Figure 1: A) Copy number analysis on SNP arrays identified 1/99 patients with focal amplification of HER2. B) whole genome sequencing resolved the breakpoints to a 1.0 MB region, containing HER2. C) This resulted in extreme up-regulation of gene expression. D) Whole exome sequencing identified 23 non-synonymous somatic variants; whole genome sequencing identified additional structural variations. E) Genes within the 1.0 MB amplicon. HER2-amplification confirmed by IHC (3+ staining; F) SISH (G) and FISH (H).

Aims 1)  Determine the prevalence of HER2-amplified PDAC 2)  Assess clinical response to targeted therapeutics

Conclusions

PANCREATIC CANCER

Repurposing therapies for treatment of HER2-amplified pancreatic cancer Mark J Cowley1^ Angela Chou1^ Nicola Waddell2^ David K Chang1 Jiamin Wu1 Mark Pinese1 Lorraine Chantrill1 Amber L Johns1 Katia Nones2 Ann-Marie Patch2 APGI3 Sean M Grimmond2 Andrew V Biankin1 1Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia. 2Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, St Lucia, QLD, Australia. 3Australian Pancreatic Cancer Genome Initiative, for a list of members, please visit http://www.pancreaticcancer.net.au/apgi/collaborators ^these authors contributed equally

Background

The 5 year survival rate of pancreatic ductal adenocarcinoma (PDAC) is a dismal 3-5%.

Only 10% of patients with PDAC demonstrate any clinical response to the standard therapy, gemcitabine.

We recently performed whole exome sequencing of 142 primary PDAC tumours, which revealed extensive molecular heterogeneity.

Defining clinically actionable molecular subtypes of PDAC is vital.

Trastuzumab (Herceptin®), a monoclonal antibody targeting HER2 has been successfully used to treat HER2-amplified breast cancer.

Trastuzumab has recently been repurposed for HER2-amplified gastric cancer.

Establishment of a genotype-guided clinical trial

•  2.1% of PDAC is HER2-amplified •  8% will stain as 2+/3+ by IHC & warrant further testing by FISH •  Like breast cancer, HER2-amplified PDAC has unusual pattern of metastasis •  1 patient with strong response to Trastuzumab • Clinical trial established to determine efficacy of Trastuzumab in HER2-amplified PDAC • HER2-amplifications identified in other cancers; potential for pan-cancer clinical trials.

Figure 1: Integrated genomic analysis identified 1/99 patients with focal amplification of HER2 (A). This resulted in up-regulated of gene expression (B). Whole exome sequencing identified somatic mutations, whole genome sequencing identified structural variationss. A 1.9MB stretch of chromosome 17 was amplified, including HER2 (ERBB2(.

HER2-amplified pancreatic cancer

Table 1: HER2-amplification was assessed by IHC and FISH in an archival cohort of 469 PDAC tumours. Diagnostic criteria for detecting HER2-amplified PDAC were established.

2.1% of PDAC is HER2-amplified

Figure 2: Algorithm for Diagnostic testing of HER2-amplification in PDAC

Figure 4: Prevalence of HER2-amplified (>4 copies) cancer, from TCGA and ICGC. 54,000 new cases of HER2-amplified cancer are expected in 2012, in USA alone (22,000 excluding breast and gastric)

Prevalence of any HER2-amplified cancer

Cancer  Type  

TCGA  frequency  of  HER2  gain  (%)  

 es;mated  new  cases  

2012    

es;mated  new  cases  in  2012  

with  HER2  gain  

 es;mated  deaths  2012    

es;mated  deaths  in  2012  with  HER2  gain  

Breast  Invasive  Carcinoma  (TCGA,  Nature  2012)   12.9    229,060      29,549      39,920      5,150    Stomach  Adenocarcinoma  (TCGA,  Provisional)   12.9    21,320      2,750      10,540      1,360    Bladder  Urothelial  Carcinoma  (TCGA,  Provisional)   6.8    73,510      4,999      14,880      1,012    Uterine  Corpus  Endometrioid  Carcinoma  (TCGA,  Provisional)   5.5    47,130      2,592      8,010      441    Cervical  Squamous  Cell  Carcinoma  (TCGA,  Provisional)   4.4    12,170      535      4,220      186    Colon  and  Rectum  Adenocarcinoma  (TCGA,  Nature  2012)   3.1    143,460      4,447      51,690      1,602    Head  and  Neck  Squamous  Cell  Carcinoma  (TCGA,  Provisional)   2.4    52,610      1,263      38,380      921    Lung  &  bronchus  cancer   2.4    226,160      5,428      160,340      3,848    Ovarian  Serous  Cystadenocarcinoma  (TCGA,  Nature  2011)   2.2    22,280      490      15,500      341    PancreaUc  Ductal  Adenocarcinoma  (ICGC,  Nature  2012)   2.1    43,920      922      37,390      785    Kidney  &  renal  pelvis  cancer   1.3    64,770      842      13,570      176    Thyroid  Carcinoma  (TCGA,  Provisional)   0.4    56,460      226      1,780      7    Brain  &  other  nervous  system   0    22,910      -­‐          13,700      -­‐        Liver  Hepatocellular  Carcinoma  (TCGA,  Provisional)   0    28,720      -­‐          20,550      -­‐        Prostate  Adenocarcinoma  (MSKCC,  Cancer  Cell  2010)   0    241,740      -­‐          28,170      -­‐        Sarcoma  (MSKCC/Broad,  Nature  GeneUcs  2010)   0    10,700      -­‐          3,800      -­‐        Skin  Cutaneous  Melanoma  (TCGA,  Provisional)   0    76,250      -­‐          9,180      -­‐        

total,  all  cancer  types  sequenced  by  TCGA/ICGC   3.94%    1,373,170      54,043      471,620      15,829    total,  excluding  Breast  &  Stomach,  and  cancers  with  0%  HER2  amp   2.93%    742,470     21,744    345,760     9,319  

HER2-amplified PDAC has an unusual pattern of metastasis & responds to targeted therapy

Table 2: Clinicopathological characteristics of HER2-amplified PDAC. A preponderance of lung, without liver metastases (χ2 P=5e-7)

Figure 3: HER2-amplified patient response to an EGFR inhibitor, Tarceva® (Erlotinib). HER2 heterodimerises with EGFR.

Acknowledgements The authors thank all the members of the Australian Pancreatic Cancer Genome Initiative (www.pancreaticcancer.net.au/apgi/collaborators) for their continuing support with provision of biospecimens. We also thank Mary-Anne Brancato, Michelle Thomas, Sarah Rowe and Mona Martyn-Smith for maintenance of the APGI database and biospecimen resource, Gerard hammond, Warren Kaplan, Derrick Lin, Ajaya Sharma and Jim McBride for database, high performance computing and IT support. The work is supported by the National Health and Medical Research Council of Australia (NHMRC; 631701, 535903, 535914); Australian Government: Department of Innovation, Industry, Science, Research and Tertiary Education (DIISRTE); Australian Cancer Research Foundation (ACRF); Queensland Government (NIRAP); University of Queensland; Cancer Council NSW (SRP06-01; ICGC09-01; SRP11- 01); Cancer Institute NSW (06/ECF/1-24, 09/CDF/2-40, 07/CDF/1-03, 10/CRF/1-01, 08/RSA/1-15, 10/CDF/2-26,10/FRL/2-03, 06/RSA/1-05, 09/RIG/1-02, 10/TPG/1-04, 11/REG/1-10, 11/CDF/3-26); Garvan Institute of Medical Research; Avner Nahmani Pancreatic Cancer Foundation; R.T. Hall Trust; Jane Hemstritch in memory of Philip Hemstritch; Gastroenterological Society of Australia (GESA); Royal Australasian College of Surgeons (RACS); Royal Australasian College of Physicians (RACP); Royal College of Pathologists of Australasia (RCPA) and the St Vincent’s Clinic Foundation.

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Figure 3

Case Report 42yo lady, primary PDAC, resected & standard first line adjuvant therapy Recurred 14mo later, with liver metastasis Confirmed pancreatic origin, strongly HER2-amplified (IHC 3+) Received 24 weeks of Capecitabine and Trastuzumab + 5 cycles of Epirubuicin Further Trastuzumab for 34 weeks Alive at 4 years since recurrence

Case Report