Table 2.
Comparison of clinical and molecular characteristics of identified CRC subtypes
|
iNMF step 1 | |||||
|---|---|---|---|---|---|
| Molecular feature | Type 1 | Type 2 | |||
| No. of tumor samples (AZTS) |
28 |
34 |
|||
| No. of tumor samples (all datasets) |
944 |
762 |
|||
| EMT expression signature |
mesenchymal |
epithelial |
|||
| Survival prognosis |
poor |
good |
|||
| Microsatellite status |
similar number of MSI and MSS CRC |
enriched with MSS CRC |
|||
|
iNMF step 2 | |||||
|
Molecular feature |
Subtype 1.1 |
Subtype 1.2 |
Subtype 1.3 |
Subtype 2.1 |
Subtype 2.2 |
| No. of tumor samples (AZTS) |
12 |
9 |
7 |
14 |
20 |
| No. of tumor samples (all datasets) |
313 |
303 |
328 |
313 |
449 |
| Average percent tumor foci area |
79.2 |
81.4 |
77.9 |
82.1 |
79.7 |
| Average percent tumor cells in foci |
76.3 |
74.5 |
80.0 |
73,8 |
73.7 |
| Average percent stromal cells in foci |
18.3 |
18.3 |
12.2 |
21.2 |
21.2 |
| Average percent inflammatory cells in foci |
3.8 |
7.2 |
6.4 |
3.5 |
4.7 |
| EMT expression signature |
strongly mesenchymal |
mesenchymal |
mesenchymal |
epithelial |
epithelial |
| Tumor location colon/left/rectum/right |
0/26/16/15 |
1/12/1/29 |
0/12/2/11 |
1/22/9/37 |
1/50/11/33 |
| Microsatellite status MSI/MSS |
14/15 |
42/9 |
2/35 |
27/31 |
4/50 |
| Tumor stage |
enriched in late stage CRC |
|
|
|
|
| Gender enrichment Female/Male/Unknown |
87/99/0 |
89/57/0 |
90/124/1 |
58/34/0 |
108/113/0 |
| Up-regulated genes | Ca-signaling and SRF-targeted | immune system-related | transporters | stress response and immune system-related | cell cycle and amino acid synthesis; genes on 13q13, 13q14, 13q32-34 and 20q11and 20q13 |
Differences in these characteristics were assessed using all datasets with available annotation.