A combined computational and functional approach identifies IGF2BP2 as a driver of chemoresistance in a wide array of pre-clinical models of colorectal cancer

AIM

Chemoresistance is a major cause of treatment failure in colorectal cancer (CRC) therapy. In this study, the impact of the IGF2BP family of RNA-binding proteins on CRC chemoresistance was investigated using in silico, in vitro, and in vivo approaches.

METHODS

Gene expression data from a well-characterized cohort and publicly available cross-linking immunoprecipitation sequencing (CLIP-Seq) data were collected. Resistance to chemotherapeutics was assessed in patient-derived xenografts (PDXs) and patient-derived organoids (PDOs). Functional studies were performed in 2D and 3D cell culture models, including proliferation, spheroid growth, and mitochondrial respiration analyses.

RESULTS

We identified IGF2BP2 as the most abundant IGF2BP in primary and metastastatic CRC, correlating with tumor stage in patient samples and tumor growth in PDXs. IGF2BP2 expression in primary tumor tissue was significantly associated with resistance to selumetinib, gefitinib, and regorafenib in PDOs and to 5-fluorouracil and oxaliplatin in PDX in vivo. IGF2BP2 knockout (KO) HCT116 cells were more susceptible to regorafenib in 2D and to oxaliplatin, selumitinib, and nintedanib in 3D cell culture. Further, a bioinformatic analysis using CLIP data suggested stabilization of target transcripts in primary and metastatic tumors. Measurement of oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) revealed a decreased basal OCR and an increase in glycolytic ATP production rate in IGF2BP2 KO. In addition, real-time reverse transcriptase polymerase chain reaction (qPCR) analysis confirmed decreased expression of genes of the respiratory chain complex I, complex IV, and the outer mitochondrial membrane in IGF2BP2 KO cells.

CONCLUSIONS

IGF2BP2 correlates with CRC tumor growth in vivo and promotes chemoresistance by altering mitochondrial respiratory chain metabolism. As a druggable target, IGF2BP2 could be used in future CRC therapy to overcome CRC chemoresistance.

Abstract 6223: PD3D®models: New age in cancer research and clinical diagnostics

Patient-derived 3D cell culture models (PD3D®) developed as a powerful tool for disease modelling, biomarker and drug discovery. Currently, they are gaining increasing significance in the field of personalized oncology, as they recapitulate the histopathology of the original tumor tissue and preserve its genetic markup. PD3D® can be used to model intratumoral heterogeneity and for medium and high throughput drug screens. Using a reverse clinical engineering approach, PD3D® models allow identification of chemoresistance/sensitivity signatures (i.e., biomarkers) and can be applied in personalized oncology to identify treatment for an individual patient. We successfully established PD3D® models from more than 300 tumor tissue samples, ranging from more prevalent cancers like colorectal, breast and pancreas carcinoma, to rare tumor entities including various sarcoma types and thymoma. PD3D® models from different tumor entities differ in morphology and culture media requirements. When treating PD3D® from the same tumor entity with standard of care drugs, we found that their response differed, as does clinical response of patients. Furthermore, we successfully used PD3D® models to identify a biomarker for predicting chemosensitivity towards a targeted drug. For application of PD3D® in truly personalized oncology, we developed a protocol that allows us to generate a PD3D® culture and perform a drug sensitivity assay for an individual patient within a therapy-relevant timeframe. Using this protocol, we identified a combination therapy for a pretreated, metastasized appendix carcinoma within 29 days, that resulted in stable disease of the patient. In conclusion, PD3D® models can be derived from various cancer entities and used to analyze drug response in cohorts of models for drug development or identification of signatures related to drug resistance or sensitivity. Furthermore, PD3D® models can be used to predict a patient tumor’s drug response in a personalized manner, supporting the oncologist to identify the best treatment option for the patient.

Citation Format: Alina Pflaume, Samantha Exner, Katja Herrera-Glomm, Jürgen Loskutov, Ulrike Pfohl, Manuela Regenbrecht, Sushmitha Sankarasubramanian, Lena Wedeken, Sabine Finkler, Larissa Ruhe, Quirin Graf Adelmann, Christoph Reinhard, Philipp Stroebel, Christian R. Regenbrecht. PD3D®models: New age in cancer research and clinical diagnostics [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6223.

Abstract 6224: The bad, the ugly and the ultra-rare: All cancers are equal in the face of personalized medicine

Cancer represents a huge health problem worldwide and is well-recognized as an extremely heterogeneous disease affecting all the tissues and organs. The incidence of the particular cancer type is directly connected to the availability of specific medication and amount of the research focused on it, resulting in a high unmet medical need for treatment options for rare cancers. Currently, NCI defines “rare cancer” as cancer with an incidence rate below 15 per 10^5 people per year and recently the term “ultra-rare cancer” was defined as cancer with an incidence rate below 1 per 10^6 people per year. These encompass drastically understudied entities, usually with poor prognosis and grim outlook for an improvement in treatment. Low incidence of such cancers makes development of targeted therapies not interesting from a commercial point of view and completely abolishes the possibility of large-scale clinical trials. Therefore, a personalized medicine approach appears to be the most promising strategy for the patients to get adequate care.

Here we report our experience with personalized oncology solutions for rare and ultra-rare cancers. We utilized patient derived 3D (PD3D) cultures to evaluate prospective therapeutic options in these exceptional cases to support the oncologists in providing personalized care to the patients. Fresh surgical specimens underwent several steps of mechanical and chemical dissociation. Subsequently, cell aggregates were seeded into 24 well plates in matrix-like scaffolds and allowed to grow until they started forming colonies. After harvesting, the cells underwent pathology evaluation to confirm origin and diagnosis. Therapies, recommended by the case leading oncologist, were used for drug sensitivity testing after transferring cells semi- automatically to 384-well plates.

Over the last 18 months, we handled 6 cases classified as rare or ultra-rare cancers. The diagnoses included: clear cell sarcoma, extra-skeletal myxoid chondrosarcoma, CIC-rearranged round cell sarcoma, pleomorphic liposarcoma, cardiac angiosarcoma and clear cell endometrial carcinoma. In all cases we were able to successfully establish PD3D cultures and perform a drug screen, identifying a potential treatment for the patient.

Overall, our results indicate that it is feasible to utilize our testing strategy for rare and ultra-rare cancer entities. Further research and rigorous follow up is required to confirm the benefit of the personalized approach vs current strategies. However, a demand for personalized care in such cases is clearly visible.

Citation Format: Juergen Loskutov, Manuela Regenbrecht, Rica Sauer, Sabine Finkler, Maya Niethard, Christoph Reinhard, Christian Regenbrecht. The bad, the ugly and the ultra-rare: All cancers are equal in the face of personalized medicine [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 6224.

A RAS-independent biomarker panel pedicts response to MEK-inhibitors in colorectal cancer

e15524

Background: Biomarker discovery and development are essential for stratifying cancer patients in order to improve treatment outcomes. In colorectal cancer (CRC), mutations in the TGF-β/BMP pathway, especially in the SMAD4 gene have been correlated with decreased overall survival and are suspected to modulate drug sensitivity on the cellular level, hence SMAD4 mutations are worthwile targets for novel targeted therapy aproaches. Methods: In the present study, we uncover the mechanistic role of a loss-of-function mutation in SMAD4 in syngeneic patient-derived organoids (PDOs). CRISPR-engineered SMAD4R361H PDOs were subjected to a comparative drug screening, RNA-Sequencing and multiplex protein profiling analysis (DigiWest®). We have confirmed the response towards MEK inhibition of the initial model in an additional set of 62 PDOs with known mutational status. Results: We show that acquisition of SMAD4 loss-of-function mutations renders PDOs sensitive to MEK-inhibitors. Further, an activation of the TGF-β/BMP signaling pathway, specifically of the BMP branch was observed in SMAD4wt PDOs; indicating that BMP signaling is likely responsible for the resistance towards MEK inhibition. It is plausible that functional loss of SMAD4 and thus loss of BMP signaling renders SMAD4 mutated tumors more sensitive to MEK-inhibitors. By looking at additional genes involved in TGF-β/BMP signaling that are frequently mutated in CRC, we identified the novel gene mutational SFAB-signature ( SMAD4, FBXW7, ARID1A, or BMPR2), when at least one pathogenic mutation is present in these genes. The frequency of SFAB in CRC patient cohort (TCGA, n = 594) was comparable to the frequency of SFAB in our PDOs. For PDOs with SFAB-signature, we found up to 95% and 70% significant positive prediction for cobimetinib and selumetinib, respectively and also up to 70% positive prediction for trametinib. Thus, the SFAB-signature predicts response to MEK inhibition in PDOs with a very high confidence. We further investigated whether the RAS status of CRC PDOs does predict sensitivity to MEK inhibition. The RAS status alone and in combination with SFAB-signature failed to yield better prediction sensitivity to MEK-inhibitors. Conclusions: The present study is a significant step forward to more personalized treatment regimens for CRC patients by early inclusion of MEK-inhibitors. The SFAB-signature should be put to clinical testing as a RAS-independent biomarker for stratification of patients providing a valuable alternative treatment option against CRC, thus ensuring that all patients receive effective and specific therapies as early as possible.

Context Matters-Why We Need to Change From a One Size Fits all Approach to Made-to-Measure Therapies for Individual Patients With Pancreatic Cancer

Pancreatic cancer is one of the deadliest cancers and remains a major unsolved health problem. While pancreatic ductal adenocarcinoma (PDAC) is associated with driver mutations in only four major genes (KRAS, TP53, SMAD4, and CDKN2A), every tumor differs in its molecular landscape, histology, and prognosis. It is crucial to understand and consider these differences to be able to tailor treatment regimens specific to the vulnerabilities of the individual tumor to enhance patient outcome. This review focuses on the heterogeneity of pancreatic tumor cells and how in addition to genetic alterations, the subsequent dysregulation of multiple signaling cascades at various levels, epigenetic and metabolic factors contribute to the oncogenesis of PDAC and compensate for each other in driving cancer progression if one is tackled by a therapeutic approach. This implicates that besides the need for new combinatorial therapies for PDAC, a personalized approach for treating this highly complex cancer is required. A strategy that combines both a target-based and phenotypic approach to identify an effective treatment, like Reverse Clinical Engineering® using patient-derived organoids, is discussed as a promising way forward in the field of personalized medicine to tackle this deadly disease.

Abstract 2980: Patient-derived 3D sarcoma model - robust system for sarcoma research and personalized therapy selection

Recent progress in 3D cell culture models largely advanced the field of personalized medicine in carcinomas. Unfortunately, the situation is different for the sarcomas: the clinical treatment of sarcoma patients has not significantly improved in the last decade. Such a discrepancy stems from the high degree of heterogeneity of sarcomas and the limited knowledge of the molecular drivers of the tumorigenesis and progression. Our group developed the patient-derived 3D (PD3D) sarcoma model as a tool for a systematic sarcoma research and personalized therapy selection. In short, fresh surgical specimens undergo mechanical and chemical dissociation, cell aggregates are embedded in matrix-like scaffolds and allowed to form colonies. After harvesting the cells undergo pathology evaluation to confirm origin and diagnosis. Standard-of-care compounds as wells as experimental drugs are used for drug sensitivity testing after transferring cells semi-automatically to 384-well plates. Here we report that our PD3D sarcoma model is suitable for the screening of multiple chemotherapeutic compounds in a wide range of sarcoma subtypes. So far, we obtained 57 sarcoma samples. As expected, the most common diagnoses within our cohort are liposarcoma (31.58%) and Undifferentiated pleomorphic sarcoma (UPS) (15.79%). As a proof of the concept, we performed 10 drug-screening experiments with different sarcoma subtypes utilizing first and second line treatment chemotherapeutic compounds. The mean time between obtaining of the sample and drug-screening result was 69 days. Epirubicin, doxorubicin and actinomycin D showed robust activity throughout the whole spectrum of sarcomas tested. Ifosfamide did not show any significant effect, probably due to the requirement for its activation by liver enzymes. Interestingly, trabectedin demonstrated the best effect through the whole samples tested with the IC50s at list 3 orders of magnitude lower than the maximally reachable plasma concentration. Trabectedin is currently only approved as a second line treatment for liposarcoma and leiomyosarcoma by the FDA. Our results indicate that it could be beneficial for patients with other sarcoma subtypes. Even with the limited number of samples we accumulated a variety of different histopathological sarcoma subtypes in our collection. We hope that further development of our collection will allow us to cover the whole spectrum of sarcomas, generating much needed tool for investigating soft-tissue tumors, and allowing for successful development of a targeted therapeutic approach. Overall, our results indicate, that sarcoma PD3D cultures are a viable option for personalized medicine approach, previously unavailable for sarcoma patients.

Citation Format: Juergen Loskutov, Manuela Regenbrecht, Saskia Scharf, Philipp Stroebel, Maya Niethard, Christoph Reinhard, Christian Regenbrecht. Patient-derived 3D sarcoma model - robust system for sarcoma research and personalized therapy selection [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2980.

Precision Oncology Beyond Genomics: The Future Is Here-It Is Just Not Evenly Distributed

Cancer is a multifactorial disease with increasing incidence. There are more than 100 different cancer types, defined by location, cell of origin, and genomic alterations that influence oncogenesis and therapeutic response. This heterogeneity between tumors of different patients and also the heterogeneity within the same patient's tumor pose an enormous challenge to cancer treatment. In this review, we explore tumor heterogeneity on the longitudinal and the latitudinal axis, reviewing current and future approaches to study this heterogeneity and their potential to support oncologists in tailoring a patient's treatment regimen. We highlight how the ideal of precision oncology is reaching far beyond the knowledge of genetic variants to inform clinical practice and discuss the technologies and strategies already available to improve our understanding and management of heterogeneity in cancer treatment. We will focus on integrating multi-omics technologies with suitable in vitro models and their proficiency in mimicking endogenous tumor heterogeneity.

Abstract 1699: IMMUcan: Broad cellular and molecular profiling of the human tumor microenvironment

The development of next generation therapeutics for cancer patients requires an improved understanding of the underlying mechanisms of resistance to existing therapies as well as novel biomarkers that can help identify patients most likely to benefit from the treatments. Most studies addressing these questions have predominantly relied on a limited set of tumor profiling techniques or have been hampered by relatively small patient numbers. In response to this need, the IMMUcan consortium has been formed. Co-led by the EORTC (Brussels, Belgium), SIB (Lausanne, Switzerland), Eli Lilly (Indianapolis, IN, USA) and Merck KGaA (Darmstadt, Germany), IMMUcan is an EU-funded, public-private partnership of expert immunologists, cell biologists, technology developers and clinical key opinion leaders. The mission of IMMUcan is to generate broad molecular and cellular profiling data of the tumor microenvironment from up to 3,000 patients derived from five indications: non-small cell lung cancer, head and neck squamous cell carcinoma, renal cell carcinoma, colorectal cancer and breast cancer. Most of these patients will be treated under standard of care and recruited via the EORTC-SPECTA infrastructure. All acquired tumor samples will undergo detailed and standardized analyses applying diverse profiling modalities including whole exome sequencing to determine the mutational landscape, total RNA sequencing for transcriptome analysis, multiplex immunofluorescence (IF) and imaging mass cytometry (IMC) facilitating the assessment of approx. 80 proteins at single cell resolution. To avoid inter-lab variations, each profiling method (sequencing, IF or IMC) will be performed by a single expert laboratory, which will process all IMMUcan samples. These data will be integrated with clinical information and centralized in a Knowledge Management System. Once published, the entire IMMUcan dataset will be made available to the scientific community for further study and interrogation. IMMUcan also acquires blood samples, including PBMCs, saliva as well as fresh-frozen stool samples. In addition, we have established workflows to generate reports documenting clinically actionable molecular alterations, which are returned to the treating physicians within 6-8 weeks. Thus far, 31 patients have been recruited and first tumor profiling data from these patients will be presented. Funding: IMI2 JU grant agreement 821558, supported by EU's Horizon 2020 and EFPIA.

Citation Format: Henoch S. Hong, Robin Liechti, Christoph Reinhard, Marie M. Morfouace, IMMUcan consortium. IMMUcan: Broad cellular and molecular profiling of the human tumor microenvironment [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1699.

Evaluation of molecular subtypes and clonal selection during establishment of patient-derived tumor xenografts from gastric adenocarcinoma

Patient-derived xenografts (PDX) have emerged as an important translational research tool for understanding tumor biology and enabling drug efficacy testing. They are established by transfer of patient tumor into immune compromised mice with the intent of using them as Avatars; operating under the assumption that they closely resemble patient tumors. In this study, we established 27 PDX from 100 resected gastric cancers and studied their fidelity in histological and molecular subtypes. We show that the established PDX preserved histology and molecular subtypes of parental tumors. However, in depth investigation of the entire cohort revealed that not all histological and molecular subtypes are established. Also, for the established PDX models, genetic changes are selected at early passages and rare subclones can emerge in PDX. This study highlights the importance of considering the molecular and evolutionary characteristics of PDX for a proper use of such models, particularly for Avatar trials.

Molecular dissection of CRC primary tumors and their matched liver metastases reveals critical role of immune microenvironment, EMT and angiogenesis in cancer metastasis

Metastasis is the primary cause of cancer mortality. The primary tumors of colorectal cancer (CRC) often metastasize to the liver. In this study, we have collected 122 samples from 45 CRC patients. Among them, 32 patients have primary tumors, adjacent normal tissues, and matched liver metastases. Thirteen patients have primary tumors without distant metastasis and matched normal tissues. Characterization of these samples was conducted by whole-exome and RNA sequencing and SNP6.0 analysis. Our results revealed no significant difference in genetic alterations including common oncogenic mutations, whole genome mutations and copy number variations between primary and metastatic tumors. We then assembled gene co-expression networks and identified metastasis-correlated gene networks of immune-suppression, epithelial–mesenchymal transition (EMT) and angiogenesis as the key events and potentially synergistic drivers associated with CRC metastasis. Further independent cohort validation using published datasets has verified that these specific gene networks are up regulated throughout the tumor progression. The gene networks of EMT, angiogenesis, immune-suppression and T cell exhaustion are closely correlated with the poor patient outcome and intrinsic anti-PD-1 resistance. These results offer insights of combinational strategy for the treatment of metastatic CRC.

Management of rare movement disorders in Europe: outcome of surveys of the European Reference Network for Rare Neurological Diseases

Background and purpose

The diagnosis of rare movement disorders is difficult and specific management programmes are not well defined. Thus, in order to capture and assess care needs, the European Reference Network for Rare Neurological Diseases has performed an explorative care need survey across all European Union (EU) countries.

Methods

This is a multicentre, cross‐sectional study. A survey about the management of different rare movement disorders (group 1, dystonia, paroxysmal dyskinesia and neurodegeneration with brain iron accumulation; group 2, ataxias and hereditary spastic paraparesis; group 3, atypical parkinsonism; group 4, choreas) was sent to an expert in each group of disorders from each EU country.

Results

Some EU countries claimed for an increase of teaching courses. Genetic testing was not readily available in a significant number of countries. Regarding management, patients’ accessibility to tertiary hospitals, to experts and to multidisciplinary teams was unequal between countries and groups of diseases. The availability of therapeutic options, such as botulinum toxin or more invasive treatments like deep brain stimulation, was limited in some countries.

Conclusions

The management of these conditions in EU countries is unequal. The survey provides evidence that a European care‐focused network that is able to address the unmet rare neurological disease care needs and inequalities is highly warranted.

Genomic characterization of intrinsic and acquired resistance to cetuximab in colorectal cancer patients

Anti-EGFR antibodies are effective in therapies for late-stage colorectal cancer (CRC); however, many tumours are unresponsive or develop resistance. We performed genomic analysis of intrinsic and acquired resistance to anti-EGFR therapy in prospectively collected tumour samples from 25 CRC patients receiving cetuximab (an EGFR inhibitor). Of 25 CRC patients, 13 displayed intrinsic resistance to cetuximab; 12 were intrinsically sensitive. We obtained six re-biopsy samples at acquired resistance from the intrinsically sensitive patients. NCOA4–RET and LMNA–NTRK1 fusions and NRG1 and GNAS amplifications were found in intrinsic-resistant patients. In cetuximab-sensitive patients, we found KRAS K117N and A146T mutations in addition to BRAF V600E, AKT1 E17K, PIK3CA E542K, and FGFR1 or ERBB2 amplifications. The comparison between baseline and acquired-resistant tumours revealed an extreme shift in variant allele frequency of somatic variants, suggesting that cetuximab exposure dramatically selected for rare resistant subclones that were initially undetectable. There was also an increase in epithelial-to-mesenchymal transition at acquired resistance, with a reduction in the immune infiltrate. Furthermore, characterization of an acquired-resistant, patient-derived cell line showed that PI3K/mTOR inhibition could rescue cetuximab resistance. Thus, we uncovered novel genomic alterations that elucidate the mechanisms of sensitivity and resistance to anti-EGFR therapy in metastatic CRC patients.

Aurora A-Selective Inhibitor LY3295668 Leads to Dominant Mitotic Arrest, Apoptosis in Cancer Cells, and Shows Potent Preclinical Antitumor Efficacy

Although Aurora A, B, and C kinases share high sequence similarity, especially within the kinase domain, they function distinctly in cell-cycle progression. Aurora A depletion primarily leads to mitotic spindle formation defects and consequently prometaphase arrest, whereas Aurora B/C inactivation primarily induces polyploidy from cytokinesis failure. Aurora B/C inactivation phenotypes are also epistatic to those of Aurora A, such that the concomitant inactivation of Aurora A and B, or all Aurora isoforms by nonisoform-selective Aurora inhibitors, demonstrates the Aurora B/C-dominant cytokinesis failure and polyploidy phenotypes. Several Aurora inhibitors are in clinical trials for T/B-cell lymphoma, multiple myeloma, leukemia, lung, and breast cancers. Here, we describe an Aurora A-selective inhibitor, LY3295668, which potently inhibits Aurora autophosphorylation and its kinase activity in vitro and in vivo, persistently arrests cancer cells in mitosis, and induces more profound apoptosis than Aurora B or Aurora A/B dual inhibitors without Aurora B inhibition-associated cytokinesis failure and aneuploidy. LY3295668 inhibits the growth of a broad panel of cancer cell lines, including small-cell lung and breast cancer cells. It demonstrates significant efficacy in small-cell lung cancer xenograft and patient-derived tumor preclinical models as a single agent and in combination with standard-of-care agents. LY3295668, as a highly Aurora A-selective inhibitor, may represent a preferred approach to the current pan-Aurora inhibitors as a cancer therapeutic agent.

Abstract 3513: The CHK1 kinase inhibitor prexasertib (LY2606368) shows potent single-agent efficacy in in vitro and in vivo models of castrate-resistant prostate cancer

Reported genomic alterations in the DNA repair pathway in studies of castrate-resistant prostate cancer (CRPC) patients have prompted interests in targeted therapies related to the DNA damage response (DDR). CHK1 kinase plays a critical role in mediating the DNA damage checkpoint response by contributing to orderly cell cycle progression, regulation of the mitotic spindle-assembly checkpoint response and is essential for homologous recombination repair. The CHK1 kinase (CHK1) inhibitor prexasertib (LY2606368) is currently in clinical development. In this study we investigated the efficacy of prexasertib as single agent in CRPC in vitro cell lines and in vivo tumors. Prexasertib inhibited cell proliferation of prostate cancer cell lines showing the more consistent and potent inhibition in androgen-receptor positive (AR) + models (n=5, IC50 value ranges from 4.3 to 13.1 nM) while AR- cell lines had IC50 values ranging from 6.4 nM to 1000 nM (n=8). A sub-set of cell lines including VCAP, LNCaP, 22RV1 and PC3 underwent additional in vitro studies including cell cycle regulation and programmed cell death induced by prexasertib. A 24-hour treatment with 50 nM prexasertib increased S-phase populations in all cell lines (VCAP, LNCaP, 22RV1 and PC3) and sub-G1 populations in VCAP and 22RV1 cells. Live-cell imaging showed 50 nM prexasertib triggered caspase 3/7 induction by 30, 19, 15 and 10 fold change in VCAP, 22RV1, LNCaP and PC3, respectively when compared with control. Western blot studies characterized the activation of the DDR pathway signaling giving rise to a time- and concentration-dependent DNA damage response leading to induction of pCHK1 (S345), γH2AX, pRPA32(S4/8) and PARP cleavage. Importantly, in all three AR+ cell lines, prexasertib yielded both time- and concentration-dependent inhibition of AR-full length and AR-variant7 expression. In addition, prexasertib demonstrated similar single-agent activity in prostate cancer patient-derived organoid (PDO) models by inhibiting proliferation and increasing apoptosis. Finally, in vivo n=1 studies of six patient-derived xenograft (PDX) models which represent heavily pretreated mCRPC patients yielded single-agent prexasertib efficacy in 4/6 models. Similarly, xenograft models including 22RV1, LNCaP and PC3 also yielded single-agent efficacy compared to vehicle groups. On-going efforts continue to deepen the understanding of the mechanisms underlying the action of prexasertib and potential markers for drug response by using RNA/gene arrays. In conclusion, prexasertib yielded potent single-agent activity in preclinical studies including cancer cell lines, PDO, xenograft and PDX models of castrate-resistant prostate cancer and these data provide rationale of the development of the prexasertib for the treatment of CRPC.

Citation Format: Ann McNulty, Greg Donoho, Jack Dempsey, Adem Abel, Jennifer Stephens, Ricardo Martinez, Damien Gerald, Carole Perruzzi, Marguerita O’Mahony, Christoph Reinhard, Aimee Lin, Wenjuan Wu. The CHK1 kinase inhibitor prexasertib (LY2606368) shows potent single-agent efficacy in in vitro and in vivo models of castrate-resistant prostate cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3513.

Abstract LB-083: Combination of an ERK1/2 inhibitor (LY3214996) with pan-RAF inhibitor enhances anti-tumor activity in KRAS mutant colorectal cancer (CRC) and non-small cell lung cancer (NSCLC)

Cancer patients with KRAS mutations have poor prognosis and represent an unmet medical need. Mutant KRAS driven MAPK activation is present in ~ 40% and ~ 30% of CRC and NSCLC patients, respectively. ERK1/2, a key downstream effector of KRAS mutations, is involved in the critical signaling network to drives cell proliferation, survival, metastasis and drug resistance. LY3214996, an ERK1/2 inhibitor which is in Phase I clinical trial (NCT02857270), has potent anti-tumor activities in KRAS mutant tumor cells in vitro and in vivo. However, some KRAS mutant cancer cells were less sensitive to LY3214996 single agent, suggesting that combination therapy is needed to maximize the benefit from ERK1/2 inhibition. The combined inhibition of RAS/RAF/MEK/ERK pathway components (such as the inhibition of both BRAF and MEK) has shown the promising anti-cancer activity in melanoma. Based on interaction between activated RAS with RAF which is responsible for cancer progression and resistance in KRAS mutant cancers, we hypothesized that inhibiting both ERK and RAF may augment efficacy of the single agents and delay the resistance. Therefore in this study we have investigated the combination effect of LY3214996 with a pan-RAF inhibitor LY3009120 in KRAS mutant CRC and NSCLC in vitro and in vivo. The combination of LY3214996 and LY3009120 showed synergistic or additive inhibition of cell proliferation in all KRAS mutant CRC (n=8) and NSCLC (n=8) cell lines tested. The LY3214996 and LY3009120 combination significantly decreased the phosphorylation levels of ERK, Rb, S6 and H3, and induced more complete cell death in NCI-H2122 (G-12C), A549 (G-12S), NCI-H441 (G-12V), HCT-116 (G-13D) and in LY3009120-resistant HCT-116 cells compared with either single agent. Subsequent combination efficacy was evaluated in the HCT-116 xenograft model. LY3214996 alone, LY3009120 alone and the combination of LY3214996 and LY3009120 resulted in 52%, 68% and 94% tumor growth inhibition, respectively; and the combination significantly augmented the efficacy (p <0.001). Furthermore the combination efficacy of LY3214996 with a different pan-RAF inhibitor (LSN3074753, a surrogate and an analogue of LY3009120) was also assessed in the H441 NSCLC orthotopic model, and the combination increased the inhibition of both primary tumor growth and spontaneous metastasis (including lymph node metastasis and chest wall metastasis) when compared with the respective single agent activity. Overall, the combined inhibition of ERK1/2 and RAF was tolerated and enhanced antitumor efficacy in KRAS mutant CRC and NSCLC preclinical models. These data support the feasibility of combining ERK inhibitor LY3214996 with a pan-RAF inhibitor as a promising strategy for the treatment of KRAS mutant CRC and NSCLC.

Citation Format: Wenjuan Wu, Shripad Bhagwat, Lisa Kindler, William McMillen, Sajan Joseph, Sean Buchanan, Christoph Reinhard, Ramon V. Tiu, Sheng-Bin Peng. Combination of an ERK1/2 inhibitor (LY3214996) with pan-RAF inhibitor enhances anti-tumor activity in KRAS mutant colorectal cancer (CRC) and non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-083.

Aurora A Kinase Inhibition Is Synthetic Lethal with Loss of the RB1 Tumor Suppressor Gene

Loss-of-function mutations in the retinoblastoma gene RB1 are common in several treatment-refractory cancers such as small-cell lung cancer and triple-negative breast cancer. To identify drugs synthetic lethal with RB1 mutation (RB1 ^mut), we tested 36 cell-cycle inhibitors using a cancer cell panel profiling approach optimized to discern cytotoxic from cytostatic effects. Inhibitors of the Aurora kinases AURKA and AURKB showed the strongest RB1 association in this assay. LY3295668, an AURKA inhibitor with over 1,000-fold selectivity versus AURKB, is distinguished by minimal toxicity to bone marrow cells at concentrations active against RB1 ^mut cancer cells and leads to durable regression of RB1 ^mut tumor xenografts at exposures that are well tolerated in rodents. Genetic suppression screens identified enforcers of the spindle-assembly checkpoint (SAC) as essential for LY3295668 cytotoxicity in RB1-deficient cancers and suggest a model in which a primed SAC creates a unique dependency on AURKA for mitotic exit and survival. SIGNIFICANCE: The identification of a synthetic lethal interaction between RB1 and AURKA inhibition, and the discovery of a drug that can be dosed continuously to achieve uninterrupted inhibition of AURKA kinase activity without myelosuppression, suggest a new approach for the treatment of RB1-deficient malignancies, including patients progressing on CDK4/6 inhibitors.See related commentary by Dick and Li, p. 169.This article is highlighted in the In This Issue feature, p. 151.

Influence of eukaryotic translation initiation factor 6 on non-small cell lung cancer development and progression

Non-small cell lung cancer (NSCLC) is the leading cause of cancer-related death worldwide. Dysregulation of protein synthesis plays a major role in carcinogenesis, a process regulated at multiple levels, including translation of mRNA into proteins. Ribosome assembly requires correct association of ribosome subunits, which is ensured by eukaryotic translation initiation factors (eIFs). eIFs have become targets in cancer therapy studies, and promising data on eIF6 in various cancer entities have been reported. Therefore, we hypothesised that eIF6 represents a crossroad for pulmonary carcinogenesis. High levels of eIF6 are associated with shorter patient overall survival in adenocarcinoma (ADC), but not in squamous cell carcinoma (SQC) of the lung. We demonstrate significantly higher protein expression of eIF6 in ADC and SQC than in healthy lung tissue based on immunohistochemical data from tissue microarrays (TMAs) and on fresh frozen lung tissue. Depletion of eIF6 in ADC and SQC lung cancer cell lines inhibited cell proliferation and induced apoptosis. Knockdown of eIF6 led to pre-rRNA processing and ribosomal 60S maturation defects. Our data indicate that eIF6 is upregulated in NSCLC, suggesting an important contribution of eIF6 to the development and progression of NSCLC and a potential for new treatment strategies against NSCLC.

Abstract 336: Anti-tumor activity of the Chk1 inhibitor prexasertib (LY2606368) as a single agent in triple negative breast cancer models

Triple-negative breast cancer (TNBC), the most aggressive subtype of breast cancer, is diagnosed in approximately 15% of all breast cancer patients and characterized by high level of genomic instability, defects in DNA damage response (DDR) and increased replication stress (RS). Currently the treatment options for TNBC are limited, and new approaches are needed. Checkpoint kinase 1 (Chk1) is a key kinase that regulates the cell cycle, DDR and RS through the modulation of cell cycle checkpoints and replication fork licensing; and has emerged as an attractive target for anti-cancer therapy. Prexasertib (LY2606368), an ATP-competitive inhibitor of Chk1 has demonstrated single agent activity in vitro and in vivo. Prexasertib is being evaluated in an ongoing TNBC Phase 2 trial sponsored by NCI; and preliminary results suggest modest single-agent activity in sporadic TNBC patients (https://academic.oup.com/annonc/article/27/suppl_6/231PD/2798970). To understand the biology and mechanisms underlying prexasertib's activity and/or identify the potential biomarkers that may predict response or identify novel combinations that could improve prexasertib's efficacy, we evaluated the anti-tumor activity of prexasertib as a single agent in TNBC cancer cell lines in vitro and in vivo, including xenograft, orthotopic and patient-derived xenograft (PDX) tumor models. Prexasertib inhibited cell proliferation in 12 TNBC cell lines with IC50 values ranging from 0.32 nM to 117.3 nM; and demonstrated inhibition of Chk1 auto-phosphorylation and activation of γH2AX, RPA32 and DNAPKc in TNBC cell lines including HCC1187, HCC1806, MX-1 and MDA-MB-231. Treatment with prexasertib inhibited tumor growth by 83.8%, 85.5% and 94.2% in HCC1187, MX-1 and HCC1806 xenograft models, respectively. Prexasertib also inhibited primary tumor growth by 74.4% and lung metastasis by 97.48% in a MDA-MB-231 mammary fat pad orthotopic model. The anti-tumor effect of prexasertib was further assessed in 40 TNBC PDX models. Prexasertib treatment resulted in 10% (4/40) of models achieving complete tumor regression, 40% (16/40) achieving partial tumor regression/stasis and 50% (20/40) not deriving benefit. Potential biomarkers of prexasertib were investigated. TNBC cells with higher phosphorylation levels of DNAPKc and RPA32 demonstrated higher sensitivity to prexasertib treatment. TNBC PDX tumors with higher RNA message levels of CyclinE1, Cyclin D1 and c-Myc showed better prexasertib response. Together these findings will inform subsets of TNBC and/or individual patient characteristics that should be considered for future clinical assessments and development of potential combination therapy strategies.

Citation Format: Wenjuan Wu, Constance King, Gregory Donoho, Philip Iversen, Andrew Capen, Mark Castanares, Jennifer Stephens, Yan Ding, Susan Pratt, Ricardo Martinez, Sean Buchanan, Christoph Reinhard, Richard Beckmann, Aimee Lin. Anti-tumor activity of the Chk1 inhibitor prexasertib (LY2606368) as a single agent in triple negative breast cancer models [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 336.

Abstract LB-185: Combination of an ERK1/2 inhibitor (LY3214996) with VEGFR-2 inhibitor enhances anti-tumor activity in KRAS mutant non-small cell lung cancer

Lung cancer is a leading cause of cancer death worldwide. ERK1/2, a key downstream effector of RAS mutations, is involved in the signaling network which drives cell proliferation, survival, metastasis and cancer resistance to drug treatment. KRAS mutation driven MAPK activation is present in ~ 30% of lung cancer patients. Non-small cell lung cancer (NSCLC) patients with KRAS mutation have poor prognosis and represents an unmet medical need. LY3214996, an ERK1/2 inhibitor which is in a phase I clinical trial, has anti-tumor activities in RAS mutant tumor cells in vitro and in vivo (http://cancerres.aacrjournals.org/content/77/13_Supplement/4973). Ramucirumab, a fully-human monoclonal antibody to human VEGFR-2 was approved as an anti-angiogenic treatment for several cancer indications including second-line NSCLC. Combination strategies in cancer including targeting both tumor cells and the surrounding stroma including endothelial cells have been shown to be effective in various tumor subtypes. In this study, the combination effect of LY3214996 with VEGFR-2 inhibitor DC101 (a monoclonal antibody specific for murine VEGFR-2 and a surrogate for ramucirumab) were evaluated in KRAS mutant NSCLC models, including NCI-H2122 (G-12C), A549 (G-12S) and NCI-H441 (G-12V). LY3214996 treatment alone resulted in 41%, 91% and 101% tumor growth inhibition in H2122, A549 and H441 xenograft tumors, respectively. DC101 treatment alone resulted in 64%, 75% and 102% tumor growth inhibition in H2122, A549 and H441, respectively. The combination of LY3214996 with DC101 led to better tumor growth inhibition 83%, 115% (i.e. 15% regression) and 146% (i.e. 46% regression) for H2122, A549 and H441, respectively when compared with single agent treatment. The molecular mechanism was further investigated in H2122 tumor xenograft tumors in terms of MAPK signaling, MAPK gene signatures, tumor vascularization, cell proliferation and apoptosis. LY3214996 together with DC101 led to greater reduction in tumor blood vessels density compared to DC101 alone. Similarly, the analysis of multiple cell cycle markers (including pRb, pH3 and Ki67) indicated that the combination treatment resulted in greater inhibited of cell proliferation compared to single agent. Moreover, the combination effect of LY3214996 with ramucirumab was also investigated via tumor cell driven cord formation assays in vitro; and the data indicated that the combination enhanced the inhibition of cord formation when compared to single agent. Overall, combined inhibition of ERK1/2 and VEGFR-2 enhanced both anti-angiogenesis and antitumor effects. Taken together, these data support further clinical development of the combination of an ERK1/2 inhibitor, LY3214996 with ramucirumab in the treatment of KRAS mutant NSCLC.

Citation Format: Wenjuan Wu, Shripad V. Bhagwat, Bonita D. Jones, Michelle L. Swearingen, Beverly L. Falcon, William T. McMillen, Sajan Joseph, Sean Buchanan, Sheng-Bin Peng, Christoph Reinhard, Ramon V. Tiu. Combination of an ERK1/2 inhibitor (LY3214996) with VEGFR-2 inhibitor enhances anti-tumor activity in KRAS mutant non-small cell lung 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 LB-185.

Genomic Aberrations that Activate D-type Cyclins Are Associated with Enhanced Sensitivity to the CDK4 and CDK6 Inhibitor Abemaciclib

Most cancers preserve functional retinoblastoma (Rb) and may, therefore, respond to inhibition of D-cyclin-dependent Rb kinases, CDK4 and CDK6. To date, CDK4/6 inhibitors have shown promising clinical activity in breast cancer and lymphomas, but it is not clear which additional Rb-positive cancers might benefit from these agents. No systematic survey to compare relative sensitivities across tumor types and define molecular determinants of response has been described. We report a subset of cancers highly sensitive to CDK4/6 inhibition and characterized by various genomic aberrations known to elevate D-cyclin levels and describe a recurrent CCND1 3'UTR mutation associated with increased expression in endometrial cancer. The results suggest multiple additional classes of cancer that may benefit from CDK4/6-inhibiting drugs such as abemaciclib.

The effect of long-term bisphosphonate therapy on trabecular bone strength and microcrack density

Objectives

Bisphosphonates (BP) are the first-line treatment for preventing fragility fractures. However, concern regarding their efficacy is growing because bisphosphonate is associated with over-suppression of remodelling and accumulation of microcracks. While dual-energy X-ray absorptiometry (DXA) scanning may show a gain in bone density, the impact of this class of drug on mechanical properties remains unclear. We therefore sought to quantify the mechanical strength of bone treated with BP (oral alendronate), and correlate data with the microarchitecture and density of microcracks in comparison with untreated controls.

Methods

Trabecular bone from hip fracture patients treated with BP (n = 10) was compared with naïve fractured (n = 14) and non-fractured controls (n = 6). Trabecular cores were synchrotron scanned and micro-CT scanned for microstructural analysis, including quantification of bone volume fraction, microarchitecture and microcracks. The specimens were then mechanically tested in compression.

Results

BP bone was 28% lower in strength than untreated hip fracture bone, and 48% lower in strength than non-fractured control bone (4.6 MPa vs 6.4 MPa vs 8.9 MPa). BP-treated bone had 24% more microcracks than naïve fractured bone and 51% more than non-fractured control (8.12/cm²vs 6.55/cm²vs 5.25/cm²). BP and naïve fracture bone exhibited similar trabecular microarchitecture, with significantly lower bone volume fraction and connectivity than non-fractured controls.

Conclusion

BP therapy had no detectable mechanical benefit in the specimens examined. Instead, its use was associated with substantially reduced bone strength. This low strength may be due to the greater accumulation of microcracks and a lack of any discernible improvement in bone volume or microarchitecture. This preliminary study suggests that the clinical impact of BP-induced microcrack accumulation may be significant.

Cite this article: A. Jin, J. Cobb, U. Hansen, R. Bhattacharya, C. Reinhard, N. Vo, R. Atwood, J. Li, A. Karunaratne, C. Wiles, R. Abel. The effect of long-term bisphosphonate therapy on trabecular bone strength and microcrack density. Bone Joint Res 2017;6:602–609. DOI: 10.1302/2046-3758.610.BJR-2016-0321.R1.

Abstract 849: Molecular characterization of primary tumor & the paired liver metastatic biopsies of colorectal cancer reveals a critical role of immunosuppression, EMT & angiogenesis in cancer metastasis

Colorectal cancer (CRC) is one of the leading causes of cancer-related mortality worldwide. In United States alone, it was estimated that nearly 137,000 people were diagnosed, and more than 50,000 were dead from the disease each year. CRC primary tumors often metastasize to liver which accounts for most of CRC death. The molecular mechanism of tumor metastasis is complicate and remains poorly understood. In this study, we have collected 79 human CRC samples, and 60 of them are paired primary tumor and liver metastatic surgically resected samples. Molecular characterization of these samples was conducted by exome and RNA sequencing, as well as SNP6.0 analysis. Genetic analysis revealed no significant difference in genetic alterations including common oncogenic mutations, whole genome mutations and copy number variations between primary and their matched liver metastatic tumors. To further characterize the molecular mechanism of metastatic progression, we have assembled gene correlation networks by utilizing a genome-wide interrogation of co-regulated networks based on RNA sequencing data of these CRC samples. Computational analysis of these correlation networks has identified gene signatures of immune-suppression, epithelial-mesenchymal transition (EMT) and angiogenesis as the key events and potentially synergistic drivers associated with CRC metastasis. Further independent cohort validation using published datasets verified that these specific gene networks of tumor microenvironment were progressively up-regulated throughout the carcinogenesis, and represented distinct biological processes. These gene networks were capable of discriminating the previously categorized CRC molecular subclasses. In addition, we also showed an association of type I interferon network with good clinical outcome of CRC, and gene networks of EMT, angiogenesis, immune-suppression and T cell exhaustion are closely associated with the poor patient outcome. We further demonstrated that the networks of EMT and angiogenesis were related to innate anti-PD-1 resistance, and the networks of immunosuppression and T cell exhaustion were associated with resistance to radiation and checkpoint blockade. Overall, we conclude that a genome-wide interrogation of co-regulated networks utilized in this study represents a valuable strategy to identify molecular mechanisms of cancer metastasis, and gene networks of immune-suppression, EMT and angiogenesis are among the key events associated with CRC metastasis.

Citation Format: Jiangang Liu, Yong Beom Cho, Hye kyung Hong, Song Wu, Philip J. Ebert, Steven M. Bray, Swee Seong Wong, Jason C. Ting, John N. Calley, Catherine F. Whittington, Shripad Bhagwat, Emma Bowden, Amit Aggarwal, Christoph Reinhard, Robert Wild, Do-Hyun Nam, Woo Yong Lee, Sheng-Bin Peng. Molecular characterization of primary tumor & the paired liver metastatic biopsies of colorectal cancer reveals a critical role of immunosuppression, EMT & angiogenesis in cancer metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 849. doi:10.1158/1538-7445.AM2017-849

Abstract 317: Combination of a novel ERK1/2 inhibitor (LY3214996) with CDK4 and CDK6 inhibitor (abemaciclib) enhances antitumor efficacy in KRAS mutant non-small cell lung cancer (NSCLC)

ERK1/2, a key downstream effector of RAS mutations, is involved in the signaling network which drives cell proliferation, survival, metastasis and cancer resistance to drug treatment (including MEK and BRAF inhibitors). Lung cancer is a leading cause of cancer death worldwide. KRAS mutation present in up to 30% of NSCLC patients is associated with a poor prognosis and represents an unmet medical need. In KRAS mutant NSCLC, enhanced ERK activation cooperates with dysregulation of the cell cycle checkpoint (e.g., cyclin D, CDK4 and CDK6 complex), and contributes to tumor progression; thus, the simultaneous inhibition of ERK and the CDK4/6 pathway is hypothesized to augment tumor growth inhibition. LY3214996, a novel and highly selective small molecule inhibitor of ERK1 and ERK2, is currently in phase I clinical trial and has been shown to inhibit cell proliferation in RAS or BRAF mutant tumor cells in vitro and xenograft tumor growth in vivo. Abemaciclib, a CDK4 and CDK6-selective inhibitor is currently in phase III studies for ER positive breast cancer and KRAS mutant NSCLC. In this study we explore the potential efficacy of combined inhibition of ERK1/2 and CDK4 and CDK6 in KRAS mutant NSCLC. The combination of LY3214996 and abemaciclib synergistically inhibited cell proliferation in 85% of KRAS mutant cells in an unbiased NSCLC panel. Combination treatment with LY3214996 and abemaciclib significantly decreased levels of phospho- p90RSK, phospho-Rb, phospho-S6 and Ki67; and synergistically inhibited cell proliferation and survival in KRAS mutant NSCLC cell lines including NCI-H2122 (G-12C), A549 (G-12S) and NCI-H441 (G-12V). Subsequent in vivo studies showed that the combination treatment with LY3214996 and abemaciclib was well tolerated and led to more robust tumor growth inhibition or regression in all KRAS mutant NSCLC xenograft models (H2122, A549 and H441) compared with either single agent treatment (p≤0.002). Furthermore, in xenograft tumors the combination of LY3214996 and abemaciclib resulted in more significant reduction of phospho-p90RSK, phospho-Rb, phospho-S6 and Ki67 in H2122 tumors compared with either single agent. Overall, the combined inhibition of ERK1/2 and CDK4 and CDK6 was tolerated and enhanced antitumor efficacy in several KRAS mutant NSCLC preclinical models. These data support the feasibility of combining ERK inhibitor LY3214996 with CDK4 and CDK6 inhibitor abemaciclib as a promising strategy for the treatment of KRAS mutant NSCLC patients, and provides the rationale for the combination study in the on-going phase I LY3214996 clinic trial (NCT02857270).

Citation Format: Wenjuan Wu, Shripad V. Bhagwat, Constance King, Susan Pratt, Xueqian Gong, Julie Stewart, Bonita Jones, Robert Flack, Richard Beckman, Beverly Falcon, Jason Manro, William T. McMillen, Ramon V. Tiu, Sheng-Bin Peng, Christoph Reinhard, Sajan Joseph, Sean Buchanan. Combination of a novel ERK1/2 inhibitor (LY3214996) with CDK4 and CDK6 inhibitor (abemaciclib) enhances antitumor efficacy in KRAS mutant non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 317. doi:10.1158/1538-7445.AM2017-317

Abstract 4104: Intrinsic and acquired resistance to cetuximab in colorectal cancer patients

Anti-EGFR antibodies, such as cetuximab, are effective therapies for many late-stage colorectal cancer (CRC) patients; unfortunately, many tumors are initially unresponsive while others show initial efficacy but eventually develop acquired resistance. Genomic studies of patient tumors, cell lines, and xenograft models have identified putative anti-EGFR resistance markers, including mutations in KRAS, NRAS, BRAF, PIK3CA, and the EGFR extracellular domain, as well as amplifications in ERBB2 and MET. In order to further confirm and identify new resistance mechanisms to anti-EGFR treatment in CRC, we performed retrospective genomic profiling of 25 CRC patients treated at Samsung Medical Center from 2006-2015. Patients received cetuximab containing chemo regimens with varying duration of responses, including acquired resistance cases. Our analysis identifies mutations in receptor tyrosine kinases, such as EGFR, NTRK1, and PDGFRA, as well as RAS/MAPK pathway genes that affect cetuximab response. We also uncover genomic alterations in ERBB2 and c-KIT as potential novel mechanisms regulating sensitivity to anti-EGFR antibodies. Additional genomic analyses of acquired resistance tumors and in vitro studies of a patient-derived cell line provide added insights into clonal selection and signaling pathways that bypass the EGFR blockade. Overall, our study elucidates important new facets in the landscape of anti-EGFR resistance mechanisms.

Note: This abstract was not presented at the meeting.

Citation Format: Steven M. Bray, Jeeyun Lee, Seung Tae Kim, Philip J. Ebert, John N. Calley, Isabella H. Wulur, Thejaswini Gopalappa, Swee Seong Wong, Hui-Rong Qian, Jason C. Ting, Jiangang Liu, Melinda D. Willard, Amit Aggarwal, Ruslan D. Novosiadly, Hee-Cheol Kim, Christoph Reinhard. Intrinsic and acquired resistance to cetuximab in colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4104. doi:10.1158/1538-7445.AM2017-4104

Abstract A07: The identification of combinations for the CDK4 and CDK6 inhibitor, abemaciclib

We developed a combination screening protocol to look for synergistic interactions with abemaciclib, an inhibitor of cyclin dependent kinases 4 and 6 (CDK4 and CDK6). Abemaciclib (LY2835219), has shown cytostatic effects in some cell lines while inducing senescence and apoptosis in particularly sensitive cell lines. Abemaciclib, combined with various compounds, was screened across panels of genomically characterized tumor cells. These screens identified several synergistic interactions that improved the activity of abemaciclib in cancer cells lines that respond to abemaciclib monotherapy (e.g. mantle cell lymphoma, ER+ breast cancer) but additionally revealed certain combinations with synergy in Rb wild-type cancers that do not respond optimally to single agent abemaciclib treatment. Most interestingly, MEK inhibitors and LY3009120, a novel Raf dimer inhibitor that inhibits all three Raf isoforms (Cancer Cell 28:384-98) were found to potentiate the cytostatic effects of abemaciclib in these cell lines leading to apoptosis in vitro and tumor regression in vivo. Further analysis of the effects of combined inhibition of CDK4 and CDK6 and Raf isoforms on downstream signaling pathways provides mechanistic clues that may help explain the observed synergy.

Citation Format: Gong Xueqian, Li-Chun Chio, Yue Webster, Maria Jose Lallena, Karsten Boehnke, Raquel Torres, Phil Iversen, Alfonso De Dios, Ian Smith, Christoph Reinhard, Sheng-Bin Peng, Jack Dempsey, Teresa Burke, Shih-Hsun Chen, Trent Stewart, Richard Beckmann, Wenjuan Wu, Sean G. Buchanan. The identification of combinations for the CDK4 and CDK6 inhibitor, abemaciclib. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Cancer Cell Cycle - Tumor Progression and Therapeutic Response; Feb 28-Mar 2, 2016; Orlando, FL. Philadelphia (PA): AACR; Mol Cancer Res 2016;14(11_Suppl):Abstract nr A07.

Abstract 2829: Preclinical analysis and characterization of abemaciclib using three-dimensional patient-derived colorectal cancer organoid cultures

Proper patient-tailoring strategy and the validation of novel therapeutic targets remain enormous challenges during drug discovery processes. Patient-derived three-dimensional organoid cell culture models possess great potential to associate compound sensitivity and disease complexity in order to provide a key missing link between compound screening and clinical trials. Abemaciclib is a reversible, ATP competitive, selective inhibitor of the kinase activity of both CDK4 and CDK6 and is currently undergoing advanced clinical testing.

In this study, we established and characterized three-dimensional organoid cultures from primary colorectal cancer patients and validated their use as drug sensitivity models. We aimed to explore the antitumor activity of abemaciclib in colon cancer organoid cultures by assessing markers for cell viability, proliferation, cell cycle, senescence and apoptosis. Single cell suspension of patient-derived samples were precultured for four days to allow for complete morphogenesis of three-dimensional organoid structures. Subsequently, the cultures were treated for at least two population doubling times and analyzed by luminescent cell viability, immunohistochemistry and flow cytometry assays.

Our data suggest that abemaciclib treatment decreased the cell viability of patient-derived colorectal cancer organoid cultures characterized by G1 cell cycle arrest and reduced Ki-67-positive cells. Furthermore, treated cultures showed elevated levels of reactive oxygen species and increased markers for early and late apoptosis. In summary, complex organoid models have the potential to further evaluate the antitumor activity of abemaciclib in various tumor types by enabling mechanistic studies in a patient-specific preclinical setting.

Citation Format: Karsten Boehnke, Bruna Calsina, Joaquín Amat, Ana Hermoso, Raquel Torres, Christoph Reinhard, Juan A. Velasco, Philip W. Iversen, Alfonso De Dios, Sean Buchanan, Richard P. Beckmann, Dirk Schumacher, Christian RA Regenbrecht, Marie-Laure Yaspo, Hans Lehrach, María José Lallena. Preclinical analysis and characterization of abemaciclib using three-dimensional patient-derived colorectal cancer organoid cultures. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2829.

Assay Establishment and Validation of a High-Throughput Screening Platform for Three-Dimensional Patient-Derived Colon Cancer Organoid Cultures

The application of patient-derived three-dimensional culture systems as disease-specific drug sensitivity models has enormous potential to connect compound screening and clinical trials. However, the implementation of complex cell-based assay systems in drug discovery requires reliable and robust screening platforms. Here we describe the establishment of an automated platform in 384-well format for three-dimensional organoid cultures derived from colon cancer patients. Single cells were embedded in an extracellular matrix by an automated workflow and subsequently self-organized into organoid structures within 4 days of culture before being exposed to compound treatment. We performed validation of assay robustness and reproducibility via plate uniformity and replicate-experiment studies. After assay optimization, the patient-derived organoid platform passed all relevant validation criteria. In addition, we introduced a streamlined plate uniformity study to evaluate patient-derived colon cancer samples from different donors. Our results demonstrate the feasibility of using patient-derived tumor samples for high-throughput assays and their integration as disease-specific models in drug discovery.

Genomic alterations and molecular subtypes of gastric cancers in Asians

Gastric cancer (GC) is a highly heterogenic disease, and it is the second leading cause of cancer death in the world. Common chemotherapies are not very effective for GC, which often presents as an advanced or metastatic disease at diagnosis. Treatment options are limited, and the prognosis for advanced GCs is poor. The landscape of genomic alterations in GCs has recently been characterized by several international cancer genome programs, including studies that focused exclusively on GCs in Asians. These studies identified major recurrent driver mutations and provided new insights into the mutational heterogeneity and genetic profiles of GCs. An analysis of gene expression data by the Asian Cancer Research Group (ACRG) further uncovered four distinct molecular subtypes with well-defined clinical features and their intersections with actionable genetic alterations to which targeted therapeutic agents are either already available or under clinical development. In this article, we review the ACRG GC project. We also discuss the implications of the genetic and molecular findings from various GC genomic studies with respect to developing more precise diagnoses and treatment approaches for GCs.

Abstract 29: Concordance of somatic mutations found in primary tumors and plasma circulating-free DNA from early and late-stage colorectal cancer patients

Circulating-free DNA (cfDNA) holds great potential for non-invasive somatic mutation detection in cancer patients as a so-called “liquid biopsy”. A liquid biopsy is especially valuable when tumor tissue is not available and for longitudinal monitoring of tumor burden or emerging resistance. In such cases, tumor-specific mutations are not known a priori and in order to detect tumor-derived somatic mutations it is best to interrogate a broad panel of cancer genes. The primary obstacle to sequencing cfDNA with broad mutation panels is achieving the necessary limit of detection to identify small amounts of tumor-derived cfDNA relative to the predominant wild-type cfDNA in the plasma of cancer patients. Tumor-derived cfDNA levels correlate with tumor stage, also making it an important consideration when investigating the sensitivity of this approach. We demonstrate the detection of somatic variants in several cancer genes in the plasma of early and late-stage colorectal cancer (CRC) patients by deep sequencing (> 8,000X) the cfDNA and matched normal DNA of N=33 CRC patients using the AmpliSeq cancer panel. The AmpliSeq panel requires less than 10ng of input DNA and amplifies hotspot loci of 50 known cancer genes for next-generation sequencing (NGS). We observe at least one somatic mutation with greater than 0.1% variant allele frequency in the cfDNA of all 33 CRC patients. We also show the sensitivity of detecting tumor-derived somatic mutations in cfDNA by exome sequencing of the primary tumor tissue. We find higher sensitivity for tumor mutations in cfDNA of late-stage patients compared to early-stage patients. Overall, we demonstrate the feasibility of using NGS on a small sized cancer panel for identifying somatic mutations, including those with low variant allele frequency, in cfDNA of early and late-stage CRC patients. Although a cfDNA approach holds promise as a tool to aid in pre-clinical and clinical research, more work is needed to understand its performance under different assay and disease conditions.

Citation Format: Steven M. Bray, Philip J. Ebert, John N. Calley, Richard E. Higgs, Isabella H. Wulur, Swee Seong Wong, Candice L. Horn, Ricardo Martinez, Christoph Reinhard. Concordance of somatic mutations found in primary tumors and plasma circulating-free DNA from early and late-stage colorectal cancer patients. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Integrating Clinical Genomics and Cancer Therapy; Jun 13-16, 2015; Salt Lake City, UT. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(1_Suppl):Abstract nr 29.

Abstract A24: Beta-klotho expression is associated with the antitumor activity of pan-FGFR inhibitor in human malignancies with FGF19 amplification

Fibroblast growth factor receptor 4 (FGFR4) is an attractive target in Oncology. A gene encoding fibroblast growth factor 19 (FGF19), the main ligand of FGFR4, is frequently amplified (A) and/or overexpressed (OE) in human malignancies according to The Cancer Genome Atlas (TCGA) (breast cancer 12.8% A, 0.6% OE; head and neck cancer 20.5% A, 7.1% OE; squamous cell carcinoma of the lung 11.6% A, 11.8% OE; hepatocellular carcinoma (HCC) 4.2% A, 21.1% OE; colorectal carcinoma 0% A, 15.4% OE; pancreatic carcinoma 0% A, 32.1% OE; endometrial carcinoma 0.8% A, 17.7% OE; bladder carcinoma 8.5% A, 1.9% OE). The objective of this study was to identify the hallmarks of FGFR4 pathway dependence in human tumors. LY2874455, a selective SMI with a potent activity against FGFR1, 2, 3 and 4, was tested in vitro using Cancer Cell Line Sensitivity Panel that included 539 histologically and genetically diverse tumor cell lines representing human malignancies. Cell lines that were most sensitive to LY2874455 were enriched for genetic FGFR pathway aberrations including FGF19 amplification. We therefore hypothesized that FGF19 amplification and/or overexpression might be molecular predictors of antitumor efficacy of LY2874455. We further tested LY2874455 in a panel of 14 HCC, 4 colorectal, 4 esophageal, 2 breast, 2 pancreatic and 1 head and neck carcinoma cell lines with FGF19 amplification and/or expression using a cell viability assay. Among all cell lines tested, LY2874455 activity was restricted to HCC cell lines with concurrent FGF19 amplification and expression (IC50 = 0.001-72 nM). It is known that endocrine effects of FGF19 require beta-klotho (KLB), a co-receptor whose expression is restricted to very few cell types including hepatocytes. We thus speculated that KLB expression could underlie FGFR4 pathway dependence in a subset of HCC with FGF19 amplification and/or overexpression. To corroborate this hypothesis, we employed doxycycline-inducible shRNA-mediated KLB knockdown in FGF19-amplified HCC cell lines, and demonstrated that ablated KLB expression decreased sensitivity to LY2874455 in JHH-7 (IC50 shift from 3.9 to 198 nM) and Hep3B (IC50 shift from 0.6 to 18 nM). Furthermore, in Hep3B cells, KLB knockdown was associated with a disrupted downstream signaling as exemplified by abrogated early growth response 1 (EGR1) and FBJ murine osteosarcoma viral oncogene homolog (FOS) expression upon FGF19 stimulation. These results suggest that FGF19 amplification or overexpression per se do not confer tumor cell sensitivity to FGFR blockade. Instead, FGFR4 inhibition seems to be most efficacious in FGF19-amplified tumor cells with concomitant FGF19, FGFR4 and KLB expression. This study established a mechanistic link between KLB expression and FGFR SMI efficacy in the setting of FGF19 amplification and/or overexpression and revealed a molecular profile of HCC patients that may benefit from FGFR inhibitors.

Citation Format: Amelie Forest, Sandra Nakasone, Ying Wang, Xuemei Guo, Timothy R. Mack, Genshi Zhao, Yong G. Yue, Xueqian Gong, Trent Stewart, Sean Buchanan, Christoph Reinhard, Ruslan Novosiadly. Beta-klotho expression is associated with the antitumor activity of pan-FGFR inhibitor in human malignancies with FGF19 amplification. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr A24.

Molecular analysis of gastric cancer identifies subtypes associated with distinct clinical outcomes

Gastric cancer, a leading cause of cancer-related deaths, is a heterogeneous disease. We aim to establish clinically relevant molecular subtypes that would encompass this heterogeneity and provide useful clinical information. We use gene expression data to describe four molecular subtypes linked to distinct patterns of molecular alterations, disease progression and prognosis. The mesenchymal-like type includes diffuse-subtype tumors with the worst prognosis, the tendency to occur at an earlier age and the highest recurrence frequency (63%) of the four subtypes. Microsatellite-unstable tumors are hyper-mutated intestinal-subtype tumors occurring in the antrum; these have the best overall prognosis and the lowest frequency of recurrence (22%) of the four subtypes. The tumor protein 53 (TP53)-active and TP53-inactive types include patients with intermediate prognosis and recurrence rates (with respect to the other two subtypes), with the TP53-active group showing better prognosis. We describe key molecular alterations in each of the four subtypes using targeted sequencing and genome-wide copy number microarrays. We validate these subtypes in independent cohorts in order to provide a consistent and unified framework for further clinical and preclinical translational research.

Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing

Gastric cancer (GC) is the second most common cause of cancer-related deaths. It is known to be a heterogeneous disease with several molecular and histological subtypes. Here we perform whole-genome sequencing of 49 GCs with diffuse (N=31) and intestinal (N=18) histological subtypes and identify three mutational signatures, impacting TpT, CpG and TpCp[A/T] nucleotides. The diffuse-type GCs show significantly lower clonality and smaller numbers of somatic and structural variants compared with intestinal subtype. We further divide the diffuse subtype into one with infrequent genetic changes/low clonality and another with relatively higher clonality and mutations impacting TpT dinucleotide. Notably, we discover frequent and exclusive mutations in Ephrins and SLIT/ROBO signalling pathway genes. Overall, this study delivers new insights into the mutational heterogeneity underlying distinct histologic subtypes of GC that could have important implications for future research in the diagnosis and treatment of GC.

Abstract LB-313: Integrative genomic profiling of Asian gastric cancers identifies four subgroups with distinct pathobiology and prognosis

Gastric cancer is the 2nd most common cause of cancer related mortality and 4th most common cancer worldwide. The molecular classification of Gastric Cancers and the relevance of pre-clinical models are not well established, creating challenges in discovering novel molecularly targeted therapies. In order to address that, we conducted integrated molecular data analysis of 300 Asian Gastric tumors through the Asian Cancer Research Group (ACRG). We identified four cancer subtypes, based on RNA/DNA profiling, Lauren's histological classification (Intestinal and Diffused) and Epstein Barr Virus (EBV) status, exhibiting differential pathobiology as well as prognosis. The groups are 1) Mesenchymal subgroup characterized by Diffused tumors with hallmarks of Epithelial to Mesenchymal transition such as CDH1 loss and co-occurring with IGF2 over-expression; 2) Microsatellite instable (MSI) subgroup characterized by predominantly hypermutated Intestinal tumors (including majority of mutations in KRAS) with likely MLH1 loss through promoter methylation; 3) TP53 pathway active subgroup with Epstein-Barr virus (EBV) infection or mutated oncogenes (e.g. PIK3CA) and 4) TP53 pathway inactive characterized by p53 loss through deleterious mutations in TP53 or MDM2 amplification and further characterized by both focal amplifications in oncogenes such as HER2, EGFR, cMET, CCNE1 as well as large scale chromosomal gains and losses. The above subtypes exhibited differential prognosis with the Mesenchymal subtype displaying the worst prognosis and the MSI subtype the best prognosis among the subtypes. The subtypes and their association with prognosis were independently validated in an additional large Gastric cancer cohort (N=277).

We studied the applicability of this classification in other gastrointestinal (GI) cancers and show the presence of our proposed molecular subtypes of Gastric cancer in Colorectal cancers as well thereby suggesting commonalities in biological processes that give rise to Gastric and Colorectal tumors and providing a common ground to classify GI cancers.

We also checked the presence of Gastric cancer subtypes in pre-clinical models of GI tract cancers and found that cell line panels often used for drug discovery shown an under-representation of p53 pathway active subtype, thus possibly creating challenges in translation to clinical studies.

Overall, we provide a stratification that will lay a more solid groundwork for rationally targeting Gastric Cancer by helping focus on specific altered mechanisms and/or oncogenes as well as allowing for a more rational choice of pre-clinical models in drug discovery and development.

Citation Format: Razvan Cristescu, Jeeyun Lee, Michael Nebozhyn, Amit Aggarwal, Jason Ting, Swee Seong Wong, Yong Yue, Christoph Reinhard, Kyoung Kim, Ingu Do, Hongyue Dai, Andrey Loboda. Integrative genomic profiling of Asian gastric cancers identifies four subgroups with distinct pathobiology and prognosis. [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-313. doi:10.1158/1538-7445.AM2014-LB-313

Abstract 2978: Generation of drug response data from 57 new patient-derived colon cancer xenografts and 3D cell cultures for systematic correlation with tumor biology within the OncoTrack* project

*OncoTrack is a project funded by the Innovative Medicines Initiative Joint Undertaking (IMI JU).

New therapies for colon cancer barely improved cure rates over the last decade and typically only a subset of patients benefits from them. The reasons for these disappointing outcomes are likely related to the inherent genetic and cellular heterogeneity and plasticity of tumors. Therefore only comprehensive approaches that correlate data from systematic molecular tumor tissue characterization with preclinical and clinical responses could improve our understanding of this disease and help to design diagnostic procedures allowing optimal therapy for individual patients.

OncoTrack is an international consortium funded by the Innovative Medicines Initiative (www.OncoTrack.eu) that has launched one of Europe's largest collaborative public-private research projects to implement novel approaches of systems biology into colon cancer therapy.

Tumor tissue and circulating tumor cells from a cohort of more than 120 patients with primary or metastatic colon cancer were subjected to high-throughput protein, epigenome, and gene expression analysis as well as next generation sequencing. Three- dimensional (3D) in vitro cultures and in vivo patient-derived xenografts (PDX) in immunodeficient mice were generated from each tissue sample and used to determine response to more than 14 approved drugs, investigational drug candidates, and tool compounds. These wet-lab data, combined with clinical data were used for in silico modeling to identify new predictors for tailored therapies.

Here we are presenting data from the subproject tumor models and therapy response. Tumor tissues from 118 colon cancer patients (87 primary tumors and 31 metastases) were transplanted into mice. To date, 44 permanent new PDX models have been generated from the primary tumors and 13 from the metastases; (establishment of 25 additional models is ongoing). These models are being used to determine sensitivity of the tumors to a broad range of drugs, targeting signaling pathways frequently activated in cancer. In parallel, in vitro cultures using a Matrigel-based, serum-free 3D system were established and adapted for high-throughput 384-well assay format for testing against a similar drug panel.

Drug response data generated from more than 30 patient specimens using both the specific 3D in vitro assays and the in vivo PDX experiments are available and will be shown and compared.

These experimental results about drug sensitivity together with the molecular signatures of the tumor tissues provide an exceptionally broad basis to analyze the relationship between tumor biology and treatment response. Such approaches may hold promise in the design of rational therapy for colon cancer in the future.

Citation Format: Maria Rivera, Marlen Keil, Karsten Boehnke, Martin Lange, Dirk Schumacher, Reinhold Schäfer, Christian RA Regenbrecht, David Henderson, Ulrich Keilholz, Alexander Kuehn, Amin El-Heliebi, Tabea Hohensee, Johannes Haybäck, Christoph Reinhard, Juan A. Velasco, Hans Lehrach, Pilar Garin-Chesa, Garry Beran, Jens Hoffmann. Generation of drug response data from 57 new patient-derived colon cancer xenografts and 3D cell cultures for systematic correlation with tumor biology within the OncoTrack* project. [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 2978. doi:10.1158/1538-7445.AM2014-2978

Abstract LB-314: Whole exome sequencing analyses of gastric cancers reveal two distinct genomic alteration patterns with implications in drug sensitivity

Gastric cancer is the fourth most common cancer diagnosed and the second most frequent cause of cancer-related death worldwide. Multiple factors can contribute to the development of gastric cancer, including H. pylori infection, dietary behaviour and life style, possibly resulting in distinct cancer subtypes with different drug sensitivity profiles. In the present study we searched for gastric cancer mutation patterns in the dataset of the “The Cancer Genome Atlas” (TCGA) and in our collection of patient derived xenografts (PDX). In a second part, we evaluated gene alteration patterns for their implications for drug sensitivity.

In both TCGA and our PDX datasets, Whole Exome Sequencing analyses revealed two subsets of gastric tumors characterized by specific mutation signatures, with different types and numbers of genomic alterations. The first subset (60% and 75% of samples) contained lower levels of mutations and was characterized by increased numbers of large chromosomal rearrangements resulting in gene loss or amplifications. The second subset of tumors (25%-40% of samples) revealed higher levels of mutations that were predominantly nucleic acid substitutions and small indels linked to mismatch repair genes including MLH1 or MSH3 and to high microsatellite instability. In both subsets, the mutation spectrum was dominated by C>T transitions with an increase of small indels in the subset of highly-mutated tumors.

At the gene level, the genes which were mutated in our gastric PDX collection overlapped to great extent with the mutations found in TCGA tumors, especially regarding the most frequently mutated genes. In the first subset, high levels of gene amplifications and deletions were found, including growth factor receptor amplifications in EGFR and HER2. Furthermore, the mutation frequency in genes associated with drug resistance such as KRAS was decreased. The tumors with growth factor receptor amplification responded consistently to therapies such as Cetuximab or Trastuzumab. In contrast, an increased frequency of mutations in oncogenes and tumor suppressors, including KRAS (n=5/10), PIK3CA (n=5/10) and PTEN (n=7/10), was found in the second subset. The mutational profile of these tumors suggest the use of compounds targeting downstream molecules, such as PIK3CA, or targeting effectors of DNA repair, such as PARP, for anti-cancer therapy. Of note, no association was found between the mutation groups and sensitivity to chemotherapeutic agents such as 5FU, Cisplatin or Paclitaxel.

In conclusion, we identified two subsets of gastric tumors both in the TCGA dataset and in our collection of PDX models, characterized by distinct genomic alteration profiles suggesting different therapeutic approaches. Currently, we are assessing drug sensitivity profiles within the two subsets in our PDX models.

Citation Format: Anne-Lise Peille, Swee-Seong Wong, Florian Kiefer, Bruno Zeitouni, Armin Maier, Frederic Foucault, Tim Kees, Vincent Vuaroqueaux, Amit Aggarwal, Christoph Reinhard, Heinz Herbert Fiebig. Whole exome sequencing analyses of gastric cancers reveal two distinct genomic alteration patterns with implications in drug sensitivity. [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-314. doi:10.1158/1538-7445.AM2014-LB-314

Abstract 3875: Functional and molecular characterization of colon cancer stem cells in tumor heterogeneity and disease relapse using a 3D-model of patient-derived tumors

Colon cancer is a heterogeneous disease. Growing evidence supports a subpopulation of cancer stem cells (CSCs) as both the drivers of tumour growth and the source of relapse following treatment. Elucidation of the cellular heterogeneity within a tumour would therefore facilitate better characterization of patient subtypes and lead to more personalized and effective treatments. Here we report the use of a Matrigel-based 3D in vitro model for the study of tumour heterogeneity and therapeutic resistance in patient derived colon tumours. To date, this system has enabled the establishment and long term culture of more than 53 patient-specific primary and metastasis derived colon tumours.

Tumour heterogeneity and the prospective isolation of CSCs within each patient-derived culture model is determined by separating cells using fluorescence assisted cell sorting (FACS) based on expression of previously defined markers of colon CSCs (e.g. ALDH+, CD133+, CD44+, CD166+, EpCAMHigh). To date, these analyses have been performed on ten of the patient derived tumour models and demonstrate both inter- and intra- tumour heterogeneity as each tumour contains varying subpopulations of cells either positive or negative for expression of CSC markers. In addition, immunofluorescence staining and 3D confocal analysis of genes important in the regulation of both normal and CSCs (e.g. Notch, Wnt and Hedgehog signalling genes) has also revealed heterogeneity of expression.

Functional characterization using in vitro and in vivo assays to determine the tumorigenic and differentiation capacity of the separated subpopulations are currently underway. Validated CSC subpopulations will be subjected to genome-wide analyses using next-generation sequencing for detailed characterization at the level of the transcriptome and methylome.

To study the effect of drug treatment on CSCs we have determined the IC50 values for standard of care drugs (e.g. 5-fluorouracil, oxaliplatin, irinotecan, receptor tyrosine kinase inhibitors) for each patient derived colon tumour. Tumour cells were treated for 72 - 96 hrs after which time treatment was terminated and the cells were allowed to recover. Surviving cells were then analyzed by FACS to determine the effect of treatment on the frequency of CSCs. Molecular characterization of the therapy resistant CSCs was then used to identify possible biomarkers and targets for more effective treatments.

These studies will provide insight into the relationship between variable tumour composition and the variable response of tumours to treatment. Ultimately, these studies will facilitate the more accurate classification and personalized treatment of colon tumours. OncoTrack is a project funded by the Innovative Medicines Initiative Joint Undertaking (IMI JU).

Citation Format: Joseph L. Regan, Dirk Schumacher, Karsten Boehnke, Cathrin Davies, Ulrich Keilholz, Johannes Haybaeck, Christoph Reinhard, Hans Lehrach, David Henderson, Reinhold Schaefer, Christian Regenbrecht, Martin Lange. Functional and molecular characterization of colon cancer stem cells in tumor heterogeneity and disease relapse using a 3D-model of patient-derived tumors. [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 3875. doi:10.1158/1538-7445.AM2014-3875

Whole-genome sequencing of asian lung cancers: second-hand smoke unlikely to be responsible for higher incidence of lung cancer among Asian never-smokers

Asian nonsmoking populations have a higher incidence of lung cancer compared with their European counterparts. There is a long-standing hypothesis that the increase of lung cancer in Asian never-smokers is due to environmental factors such as second-hand smoke. We analyzed whole-genome sequencing of 30 Asian lung cancers. Unsupervised clustering of mutational signatures separated the patients into two categories of either all the never-smokers or all the smokers or ex-smokers. In addition, nearly one third of the ex-smokers and smokers classified with the never-smoker-like cluster. The somatic variant profiles of Asian lung cancers were similar to that of European origin with G.C>T.A being predominant in smokers. We found EGFR and TP53 to be the most frequently mutated genes with mutations in 50% and 27% of individuals, respectively. Among the 16 never-smokers, 69% had an EGFR mutation compared with 29% of 14 smokers/ex-smokers. Asian never-smokers had lung cancer signatures distinct from the smoker signature and their mutation profiles were similar to European never-smokers. The profiles of Asian and European smokers are also similar. Taken together, these results suggested that the same mutational mechanisms underlie the etiology for both ethnic groups. Thus, the high incidence of lung cancer in Asian never-smokers seems unlikely to be due to second-hand smoke or other carcinogens that cause oxidative DNA damage, implying that routine EGFR testing is warranted in the Asian population regardless of smoking status.

Abstract A104: A screening method for the identification of potentially effective drug-drug combinations reveals a synergistic interaction between Aurora-A inhibitor MK-5108 and Bcl-xL inhibitor navitoclax

Recent developments in understanding the molecular mechanisms of cancer, coupled with large genomic datasets that detail the heterogeneity of the disease, have together led to a wealth of new cancer targets and therapeutic options. However, the restricted efficacy of these new agents and the emergence of resistance suggest that broader and more durable responses may be achieved through combination of these new drugs. To identify drug-drug combinations that may be effective in particular tumor types, we have developed an unbiased "synthetic lethal" screening approach to survey combination space across a diverse panel of tumor cell lines. We used this approach to test a panel of targeted drugs in all-versus-all fashion across 63 cell lines. Synergistic interactions were observed with the combination of an Aurora-A inhibitor, MK-5108, with navitoclax, an inhibitor of Bcl-2 family survival proteins. This combination, which was synergistic in a subset of the tumor cells, was further examined to identify the molecular determinants of synergy. Several features emerged from this analysis including the observation that Bcl-xL expression levels predict resistance to the single agent Aurora-A inhibitor and to synergy of combined MK-5108 and navitoclax.

Citation Information: Mol Cancer Ther 2013;12(11 Suppl):A104.

Citation Format: Xueqian Gong, Shaoling Jin, Farhana Merzoug, Xiang S. Ye, MaryJo Lallena, Jian Du, Yue Webster, Xiwen Ma, Christoph Reinhard, Phillip Iversen, Sean G. Buchanan. A screening method for the identification of potentially effective drug-drug combinations reveals a synergistic interaction between Aurora-A inhibitor MK-5108 and Bcl-xL inhibitor navitoclax. [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 A104.

Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole-genome sequencing (WGS) study of 88 matched HCC tumor/normal pairs, 81 of which are Hepatitis B virus (HBV) positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find beta-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumor suppressor (35.2%). The Wnt/beta-catenin and JAK/STAT pathways, altered in 62.5% and 45.5% of cases, respectively, are likely to act as two major oncogenic drivers in HCC. This study also identifies several prevalent and potentially actionable mutations, including activating mutations of Janus kinase 1 (JAK1), in 9.1% of patients and provides a path toward therapeutic intervention of the disease.

Abstract LB-229: Whole genome sequencing reveals genetic landscape of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the most deadly cancers worldwide and has no effective treatment, yet the molecular basis of hepatocarcinogenesis remains largely unknown. Here we report findings from a whole genome sequencing (WGS) study of 88 matched HCC tumour/normal pairs, 81 of which are HBV positive, seeking to identify genetically altered genes and pathways implicated in HBV-associated HCC. We find β-catenin to be the most frequently mutated oncogene (15.9%) and TP53 the most frequently mutated tumour suppressor (35.2%). The Wnt/β-catenin pathway, altered in 62.5% of cases, is likely to act as the major oncogenic driver in HCC. TP53 alterations appear to cause increased levels of genomic arrangement and chromosomal instability. We identified chromothripsis in 5 HCC genomes (5.7%) recurrently affecting chromosomal arms 1q and 8q. We also identified recurrent HBV integration events at the known and putative cancer-related genes such as TERT, MLL4 and CCNE1, which showed upregulated gene expression in tumour versus normal tissue. The frequently altered genes and pathways in HCC reflect classical cancer hallmarks. This study identified several prevalent and actionable mutations that provide a path towards therapeutic intervention of the disease.

Citation Format: Mao Mao, Hancheng Zheng, Zhengyan Kan, Jiangchun Xu, Xiao Liu, Shuyu Li, Thomas Barber, Zhuolin Gong, Huan Gao, Ke Hao, Melinda Willard, Robert Hauptschein, Paul Rejto, Julio Fernandez, Guan Wang, Qinghui Zhang, Bo Wang, Ronghua Chen, Jian Wang, Nikki Lee, Wei Zhou, Zhao Lin, Zhiyu Peng, Kang Yi, Shengpei Chen, Lin Li, Xiaomei Fan, Jie Yang, Rui Ye, Jia Ju, Kai Wang, Heather Estrella, Shibing Deng, Ping Wei, Ming Qiu, Isabella Wulur, Jiangang Liu, Mariam Ehsani, Chunsheng Zhang, Andrey Loboda, Wing Kin Sung, Amit Aggarwal, Ronnie Poon, Sheung Tat Fan, Jun Wang, James Hardwick, Christoph Reinhard, Hongyue Dai, Yingrui Li, John Luk. Whole genome sequencing reveals genetic landscape of hepatocellular carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-229. doi:10.1158/1538-7445.AM2013-LB-229

Abstract 2339: Prevalence of MET expression, activating mutations of KRAS and IDH1/2, and ROS1 fusions in cholangiocarcinoma patient tumor samples

Cholangiocarcinoma (CCA) originates from biliary tract epithelium and can be classified anatomically into intrahepatic or extrahepatic CCA. Although a relatively rare disease in the United States and Europe, the incidence of intrahepatic CCA is on the rise with unknown causes. CCA incidence is higher in Asia and the etiology is associated with infections such as liver fluke and hepatitis B/C. Prognosis at diagnosis is poor with median survival time of < 1 year, and only 10-20% of patients are eligible for tumor resection at diagnosis. This study examined the prevalence of MET over-expression, activating single point mutations of KRAS and IDH1/2, and ROS1 gene fusions in ∼100 intrahepatic and extrahepatic CCA FFPE tumor tissues obtained from non-Asian (n=40) and Asian (n=60) patients. Immunohistochemistry performed with an anti-MET-specific antibody (A2) demonstrated that MET is expressed in the majority of all intrahepatic CCA samples analyzed, with ∼50% of samples reported with membranocytoplasmic scores of 2+ (moderate intensity) or 3+ (strong intensity) on a 0-3+ scale. Interestingly, most non-malignant bile ducts and much vascular endothelia also stained lightly positive for MET. To determine mutation frequencies of KRAS and IDH1/2, competitive allele-specific Taqman® PCR (castPCR) was performed on DNA extracted from FFPE CCA tissue (limit of mutation detection 0.1%). Fourteen KRAS activating mutations (G12S, G12R, G12A, G13C, G13S, G13R, G12D, G13D, G12V, G12C, Q61R, Q61L, Q61H (c.183A>C and c.183A>T for Q61H), 5 IDH1 mutations (R132G, R132S, R132H, R132C, R132L), and 5 IDH2 mutations (R172G, R172M, R172K, R172W, R172S) were analyzed. Overall, 25% of analyzed samples were positive for KRAS mutation, and G12D was the predominant mutation (∼60%). One-third of Asian samples were positive for KRAS mutation, whereas less than one-fifth of non-Asian samples contained KRAS mutations. For IDH1, the frequency of mutation was less than 10% overall, and the majority of patients with IDH1 mutations were non-Asian. The R132C mutation was the predominant IDH1 mutation, and all tissues that were positive for IDH1 mutations were of intrahepatic origin. Interestingly, 2 out of the 7 samples positive for IDH1 mutations (R132C) were also positive for G12D KRAS mutation. There is no trend of MET expression correlating with either KRAS or IDH1 mutations. IDH2 analyses by castPCR and FISH studies examining ROS1 gene fusion are ongoing. Based on these data, inhibitors of receptor tyrosine kinases and their signaling pathways such as MET and ROS1 may merit clinical evaluation in CCA patients. LY2801653, a MET inhibitor which also has inhibitory activity against ROS1 and MKNK1/2 is currently in phase 1 clinical testing in patients with advanced cancer (trial I3O-MC-JSBA, NCT01285037).

Citation Format: Megan N. Thobe, S. Betty Yan, Kelly M. Credille, Aejaz Nasir, Jessica A. Roseberry Baker, Mary Lajiness, Nathan A. Brooks, Darryl W. Ballard, Donna M. Farley, Victoria L. Peek, Suzane L. Um, G. Jason Jin, Raymond Gilmour, Christoph Reinhard, Jeremy R. Graff, Andrew E. Schade, Aaron M. Gruver, Bruce Colligan, Larry Douglass, Julia Carter, Richard A. Walgren. Prevalence of MET expression, activating mutations of KRAS and IDH1/2, and ROS1 fusions in cholangiocarcinoma patient tumor samples. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2339. doi:10.1158/1538-7445.AM2013-2339

Abstract 817: Genomic evolution landscape of patient tumor derived xenograft of gastric cancer

Patient-derived xenograft (PDX) models have emerged as key model systems to understand the efficacy of anti-cancer agents. PDX systems have demonstrated superiority over cell lines with regards to higher histological resemblance to primary tumor, presence of stroma and also in mimicking response to therapeutic agents. However, the genomic evolution landscape of model establishment is not a well studied topic. In order to do that, we systematically collected materials from the first three passages of xenografts derived from eight gastric cancer patients from Seoul National University, Korea from 2008-2011. We subsequently generated comprehensive genomic profiles of the first three passages, parent primary tumor, and matched normal tissues for the eight patients. The genomic profiling data included whole-exome sequencing data (Agilent exome capture, paired-end sequencing on Illumina HiSeq 2000), mRNA expression (Affymetrix U133 Plus2.0), copy number data (Affymetrix SNP6), miRNA expression (Agilent miRNA array v16.0) and DNA methylation data (Illumina HumanMethylation27). The analysis is focused on two types of events: a) Cancer-related genomic changes derived from normal vs. tumor comparison, and their subsequent assessment in early passages; b) Passage-specific genomic changes derived from tumor vs. passages comparison. A further refinement of passage-specific genomic changes is done to differentiate ‘true’ passage-specific events from the ones that appear due to the difference in tumor purity that is lower in primary tumor due to the normal contamination. Overall, we describe the genomic landscape of evolution along xenograft establishment in gastric cancer and provide a comprehensive picture of genetic and genomic similarities (and differences) of xenografts to the primary tumor. This analysis will help us to better interpret the in vivo results emanating from experiments using xenografts and to translate the findings appropriately to the clinic.

Citation Format: Kun Yu, Swee Seong Wong, Jason C. Ting, Thompson N. Doman, Yong Yue, Amit aggarwal, Gregory P. Donoho, Rebekka Krumbach, Heiner H. Feibig, Seong-Ho kong, Woo-ho Kim, Han-kwang Yang, Christoph Reinhard. Genomic evolution landscape of patient tumor derived xenograft of gastric cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 817. doi:10.1158/1538-7445.AM2013-817

Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Abstract 2789: Functional and molecular characteristics of 20 novel patient-derived xenografts of Asian gastric cancer

Introduction: Asian and Caucasian populations are distinct regarding the prevalence of different tumor types due to differences in lifestyle and genetics. The molecular makeup of tumors of the same type can also vary. When developing drugs for the treatment of stomach cancer it is important to study tumors in both Asian and Caucasian backgrounds. In East Asia stomach cancer is the 2nd most common malignancy. The development of patient derived xenografts (PDX) from patients of East Asian origin is therefore critical. Oncotest established xenografts from stomach cancer patients who underwent surgery for the treatment of their cancer at the Seoul National University, South Korea. These Asian gastric cancer xenografts (GXA) were utilized for the investigation of molecular characteristics and sensitivity to anticancer agents.

Material and Methods: 78 gastric tumor samples from SNU were implanted subcutaneously in nude mice and sequentially passaged. Tumor material was collected for molecular profiling, including mutational analysis by Sanger sequencing and OncoCarta panels I, II, III. The efficacy of standard of care drugs 5-fluoruracil, cisplatin and taxol was tested in vivo.

Results: From the 78 implantations we were able to establish 21 Asian patient-derived gastric cancer xenografts, representing a take rate of 27%. The majority of tumors from which GXA xenografts were derived were poorly or moderately differentiated adenocarcinomas. The panel also includes mucinous adenocarcinomas and squamous cell carcinomas. The morphological features of the tumors (degree of differentiation) were preserved throughout serial passages.

Mutational analysis for 18 established models revealed that TP53 (13/18, 72%), PTEN (6/9, as well as one with PTEN RNA levels too low for RT-PCR), KRAS (5/18, 28%) and PIK3CA (4/18, 22%) were frequently mutated in these gastric cancers. Mutations in EGFR, MLH1 and APC were also detected, but no mutations in NRAS (0/18) or BRAF (0/17) were found.

Regarding sensitivity to anticancer agents, the response of the tumors varied strongly. Tumors were considered sensitive if the optimal treatment / control (T/C [%]) value was lower than 30%. 6 of 18 (33%) tumors were sensitive to 5-fluoruracil, 5 of 18 (28%) to paclitaxel and 3/18 (17 %) to cisplatin. Some gastric PDX were responsive to more than one chemotherapy, whereas 7 of 18 (39%) were not sensitive to any of these standard of care therapies.

These results demonstrate (i) that standard of care therapies are not the therapy of choice for a large proportion of these tumors and (ii) great heterogeneity within the 18 analyzed gastric Asian patient- derived xenografts.

Conclusion: In this study we developed a panel of Asian patient-derived gastric cancer xenografts with diverse molecular characteristics and responses to standard of care drugs.

Citation Format: Rebekka Krumbach, Seong-Ho Kong, Woo Ho Kim, Julia Schüler, Andreas Ackermann, Vincent Vuaroqueaux, Gregory P. Donoho, Amit Aggarwal, Christoph Reinhard, Han-Kwang Yang, Thomas Beckers, Heiner Fiebig. Functional and molecular characteristics of 20 novel patient-derived xenografts of Asian gastric cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2789. doi:10.1158/1538-7445.AM2013-2789

Network Expansion and Pathway Enrichment Analysis towards Biologically Significant Findings from Microarrays

In many cases, crucial genes show relatively slight changes between groups of samples (e.g. normal vs. disease), and many genes selected from microarray differential analysis by measuring the expression level statistically are also poorly annotated and lack of biological significance. In this paper, we present an innovative approach - network expansion and pathway enrichment analysis (NEPEA) for integrative microarray analysis. We assume that organized knowledge will help microarray data analysis in significant ways, and the organized knowledge could be represented as molecular interaction networks or biological pathways. Based on this hypothesis, we develop the NEPEA framework based on network expansion from the human annotated and predicted protein interaction (HAPPI) database, and pathway enrichment from the human pathway database (HPD). We use a recently-published microarray dataset (GSE24215) related to insulin resistance and type 2 diabetes (T2D) as case study, since this study provided a thorough experimental validation for both genes and pathways identified computationally from classical microarray analysis and pathway analysis. We perform our NEPEA analysis for this dataset based on the results from the classical microarray analysis to identify biologically significant genes and pathways. Our findings are not only consistent with the original findings mostly, but also obtained more supports from other literatures.

Genome-wide survey of recurrent HBV integration in hepatocellular carcinoma

To survey hepatitis B virus (HBV) integration in liver cancer genomes, we conducted massively parallel sequencing of 81 HBV-positive and 7 HBV-negative hepatocellular carcinomas (HCCs) and adjacent normal tissues. We found that HBV integration is observed more frequently in the tumors (86.4%) than in adjacent liver tissues (30.7%). Copy-number variations (CNVs) were significantly increased at HBV breakpoint locations where chromosomal instability was likely induced. Approximately 40% of HBV breakpoints within the HBV genome were located within a 1,800-bp region where the viral enhancer, X gene and core gene are located. We also identified recurrent HBV integration events (in ≥ 4 HCCs) that were validated by RNA sequencing (RNA-seq) and Sanger sequencing at the known and putative cancer-related TERT, MLL4 and CCNE1 genes, which showed upregulated gene expression in tumor versus normal tissue. We also report evidence that suggests that the number of HBV integrations is associated with patient survival.