Background
Methods
Study design and participants
Prospective CCP cohort study
Patient assessments
Pilot and validation-phase patient cohorts
Isolation and profiling of serum miRNA
Quantitative reverse transcription (qRT)-PCR on custom miRNA cards
miRNAs network analysis
Statistical analysis
Results
Patient cohorts - progression from CCP+ status to VERA
Pilot phase of serum miRNA profiling
HC | CCP | VERA | CCP vs. HC | VERA vs. HC | CCP to VERA (within progressors) | |||
---|---|---|---|---|---|---|---|---|
miR | dCt median (IQR) | dCt median (IQR) | dCt median (IQR) | FD between medians | FD between medians | Median (IQR) ddCt | Median FC | Number upregulated (/12) |
miR-16 | -6.3 (-7.1, -6.0) | -7.1 (-7.6, -7.0) | -7.6 (-8.2, -7.4) | 1.7 | 2.4 | -0.4 (-1.1, -0.1) | 1.3 | 10 |
miR-18a | 0.1 (-0.8, 1.3) | 1.3 (0.3, 2.0) | -0.1 (-1.0, 0.4) | -2.4 | 1.1 | -1.6 (-2.0, -1.0) | 3.1 | 10 |
miR-19a | -0.9 (-1.6, 1.0) | -2.4 (-2.8, -1.9) | -3.2 (-3.5, -2.8) | 2.9 | 5.0
| -0.6 (-1.7, 0.1) | 1.5 | 9 |
miR-21 | -2.8 (-4.1, -2.5) | -3.8 (-4.4, -3.3) | -4.3 (-4.8, -4.1) | 2.0 | 2.7 | -0.7 (-1.2, -0.2) | 1.6 | 9 |
miR-22 | 4.2 (0.5, 4.8) | 3.0 (1.5, 5.1) | 0.9 (0.6, 1.5) | 2.2 | 9.4
| -2.1 (-3.6, -1.5) |
4.3
|
12
|
miR-26b | -1.4 (-3.0, 0.2) | -3.1 (-3.4, -1.8) | -3.6 (-4.2, -2.8) | 3.3 | 4.7
| -0.7 (-2.3, -0.3) | 1.7 | 10 |
miR-34a | -0.2 (-2.1, 0.8) | -0.1 (-0.3, 1.0) | -0.6 (-2.1, 0.2) | -1.1 | 1.3 | -0.1 (-0.9, 0.3) | 1.1 | 6 |
miR-101 | 2.5 (1.7, 3.2) | 1.6 (1.3, 1.8) | 0.4 (-0.3, 0.9) | 1.9 | 4.3
| -1.1 (-1.9, -0.6) | 2.1 | 11 |
miR-132 | -1.6 (-2.0, -1.4) | -1.7 (-2.1, -1.6) | -2.5 (-2.7, -2.2) | 1.0 | 1.8 | -0.8 (-1.1, -0.3) | 1.7 | 11 |
miR-142-3p | -2.3 (-4.5, -1.3) | -4.4 (-4.5, -3.8) | -5.0 (-5.2, -4.5) | 4.2
| 6.2
| -0.4 (-1.1, -0.3) | 1.4 | 10 |
miR-142-5p | 3.9 (2.9, 5.7) | 3.0 (2.4, 5.5) | 1.7 (1.5, 4.3) | 1.9 | 4.7
| -1.3 (-1.4, -0.3) | 2.4 | 10 |
miR-146a | -7.3 (-7.5, -6.5) | -7.1 (-7.6, -7.0) | -7.5 (-7.7, -7.3) | -1.2 | 1.1 | -0.5 (-0.8, 0.2) | 1.4 | 8 |
miR-155 | -0.9 (-2.3, 1.5) | 0.1 (-0.5, 1.1) | -0.5 (-0.7, -0.3) | -2.1 | -1.4 | -0.3 (-1.3, 0.1) | 1.2 | 8 |
miR-195 | -2.5 (-3.0, -1.6) | -0.4 (-3.4, 0.2) | -2.9 (-4.2, -0.5) | -4.6
| 1.3 | -1.1 (-2.0, -0.5) | 2.1 | 11 |
miR-197 | -3.5 (-3.3, -1.3) | 0.6 (-1.5, 2.9) | 0.6 (-2.5, 2.2) | -16.8
| -16.5
| -0.6 (-2.7, 1.3) | 1.5 | 7 |
miR-203 | 2.3 (1.8, 3.0) | 3.0 (2.1, 3.0) | 2.9 (2.6, 3.4) | -1.5 | -1.5 | 0.0 (-0.4, 0.6) | 1.0 | 6 |
miR-210 | 3.9 (0.1, 5.0) | 3.1 (2.2, 3.4) | 1.5 (1.1, 1.8) | 1.8 | 5.1
| -1.8 (-2.9, -0.3) | 3.4 | 10 |
miR-223 | -9.3 (-9.6, -8.8) | -9.9 (-9.9, -9.6) | -10.3 (-10.4, -10.0) | 1.5 | 2.0 | -0.4 (-0.6, 0.2) | 1.3 | 6/9a
|
miR-361 | -0.1 (-1.1, 1.1) | 2.1 (-0.5, 2.5) | 0.6 (-0.2, 0.7) | -4.7
| -1.7 | -1.5 (-2.1, -1.0) | 2.9 | 11 |
miR-374d
| -2.2 (-3.4, -2.1) | -3.2 (-3.7, -2.0) | -4.1 (-4.3, -3.9) | 2.0 | 3.8 | -0.6 (-1.0, -0.4) | 1.5 | 12 |
miR-382 | -0.7 (-1.2, 0.5) | 1.4 (0.9, 2.7) | -0.1 (-1.2, 0.5) | -4.1
| -1.5 | -2.0 (-2.8, -0.8) |
4.1
|
11
|
miR-454d
| -1.3 (-2.8, 0.2) | -2.3 (-3.2, -0.1) | -3.0 (-3.3, -1.3) | 1.9 | 3.3 | -0.5 (-1.1, -0.2) | 1.4 | 10 |
miR-486-3p | 4.3 (2.5, 5.6) | 4.9 (2.5, 6.2) | 3.5 (3.1, 4.3) | -1.5 | 1.8 | -2.0 (-3.1, 0.2) |
4.1
|
9
|
miR-520c-3p | 2.3 (0.3, 2.9) | -0.4 (-1.6, 2.4) | -1.1 (-1.4, 0.5) | 6.3
| 10.6
| 0.3 (-1.7, 0.6) | -1.3 | 5 |
miR-579c
| 4.2 (3.5, 5.0) | 3.5 (3.1, 3.7) | 2.4 (1.8, 2.9) | 1.6 | 3.6 | -1.2 (-1.7, -0.3) | 2.2 | 11 |
miR-590-3P | 5.2 (2.9, 5.8) | 3.2 (2.3, 3.9) | 2.4 (2.2, 3.1) | 3.9 | 6.9
| -0.9 (-1.1, 0.2) | 1.9 | 8 |
miR-590-5p | 1.2 (0.7, 1.4) | -0.4 (-1.2, -0.2) | -1.3 (-1.6, -0.7) | 3.0 | 5.6
| -0.5 (-1.1, -0.3) | 1.4 | 10 |
miR-598 | 3.7 (3.1, 4.3) | 2.8 (2.5, 3.6) | 1.5 (1.4, 1.9) | 1.8 | 4.6
| -1.2 (-1.7, -0.8) | 2.2 | 12 |
miR-628-5p | 3.0 (-8.4, 7.9) | -7.2 (-8.3, 3.9) | -2.9 (-7.8, 2.2) | 1174.6
| 61.3
| 0.4 (-1.6, 1.7) | -1.3 | 5 |
miR-15b# | 9.9 (2.6, 11.4) | 6.2 (5.6, 8.4) | 4.0 (2.0, 4.4) | 13.3b
| 58.5b
| -2.6 (-4.0, -1.8) | 6.1b
| 11/11 |
miR-335# | 6.1 (5.6, 8.3) | 6.5 (5.2, 8.1) | 4.2 (3.9, 5.1) | -1.4b
| 3.6b
| -1.9 (-3.9, -1.0) | 3.8b
| 12 |
HC-CCP+ and HC-VERA comparison
Matched CCP+ to VERA serum miRNA evaluation
Validation phase of serum microRNA profiling
HC-CCP+ (progressor or non-progressor) and HC-VERA comparison
Baseline miRNA profile of progressors vs non-progressors
CCP+ to VERA | CCP+ to no progression | CCP+ non progressor | CCP+ progressor | Progressors vs. non progressors | ||||
---|---|---|---|---|---|---|---|---|
Median FC (IQR 1st, 3rd) | Median FC (IQR 1st, 3rd) | B/L median dCt (IQR) | B/L median dCt (IQR) | FD between medians | Area under ROC curve (90% CI) | Sens | Spec | |
Pilot phase | ||||||||
miR-22 | 4.3 (2.8, 12.1) | - | - | - | - | - | - | |
miR-382 | 4.1 (1.7, 6.9) | - | - | - | ||||
miR-486-3p | 4.1 (0.9, 8.6) | - | - | - | - | - | - | |
Validation Phase | ||||||||
miR-22 | 2.5 (-2.2, 15.3) | 3.4 (2.3, 12.6) | 7.4 (4.1, 8.2) | 3.1 (1.8, 7.3) | 19.7 | 0.68 (0.48, 0.82) | 63% | 100% |
miR-382 | 1.2 (-2.1, 2.7) | 2.4 (1.0, 2.6) | 1.1 (0.0, 1.8) | -0.2 (-0.5, 1.9) | 2.5 | 0.57 (0.40, 0.75) | 75% | 58% |
miR-486-3p | 2.2 (-2.5, 6.0) | 1.0 (-1.4, 3.0) | 3.4 (1.7, 3.9) | 3.9 (2.6, 5.0) | -1.4 | 0.55 (0.36, 0.72) | 50% | 75% |