Background
Methods
Tissue specimens
Biopsy | Group2
| Histology1
| L-score6
| pTpNM-stage (age, sex) | Relapse (years)3
| Tumour4
| Obs. (years) |
---|---|---|---|---|---|---|---|
181-I | PTC | L0 | T2AN0M0, (37, M) | No | PT | 15 | |
197-I | PTC-FV, thyroiditis | L2 | T1BN0M0, (50, M) | No | PT | 14 | |
198-IV | PTC, some histologic dediff. | L0 | T2AN1BM0, (13, F) | No | PT | 14 | |
219-II | PTC(diff) | PTC | L0 | T4AN0M0, (67, M) | No | PT | 6.0 (dead)5
|
222-IV | PTC | L0 | T1BN1BM0, (37, F) | No | PT | 14 | |
283-III | PTC, thyroiditis | L1 | T2AN1BM0, (22, F) | No | PT | 12 | |
300-V | PTC, squamous cell metaplasia | L1 | T3AN0M0, (43, F) | No | PT | 11 | |
317-IV | PTC | L0 | T1N1AM0, (30, F) | LN (9.1) | LN (r) | 11 | |
328-V | PTC | L0 | T2BN1AM0, (27, F) | No | PT | 10 | |
353-I | PTC-FV | L0 | T3BN0M0, (70, M) | No | PT | 9.0 (dead) | |
246-I | PTC-R-M1 | L0 | T4AN1AM0, (79, F) | LN, Lung (4.7) | LN (r) | 9.0 (dead) | |
247-IV | PTC-PD-M1, thyroiditis | L2 | T4AN1AM1, (83, F) | Lung metastases at diagnosis | PT | 0.4 (dead) | |
319-V | PTC-PD | L1 | T4AN1AM0, (79, F) | Residual tumour in trachea | LN | 2.0 (dead) | |
326-III | PTC(agg) | PTC-UD-M1 | L0 | T4AN1AM1, (72, M) | Lung metastases at diagnosis | PT | 0.1 (dead) |
345-III | PTC-PD, squamous cell metaplasia | L1 | T1BN1BM0, (37, M) | LN | LN | 3.4 (dead) | |
354-II | PTC-PD | L0 | T4AN0M0, (80, F) | No | PT | 10 | |
367-I | PTC-PD-R-M1 | L0 | T4AN0M1, (81, F) | Lung metastases at diagnosis | LN | 1.3 (dead) | |
379-I | PTC-PD | L1 | T4BN1BM0, (74, F) | No | PT | 9.0 |
Semiquantitative assessment of lymphocytes
RNA extraction and cDNA synthesis
TaqMan qRT-PCR
Gene Sequence (5'-> 3') | Amplicon (bp) | Genebank Acc.No |
---|---|---|
PDGFA | ||
(+) TCGATGAGATGGAGGGTCG | 71 | NM_033023 |
(-) ACCCGGACAGAAATCCAGTCT | ||
FAM-TGAGACCTCTGCACTTCCATCCCACG-TAMRA | ||
PDGFB
| ||
Applied Biosystems Assay On Demand, Hs00234042_m1 | 80 | NM_033016.1 |
PDGFC
| ||
(+) TATCTGATGAATATTTTCCTTCTGAACCAG | 96 | NM_016205 |
(-) GTAGCACTGAAGGACTCACAGCTTCT | ||
FAM-TTCTGCATCCACTACAACATTGTCATGCCACAATTC-TAMRA | ||
PDGFD
| ||
Applied Biosystems Assay On Demand, Hs00228671_m1 | 73 | NM_033135.3 |
PDGFRA
| ||
(+) CAAGAGGAACAGACACAGCTCGCAGA | 84 | NM_006206 |
(-) CTGCTGGAACCCGTCTCAAT | ||
FAM - CAAGAGGAACAGACACAGCTCGCAGA-TAMRA | ||
PDGFRB
| ||
Applied Biosystems Assay On Demand, Hs00182163_m1 | 86 | NM_002609.3 |
LTB2
| ||
Applied Biosystems Assay On Demand, Hs00242739_m1 | 78 | NM_002341.1 |
IL2RG
| ||
Applied Biosystems Assay On Demand, Hs00173950_m1 | 76 | NM_000206.1 |
FYB
| ||
Applied Biosystems Assay On Demand, Hs01061565_m1 | 123 | NM_001465.3 |
IL32
| ||
Applied Biosystems Assay On Demand, Hs00992441_m1 | 85 | NM_004221.4 |
Integration of TaqMan and microarray data
Data analysis
Analysis of networks based on recognized interactions
Results
TaqMan qRT-PCR of PDGF
TaqMan qRT-PCR of lymphocyte-specific gene expression
Semiquantitative assessment of tumour-infiltrating lymphocytes
Expression profiling
ID | Molecules in Network | Score | Top Functions |
---|---|---|---|
1 | ALP, ANXA6, C1R, CD37, COL5A1, CXCL9, CXCL10, ERK, FCER1G, Ifn gamma, Ige, IGFBP5, IgG, IGHG1, IGL@, Igm, IL12, IL2RG, IL7R, Interferon alpha, JAG1, MAFB, MBL2, MHC Class II, Notch, NOTCH1, NOTCH3, NTN4, OXTR, PDGFC, SET, TGFB3, TNFRSF17, TNFSF13B, ZNF354C
| 44 | Hematological System Development and Function, Tissue Development, Cellular Growth and Proliferation |
2 |
ABCD3, CACYBP, CD3, CSF2RB, CXCL5, IFN Beta, IL1, IL32, IL23A, ISG15, JAK, KYNU, LCP2, LSP1, LTA, LTB, NF-κB, NFAT complex, NFkB, NGFR, NPM1 (includes EG:4869), peptidase, PPIF, PSCDBP, REN, RIPK4, S100B, STAT4, TLR5, Tnf receptor, TNFAIP3, TYROBP, UBA7, VAV, VAV1
| 44 | Hematological System Development and Function, Immune and Lymphatic System Development and Function, Tissue Morphology |
3 |
ACTA2 (includes EG:59), Akt, Ap1, Calpain, CAPN3, CD4, CD53, COL4A2, COTL1, Cpla2, DOCK10, ENG, F Actin, FYB, HLA-DQB1, IL10RA, Integrin, LDL, MB, Myosin, NCK, Nfat, Pdgf, PER2, PER3, Pkc(s), Ras, SHROOM3, SUB1, SYF2, TCR, Tgf beta, TRA@, VCAM1, WIPF1
| 32 | Cell-To-Cell Signaling and Interaction, Hematological System Development and Function, Immune and Lymphatic System Development and Function |
4 |
AOF2, BAZ2A, BIRC5, Caspase, CBL, CCNA2, Cytochrome c, ELP3, GZMK, HCLS1, HIF1A, Histone h3, Hsp70, Hsp90, IFI27, IL2RB, Insulin, Mapk, NFKBIA, NR2F2, P38 MAPK, PFN1, PI3K, PLA2G7, Proteasome, RAD23B, RNA polymerase II, STAT, STAT1, STAT5a/b, UBD, Ubiquitin, Vegf, VIP, ZNF83 | 32 | Cell Cycle, Cardiac Hypertrophy, Cardiovascular Disease |
5 | Actin, BST2, C1R, CAMSAP1, CAP2, CCL17, CXCL9, DUSP5, FCGR2B, HLA-DMA, HLA-DOA, HLA-DQB1, HLA-DQB2, HMGN3, IFI44L, IFNG, IL17F, IL18R1, IL18RAP, IL1B, IL23A, LCP1, MARCH5, NFYB, PDE4B, PLEK, PRPF40A, PXMP3, RAB8B, SF1, SMAD1, SP110, SPAG16, TREM2, TYMP | 28 | Immunological Disease, Immune Response, Connective Tissue Disorders |
6 |
ABCD3, AHNAK, ARMCX3, ATF7IP, ATPase, BNIP3 (includes EG:664), C3, CLTC, COL4A2, COTL1, DAB2, ECM2, FBXO4, FBXO21, GRPEL1, HLTF, IFITM1, IKZF1, IKZF3, KIF1B, MYH6, NAE1, NEDD8, PPP2R4, retinoic acid, RNF10, SFTPC, SKP1, SMARCA4, SMARCA5, TERF1, TMEM150, UBE2M, VCAM1, VHL | 22 | Cell Cycle, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair |
7 | BCL2L1, COL6A1, COL6A2, EGFR, ERBB2, FOXN2, FYB, GALNT10, GKAP1, GULP1, HBB (includes EG:3043), HGS, HP, HPR, ITGB1, KRT7, LTA, LTB, MIST, MYST1, NFIB, NPTN, NUP210, PLAC8, POLD1, PTPRA, PTPRS (includes EG:5802), SH3BGRL, SKAP1, THBS2, TP53, TRIM22, UPF3A, WAP, ZFP36L2
| 22 | Immune and Lymphatic System Development and Function, Tissue Development, Cancer |
8 |
ADSSL1, ANG, APOD, ARNT2, beta-estradiol, bilirubin, C3, CACNG1, CALCR, CGRRF1, ESR2, GARS, GYPA, HGF, IPO7, LCAT, MAMLD1, NPM1 (includes EG:4869), OCLN, PLEKHA4, POLD4, PRIM2, PTPN2, RAP1GAP (includes EG:5909), RBM9, RBM17, RGS3, RPL5, S100A13, SFRS10, SNAP25, STX4, STX1A, STXBP6, YWHAZ | 18 | Drug Metabolism, Molecular Transport, Small Molecule Biochemistry |
9 | AEBP1, CD79A, CD79B, CDC34 (includes EG:997), CDC45L, CDON, CHST10, EBF1, FSH, GATAD2A, GFI1, GLRX, H2-M1, HLA-B, hydrogen peroxide, IDH2, IGHM, IGLL1, INSM1, KIAA0247, MAN2A1, MBD2, MIF, MYC, NEO1, PHKA2, SERINC3, TCF3, TERT, TGFBR3, UBE2L3, VPREB1 (includes EG:7441), YAF2, ZBTB7A, ZRANB1
| 18 | Cellular Development, Hematological System Development and Function, Immune and Lymphatic System Development and Function |