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1 SUPPLEMENTARY FILES – DESCRIPTION AND LEGENDS Supplementary Data: Validation of amplicons, analysis of grade III IDC-NST of indeterminate phenotype and quantification of PPM1D protein levels by densitometric analysis. Supplementary Figure 1: Validation of CCND1 and EGFR amplifications in a series of 91 grade III-IDC-NST and CCNE1 amplifications on selected cases. (A) i) H&E ii) CISH iii) IHC for a) luminal tumour for CCND1 showing amplification and protein over-expression, b) basal-like tumour for CCND1 with normal copy number and no protein expression, c) EGFR non-amplified tumour with no protein expression d) EGFR amplified tumour showing strong protein expression. Amplification of CCNE1 in basal-like breast cancers. (B) Genome plots of two cases exhibiting amplification with the smallest region of overlap highlighted (i). FISH confirmation of CCNE1 amplification with RP11-327I05 (CCNE1) (red), showing amplification > 5 copies per nucleus (Bii). Supplementary Figure 2: Microarray-based comparative genomic hybridisation analysis of five grade III invasive ductal carcinomas of no special type of indeterminate phenotype. A) Representative genome plots. Log2 ratios are plotted on the Y axis against each clone according to genomic location on the X axis. The centromere is represented by a vertical dotted line. BACs categorised as displaying genomic gains as defined by aws ratios > 0.08 are highlighted in green and those categorised as genomic losses as defined by aws ratios < -0.08 are highlighted in red. Bi) The proportion of tumours in which each clone is gained (green bars) or lost (red bars) is plotted (Y axis) for each BAC clone according to genomic location (X axis). Vertical dotted lines represent chromosome centromeres. Bii) The proportion of tumours in which each clone is amplified (green bars) is plotted (Y axis) for each 2 BAC clone according to genomic location (X axis). Vertical dotted lines represent chromosome centromeres. Supplementary Figure 3: Densitometric analysis of western blots comparing the protein expression levels of PPM1D and β-tubulin. Cell lines harbouring PPM1D gene amplification: MCF-7, KPL-1, MCF-3B, BT474 and ZR-75.3; cell lines with normal PPM1D copy numbers: HeLa, MDA-MB-361, ZR-75.1, CAMA1, T47D and MDA-MB-231. Supplementary Table S1: Summary of the results of the immunohistochemical expression of oestrogen receptor, HER2, progesterone receptor, cytokeratins 5/6 and 14, EGFR and p53; chromogenic in situ hybridisation with probes for HER2, EGFR and CCND1; amplification status of PPM1D and mRNA expression levels of PPM1D as defined by qRT-PCR of all grade III invasive ductal carcinomas of no special type subjected to microarray-based comparative genomic hybridisation analysis and used for the construction of tissue microarrays 1 and 2. Supplementary Table S2: Summary of antibodies, clones, dilutions and scoring systems used for immunohistochemical analysis. Supplementary Table S3: Results of multi-Fisher’s exact test of gains and losses between basal-like, luminal and HER2 tumours. Supplementary Table S4: Recurrent amplifications in basal-like breast cancers. Supplementary Table S5: Results of multi-Fisher’s exact test of gains and losses between basal-like, luminal and HER2 tumours compared in a pair-wise fashion. 3 Supplementary Table S6: Results of multi-Fisher’s exact test of amplifications between basal-like, luminal and HER2 tumours. Supplementary Table S7: Results of multi-Fisher’s exact test of amplifications between basal-like, luminal and HER2 tumours compared in a pair-wise fashion. Supplementary Table S8: Recurrent amplifications in luminal breast cancers. Supplementary Table S9: Recurrent amplifications in HER2 breast cancers. Supplementary Table S1 aCGH series sample ER HER 2 PgR ck5/6 ck14 EGFR TP53 basal marker Nielsen groups Genomic pattern HER2 aCGH HER2 CISH CCND1 CCND1 CISH EGFR aCGH EGFR CISH PPM1D aCGH PPM1D expression number aCGH (Taqman) 1004 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified amplified 3.1256 1005 Positive Negative Positive Negative Negative Negative Positive Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.1132 1008 Positive Negative Positive Negative Negative Negative Positive Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5775 1010 Negative Negative Negative Positive Positive Negative Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.4085 1011 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.1381 1012 Negative Positive Negative Negative Negative Negative Negative Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified 1.2885 1013 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified not amplified 0.6439 1014 Negative Positive Negative Negative Negative Negative Positive Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified amplified 3.3754 1015 Positive Positive Positive Negative Negative Negative Negative Negative HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified not amplified 0.7452 1016 Negative Negative Negative Positive Positive Negative Positive Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.8112 1019 Positive Negative Positive Negative Negative Negative Positive Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1020 Positive Negative Positive Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified 0.8683 1021 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.5526 1022 Positive Negative Negative Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 0.5418 1024 Positive Negative Positive Negative Negative Negative Negative Negative Luminal simplex not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1.2073 1025 Positive Positive Negative Negative Negative Negative Negative Negative HER2 amplifier amplified amplified amplified amplified not amplified not amplified amplified 2.0300 1026 Positive Negative Negative Negative Positive Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 0.9993 1027 Positive Negative Negative Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified not amplified 1028 Negative Negative Negative Positive Negative Negative Negative Positive Basal sawtooth not amplified not amplified not amplified 0.5787 1029 Positive Negative Negative Positive Negative Negative Negative Positive Luminal simplex not amplified not amplified not amplified 0.5330 1030 Positive Positive Negative Negative Negative Negative Negative Negative HER2 sawtooth amplified amplified amplified not amplified not amplified not amplified not amplified 1.0201 1031 Negative Positive Negative Positive Negative Negative Positive Positive HER2 amplifier amplified amplified not amplified not amplified not amplified not amplified 0.4661 1032 Positive Negative Negative Negative Negative Negative Positive Negative Luminal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified 0.6805 1033 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified 0.4493 1035 Positive Negative Positive Negative Negative Negative Negative Negative Luminal amplifier not amplified not amplified amplified amplified not amplified not amplified not amplified 0.4849 1037 Positive Negative Negative Negative Positive Negative Negative Positive Luminal sawtooth not amplified not amplified amplified amplified not amplified not amplified not amplified 2.4002 1038 Positive Positive Negative Negative Negative Negative Negative Negative HER2 sawtooth amplified amplified not amplified not amplified not amplified not amplified amplified 2.3594 1040 Negative Negative Negative Positive Positive Positive Negative Positive Basal sawtooth not amplified not amplified not amplified not amplified not amplified not amplified 0.2890 1041 Positive Negative Positive Negative Negative Negative Negative Negative Luminal sawtooth not amplified not amplified amplified amplified not amplified not amplified not amplified 0.5934 1042 Positive Negative Positive Negative Negative Negative Positive Negative Luminal amplifier not amplified not amplified not amplified not amplified not amplified not amplified amplified 2.7133 1043 Positive Positive Negative Positive Negative Positive
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  • Differentially Methylated Genes

    Differentially Methylated Genes

    10/30/2013 Disclosures Key Rheumatoid Arthritis-Associated Pathogenic Pathways Revealed by Integrative Analysis of RA Omics Datasets Consultant: IGNYTA Funding: Rheumatology Research Foundation By John W. Whitaker, Wei Wang and Gary S. Firestein DNA methylation and gene regulation The RA methylation signature in FLS DNA methylation – DNMT1 (maintaining methylation) OA – DNMT3a, 3b (de novo methylation) RA % of CpG methylation: 0% 100% Nakano et al. 2013 ARD AA06 AANAT AARS ABCA6 ABCC12 ABCG1 ABHD8 ABL2 ABR ABRA ACACA ACAN ACAP3 ACCSL ACN9 ACOT7 ACOX2 ACP5 ACP6 ACPP ACSL1 ACSL3 ACSM5 ACVRL1 ADAM10 ADAM32 ADAM33 ADAMTS12 ADAMTS15 ADAMTS19 ADAMTS4 ADAT3 ADCK4 ADCK5 ADCY2 ADCY3 ADCY6 ADORA1 ADPGK ADPRHL1 ADTRP AFAP1 AFAP1L2 AFF3 AFG3L1P AGAP11 AGER AGTR1 AGXT AIF1L AIM2 AIRE AJUBA AK4 AKAP12 AKAP2 AKR1C2 AKR1E2 AKT2 ALAS1 ALDH1L1-AS1 ALDH3A1 ALDH3B1 ALDH8A1 ALDOB ALDOC ALOX12 ALPK3 ALS2CL ALX4 AMBRA1 AMPD2 AMPD3 ANGPT1 ANGPT2 ANGPTL5 ANGPTL6 ANK1 ANKMY2 ANKRD29 ANKRD37 ANKRD53 ANO3 ANO6 ANO7 ANP32C ANXA6 ANXA8L2 AP1G1 AP2A2 AP2M1 AP5B1 APBA2 APC APCDD1 APOBEC3B APOBEC3G APOC1 APOH APOL6 APOLD1 APOM AQP1 AQP10 AQP6 AQP9 ARAP1 ARHGAP24 ARHGAP42 ARHGEF19 ARHGEF25 ARHGEF3 ARHGEF37 ARHGEF7 ARL4C ARL6IP 5 ARL8B ARMC3 ARNTL2 ARPP21 ARRB1 ARSI ASAH2B ASB10 ASB2 ASCL2 ASIC4 ASPH ATF3 ATF7 ATL1 ATL3 ATP10A ATP1A1 ATP1A4 ATP2C1 ATP5A1 ATP5EP2 ATP5L2 ATP6V0CP3 ATP6V1C1 ATP6V1E2 ATXN7L1 ATXN7L2 AVPI1 AXIN2 B3GNT7 B3GNT8 B3GNTL1 BACH1 BAG3 Differential methylated genes in RA FLS BAIAP2L2 BANP BATF BATF2 BBS2 BCAS4 BCAT1 BCL7C BDKRB2 BEGAIN BEST1 BEST3