Dataset: Network Analysis of Skin Tumor Progression Identifies a Rewired Genetic Architecture Affecting Inflammation and Tumor Susceptibility (carcinomas)
Germline polymorphisms influence gene expression networks in normal mammalian tissues. Analysis of this genetic architecture can identify...
Germline polymorphisms influence gene expression networks in normal mammalian tissues. Analysis of this genetic architecture can identify single genes and whole pathways that influence to complex traits including inflammation and cancer susceptibility. Changes in the genetic architecture during the development of benign and malignant tumours have not been investigated. Here, we document major changes in germline control of gene expression during skin tumour development as a consequence of cell selection, somatic genetic events, and changes in tumour microenvironment. Immune response genes such as Interleukin 18 and Granzyme E are under germline control in tumours but not in normal skin. Gene expression networks linked to tumour susceptibility and hair follicle stem cell markers in normal skin undergo significant reorganization during tumour progression. Our data highlight opposing roles of Interleukin-1 signaling networks in tumour susceptibility and tumour progression and have implications for the development of chemopreventive strategies to reduce cancer incidence. Skin tumors were induced on dorsal back skin from a Mus spretus / Mus musculus backcross ([SPRET/Ei X FVB/N] X FVB/N) mice by treatment of dorsal back skin with dimethyl benzanthracene (DMBA) and tetradecanoyl-phorbol acetate (TPA). This treatment induced multiple benign papillomas as well as malignant squamous cell carcinomas (SCC) and spindle cell carcinomas. 60 carcinomas were harvested from 55 mice; five mice provided two carcinomas each.
- Species:
- mouse
- Samples:
- 60
- Source:
- E-GEOD-21247
- Updated:
- Dec.12, 2014
- Registered:
- Nov.11, 2014
| Sample | ORIGIN | MOUSE_ID | TAIL_ARRAY | COAT | NODAL_STATUS | SEX | WEEKS_TO_PAP | TUMOR_CLASS | DX | P53.MUTANT | DIFFERENTIATION | PAP_NO_20_WKS | CAGE | PAP_NO_24_WEEKS |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GSM531054 | F1BSF2 | 412103373C | MT-002 | White | nan | F | 10.0 | 2 | SCC | 0 | mod | 17 | 3 | 24 |
| GSM531055 | F1BSF2 | 4121093316 | MT-003 | White | 0.0 | F | 10.0 | 2 | SCC | 1 | mod | 9 | 3 | 10 |
| GSM531056 | F1BSF4 | 41214F7246 | MT-006 | White | 0.0 | M | 10.0 | 2 | spindle | 0 | poor | 12 | 4 | 10 |
| GSM531057 | F1BSF4 | 4121057439 | MT-007 | White | 1.0 | M | 10.0 | 1 | SCC | 0 | well | 7 | 5 | 18 |
| GSM531057 | F1BSF4 | 4121057439 | MT-007 | White | 1.0 | M | 10.0 | 1 | SCC | 0 | well | 7 | 5 | 18 |
| GSM531059 | F1BSF4 | 4020685C21 | MT-009 | Agouti | 0.0 | M | 10.0 | 2 | SCC | 1 | poor | 0 | 7 | 1 |
| GSM531060 | F1BSF4 | 4121484549 | MT-011 | White | nan | F | 10.0 | 2 | SCC | 0 | well | 13 | 8 | 12 |
| GSM53106 | F1BSF4 | 4121514D20 | MT-012 | Agouti | 0.0 | F | 10.0 | 2 | SCC | 0 | well | 10 | 8 | 14 |
| GSM53106 | F1BSF4 | 4121514D20 | MT-012 | Agouti | 0.0 | F | 10.0 | 2 | SCC | 0 | well | 10 | 8 | 14 |
| GSM531063 | F1BSF1 | 41216B4F5F | MT-014 | White | nan | M | 10.0 | 2 | nan | 1 | nan | 0 | 9 | 0 |
| GSM531064 | F1BSF1 | 41214E3C43 | MT-015 | Agouti | 1.0 | F | 10.0 | 2 | spindle | 1 | poor | 0 | 10 | 1 |
| GSM531065 | F1BSF2 | 41211A1A6F | MT-018 | White | 1.0 | M | 10.0 | 2 | SCC | 0 | mod | 7 | 11 | 14 |
| GSM531066 | F1BSF2 | 4123071F02 | MT-019 | White | nan | F | 10.0 | 1 | spindle | 0 | poor | 4 | 12 | 5 |
| GSM531067 | F1BSF3 | 41212C0A01 | MT-020 | White | nan | F | 10.0 | 1 | spindle | 1 | poor | 7 | 12 | 12 |
| GSM531068 | F1BSF3 | 4121362436 | MT-021 | White | nan | F | 10.0 | 2 | SCC | 0 | poor | 2 | 12 | 3 |
| GSM531069 | F1BSF4 | 412115080D | MT-022 | Agouti | 0.0 | M | 8.0 | 2 | SCC | 0 | well | 12 | 13 | 17 |
| GSM531070 | F1BSF4 | 4121192A61 | MT-023 | Agouti | 1.0 | M | 8.0 | 2 | SCC | 1 | mod | 1 | 13 | 3 |
| GSM53107 | F1BSF4 | 40674E112D | MT-024 | Agouti | 1.0 | F | 10.0 | 2 | SCC | 0 | well | 4 | 14 | 3 |
| GSM531072 | F1BSF4 | 41211B6A7F | MT-025 | Agouti | nan | F | 28.0 | 2 | SCC | 0 | mod | 0 | 14 | 0 |
| GSM531073 | F1BSF4 | 4121141A53 | MT-026 | Agouti | nan | F | 10.0 | 2 | SCC | 0 | well | 35 | 14 | 30 |
| GSM531074 | F1BSF1 | 412154011D | MT-027 | Agouti | 0.0 | M | 12.0 | 2 | SCC | 0 | mod | 6 | 15 | 9 |
| GSM531075 | F1BSF1 | 4121194F22 | MT-028 | White | 1.0 | M | 10.0 | 2 | spindle | 0 | poor | 9 | 15 | 13 |
| GSM531076 | F1BSF1 | 412156293F | MT-029 | White | 0.0 | F | 12.0 | 2 | spindle | 1 | mod | 0 | 16 | 1 |
| GSM531077 | F1BSF1 | 41212B5706 | MT-030 | Agouti | nan | F | 22.0 | 1 | spindle | 0 | poor | 0 | 16 | 1 |
| GSM531078 | F1BSF3 | 4121340F03 | MT-031 | White | 0.0 | F | 10.0 | 2 | SCC | 0 | well | 12 | 16 | 12 |
| GSM531079 | F1BSF3 | 4121134677 | MT-032 | Agouti | nan | F | 18.0 | 2 | SCC | 0 | well | 16 | 16 | 17 |
| GSM531080 | F1BSF3 | 412112404D | MT-033 | Agouti | 0.0 | M | 12.0 | 2 | SCC | 0 | well | 16 | 17 | 12 |
| GSM53108 | F1BSF3 | 41212B6361 | MT-035 | Agouti | 1.0 | M | 10.0 | 1 | spindle | 1 | poor | 6 | 17 | 3 |
| GSM531082 | F1BSF3 | 41212B6361 | MT-035 | Agouti | 1.0 | M | 10.0 | 2 | spindle | 1 | poor | 6 | 17 | 3 |
| GSM531083 | F1BSF3 | 4121533C60 | MT-036 | White | 0.0 | M | 20.0 | 2 | SCC | 0 | well | 3 | 18 | 5 |
| GSM531084 | F1BSF3 | 4122793F43 | MT-037 | Agouti | 0.0 | F | 24.0 | 1 | spindle | 0 | poor | 0 | 19 | 1 |
| GSM531085 | F1BSF4 | 41207B5D1D | MT-039 | Agouti | 1.0 | F | 24.0 | 1 | SCC | 0 | poor | 0 | 21 | 2 |
| GSM531086 | F1BSF4 | 412254156A | MT-040 | Agouti | 0.0 | F | nan | 1 | SCC | 0 | mod | 0 | 21 | 0 |
| GSM531087 | F1BSF4 | 412254156A | MT-040 | Agouti | 0.0 | F | nan | 2 | SCC | 0 | mod | 0 | 21 | 0 |
| GSM531088 | F1BSF4 | 4122660C6D | MT-042 | White | nan | M | 22.0 | 2 | nan | 0 | nan | 0 | 22 | 1 |
| GSM531089 | F1BSF1 | 4120627743 | nan | Agouti | 1.0 | M | 21.0 | 2 | nan | 0 | nan | 0 | 23 | 1 |
| GSM531090 | F1BSF1 | 412153120B | MT-043 | Agouti | 1.0 | F | 10.0 | 1 | SCC | 0 | well | 3 | 24 | 6 |
| GSM53109 | F1BSF2 | 4122537175 | MT-044 | White | nan | F | 18.0 | 2 | SCC | 0 | poor | 2 | 24 | 4 |
| GSM531092 | F1BSF2 | 41214E6B49 | MT-045 | Agouti | 0.0 | F | 20.0 | 2 | SCC | 1 | poor | 1 | 24 | 2 |
| GSM531093 | F1BSF2 | 41205E4B42 | MT-046 | Agouti | nan | F | 12.0 | 2 | SCC | 0 | mod | 7 | 24 | 10 |
| GSM531094 | F1BSF1 | 417F001308 | MT-047 | Agouti | 1.0 | F | 14.0 | 2 | SCC | 0 | well | 5 | 26 | 5 |
| GSM531095 | F1BSF1 | 417E3B343D | nan | White | nan | F | 18.0 | 2 | nan | 0 | nan | 3 | 26 | 6 |
| GSM531096 | F1BSF1 | 417F000558 | MT-049 | White | 1.0 | F | 12.0 | 1 | spindle | 0 | poor | 23 | 26 | 19 |
| GSM531097 | F1BSF3 | 417E3F3431 | MT-050 | White | 0.0 | M | 14.0 | 1 | spindle | 0 | poor | 2 | 28 | 3 |
| GSM531098 | F1BSF3 | 417E2B3451 | MT-052 | Agouti | nan | M | 16.0 | 2 | nan | 0 | nan | 3 | 28 | 2 |
| GSM531099 | F1BSF3 | 417F00555F | MT-053 | White | 0.0 | F | nan | 2 | SCC | 0 | mod | 5 | 29 | 6 |
| GSM531100 | F1BSF4 | 417F254972 | MT-055 | Agouti | 0.0 | M | 18.0 | 2 | SCC | 1 | poor | 3 | 30 | 2 |
| GSM53110 | F1BSF4 | 4122726431 | MT-058 | White | nan | M | 10.0 | 1 | spindle | 0 | poor | 17 | 31 | 17 |
| GSM531102 | F1BSF4 | 4122702E5D | MT-060 | Agouti | nan | M | 18.0 | 2 | SCC | 0 | mod | 1 | 31-2 | 1 |
| GSM531103 | F1BSF4 | 4100614925 | MT-062 | Agouti | 1.0 | F | 10.0 | 2 | SCC | 0 | poor | 21 | 32 | 17 |
| GSM531104 | F1BSF4 | 4120762510 | MT-063 | White | 0.0 | F | nan | 2 | SCC | 0 | mod | 0 | 32 | 0 |
| GSM531105 | F1BSF1 | 41247A0B40 | MT-066 | Agouti | nan | M | 10.0 | 1 | nan | 0 | nan | 14 | 35 | 29 |
| GSM531106 | F1BSF1 | 41247A0B40 | MT-066 | Agouti | nan | M | 10.0 | 2 | nan | 0 | nan | 14 | 35 | 29 |
| GSM531107 | F1BSF1 | 4217072C08 | MT-068 | Agouti | 0.0 | M | 14.0 | 1 | spindle | 0 | poor | 2 | 35 | 7 |
| GSM531108 | F1BSF1 | 412254163 | MT-070 | White | 1.0 | M | 16.0 | 2 | SCC | 0 | mod | 3 | 36 | 4 |
| GSM531109 | F1BSF1 | 4217037671 | MT-071 | White | 0.0 | F | 14.0 | 2 | SCC | 0 | mod | 6 | 37 | 4 |
| GSM531110 | F1BSF2 | 4121663E37 | MT-005 | White | 1.0 | F | 10.0 | 2 | SCC | 1 | poor | 15 | 3 | 17 |
| GSM53 | F1BSF4 | 41215B6D13 | MT-064 | White | nan | F | nan | 2 | SCC | 1 | poor | 0 | 32 | 0 |
| GSM531112 | F1BSF1 | 41207A546C | MT-069 | White | nan | M | 22.0 | 2 | SCC | 1 | well | 0 | 35 | 0 |
| GSM531113 | F1BSF1 | 4121683825 | MT-072 | White | nan | F | 12.0 | 1 | nan | 1 | nan | 2 | 37 | 5 |