Australian Pancreatic Cancer Genome Initiative Research Articles

Abstract 6575: Selective targeting of integrins αVβ8 and αVβ1 within the dynamic ecosystem of pancreatic cancer to improve the overall anti-tumor response

Abstract Pancreatic ductal adenocarcinoma (PDA) has a 5-year survival of less than 10% and remains the 3rd leading cause of cancer-related death in Western societies. New treatment options are urgently needed. TGF-β promotes stromal cell reprogramming, immunosuppression, and fibrinogenesis in cancers, including PDA. Integrins αVβ8 and αVβ1 are important activators of TGF-β signalling. Selective integrin blockade has recently emerged as a promising therapeutic approach to address TGF-β-mediated immunotherapy resistance and improve anti-tumour response across cancer models. The purpose of this study was to assess the in vivo efficacy of small molecule inhibitor PLN-104, a selective inhibitor of αVβ1, and PLN-101095, a dual inhibitor of αVβ8 and αVβ1, in well-annotated models of advanced PDA. We determined the preclinical efficacy and detailed anti-stromal effect of PLN-101095 inhibitor in genetically defined and patient-derived PDA models, including clinically relevant combinations with standard of care (SoC) chemotherapy and anti-programmed death receptor-1 antibody (anti-mPD-1). Mechanistic assessment of alterations in tumour cell-stromal cell crosstalk was performed using comprehensive transcriptomics and immunofluorescence approaches. Dual targeting of αVβ8 and αVβ1 with PLN-101095 in the syngeneic LSL-KrasG12D/+;LSL-Trp53R172H/+;Pdx1-Cre (KPC) model effectively reduced tumour growth by 45% in comparison to the vehicle, and significantly delayed disease progression in vivo. Single-cell analysis of PLN-101095-treated KPC pancreatic tumours revealed a positive reprogramming of malignant cells from a mesenchymal to a more epithelial-like state. This effect was further associated with an upregulation of MHC type I/II markers and corresponding downregulation of pro-metastatic factors across diverse cancer sub-populations. Additionally, combining PLN-101095 with anti-mPD-1 antibody further improved survival in this aggressive model of metastatic PDA. In a second syngeneic model, Pan02, PLN-101095 in combination with anti-mPD-1 antibody significantly reduced tumour growth, while increasing CD8+ lymphocyte infiltration. The combination of PLN-101095 with Anti-PD1 increased MHC and IFN gene expression. Finally, utilizing patient-derived models of metastatic PDA revealed that both PLN-104 and PLN-101095 significantly blocked tumour growth, improved the response to SoC chemotherapy Gemcitabine/Abraxane, and reduced metastatic spread to distant sites. In conclusion, these data provide scientific rationale for the design of future PLN-101095 and SoC chemotherapy as well as immunotherapy combinations in pancreatic cancer, with Phase I first-in-human oncology studies with PLN-101095 plus ICB already underway. Citation Format: Dannielle Upton, Diego Chacon Fajardo, Sofia Omari, Sean Porazinski, Benjamin McLean, Diana Schuhmacher, Aji Istadi, Australian Pancreatic Cancer Genome Initiative, Vishal Kothari, Darren Finkelstein, Tim Machajewski, Fernando Rock, Scott Turner, Marina Pajic. Selective targeting of integrins αVβ8 and αVβ1 within the dynamic ecosystem of pancreatic cancer to improve the overall anti-tumor response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6575.

ROR1 and ROR2 expression in pancreatic cancer

BackgroundThe Wnt receptors ROR1 and ROR2 are generating increased interest as cancer therapeutic targets but remain understudied in pancreatic ductal adenocarcinoma (PDAC). Compared to canonical Wnt/ β-catenin signalling, the role of noncanonical Wnt signalling in PDAC remains largely unknown. Only one study has investigated the prognostic significance of the noncanonical Wnt signalling receptor, ROR2 in PDAC. No studies have investigated the prognostic role of ROR1 in PDAC.MethodsHere, we performed analysis of ROR1 and ROR2 mRNA expression in three publicly available datasets ICGC-PACA-AU (n = 81), TCGA-PAAD (n = 150) and CPTAC-PDAC (n = 137). ROR1 and ROR2 protein expression from the CPTAC-PDAC discovery cohort were also analysed. Immunohistochemistry (IHC) using the validated anti ROR1 monoclonal antibody (4A5) was performed on the Australian Pancreatic Cancer Genome Initiative (APGI) cohort of PDAC samples (n = 152). Association between ROR1 cytoplasmic staining intensity and clinicopathological parameters including stage, grade and overall survival (OS) was investigated.ResultsHigh ROR1 mRNA expression levels correlated with a favourable OS outcome in all of the ICGC-PACA-AU, TCGA-PAAD and CPTAC-PDAC cohorts. ROR1 protein expression was not associated with stage, grade or OS in the APGI cohort.ConclusionROR1 and ROR2 have potential as prognostic markers when measured at the mRNA level in PDAC. Our IHC cohort did not support ROR1 protein expression in predicting OS, and highlighted the discrepancy of prognostic biomarkers when measured by MS, IHC and RNAseq.

Genomic and Molecular Analyses Identify Molecular Subtypes of Pancreatic Cancer Recurrence

Genomic and Molecular Analyses Identify Molecular Subtypes of Pancreatic Cancer Recurrence

Abstract A100: ROBO2 is a stroma suppressor gene in the pancreas through regulation of TGF-β

Abstract Pancreatic ductal adenocarcinoma (PDAC) has a dismal prognosis, being predicted to become the second leading cause of cancer-related death by 2030. Chronic pancreatitis is a risk factor for PDAC and both diseases are characterized by a strong desmoplastic response, comprised of activated myofibroblasts and immune cell infiltrates. Genomic aberrations in the SLIT-ROBO pathway are frequent in PDAC. Nevertheless, their role in the pancreas is unclear. We have used an integrative approach combining the study of murine models and PDAC patients with the objective of unraveling the function of the SLIT-ROBO signaling pathway in pancreatic disease. RNA expression of SLIT-ROBO genes was analyzed in murine normal pancreas, pancreatitis and PDAC. Primary cell cultures and experimental pancreatitis were studied using pancreas-specific Robo2 (Pdx1-Cre;Robo2F/F) and whole-body Slit1 (Slit1-/-) knockout mice. Gene and protein expression were assessed in a cohort of PDAC patients (n=109). In mouse pancreatitis and PDAC, epithelial Robo2 expression is lost while Robo1 expression becomes most prominent in the stroma. Pdx1Cre;Robo2F/F pancreatic cell cultures showed increased activation of Robo1-positive myofibroblasts and induction of TGF-β and Wnt pathways. Likewise, induction of pancreatitis in Pdx1Cre;Robo2F/F mice enhanced myofibroblast activation, collagen crosslinking, T-cell infiltration and tumorigenic immune markers. Similar results were obtained using Slit1-/- animals. Moreover, TGF-β inhibition using galunisertib treatment suppressed Robo2-mediated effects in the microenvironment. In patients, ROBO2 expression is overall low in PDAC, while ROBO1 is variably expressed in epithelium and high in the stroma. ROBO1 expression is correlated with markers of activated stroma, Wnt and TGF-β pathways. ROBO2low;ROBO1high subpopulation of patients present the poorest survival rates. In conclusion, Robo2 acts nonautonomously as a stroma suppressor gene by restraining myofibroblast activation and inflammation in the pancreatic microenvironment. ROBO1/2 expression is prognostic in PDAC patients and may guide therapy with TGF-β inhibitors or immunotherapies, currently being tested in clinical trials for advanced pancreatic cancer. Citation Format: Andreia V. Pinho, Mathias Van Bulck, Lorraine Chantrill, Mehreen Arshi, David Herrmann, Claire Vennin, APGI - Australian Pancreatic Cancer Genome Initiative, Anthony Gill, Paul Timpson, Andrew Biankin, Jianmin Wu, Ilse Rooman. ROBO2 is a stroma suppressor gene in the pancreas through regulation of TGF-β [abstract]. In: Proceedings of the Fourth CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; Sept 30-Oct 3, 2018; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2019;7(2 Suppl):Abstract nr A100.

Defining the molecular pathology of pancreatic body and tail adenocarcinoma.

BackgroundPancreatic ductal adenocarcinoma (PDAC) remains a dismal disease, with very little improvement in survival over the past 50 years. Recent large-scale genomic studies have improved understanding of the genomic and transcriptomic landscape of the disease, yet very little is known about molecular heterogeneity according to tumour location in the pancreas; body and tail PDACs especially tend to have a significantly worse prognosis. The aim was to investigate the molecular differences between PDAC of the head and those of the body and tail of the pancreas.MethodsDetailed correlative analysis of clinicopathological variables, including tumour location, genomic and transcriptomic data, was performed using the Australian Pancreatic Cancer Genome Initiative (APGI) cohort, part of the International Cancer Genome Consortium study.ResultsClinicopathological data were available for 518 patients recruited to the APGI, of whom 421 underwent genomic analyses; 179 of these patients underwent whole-genome and 96 RNA sequencing. Patients with tumours of the body and tail had significantly worse survival than those with pancreatic head tumours (12·1 versus 22·0 months; P = 0·001). Location in the body and tail was associated with the squamous subtype of PDAC. Body and tail PDACs enriched for gene programmes involved in tumour invasion and epithelial-to-mesenchymal transition, as well as features of poor antitumour immune response. Whether this is due to a molecular predisposition from the outset, or reflects a later time point on the tumour molecular clock, requires further investigation using well designed prospective studies in pancreatic cancer.ConclusionPDACs of the body and tail demonstrate aggressive tumour biology that may explain worse clinical outcomes.

Effect of Rho/ROCK pathway inhibition on metastasis-free and overall survival in biomarker selected, orthotopic, patient-derived models of pancreatic cancer.

e15759 Background: PC is a highly lethal disease which metastasises early. The sequencing efforts of the Australian Pancreatic Cancer Genome Initiative (APGI) identified ROCK-1 as a target of interest. The Rho/ROCK pathway is essential in cellular movement, metastasis, vasculogenesis and stromal signaling. Fasudil (F) is a ROCK inhibitor which has been shown to be safe for human use. Using unique, patient derived models, we have previously shown that F plus gemcitabine (G) does not reduce cellular proliferation in vitro but reduces tumour size and improves overall survival (OS) in subcutaneous patient-derived xenografts (PDX). However, PDXs are critisised for not fully recapitulating the human condition. Here we aimed to generate a patient-derived orthotopic xenograft (O-PDX) which could be used to assess the effects of F + G on metastasis formation and OS. Methods: One patient-derived cell line (PDCL) was labled with firefly luciferase. This was injected into the pancreas of NOD/Shi- scid/IL-2Rγnull (NSG) mice to generate the O-PDX model. The O-PDX was imaged weekly with the IVIS imaging system. The O-PDXs were treated with saline control (S) (n = 8), gemcitabine (G) (n = 10) fasudil (F) (n = 6) or gemcitabine + fasudil (GF) (n = 10). Mice were culled once radiographic or clinical evidence of ascites was detected. Metastasis free (MFS) and OS were recorded. Vessel quantification was performed via CD-31 staining. Results: Metastases seen (spleen, liver, lung, ovary) on imaging were confirmed using GFP stains on immunohistochemistry. F prolonged MFS but not OS when compared with S. GF significantly prolonged MFS (33.5 versus 43 days; p = 0.0339) and OS (51.5 versus 64 days; p = 0.0035). CD-31 staining showed that treatment with F resulted in increased vascularity in the liver metastases and normal liver tissue but not in the pancreas tumour. Conclusions: The addition of Fasudil to gemcitabine improves MFS and OS in an orthotopic model of PC and is a promising new therapeutic option. The increase in vascularity of the metastases and normal liver tissue suggest that changes in vascularity are important and may result in improved delivery of gemcitabine.

Lost in translation: returning germline genetic results in genome-scale cancer research

BackgroundThe return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have on clinical care and health outcomes, is sorely lacking. Through the work of the Australian Pancreatic Cancer Genome Initiative (APGI) we: (1) delineate the pathway back to the patient where actionable research data were identified; and (2) report the clinical utilisation of individual results returned. Using this experience, we discuss barriers and opportunities associated with a comprehensive process of RoR in large-scale genomic research that may be useful for others developing their own policies.MethodsWe performed whole-genome (n = 184) and exome (n = 208) sequencing of matched tumour-normal DNA pairs from 392 patients with sporadic pancreatic cancer (PC) as part of the APGI. We identified pathogenic germline mutations in candidate genes (n = 130) with established predisposition to PC or medium–high penetrance genes with well-defined cancer associated syndromes or phenotypes. Variants from candidate genes were annotated and classified according to international guidelines. Variants were considered actionable if clinical utility was established, with regard to prevention, diagnosis, prognostication and/or therapy.ResultsA total of 48,904 germline variants were identified, with 2356 unique variants undergoing annotation and in silico classification. Twenty cases were deemed actionable and were returned via previously described RoR framework, representing an actionable finding rate of 5.1%. Overall, 1.78% of our cohort experienced clinical benefit from RoR.ConclusionReturning research results within the context of large-scale genomics research is a labour-intensive, highly variable, complex operation. Results that warrant action are not infrequent, but the prevalence of those who experience a clinical difference as a result of returning individual results is currently low.

Abstract A02: Assessment of germline cancer predisposition genes in 392 unselected pancreatic cancer patients

Abstract Aim: To determine the prevalence of pathogenic germline mutations in known pancreatic cancer (PC) predisposition genes in an unselected PC cohort; identify clinico-pathological characteristics associated with gene carrier status; and analyse somatic genomic data for evidence of biallelic inactivation. Methods: Whole-genome (n = 184) and exome (n = 208) sequencing was performed on matched tumor-normal DNA pairs from 392 predominantly sporadic cases of PC. Pathogenic mutations were assessed in 13 cancer predisposition genes associated with PC risk (APC, ATM, BRCA1, BRCA2, CDKN2A, MLH1, MSH2, MSH6, PALB2, PMS2, PRSS1, STK11, TP53. Results: A total of 377 unique high confidence germline variants were observed in the 13 PC predisposition genes. 22 were classified as pathogenic and identified in 23/392 (5.9%) PC patients. The mutations occurred in BRCA2 (n=9), ATM (n=4), BRCA1 (n=3), PALB2 (n=3), CDKN2A (n=2) and one each in PMS2 and STK11. Truncating BRCA2 and PALB2 mutations were detected in 2 cases classified as familial PC. There was no significant difference in average age at diagnosis (67.9 vs 66.6, P = 0.5468), post-resection survival (20.3 vs 20.5 months, P = 0.9788), family history of malignancy (55.6% vs 40.5%, P = 0.2249) or personal history of malignancy (31.8% vs 15.0%, P = 0.0642) between those with and those without a pathogenic germline PC risk mutation. Patients harboring BRCA1, BRCA2 or PALB2 mutations were associated with an increased family history of breast or ovarian cancer (27.3% vs 6.3%, P = 0.0348). The second-hit mechanism could be assessed in tumors with >30% cellularity (n=16), of which 75% (7 BRCA2, 4 ATM, 1 BRCA1) showed evidence of biallelic inactivation. Conclusion: 5.9% of PC patients with predominantly sporadic disease have a pathogenic germline mutation in cancer predisposition genes associated with PC risk. However, carrier status did not significantly affect age at diagnosis, survival, personal or family history of malignancy in this cohort. Second hit mechanisms were identified in 12 (52.2%) cases, supporting a potential role in pancreatic tumorgenesis. An expanded analysis of the germline data is required to further understand the genetic basis of both sporadic and familial PC. Citation Format: Skye McKay, Jeremy Humphris, Amber Johns, Mark Pinese, Ann-Marie Patch, Katia Nones, Australian Pancreatic Cancer Genome Initiative (APGI), Sean Grimmond, Andrew Biankin, Nicola Waddell.{Authors}. Assessment of germline cancer predisposition genes in 392 unselected pancreatic cancer patients. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Advances in Science and Clinical Care; 2016 May 12-15; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2016;76(24 Suppl):Abstract nr A02.

Targeting the Rho-ROCK pathway to treat pancreatic cancer: The use of unique preclinical models to ascertain the effects on cancer growth and metastasis.

312 Background: Pancreatic cancer (PC) is a highly lethal and genetically heterogenous disease. Genomic sequence data from the Australian Pancreatic Cancer Genome Initiative (APGI) has identified a subset of patients with ROCK-1 amplification. ROCK-1 is a downstream target of Rho, a small GTPase that plays an important role in regulating proliferation, invasion and metastasis of cancer cells. Our aim was to analyse the effects of inhibiting ROCK-1 using specific small molecule inhibitors (Fasudil and Y-27632) in well annotated and robust pre-clinical model systems generated as part of our APGI efforts. Methods: Patient derived cell lines (PDCL) and xenografts (PDX) were used to test the effectiveness of ROCK-1 inhibitors (RI). Colony formation and 3-D organotypic assays tested cellular proliferation and invasion. In vivo, pre-clinical trials assessed the effect gemcitabine (G) +/- RI on a range of PDXs with varying tumour ROCK expression, including one G resistant model. A PDCL shown to form metastases when injected orthotopically into mice has been labeled with firefly luciferase. The effect of RI on metastasis formation will be assessed in vivo using real time imaging. Results: ROCK inhibition has a differential effect on colony formation on PDCLs in vitro, and inhibits cellular invasion. A statistically significant increase in median survival in the G + RI group compared with G alone, was seen in 3 PDXs, including the G resistant tumour. 1 PDX showed a decrease in tumour size at 200 days in the G + RI group. Conclusions: ROCK inhibition has a differential effect in vitro, but an anti-tumour effect in vivo, including overcoming resistance to G. This suggests that effects on the tumour micro-environment are an important mechanism of action. RI have the potential to be an effective therapy in PC.

Expression of the axon guidance protein Robo1 in pancreatic ductal adenocarcinoma from smokers compared to nonsmokers.

305 Background: The most important modifiable risk factor for the development of pancreas cancer is smoking, which accounts for up to 25% of pancreatic ductal adenocarcinomas (PDAC; Maisonneuve P, Lowenfels AB: Epidemiology of pancreatic cancer: an update. Digestive Diseases 28:645-656, 2010), and the incidence of PDAC correlates with smoking prevalence (Weiss W, Benarde MA: The temporal relation between cigarette smoking and pancreatic cancer. American journal of public health 73:1403-1404, 1983). A recently published Ingenuity Pathway Analysis of GWAS genotype and risk factor data from the Pancreatic Cancer Case Control Consortium demonstrated that axon guidance signalling genes were significantly overrepresented in smokers (Tang H, Wei P, Duell EJ, et al: Axonal guidance signaling pathway interacting with smoking in modifying the risk of pancreatic cancer: A gene and pathway-based interaction analysis of GWAS data. Carcinogenesis:bgu010, 2014) and we aimed to investigate this link in our cohort. Methods: Tissue from resected PDAC were obtained from 200 patients via the Australian Pancreatic Cancer Genome Initiative with patient consent and ethical approval. Immunohistochemistry was performed on TMAs with the anti-Robo1 antibody (ab7279). The sections were scored on a 4-point scale of 0, 1, 2 and 3 intensity. All sections were scored blindly by two independent reviewers. Results: Robo1 protein expression is found in the normal pancreas, predominantly in acinar cells. In PDAC, Robo1 expression is predominantly in epithelial ductal cells. Most PDACs have Robo1 expression with an overall mean score of 1.65±0.05. 20 out of 200 patients were current smokers at the time of their pancreatectomy, 97 were never smokers, the remainder were ex-smokers. The mean score for smokers was 2.1± 0.1 and for never smokers 1.6±0.1 (p = 0.0003). Genomic analysis did not demonstrate any mutations in the Robo1 gene. There were 7 cases of loss of heterozygosity for Robo1; none of these were current smokers and they had an average score of 1.25±0.17. Conclusions: In addition to our genomic (Biankin AV, Waddell N, Kassahn KS, et al: Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature 491:399-405, 2012) and methylation data (Nones K, Waddell N, Song S, et al: Genome‐wide DNA methylation patterns in pancreatic ductal adenocarcinoma reveal epigenetic deregulation of SLIT‐ROBO, ITGA2 and MET signaling. International Journal of Cancer, 2014), we provide the results of protein expression of Robo1 in a clinically annotated cohort of 200 cases of PDAC. We demonstrate that patients who are currently smoking have enhanced Robo1 expression. Preliminary results indicate that this may confer a poorer prognosis when coupled with high SLIT2 expression.

Abstract LB-73: SOX9 regulates EGFR/ERBB signaling in pancreatic cancer

Abstract The transcription factor SOX9 has recently been shown to have a role in the ontogenesis of pancreatic ductal adenocarcinoma (PDAC) through metaplastic changes in pancreatic acinar cells. Nevertheless, the mechanisms through which SOX9 operates remain to be explored. We analyzed genomic and transcriptomic data from a cohort of surgically resected cases of PDAC (n=90) from the Australian Pancreatic cancer Genome Initiative (APGI). Genetic aberrations (mutation and copy number changes) in the SOX9 gene were found in 15% of patient tumors. Protein expression analysis revealed that most PDAC samples strongly express SOX9 protein and differential SOX9 expression correlates with patient survival. SOX9 gene expression was higher in the classical PDAC subtype, which relates with better patient outcome and increased response to epidermal growth factor receptor (EGFR)-directed therapy. In patient tumors, we found that SOX9 expression correlates with expression of EGFR signaling pathway genes, including ErbB2. Analysis of patient-derived xenografts confirmed strong correlation of SOX9 and ErbB2 expression and manipulation of human tumor cell lines demonstrated that Sox9 regulates the expression of ErbB2. We extended these findings by using a mouse model lacking pancreatic Sox9 expression where we found reduced expression of Egfr/ErbB signaling components. Sox9-deficient pancreatic acinar cells failed to generate PDAC precursor lesions and did not respond to EGF, indicating that Sox9 is required for Egfr/ErbB signaling pathway activity. In conclusion, by using an integrative approach that combines human and mouse models data, we discovered a new function of SOX9 in the regulation of EGFR/ERBB signaling throughout pancreatic tumorigenesis. This provides a novel mechanistic insight of potential therapeutic significance for pancreatic cancer patients. Citation Format: Andreia V. Pinho, Adrien Grimont, Mark J. Cowley, Cecile Augereau, Amanda Mawson, Marc Giry-Laterriere, Geraldine Van den Steen, Nicola Waddell, Marina Pajic, Christine Sempoux, Australian Pancreatic Cancer Genome Initiative, Jianmin Wu, Sean M. Grimmond, Andrew V. Biankin, Frederic P. Lemaigre, Patrick Jacquemin, Ilse Rooman. SOX9 regulates EGFR/ERBB signaling in pancreatic cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-73. doi:10.1158/1538-7445.AM2014-LB-73

10. Clinicopathological features of HER2 amplified pancreatic cancer

Background Pancreatic cancer is one of the most lethal and molecularly diverse malignancies. Although HER2 amplification occurs in pancreatic cancer, it is inadequately characterised to define its clinical relevance and to exploit the potential of anti-HER2 therapies. Aims We aim to characterise the clinicopathological features of HER2 amplified pancreatic cancer. Our work extends the clinical relevance of our effect as part of the Australian Pancreatic Cancer Genome Initiative (APGI) in cataloguing genomic aberrations that characterise pancreatic cancer. Methods 469 cases of surgically resected pancreatic ductal adenocarcinoma (PDAC) from 12 institutions associated with the APGI from 1990 to 2012 were assessed for HER2 overexpression by immunohistochemistry and HER2 gene amplification by in situ hybridization. 55 of these cases were also assessed for DNA copy number changes and mRNA expression. Results HER2 amplification was found in 10 of 469 (2.1%) of samples. HER2 gene amplification was found in 100% (7/7) of HER2 3+, 11% (3/27) of HER2 2+ and none of 1+ overexpres-siong tumours. In all but one case, HER2 overexpression was uniform throughout tumours rather than showing clonal heterogeneity. HER2 amplification was associated with moderately differentiated tumours with distinctive macroglandular morphology. HER2 amplified tumours were also distinctive in their pattern of metastasis, with involvement of the lung ± brain without liver metastasis. Conclusions HER2 amplification occurs in 2% of PDAC and has distinct clinicopathological features with implications to clinical practice. The molecular heterogeneity of PDAC implies that even an incidence of 2% represents an attractive target for anti-HER2 therapies, as options for PDAC are limited. Recruiting patients based on HER2 amplification rather than organ of origin could make clinical trials of anti-HER2 therapies more feasible but needs to be well defined with robust diagnostic assays.

Returning individual research results for genome sequences of pancreatic cancer.

BackgroundDisclosure of individual results to participants in genomic research is a complex and contentious issue. There are many existing commentaries and opinion pieces on the topic, but little empirical data concerning actual cases describing how individual results have been returned. Thus, the real life risks and benefits of disclosing individual research results to participants are rarely if ever presented as part of this debate.MethodsThe Australian Pancreatic Cancer Genome Initiative (APGI) is an Australian contribution to the International Cancer Genome Consortium (ICGC), that involves prospective sequencing of tumor and normal genomes of study participants with pancreatic cancer in Australia. We present three examples that illustrate different facets of how research results may arise, and how they may be returned to individuals within an ethically defensible and clinically practical framework. This framework includes the necessary elements identified by others including consent, determination of the significance of results and which to return, delineation of the responsibility for communication and the clinical pathway for managing the consequences of returning results.ResultsOf 285 recruited patients, we returned results to a total of 25 with no adverse events to date. These included four that were classified as medically actionable, nine as clinically significant and eight that were returned at the request of the treating clinician. Case studies presented depict instances where research results impacted on cancer susceptibility, current treatment and diagnosis, and illustrate key practical challenges of developing an effective framework.ConclusionsWe suggest that return of individual results is both feasible and ethically defensible but only within the context of a robust framework that involves a close relationship between researchers and clinicians.

Abstract A75: The IMPaCT trial: Individualised Molecular Pancreatic Cancer Therapy. A pilot, randomized, open label Phase II trial assessing first line treatment with gemcitabine or personalized treatment based on tumour molecular signature in patients with metastatic pancreatic cancer.

Abstract Background: Less than 5% of patients with metastatic pancreatic cancer survive to 5 years and there have been no major improvements in outcomes over the last 20 years. The use of treatments targeted according to the molecular phenotype of individual tumours may result in improved response and survival compared to standard therapy. Methods: The IMPaCT trial is a multidisciplinary collaboration between the AGITG, NHMRC Clinical Trials Centre, Sydney Catalyst, and the Kinghorn Cancer Centre at Garvan Institute of Medical Research, which houses the Australian Pancreatic Cancer Genome Initiative (APGI). Patients who have available sequence data will be screened for actionable molecular phenotypes and randomized 1:1 to receive standard therapy (gemcitabine) or personalized treatment. Recruitment to the IMPaCT trial is based on the following defined molecular phenotypes: HER2/neu overexpression: personalized treatment with gemcitabine + trastuzumab; BRCA1, BRCA2, and PALB2 mutations: personalized treatment with 5-FU and mitomycin C; Kras wildtype: personalized treatment with gemcitabine + erlotinib. The study will be conducted in two parts: an initial 20 patient pilot trial across 4 Australian sites assessing feasibility, followed by an additional 70 patients to assess progression (90 patients in total). The pilot study is now open and active. Results: The novel trial design involves personalized treatment, where therapies are assigned based on a defined molecular phenotype, in a standard care setting. Stratifying randomization for individual molecular signatures will provide evidence, albeit in small numbers, for confirmation in a larger Phase III trial and broader clinical applicability. Additionally, the study offers the opportunity to explore a number of unique tertiary/correlative objectives, including the planned examination of circulating DNA as a surrogate of survival. Conclusion: The IMPaCT trial exemplifies a strong collaboration between basic scientists, clinicians and clinical trial investigators to illustrate the promises and challenges facing the development and successful testing of personalized therapeutic strategies. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A75. Citation Format: Lorraine Chantrill, Amber Johns, Adnan Nagrial, Venessa Chin, Angela Chou, Mark Pinese, Scott Mead, Val Gebski, Katrin Sjoquist, Chee Lee, Sonia Yip, Danielle Miller, Lucille Sebastian, Ray Asghari, Sandra Harvey, Nick Pavlakis, Sanjay Mukhedkar, Peter Grimison, David Miller, John Pearson, Nicola Waddell, Sean Grimmond, John Simes, Andrew Biankin. The IMPaCT trial: Individualised Molecular Pancreatic Cancer Therapy. A pilot, randomized, open label Phase II trial assessing first line treatment with gemcitabine or personalized treatment based on tumour molecular signature in patients with metastatic pancreatic cancer. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr A75.

Understanding pancreatic cancer genomes

Pancreatic cancer is the fourth leading cause of cancer death in our society, with a mortality that virtually parallels its incidence, a median survival of <12 months even with maximal therapy, and a 5-year survival rate of <5 %. The diversity of clinical outcomes and the molecular heterogeneity of histopathologically similar cancer types, incomplete knowledge of the genomic aberrations that drive carcinogenesis and the lack of therapeutics that specifically target most known genomic aberrations necessitates large-scale detailed analysis of cancer genomes to identify novel potential therapeutic strategies. As part of the International Cancer Genome Consortium (ICGC), the Australian Pancreatic Cancer Genome Initiative (APGI) used exomic sequencing and copy number analysis to define genomic aberrations that characterize a large, clinically focused, prospectively accrued cohort of patients with pancreatic cancer. The cohort consisted of early (clinical stages I and II) non-pre-treated patients with pancreatic ductal adenocarcinoma who underwent operative resection with curative intent. We devised approaches to adjust for low epithelial content in primary tumours and to define the genomic landscape of pancreatic cancer to identify novel candidate driver genes and mechanisms. We aim to develop stratified, molecular phenotype-guided therapeutic strategies using existing therapeutics that are either rescued, repurposed, in development, or are known to be effective in an undefined subgroup of PC patients. These are then tested in primary patient-derived xenografts and cell lines from the above deeply characterized cohort. In addition, we return information to treating clinicians that influences patient care and are launching a clinical trial called IMPaCT (Individualized Molecular Pancreatic Cancer Therapy). This umbrella design trial randomizes patients with metastatic disease to either standard first-line therapy with gemcitabine, or a molecular phenotype-guided approach using next-generation sequencing strategies to screen for actionable mutations defined through the ICGC effort.

A transposon-based tumor resection model of pancreatic ductal adenocarcinoma (PDAC) with extrahepatic distant metastases

A transposon-based tumor resection model of pancreatic ductal adenocarcinoma (PDAC) with extrahepatic distant metastases

Erratum: Corrigendum: The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

Nature 486, 266–270 (2012); doi:10.1038/nature11114 In this Letter, several authors from the Australian Pancreatic Cancer Genome Initiative were inadvertently omitted: Christopher J. Scarlett and Warren Kaplan from the The Kinghorn Cancer Centre; and Aldo Scarpa from the ARC-NET Center for Applied Research on Cancer.

Abstract 5071: The genomic landscape of pancreatic cancer: from discovery to patient care

Abstract Pancreatic Cancer is the fourth leading cause of cancer death in our society, with a mortality that virtually parallels its incidence, a median survival of &amp;lt; 12 months even with maximal therapy, and a 5-year survival rate of &amp;lt; 5%. The diversity of clinical outcomes and the molecular heterogeneity of histopathologically similar cancer types, incomplete knowledge of the genomic aberrations that drive carcinogenesis and the lack of therapeutics that specifically target most known genomic aberrations necessitates large scale detailed analysis of cancer genomes to identify novel potential therapeutic strategies. As part of the International Cancer Genome Consortium (ICGC), the Australian Pancreatic Cancer Genome Initiative (APGI), together with the Baylor College of Medicine and the Ontario Institute of Cancer Research used exomic sequencing and copy number analysis to define genomic aberrations that characterise a large clinically focused prospectively accrued cohort of patients with pancreatic cancer (n = 142). The cohort consists of early (clinical stages I and II) non-pretreated patients with pancreatic ductal adenocarcinoma who underwent operative resection with curative intent. We devise approaches to adjust for low epithelial content in primary tumours and define the genomic landscape of pancreatic cancer to identify novel candidate driver genes and mechanisms. We develop stratified, molecular phenotype guided therapeutic strategies using existing therapeutics that are either rescued, repurposed, in development, or are known to be effective in an undefined subgroup of PC patients. These are then tested in primary patient derived xenografts and cell lines from the above deeply characterised cohort. In addition, we are launching a clinical trial named IMPaCT (Individualised Molecular Pancreatic Cancer Therapy). This trial randomises patients with metastatic disease to either standard first line therapy with gemcitabine, or a molecular phenotype guided approach using next generation sequencing strategies to screen for actionable mutations defined through the ICGC effort. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5071. doi:1538-7445.AM2012-5071

Cancer genomes and clinical care

Stratifying individual patients for specific therapies based on the clinical stage and morphological features (phenotype) of their disease is the basis of modern clinical oncology. Appropriate therapeutic regimens are selected in light of the characteristics of an individual’s cancer based on imaging and histopathology, which are indirect ‘surrogate’ measures of disease biology. Advances in molecular pathology and our understanding of cancer biology have led to refinement of existing clinico-pathological phenotypes, and in some cases such as leukaemia and breast cancer, a new molecular taxonomy has emerged which is integral to the modern management of these diseases. Increasingly, the development of a novel targeted therapy involves defining drug-diagnostic combinations where the presence of a molecular marker identifies patients who are most likely to respond to treatment. This model of developing treatment and diagnostic/companion biomarker combinations in order to target patient populations with a greater chance of benefiting from treatment is the emerging paradigm for new drug and diagnostic development. This strategy is facilitating significant advances in some cancer types, with one of the more recent examples being the successful use of the BRAF inhibitor PLX4032, which targets a specific mutation (V600E) in melanoma. The number of target-drug combinations with efficacy is growing, and some are suggesting that the era of personal genomic cancer therapy is already here. This emerging paradigm is changing the focus from therapeutic strategy development to diagnostics and will create significant challenges in the development and delivery of personalised medicine strategies. The Australian Pancreatic Cancer Genome Initiative, a part of the International Cancer Genome Consortium, aims to define, interpret and apply cancer genomic data. Direct potential clinical applications include the delineation of phenotypes based on patterns of genomic aberrations co-segregating with clinico-pathological end-points and identifying druggable mutations. In addition, other approaches such as the detection of tumour specific genomic abnormalities in blood would have applications in early detection of recurrence and surrogate markers of therapeutic responsiveness. These advances are rapidly altering diagnostic and therapeutic strategies for cancer, and potentially other diseases, paving the way to genomic health. These advances in genetic pathology have the potential to refine, and possibly replace current morphology based diagnostic approaches. Stratifying individual patients for specific therapies based on the clinical stage and morphological features (phenotype) of their disease is the basis of modern clinical oncology. Appropriate therapeutic regimens are selected in light of the characteristics of an individual’s cancer based on imaging and histopathology, which are indirect ‘surrogate’ measures of disease biology. Advances in molecular pathology and our understanding of cancer biology have led to refinement of existing clinico-pathological phenotypes, and in some cases such as leukaemia and breast cancer, a new molecular taxonomy has emerged which is integral to the modern management of these diseases. Increasingly, the development of a novel targeted therapy involves defining drug-diagnostic combinations where the presence of a molecular marker identifies patients who are most likely to respond to treatment. This model of developing treatment and diagnostic/companion biomarker combinations in order to target patient populations with a greater chance of benefiting from treatment is the emerging paradigm for new drug and diagnostic development. This strategy is facilitating significant advances in some cancer types, with one of the more recent examples being the successful use of the BRAF inhibitor PLX4032, which targets a specific mutation (V600E) in melanoma. The number of target-drug combinations with efficacy is growing, and some are suggesting that the era of personal genomic cancer therapy is already here. This emerging paradigm is changing the focus from therapeutic strategy development to diagnostics and will create significant challenges in the development and delivery of personalised medicine strategies. The Australian Pancreatic Cancer Genome Initiative, a part of the International Cancer Genome Consortium, aims to define, interpret and apply cancer genomic data. Direct potential clinical applications include the delineation of phenotypes based on patterns of genomic aberrations co-segregating with clinico-pathological end-points and identifying druggable mutations. In addition, other approaches such as the detection of tumour specific genomic abnormalities in blood would have applications in early detection of recurrence and surrogate markers of therapeutic responsiveness. These advances are rapidly altering diagnostic and therapeutic strategies for cancer, and potentially other diseases, paving the way to genomic health. These advances in genetic pathology have the potential to refine, and possibly replace current morphology based diagnostic approaches.

Cancer genomes and clinical care

Stratifying individual patients for specific therapies based on the clinical stage and morphological features (phenotype) of their disease is the basis of modern clinical oncology. Appropriate therapeutic regimens are selected in light of the characteristics of an individual’s cancer based on imaging and histopathology, which are indirect ‘surrogate’ measures of disease biology. Advances in molecular pathology and our understanding of cancer biology have led to refinement of existing clinico-pathological phenotypes, and in some cases such as leukaemia and breast cancer, a new molecular taxonomy has emerged which is integral to the modern management of these diseases. Increasingly, the development of a novel targeted therapy involves defining drug-diagnostic combinations where the presence of a molecular marker identifies patients who are most likely to respond to treatment. This model of developing treatment and diagnostic/companion biomarker combinations in order to target patient populations with a greater chance of benefiting from treatment is the emerging paradigm for new drug and diagnostic development. This strategy is facilitating significant advances in some cancer types, with one of the more recent examples being the successful use of the BRAF inhibitor PLX4032, which targets a specific mutation (V600E) in melanoma. The number of target-drug combinations with efficacy is growing, and some are suggesting that the era of personal genomic cancer therapy is already here. This emerging paradigm is changing the focus from therapeutic strategy development to diagnostics and will create significant challenges in the development and delivery of personalised medicine strategies. The Australian Pancreatic Cancer Genome Initiative, a part of the International Cancer Genome Consortium, aims to define, interpret and apply cancer genomic data. Direct potential clinical applications include the delineation of phenotypes based on patterns of genomic aberrations co-segregating with clinico-pathological endpoints and identifying druggable mutations. In addition, other approaches such as the detection of tumour specific genomic abnormalities in blood would have applications in early detection of recurrence and surrogate markers of therapeutic responsiveness. These advances are rapidly altering diagnostic and therapeutic strategies for cancer, and potentially other diseases, paving the way to genomic health. These advances in genetic pathology have the potential to refine, and possibly replace current morphology based diagnostic approaches.