Genomics, cancer, and medicine: 10 years after the

Human Genome Project

Edison Liu, M.D.April 13, 2012

We are entering one of the most profound periods of advancement in biology and medicine – one that will

transform:

Health and Medicine

Driven by technologies in genetics, genomics, and computational biology

Declaration

Genomics and Genetics

Genetics: study of genes and their function

Genomics: study of all genes and how they function together

“Discover all possible genes involved in a biological process or a human disease”

Genomics enables the

complete genetic “view” of a disease

Transformative technologies enabling this revolution:

•New generation of ultra-fast sequencing

technologies

“Massive Data Generation”

• Enabling computational advances

“”Analytical power“•Genetic engineering to model organisms of disease

“Surrogates of disease”

CTAGCTGATTCAG

CTAGCTGATTCAG

AAGT

T*

A*C*

G*

T*

T*

AGT

A*

Massively Parallel Sequencing:

Sequencing by Synthesis

~105-107 kb per run = 0.1-3 X human genome equivalents / run

MR Stratton et al. Nature 458, 719-724 (2009)

7 orders of magnitudeincrease in throughput

Cost of sequencing a human genome

300,000 USD -

30 million USD -

300 million USD -

2003

2005

2007

2009

2001

300 million

1 million

$60,000

$ 3,000

2011

3 million USD -

30,000 USD -

Cost-effective sequencing =Accessibility of genomic data

Low complexityimage

Data complexity when ordered

appropriately giveshigh resolution

picture

Genomic scale information providesunique biological insights

Genomics & Personalized Medicine

Conventional chemothrapy

Towards personalized cancer medicine

Non-selective

No benefit

RespondersSevere side effect

Personalized cancer medicine

Molecular marker&

target

Selection

by marker

Other therapyNo treatment

Molecular specific

drug

High response rate

CAT ATE RAT Wild Type

BAT ATE RAT Point Mutation

RAT ATE CAT Rearrangement

Cathryn Polymorphism

Kathryn Polymorphism

Kathrine Polymorphism

Chronic Myelogenous Leukemia:and the 9;22 chromosomal rearrangement

• Ph1 chromosome identified 1960 as a marker for CML (Nowell)• bcr-abl cloned and shown to be the molecular mechanism 1984-1990 (Groffen and Lugo)

Molecular Mechanisms: How to make a Leukemia

BCR

ABL

ChronicMyelogenous

Leukemia

Chronic Myelogenous Leukemia: Mortality 1969 - 2002

Gleevec Approved By FDA

Large scale clinical

trials begin with Gleevec

BCR ABL

STI521:Gleevec

• Ph1 chromosome identified 1960 as a marker for CML (Nowell)• bcr-abl cloned and shown to be the molecular mechanism 1984-1990 (Groffen and Lugo)• Specific drug (Gleevec) to target gene abnormality 1999 (Druker)

From discovery of a single oncogene to treatment: 39 years

From Concept to Molecular Mechanism to Treatment

EML

ALK

LungCancer

Nature 2007

In 2007, the genomic analysis of one lung cancer from a 62 year-old smoker EML-ALK fusion in 6% of lung cancer patients

Crizotinib 60% response rate in those 6% of patients with lung cancer with the EML-ALK mutation. On August 26, 2011, the US FDA gave approval of crizotinib by for the treatment of ALK-rearranged lung cancer

Ou, Drug Des Devel Ther. 2011; 5: 471–485.

4 years from genomic discovery to treatment

Chronic Myelogenous Leukemia (CML)

Optimizing treatment for CML based on genetic makeup of the patient

Clinical Challenge: Drug resistance•Acquired resistance – resistance after long term treatment - due to second ABL mutation•Primary resistance – resistance at the beginning of treatment. •In Asia, complete cytogenetic response rates are lower - 50% vs. 74%. Mechanism unknown

Question: is there a reason why 25% of CML cases do notrespond to imatinib?

Approach: We compared the genomes of three CML cases with primary resistance to Imatinib with two CML cases sensitive to Imatinib therapy

Results:

3/3 resistance cases had the same 2.9kb deletion in the BIM gene not seen in sensitive cases (0/2)

BIM:

•BIM is a gene that activates cell death (pro-apoptotic). •Activated BCR-ABL1, suppresses BIM function thus allowing leukemia cells to survive. When CML cells are treated with Imatinib, BIM expression goes up cell death

Bcr-ABL: CML Intact BIMDeath of

Leukemia cells

Imatinib

BIM deletion polymorphism:

•This deletion polymorphism is 3-5X more common in CML cases resistant to imatinib that sensitive cases

•This 2.9 kb 2 deletion of BIM is not a mutation, but is a polymorphism present in normal genomes (a germline polymorphism):

12% in Asian individuals 0% in Africans

0% in Caucasians

How does it work?: The 2.9kb BIM deletion polymorphism results an abnormal transcript (E3) that a produces a truncated and inactive BIM protein

Bcr-ABL: CML Intact BIMDeath of

Leukemia cells

Imatinib

Bcr-ABL: CML BIM E3

Primary Drug Resistance

Imatinib

NormalTranscripts

E3

We used this genomic intelligence to overcome this resistance:

Bcr-ABL: CML BIM 3 Primary Drug

Resistance

Imatinib

Imatinib

Bcr-ABL: CML BIM

BH3 mimetics

Death of Leukemia

cells

This genomic experiment with 5 patients explains the lower response rate In North Asians to a life saving treatment in CML. Personalizing medicine in Asia

Now: New

CML Patientin Asia Check for bcr-ABL

rearrangementCheck for 2.9kb

deletion polymorphism in BIM

YES

~50% cytogenetic response

YESNO

Imatinib

Imatinib&

BH3-mimetic

75% cytogenetic response

>75% cytogenetic response

LOHCopyNumber

StructuralVariations

BT55

17

Visualizing the Cancer Genome

‘Conductor’ mutation = early event that conducts the direction of further cancer mutations

Mutation patternappears to be generated by separate cuts when mapped to the original physical “map”

Chromosomal “origami” simultaneously generates oncogenic “pattern”

Chromosomal origami to generate cancer gene cassette

ERBB2P53 BRCA1

ERBB2

ERBB2

ERBB2

ERBB2ERBB2

17q21.3

17q21.3

17q21.3

Oncogenes 17q21.3

BT55 (ER+, ERBB2++)Luminal B

ERBB2/HER217q21.3 amplicon

BRCA1

TD207

U-Inv331

U-Inv75Del51TD49 + Del67

Amplification

ERBB217q21.3 17q21.3

Oncogene

There are 16 weak oncogenes here.4 that are synergisticwith ERBB2 oncogenesis

Tumor Suppressor

Gene

Chr17 ‘evolutionary origami’ has treatment implications for Combination therapy

17p (TP53) loss17p (TP53) loss

BRCA1 locus lossBRCA1 locus loss

Tandem duplication in ERBB2 locus

Tandem duplication in ERBB2 locus

Recurrent Unpaired-Inversion:

“Conductor” Mutation

Recurrent Unpaired-Inversion:

“Conductor” Mutation

Chromosomal instabilityChromosomal instability

Cancer progression

17q21.3 amplification

17q21.3 amplification

Tumor Suppressor

genes

Tumor Suppressor

genes

OncogenesOncogenes

Massive ERBB2 amplification

Massive ERBB2 amplification

Lapatinib

PARP inhibitor

New Target

Nutlins

Cancer Genomics Consultation Model Using Mouse Avatars for Human Disease

Tumor DNA sample

Germline DNA sample

Generation of serum-based

personalized and private cancer biomarker test

Monitor for recurrence and clonal variation

Visualization formatted report

Sequence Tumor

Expand tumor inNSG mice

Automated sequence

analysis of tumorand germline

Druggable mutations

Prognostic information

Germline pharmacogenetic

analysis

Identification of cancer specific

rearrangements

Test specified drugs for

response in vivo

Devise optimal combination

therapy

Consultation with patient and

physicianfor treatment

plan

RadiologistRadiologist of the Genome

Interprets complex datarendered through

computational algorithms

Is the consultants to doctors

Genomics, cancer, and medicine: 10 years after the

Human Genome Project

Edison Liu, M.D.April 13, 2012

1990

Age Adjusted Mortality for breast cancer is declining since 1990

T2N1M0

ER (IHC) positiveHER2 (FISH) PositiveKi67: +++ GHI recurrence score: XXX Age: 56 family history: negative

Sequence performance: 9.6 million reads; 75 base pair, paired end on Illumina HiSeq

Comparison of germline and cancer genomesThis is a visual representation of the cancer genome of your patient as compared to her constitutional (germline) genome.The 23 chromosomes are arrayed in a circle; amplifications are on the outer circle, and the deletions and inversions are in the inner circles. In the innermost circle is a representation of the chromosomal translocations. Each arc represents a translocation, and the intensity of the arcs is an indication ofAmplification of that translocation. By clicking onto the figure, you will get a blow up of the schematic and a detailed legend.

The mutational load score is a composite score the integrates the mutational load that is seen in the tumor of your patient. It is made up of two components: sequence mutations, structuralmutations/rearrangements. Your patient’s mutational score when compared to a panel of XXX tumors of the same type is in the following distribution:

Nor

mal

Max

imal

1990

2020

Can death from breast cancer be eliminated?

What if this trend continues?