Analysis Of Patient-derived Xenografts Research Articles

HLF promotes ovarian cancer progression and chemoresistance via regulating Hippo signaling pathway

Hepatic leukemia factor (HLF) is aberrantly expressed in human malignancies. However, the role of HLF in the regulation of ovarian cancer (OC) remains unknown. Herein, we reported that HLF expression was upregulated in OC tissues and ovarian cancer stem cells (CSCs). Functional studies have revealed that HLF regulates OC cell stemness, proliferation, and metastasis. Mechanistically, HLF transcriptionally activated Yes-associated protein 1 (YAP1) expression and subsequently modulated the Hippo signaling pathway. Moreover, we found that miR-520e directly targeted HLF 3′-UTR in OC cells. miR-520e expression was negatively correlated with HLF and YAP1 expression in OC tissues. The combined immunohistochemical (IHC) panels exhibited a better prognostic value for OC patients than any of these components alone. Importantly, the HLF/YAP1 axis determines the response of OC cells to carboplatin treatment and HLF depletion or the YAP1 inhibitor verteporfin abrogated carboplatin resistance. Analysis of patient-derived xenografts (PDXs) further suggested that HLF might predict carboplatin benefits in OC patients. In conclusion, these findings suggest a crucial role of the miR-520e/HLF/YAP1 axis in OC progression and chemoresistance, suggesting potential therapeutic targets for OC.

Predictive biomarkers for 5-fluorouracil and oxaliplatin-based chemotherapy in gastric cancers via profiling of patient-derived xenografts

Gastric cancer (GC) is commonly treated by chemotherapy using 5-fluorouracil (5-FU) derivatives and platinum combination, but predictive biomarker remains lacking. We develop patient-derived xenografts (PDXs) from 31 GC patients and treat with a combination of 5-FU and oxaliplatin, to determine biomarkers associated with responsiveness. When the PDXs are defined as either responders or non-responders according to tumor volume change after treatment, the responsiveness of PDXs is significantly consistent with the respective clinical outcomes of the patients. An integrative genomic and transcriptomic analysis of PDXs reveals that pathways associated with cell-to-cell and cell-to-extracellular matrix interactions enriched among the non-responders in both cancer cells and the tumor microenvironment (TME). We develop a 30-gene prediction model to determine the responsiveness to 5-FU and oxaliplatin-based chemotherapy and confirm the significant poor survival outcomes among cases classified as non-responder-like in three independent GC cohorts. Our study may inform clinical decision-making when designing treatment strategies.

MicroRNA-454 promotes liver tumor-initiating cell expansion by regulating SOCS6

Tumor-initiating cells (T-ICs) are involved in the tumorigenesis, progression, drug resistance and recurrence of hepatocellular carcinoma (HCC). However, the underlying mechanism for the propagation of liver T-ICs remains unclear. Herein, we find that miR-454 is upregulated in liver T-ICs and has an important function in liver T-ICs. Functional studies have revealed that knockdown of miR-454 inhibits liver T-IC self-renewal and tumorigenesis. Conversely, forced miR-454 expression promotes liver T-IC self-renewal and tumorigenesis. Mechanistically, we found that miR-454 downregulates SOCS6 expression in liver T-ICs. The correlation between miR-454 and SOCS6 is validated in human HCC tissues. Furthermore, HCC cells that overexpress miR-454 are resistant to sorafenib treatment. Analysis of patient-derived xenografts (PDXs) further demonstrates that miR-454 may predict sorafenib benefits in HCC patients. In conclusion, our findings reveal the crucial role of miR-454 in liver T-IC expansion and sorafenib response.

MicroRNA-29a regulates liver tumor-initiating cells expansion via Bcl-2 pathway

MicroRNAs (miRNAs) participate in tumorigenesis, progression, recurrence and drug resistance of hepatocellular carcinoma (HCC). However, few miRNAs have been identified and entered clinical practice. Herein, we report that miR-29a is downregulated in tumor-initiating cells (T-ICs) and has an important function in liver T-ICs. Functional studies revealed that miR-29a knockdown promotes liver T-ICs self-renewal and tumorigenesis. Conversely, a forced miR-29a expression inhibits liver T-ICs self-renewal and tumorigenesis. Mechanistically, we find that miR-29a downregulates Bcl-2 via binding its mRNA 3′UTR in liver T-ICs. The correlation between miR-29a and Bcl-2 is validated in human HCC tissues. Furthermore, the miR-29a expression determines the responses of hepatoma cells to sorafenib treatment. Analysis of patient-derived xenografts (PDXs) further demonstrated that the miR-29a high patients are more sensitive to sorafenib treatment. In conclusion, our findings revealed the crucial role of the miR-29a in liver T-ICs expansion and sorafenib response, rendering miR-29a as an optimal target for the prevention and intervention of HCC.

MicroRNA-28-5p Regulates Liver Cancer Stem Cell Expansion via IGF-1 Pathway

Background MicroRNAs (miRNAs) play a critical role in the regulation of cancer stem cells (CSCs). However, the role of miRNAs in liver CSCs has not been fully elucidated. Methods Real-time PCR was used to detect the expression of miR-miR-28-5p in liver cancer stem cells (CSCs). The impact of miR-28-5p on liver CSC expansion was investigated both in vivo and in vitro. The correlation between miR-28-5p expression and sorafenib benefits in HCC was further evaluated in patient-derived xenografts (PDXs). Results Our data showed that miR-28-5p was downregulated in sorted EpCAM- and CD24-positive liver CSCs. Biofunctional investigations revealed that knockdown miR-28-5p promoted liver CSC self-renewal and tumorigenesis. Consistently, miR-28-5p overexpression inhibited liver CSC's self-renewal and tumorigenesis. Mechanistically, we found that insulin-like growth factor-1 (IGF-1) was a direct target of miR-28-5p in liver CSCs, and the effects of miR-28-5p on liver CSC's self-renewal and tumorigenesis were dependent on IGF-1. The correlation between miR-28-5p and IGF-1 was confirmed in human HCC tissues. Furthermore, the miR-28-5p knockdown HCC cells were more sensitive to sorafenib treatment. Analysis of patient-derived xenografts (PDXs) further demonstrated that the miR-28-5p may predict sorafenib benefits in HCC patients. Conclusion Our findings revealed the crucial role of the miR-28-5p in liver CSC expansion and sorafenib response, rendering miR-28-5p an optimal therapeutic target for HCC.

PS915 HIGH‐THROUGHPUT IMAGING ANALYSIS FOR DRUG COMBINATION EFFICACY AND SPECIFICITY IN CHILDHOOD ACUTE LYMPHOBLASTIC LEUKAEMIA

Background:Childhood acute lymphoblastic leukaemia (ALL) responds well to conventional treatment, however there is a need to find more targeted therapies without the associated toxicities. There is great inconsistency of drug responses in cell lines, and often these do not represent the outcomes observed in the clinic. Patient‐derived xenografts (PDXs) have been shown to more closely represent patient cancers, and increasingly better demonstrate the drug response clinically observed. However, in vivo assessment of multiple drug combinations is costly and time consuming. The development of an ex vivo ALL patient‐derived xenograft/mesenchymal stromal cell (MSC) co‐culture platform has allowed for screening of novel drug combinations in multiple childhood ALL cytogenetic subtypes.Aims:The aim of this study was to develop a high‐throughput whole‐well image‐based analysis of PDX and MSC cell numbers after exposure to double combinations of 4 drugs. A panel of PDXs were assessed to take into account heterogeneity in pharmacological response.Methods:A previously reported PDX/MSC platform was utilised to assess double drug combinations of dexamethasone, palbociclib, idasanutlin and ABT‐199 in a panel of childhood ALL PDXs. Thawed PDXs were seeded on MSCs and treated with drug combinations in a 7x7 matrix format for 96 h. These were subsequently stained with a fluorescent DNA dye, and high‐throughput microscopy was conducted to obtain whole‐well images of PDX and MSC nuclei. Images were segmented and measurements of nuclear intensity, size and shape were produced with CellProfiler software. Segmented images were used to train a random forest classifier, within CellProfiler Analyst software, to distinguish PDX and MSC nuclei, utilising a multitude of image features. Combination treatments were assessed for synergy with the zero interaction potency model (ZIP).Results:Whole‐well cell numbers were achieved for PDXs and MSCs in the context of drug combinations across a range of ALL cytogenetic subgroups. Comparing fluorescence intensity readings with imaging and cell scoring revealed a background fluorescence level that previously could not be removed, leading to the underestimation of drug response. Combination of dexamethasone and ABT‐199, previously shown to be additive or synergistic was also confirmed across our panel. Cell numbers in control wells were consistently equal to or higher than the original seeding densities, demonstrating the capacity of the platform to support PDX proliferation. Interestingly, the CDK4/6 inhibitor palbociclib scored strongly across many of the PDXs, and even more so in combination with ABT‐199: something which has not been previously observed. Particularly strong synergy of ABT‐199 and idasanutlin was observed in a PDX with a t(9;22) translocation (max ZIP score 69). None of the double combinations tested had an effect on MSC cell number.Summary/Conclusion:This platform allows accurate quantification of absolute PDX cell number and relative MSC cell number. DNA stains have previously been shown to be superior to many standard viability assays such as fluorescent metabolic readouts. This methodology goes further to enable stratification of different cell types. The effective combination of dexamethasone and ABT‐199 in childhood ALL, previously seen in mice, was confirmed with this platform, and several novel combinations were identified which appeared to show synergy, and will be taken forward to in vivo testing. This image‐based platform is now being expanded to increase the complexity of the co‐culture model with other haematopoietic niche cells.

Abstract 2973: A comprehensive panel of patient-derived xenografts representing the molecular heterogeneity and diversity of triple-negative breast cancer

Abstract Purpose: Triple-negative breast cancer (TNBC) is a heterogeneous disease. Patients diagnosed with TNBC have a poor prognosis and identification of new biomarkers and therapeutic agents is a high priority. Patient-derived xenografts (PDX) are clinically relevant models that have emerged as important tool for the analysis of drug activity and predictive biomarker discovery. The purpose of this work was to analyze the molecular heterogeneity of a large panel of TNBC PDX with the perspective to test targeted therapy and to identify biomarkers of response. Experimental Design: PDX of early-stage TNBC established from 2003 to 2016 (N=60) were analyzed by high-resolution array CGH and gene expression profiling (Cytoscan HD and Human Gene 1.1 ST arrays). Subtypes were identified with the tool TNBCtype (Chen et al., 2012) based on transcriptomic data. A targeted next-generation sequencing (NGS) of 100 genes (the top frequently mutated genes in breast cancer) was performed on Illumina HiSeq2500 sequencer. COSMIC, Tumorportal and cBioportal databases were used for the interpretation of genomic variants. Immunohistochemistry (IHC) and morphologic analysis of PDX were performed as compared to the corresponding patients' tumors. PDX carrying targetable genomic alterations in the PI3K/AKT/mTOR and MAPK signaling pathways were treated by specific inhibitors (selumetinib, BAY 80-6946 and PF-04691502). Results: At the gene expression level, TNBC PDX represent all the different TNBC subtypes identified by the Lehmann classification. The frequency of the different TNBC subtypes was similar to the TGCA TNBC, except for the immunomodulatory subtype, underrepresented in PDX. Somatic pathologic mutations and copy number alterations were similar in PDX and TCGA TNBC patients. Among the top altered genes are TP53 and oncogenes and tumor suppressors of the PI3K/AKT/mTOR and MAPK pathways (including PIK3CA, AKT1, NF1 and NRAS/KRAS). At the histologic level, TNBC PDX were mainly composed of invasive ductal carcinoma of no special type, with some tumors being classified as apocrine or metaplastic carcinomas. Comparison with the original tumors show similar patterns (based on IHC analysis of CK5, CK8/18, CK14 and AR, FOXA1, EGFR and Ki67). In vivo efficacy experiments with PI3K and MAPK pathways inhibitors showed marked antitumor activity in PDX carrying genomic alterations of PIK3CA, AKT1 and NRAS, NF1 genes. Drug combination experiments are currently ongoing in PDX with simultaneous genomic alterations of PI3KCA and MAPK related genes. Conclusions: TNBC PDX reproduce the molecular heterogeneity and diversity of TNBC patients. This large collection of PDX is a clinically relevant platform for drug testing, biomarker discovery and translational research. Citation Format: Florence Coussy, Virginie Bernard, Marion Lavigne, Anais Boulai, Sophie Chateau-Joubert, Ahmed Dahmani, Elodie Montaudon, Cécile Reyes, Rania El Botty, Gaëlle Pieron, Cécile Laurent, Samia Melaabi, Anne Vincent Salomon, Ivan Bièche, Elisabetta Marangoni. A comprehensive panel of patient-derived xenografts representing the molecular heterogeneity and diversity of triple-negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2973.

Abstract 3596: Biomarkers of response to CDK4/6 inhibitor (CDK4/6i) in hormone receptor (HR) positive and HER2-positive breast cancer (BC) patient-derived xenografts (PDX)

Abstract The cell cycle G1-restriction point is frequently deregulated in HR+ BC by alterations of cyclin D1 (CCND1), p16 (CDKN2A) or pRb (RB1). CDK4/6i (ribociclib, abemaciclib and palbociclib) have shown clinical activity in metastatic HR+ BC, both as single agents and in combination with endocrine therapy. Currently, no biomarkers of response to CDK4/6i have been identified beyond HR expression and little is known about mechanisms of acquired resistance. Twenty-one PDXs were established from HR+, HER2+ or HR+/HER2+ BC patient biopsies and their response to ribociclib was evaluated in vivo and ex vivo in matrigel cultures. Acquired-resistance was generated in vivo by isolating tumors that escaped therapy overtime. In order to identify response biomarkers, genetic and proteomic analysis of PDXs were performed and correlated with ribociclib antitumor activity. Candidates were validated in a cohort of 8 tumor samples from patients treated with abemaciclib monotherapy and in vitro. Combination with the PI3K-alpha inhibitor (PI3Ki) BYL719 was explored in vivo. In vivo, ribociclib exhibited antitumor activity in five out of 21 PDXs (24%), two of which acquired resistance after continuous dosage (75mg/kg, 6IW). Ex vivo matrigel cultures recapitulated the in vivo response with 75% sensitivity and 92% specificity (p=0.01), providing a novel approach for high throughput screening. Baseline levels of ER, PR and Ki67 protein or PIK3CA/ESR1 mutations did not discriminate between ribociclib-resistant/sensitive PDXs, whereas CCND1/D2-amplification/overexpression were only found in ribociclib-resistant models. Importantly, sensitive PDXs exhibited significant Ki67 reduction upon ribociclib treatment, higher baseline pRb- and lower p16-staining compared to ribociclib-resistant PDXs (p=0.004, 0.02 and 0.03, respectively). Three out of 8 acquired-resistant tumors (37.5%) exhibited pRb loss. In vitro, RB1 knockdown and cyclin D1/D2-overexpression resulted in higher BrdU incorporation and higher IC50 than control cells upon ribociclib treatment. p16 expression was significantly lower in samples of patients exhibiting clinical benefit with abemaciclib monotherapy (p=0.04). Remarkably, combination of ribociclib with a PI3Ki resulted in appreciable antitumor activity in 18 out of 20 PDXs (90%), including two models resistant to fulvestrant given in combination with ribociclib. In conclusion, HR+, HER2+ and HR+/HER2+ BC PDXs expressing both high Rb- and low p16-protein levels are sensitive to CDK4/6i whereas deregulation of the G1-restriction point due to low pRb or high cyclin D1/D2 protein levels is associated with resistance to ribociclib monotherapy. Addition of a PI3Ki markedly improves the antitumor response of ribociclib in most of PDXs, suggesting that the PI3K pathway may play a pivotal role in limiting the efficacy of CDK4/6 inhibition. Citation Format: Marta Palafox, María Teresa Herrera-Abreu, Meritxell Bellet, Mafalda Oliveira, Alejandra Bruna, Olga Rodriguez, Marta Guzmán, Judit Grueso, Cristina Vilaplana, Joaquín Arribas, Emmanuelle di Tomaso, Faye Su, Carlos Caldas, Nicholas C. Turner, Rodrigo Dienstmann, José Baselga, Maurizio Scaltriti, Javier Cortés, Cristina Saura, Violeta Serra. Biomarkers of response to CDK4/6 inhibitor (CDK4/6i) in hormone receptor (HR) positive and HER2-positive breast cancer (BC) patient-derived xenografts (PDX) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3596.

Abstract B209: Transcriptomic analysis of patient-derived xenografts reveals heterogeneity in human and mouse stroma/immune compartments

Abstract Introduction: Cancers are increasingly recognized as diverse collections of not only genetic diseases but also immune diseases. The heterogeneous tumor microenvironment (TME), including immune components, plays critical roles in tumor growth/progression and response to pharmaceutics, particularly immuno-oncology therapeutics. However, investigating stroma-specific components is rather challenging due to the difficulty in separating stroma from tumor cells, either physically via microdissection or in silico via bioinformatics. Experimental animal models are excellent system to investigate TME1. For example, patient-derived xenograft (PDX), where human and mouse content can readily be separated in silico2, provides a model to study tumor microenvironment, including tumor-stroma interactions. Methods: Whole transcriptome sequencing was performed on subcutaneous PDXs in athymic mice3 and all reads were aligned to human and mouse genomes to discriminate human and mouse content, respectively. Low expressed/less variable genes were removed across the two components. MCP-counter algorithm4 was used to estimate infiltration by various human immune and other stromal cell populations from human gene expression data. The gene expression profiles of 35 cell types from Immunological Genome Consortium (ImmGen)5 were used to create lineage-specific signatures and compute mouse stroma composition by CIBERSORT6. Weighted gene coexpression network analysis (WGCNA)7 was applied on human and mouse gene expression data, respectively, to identify distinct gene modules associated with different biologic functions. Human-mouse gene correlation analysis was performed to construct cross-species expression networks. Results: We have established and profiled ~1800 subcutaneous PDXs, with ~1500 of them whole transcriptome-sequenced (http://crownbio.com/eortc17/stromalposter)8. The average mouse-to-human sequencing read ratio is around 11%, consistent with the previous report2. By deconvolution analysis of human and mouse gene expression data, we identified all types of adaptive and innate immune cells in mouse stroma of these immune-deficient mice. Most surprisingly, a variety of human immune components were also observed in human expression contents. The corresponding fractions vary across cancer subtypes and individual models. The heterogeneity has been also validated by flow cytometry. Distinct coexpressed gene modules from human (50x) and mouse (28x) revealed that human clusters were more correlated to cancer type than mouse clusters, particularly strong in pancreatic, colorectal, and lung cancers. Knowledge-based functional analysis of these gene modules revealed the association of diverse biologic processes. Moreover, cross-species correlation network identified a novel relationship between human and mouse genes over all PDXs and in specific cancers. Conclusions: Both human and mouse stroma/immune composition exists and varies across cancers in subcutaneous PDXs, with each cancer type and each individual model within subtypes, suggesting PDX as a useful experimental model to study TME. Citation Format: Jia Xue, Wubin Qian, Sheng Guo, Jie Cai, Xuesong Ouyang, Henry Qixiang Li. Transcriptomic analysis of patient-derived xenografts reveals heterogeneity in human and mouse stroma/immune compartments [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2017 Oct 26-30; Philadelphia, PA. Philadelphia (PA): AACR; Mol Cancer Ther 2018;17(1 Suppl):Abstract nr B209.

Novel therapeutic targets for pancreatic adenocarcinoma revealed by a multi-omics analysis of patient-derived xenografts

Novel therapeutic targets for pancreatic adenocarcinoma revealed by a multi-omics analysis of patient-derived xenografts

Abstract B37: Chemi-genomic analysis of patient-derived xenografts to identify personalized therapies for medulloblastoma

Abstract Medulloblastoma (MB) is the most common malignant brain tumor in children. Even with an intensive regimen of surgery, radiation and chemotherapy, one-third of patients still die from their disease. Moreover, survivors suffer devastating side effects including cognitive deficits, endocrine disorders and an increased incidence of secondary cancers later in life. Thus, more effective and less toxic therapies are desperately needed. Recent genomic analyses have identified 4 major subgroups of MB—WNT, SHH, Group 3 and Group 4—that differ in terms of mutations, gene expression profiles and patient outcomes. Despite this heterogeneity, all MB patients currently receive the same therapy. To identify novel therapies for each subgroup of MB, we have assembled a diverse panel of patient-derived xenograft (PDX) lines. These lines, established by orthotopic transplantation of tumor cells obtained from surgery, recapitulate the properties of patients' tumors more accurately than cultured cell lines. We are using these PDX lines to screen small molecule libraries and identify compounds that can inhibit tumor growth and survival. To date we have completed screening of 18 lines, including 10 representing Group 3 MB, the most aggressive and lethal form of the disease. Among the ~7800 compounds tested, we have found 20 that are effective against the majority of Group 3 PDX lines. Ongoing studies are focused on validating the activity of these compounds against additional Group 3 lines and moving the most promising ones forward into in vivo efficacy studies. Similar approaches will be pursued for each of the other subgroups of MB. Drug response data will also be compared with genomic and epigenomic data (whole exome and low coverage whole genome DNA sequencing, DNA methylation analysis, and gene expression profiling) to identify biomarkers of drug responsiveness and key pathways that may be exploited for therapy. Based on these studies, we hope to move away from a one-size-fits-all approach, and begin to treat each patient with therapies that are likely to be effective against their tumor. Citation Format: Jessica M. Rusert, Alexandra Garancher, Yoko T. Udaka, Sebastian Brabetz, Lourdes A. Esparza, Huriye Seker-Cin, Lin Qi, Mari Kogiso, Simone Schubert, Till Milde, Yoon-Jae Cho, Xiao-Nan Li, James M. Olson, John R. Crawford, Michael L. Levy, Marcel Kool, Stefan M. Pfister, Robert J. Wechsler-Reya. Chemi-genomic analysis of patient-derived xenografts to identify personalized therapies for medulloblastoma. [abstract]. In: Proceedings of the AACR Special Conference: Patient-Derived Cancer Models: Present and Future Applications from Basic Science to the Clinic; Feb 11-14, 2016; New Orleans, LA. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(16_Suppl):Abstract nr B37.

Intra‐ and inter‐tumor heterogeneity in a vemurafenib‐resistant melanoma patient and derived xenografts

The development of targeted inhibitors, like vemurafenib, has greatly improved the clinical outcome of BRAFV600E metastatic melanoma. However, resistance to such compounds represents a formidable problem. Using whole-exome sequencing and functional analyses, we have investigated the nature and pleiotropy of vemurafenib resistance in a melanoma patient carrying multiple drug-resistant metastases. Resistance was caused by a plethora of mechanisms, all of which reactivated the MAPK pathway. In addition to three independent amplifications and an aberrant form of BRAFV600E, we identified a new activating insertion in MEK1. This MEK1T55delinsRT mutation could be traced back to a fraction of the pre-treatment lesion and not only provided protection against vemurafenib but also promoted local invasion of transplanted melanomas. Analysis of patient-derived xenografts (PDX) from therapy-refractory metastases revealed that multiple resistance mechanisms were present within one metastasis. This heterogeneity, both inter- and intra-tumorally, caused an incomplete capture in the PDX of the resistance mechanisms observed in the patient. In conclusion, vemurafenib resistance in a single patient can be established through distinct events, which may be preexisting. Furthermore, our results indicate that PDX may not harbor the full genetic heterogeneity seen in the patient’s melanoma.

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

Abstract LB-226: Integrative pharmacogenomic analysis of patient-derived xenografts of Chinese hepatocellular carcinoma

Abstract Hepatocellular carcinoma (HCC) is the sixth most common cancer worldwide and the third leading cause of cancer-related deaths. Patient derived xenografts (PDX), generated by direct engraftment of tumor samples from the patients into immunocompromised mice can be used as an in vivo platform that provides the opportunity to test proposed personalized medicine strategies. In this study, comprehensive molecular characterizations of 28 Chinese HCC PDX models were done by both whole genome sequencing (WGS) and RNAseq technology. After removing contaminated murine DNA/RNA reads by a proprietary algorithm (unpublished) to eliminate homology bias, more than 35 million reads per sample were analyzed in the RNAseq experiment, and at least average 40X coverage at each base of DNA in the WGS experiment. In order to find meaningful targets with high confidence, we integrated multiple lines of evidences from both DNA and RNA levels. Out of 346 gene fusion events were identified in 28 HCC PDXs, 51 occurred in more than one sample and 13 were supported by structural variation evidence from WGS dataset. The same passages (between p3-p5) of 24 PDX tissues were also treated with Sorafenib in the efficacy studies and showed differential responses. The expression of 482 genes (2%) is statistically significantly correlated with drug sensitivity (p-value <0.05), 198 of them (41%) are positively correlated. In the single nucleotide variation (SNV) and indel analysis of WGS dataset, 162 genes were identified as highly mutated genes (p-value <0.05), including classical cancer driver gene TP53. Total 27401 novel SNVs in these 162 genes were identified, 991 (3.6%) of them are nonsynonymous. 557 (2%) SNVs are statistically significantly correlated with drug sensitivity status (p-value<0.05), 28 are nonsynonymous. Pathway analysis shows that these drug responses related genes are enriched in focal adhension formation, induction of apoptosis, P53 signaling pathway, DNA damage response and cell cycle checkpoint. Comparing to other similar studies, our approach of integrative analysis of WGS (vs. Whole exome sequencing) and RNAseq (vs. microarray) provided the most comprehensive genetic insights/landscapes of HCC patients and genetic alterations’ relationship to the drug responses. It also demonstrated that PDX models provide rich information for preclinical studies of experimental therapeutics, and an excellent resource for biomarker discovery and translational research. Citation Format: Hui Zhou, Haisong Lu, Yujian Shi, Gang Hu, He Zhou, Xueyan Yang, Limei Ouyang, Xiaolong Zhu, Zhuolin Gong, Weikang Tao. Integrative pharmacogenomic analysis of patient-derived xenografts of Chinese hepatocellular carcinoma. [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-226. doi:10.1158/1538-7445.AM2014-LB-226