Binds to IL6 with low affinity, but does not transduce a signal. Signal activation necessitates an association with IL6ST. Activation may lead to the regulation of the immune response, acute-phase reactions and hematopoiesis

MIF macrophage migration Pro-inflammatory cytokine. Involved in the innate immune response to bacterial pathogens. The expression of MIF at sites of inflammation suggests a role as mediator in inhibitory factor regulating the function of macrophages in host defense.

MMP2 matrix metallopeptidase 2 Ubiquitinous metalloproteinase that is involved in diverse functions such as remodelling of the vasculature, angiogenesis, tissue repair, tumor invasion, inflammation, and atherosclerotic plaque rupture. As well as degrading extracellular matrix proteins, can also act on several non-matrix proteins such as big endothelial 1 and beta-type CGRP promoting vasoconstriction.

MMP9 matrix metallopeptidase 9 May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration.

MYC v-myc avian Transcription factor that binds DNA in a non-specific manner, yet also specifically myelocytomatosis viral recognizes the core sequence 5'-CAC[GA]TG-3'. Activates the transcription of growth- oncogene homolog related genes

RAB14 RAB14, member RAS Involved in membrane trafficking between the Golgi complex and endosomes during early oncogene family embryonic development.

RAB5A RAB5A, Member RAS RAB5A (RAB5A, Member RAS Oncogene Family) is a Protein Coding gene. Diseases Oncogene Family associated with RAB5A include borna disease and choroideremia. Among its related pathways are Ras signalling pathway and Endocytosis.

TMED7 transmembrane emp24 Potential role in vesicular protein trafficking, mainly in the early secretory pathway. protein transport domain Appears to play a role in the biosynthesis of secreted cargo including processing and post- containing 7 translational modifications