PDF file - 219K, Genotyping assays.

PDF file - 1893K, FM108 ovarian cell line production.

PDF file - 1995K, Isolation of pancreatic cancer cell line, Panc486.

PDF file - 87K, Breeding strategy for production and maintenance of the SCID hprt-null mouse.

XLSX file - 165K, Response of Panc502 to 125 anti-neoplastic drugs.

PDF file - 105K, Pharmagram of Panc502 to all drugs in the JHDL.

PDF file - 1505K, Selection of pancreatic cancer cell line, Panc502.

Abstract Purpose: High-throughput chemosensitivity testing of low-passage cancer cell lines can be used to prioritize agents for personalized chemotherapy. However, generating cell lines from primary cancers is difficult because contaminating stromal cells overgrow the malignant cells. Experimental Design: We produced a series of hypoxanthine phosphoribosyl transferase (hprt)-null immunodeficient mice. During growth of human cancers in these mice, hprt-null murine stromal cells replace their human counterparts. Results: Pancreatic and ovarian cancers explanted from these mice were grown in selection media to produce pure human cancer cell lines. We screened one cell line with a 3,131-drug panel and identified 77 U.S. Food and Drug Administration (FDA)–approved drugs with activity, and two novel drugs to which the cell line was uniquely sensitive. Xenografts of this carcinoma were selectively responsive to both drugs. Conclusion: Chemotherapy can be personalized using patient-specific cell lines derived in biochemically selectable mice. Clin Cancer Res; 19(5); 1139–46. ©2012 AACR.

PDF file - 77K, Chemosensitivity to topoisomerase inhibitors.

PDF file - 79K, Breeding strategy for production and maintenance of the nude hprt-null mouse.

Supplementary Data from Ligand-dependent Notch Signaling Is Involved in Tumor Initiation and Tumor Maintenance in Pancreatic Cancer

The therapeutic efficacy of temozolomide (TMZ) is hindered by inherent and acquired resistance. Biomarkers such as MGMT expression and MMR proficiency are used as predictors of response. However, not all MGMTlow/-ve/MMRproficient patients benefit from TMZ treatment, indicating a need for additional patient selection criteria. We explored the role of ATR in mediating TMZ resistance and whether ATR inhibitors (ATRi) could reverse this resistance in multiple cancer lines. We observed that only 31% of MGMTlow/-ve/MMRproficient patient-derived and established cancer lines are sensitive to TMZ at clinically relevant concentrations. TMZ treatment resulted in DNA damage signaling in both sensitive and resistant lines, but prolonged G2/M arrest and cell death were exclusive to sensitive models. Inhibition of ATR but not ATM, sensitized the majority of resistant models to TMZ and resulted in measurable DNA damage and persistent growth inhibition. Also, compromised homologous recombination (HR) via RAD51 or BRCA1 loss only conferred sensitivity to TMZ when combined with an ATRi. Furthermore, low REV3L mRNA expression correlated with sensitivity to the TMZ and ATRi combination in vitro and in vivo. This suggests that HR defects and low REV3L levels could be useful selection criteria for enhanced clinical efficacy of an ATRi plus TMZ combination.

Background: The National Cancer Institute (NCI) has developed a Patient-Derived Models Repository (PDMR; https://pdmr.cancer.gov) of preclinical models including patient-derived xenografts (PDX), organoids (PDOrg) and patient-derived cell cultures (PDC). Extensive clinical annotation and genomic datasets are available for these preclinical models. However, it is unclear if the molecular profiles of the corresponding patient tumors are stably propagated in these models. We have previously demonstrated that PDX models from the NCI PDMR faithfully represent the patient tumors both in terms of genomic stability and tumor heterogeneity. Here, we conduct an in-depth investigation of genomic representation of patient tumors in the PDOrgs and PDCs. Methods: PDOrgs (n=64) and PDCs (n=94) were established from tumor fragments (i.e., initiator specimens) obtained either from patient specimens or from PDX specimens of early passage. For some models (n=19), both PDOrgs and PDCs were generated from the same tumor tissue; in fewer cases (n=4), PDCs were established from organoids derived from patient specimens. Whole Exome Sequencing and RNA-Seq were performed on all PDCs and PDOrgs, and data were compared with patient specimens or early passage PDXs. Results: A majority of the PDOrgs and PDCs have stably inherited the genome of the corresponding patient specimens based on the following observations: (1) >87% of PDOrgs and PDCs maintained similar copy number alteration profiles compared with the initiator specimens of the preclinical model; (2) the variant allele frequency (VAF) of clinically relevant mutations remained consistent between the PDOrgs, PDCs, and the initiator specimens, with none of the PDCs or PDOrgs deviating by >15% VAF; and (3) clinically relevant biomarkers (e.g., MSI, LOH, mutational signatures etc.) are concordant amongst the PDOrgs, PDCs, and the initiator specimens. We observed that the majority of SNVs and indels present in the initiator specimens were also found in the PDOrgs and PDCs, suggesting almost all the tumor heterogeneity was preserved in these preclinical models. Conclusions: This large and histologically diverse set of PDOrgs and PDCs from the NCI PDMR exhibited genomic stability and faithfully represented the tumor heterogeneity observed in corresponding patient specimens. These preclinical models thus represent a valuable resource for researchers interested in pre-clinical drug or other studies. Citation Format: Biswajit Das, Yvonne A. Evrard, Li Chen, Rajesh Patidar, Tomas Vilimas, Justine N. McCutcheon, Amanda L. Peach, Nikitha V. Nair, Thomas D. Forbes, Brandie A. Fullmer, Anna J. Lee Fong, Luis E. Romero, Alyssa K. Chapman, Kelsey A. Conley, Robin D. Harrington, Shahanawaz S. Jiwani, Peng Wang, Michelle M. Gottholm-Ahalt, Erin N. Cantu, Gloryvee Rivera, Lindsay M. Dutko, Kelly M. Benauer, Vishnuprabha R. Kannan, Carrie A. Bonomi, Kelly M. Dougherty, Joseph P. Geraghty, Marion V. Gibson, Savanna S. Styers, Abigail J. Walke, Jenna E. Moyer, Anna Wade, Mariah L. Baldwin, Kaitlyn A. Arthur, Kevin J. Plater, Luke Stockwin, Matthew R. Murphy, Michael E. Mullendore, Dianne L. Newton, Melinda G. Hollingshead, Chris A. Karlovich, Paul M. Williams, James H. Doroshow. Patient-derived organoid and cell culture models from the NCI Patient-Derived Models Repository (NCI PDMR) preserve genomic stability and heterogeneity of patient tumor specimens [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 3916.

BACKGROUND:Development of cancer therapeutics partially depends upon selection of appropriate animal models. Therefore, improvements to model selection are beneficial.RESULTS:Forty-nine human tumor xenografts at in vivo passages 1, 4 and 10 were subjected to cDNA microarray analysis yielding a dataset of 823 Affymetrix HG-U133 Plus 2.0 arrays. To illustrate mining strategies supporting therapeutic studies, transcript expression was determined: 1) relative to other models, 2) with successive in vivo passage, and 3) during the in vitro to in vivo transition. Ranking models according to relative transcript expression in vivo has the potential to improve initial model selection. For example, combining p53 tumor expression data with mutational status could guide selection of tumors for therapeutic studies of agents where p53 status purportedly affects efficacy (e.g., MK-1775). The utility of monitoring changes in gene expression with extended in vivo tumor passages was illustrated by focused studies of drug resistance mediators and receptor tyrosine kinases. Noteworthy observations included a significant decline in HCT-15 colon xenograft ABCB1 transporter expression and increased expression of the kinase KIT in A549 with serial passage. These trends predict sensitivity to agents such as paclitaxel (ABCB1 substrate) and imatinib (c-KIT inhibitor) would be altered with extended passage. Given that gene expression results indicated some models undergo profound changes with in vivo passage, a general metric of stability was generated so models could be ranked accordingly. Lastly, changes occurring during transition from in vitro to in vivo growth may have important consequences for therapeutic studies since targets identified in vitro could be over- or under-represented when tumor cells adapt to in vivo growth. A comprehensive list of mouse transcripts capable of cross-hybridizing with human probe sets on the HG-U133 Plus 2.0 array was generated. Removal of the murine artifacts followed by pairwise analysis of in vitro cells with respective passage 1 xenografts and GO analysis illustrates the complex interplay that each model has with the host microenvironment.CONCLUSIONS:This study provides strategies to aid selection of xenograft models for therapeutic studies. These data highlight the dynamic nature of xenograft models and emphasize the importance of maintaining passage consistency throughout experiments.

Oxyphenisatin (3,3-bis(4-hydroxyphenyl)-1H-indol-2-one) and several structurally related molecules have been shown to have in vitro and in vivo antiproliferative activity. This study aims to confirm and extend mechanistic studies by focusing on oxyphenisatin acetate (OXY, NSC 59687), the pro-drug of oxyphenisatin. Results confirm that OXY inhibits the growth of the breast cancer cell lines MCF7, T47D, HS578T, and MDA-MB-468. This effect is associated with selective inhibition of translation accompanied by rapid phosphorylation of the nutrient sensing eukaryotic translation initiation factor 2α (eIF2α) kinases, GCN2 and PERK. This effect was paralleled by activation of AMP-activated protein kinase (AMPK) combined with reduced phosphorylation of the mammalian target of rapamycin (mTOR) substrates p70S6K and 4E-BP1. Microarray analysis highlighted activation of pathways involved in apoptosis induction, autophagy, RNA/protein metabolism, starvation responses, and solute transport. Pathway inhibitor combination studies suggested a role for AMPK/mTOR signaling, de novo transcription and translation, reactive oxygen species (ROS)/glutathione metabolism, calcium homeostasis and plasma membrane Na(+) /K(+) /Ca(2+) transport in activity. Further examination confirmed that OXY treatment was associated with autophagy, mitochondrial dysfunction, and ROS generation. Additionally, treatment was associated with activation of both intrinsic and extrinsic apoptotic pathways. In the estrogen receptor (ER) positive MCF7 and T47D cells, OXY induced TNFα expression and TNFR1 degradation, indicating autocrine receptor-mediated apoptosis in these lines. Lastly, in an MCF7 xenograft model, OXY delivered intraperitoneally inhibited tumor growth, accompanied by phosphorylation of eIF2α and degradation of TNFR1. These data suggest that OXY induces a multifaceted cell starvation response, which ultimately induces programmed cell death.

Abstract Several indole-3-carbinol analogs are under preclinical evaluation at the National Cancer Institute. One analog, NSC743380 (1-[(3-chlorophenyl)-methyl]-1H-indole-3-carbinol), is selectively toxic to a subset of NCI 60 cell lines in vitro and has undergone extensive in vivo testing. In vivo, NSC743380 produced complete regressions in A498 renal xenograft models at doses as low as 45 mg/kg when administered intraperitoneally. Additional studies demonstrated that NSC743380 is orally bioavailable. To extend knowledge regarding the mechanism of action, two pairs of resistant and sensitive cell lines [A498/ACHN (renal) and NCI-H226/A549 (NSCLC), sensitive/resistant, respectively] were used. Results showed that 5-10 min following NSC743380 treatment, phosphorylation of p38 and JNK were enhanced in sensitive but not resistant lines. Two hrs of treatment resulted in an inhibition of transcription and translation (45% and 75% inhibition, respectively) and by 4 hrs NSC743380 induced caspase-dependent apoptosis with loss of c-FLIP. Pathway-specific inhibitors were then used to gain mechanistic insight. Diverse antioxidants and NSAIDs, inhibitors of JNK, RAS/RAF, PPAR, lipid 2nd messenger signaling, transcription and actin polymerization were shown to completely inhibit NSC743380 activity. Microarray analysis of three sensitive cell lines using Affymetrix U133 Plus 2 chipset identified several trends in the transcriptome notably the upregulation of diverse immediate-early genes (IEGs) including; transcriptional regulators [EGR1, FOS/FOSB, HES1, MAFF and SOX9], secreted factors [HBEGF, IL-8 and GDF-15] and several general IEGs [ARC, ERRFI1, GADD45A/B, GEM and IER2]. A second noteworthy trend involved increased expression of the IL-6 family members, IL-6, IL-11 and LIF. These data led to an exploration as to whether enhanced JAK/STAT signaling was responsible for the above effects. Short time course lysates from 3 sensitive (A498, CAKI-1 and NCI-H226) cell lines and 1 resistant (A549) cell line showed that in sensitive lines only, NSC743380 rapidly (5 minutes) enhanced phosphorylation of the JAK family member Tyk2 at Y1054/55 and STAT3 at Y705. Additionally several phosphostate changes were observed in a subset of sensitive cell lines such as JAK1 phosphorylation in A498 cells and transient increase in pSTAT1 in A498 and CAKI-1 cell lines. Furthermore, two inhibitors of JAK/STAT signaling, AG490 and resveratrol, completely inhibited NSC743380 activity and p38/JNK phosphorylation. Subsequent siRNA knockdown experiments showed that Tyk2 siRNA inhibited NSC743380 activity whereas STAT3 and JAK1 siRNA along with scrambled siRNA had no effect. These data suggest that signaling through the JAK family member Tyk2 contributes towards NSC743380 activity and the data are being evaluated to determine how best to move forward. Funded by NCI Contract No. HHSN261200800001E. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2810. doi:1538-7445.AM2012-2810

PURPOSE:To establish whether NSC80467, a novel fused naphthquinone imidazolium, has a similar spectrum of activity to the well-characterized "survivin suppressant" YM155 and to extend mechanistic studies for this structural class of agent.METHODS:NSC80467 and YM155 were analyzed in parallel using assays measuring viability, survivin suppression, inhibition of DNA/RNA/protein synthesis and the cellular response to DNA damage.RESULTS:GI(50) values generated for both compounds in the NCI-60 screen yielded a correlation coefficient of 0.748, suggesting significant concordance. Both agents were also shown to inhibit protein expression of survivin [BIRC5]. COMPARE analysis identified DNA damaging agents chromomycin A3 and bisantrene HCl and one DNA-directed inhibitor of transcription, actinomycin D, as correlating with the activity of NSC80467 and YM155. Furthermore, both agents were shown to preferentially inhibit DNA, over RNA and protein synthesis. Thus, the ability of NSC80467 and YM155 to induce a DNA damage response was examined further. Treatment of PC3 cells with either agent resulted in dose-dependent induction of γH2AX and pKAP1, two markers of DNA damage. The concentrations of agent required to stimulate γH2AX were considerably lower than those required to inhibit survivin, implicating DNA damage as an initiating event. The DNA damage response was then confirmed in a panel of cell lines treated with NSC80467 or YM155, suggesting that γH2AX and pKAP1 have potential as response biomarkers.CONCLUSIONS:These data provide the first evidence that NSC80467 and YM155 are DNA damaging agents where suppression of survivin is a secondary event, likely a consequence of transcriptional repression.

Intraductal papillary mucinous neoplasms (IPMN) are non-invasive precursor lesions of pancreatic cancer (PC), which originate in ductal cells and can be macroscopically identified. These lesions can be classified in IPMN-adenoma, moderate dysplasia and carcinoma in situ. The differentiation of the IPMN epithelium correlates- besides the histological grading- with the potential for the development of PC. Differences in miRNA expression, small, highly conserved RNAs of 18–24 bp length, have been extensively examined in PC. In contrast, changes in miRNA expression in precursor lesions of PC have not been demonstrated thus far. In this study, we demonstrate miRNA expression differences in PC precursor lesions for the first time and evaluate the potential of those miRNAs as biomarkers of early pancreatic neoplasia. Material and Methods: Relative expression levels of 12 miRNAs, which elevated expression levels in PC have previously been identified, were examined using qRT-PCR on microdissected epithelium of 15 non-invasive IPMN and matched normal tissue. Two highly expressed miRNAs, miR-155 and miR-21, have been further evaluated using locked nucleic acid in-situ-hybridization (LNA-ISH) on 64 archival IPMN (tissue microarrays). Furthermore, the expression of miR-155 and miR-21 in pancreatic juice of 10 resected and confirmed patients with IPMN and 5 patients with non-neoplastic pancreatic diseases has been examined. Results: Ten out of 12 miRNAs revealed significantly higher expression levels when compared to the matched normals (p<0.05), in which miR-155 (11.6 fold) and miR-21 (12.1 fold) demonstrated the highest expression differences. LNA-ISH verified the expression of miR-155 in 53 out of 64 (83%) IPMNs, whereas only 4 out of 54 (7%) normal ducts revealed miR-155 expression. Expression of miR-21 could be identified in 52 out of 64 (81%) IPMNs. Only one sample out of 54 normal ducts revealed miR-21 expression. Furthermore, higher expression levels of miR-155 could be identified in 6 out of 10 (60) IPMN-pancreatic juice samples using qRT-PCR, whereas no miR-155 expression could be detected in the control group. Conclusion: We were able to demonstrate for the first time that differences in miRNA expression occur not only in PC but also in precursor lesions, exhibiting one mechanism of multistep progression of PC. Furthermore, we were able to prove that miRNA expression patterns, especially miR-155, reveal a potential as biomarkers for the early detection of PC.

Abstract Purpose: Aberrant activation of the Notch signaling pathway is commonly observed in human pancreatic cancer, although the mechanism(s) for this activation has not been elucidated. Experimental Design: A panel of 20 human pancreatic cancer cell lines was profiled for the expression of Notch pathway-related ligands, receptors, and target genes. Disruption of intracellular Notch signaling, either genetically by RNA interference targeting NOTCH1 or pharmacologically by means of the γ-secretase inhibitor GSI-18, was used for assessing requirement of Notch signaling in pancreatic cancer initiation and maintenance. Results: Striking overexpression of Notch ligand transcripts was detectable in the vast majority of pancreatic cancer cell lines, most prominently JAGGED2 (18 of 20 cases, 90%) and DLL4 (10 of 20 cases, 50%). In two cell lines, genomic amplification of the DLL3 locus was observed, mirrored by overexpression of DLL3 transcripts. In contrast, coding region mutations of NOTCH1 or NOTCH2 were not observed. Genetic and pharmacologic inhibition of Notch signaling mitigated anchorage-independent growth in pancreatic cancer cells, confirming that sustained Notch activation is a requirement for pancreatic cancer maintenance. Further, transient pretreatment of pancreatic cancer cells with GSI-18 resulted in depletion in the proportion of tumor-initiating aldehyde dehydrogenase–expressing subpopulation and was associated with inhibition of colony formation in vitro and xenograft engraftment in vivo, underscoring a requirement for the Notch-dependent aldehyde dehydrogenase–expressing cells in pancreatic cancer initiation. Conclusions: Our studies confirm that Notch activation is almost always ligand dependent in pancreatic cancer, and inhibition of Notch signaling is a promising therapeutic strategy in this malignancy.

The transcription factor Snail represses E-cadherin and induces epithelial-mesenchymal transition (EMT), a process also exploited by invasive cancer cells. Aberrant Hedgehog (Hh) signaling was recently observed in a variety of epithelial cancers and it has been shown that the Hh target gene Gli1 induces expression of Snail. In this study, we examined whether Snail and Sonic Hedgehog (SHH) are expressed in neuroendocrine tumors (NETs) of the ileum. Using immunohistochemistry, we found expression of Snail in 22/37 (59 %) of evaluated NET samples, but not in adjacent normal tissues. Snail expression was mostly restricted to the invasive front of the tumors. Six of seven liver metastases analyzed were positive for Snail. Intratumoral expression of SHH was detected in 27/37 (73 %) tumors. As opposed to Snail, cells expressing SHH were found to be distributed more randomly throughout the tumors. 16 of 30 (53 %) primary NETs showed both Snail and SHH expression. Furthermore we found downregulation of E-cadherin in Snail-expressing cells by immunofluorescence. RT-PCR revealed conservation of the Hh target genes Gli1, Gli2, and Ptch in the pancreatic carcinoid cell line BON1, which were downregulated upon Hh-inhibition with cyclopamine. Moreover, Hh-inhibition attenuated in vitro cell growth in a dose-dependent manner. In conclusion, we describe for the first time that Snail and SHH are overexpressed in a large subset of NETs of the ileum. Aberrant activation of these pathways might be involved in invasion and metastatic spread in NETs.