Exploitation of Epigenetic Changes to Distinguish Benign from Malignant Prostate Biopsies

Exploitation of Epigenetic Changes to Distinguish Benign from Malignant Prostate Biopsies

Disclosures MDxHealth Scientific Advisor 2

Case Study 54-year-old man referred for a PSA of 7 - Healthy, minimal LUTS, normal DRE - Evaluation leads to TRUS/BX (12-core) Results: 40 cc prostate, negative for malignancy Now what? 3

Defining the Problem: Prostate Cancer in the USA 30 million PSA screenings 1,2 1.5 million abnormal PSA test results 3 >900,000 prostate biopsy procedures 4 ~240,000 diagnosed with prostate cancer 6 Lung & Bronchus Colon & rectum Urinary bladder Melanoma of the skin Non-Hodgkin lymphoma Kidney & renal pelvis Oral cavity & pharynx Most Prevalent Men's Cancers Prostate Leukemia 32,000 deaths 6 Pancreas 0 50,000 100,000 150,000 200,000 250,000 Confidential Information 2013 MDxHealth Inc. All rights reserved. 1) Ross et al, Cancer Epidemiol Biomarkers Prev 2008 2) Cost Analysis of Screening for, Diagnosing, and Staging Prostate Cancer_CDC_2007 3) Lin et al., Ann Intern Med. 2008; 149:192-199. 4) Mosquera et al, Clin Cancer Res 2009.pdf 5) Fadare et al, Arch Pathol Lab Med. 2004;128:557 560 6) American Cancer Society, Inc., Surveillance and Health Policy Research, 2012 4 4

Defining the Problem: Prostate Cancer in the USA 900,000 biopsies a year in US Approximately 240,000 positive for malignancy This leaves ~700,000 men with uncertainty - What can we say to these men about their risk of malignancy? - In other words, how accurate is prostate biopsy? 5

Prostate Cancer in the USA ~700,000 Patients with negative biopsy result but false negative in 20-25% Or approximately 175,000 with false-negative results 1 1.National Cancer Institute Trends Progress Report-2009/2010 Updated; Predicting cancer following a diagnosis of high-grade prostatic intraepithelial neoplasia on needle biopsy: data on men with more than one follow-up biopsy. Epstein et al Am J Surg Pathol. 2001 Aug;25(8):1079-85 6

Wanted: A Biomarker to avoid unnecessary repeat biopsies But also one that tells us which patients need another PSAV, PSAD, fpsa, others all help a little bit Biopsies cause discomfort, psychological distress, ED Biopsies increasingly associated with hospitalization and infectious complications Risk now estimated to be 4%, due to bacterial resistance Need to decrease number of biopsies, both initial and repeat, but how? >40% of screen abnormal patients have repeat biopsies Cycle of Follow Up & Anxiety Negative Pathology Results Elevated PSA Prostate Biopsy Terris, Curr Pros Rep., 2009, Welch, J Natl Cancer Inst 2007, Pinsky BJU International 2007 7

Epigenetics: Genetic Control Without DNA Changes DNA methylation inactivates gene expression (CpG islands in promoter regions) Benign situations: cell differentiation, embryogenesis Malignancy: silencing of tumor suppressor genes Methylation is one form of epigenetic change commonly seen in cancer 8

Methylation Changes in Prostate Cancer Development K. Chiam et al., Cancer Lett. (2012) 9

Evaluation of Biomarkers for Diagnostic Purposes We are entering the age of personalized medicine, driven by molecular analysis of cancers and the patients it affects Many assays out and forthcoming Which assay to use? - Best way is to evaluate the evidence - Be sure the assay chosen is appropriate for the context 10

ConfirmMDx: > 15 Years in the Making >40 papers Clinical trials involving >4000 patients 2 large multi-institutional trials 11

Genes Selected for Assay 1. GSTP1: Encodes enzyme for detoxification/protection of DNA from oxidants and electrophilic metabolites >90% specificity for prostate cancer Levels of methylation of GSTP1 promoter region distinguish benign, PIN, and cancer Levels also correlate with stage of cancer and disease recurrence Can be assayed in tissue but also serum, urine, plasma 2. APC: Tumor suppressor gene involved in signaling, migration, adhesion Hypermethylated in all stages of disease 3. RASSF1: Tumor suppressor gene involved in cell cycle and apoptosis Hypermethylated in early stages of disease K. Chiam et al,: Cancer Lett. (2012) 12

An Epigenetic Solution 1. ConfirmMDx for Prostate Cancer RT PCR based assay derived from FFPE biopsy samples Detects the degree of GSTP1, APC and RASSF1 gene promoter methylation Takes advantage of field effect - Presence of epigenetic changes in prostate that appears histologically benign - Changes are present in the field around a focus of malignancy that otherwise looks histologically benign 2. Results identify negative biopsy patients who are either: At increased risk of prostate cancer despite the negative biopsy, or Who have a low likelihood of prostate cancer and can be offered a higher degree of reassurance This test is an adjunct to standard of care procedures Van Neste,et al., The Prostate, 2011 13

Diagnosis of Prostate Cancer Prostate biopsy is the standard of care - Percentage sampled = <1% The needle may miss the mark Pathologists can only call what they see on the slide Follow up is often repeat biopsy due to ongoing concern 14

Epigenetic Changes Influence Gene Expression Without Changing the Genome ConfirmMDx detects an epigenetic field effect with the cancerization process at the DNA level This field effect around the cancer lesion can be present despite the normal appearance of cells Detection of field effects extends the coverage of the biopsy helping to rule out, or rule in, occult cancers 15

Case Study Continued Patient followed every 6 months for two years - PSA remains relatively stable in 7-8 range, DRE nl - After 2 years, another biopsy is recommended - Results: 44 cc prostate, 3/12 cores GG 3+3 CaP Was this predictable? Should he have had another biopsy? What if he refused biopsy? Would missing this cancer matter? 16

Is it Worth Identifying Prostate Cancer on Repeat Biopsy? Biopsy number when cancer identified Cancer insignificant Cancer significant 1 st biopsy 31% 65% 2 nd biopsy 44% 53% 3+ biopsy 47% 52% Resnick et al., Urology 2011 17

Clinical Application PSA Screening Prostate DRE Elevated PSA Abnormal DRE Biopsy Pathology Negative ConfirmMDx for Prostate Cancer Repeat Biopsy 18

MATLOC STUDY: AUA 2012, J UROL MARCH 2013 MATLOC: Methylation Analysis To Locate Occult Cancer evaluate clinical utility of an epigenetic test which: Increases negative predictive value (NPV) of histology (~75%) thus confirming the absence of cancer and avoiding unnecessary repeat biopsies Might indicate the molecular presence of prostate cancer despite negative read by pathologist 19

Epigenetic Analysis and Clinical Performance Analysis of GSTP1, APC and RASSF1 gene promoter methylation, in initial, negative prostate biopsies DNA extracted from the initial, non-cancerous FFPE biopsy core specimens (20 microns/core), processed using methylation-specific PCR (MSP) technology Cutoff points determined for each gene. A positive assay result was determined as a methylation signal above the analytical cutoff for at least one of the 3 gene markers All samples were tested in a blinded manner without knowledge of cancer detection outcome in the repeat biopsy Results validated using 4-fold cross validation methods in varying patient cohorts 20

MATLOC Results All Cases Controls p-value Patients (n) 483 87 396 (n) 85 GS < 6 6 (7%) Gleason Score (GS) GS 6 50 (59%) GS 7 22 (26%) GS > 7 7 (8%) (n) 77 Cancer Location Right 33 (43%) Left 23 (30%) Bilateral 21 (27%) Median (range) 5% (1%-70%) % Tumor Involvement # Positive Cores Maximum Methylation Levels (n) 73 < 5 12 (16%) >= 5 & < 10 32 (44%) >= 10 29 (40%) Median (range) 2 (1-7) (n) 67 < 2 25 (37%) 2 22 (33%) > 2 20 (30%) Median APC (range) 27 (0-587) 51 (0-587) 24 (0-493) 0.00082 Mean APC 53 84 46 Median GSTP1 (range) 0 (0-371) 0 (0-261) 0 (0-371) < 0.0001 Mean GSTP1 4 11 3 Median RASSF1 (range) 57 (0-1447) 62 (0-542) 55 (0-1447) 0.047 23 Mean RASSF1 80 98 76

MATLOC Results: Relative Contribution of Each Gene 87 cancer cases identified on repeat biopsy, 59 of which showed positive methylation of at least one of the three genes. Note that (+) test of any one or more genes identified prostate cancer Genes positive 59 Cases % of Cases 1 Gene 2 Genes APC 14 24% GSTP1 9 15% RASSF1 10 17% Total 33 56% APC + GSTP1 9 15% APC & RASSF1 4 7% GSTP1 & RASSF1 1 2% Total 14 24% 3 Genes APC & GSTP1 & RASSF1 12 20% 24

MATLOC Results: Multivariate Analysis of Known Risk Factors and Assay Performance 87 cancer cases identified on repeat biopsy, 59 of which showed positive methylation of at least one of the three genes. Note that (+) test of any one or more genes identified prostate cancer Genes positive 59 Cases % of Cases 1 Gene 2 Genes APC 14 24% GSTP1 9 15% RASSF1 10 17% Total 33 56% APC + GSTP1 9 15% APC & RASSF1 4 7% GSTP1 & RASSF1 1 2% Total 14 24% 3 Genes APC & GSTP1 & RASSF1 12 20% 25

MATLOC Results: Clinical Utility of the Epigenetic Test Increased Negative Predictive Value - Confirm absence of cancer, reassuring (90% in this study) - These patients don t need another biopsy in short term Identify false-negative biopsy patients with high risk of harboring prostate cancer - Recommend repeat biopsy - Increased sensitivity: ~2/3 of cancer cases identified on initial negative biopsy tissue Non-invasive: Test performed on residual prostate tissue from previous biopsy Mapping to guide repeat biopsy (treat like an ASAP result) 26

Cost Analysis Budget Impact Model: Epigenetic assay can help avoid unnecessary repeat prostate biopsies and reduce healthcare spending Savings per patient managed: > $588 28

31 Health Economic Continued

Sample Patient Report Negative for DNA Methylation Positive for DNA Methylation 32

Conclusion ConfirmMDx assay, when performed on histologically negative biopsy tissue, is a powerful tool for stratification of patients as true-negative vs. prostate cancer detection in subsequent biopsies. ConfirmMDx assay helps identify which patients should have another biopsy, and which patients may not need one Adds significantly to the result of prostate biopsy Available in US as of May 1, 2012 Published in Journal of Urology March 2013 Further validation: US DOCUMENT trial results imminent 33