Supplementary data Fig 1: Comparison of differential mRNA expression data obtained by qRT-PCR and microarray (relative expression in tumors compared to normal tissues).

The upper and lower limits of each box stand for the upper and the lower quartiles, respectively; bold lines represent medians; whiskers represent extreme measurements. Regulation of CA12, BID, CLU, CCND2, TFF3, LRP1B, DUSP1, THSD7A was confirmed on 11 tumor/non-tumor pairs of PTC

Supplementary data Fig 2 Median age at operation in the exposed and non exposed samples

Age

at

aper

atio

n

Non exposedExposed

p = 0.006

Supplementary data Figure 3 Hierarchical Clustering (pearson correlation, pairwise average-linkage) (Gene Pattern) on the basis of all probes after age-adjustment; Arrows point the exposed tissues

Supplementary data Fig 4: Enrichment plot of the gene signature identified by SAM in the Polish data setof normal exposed and non exposed thyroid tissues

Supplementary Table 1: Patient information, clinical data and gene alterations for the PTC samples used for microarray analyses.

Exposed Paired

samples oblast sexAge at

operationdominant subtype TNM

Ret_exp_status ret/ptc_type

BRAF mutation

Lymphocytic infiltration

% epithelial.cells (tumour)

% epithelial.cells (normal)

lesion_size(cm)

UA147 Zhytomyr F 16.5 P T2N0M0 NRE neg pos 0% 60-70 50-60 2.30UA242 Kiev F 17.7 P T3N1aM0 unbalanced TK not-defined neg 0% 30-40 40-50 4.50UA144 Chernigov F 14.7 F T3N1aM0 unbalanced TK RET/PTC1 neg 0% 50-60 50-60 1.20UA343 Kiev F 18.5 S T2N1aM0 unbalanced TK NA neg 30-40% 70-80 40-50 2.80UA145 Zhytomyr M 15.8 Mixed (SF) T1N1aM0 balanced neg neg 0% 70-80 50-60 1.10UA103 Zhytomyr F 15.0 Mixed (FS) T3N1abM1 unbalanced TK RET/PTC3 neg 1-10% 60-70 40-50 2.70UA130 Pripyat F 17.7 Mixed (SF) T1N1aM0 N/A neg N/A 0% 60-70 50-60 0.80UA243 Kiev M 17.0 F T3N1aM0 NRE neg neg 0% 50-60 30-40 2.50UA366 Sumy M 15.6 P T1N0M0 NRE neg neg 0% 40-50 40-50 0.90UA446 Kiev M 17.1 P T1N0M0 NRE neg neg 0% 60-70 30-40 1.40UA502 Zhytomyr F 16.9 Mixed (PS) T3N1abM1 unbalanced TK RET/PTC3 neg 0% 60-70 40-50 3.00UA165 Chernigov F 16.7 F T1N0M0 NRE neg neg 0% 40-50 40-50 1.50UA686 Chernigov M 18.1 Mixed (PF) T3N1aM0 NRE neg neg 0% 40-50 40-50 3.20UA601 Kiev M 16.9 F T3N1abM0 NRE RET/PTC3 pos 1-10% 50-60 40-50 5.00UA758 Zhytomyr F 18.8 S (F areas) T2N1aM0 unbalanced TK RET/PTC1 neg 1-10% 60-70 40-50 1.70UA771 Kiev F 20.0 FP T1N0M0 unbalanced EC RET/PTC1 neg 1-10% 60-70 40-50 1.70UA886 Chercassy F 24.5 SP T3N0M0 NRE RET/PTC1 neg 40-50% 60-70 30-40 1.00UA905 Sumy F 21.2 SP T3N0M0 NRE neg pos 1-10% 40-50 30-40 0.90UA954 Kiev F 19.8 F (S areas) T3N1aM0 unbalanced TK neg neg 1-2% 20-30 40-50 0.50UA249 Rovno F 16.8 F T2N1aM0 NRE RET/PTC3 (weak) neg 0% 50-60 40-50 3.50UA515 Chernigov F 17.7 P T1N0M0 NRE neg pos 0% 50-60 40-50 0.70UA501 Chernigov F 16.6 P T3N1aM0 N/A NA N/A 0% 30-40 50-60 1.60

Non exposed Paired

samplesUA1030 Sumy M 12.8 S T3N1aM0 unbalanced TK RET/PTC3 neg 0% 80-90 50-60 0.80UA939 Sumy F 17.7 Mixed (PF) T1N0M0 NRE neg pos 0% 20-30 30-40 0.60UA710 Chernigov F 16.7 P T1N1aM0 NRE neg neg 10-20% 40-50 40-50 1.30UA615 Sumy F 15.4 Mixed (FS) T3N1abM0 unbalanced TK RET/PTC3 neg 1-10% 20-30 40-50 3.50UA691 Chercassy F 7.7 P T3N0M0 NRE neg neg 0% 40-50 40-50 1.80UA964 Sumy F 15.2 P T3N1aM0 NRE neg pos 0% 60-70 40-50 4.50UA307 Zhytomyr F 13.1 F T1N0M0 unbalanced TK RET/PTC1 neg 30-40% 30-40 30-40 1.00

UA1144 Sumy M 16.3 P T1N0M0 NRE neg neg 0% 20-30 50-60 1.30UA1175 Kiev M 16.6 F T1N0M0 NRE neg neg 0% 60-70 50-60 2.50UA1502 Kiev M 19.3 FS T3N0M0 NRE neg NA 0% 30-40 50-60 4.30UA1190 Kiev F 16.6 PS T1N0M0 unbalanced TK neg neg 1-10% 40-50 50-60 1.50UA1208 Kiev F 15.2 P T2N1aM0 unbalanced TK RET/PTC1 neg 1-10% 40-50 40-50 2.40UA1224 Chernigov F 17.0 PF T3N0M0 NRE neg NA 1-10% 60-70 50-60 0.80UA1243 Chernigov F 18.2 S(P areas) T3N1a,bM0 NRE neg neg 1-10% 70-80 40-50 2.80UA1247 Zhytomyr F 15.6 P T1N0M0 NRE neg pos 0% 60-70 60-70 1.70UA1328 Sumy F 18.0 SP T3N1a,bM0 NRE neg neg 40-50% 40-50 30-40 3.80UA1337 Sumy F 18.3 P (S areas) T3N0M0 unbalanced TK neg neg 0% 80-90 40-50 5.20UA1367 Kiev F 17.7 F (S areas) T1N0M0 NRE neg neg 50-60% 50-60 40-50 1.50UA1426 Kiev F 16.6 PF T2N0M0 NRE neg neg 0% 70-80 40-50 3.00UA1486 Chercassy F 20.7 F T1N1aM0 NRE NA pos 1-2% 50-60 40-50 1.50UA1319 Zhytomyr F 12.4 PS T3N1a,bM0 unbalanced TK RET/PTC1 neg 10-20% 40-50 40-50 3.00UA574 Kiev F 13.6 Mixed (SP) T2N1aM0 balanced neg neg 20-30% 70-80 40-50 2.50

UA1053 Sumy F 16.1 F T1N0M0 unbalanced TK RET/PTC1 neg 0% 70-80 50-60 1.20

TumorsUA465T Chernigov M 13.9 S T3N0M0 unbalanced TK RET/PTC3 neg 80-90 2.10UA411T Kiev F 13.2 S T1N0M0 N/A neg N/A 70-80 1.30UA752T Kiev M 16.5 Mixed (FS) T1N0M0 N/A neg N/A 40-50 1.10UA607T Kiev F 14.0 Mixed (PFS) T3N1abM0 NRE neg neg 40-50 4.50UA557T Kiev F 13.1 Mixed (PF) T3N1aM0 N/A neg N/A 50-60 1.70

The PTCs were characterized for the presence of RET/PTC rearrangements and for the most frequent BRAF mutation, V600E, via DNA direct sequencing (details in ref. 3). Expression of the RET gene was classified as balanced (BAL) when expression of the extracellular domain (EC) and tyrosine kinase domain (TK) were the same, as unbalanced TK when the expression of the TK was significantly higher than expression of the EC domain, as unbalanced EC when the EC domain was more highly expressed compared with expression of the TK domain, and as nonRET expressor (nre) when no expression, or very low expression, of both domains was detectable.NA= not available, F = female, M = male, tbno = Chernobyl Tissue Bank number, age op = age at operation;Subtypes: P = papillary, F = follicular variant, S = solid.TNM = tumor node metatstasis status according to classification of malignant tumors of UICC (Union for International Cancer Control)

Suppl. Table 1 (continued):

Supplementary data Table 2: Sequences of the primers used for real-time RT-PCR (fwd: forward, rev: reverse)

Supplementary data Table 3: Top of the 50 most upregulated genes in the normal exposed tissues compared to the normal non exposed tissues (SAM Stanford)

Gene symbol Gene Name Fold Change q-value(%)TMEM49 transmembrane protein 49 2.99 4.51RBM47 RNA binding motif protein 47 2.55 0.64IL6ST interleukin 6 signal transducer (gp130, oncostatin M receptor) 2.51 0.00DUSP1 dual specificity phosphatase 1 2.32 1.31SFRS6 splicing factor, arginine/serine-rich 6 2.28 0.87GNAL guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type 2.28 1.31MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non-protein coding) 2.27 4.95S100A10 S100 calcium binding protein A10 2.26 4.17SFRS4 splicing factor, arginine/serine-rich-4 2.24 4.17CALD1 caldesmon 1 2.22 3.13SAR1A SAR1 homolog A (S. cerevisiae) 2.19 1.31CHP calcium binding protein P22 2.18 0.87DLG1 discs, large homolog 1 (Drosophila) 2.17 0.00SLC39A14 solute carrier family 39 (zinc transporter), member 14 2.17 0.64MBNL2 muscleblind-like 2 (Drosophila) 2.17 0.00CTDSPL2 CTD (carboxy-terminal domain, RNA polymerase II, polypeptide A) small phosphatase like 2 2.15 0.64AFF4 AF4/FMR2 family, member 4 2.15 0.87RHOB ras homolog gene family, member B 2.13 0.64TFRC transferrin receptor (p90, CD71) 2.11 0.87MALAT1 metastasis associated lung adenocarcinoma transcript 1 (non-protein coding) 2.07 3.85EIF2AK2 eukaryotic translation initiation factor 2 2.06 3.48RBBP9 retinoblastoma binding protein 9 2.03 1.31TRIB1 tribbles homolog 1 (Drosophila) 1.99 0.87C5orf22 chromosome 5 open reading frame 22 1.99 0.00FAM62B family with sequence similarity 62 (C2 domain containing) member B 1.98 0.00EIF1 eukaryotic translation initiation factor 1 1.97 3.85BCL2L2 BCL2-like 2 1.96 0.64SSFA2 sperm specific antigen 2 1.95 0.64AFF4 AF4/FMR2 family, member 4 1.94 2.14GNAL guanine nucleotide binding protein (G protein), alpha activating activity polypeptide, olfactory type 1.93 3.48PURB purine-rich element binding protein B 1.93 4.95SUPT16H suppressor of Ty 16 homolog (S. cerevisiae) 1.91 1.31NCRNA00084 non-protein coding RNA 84 1.91 4.51RBBP9 retinoblastoma binding protein 9 1.91 4.95GALC galactosylceramidase 1.91 4.17AKT2 v-akt murine thymoma viral oncogene homolog 2 1.90 4.95AP1S3 adaptor-related protein complex 1, sigma 3 subunit 1.90 1.57FUS fusion (involved in t(12;16) in malignant liposarcoma) 1.90 4.17FLT1 fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor) 1.89 4.95TTC26 tetratricopeptide repeat domain 26 1.89 0.64RNF38 ring finger protein 38 1.88 0.87CXADR coxsackie virus and adenovirus receptor 1.88 3.85AHCYL2 S-adenosylhomocysteine hydrolase-like 2 1.87 1.62C10orf18 chromosome 10 open reading frame 18 1.87 0.64SCAMP1 secretory carrier membrane protein 1 1.86 2.14EXOC4 exocyst complex component 4 1.86 1.57TOB1 transducer of ERBB2, 1 1.85 0.64OGDH oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) 1.85 0.00NCAM1 neural cell adhesion molecule 1 1.85 4.17USP33 ubiquitin specific peptidase 33 1.85 0.87

Supplementary data Table 4: molecular functions of gene ontology categories enriched in exposed normal tissues and statistical signifiance following the analysis of the 793 probes discriminating normal non exposed/exposed tissues with DAVID software

Term PValue FDRGO:0000166: nucleotide binding 1.27E-08 1.91E-05GO:0003723: RNA binding 4.44E-08 6.67E-05GO:0019787: small conjugating protein ligase activity 6.47E-05 0.0971797GO:0017076: purine nucleotide binding 9.45E-05 0.1418328GO:0032553: ribonucleotide binding 1.14E-04 0.170456GO:0032555: purine ribonucleotide binding 1.14E-04 0.170456GO:0019901: protein kinase binding 1.56E-04 0.2341273GO:0019900: kinase binding 1.71E-04 0.2565218GO:0016881: acid-amino acid ligase activity 2.55E-04 0.3824837GO:0003924: GTPase activity 4.70E-04 0.7041631GO:0019899: enzyme binding 9.11E-04 1.3600265GO:0016879: ligase activity, forming carbon-nitrogen bonds 0.001401 2.0840762GO:0030554: adenyl nucleotide binding 0.0030592 4.4983173GO:0001883: purine nucleoside binding 0.0031182 4.5831353GO:0032561: guanyl ribonucleotide binding 0.0032155 4.7229929GO:0019001: guanyl nucleotide binding 0.0032155 4.7229929GO:0019887: protein kinase regulator activity 0.0036581 5.3565547

Supplementary data Table 5: GSEA analysis with previously published radiation signatures (11-13,40): class phenotypes: normal non exposed versus normal exposed tissues (Metric for ranking genes: signal to noise).DNA repair signatures: NER, NER-RELATED, BER, MMR, HR, NHEJ: Wood R et al 2005: Human DNA repair genes. Mutation Research 577: 275–283.