Sarkaria, Jann N.

Abstract Biomarkers that select patients for therapeutics would benefit clinical trial design and patient care. The Akt pathway is a therapeutic target in Glioblastoma Multiforme (GBM) and an important determinant of patient outcome. However, it is not known whether activity of this pathway varies among GBM tumors. To investigate we used Akt pathway genes from published GBM expression datasets. We detected 5 patterns of Akt pathway gene expression and these Akt subgroups correlated with prognosis. We analyzed networks within subgroups using both gene set enrichment analysis and a novel method that scores relevance based on both expression and local network connectivity (Komurov et al., PLoS Comput Biol. 2010 6:8, 1-10). The results suggest therapeutic targets within the individual subgroups. Furthermore, preliminary analysis indicates that human GBM xenograft models and primary human GBM manifest similar Akt subgroups. We are investigating rodent xenograft models of Akt subgroups to evaluate subgroup-specific drug sensitivity, and will present a method and examples of analysis integrating gene expression data from human GBM xenografts and primary human GBM. We hypothesize that Akt subgroups will help personalize treatment for GBM therapeutics. Supported by Barrow Neurological Foundation, Halle Family Foundation, and NIH 1 K01 NS064952-01A1 (AMJ). Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4138. doi:10.1158/1538-7445.AM2011-4138

Abstract Glioblastoma multiforme (GBM) is the most common primary brain tumor in adults and is associated with a poor prognosis. Progress in developing effective therapies for this disease is significantly limited by the blood-brain barrier (BBB), which limits the delivery of many anti-cancer agents to infiltrative tumor cells. In addition to physical barriers, such as tight junctions, the efflux proteins bcrp and P-gp in the BBB limit the brain distribution of numerous anti-cancer agents. Palbociclib (PD0332991) is a potent Cdk4/6 inhibitor which has shown remarkable efficacy in treating peripheral (non-brain) tumors. The Cdk4 pathway is dysregulated in approximately 75% of GBM; most commonly, the pathway is hyperactivated through the homozygous deletion of p16 (52%), amplification of Cdk4 (18%), or amplification of Cdk6 (1%). The purpose of this study is to define the role of the efflux transporters P-gp and bcrp in the brain distribution of palbociclib and to examine if an intact BBB limits efficacy. Palbociclib brain distribution studies were performed in FVB wild-type, P-gp knockout (PKO; Mdr1a/b(-/-)), bcrp knockout (BKO; Bcrp1(-/-)), and triple knockout (TKO; Mdr1a/b(-/-)Bcrp1(-/-)) mice after an oral dose (10mg/kg). The concentrations of palbociclib from all distribution studies were determined by a sensitive and specific LC-MS/MS assay. Survival studies were conducted in patient-derived primary GBM xenograft models in athymic nu/nu mice. The brain exposure of palbociclib (AUCbrain-to-AUCplasma ratio) was ∼ 33.5, 3.2, and 150-fold higher as compared to WT mice (WT: .044; PKO: 1.34; BKO: 0.13; TKO: 6.24). Further, the steady-state brain-to-plasma ratio (B/P) of palbociclib after a constant intra-peritoneal infusion of 10 µg/hr for 48hrs was ∼120-fold higher in the TKO mice than the WT mice [WT: (0.21 ± 0.07); PKO: (2.48 ± .13); BKO: (0.43 ± 0.12); TKO: (26.5 ± 5.4) p < 0.0001]. Inhibition of P-gp and bcrp with elacridar (10 mg/kg IP) resulted in a marked increase in palbociclib brain distribution [control B/P (0.06 ± 0.02); elacridar treatment (2.0 ± 1.4)]. For survival studies, palbociclib was dosed at 150 mg/kg/day continuously. Consistent with limited brain penetration, palbociclib did not improve the median survival of an orthotopic GBM xenograft model. In contrast, treatment of GBM22 xenografts grown as flank tumors resulted in profound efficacy with a 70 day prolongation in the time for tumor volume to reach 1000mm3. These data suggest the clinical paradigm of a potent anti-cancer agent (for instance, palbociclib) used in the treatment of peripheral disease is less effective in the treatment of brain tumors due to the BBB and active efflux by P-gp and bcrp. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):C81. Citation Format: Karen E. Parrish, Jenny L. Pokorny, Rajendar K. Mittapalli, Katrina Bakken, Jann N. Sarkaria, William F. Elmquist. BBB efflux pump activity limits brain penetration of palbociclib (PD0332991) in glioblastoma. [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 C81.

Abstract Glioblastoma (GBM) is the most common and malignant form of primary brain tumor. Average survival rate of GBM is 12-15 months from diagnosis. Due to its highly invasive nature, current treatment options have not been able to improve the survival rate in past 20 years. In order to discover GBM therapeutic targets, omics technologies have been widely used in order to identify potential biomarkers. Identification of cancer biomarkers for diagnosis and prognosis continues to evolve as clinical specimen pipelines and technologies are optimized. This research study focused on investigating proteins, metabolites and lipids biomarkers and patterns of human GBM xenografts employing mass spectrometry. Human tumor cell lines GBM 10 and GBM 43 were injected in the right cerebral hemisphere and flank sites in NOD/SCID mice (n = 10 mice per group). After harvesting brain and flank tumors and control brain from mouse models, protein, metabolites, and lipids of tumor samples were collected through one simple extraction procedure, which may solve sample preparation difficulties in omics studies, developed by Dr. Jiri Adamec. These samples were analyzed by reverse phase high performance liquid chromatography - Fourier transform ion cyclotron resonance mass spectrometry (LC-FTMS). FTMS analyzers have the highest resolving power of all MS instruments, which is ideal for complex mixtures such as GBM tissue. Spectra obtained from the FTMS analysis were analyzed using Student t-tests to detect significant differences in tissue profiles at a level of p = 0.05. Compounds below this threshold were identified through a database using the m/z ratio. Lipidomic analysis indicated the possible up and down-regulation of several lipids classes in GBM tissue connected to metabolic pathways, tumor proliferation and immunodepression, such as glycerophospholipids, both up- and down-regulated (e.g. PC38:4 or PG 35:2, respectively), and down-regulated glycosphingolipids (Galβ1-3GlcNAcβ1-3Galβ1-4Glc-Cer, Galβ1-4GlcNAcβ1-3Galβ1-4Glc-Cer), and triglycerides (TG 55:9, 53:4,52:8). We expect that integrated studies of proteomics, metabolomics, and lipidomics increase the confidence of identification of potential biomarkers. Accompanying these studies is a collaborative effort to improve the effectiveness and efficiency of computational pipelines that are imperative to the analytics, visualization, identification, and interpretation of the omics data. Only by carefully integrating the computational pipelines can we successfully perform the types of integrative studies needed to advance the identification of cancer biomarkers for diagnosis and prognosis, and our integrative studies serve as a case study for our pipeline advancement efforts. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B37. Citation Format: Soo Jung Ha, Gordon Showalter, Jenna Rickus, Shanbao Cai, Haiyan Wang, Wei Michael Liu, Jann N. Sarkaria, John Springer, Jiri Adamec, Karen E. Pollok, Kari L. Clase. Proteomic and metabolomic analyses of glioblastoma using mass spectrometry. [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 B37.

Abstract Purpose: Effective sensitizing strategies potentially can extend the benefit of temozolomide (TMZ) therapy in patients with glioblastoma (GBM). We previously demonstrated that robust TMZ-sensitizing effects of the [poly (ADP-ribose) polymerase] (PARP) inhibitor veliparib (ABT-888) are restricted to TMZ-sensitive GBM xenografts. The focus of this study is to provide an understanding for the differential sensitization in paired TMZ-sensitive and -resistant GBM models. Experimental Design: The impact of veliparib on TMZ-induced cytotoxicity and DNA damage was evaluated in vitro and in vivo in models of acquired TMZ resistance (GBM12TMZ-mgmtHigh, GBM12TMZ-mgmtLow, and U251TMZ), inherent TMZ resistance (T98G), and TMZ-sensitive (U251 and GBM12). In vivo drug efficacy, pharmacokinetics, and pharmacodynamics were analyzed using clinically relevant dosing regimens. Results: Veliparib enhanced TMZ cytotoxicity and DNA-damage signaling in all GBM models in vitro with more pronounced effects in TMZ-resistant lines at 3 to 10 μmol/L veliparib. In vivo, combined TMZ/veliparib, compared with TMZ alone, significantly delayed tumor growth and enhanced DNA-damage signaling and γH2AX levels in the sensitive GBM12 xenograft line but not in the resistant GBM12TMZ lines. The pharmacokinetic profile of veliparib was similar for GBM12 and GBM12TMZ tumors with Cmax (∼1.5 μmol/L) in tissue significantly lower than concentrations associated with optimal in vitro sensitizing effects for resistant tumors. In contrast, robust suppression of PARP-1 expression by shRNA significantly increased TMZ sensitivity of U251TMZ in vitro and in vivo. Conclusions: In vitro cytotoxicity assays do not adequately model the therapeutic index of PARP inhibitors, as concentrations of veliparib and TMZ required to sensitize TMZ-resistant cancer cells in vivo cannot be achieved using a tolerable dosing regimen. Clin Cancer Res; 20(14); 3730–41. ©2014 AACR.

Abstract Purpose: Ovarian cancer has a high recurrence and mortality rate. A barrier to improved outcomes includes a lack of accurate models for preclinical testing of novel therapeutics. Experimental Design: Clinically relevant, patient-derived tumorgraft models were generated from sequential patients and the first 168 engrafted models are described. Fresh ovarian, primary peritoneal, and fallopian tube carcinomas were collected at the time of debulking surgery and injected intraperitoneally into severe combined immunodeficient mice. Results: Tumorgrafts demonstrated a 74% engraftment rate with microscopic fidelity of primary tumor characteristics. Low-passage tumorgrafts also showed comparable genomic aberrations with the corresponding primary tumor and exhibit gene set enrichment of multiple ovarian cancer molecular subtypes, similar to patient tumors. Importantly, each of these tumorgraft models is annotated with clinical data and for those that have been tested, response to platinum chemotherapy correlates with the source patient. Conclusions: Presented herein is the largest known living tumor bank of patient-derived, ovarian tumorgraft models that can be applied to the development of personalized cancer treatment. Clin Cancer Res; 20(5); 1288–97. ©2014 AACR.

Abstract Glioblastoma multiforme is an aggressive, treatment-refractory type of brain tumor for which effective therapeutic targets remain important to identify. Here, we report that cyclophilin B (CypB), a prolyl isomerase residing in the endoplasmic reticulum (ER), provides an essential survival signal in glioblastoma multiforme cells. Analysis of gene expression databases revealed that CypB is upregulated in many cases of malignant glioma. We found that suppression of CypB reduced cell proliferation and survival in human glioblastoma multiforme cells in vitro and in vivo. We also found that treatment with small molecule inhibitors of cyclophilins, including the approved drug cyclosporine, greatly reduced the viability of glioblastoma multiforme cells. Mechanistically, depletion or pharmacologic inhibition of CypB caused hyperactivation of the oncogenic RAS–mitogen-activated protein kinase pathway, induction of cellular senescence signals, and death resulting from loss of MYC, mutant p53, Chk1, and Janus-activated kinase/STAT3 signaling. Elevated reactive oxygen species, ER expansion, and abnormal unfolded protein responses in CypB-depleted glioblastoma multiforme cells indicated that CypB alleviates oxidative and ER stresses and coordinates stress adaptation responses. Enhanced cell survival and sustained expression of multiple oncogenic proteins downstream of CypB may thus contribute to the poor outcome of glioblastoma multiforme tumors. Our findings link chaperone-mediated protein folding in the ER to mechanisms underlying oncogenic transformation, and they make CypB an attractive and immediately targetable molecule for glioblastoma multiforme therapy. Cancer Res; 74(2); 484–96. ©2013 AACR.

Abstract Growing evidence supports a role for the unfolded protein response (UPR) in carcinogenesis; however, the precise molecular mechanisms underlying this phenomenon remain elusive. Herein, we identified the circadian clock PER1 mRNA as a novel substrate of the endoribonuclease activity of the UPR sensor IRE1α. Analysis of the mechanism shows that IRE1α endoribonuclease activity decreased PER1 mRNA in tumor cells without affecting PER1 gene transcription. Inhibition of IRE1α signaling using either siRNA-mediated silencing or a dominant-negative strategy prevented PER1 mRNA decay, reduced tumorigenesis, and increased survival, features that were reversed upon PER1 silencing. Clinically, patients showing reduced survival have lower levels of PER1 mRNA expression and increased splicing of XBP1, a known IRE-α substrate, thereby pointing toward an increased IRE1α activity in these patients. Hence, we describe a novel mechanism connecting the UPR and circadian clock components in tumor cells, thereby highlighting the importance of this interplay in tumor development. Cancer Res; 73(15); 4732–43. ©2013 AACR.

Abstract Purpose: Glioblastoma multiforme (GBM) is a devastating disease. Recent studies suggest that the stem cell properties of GBM contribute to the development of therapy resistance. Experimental Design: The expression of Survivin and Ran was evaluated by immunohistochemistry with GBM tissues, and quantitative reverse transcriptase (qRT)-PCR and immunocytochemistry with patient-derived GBM sphere cultures. With a computational structure-based drug design, 11 small-molecule compounds were designed, synthesized, and evaluated as inhibitor candidates for the molecular interaction of Survivin protein. The molecular mechanism of the lead compound, LLP-3, was determined by Western blot, ELISA, in situ proximity ligation assay, and immunocytochemistry. The effects of LLP-3 treatment on GSCs were evaluated both in vitro and in vivo. Quantitative immunohistochemistry was carried out to compare Survivin expression in tissues from 44 newly diagnosed and 31 recurrent post-chemoradiation GBM patients. Lastly, the sensitivities of temozolomide-resistant GBM spheres to LLP-3 were evaluated in vitro. Results: Survivin and Ran were strongly expressed in GBM tissues, particularly in the perivasculature, and also in patient-derived GSC cultures. LLP-3 treatment disrupted the Survivin–Ran protein complex in cancer cells and abolished the growth of patient-derived GBM spheres in vitro and in vivo. This inhibition was dependent on caspase activity and associated with p53 status of cells. Immunohistochemistry showed that Survivin expression is significantly increased in recurrent GBM compared with newly diagnosed tumors, and temozolomide-resistant GBM spheres exhibited high sensitivities to LLP-3 treatment. Conclusions: Disruption of the Survivin–Ran complex by LLP-3 abolishes survival and growth of GSCs both in vitro and in vivo, indicating an attractive novel therapeutic approach for GBM. Clin Cancer Res; 19(3); 631–42. ©2012 AACR.

Abstract Purpose: Glioblastoma (GBM), the most common primary brain tumor in adults, presents a high frequency of alteration in the PI3K pathway. Our objectives were to identify a dual PI3K/mTOR inhibitor optimized to cross the blood–brain barrier (BBB) and characterize its brain penetration, pathway modulation in the brain and efficacy in orthotopic xenograft models of GBM. Experimental Design: Physicochemical properties of PI3K inhibitors were optimized using in silico tools, leading to the identification of GNE-317. This compound was tested in cells overexpressing P-glycoprotein (P-gp) or breast cancer resistance protein (BCRP). Following administration to mice, GNE-317 plasma and brain concentrations were determined, and phosphorylated biomarkers (pAkt, p4EBP1, and pS6) were measured to assess PI3K pathway suppression in the brain. GNE-317 efficacy was evaluated in the U87, GS2, and GBM10 orthotopic models of GBM. Results: GNE-317 was identified as having physicochemical properties predictive of low efflux by P-gp and BCRP. Studies in transfected MDCK cells showed that GNE-317 was not a substrate of either transporter. GNE-317 markedly inhibited the PI3K pathway in mouse brain, causing 40% to 90% suppression of the pAkt and pS6 signals up to 6-hour postdose. GNE-317 was efficacious in the U87, GS2, and GBM10 orthotopic models, achieving tumor growth inhibition of 90% and 50%, and survival benefit, respectively. Conclusions: These results indicated that specific optimization of PI3K inhibitors to cross the BBB led to potent suppression of the PI3K pathway in healthy brain. The efficacy of GNE-317 in 3 intracranial models of GBM suggested that this compound could be effective in the treatment of GBM. Clin Cancer Res; 18(22); 6239–48. ©2012 AACR.

Abstract The importance of the blood–brain barrier in preventing effective pharmacotherapy of glioblastoma has been controversial. The controversy stems from the fact that vascular endothelial cell tight junctions are disrupted in the tumor, allowing some systemic drug delivery. P-glycoprotein (Pgp) and breast cancer resistance protein (BCRP) efflux drugs from brain capillary endothelial cells into the blood. We tested the hypothesis that although the tight junctions are “leaky” in the core of glioblastomas, active efflux limits drug delivery to tumor-infiltrated normal brain and consequently, treatment efficacy. Malignant gliomas were induced by oncogene transfer into wild-type (WT) mice or mice deficient for Pgp and BCRP (knockout, KO). Glioma-bearing mice were orally dosed with dasatinib, a kinase inhibitor and dual BCRP/PgP substrate that is being currently tested in clinical trials. KO mice treated with dasatinib survived for twice as long as WT mice. Microdissection of the tumor core, invasive rim, and normal brain revealed 2- to 3-fold enhancement in dasatinib brain concentrations in KO mice relative to WT. Analysis of signaling showed that poor drug delivery correlated with the lack of inhibition of a dasatinib target, especially in normal brain. A majority of human glioma xenograft lines tested expressed BCRP or PgP and were sensitized to dasatinib by a dual BCRP/Pgp inhibitor, illustrating a second barrier to drug delivery intrinsic to the tumor itself. These data show that active efflux is a relevant obstacle to treating glioblastoma and provide a plausible mechanistic basis for the clinical failure of numerous drugs that are BCRP/Pgp substrates. Mol Cancer Ther; 11(10); 2183–92. ©2012 AACR.