1. Identification of PDX model cohorts with aberrant HER2 genomics and protein expression

While HER2-directed agents are most often used for treating breast cancer, there is increasing evidence that these therapies may be of value in other solid

tumors. Sequencing efforts and immunohistochemistry (IHC) have identified mutations, amplifications, and overexpression of HER2 in ovarian, HNSCC,

NSCLC, melanoma, and GI cancers. PDX models could permit evaluation of HER2 response/resistance mechanisms to optimize therapeutic strategies. In

this pilot study, we evaluated the response of PDX models to HER2-targeted therapies and correlated responses to clinical outcomes.

Patient-derived xenograft (PDX) models expressing HER2 reflect clinical responses to targeted HER2 inhibition1 2 1 1 3Daniel Ciznadija , Amir Sonnenblick , Jennifer Jaskowiak ,Angela Davies , and David Sidransky

1 2 3 Champions Oncology, USA. Sharett Institute of Oncology, Israel. Johns Hopkins University School of Medicine, USA

Incorporation of PDX models into clinical trial strategies could enable real-time analysis of patient treatment outcomes and response biomarkers.

Hypotheses generated from NGS can be tested in clinically-relevant PDX cohorts to improve selection of optimally effective drugs for further development.

Patient-derived xenografts are an important and relevant model for gaining a deeper understanding of drug resistance mechanisms.

A co-clinical trial in metastatic HER2+ breast cancer patients after progression on HER2-directed therapy is planned, incorporating PDX models to further

interrogate mechanisms of resistance in this patient population.

Prospective evaluation of PDX model responses and patient outcomes in response to HER-targeted therapies is ongoing.

Perform extensive integrated genomic analysis and therapeutic screens against anti-HER2 agents to identify potential response biomarkers.

Control

HER2i

We are grateful to the patients who participated in this study and to collaborating oncologists for providing valuable resources and guidance during the course of

this work. For further information, please contact Dr. Angela Davies, Chief Medical Officer (adavies@championsoncology.com).

References: Gao, H et al., Nature Medicine, 21(11): 1318-25. 2015

No alterationLow level gainAmplification Heterozygous deletion

Homozygous deletion

Missense mutation

Truncating mutation

HER2 inhibitors(n=14)

Patient population (n=507)

WES sequencing(gene mutations/CNV)

HER2 IHC staining

HER2i screening(modified RECIST)

A

B

ERBB2

ERBB3

ERBB4

EGFR

ERBB2 amplifications

Future directions

Introduction

Methods

Results

Conclusions

Acknowledgments and References

C

2. Response of PDX models to relevant anti-HER2 therapies stratified by tumor type, HER2 IHC, and HER2 CNV

3. Response of PDX models to HER2-targeted therapy correlates with patient clinical outcomes

B

A

C

Total

Patient response

Positive Negative

PDX response

Total

Positive

Negative

6

0

6 5

2 8

33

11

Number of patients = 9

Clinical accuracy

Positive Predictive Value (PPV)

Analytical accuracy

Sensitivity

Specificity

Negative Predictive Value (NPV)

75% (6/8)

100% (3/3)

100% (6/6)

60% (3/5)

Result

Result

52% - 100%

17% - 93%

36% - 96%

31% - 100%

95% CI

95% CI

5. Uncovering HER2 resistance and identifying new clinical regimens - a PDX case report

4. PDXs allow identification of HER2 resistance pathways when integrated with drug testing

* Includes doublet therapies where

one agent is a HER2-targeted drug.

Intracellular domain Extracellular domain

39 year-old female

HER2+ tumor

Invasive ductal carcinoma

Placed on trastuzumab

No clinical response

Clinical response Clinical response

Metastatic deposits

found in the lungs

Primary and metastatic

sites stable - 5 months

Primary/metastatic

sites regressed

Surgery to de-bulk

Sample from lung metastasis taken

PDX model developed

from lung metastasis

HER2+ confirmed

in PDX model

PDX model fails to

respond to trastuzumab

Correlates with clinical outcome

IHC analysis of PDX model shows it expresses

p95HER2, which lacks the extracellular domain

that trastuzumab needs to bind receptor

Trastuzumab resistance

retained in new clone

PDX model treated simultaneously

with same regimen to develop

lapatinib/capecitabine resistant clone

Patient receives

lapatinib/capecitabine

Patient on

Nab-paclitaxel

Lapatinib inhibits HER2 by

binding intracellular ATP-pocket in

kinase domain, inhibiting auto-phosphorylation

Control

Trastuzumab

Nab-paclitaxel

Day

3T

um

or

volu

me (

mm

)

0 147 210

800

1600

2400

28 35

Control

Lapatinib/Capecitabine

3T

um

or

volu

me (

mm

)

0 73 100

500

250

750

1000

14 2117

Day

Control

Trastuzumab

Day

3T

um

or

volu

me (

mm

)

0 2010 300

1000

500

2000

1500

2500

40 50

A

B

C

Responsive to Nab-paclitaxel

TrastuzumabTrastuzumab emtansine Lapatinib Trastuzumab/PertuzumabPertuzumab Trastuzumab emtansine/PertuzumabAfatinib

0 200 400 600 800 1000 1255

Tyrosine kinase domain C-terminal tailGrowth factor

receptor domainReceptor L

(ligand binding)Receptor L

(ligand binding)Furin-like

cysteine-rich

R74H

R143Q

S310F

P391fs

S463N

P489L

L535F

V666fs R678Q

P699S

L726I

I767M

V842I

E930D

D982fs

Q984fs Q1028K

P1074A

S11

07fs

A1216D

SNV DeletionsERBB2 (n=20/507 models)

n=507 models

Breast

+++

Melanoma Colorectal Breast

++ + -

Esophageal Colorectal Pancreatic NSCLC Gastric ColorectalEsophageal Breast

A

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

BRC

CRC

CRC

CRC

CRC

CRC

CRC

CRC

CRC

CRC

CRC

CRC

NSC

LCESO

ESO

PANC

PANC

PANC

H&N

H&N

GBM

CHOL

GAST

GAST

GAST

GAST

100

75

50

25

-50

-25

-75

-100

Be

st a

vera

ge

% t

um

or

volu

me

ch

an

ge

0

Bars marked with an asterisk represent the median of response for models tested against the same agent multiple times

CR

PR

SD

PD

Modified RECIST (PDX response)

By tumor type (n=34)

Breast Breast Breast BreastBreast BreastColorectalColorectal H&N H&NCholangio

Patient

PDX model

PR CRSDPD

Trastuzumabemtansine

LapatinibCapecitabine

VinorelbineTrastuzumab

AfatinibMethotrexate

AfatinibLapatinib

Capecitabine Trastuzumab TrastuzumabTrastuzumab

emtansineTrastuzumab

emtansineTrastuzumab

emtansine

Responded

By HER2 CNV status (n=25)

Am

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pAm

pGai

nGai

nDip

Dip

Dip

Dip

Dip

100

75

50

25

-50

-25

-75

-100

Be

st a

vera

ge

% t

um

or

volu

me

ch

an

ge

0

CR

PR

SD

PD

Modified RECIST (PDX response)

Bars marked with an asterisk represent the median of response for models tested against the same agent multiple times

Am

pAm

pDip

Dip

Dip

Het

Loss+++++ ++ ++++ ++ ++++++ ++++ ++ ++++ +++

+++

+++

+++

+++

By HER2 IHC score (n=18)

No alteration

Low level gain

Amplification

Heterozygous deletion

Homozygous deletion

Missense mutation

Truncating mutation

Inframemutation

PTEN

PIK3CA

MET

IGF-1R

MTOR

AKT1

AKT2

surgeryor

biopsy

PDX models

Patient therapy

Clinical response(RECIST criteria)

Radiologicalmeasurements

Tumor volume calculated by:

2width x length x (p/6)

Patient-PDX

correlations

(A) Models were stained with anti-HER2 antibodies (Dako, USA) and scored by a pathologist for intensity of HER2 expression (using the -/+/++/+++

nomenclature). Representative examples of each HER2 staining score are depicted. (B) OncoPrints (cBioPortal) created from whole-exome sequencing

demonstrating mutations and copy number variations amongst HER2 family members. Models with amplifications and focal gains at the ERBB2 locus are

indicated. (C) Lollipop diagram (cBioPortal) highlighting the mutational spectrum of the ERBB2 gene across twenty PDX models harboring SNVs and indels

at that locus (of 507 sequenced). SNVs are indicated by red circles and focal deletions by blue triangles. No focal amplifications were found.

n=11 correlations

Models with HER2 amplifications

Models staining positive for HER2

Poster #1836