Multi-omic serum biomarkers for prognosis of disease progression in prostate cancer

Background

Predicting the clinical course of prostate cancer is challenging due to the wide biological spectrum of the disease. The objective of our study was to identify prostate cancer prognostic markers in patients ‘sera using a multi-omics discovery platform.

Methods

Pre-surgical serum samples collected from a longitudinal, racially diverse, prostate cancer patient cohort (N = 382) were examined. Linear Regression and Bayesian computational approaches integrated with multi-omics, were used to select markers to predict biochemical recurrence (BCR). BCR-free survival was modeled using unadjusted Kaplan–Meier estimation curves and multivariable Cox proportional hazards analysis, adjusted for key pathologic variables. Receiver operating characteristic (ROC) curve statistics were used to examine the predictive value of markers in discriminating BCR events from non-events. The findings were further validated by creating a training set (N = 267) and testing set (N = 115) from the cohort.

Results

Among 382 patients, 72 (19%) experienced a BCR event in a median follow-up time of 6.9 years. Two proteins—Tenascin C (TNC) and Apolipoprotein A1V (Apo-AIV), one metabolite—1-Methyladenosine (1-MA) and one phospholipid molecular species phosphatidic acid (PA) 18:0-22:0 showed a cumulative predictive performance of AUC = 0.78 [OR (95% CI) = 6.56 (2.98–14.40), P < 0.05], in differentiating patients with and without BCR event. In the validation set all four metabolites consistently reproduced an equivalent performance with high negative predictive value (NPV; > 80%) for BCR. The combination of pTstage and Gleason score with the analytes, further increased the sensitivity [AUC = 0.89, 95% (CI) = 4.45–32.05, P < 0.05], with an increased NPV (0.96) and OR (12.4) for BCR. The panel of markers combined with the pathological parameters demonstrated a more accurate prediction of BCR than the pathological parameters alone in prostate cancer.

Conclusions

In this study, a panel of serum analytes were identified that complemented pathologic patient features in predicting prostate cancer progression. This panel offers a new opportunity to complement current prognostic markers and to monitor the potential impact of primary treatment versus surveillance on patient oncological outcome.

Cold-Activated Lipid Dynamics in Adipose Tissue Highlights a Role for Cardiolipin in Thermogenic Metabolism

Thermogenic fat expends energy during cold for temperature homeostasis, and its activity regulates nutrient metabolism and insulin sensitivity. We measured cold-activated lipid landscapes in circulation and in adipose tissue by MS/MS^ALL shotgun lipidomics. We created an interactive online viewer to visualize the changes of specific lipid species in response to cold. In adipose tissue, among the approximately 1,600 lipid species profiled, we identified the biosynthetic pathway of the mitochondrial phospholipid cardiolipin as coordinately activated in brown and beige fat by cold in wild-type and transgenic mice with enhanced browning of white fat. Together, these data provide a comprehensive lipid bio-signature of thermogenic fat activation in circulation and tissue and suggest pathways regulated by cold exposure.

A Data-Driven Approach to Predicting Septic Shock in the Intensive Care Unit

Early diagnosis of sepsis and septic shock has been unambiguously linked to lower mortality and better patient outcomes. Despite this, there is a strong unmet need for a reliable clinical tool that can be used for large-scale automated screening to identify high-risk patients. We addressed the following questions: Can a novel algorithm to identify patients at high risk of septic shock 24 hours before diagnosis be discovered using available clinical data? What are performance characteristics of this predictive algorithm? Can current metrics for evaluation of sepsis be improved using novel algorithm? Publicly available data from the intensive care unit setting was used to build septic shock and control patient cohorts. Using Bayesian networks, causal relationships between diagnosis groups, procedure groups, laboratory results, and demographic data were inferred. Predictive model for septic shock 24 hours prior to digital diagnosis was built based on inferred causal networks. Sepsis risk scores were augmented by de novo inferred model and performance was evaluated. A novel predictive model to identify high-risk patients 24 hours ahead of time, with area under curve of 0.81, negative predictive value of 0.87, and a positive predictive value as high as 0.65 was built. The specificity of quick sequential organ failure assessment, systemic inflammatory response syndrome, and modified early warning score was improved when augmented with the novel model, whereas no improvements were made to the sequential organ failure assessment score. We used a data-driven, expert knowledge agnostic method to build a screening algorithm for early detection of septic shock. The model demonstrates strong performance in the data set used and provides a basis for expanding this work toward building an algorithm that is used to screen patients based on electronic medical record data in real time.

12-Lipoxygenase Regulates Cold Adaptation and Glucose Metabolism by Producing the Omega-3 Lipid 12-HEPE from Brown Fat

Distinct oxygenases and their oxylipin products have been shown to participate in thermogenesis by mediating physiological adaptations required to sustain body temperature. Since the role of the lipoxygenase (LOX) family in cold adaptation remains elusive, we aimed to investigate whether, and how, LOX activity is required for cold adaptation and to identify LOX-derived lipid mediators that could serve as putative cold mimetics with therapeutic potential to combat diabetes. By utilizing mass-spectrometry-based lipidomics in mice and humans, we demonstrated that cold and β3-adrenergic stimulation could promote the biosynthesis and release of 12-LOX metabolites from brown adipose tissue (BAT). Moreover, 12-LOX ablation in mouse brown adipocytes impaired glucose uptake and metabolism, resulting in blunted adaptation to the cold in vivo. The cold-induced 12-LOX product 12-HEPE was found to be a batokine that improves glucose metabolism by promoting glucose uptake into adipocytes and skeletal muscle through activation of an insulin-like intracellular signaling pathway.

bAIcis: A Novel Bayesian Network Structural Learning Algorithm and Its Comprehensive Performance Evaluation Against Open-Source Software

Structural learning of Bayesian networks (BNs) from observational data has gained increasing applied use and attention from various scientific and industrial areas. The mathematical theory of BNs and their optimization is well developed. Although there are several open-source BN learners in the public domain, none of them are able to handle both small and large feature space data and recover network structures with acceptable accuracy. bAIcis^® is a novel BN learning and simulation software from BERG. It was developed with the goal of learning BNs from “Big Data” in health care, often exceeding hundreds of thousands features when research is conducted in genomics or multi-omics. This article provides a comprehensive performance evaluation of bAIcis and its comparison with the open-source BN learners. The study investigated synthetic datasets of discrete, continuous, and mixed data in small and large feature space, respectively. The results demonstrated that bAIcis outperformed the publicly available algorithms in structure recovery precision in almost all of the evaluated settings, achieving the true positive rates of 0.9 and precision of 0.8. In addition, bAIcis supports all data types, including continuous, discrete, and mixed variables. It is effectively parallelized on a distributed system and can work with datasets of thousands of features that are infeasible for any of the publicly available tools with a desired level of recovery accuracy.

Abstract 3608: BPM31510 exploits differential redox vulnerabilities between normal and glioblastoma cells to mediate its anti-cancer effect

Glioblastoma is an aggressive cancer, the proliferative capacity of which is correlated with glycolytic metabolism. BPM31510 is a novel formulation for delivery of supraphysiological levels of ubidecarenone to the mitochondria, enabling cancer specific metabolic switches. It is being studied in Phase I clinical trials versus a number of tumors, including glioma. Here, the effects of ubidecarenone on viability and redox homeostasis of glioma and non-tumorigenic cells was assessed using in vitro monoculture and coculture systems and an in vivo preclinical model. BPM31510 administration (50 mg/kg bid i.p., beginning 4-8 days post-inoculation) resulted in over a 20% long term survival rate in C6 tumor-bearing rats. We next compared BPM31510 effects in vitro between glioma lines (rat C6, human U251) and murine NIH3T3 fibroblasts, as a stromal control. In monocultures, decreased growth was observed in glioma lines and NIH3T3 with increasing BPM31510 doses; however, glioma lines were 2-fold more sensitive to BPM31510 compared to NIH3T3 cells (IC50 glioma lines: 230 µM vs IC50 NIH3T3: &gt;460 µM). To investigate the differential sensitivity to BPM31510, a coculture system was developed by coincubating 2 x 105 C6-GFP labeled cells and NIH3T3 cells. After 6 days of coculture, the percentage of C6 relative to NIH3T3 cells was lowest at doses of BPM31510 between 115 µM and 230 µM, evidence of greater sensitivity to BPM31510-induced cytotoxicity in the C6 glioma cells than the non-tumorigenic component. At higher doses, differential effects on cell viability were less apparent. The level of superoxide, a central reactive oxygen species important in redox homeostasis, was also assessed using Mitosox in cocultures. At a BPM31510 dose which resulted in maximal differential viability between C6 and NIH3T3 cells (230 μM), the maximal differential superoxide level was likewise greatest. The basal differential in Mitosox signal was 9-fold between C6 and NIH3T3 cells, and it increased to over 50-fold upon treatment with BPM31510 (230 μM), implying that BPM31510 exploits differential redox vulnerabilities between C6 and NIH3T3 to mediate its anti-cancer activity. At high doses of BPM31510, differential effects on superoxide levels were less apparent. In summary, BPM31510 has marked anti-cancer activity in rats implanted with C6 glioma, and its differential effects on the viability of normal and transformed cells are associated with maximal differences in BPM31510-induced superoxide production. Together, these data suggest that differential redox vulnerabilities between tumorigenic and non-tumorigenic cells may underpin the anti-cancer activity of BPM31510, and identification of in vivo correlates of redox indices may represent an avenue to improved measurement of anti-cancer efficacy as well as define patient populations responsive to BPM31510.

Citation Format: Jiaxin Sun, Seema Nagpal, Chirag Patel, Milton Merchant, Tiachang Jang, Anne R. Diers, Shiva Kazerounian, Stephane Gesta, Niven R. Narain, Rangaprasad Sarangarajan, Lawrence Recht. BPM31510 exploits differential redox vulnerabilities between normal and glioblastoma cells to mediate its anti-cancer effect [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 3608.

Abstract 4900: Dynamic metabolic response of prostate cancer patients treated with ADT and low carb diet

Background: Prostate cancer (PrCa) is one of the most common cancers among men and managed through surgery, hormonal therapy, chemotherapy, radiation, and cryotherapy. Depending on the stage of PrCa, androgen deprivation therapy (ADT) is commonly utilized as an intervention. ADT has proven effective in intervening in PrCa progression, although there are several side effects. Recently, the use of low carb diets has been shown to alter patients’ metabolic phenotype and as such may reduce the side effects of ADT.

Methods: In this study 35 men, who were beginning ADT, were randomized to low carb diet intervention with recommended exercise or control (no lifestyle change) for 6 months. Primary results have been reported showing significant weight loss at both 3-month (17lb, p&lt;0.01) and 6-month (23 lbs, p&lt;0.01) and improved insulin control at 3-month (HOMA=-19 as compared to baseline, p=0.02) but not at 6-month (HOMA=-4 as compared to baseline, p=0.13). For this exploratory analysis, sera collected at baseline, 3, and 6 months was used for metabolomics analysis utilizing GC/MS TOF, QqQ LC-HILIC-MS/MS, and TripleTOF 6600 LC-RP-MS and lipidomics analysis using TripleTOF 5600+ MS/MSALL workflows to quantify the chemical diversity of the metabolome and lipidome.

Results: Over 450 metabolites and 1000 lipid species were quantified. Metabolomics analysis of sera from the control patients (ADT alone) demonstrated alterations in steroid biosynthesis, androgen/estrogen metabolism, fatty acid metabolism, and lysine degradation. Lipidomics analysis of the control patients demonstrated changes in selective long chain polyunsaturated phosphatidylcholine species. Analysis of the ADT plus low carb patients revealed a change in pyruvate, glucose-alanine cycle, selenoamino acid, phenylalanine/tyrosine, and taurine metabolism. Further, lipidomic analysis revealed changes in several triglycerides, plasmalenylethanolamine, and phosphatidic acid species.

Conclusion: In summary, integration of metabolomic and lipidomic analysis in hormonal and metabolic interventions of PrCa patients revealed dynamic changes providing novel insight for tailoring therapeutic intervention and monitoring.

Citation Format: Stephen Freedland, Pao-Hwa Lin, Emily Y. Chen, Vladimir Tolstikov, Jen-Tsan Chi, Rangaprasad Sarangarajan, Niven R. Narain, Michael A. Kiebish. Dynamic metabolic response of prostate cancer patients treated with ADT and low carb diet [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 4900.

Abstract 4945: Project Survival: Engineering a phenomic and artificial intelligence driven precision medicine biomarker pipeline for pancreatic adenocarcinomas

Pancreatic cancer is a complex and dynamic disorder necessitating a comprehensive clinical design integrated with robust OMICS technologies and AI analytics to identify potential molecular and clinical signatures of diagnosis, progression, and treatment outcomes. Project Survival is a multisite prospective longitudinal study currently in the 4th year of a 6 year initiative of sampling and analysis of subjects in 6 categories: healthy volunteers with a first degree relative with pancreatic cancer (N=39), pancreatitis (N=34), pancreatic cystic neoplasm (N=52), suspicious pancreatic masses with pathology other than pancreatic cancer (N=22), early stage (N=66), locally advanced (N=123), and metastatic pancreatic cancer (N=99). All diseased patients are longitudinally sampled multiple times per year for sera, plasma, buffy coat, saliva, urine, and tumor/adjacent normal tissue. The BERG Interrogative Biology® platform is employed for multi-omic mass spectrometry analysis (metabolomics, lipidomics and proteomics) and applies artificial intelligence (bAIcis®, BERG Artificial Intelligence Clinical Information System) technologies. bAIcis® is harnessed to align the multi-omic profiles with longitudinal clinical information to infer probabilistic cause-and-effect relationships among molecular and clinical variables in a network-based model. Multiple longitudinal time points continue to be collected during the course of the six-year timeline enabling dynamic modeling. The value of this longitudinal study is in the epidemiological assessment of patient type progression to more advanced stages and identification of biomarkers and clinical features that align with the shifts observed in the patient populations. Collectively, we are incorporating patient progression with longitudinal sampling to investigate predictive signatures of disease advancement. Biomarker panels with AUC &gt; 0.7 will be pursued in a further prospective clinical study with a larger subject number. The integration of multi-omic analysis with artificial intelligence has identified several biomarker panels that meet numerous unmet needs for the identification and clinical stratification of pancreatic adenocarcinoma.

Citation Format: Eric Michael Grund, Michael A. Kiebish, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, John J. Crowley, Amy Stoll-D'Astice, Tori Singer, Corinne Decicco, Wendy Hori, Abena Darkwah, Lixia Zhang, Valerie Bussberg, Leonardo O. Rodrigues, Emily Y. Chen, Tomislav Dragovich, Manuel Hidalgo, Niven R. Narain, A James Moser. Project Survival: Engineering a phenomic and artificial intelligence driven precision medicine biomarker pipeline for pancreatic adenocarcinomas [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 4945.

Therapeutic benefit of combining calorie-restricted ketogenic diet and glutamine targeting in late-stage experimental glioblastoma

Glioblastoma (GBM) is an aggressive primary human brain tumour that has resisted effective therapy for decades. Although glucose and glutamine are the major fuels that drive GBM growth and invasion, few studies have targeted these fuels for therapeutic management. The glutamine antagonist, 6-diazo-5-oxo-L-norleucine (DON), was administered together with a calorically restricted ketogenic diet (KD-R) to treat late-stage orthotopic growth in two syngeneic GBM mouse models: VM-M3 and CT-2A. DON targets glutaminolysis, while the KD-R reduces glucose and, simultaneously, elevates neuroprotective and non-fermentable ketone bodies. The diet/drug therapeutic strategy killed tumour cells while reversing disease symptoms, and improving overall mouse survival. The therapeutic strategy also reduces edema, hemorrhage, and inflammation. Moreover, the KD-R diet facilitated DON delivery to the brain and allowed a lower dosage to achieve therapeutic effect. The findings support the importance of glucose and glutamine in driving GBM growth and provide a therapeutic strategy for non-toxic metabolic management.

Safety, tolerability, and PK of topical calcitriol formulation for treatment of chemotherapy-induced alopecia (CIA) in patients receiving taxane-based regimen: Final results

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Background: Chemotherapy-induced alopecia (CIA) following taxane-based treatment regimen is due to direct toxicity of these agents on rapidly dividing cells within hair follicles. Currently no oral or topical agents have been approved for prevention of CIA. In murine studies, topical calcitriol reduced CIA, likely due to arrest of cell cycle in healthy hair follicles, and reduction in the sensitivity of follicular epithelium to chemotherapy. Methods: A 3+3 dose-escalation strategy was used in this Phase 1 study with 3-6 patients at six dose levels (5/10/20/40/60/80 μg/mL) were assessed for safety and tolerability of BPM31543. Patients with a diagnosis of breast cancer, gynecologic cancer or sarcomas receiving a taxane-based chemotherapy regimen applied 1mL of the formulation to the scalp BID, ≥ 5 days prior to starting chemotherapy for at least 3 months or until treatment completed. Safety and efficacy assessments included AE monitoring, PK analysis, blinded photographic assessments and patient self-assessment. Results: 22/23 (95.7%) female patients receiving treatment and included in the safety population experienced at least one TEAE. The most frequently experienced TEAEs were alopecia (14 pts; 60.9%), fatigue (11 pts; 47.8%), nausea (9 pts; 39.1%), peripheral sensory neuropathy (7 pts; 30.4%), and maculopapular rash and vitamin D increased each in six patients (26.1%). Of these, elevated vitamin D and rash were possibly or probably related to treatment. Fatigue, nausea, and neuropathy were likely due to chemotherapy. In 18 patients included in the post-dose versus pre-treatment comparison, there was no dose-dependency on systemic levels of calcitriol. Hair loss < 50% from baseline was observed in 8 patients at week 7 that was maintained at week 15 in 2 patients. Conclusions: Study results showed BPM31543 applied topically twice daily to the scalp in patients receiving taxane-based chemotherapy was safe and well-tolerated. No DLT was observed up to 80 µg/mL dose and no MTD level was reached. There was a signal of potential efficacy detected at each dose level. A seamless Phase 2/3 trial strategy for clinical development is planned. Clinical trial information: NCT01588522.

The importance of altruism to biomarker development for pancreatic cancer

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Background: Longitudinal donation of tissue and health information by patients with pancreatic ductal adenocarcinoma (PDAC) is critical to validating algorithms for precision treatment. Unlike therapeutic trials offering potential survival benefit, factors motivating long-term participation in biomarker studies are poorly understood. We hypothesized that long-term participation (PART) depends on identifiable factors motivating study volunteers in non-therapeutic biomarker studies. Methods: A prospective, single-institution biomarker study was screened to identify participants with, or at elevated risk for, PDAC and periampullary cancer (Jul 2015-Dec 2018). Study consent precluded individual receipt of value or research benefit. Detailed biospecimen and clinical data (n = 294) were analyzed using multivariable modeling and Bayesian AI (bAIcis) to characterize motivators of PART. Results: Of 294 participants, 185 had PDAC (63%); 89 had premalignant lesions (30%) or tumors (20; 7%) mimicking PDAC. Mean age was 68 years, 54% male, 26% with prior cancers, and 18% family PDAC history. Treatment was not indicated (37% no cancer), potentially curative (27%), non-curative (35%); or refused (1.4%). Bayesian AI showed PDAC diagnosis to be the leading predictor of PART. Using multivariable modeling and adjusting for the competing risk of death, none of the following domains predicted PART: demographics, perceived personal/family cancer risk, health insurance type, median income, housing price, travel time/distance or charitable expense, or primary institution providing clinical treatment. The following motivators were significant predictors of PART: worsening symptoms (McGill Brisbane > 9; HR 0.54; p = 0.045), non-curative treatment (HR 0.55; p = 0.042); and shorter AJCC predicted survival (HR 0.77, p = 0.042). Conclusions: Volunteers with symptomatic PDAC and shorter predicted survival who received non-curative treatment were more motivated to participate in biomarker discovery. Volunteers were undeterred by apparent self-interests such as travel time, insurance type, income, charitable expense, and personal life expectancy. We attribute these findings to altruistic behaviors among patients most likely to die of PDAC.

Adapted MS/MSALL Shotgun Lipidomics Approach for Analysis of Cardiolipin Molecular Species

Cardiolipin (Ptd₂ Gro) is a complex, doubly charged phospholipid located in the inner mitochondrial membrane where it plays an essential role in regulating bioenergetics. Abnormalities in Ptd₂ Gro content or composition have been associated with mitochondrial dysfunction in a variety of disease states. Here, we report the development of an adapted high-resolution data-independent acquisition (DIA) MS/MS^ALL shotgun lipidomic method to enhance the accuracy and reproducibility of Ptd₂ Gro molecular species quantitation from biological samples. Utilizing the doubly charged molecular ions and the isotopic pattern with negative mode electrospray ionization mass spectrometry (ESI-MS) using an adapted MS/MS^ALL approach, we profiled more than 150 individual Ptd₂ Gro species, including monolysocardiolipin (MLPtd₂ Gro). The method described in this study demonstrated high reproducibility, sensitivity, and throughput with a wide dynamic range. This high-resolution MS/MS^ALL shotgun lipidomics approach could be extended to screening aberrations of Ptd₂ Gro metabolism involved in mitochondrial dysfunction in various pathological conditions and diseases.

Genomic alterations of Tenascin C in highly aggressive prostate cancer: a meta-analysis

Tenascin C (TNC), an extra-cellular matrix (ECM) family gene, is expressed in several cancer tissues of breast, lung, colon, and gastrointestinal tract leading to proliferation, migration, invasion, angiogenesis and metastasis, but its role in tumorigenesis of prostate cancer is poorly understood. We took a meta-analysis approach to characterize the alterations of TNC gene in prostate cancer using publicly available databases (cBioportal Version 2.2.0, http://www.cBioportal.org/index.do). The analysis identified TNC alterations (gene amplification) significantly in the neuroendocrine prostate cancer dataset (Trento/Broad/Cornell, N = 114), which was further validated in other prostate cancer datasets, including The Cancer Genome Atlas (TCGA) prostate cancer (2015). In the TCGA prostate cancer dataset (N = 498), high TNC (alteration frequency, 36%) revealed a strong association with high diagnostic Gleason score. Genomic alterations of TNC was also significantly associated (P < 0.05) with expression level of genes from NOTCH, SOX and WNT family, implicating a link between TNC and poorly differentiated aggressive phenotype in NEPC. TCGA prostate adenocarcinoma cases with TNC alteration also demonstrated prominent decrease in disease-free survival (P = 0.0637). These findings indicate a possible association of TNC to the aggressive subtype of prostate cancer and warrant further functional studies to evident the involvement of TNC in prostate cancer progression.

Regulation of Human Adipose Tissue Activation, Gallbladder Size, and Bile Acid Metabolism by a β3-Adrenergic Receptor Agonist

β3-adrenergic receptor (AR) agonists are approved to treat only overactive bladder. However, rodent studies suggest that these drugs could have other beneficial effects on human metabolism. We performed tissue receptor profiling and showed that the human β3-AR mRNA is also highly expressed in gallbladder and brown adipose tissue (BAT). We next studied the clinical implications of this distribution in 12 healthy men given one-time randomized doses of placebo, the approved dose of 50 mg, and 200 mg of the β3-AR agonist mirabegron. There was a more-than-dose-proportional increase in BAT metabolic activity as measured by [18F]-2-fluoro-D-2-deoxy-d-glucose positron emission tomography/computed tomography (medians 0.0 vs. 18.2 vs. 305.6 mL ⋅ mean standardized uptake value [SUVmean] ⋅ g/mL). Only the 200-mg dose elevated both nonesterified fatty acids (68%) and resting energy expenditure (5.8%). Previously undescribed increases in gallbladder size (35%) and reductions in conjugated bile acids were also discovered. Therefore, besides urinary bladder relaxation, the human β3-AR contributes to white adipose tissue lipolysis, BAT thermogenesis, gallbladder relaxation, and bile acid metabolism. This physiology should be considered in the development of more selective β3-AR agonists to treat obesity-related complications.

Dysregulation of the calcium handling protein, CCDC47, is associated with diabetic cardiomyopathy

Background

Diabetes mellitus is associated with an increased risk in diabetic cardiomyopathy (DCM) that is distinctly not attributed to co-morbidities with other vasculature diseases. To date, while dysregulation of calcium handling is a key hallmark in cardiomyopathy, studies have been inconsistent in the types of alterations involved. In this study human cardiomyocytes were exposed to an environmental nutritional perturbation of high glucose, fatty acids, and l-carnitine to model DCM and iTRAQ-coupled LC–MS/MS proteomic analysis was used to capture proteins affected by the perturbation. The proteins captured were then compared to proteins currently annotated in the cardiovascular disease (CVD) gene ontology (GO) database to identify proteins not previously described as being related to CVD. Subsequently, GO analysis for calcium regulating proteins and endoplasmic/sarcoplasmic reticulum (ER/SR) associated proteins was carried out.

Results

Here, we identified CCDC47 (calumin) as a unique calcium regulating protein altered in our in vitro nutritional perturbation model. The cellular and functional role of CCDC47 was then assessed in rat cardiomyocytes. In rat H9C2 myocytes, overexpression of CCDC47 resulted in increase in ionomycin-induced calcium release and reuptake. Of interest, in a diet-induced obese (DIO) rat model of DCM, CCDC47 mRNA expression was increased in the atrium and ventricle of the heart, but CCDC47 protein expression was significantly increased only in the atrium of DIO rats compared to lean control rats. Notably, no changes in ANP, BNP, or β-MHC were observed between DIO rats and lean control rats.

Conclusions

Together, our in vitro and in vivo studies demonstrate that CCDC47 is a unique calcium regulating protein that is associated with early onset hypertrophic cardiomyopathy.

Electronic supplementary material

The online version of this article (10.1186/s13578-018-0244-0) contains supplementary material, which is available to authorized users.

Prophylactic ketamine alters nucleotide and neurotransmitter metabolism in brain and plasma following stress

Recently, we have shown that ketamine given prior to stress exposure protects against the development of depressive-like behavior in mice. These data suggest that it may be possible to prevent the induction of affective disorders before they develop by administering prophylactic pharmaceuticals, a relatively nascent and unexplored strategy for psychiatry. Here, we performed metabolomics analysis of brain and plasma following prophylactic ketamine treatment in order to identify markers of stress resilience enhancement. We administered prophylactic ketamine in mice to buffer against fear expression. Following behavioral analyses, untargeted metabolomic profiling was performed on both hemispheres of the prefrontal cortex (PFC) and the hippocampus (HPC), and plasma. We found that prophylactic ketamine attenuated learned fear. Eight metabolites were changed in the PFC and HPC upon ketamine treatment. Purine and pyrimidine metabolism were most significantly changed in the HPC, PFC, and, interestingly, plasma of mice two weeks after prophylactic administration. Moreover, most precursors to inhibitory neurotransmitters were increased whereas precursors to excitatory neurotransmitters were decreased. Strikingly, these long-term metabolomic changes were not observed when no stressor was administered. Our results suggest that prophylactic treatment differentially affects purine and pyrimidine metabolism and neurotransmission in brain and plasma following stress, which may underlie the long-lasting resilience to stress induced by a single injection of ketamine. These data may provide novel targets for prophylactic development, and indicate an interaction effect of prophylactic ketamine and stress. To our knowledge, this is the first study that identifies metabolomic alterations and biomarker candidates for prophylactic ketamine efficacy in mice.

Abstract 4915: Preclinical pharmacology and toxicology of intravenous BPM31510, a coenzyme Q10-containing lipid nanodispersion

Coenzyme Q10 (CoQ10) plays an important role in cellular metabolism with redox capabilities beyond the mitochondria. Although, the role of CoQ10 in providing benefit in diseases such as cardiovascular, neurodegeneration, and cancer is well established, it has been limited by the absence of delivery methods to achieve physiologically relevant bio-availability. BPM31510 is a CoQ10 (ubidecarenone) containing lipid nanodispersion that delivers supraphysiological concentrations of CoQ10 to tissues, cells and mitochondria. BPM31510 is currently in clinical trials for the treatment of solid tumors including pancreatic cancer and glioblastoma multiforme. This study describes the preclinical pharmacokinetic (PK) and toxicokinetic assessment of BPM31510 (62.5, 125, and 250 mg/kg) after acute (single) intravenous (IV) administration and chronic (3 times a week for 4 weeks), and after a two week recovery from the last exposure in rats. Here, it was demonstrated that the formulation enables an effective delivery of CoQ10 with a robust increase in plasma level and dose-dependent accumulation in several tissues. PK analysis of mean plasma concentration of CoQ10 after a single and repeat dose administration revealed a dose proportion effect on peak (Cmax) and total exposure (AUC0-t). Tissue analysis of CoQ10 levels demonstrates a dose-dependent increase in liver, lung and pancreas 72 hours post-last dose. A dose dependent elimination was observed in both male and females. No difference in pharmacokinetic of CoQ10 using this formulation was observed between males and females. Notably, chronic exposure to BPM31510 does not lead to toxicities as assessed by hematology and coagulation, clinical chemistry, histopathology and gross necropsy. These results indicate that the effective delivery and bioavailability of supraphysiological levels of CoQ10 after IV administration of BPM31510 is well tolerated.

Citation Format: David Linsenmayer, Shiva Kazerounian, Khampaseuth Thapa, Carrie Spencer, Aishwarya Sarma, John McCook, Stephane Gesta, Vivek Vishnudas, Niven R. Narain, Rangaprasad Sarangarajan. Preclinical pharmacology and toxicology of intravenous BPM31510, a coenzyme Q10-containing lipid nanodispersion [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 4915.

Abstract LB-219: Clinical utility of a serum protein biomarker panel (FLNA, KRT19) in stratification of prostate cancer from benign prostate hyperplasia patients

Background: Prostate-specific antigen (PSA) based screening tests have been considered as a benchmark for PCa diagnosis (PSA &gt;4 ng/mL), however, in recent years their use has been widely debated due to various limitations. In particular, increased PSA levels are also observed in patients with benign prostatic hyperplasia (BPH) thus generating a false positive. These patients are often subjected to unnecessary prostate biopsies and have to endure both physical and mental anguish. Thus, there is a clear unmet need to develop molecular diagnostics that stratifies men with BPH from those that have PCa and prevent unwarranted prostate biopsies in symptomatic, DRE negative men. Here in, we demonstrate clinical utility of a validated biomarker panel (FLNA, KRT 19) in combination with age and prostate volume in stratifying BPH from PCa patients.

Methods: This study was conducted using retrospectively collected and clinically annotated serum samples from 203 BPH patients and 333 PCa patients with PSA values ranging from 4-10ng/mL. These samples included BPH patients with negative Digital Rectum Exam, single biopsy and repeat biopsies, and prostate cancer patients undergoing radical prostatectomy. Validated bioanalytical assays (FLNA ELISA, FLNA IPMRM and KRT19 ELISA) were used to quantitate the serum biomarkers. Regression models were built and compared for their ability to distinguish patients with BPH from those with PCa.

Results: Table 1: Summary of predictive power analysis of PCa panel (49 characters)

BERG TestPSAAUC0.80.54Sensitivity0.8n/aSpecificity0.62n/aPPV0.78n/aNPV0.65n/aOR (CI)6.67 (4.49,9.90)n/a

Conclusion: The data demonstrates that these PCa biomarkers in combination with age, and prostatic volume were significantly better than (0.8) PSA (0.54 AUC in this population) in identifying men with BPH rather than PCa thus preventing unnecessary biopsies for this population. Moreover, this panel may be used in clinical decision support to physicians to fill a clinical unmet need.

Citation Format: Michael A. Kiebish, Poornima Tekmulla, Shobha Ravipaty, Wenfang Wu, Tracey Friss, Chenchen Liao, Allison Klotz, Joe Andreazi, Elisabeth Hutchins, Albert Dobi, Shiv Srivastava, Jennifer Cullen, Amina Ali, Stephen Freedland, Kagan Griffin, Sandra Laszlo, Michele Petrovic, Neil Fleshner, Jeonifer Garren, Leonardo Rodrigues, Mark D. Kellog, Viatcheslav R. Akmaev, Rangaprasad Sarangarajan, Niven R. Narain. Clinical utility of a serum protein biomarker panel (FLNA, KRT19) in stratification of prostate cancer from benign prostate hyperplasia patients [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-219.

Abstract 3530: Coenzyme Q10 (BPM31510-IV in clinical trials) increases mitochondrial Q-pool and modulates electron transport chain function to elicit cell death in pancreatic cancer cells

Mitochondria play a multifaceted role in tumorigenesis through regulation of energy production, biomass, redox state, and engagement of cell death pathways. The mitochondrial Q (coenzyme Q10)-pool facilitates electron transport from Complexes I and II to III and is essential for regulating these activities. Therefore, altering mitochondrial Q-pool homeostasis represents a potential therapeutic strategy in cancer. BPM 31510 is a Coenzyme Q10 containing lipid nanodispersion currently in clinical trials for pancreatic cancer. Here, we used BPM 31510 to assess how modulation of mitochondrial Q-pool homeostasis impacts mitochondrial electron transport chain function to activate regulated cell death. Pancreatic cancer cell lines (MIA PaCa-2 and Panc-1) represent models with sensitivity to BPM 31510 both in vitro and in vivo. Treatment with BPM 31510 (EC50 dose, 24 h) resulted in significant mitochondrial enrichment of CoQ10 compared to other subcellular compartments, and quantitatively, CoQ10 levels were 100 times higher in mitochondria isolated from BPM 31510 treated cells over untreated controls (MIA PaCa-2 untreated, 0.31 nmol/mg; treated, 39.4 nmol/mg; Panc1 untreated, 0.21 nmol/mg; treated, 29.3 nmol/mg). Alterations in mitochondrial respiration characterized by dose-dependent decreases in succinate- or glycerol-3-phosphate-fueled respiration were observed in cells treated with BPM 31510, while pyruvate or TMPD/ascorbate-fueled respiration was only modestly affected, suggesting that BPM31510 specifically impairs respiratory responses dependent on Complexes II/III. Moreover, in the presence of multiple mitochondrial substrates, total respiratory capacity was decreased and reliance on pyruvate (Complex I)-fueled respiration was increased with BPM 31510 treatment, indicative of bioenergetic remodeling. Concomitantly to BPM 31510-dependent changes in mitochondrial respiratory responses, BPM 31510 exposure increased oxidation of the reactive oxygen species (ROS) probes, CellROX Green and DCF-DA, increased oxidized glutathione, and decreased levels of the cellular reducing equivalent NADPH. Importantly, BPM 31510-induced death could be partially rescued by agents which alleviate electron transport chain impairment linking respiratory function to the anti-cancer mechanism of action of BPM 31510. Together, these data indicate that BPM31510 directly impairs the mitochondrial Q-pool and respiratory function resulting in oxidative stress and consequential cell death and thus provide mechanistic understanding of the anti-cancer activity of BPM31510.

Citation Format: Pallavi Awate, Tulin Dadali, Ryan Ng, Saie Mogre, Anne R. Diers, Hannah Rockwell, Justice McDaniel, Emily Chen, Fei Gao, Michael Kiebish, Stephane Gesta, Vivek Vishnudas, Niven R. Narain, Rangaprasad Sarangarajan. Coenzyme Q10 (BPM31510-IV in clinical trials) increases mitochondrial Q-pool and modulates electron transport chain function to elicit cell death in pancreatic cancer cells [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 3530.

Abstract 4724: Immuno-modulatory activity of BPM31510 supports T cell viability, proliferation, and function while reversing early signs of exhaustion

Regulation of mitochondrial metabolism is crucial to alter immune cell differentiation and function; therefore, therapeutic agents which regulate mitochondrial metabolism may have efficacy in immune-mediated tumor elimination. BPM31510 is a clinical stage, nanodispersion of ubidecarenone (coenzyme Q10), an electron transfer molecule in the mitochondrial electron transport chain required for oxidative phosphorylation. Here, we used BPM31510 to assess the role of CoQ10 in the regulation of T cell function. Healthy donor peripheral blood mononuclear cells (PBMCs) activated ex vivo with αCD3/CD28 beads were used as model system to test the effects of BPM31510 on viability and functionality of T cell subpopulations. In contrast to its ability to initiate regulated cell death in cancer cells, treatment of PBMCs with increasing concentrations of BPM31510 lead to an increased frequency of viable CD3+ cells. Further phenotypic analysis revealed that cytotoxic T cells (CD8+/CD3+) and T helper cells (CD4+/CD3+), as well as NKT cells (CD56+/CD3+), contributed to the observed increase in T cell frequency. Proliferation measurements by EdU-incorporation indicated enhanced cytotoxic T cell proliferation in BPM31510 treated PBMCs, and likewise, BPM31510 increased degranulation of activated cytotoxic T cells, as indicated by measurement of plasma membrane-exposed lysosomal-associated membrane protein 1 (CD107a). Consistent with the ex vivo observations, in vivo studies using the syngeneic MC38 murine tumor model demonstrated that BPM31510 administration resulted in a dose-dependent enhancement of the number of CD3+ cells in the tumor microenvironment with cytotoxic T cells (CD8+/CD3+) representing the largest population. Together, these data define a supportive effect of BPM31510 on T cell frequency, viability, and functionality. In addition, in ex vivo activated PBMCs, BPM31510 decreased the percentage of PD1+ T cells while simultaneously increasing the percentage of PD1- T cells in the population. Moreover, in the PD1+ T cell population, PD1 expression on the cell surface was increased while PD1- T cells experienced no change in cell surface expression of PD1. These data suggest BPM31510 treatment promotes highly functional cytotoxic T cells while cells with early signs of exhaustion are induced to follow the path of exhaustion and elimination. Collectively, these results define an immune-modulatory activity for BPM31510, particularly in the T cell compartment, in part, through regulation of T cell exhaustion; this may have important implications for the use of BPM31510 in ‘immunologically cold' tumor types or in combination with immune checkpoint blockade strategies.

Citation Format: Maria Nastke, Shiva Kazerounian, Nidhi Gaur, Shyamali Jayashankar, David Linsenmayer, Carrie Spencer, Arun Nambiar, Aishwarya Sarma, Anne R. Diers, Stephane Gesta, Vivek Vishnudas, Vikas P. Sukhatme, Niven R. Narain, Rangaprasad Sarangarajan. Immuno-modulatory activity of BPM31510 supports T cell viability, proliferation, and function while reversing early signs of exhaustion [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 4724.

Abstract 873: BPM 31510, a clinical stage metabolic modulator, demonstrates therapeutic efficacy in glioblastoma models of temozolomide chemo-sensitive and resistance by targeting mitochondrial function

BPM31510 is a metabolic modulating agent composed of a parenteral nanodispersion of ubidecarenone which is currently in clinical studies for glioblastoma. Glioblastoma is a highly metabolic and aggressive malignancy with limited treatment options and dismal median survival. Temozolomide (TMZ) as a first line treatment option, however, 90% of recurrent gliomas acquire TMZ chemoresistance. Recently, acquisition to TMZ resistance has been correlated to alterations in mitochondrial metabolism. Thus, in the present study we sought to investigate whether BPM31510 could elicit anti-cancer activity in TMZ naïve and TMZ-chemoresistant glioma models. In vitro, in a 2D model BPM31510 treatment demonstrated anti-cancer activity in a panel of glioma cell lines (rat C6 and human U251-MG and U87-MG), and this effect was translatable in spheroidal 3D cultures. Importantly, in an aggressive rat C6 orthotopic glioma model, treatment with BPM31510 (50mg/kg/day, b.i.d) starting between 4 and 8 days post-implantation resulted in a 32% cure rate compared to 0% in controls (P &lt; 0.001, Fisher's exact test), demonstrating an improved survival (P &lt; 0.01, log rank survival), despite producing a minimal change in median survival (13 vs. 12 days). A marked increase in caspase3 staining was observed in tumors from BPM31510 treated animals compared to controls assessed at a similar time point post-tumor implantation, suggesting a strong apoptotic effect of this agent in vivo. Next, BPM31510 was examined in a cellular model of acquired TMZ resistance (TMZ-R) generated by exposing parental (chemosensitive naïve) U251-MG and U87-MG cells to increasing concentrations of TMZ for 9-12 months. Similar to parental cells, BPM31510 displayed anti-cancer activity in both TMZ-R cell models, as decreased cell viability and an increase in the percentage of apoptotic cells was observed upon BPM31510 treatment. Consistent with prior studies, compared to parental cells, TMZ-R cells demonstrated metabolic rewiring characterized by increases in mitochondrial function parameters and decreased extracellular acidification rate, indicative of glycolytic flux. Regardless of chemosensitivity, BPM31510 decreased mitochondrial substrate oxidation (e.g., succinate, glycerol-3-phosphate) at doses which induce cell death. Concomitantly, increases in the reactive oxygen species production were observed with BPM 31510 treatment in both parental and TMZ-R cell lines. Together, these data define a link between regulation of mitochondrial function and the anti-cancer activity of BPM31510 in both TMZ chemo-sensitive and resistant glioblastoma models, demonstrating a distinct approach in targeting mitochondrial metabolism for the treatment of this clinically intractable disease.

Citation Format: Tulin Dadali, Shreya Kulkarni, Ryan Ng, Pallavi Awate, Saie Mogre, Anne R. Diers, Taichang Jang, Milton Merchant, Jiaxin Sun, Stephane Gesta, Khampaseuth Thapa, Seema Nagpal, Lawrence Recht, Niven R. Narain, Rangaprasad Sarangarajan. BPM 31510, a clinical stage metabolic modulator, demonstrates therapeutic efficacy in glioblastoma models of temozolomide chemo-sensitive and resistance by targeting mitochondrial function [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 873.