Epigenetics and Cancer

Assistant Professor, Gastrointestinal Oncology/Phase I Program Sidney Kimmel Comprehensive Cancer Center October 19, 2010


Nilofer Azad, MD

Simplified Model of Epigenetic Regulation of Gene Expression

CMAJ 2006;174(3):341-8

How do genes get turned on and off?
Protein Complex Protein Complex M M M Coding section Non-coding section Coding section


DNA of Gene X


Gene is transcribed = ON


Gene blocked from being transcribed = OFF

• Two currently FDA approved agents
• 5-azacytidine (Vidaza)

DNA Methyltransferase inhibitors

• 5-aza-2'-deoxycytidine (decitabine, Dacogen)

• FDA approved in 2004 for myelodysplasia • Dose: 75 mg/m2 SQ daily x 7 d / 28 d cycle • Mechanism of action: Incorporated into DNA → suicide inhibitor of DNMT Induces global hypomethylation • Time to clinical response: Average = 4 months

Histone deacetylase inhibitors
• Three currently FDA approved agents • Vorinostat (Pan-HDACi) (SAHA, Zolinza) Oral agent
Approved for cutaneous T-cell lymphoma

• Depsipeptide (Pan-HDACi) (Istodax) Intravenous agent

Approved for cutaneous T-cell lymphoma
• Valproic acid (weak inhibitor) anti-seizure


Rationale for double epigenetic blockage in lung cancer
• Epigenetic gene silencing mediated by DNA methylation and histone deaceylation is a key contributor to lung carcinogenesis • Preclinical studies suggest that combining DMNTi with HDACi synergistically enhances expression of silenced tumor suppressor genes • Clinical studies combining DMNTi and HDACi have shown remarkable clinical activity in MDS/AML • Hypothesis: similar effect in NSCLC

Trial Schema

MS275 SNDX-275 5-AC 5-Aza Day Day 11 8 8 15 15 22 29 29 36 36

• 5AC Dosing = 40 mg/m2 SQ daily on days 1-6 and 8-10 • SNDX-275 dosing = 7 mg PO (fixed dose) days 3 and 10 • Cycle length = 28 days

Phase I Toxicity Data
Phase I Toxicities
Injection Site Reaction Nausea / Vomiting Constipation Anorexia Lower Extremity Edema Hyperglycemia Low Electrolytes Fatigue Neuropathy Neutropenia Lymphopenia Anemia Thrombocytopenia
Grade 1 Grade 2 Grade 3







Number of Patients

Updated Response Data 28 Evaluable Patients
• 1 Complete Response – On treatment for 14 months • 1 Partial Response
Responded for 8 months – then new SCLC Still no progression of his NSCLC 9 months off epigenetic therapy

• 8 Stable Disease
One on treatment for 18 months; Five treated for 4 months One treated for 3 months then stopped due to schedule One still being treated (on cycle 12 now) • 17 Progressive Disease • 8 Not evaluable (finished less than 1 cycle) • 5 Actively being treated

Overall Survival
Median OS: 8.2 months

Images of Patient with Complete Response

56 year old woman with stage I lung cancer that was resected and treated with adjuvant chemotherapy. She progressed after salvage chemotherapy with radiation at relapse. She had a response after 2 cycles, continued improvement after 4; 14 cycles were given. She had 3 prior therapies for advanced disease.

Images of patient with Partial Response

58 year old male treated with 3 prior therapies; Chemotherapy refractory disease. He completed 8 cycles.

Images of patient with partial response: liver metastases
Pre-treatment Cycle 2 Cycle 4 Cycle 8

Hypotheses for biology of the complete responder

5AC C (ng/mL) max

• Fewer number of previous therapies… • Higher serum level of 5-azacitidine… • Epigenetics…
15000 14500 2000 1500

• Responding patient was a previously resected stage I 1000 NSCLC patient • 500 Analysis of her tumor and mediastinal lymph nodes found a methylation pattern that predicted she was at 0 high risk for early recurrence


Gene DNA Hypermethylation Markers Are Better for Prognosis than Standard Staging

p16 and H-cadherin
Negative (U) n=79


Proportion Disease-Free


Positive (M) N=11

Stag e1 OR = 25 fold Stage 3


0.00 0

Molecular Restaging
1 2




Years After Surgery

Brock et al, 2008

Epigenetic Therapy Study Design: Treatment Schema

Stage IA or IB NSCLC s/p surgery with curative intent



2 5-Azacitidine 40 mg/m2 SQ Day 1-5, 8-10 Entinostat 7mg PO Day 3 and 10 Every 28 days, for 6 cycles

Intended Accrual: 172 patients


Standard Care Intended Accrual: 86 patients

Within 4-8 weeks of completing surgery


Colorectal Cancer is Common
2009 Estimated U.S. Cancer Deaths
Available at: http://www.cancer.org.

Men 294,120

Women 271,530
26% Lung and bronchus 15% Breast 9% Colon and rectum 6% 6% 4% 3% 3% 2% 2% Pancreas Ovary Non-Hodgkin lymphoma Leukemia Uterine corpus Brain/other nervous system Liver/bile duct

Lung and bronchus Prostate Colon and rectum Pancreas Leukemia Liver/bile duct Esophagus Urinary bladder Kidney All other sites

31% 10% 8% 6% 4% 4% 4% 3% 3% 24%

Non-Hodgkin Lymphoma 3%

25% All other sites

Colorectal cancer represents 2nd leading cause of death
Available at: http://www.cancer.org.

Colorectal Cancer Staging
Adenoma Pre-cancer lesion Stage I localized, not through “muscularis” (muscle wall in the colon) Stage II through muscularis, but no lymph nodes Stage III cancer in nodes, but not other organs Stage IV metastatic (liver, lung, etc)

Stage I-II

Stage III


Disease Stage at Time of Diagnosis
Stage I Stage II Stage III Stage IV 15% 20%–30% 30%–40% 20%–25%

Hamilton IM, Grem JL. Current Cancer Therapeutics. 3rd ed. 1998;157.

Risk of recurrence after primary resection in Stage II and III Colon Cancer

85% recur within 3 years 85%

Sargent, D. et al. J Clin Oncol; 27:872-877 2009
Copyright © American Society of Clinical Oncology

Metastatic Disease

History of Treatment for Colorectal Cancer
• ~1960: 5-FU is a cornerstone of first-line therapy; bolus/infusion • ~1985: Addition of LV (biomodulator) to 5-FU bolus regimens • • • • • • • • 1998: Irinotecan as single agent approved as second-line 2000: Irinotecan approved as first-line in CRC (bolus IFL) 2001: Capecitabine approved as first-line in CRC in selected pts 2002: Oxaliplatin approved as second-line agent (FOLFOX) 2004: Oxaliplatin approved as first-line agent in infusional regimen 2004: Approval of Cetuximab (Erbitux) & Bevacizumab (Avastin) 2006: Approval of Panitumumab (Vectibix) 2008: KRAS mutations predict lack of benefit of EGFR mAb’s

Incremental Survival Advantage in First-Line Metastatic Colorectal Cancer
No active drug 5-FU/LV IFL FOLFOX4 IFL + bevacizumab FOLFOX/FOLFIRI FOLFOX/FOLFIRI + biologics 0 6 12 18 24

~4-6 mo 12-14 mo ~ 15-16 mo ~ 20 mo 20.3 mo 21.5 mo ?

Are we hitting a wall with current drugs?

Median OS (mo)

Therapy for Advanced Colorectal Cancer: Response rates and survival
First Line - FOLFOX or - CAPOX or - FOLFIRI +/- Bevacizumab Second Line Third Line - FOLFOX or - Irinotecan + - FOLIRI or Cetuximab - Irinotecan alone - Cetuximab - Irinotecan/Cetuximab - Panitumumab +/- Bevacizumab

Response Rates in Randomized Trials:

50-60% Yes

15% Yes

10% Yes

Survival Benefit in Randomized Trials:

Epigenetics in CRC
• Many genes have silenced expression due to epigenetic changes • Targeting epigenetically abnormal tumors may be more effective than targeting abnormal mutations in genes • CRC may be uniquely appropriate for this strategy • A subset of colon cancer have more gene promoter methylation

Ahuja et al.

Combination Epigenetic Therapy
• First study of epigenetic therapy in CRC • Primary Objective: • To determine the preliminary efficacy via tumor shrinkage rate of the combination of 5-azacitadine and entinostat in patients with metastatic colorectal cancer • Secondary Objective: • To see what is happening in the tumor itself and circulating cells in blood before and after treatment with these drugs

Study Schema
28 days

C1d1 C1d3


C2d1 C2d3



entinostat entinostat

entinostat entinostat

5-aza days 1-5 and 8-10 q cycle

5-aza days 1-5 and 8-10 q cycle

= plasma sampling for research purpose

= tumor sampling for research purpose

Ongoing and Upcoming Studies
• Lung Cancer
– New schedule – Adjuvant treatment of early stage disease

• Breast
– Same schedule in triple negative and hormone resistant metastatic cancer

• Despite progress, colon cancer is a still leading source of death • Epigenetic therapy offers a novel way to approach treating cancer, based on the abnormal gene expression seen in cancers compared to normal cells • We are presently enrolling a trial of patients with late-stage colon cancer an treating them with epigenetic agents, 5azacitidine and entinostat


Epigenetics and breast cancer
• Multiple genes are methylated and thus silenced in breast cancer1 • ER, RAR beta, cyclin D, Twist, RASSF1A, and HIN-1

Pu RT. Mod Pathol 2003;16(11):1095-101.

Zebularine inhibits growth of MDA-MB-231 cell lines alone or in combination

Billam M.

Clinical studies: Vorinostat in MBC
• Phase 2

SKCCC J0785/TBCRC 008 A Multi-Institutional Randomized Phase II Study Evaluating Response and Surrogate Biomarkers to Carboplatin and nab-Paclitaxel (CP) with or without Vorinostat (SAHA) in HER2- Negative Breast Cancer
Principal Investigator: Vered Stearns, MD Fellow: Roisin Connolly, MB.BCh

Study schema
Eligible patients with locally advanced or metastatic breast cancer (up to 60)

Cohort B (up to 30) Hormone-resistant 5-AZA + entinostat

Cohort A (up to 30) Triple-negative 5-AZA + entinostat

Disease Progression at Any Time Cohort A or Cohort B

5-AZA + etinostat + hormonal therapy MD discretion

Event Monitoring

• Epigenetics is a new way to look at cancer biology and therapy • Ongoing trials in major tumor types in the metastatic setting • Plans to move therapy into earlier stage disease may be even more successful

• First and foremost, our patients • SU2C researchers • Research support staff at all our institutions

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