Predictive Blood DNA Markers for Breast Cancer Xiang Zhang, Ph.D.

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1 Predictive Blood DNA Markers for Breast Cancer Xiang Zhang, Ph.D. Department of Environmental Health University of Cincinnati

2 Background Breast cancer (BCa) The second most common cancer among women in the United States Aberrant DNA methylation is frequently found in BCa Blood DNA methylation as BCa predictive biomarkers High stability of DNA DNA methylation in response to cancer-causing insults offers opportunities to develop predictive biomarkers Molecular lesions early events during cancer development Methylation markers can be expected to be found years before the actual diagnosis of BCa Fernald Medical Monitoring Program A uranium processing plant was built in the 1950s near Fernald, Ohio Uranium exposure in the community residents 71% increased incidence of BCa Blood samples were collected for each participant, along with full physical examination

3 Materials and Methods Group-matched blood DNA samples Cancer group (short interval to cancer) Blood collected 2-3 years before BCa diagnosis Normal group (control, no caner) Blood collected 10 years before without cancer Promoter methylation array To identify differential DNA methylation in gene promoter regions between the two groups Validation of DNA methylation Bisulfite sequencing analysis (gold standard technique)

4 NimbleGen DNA methylation promoter array DNA sonication 100 to 1000 bp Immuoprecipitation Antibody: anti-methylated DNA Amplification and labeling Hybridization on chip Data analysis 2 kb fixed window 750 bp sliding window

5 Bisulfite sequencing PCR TCCCGGGAGGCC m GG Bisulfite modification TUUUGGGAGGUC m GG PCR TTTTGGGAGGTCGG DNA sequencing

6 Results and Discussion Distribution of uranium exposure index scores

7 Blood DNA sample selection Groups UC ID Sample number High exposure with cancer and short interval High exposure with cancer and long interval Low exposure with cancer and short interval U- Exposure Age at entry Age at diagnosis BMI at enrollement Maternal history of Breast Cancer Total number of relatives with BC Total number of first degree relatives with BC BMI at BC Dx Date Age at first mammogram BREAST DENSITY at first Age at last mammogram BREAST DENSITY at last mammogram B26-B Case-Hi No LOW LOW Never B25 Case-Hi No LOW 60.8 ELSE Never B-21 Case-Hi No LOW ELSE Never B-22 Case-Hi No LOW ELSE Never B-24 Case-Hi No LOW LOW Never B-23 Case-Hi No LOW ELSE Never B-13 Case-Low No LOW ELSE Never B-15 Case-Low No ELSE LOW Never B-16 Case-Low No LOW LOW Never HRT use Cancer Group Low exposure with cancer and long interval B-12 Case-Low No ELSE ELSE Never B-11 Case-Low No LOW ELSE Never B-14 Case-Low No LOW 55.7 ELSE Never A-21 Cont-Hi Yes LOW LOW Never High exposure A-22 Cont-Hi No ELSE LOW Never without cancer A-2(A-23) Cont-Hi No LOW LOW Never Low exposure without cancer A-2(A-24) Cont-Hi Yes LOW LOW Never A-11B Cont-Low No 0 0 Never A12B Cont-Low No ELSE ELSE Never A-14 Cont-Low No LOW HIGH Never Normal Group

8 Methylation array: Methylation candidates selection Fold change of the methylation % CpG island in the promoter region P value

9 Methylation candidates selection (2 kb fixed window) Promoter CpG island Hypomethylated Hypomethylated

10 Bisulfite sequencing PCR (2 kb fixed window) ASB3 (primer #4) C18orf55 (primer #5) Sample (-) C18orf55 (primer #5) FBXO15 (primer #6) Sample (-) FBXO15 (primer #6) PCDHA (Primer #7, no amplification) Sample (-)

11 Methylation candidates selection (750 bp sliding window)

12 Bisulfite sequencing PCR (750 bp sliding window) X (-) DNMT3b FAM151A X (-) X FAM151A MAP3K (-) X MAP3K1 MRPS21 51 X (-) X X (-) MRPS21 SLC25A24

13 Methylation status of SlC25A24 gene promoter (hyper-methyalted) Control no cancer 4-G7 4-G8 4-G9 4-G10 4-G11 4-G12 4-H1 4-H2 4-H3 4-H4 4-H5 4-H6 4-H7 4-H8 4-H9 4-H10 4-H11 4-H12 5-A1 5-A2 5-A3 5-A4 5-A5 5-A6 Methylated CpG site Unmethylated CpG site Short interval to Cancer 5-A7 5-A8 5-A9 5-A10 5-A11 5-A12 5-B1 5-B2 5-B3 5-B4 5-B5 5-B6 5-B7 5-B8 5-B9 5-B10 5-B11 5-B12 5-C1 5-C2 5-C3 5-C4 5-C5 5-C6 5-C7 5-C8 5-C9 5-C10 5-C11 5-C12 5-D1 5-D2 5-D4 5-D5 5-D6 5-D7 5-D8 5-D9 5-D10 5-D11 5-D12

14 Methylation status of MRPS21 gene promoter (hypo-methylated) Control no cancer 4-A7 4-A8 4-A9 4-A10 4-A11 4-A12 4-B1 4-B3 4-B4 4-B5 4-B6 4-B7 4-B8 4-B10 4-B11 4-B12 4-C1 4-C11 4-D1 4-D2 4-D3 4-D4 4-D5 4-D6 4-D7 4-D8 4-D9 4-D10 Methylated CpG site Unmethylated CpG site Short interval to Cancer 4-D11 4-D12 4-E4 4-E6 4-E7 4-E8 4-E9 4-E10 4-E12 4-F1 4-F2 4-F4 4-C5 4-C6 4-C7 4-C8 4-C9 4-C10 4-F6 4-F7 4-F8 4-F9 4-F11 4-G1 4-G3 4-G4 4-G5 4-G6

15 Possible explanation Human blood DNA are the most difficult-to-verify samples Human blood>animal tissue>cultured cells Methylation array Methylation array sensitivity and resolution Antibodies for methylated DNA: CpG cluster CpG site DNA size selection: bp bp Alternative approach in the future Improved methylated array Deep bisulfite sequencing

16 Acknowledgement Dr. Susan Pinney Dr. Shuk-mei Ho Dr. Jing Chen Mr. Saikumar Karyala Thank you