PAGE 7 OF 11 GeneName Methylated EPHA2 HOXD11 HOXD9 PPM1G RAB6B MFI2 IL17RB HHIP SFRP2 CRMP1 PKD2 PCDHGA10 HOXA2 HOXA3 EPDR1 TAC1 MTSS1 TNFRSF10D CUGBP1 NFYB PCDH8 ONECUT1 CDH8 PPP1R14A IL28A/B FOXA2 PLCG1 RTEL1 PRR5 SHOX Demethylated BRDT RRM2 BCL11A DUB3 RHOG SULT1A1 BECN1 STRA13 MAPK1 Nucleic Acids Research, 2009, Vol. 37, No. 12 e89 Table 1. Short list of genes selected from Supplementary Table 4 with altered CpG islandsa Name Location Importance Ephrin receptor A2 Homeodomain protein Homeodomain protein Protein phos’tase 1G Ras oncogene family Melanoma-associated Ag 2 Interleukin 17 receptor B Hedgehog interacting protein Secreted frizzled related protein 2 Collapsin response mediator prot 1 Polycystic kidney disease 2 Protocadherin gamma, subfam A Homeodomain protein Homeodomain protein Ependymin related protein 1 Tachykinin, precursor 1 Metastasis suppressor 1 Tumor necrosis factor superfamily CUG triplet rpt, RNA bind prot Nuc. transcr. fctr Y beta Protocadherin 8 Onecut homeobox domain 1 Cadherin 8, type 2 Protein phos’tase 1 reg subunit 14A Interleukin 23 interferon like Forkhead box A2 Phospholipase C gamma 1 Regulator telemere elong.helicase Proline rich 5 (renal) Short stature homeobox Bromo domain prot testis spec. Ribonucleotide reductase M2 B cell lymphoma protein 11A Deubiquinating enzyme 3 Ras homolog gene family G Sulfotransferase family BCL2 interacting protein Stimulated by retinoic acid 13 Map kinase 1/ERK chr1_16196139_16227870 chr2_176795292_176795763 chr2_176807548_176807855 chr2_27544151_27545066 chr3_135097550_135098100 chr3_198245561_198245644 chr3_53855151_53855185 chr4_145923993_145924160 chr4_155067811_155068195 chr4_6010436_6010699 chr4_89285337_89285745 chr5_140768066_140768556 chr7_26919212_26919376 chr7_26942376_26942852 chr7_37728939_37729281 chr7_97005815_97006071 chr8_125810238_125810819 chr8_23077244_23077520 chr11_47531208_47531279 chr12_103034912_103035336 chr13_52320446_52320832 chr15_50874380_50874668 chr16_60627191_60627579 chr19_43439132_43439444 chr19_44447259_44447674 chr20_22514937_22515431 chr20_39198472_39198934 chr20_61758790_61759467 chr22_43445548_43445907 chrX_551021_551222 chr1_92126308_92126790 chr2_10212057_10212966 chr2_60694090_60694350 chr4_9040795_9041453 chr11_3819507_3820119 chr16_28542367_28542407 chr17_38229845_38229898 chr17_77574908_77575250 chr22_20546877_20547317 With E cadherin, mult roles in cancer Development and diﬀerentiation Development and diﬀerentiation Cell cycle progression G protein regulation of proliferation Melanoma tumor progression With HOXB13 progression in breast cancer Metastasis in panc cancer Methylated is marker for colon cancer Wnt pathway, lung met suppression Cell cycle Cell adhesion Development and diﬀerentiation Development and diﬀerentiation Ca++ dependent cell adhesion Inﬂam prohormones; low act’y in brst cncr Metastasis suppressor Progresssion neuroblastoma/breast cancer Reg p21, cell cycle control p53 cell cycle Cell adhesion Reg.expression of FOXA2 Cell adhesion; freq deleted in brst cncr Reg act’y RAS and ERK in tumor lines Inhibit tumor proliferation Lung/prostate cancer Implicated in cancer and metastatsis Req for telomer elong.; chr breaks/loss Downreg in breast cancer Reg of proliferation and viability Spermatogenesis Chemotherapy target Cofactor w/ SIRT1 in transcrip’n regulation Proliferation Apoptosis, migration Response to therapy and prog. brst cancer Multiple roles in cancer Role in cell cycle and carcinogenesis Proliferation aGenes of possible functional interest were tabulated from the two categories based on TSS association. The gene abbreviation, full gene name, fragment location, and description of the gene are given. Figure 4. McrBC PCR of two diﬀerent fragments of the MTSS1 CpG island for tumors identiﬁed of having methylation of this island compared to matched normal samples. Fragment 1 encompasses the MspI fragment we have identiﬁed as being methylated and overlaps the gene TSS. Fragment 5, we do not detect methylation. Both Normal and Tumor were digested with McrBC or mock digested for both matched pairs. Others have utilized McrBC combine with PCR to study methylation (39,54). Due to the constraints on us we chose to perform McrBC PCR (40) to validate the region of the island detected as methylated (Figure 4). The island was broken down into ﬁve fragments where fragment one overlaps the TSS up to fragment ﬁve that is the farthest away from the TSS. For tumors that were suspect to have methylation, fragment 1, which overlaps the gene TSS could not be ampliﬁed in the tumor samples (due to digestion by McrBC demonstrating methylation) as