Abstract 1331: Inhibition of mitochondrial reprogramming regulated c-Src in triple-negative breast cancer activates autophagy-mediated survival mechanism

c-Src is a proto-oncogene involved in signaling that culminates in the control of multiple biological functions. Src is also one of the most frequently upregulated pathways in triple negative breast cancer (TNBC). Dysregulation of Src has been detected in TNBC and is strongly associated with tumor metastasis and poor prognosis. However, even after promising preclinical studies, Src inhibitors did not show major clinical advantage in unselected TNBC populations. Thus, understanding the mechanism of drug resistance to Src inhibition has major clinical significance in TNBC patients. The full activation of Src signature depends on the autophosphorylation at Y419 that allows the substrate to gain access. We have previously published that metastatic TNBC has high energy-dependency to mitochondrial fatty acid beta-oxidation (FAO) and FAO activate Src by inducing autophosphorylation at Y419. However, our recent analysis suggests that as observed with the Src inhibitors, treatment with FAO inhibitors only attenuate the TNBC tumor growth, but do not result in complete regression. Evaluation of their drug resistance mechanism revealed that while short-term inhibition of FAO or Src induces autophagic and apoptotic cell deaths, long-term inhibition results in autophagy-mediated drug resistance and survival. Studies using p53 knocked out TNBC cells confirmed that the autophagy-mediated resistance to Src inhibition is independent of their p53 status. Further analyses suggest that FAO and Src inhibitors increase the phosphorylation of ERK1/2 in TNBC. Treatment with MAPK/ERK inhibitors abolished the FAO or Src inhibitor-mediated autophagy activation. Validation of in vitro findings using in vivo TNBC patient-derived xenograft (PDX) models confirmed that Src inhibition enhances ERK1/2 activity and induces autophagy in TNBC. Overall, our results suggest that long-term FAO or Src inhibition results in ERK-mediated autophagy activation and therapeutic resistance in TNBC. This finding will have major therapeutic impact in the management of currently non-targetable aggressive TNBC.

Citation Format: Kwang Hwa Jung, Jun Hyoung Park, Tirupataiah Sirupangi, Dongya Jia, Shivanand Pudakalakatti, Nishant Gandhi, Jessica Elswood, Vasanta Putluri, Chad J. Creighton, Weston Porter, Michael T. Lewis, Xi Chen, Nagireddy Putluri, Pratip K. Bhattacharya, Lee-Jun C. Wong, Gokul M. Das, Benny A. Kaipparettu. Inhibition of mitochondrial reprogramming regulated c-Src in triple-negative breast cancer activates autophagy-mediated survival mechanism [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 1331.

Dimethyl fumarate targets GAPDH and aerobic glycolysis to modulate immunity

Activated immune cells undergo a metabolic switch to aerobic glycolysis akin to the Warburg effect, thereby presenting a potential therapeutic target in autoimmune disease. Dimethyl fumarate (DMF), a derivative of the Krebs cycle intermediate fumarate, is an immunomodulatory drug used to treat multiple sclerosis and psoriasis. Although its therapeutic mechanism remains uncertain, DMF covalently modifies cysteine residues in a process termed succination. We found that DMF succinates and inactivates the catalytic cysteine of the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in mice and humans, both in vitro and in vivo. It thereby down-regulates aerobic glycolysis in activated myeloid and lymphoid cells, which mediates its anti-inflammatory effects. Our results provide mechanistic insight into immune modulation by DMF and represent a proof of concept that aerobic glycolysis is a therapeutic target in autoimmunity.

Cisplatin generates oxidative stress which is accompanied by rapid shifts in central carbon metabolism

Cisplatin is commonly utilized in the treatment of solid tumors. Its mechanism of action is complex and multiple mechanisms of resistance have been described. We sought to determine the impact of cisplatin-generated oxidative stress on head and neck squamous cell carcinoma (HNSCC) proliferation, survival and metabolic activity in order to identify a potential metabolic signature associated with cisplatin response. DNA-bound cisplatin represents a small fraction of total intra-cellular cisplatin but generates a robust oxidative stress response. Neutralization of oxidative stress reverses cisplatin toxicity independent of the mechanism of cell death and TP53 mutational status. Cisplatin-induced oxidative stress triggers rapid shifts in carbon flux in 3 commonly utilized catabolic pathways: glycolysis, pentose phosphate pathway and citric acid cycle. Among these metabolic shifts, decreased flux from pyruvate into lactate is the only metabolic effect consistently observed across multiple HNSCC cell lines of varying genomic backgrounds and may reflect differential cisplatin sensitivity. Oxidative stress is a critical component of cisplatin cytotoxicity in HNSCC and is reflected in acute changes in carbon flux from pyruvate into lactate. This suggests that lactate may contribute to a metabolic signature of acute cisplatin toxicity, and could prove useful in optimizing cisplatin-based treatment regimens in HNSCC.

High throughput microscopy identifies bisphenol AP, a bisphenol A analog, as a novel AR down-regulator

Prostate cancer remains a deadly disease especially when patients become resistant to drugs that target the Androgen Receptor (AR) ligand binding domain. At this stage, patients develop recurring castrate-resistant prostate cancers (CRPCs). Interestingly, CRPC tumors maintain dependency on AR for growth; moreover, in CRPCs, constitutively active AR splice variants (e.g., AR-V7) begin to be expressed at higher levels. These splice variants lack the ligand binding domain and are rendered insensitive to current endocrine therapies. Thus, it is of paramount importance to understand what regulates the expression of AR and its splice variants to identify new therapeutic strategies in CRPCs. Here, we used high throughput microscopy and quantitative image analysis to evaluate effects of selected endocrine disruptors on AR levels in multiple breast and prostate cancer cell lines. Bisphenol AP (BPAP), which is used in chemical and medical industries, was identified as a down-regulator of both full length AR and the AR-V7 splice variant. We validated its activity by performing time-course, dose-response, Western blot and qPCR analyses. BPAP also reduced the percent of cells in S phase, which was accompanied by a ~60% loss in cell numbers and colony formation in anchorage-independent growth assays. Moreover, it affected mitochondria size and cell metabolism. In conclusion, our high content analysis-based screening platform was used to classify the effect of compounds on endogenous ARs, and identified BPAP as being capable of causing AR (both full-length and variants) down-regulation, cell cycle arrest and metabolic alterations in CRPC cell lines.

ADHFE1 is a breast cancer oncogene and induces metabolic reprogramming

Metabolic reprogramming in breast tumors is linked to increases in putative oncogenic metabolites that may contribute to malignant transformation. We previously showed that accumulation of the oncometabolite, 2-hydroxyglutarate (2HG), in breast tumors was associated with MYC signaling, but not with isocitrate dehydrogenase (IDH) mutations, suggesting a distinct mechanism for increased 2HG in breast cancer. Here, we determined that D-2HG is the predominant enantiomer in human breast tumors and show that the D-2HG-producing mitochondrial enzyme, alcohol dehydrogenase, iron-containing protein 1 (ADHFE1), is a breast cancer oncogene that decreases patient survival. We found that MYC upregulates ADHFE1 through changes in iron metabolism while coexpression of both ADHFE1 and MYC strongly enhanced orthotopic tumor growth in MCF7 cells. Moreover, ADHFE1 promoted metabolic reprogramming with increased formation of D-2HG and reactive oxygen, a reductive glutamine metabolism, and modifications of the epigenetic landscape, leading to cellular dedifferentiation, enhanced mesenchymal transition, and phenocopying alterations that occur with high D-2HG levels in cancer cells with IDH mutations. Together, our data support the hypothesis that ADHFE1 and MYC signaling contribute to D-2HG accumulation in breast tumors and show that D-2HG is an oncogenic metabolite and potential driver of disease progression.

Tobacco-Specific Carcinogens Induce Hypermethylation, DNA Adducts, and DNA Damage in Bladder Cancer

Smoking is a major risk factor for the development of bladder cancer; however, the functional consequences of the carcinogens in tobacco smoke and bladder cancer-associated metabolic alterations remain poorly defined. We assessed the metabolic profiles in bladder cancer smokers and non-smokers and identified the key alterations in their metabolism. LC/MS and bioinformatic analysis were performed to determine the metabolome associated with bladder cancer smokers and were further validated in cell line models. Smokers with bladder cancer were found to have elevated levels of methylated metabolites, polycyclic aromatic hydrocarbons, DNA adducts, and DNA damage. DNA methyltransferase 1 (DNMT1) expression was significantly higher in smokers than non-smokers with bladder cancer. An integromics approach, using multiple patient cohorts, revealed strong associations between smokers and high-grade bladder cancer. In vitro exposure to the tobacco smoke carcinogens, 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone and benzo[a]pyrene (BaP) led to increase in levels of methylated metabolites, DNA adducts, and extensive DNA damage in bladder cancer cells. Cotreatment of bladder cancer cells with these carcinogens and the methylation inhibitor 5-aza-2'-deoxycytidine rewired the methylated metabolites, DNA adducts, and DNA damage. These findings were confirmed through the isotopic-labeled metabolic flux analysis. Screens using smoke-associated metabolites and DNA adducts could provide robust biomarkers and improve individual risk prediction in bladder cancer smokers. Noninvasive predictive biomarkers that can stratify the risk of developing bladder cancer in smokers could aid in early detection and treatment. Cancer Prev Res; 10(10); 588-97. ©2017 AACR.

Expression of ganglioside GD2, reprogram the lipid metabolism and EMT phenotype in bladder cancer

High-grade Bladder Cancer (BLCA) represents the most aggressive and treatment-resistant cancer that renders the patients with poor survival. However, only a few biomarkers have been identified for the detection and treatment of BLCA. Recent studies show that ganglioside GD2 can be used as cancer biomarker and/or therapeutic target for various cancers. Despite its potential relevance in cancer diagnosis and therapeutics, the role of GD2 is unknown in BLCA. Here, we report for the first time that high-grade BLCA tissues and cell lines have higher expression of GD2 compared to low-grade by high-resolution Mass Spectrometry. The muscle invasive UMUC3 cell line showed high GD2, mesenchymal phenotype, and cell proliferation. Besides, we have shown the cancer stem cells (CSC) property (CD44hiCD24lo) of GD2+ UMUC3 and J82 cells. Also, the evaluation of lipid metabolism in GD2+ BLCA cell lines revealed higher levels of Phosphatidylinositol (PI), Phosphatidic acid (PA), Cardiolipin (CL) and lower levels of Phosphatidylserine (PS), plasmenyl-phosphatidylethanolamines (pPE), plasmenyl-phosphocholines (pPC), sphingomyelins (SM), triglycerides (TGs) and N-Acetylneuraminic acid. These findings are significantly correlated with the tissues of BLCA patients. Based on this evidence, we propose that GD2 may be used as an effective diagnostic and therapeutic target for aggressive BLCA.

Abstract 2518: Accumulation of a liver- and microbiome-derived metabolite in human breast tumors is associated with patient survival

Breast cancer is the most common cancer in women in the United States. Gene expression profiling studies of breast tumors led to the discovery of disease subtypes with different biologies. These studies also described novel biomarkers for therapy response and disease survival. However, it remains a challenge to define breast cancer biology solely based on gene expression. Recently, metabolomics emerged as a new discovery tool with the promise of identifying prognostic biomarkers and targetable metabolic dependencies of cancer cells. We previously measured the abundance of 536 metabolites in 67 breast tumor and their tumor adjacent noncancerous tissue by untargeted mass spectrometry. In the current study, we explored the prognostic power of the metabolome and conducted an integrated analysis comprising of the metabolome, transcriptome, and proteome to explore the association of metabolites with cell systems, tumor biology, and disease outcome. We built a predictive model based on multivariable Cox proportional hazards using the L1 penalized log partial likelihood (LASSO) method after pre-selecting prognostic metabolites following cross-validation with 1000 iterations. The median C-index was 0.73, indicating a certain robustness of metabolites as classifiers of breast cancer outcome. The models identified five metabolites including a bile acid-related metabolite, glycochenodeoxycholate (GCDC), as the most frequently selected features and outcome markers among these metabolites. An increased GCDC tumor content was associated with improved patient survival. We corroborated the presence of GCDC and three other bile acids in the human breast tissues using absolute measurements and confirmed their occurrence in breast tumors. Because additional large-scale transcriptome and proteome data were available for the same tissue samples, we further characterized the tumors based on their GCDC abundance, which showed that cell cycle-related pathways were enriched for differently expressed genes and tumors with a high GCDC content tended to have a low cell proliferation score, indicating that accumulation of GCDC leads to growth inhibition. We also conducted a correlation analysis for the relationship between GCDC abundance with other metabolites and identified 51 metabolites that were significantly correlated with GCDC. In this analysis, metabolite abundance in the sterol/steroid pathway associated most strongly with the GCDC tissue content. Lastly, we evaluated the effect of bile acids on breast cancer cell lines. The data showed a strong reduction of cancer cell proliferation under bile acid treatment, consistent with the tumor data, and distinct changes in gene expression. In conclusion, we propose that integrated metabolomics can provide powerful prognostic information with GCDC being a novel prognostic marker in breast cancer because accumulation of GCDC reduces cancer cell proliferation.

Citation Format: Wei Tang, Tiffany Dorsey, Vasanta Putluri, Nagireddy Putluri, Stefan Ambs. Accumulation of a liver- and microbiome-derived metabolite in human breast tumors is associated with patient survival [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 2518. doi:10.1158/1538-7445.AM2017-2518

Abstract P6-01-07: Mitochondria-nuclear communication regulates epithelial-mesenchymal transition and metastasis in triple negative breast cancer

For triple negative breast cancer (TNBC), the driver pathways are still poorly understood. Advances in cancer metabolism research over the last decade have enhanced and modified our understanding on Warburg effect. It is now known that mitochondria in tumors are not always defective in their ability to carry out oxidative phosphorylation. Instead, in proliferating cells, mitochondrial energy pathways are reprogrammed to meet the challenges of macromolecular synthesis and to escape from apoptosis. Tumor initiating cells (TICs) maintain cancer stem cell properties and are known to play significant role in TNBC metastasis. Mitochondrial retrograde regulation (MRR) is a bidirectional communication between mitochondria and nucleus. MRR is triggered by mitochondrial functional demands and it responds in a continuous manner to change metabolic needs of the cell. Using transmitochondrial cybrid (cybrid) technology, we generated different cybrid models under common nuclear backgrounds of benign breast epithelium or TNBC. Mitochondria from cells with different cancer potential such as benign breast epithelium, moderately metastatic and highly metastatic breast cancer cell lines were studied under the common nuclear background to understand MRR-regulated TIC properties and cancer pathways. Using genomic, metabolomic, and proteomic approaches, we confirmed the significance of mitochondrial character in the regulation of epithelial mesenchymal transition (EMT), TIC and metastatic properties. Altogether, our results suggest that MRR is critical in TNBC TIC character and stemness.

Citation Format: Park JH, Jung KH, Sirupangi T, Vithayathil S, Jin F, Putluri V, Piyarathna DWB, Yotnda P, Bhat VB, Sreekumar A, Lewis MT, Coarfa C, Putluri N, Creighton CJ, Wong L-JC, Kaipparettu BA. Mitochondria-nuclear communication regulates epithelial-mesenchymal transition and metastasis in triple negative breast cancer [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-01-07.

Loss of Nardilysin, a Mitochondrial Co-chaperone for α-Ketoglutarate Dehydrogenase, Promotes mTORC1 Activation and Neurodegeneration

We previously identified mutations in Nardilysin (dNrd1) in a forward genetic screen designed to isolate genes whose loss causes neurodegeneration in Drosophila photoreceptor neurons. Here we show that NRD1 is localized to mitochondria, where it recruits mitochondrial chaperones and assists in the folding of α-ketoglutarate dehydrogenase (OGDH), a rate-limiting enzyme in the Krebs cycle. Loss of Nrd1 or Ogdh leads to an increase in α-ketoglutarate, a substrate for OGDH, which in turn leads to mTORC1 activation and a subsequent reduction in autophagy. Inhibition of mTOR activity by rapamycin or partially restoring autophagy delays neurodegeneration in dNrd1 mutant flies. In summary, this study reveals a novel role for NRD1 as a mitochondrial co-chaperone for OGDH and provides a mechanistic link between mitochondrial metabolic dysfunction, mTORC1 signaling, and impaired autophagy in neurodegeneration.

EMT-induced metabolite signature identifies poor clinical outcome

Metabolic reprogramming is a hallmark of cancer. Epithelial-mesenchymal transition (EMT) induces cancer stem cell (CSC) characteristics and promotes tumor invasiveness; however relatively little is known about the metabolic reprogramming in EMT. Here we show that breast epithelial cells undergo metabolic reprogramming following EMT. Relative to control, cell lines expressing EMT transcription factors show ≥1.5-fold accumulation of glutamine, glutamate, beta-alanine and glycylleucine as well as ≥1.5-fold reduction of phosphoenolpyruvate, urate, and deoxycarnitine. Moreover, these metabolic alterations were found to be predictive of overall survival (hazard ratio = 2.3 (95% confidence interval: 1.31–4.2), logrank p-value = 0.03) and define breast cancer molecular subtypes. EMT-associated metabolites are primarily composed of anapleurotic precursors, suggesting that cells undergoing EMT have a shift in energy production. In summary, we describe a unique panel of metabolites associated with EMT and demonstrate that these metabolites have the potential for predicting clinical and biological characteristics associated with patient survival.

Differential regulation of metabolic pathways by androgen receptor (AR) and its constitutively active splice variant, AR-V7, in prostate cancer cells

Metastatic prostate cancer (PCa) is primarily an androgen-dependent disease, which is treated with androgen deprivation therapy (ADT). Tumors usually develop resistance (castration-resistant PCa [CRPC]), but remain androgen receptor (AR) dependent. Numerous mechanisms for AR-dependent resistance have been identified including expression of constitutively active AR splice variants lacking the hormone-binding domain. Recent clinical studies show that expression of the best-characterized AR variant, AR-V7, correlates with resistance to ADT and poor outcome. Whether AR-V7 is simply a constitutively active substitute for AR or has novel gene targets that cause unique downstream changes is unresolved. Several studies have shown that AR activation alters cell metabolism. Using LNCaP cells with inducible expression of AR-V7 as a model system, we found that AR-V7 stimulated growth, migration, and glycolysis measured by ECAR (extracellular acidification rate) similar to AR. However, further analyses using metabolomics and metabolic flux assays revealed several differences. Whereas AR increased citrate levels, AR-V7 reduced citrate mirroring metabolic shifts observed in CRPC patients. Flux analyses indicate that the low citrate is a result of enhanced utilization rather than a failure to synthesize citrate. Moreover, flux assays suggested that compared to AR, AR-V7 exhibits increased dependence on glutaminolysis and reductive carboxylation to produce some of the TCA (tricarboxylic acid cycle) metabolites. These findings suggest that these unique actions represent potential therapeutic targets.

Abstract 9: Metabolic profiling of bladder cancer cell lines reveals molecular alterations involved in methylation and novel epigenetic phenotype

Background: Bladder cancer (BCa) is primarily “carcinogen driven cancer”. Epidemiological studies indicate environmental factors play a major causative role compared to genetic factors. Xenobiotic metabolism is highly perturbed and precise mechanisms involved are poorly understood during BCa progression. We identified metabolic signature that can distinguish bladder cancer from controls and reveals major alterations in phaseI/II enzymes involved in xenobiotic metabolism and suggest a key role for epigenetic modifications.

Material and Methods:

In this study, we used mass spectrometry based metabolomics profiling coupled with enrichment-based bioprocess mapping to obtain insight into biochemical alterations in bladder cancer cell lines. We further validated related gene expression using real time quantitative PCR (qPCR) and proteins using western blotting.

Results:

In this study, we used high-throughput mass spectrometry to measure over 350 compounds in seven bladder cell lines, identifying 91 metabolites which exhibited significant changes in bladder Cancer. Most importantly, methylated, hydroxylated and acetylated metabolites are altered. Interestingly, S-Adenosyl methionine (SAM) is the most prominent pathway upregulated corroborated with our previous findings obtained using patient derived metabolomic data from two independent cohorts. Second, we observe many of phaseI/phaseII metabolic enzymes including aldehyde oxidase (AOX1), cytochrome P450 1A1 (CYP1A1), CYP1B1, Glutathione S-transferase T1 (GSTT1), Glutathione S-transferase M2 (GSTM2), N-acetyl transferase I NAT1 and NAT2 are transcriptionally repressed in BCa cell line compared to benign indicating the pivotal role of methylation in gene silencing. Interestingly, we observe differential expression of polycomb group of proteins (Pcg) associated with PRC2 and PRC1 complex. Specifically, histone-lysine N-methyl transferase (EZH2) protein, which is SAM dependent histone methyl transferase and concomitant 3meHK27 trimethylated histone K27, is highly expressed in metastatic UMUC3 BCa cell line further indicating prominence of epigenetic modifications.

Conclusion:

We present an integrative pathway analysis of a metabolic gene signature which has not been previously described in the context of bladder cancer cell lines. Further mechanistic analyses reveals prominent role for methylation status and associated epigenetic modifications being played in the transcriptional repression of key xenobiotic enzymes. Collectively, our novel findings provide an opportunity for development of efficient biomarker implications and epigenetic therapy targeting BCa progression.

Citation Format: Rashmi Krishnapuram, Franklin Gu, Salil Kumar Bhowmik, Suman Maity, Mohan Manikkam, Friedrich-Carl von Rundstedt, Vasanta Putluri, Yair Lotan, Jonathan M. Levitt, Seth P. Lerner, Cristian Coarfa, Arun Sreekumar, Nagireddy Putlurip. Metabolic profiling of bladder cancer cell lines reveals molecular alterations involved in methylation and novel epigenetic phenotype. [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 9.

Abstract 217: Mitochondrial reprogramming regulated cancer pathway in triple negative breast cancer

Compared to other subtypes of tumors, triple negative breast cancers (TN BCa) currently suffer from limited knowledge on its etiology and treatment options. Transmitochondrial cybrids (cybrid) and multiple OMICs approaches were used to understand mitochondrial reprogramming and mitochondria-regulated cancer pathways in TN BCa. Analysis of cybrids and established BCa cell lines showed that metastatic TN BCa maintain high levels of ATP through fatty acid β-oxidation and activate Src oncoprotein by its autophosphorylation. Inhibition and induction of β-oxidation including the shRNA mediated knockdown strategies, and analysis of patient derived xenograft (PDX) models confirmed the role of mitochondrial β-oxidation in Src activation and metastasis. Analysis of BCa clinical data further reaffirmed the role of mitochondrial β-oxidation in Src regulation and their significance in BCa metastasis. This study is innovative in showing the mitochondrial reprogramming mediated regulation of a major cancer pathway by its post-translation modification.

Citation Format: Jun H. Park, Sajna Vithayathil, Danli Wu, Vasanta Putluri, Pi-Lin Sung, Efrosini Tsouko, Vadiraja B. Bhat, Cristian Coarfa, Daniel E. Frigo, Michael T. Lewis, Arun Sreekumar, Patricia Yotnda, Chad J. Creighton, Nagireddy Putluri, Lee-Jun C. Wong, Benny A. Kaipparettu. Mitochondrial reprogramming regulated cancer pathway in triple negative breast cancer. [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 217.

Abstract 1056: Inhibition of hexose monophosphate pathway promotes castration resistant prostate cancer

Prostate Cancer (PCa) is the second highest cause of cancer-related death in men in the US. PCa is androgen dependent when organ-confined and is conventionally treated using surgery or using a combination of anti-androgens and radiation therapy. However, in about 30% of the patients tumor recurs and are initially administered androgen deprivation therapy (ADT). Majority of the patients become resistant to ADT and develop hormone-refractory disease also termed castration-resistant prostate cancer (CRPC), which is lethal. Currently, the molecular and biochemical alterations driving CRPC are not well understood. Using a novel network-based integrative approach, we show distinct alterations in the Hexosamine Biosynthetic Pathway (HBP) to be critical for sustaining the castrate resistant state. Our data suggests expression of key HBP enzymes to be significantly elevated in androgen dependent (AD) PCa while interestingly enough, relatively diminished in CRPC. Genetic loss of function experiments for these HBP enzymes in CRPC-like cells had tumor promoting effect both in vitro and in vivo. This was mediated by alterations in either PI3K-AKT pathway or SP1-ChREBP (SP1- carbohydrate response element binding protein) network in CRPC cells containing full length androgen receptor (AR) or its splice variant AR-V7, respectively. Strikingly, addition of HBP metabolite UDP-N-acetylglucosamine (UDP-GlcNAc) or glucosamine (GlcN) to CRPC-like cells attenuated tumor cell proliferation, both in vitro and in animal studies. Interestingly, these metabolites demonstrated additive efficacy when combined with enzalutamide in vitro. These findings are particularly significant given that the CRPC-like cells tested, inclusive of those containing AR-V7 variant, are inherently resistant to enzalutamide. These observations demonstrate the therapeutic value of targeting altered HBP in CRPC.

Citation Format: Akash K. Kaushik, Ali Shojaie, Katrin Panzitt, Rajni Sonavane, Harene Venghatakrishnan, Mohan Manikkam, Alexander Zaslavsky, Vasanta Putluri, Vihas Vasu, Yiqing Zhang, Ayesha Khan, Stacy Lloyd, Adam Szafran, Subhamoy Dasgupta, David Bader, Fabio Stossi, Hangwen Li, Susmita Samanta, Xuhong Cao, Efrosini Tsouko, Shixia Huang, Daniel Frigo, Lawrence Chan, Dean Edwards, Benny Kaipparettu, Nicholas Mitsiades, Nancy Weigel, Michael Mancini, Michael Ittmann, Arul Chinnaiyan, Nagireddy Putluri, Ganesh Palapattu, George Michailidis, Arun Sreekumar. Inhibition of hexose monophosphate pathway promotes castration resistant prostate cancer. [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 1056.

Abstract A65: An integromics approach identifies immune escape as a potential mechanism for prostate cancer disparities

Background: AA men with PCa will die at a rate nearly 2.5 times higher than their EA counterparts. Presently, no mechanism has been described to explain the differences observed between AA and EA men with PCa; yet, many have interrogated the role of social and anthropometric data on PCa outcomes within these populations. However, when these factors are statistically controlled, the differences in incidence, morbidity, and mortality between AA and EA PCa persist. These findings support the notion that biological factors are one of the major driving forces of PCa disparities. Therefore, to obtain better insights into the molecular aspects of PCa disparities, we examined metabolomic and gene expression profiles of PCa and matched adjacent benign tissue from AA and EA men. Metabolomics is defined as the study of all the small molecule metabolites produced by cellular processes in the body. We hypothesize that racially distinct metabolic pathways and the associated bioprocesses, may contribute to PCa health disparities

Methodology: A total of 190 polar and mid-polar metabolites were measured using mass spectrometry across 50 and 28 PCa/benign tissue pairs from AA and EA men, respectively. Likewise, gene expression microarray analysis was performed on 48 and 21 PCa/benign tissue pairs from AA and EA men. Ancestry informative markers were genotyped and ancestry estimates were determined. Metabolic profiles of AA and EA PCa and benign adjacent pairs were compared using paired t-tests. FDR corrected p-values were used to detect differential metabolites and genes.

Results: Unique biochemical alterations associated with AA tumors were identified. Pathways such as cysteine/methionine, arginine/proline and de novo purine biosynthesis were enhanced in AA PCa. Metabolites such as cystathione, cysteine, and S-Adenosylhomocysteine (SAH), are elevated in AA PCa compared to matched adjacent benign. Consistent with this, transcript and protein levels of DNA Methyl Transferase 1 (DNMT1) and Cystathione Beta Synthase (CBS) were elevated in AA PCa tissues and cell lines. Interestingly, protein and transcript levels of Adenosine Deaminase, an enzyme that converts SAM-derived adenosine to inosine was significantly down regulated in AA PCa, both in tissues and cell lines. Consistent with this, accumulated levels of adenosine were found in AA PCa.

Conclusions: Taken together, the metabolomics data alludes to the existence of an efficient immune escape mechanism in AA PCa. Corroborating this, analysis of gene expression data from AA men with PCa also reveals enriched immune escape pathways.

Citation Format: Stacy M. Lloyd, Jie Gohlke, Sumanta Basu, Salil Bhowmik, Vasanta Putluri, Rashmi Krishnapurnam, Kimal Rajapakshe, Cristian Coarfa, Nilanjan Guha, SA Deepak, Arunkumar Padmanabhan, Mohammed Sayeeduddin, Patricia Castro, Michael Ittmann, Ganesh Palapattu, Nagireddy Putluri, George Michailidis, Arun Sreekumar. An integromics approach identifies immune escape as a potential mechanism for prostate cancer disparities. [abstract]. In: Proceedings of the Eighth AACR Conference on The Science of Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; Nov 13-16, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2016;25(3 Suppl):Abstract nr A65.

Fatty Acid Oxidation-Driven Src Links Mitochondrial Energy Reprogramming and Oncogenic Properties in Triple-Negative Breast Cancer

Transmitochondrial cybrids and multiple OMICs approaches were used to understand mitochondrial reprogramming and mitochondria-regulated cancer pathways in triple-negative breast cancer (TNBC). Analysis of cybrids and established breast cancer (BC) cell lines showed that metastatic TNBC maintains high levels of ATP through fatty acid β oxidation (FAO) and activates Src oncoprotein through autophosphorylation at Y419. Manipulation of FAO including the knocking down of carnitine palmitoyltransferase-1A (CPT1) and 2 (CPT2), the rate-limiting proteins of FAO, and analysis of patient-derived xenograft models confirmed the role of mitochondrial FAO in Src activation and metastasis. Analysis of TCGA and other independent BC clinical data further reaffirmed the role of mitochondrial FAO and CPT genes in Src regulation and their significance in BC metastasis.

Integrative Pathway Analysis of Metabolic Signature in Bladder Cancer: A Linkage to The Cancer Genome Atlas Project and Prediction of Survival

Purpose

We used targeted mass spectrometry to study the metabolic fingerprint of urothelial cancer and determine whether the biochemical pathway analysis gene signature would have a predictive value in independent cohorts of patients with bladder cancer.

Materials and Methods

Pathologically evaluated, bladder derived tissues, including benign adjacent tissue from 14 patients and bladder cancer from 46, were analyzed by liquid chromatography based targeted mass spectrometry. Differential metabolites associated with tumor samples in comparison to benign tissue were identified by adjusting the p values for multiple testing at a false discovery rate threshold of 15%. Enrichment of pathways and processes associated with the metabolic signature were determined using the GO (Gene Ontology) Database and MSigDB (Molecular Signature Database). Integration of metabolite alterations with transcriptome data from TCGA (The Cancer Genome Atlas) was done to identify the molecular signature of 30 metabolic genes. Available outcome data from TCGA portal were used to determine the association with survival.

Results

We identified 145 metabolites, of which analysis revealed 31 differential metabolites when comparing benign and tumor tissue samples. Using the KEGG (Kyoto Encyclopedia of Genes and Genomes) Database we identified a total of 174 genes that correlated with the altered metabolic pathways involved. By integrating these genes with the transcriptomic data from the corresponding TCGA data set we identified a metabolic signature consisting of 30 genes. The signature was significant in its prediction of survival in 95 patients with a low signature score vs 282 with a high signature score (p = 0.0458).

Conclusions

Targeted mass spectrometry of bladder cancer is highly sensitive for detecting metabolic alterations. Applying transcriptome data allows for integration into larger data sets and identification of relevant metabolic pathways in bladder cancer progression.

A Novel [15N] Glutamine Flux using LC-MS/MS-SRM for Determination of Nucleosides and Nucleobases

The growth of cancer cells relies more on increased proliferation and autonomy compared to non-malignant cells. The rate of de novo nucleotide biosynthesis correlates with cell proliferation rates. In part, glutamine is needed to sustain high rates of cellular proliferation as a key nitrogen donor in purine and pyrimidine nucleotide biosynthesis. In addition, glutamine serves as an essential substrate for key enzymes involved in the de novo synthesis of purine and pyrimidine nucleotides. Here, we developed a novel liquid chromatography (LC-MS) to quantify glutamine-derived [15N] nitrogen flux into nucleosides and nucleobases (purines and pyrimidines). For this, DNA from 5637 bladder cancer cell line cultured in 15N labelled glutamine and then enzymatically hydrolyzed by sequential digestion. Subsequently, DNA hydrolysates were separated by LC-MS and Selected Reaction Monitoring (SRM) was employed to identify the nucleobases and nucleosides. Thus, high sensitivity and reproducibility of the method make it a valuable tool to identify the nitrogen flux primarily derived from glutamine and can be further adaptable for high throughput analysis of large set of DNA in a clinical setting.

Pathway-centric integrative analysis identifies RRM2 as a prognostic marker in breast cancer associated with poor survival and tamoxifen resistance

Breast cancer (BCa) molecular subtypes include luminal A, luminal B, normal-like, HER-2-enriched, and basal-like tumors, among which luminal B and basal-like cancers are highly aggressive. Biochemical pathways associated with patient survival or treatment response in these more aggressive subtypes are not well understood. With the limited availability of pathologically verified clinical specimens, cell line models are routinely used for pathway-centric studies. We measured the metabolome of luminal and basal-like BCa cell lines using mass spectrometry, linked metabolites to biochemical pathways using Gene Set Analysis, and developed a novel rank-based method to select pathways on the basis of their enrichment in patient-derived omics data sets and prognostic relevance. Key mediators of the pathway were then characterized for their role in disease progression. Pyrimidine metabolism was altered in luminal versus basal BCa, whereas the combined expression of its associated genes or expression of one key gene, ribonucleotide reductase subunit M2 (RRM2) alone, associated significantly with decreased survival across all BCa subtypes, as well as in luminal patients resistant to tamoxifen. Increased RRM2 expression in tamoxifen-resistant patients was verified using tissue microarrays, whereas the metabolic products of RRM2 were higher in tamoxifen-resistant cells and in xenograft tumors. Both genetic and pharmacological inhibition of this key enzyme in tamoxifen-resistant cells significantly decreased proliferation, reduced expression of cell cycle genes, and sensitized the cells to tamoxifen treatment. Our study suggests for evaluating RRM2-associated metabolites as noninvasive markers for tamoxifen resistance and its pharmacological inhibition as a novel approach to overcome tamoxifen resistance in BCa.

Metabolomic profiling identifies biochemical pathways associated with castration-resistant prostate cancer

Despite recent developments in treatment strategies, castration-resistant prostate cancer (CRPC) is still the second leading cause of cancer-associated mortality among American men, the biological underpinnings of which are not well understood. To this end, we measured levels of 150 metabolites and examined the rate of utilization of 184 metabolites in metastatic androgen-dependent prostate cancer (AD) and CRPC cell lines using a combination of targeted mass spectrometry and metabolic phenotyping. Metabolic data were used to derive biochemical pathways that were enriched in CRPC, using Oncomine concept maps (OCM). The enriched pathways were then examined in-silico for their association with treatment failure (i.e., prostate specific antigen (PSA) recurrence or biochemical recurrence) using published clinically annotated gene expression data sets. Our results indicate that a total of 19 metabolites were altered in CRPC compared to AD cell lines. These altered metabolites mapped to a highly interconnected network of biochemical pathways that describe UDP glucuronosyltransferase (UGT) activity. We observed an association with time to treatment failure in an analysis employing genes restricted to this pathway in three independent gene expression data sets. In summary, our studies highlight the value of employing metabolomic strategies in cell lines to derive potentially clinically useful predictive tools.

MYC-driven accumulation of 2-hydroxyglutarate is associated with breast cancer prognosis

Metabolic profiling of cancer cells has recently been established as a promising tool for the development of therapies and identification of cancer biomarkers. Here we characterized the metabolomic profile of human breast tumors and uncovered intrinsic metabolite signatures in these tumors using an untargeted discovery approach and validation of key metabolites. The oncometabolite 2-hydroxyglutarate (2HG) accumulated at high levels in a subset of tumors and human breast cancer cell lines. We discovered an association between increased 2HG levels and MYC pathway activation in breast cancer, and further corroborated this relationship using MYC overexpression and knockdown in human mammary epithelial and breast cancer cells. Further analyses revealed globally increased DNA methylation in 2HG-high tumors and identified a tumor subtype with high tissue 2HG and a distinct DNA methylation pattern that was associated with poor prognosis and occurred with higher frequency in African-American patients. Tumors of this subtype had a stem cell-like transcriptional signature and tended to overexpress glutaminase, suggestive of a functional relationship between glutamine and 2HG metabolism in breast cancer. Accordingly, 13C-labeled glutamine was incorporated into 2HG in cells with aberrant 2HG accumulation, whereas pharmacologic and siRNA-mediated glutaminase inhibition reduced 2HG levels. Our findings implicate 2HG as a candidate breast cancer oncometabolite associated with MYC activation and poor prognosis.

Application of 13C isotope labeling using liquid chromatography mass spectrometry (LC-MS) to determining phosphate-containing metabolic incorporation

Here, we describe an approach wherein negative electrospray ionization mass spectrometry has used to understand the relative flux through phosphate containing metabolic intermediates associated with central carbon metabolism after administering cells with 13C-labeled substrates. The method was applied to examine the 13C incorporation through glycolysis in T47D breast cancer cells and showed reduction of glycolytic relative flux upon treatment with 2-Deoxyglucose.

Abstract 5387: Integrative analysis of transcriptomic and metabolomic data reveals a critical role for aminosugar metabolism in prostate cancer

Prostate Cancer is the second most common cause of cancer-related death in men in the US. Like other tumors, prostate cancer development and progression is dictated by multiple molecular events that include changes in levels of genes, transcripts, proteins and metabolites. To better understand the biology of prostate cancer development it is essential to integrate these disparate yet related datasets. Our laboratory has identified matched transcriptomic, proteomic and metabolomic changes in localized prostate cancer relative to adjacent benign tissue as well in metastatic disease compared to organ-confined tumor. To study this using a System's Biology approach we have recently embarked on a pilot study aimed at integrating transcriptomic and metabolomic data to obtain biochemical pathways that key to prostate cancer development. Using an in-house network-based enrichment strategy, amino sugar metabolism was found to be significantly enriched in organ-confined prostate cancer but not in metastatic disease. Amino sugar metabolism describes the utilization of glucose-derived carbon and amino acid (mostly glutamine)-derive nitrogen to produce glucosamines. These amino sugars participate in synthesis of immune modulatory compounds as well as in glycosylation cascades. In this study, we describe the molecular analyses of Glucosamine-6 phosphate-N-acetyl Transferase (GNPNAT1), a key enzyme that converts D-glucosamine 6-phosphate to N-acetyl-D-glucosamine 6-phosphate, in prostate cancer. Our results indicate upregulation of GNPNAT1 in organ-confined prostate cancer as compared to benign adjacent tissue as well as metastatic tissue and regulation of the pathway by androgen. Stable knockdown of GNPNAT1 in androgen dependent LNCap cells leads to diminished cell growth and cell cycle arrest. In contrast, growth and cell cycle are not affected by the knockdown of GNPNAT1 in androgen independent C4-2 cells. Knockdown of GNPNAT1 in C4-2 cells enhances invasiveness which is not observed in LNCap knockdown cells. In this work we show that GNPNAT1 is linked to androgen receptor (AR) action and thus is a critical enzyme for the survival of androgen dependent prostate cancer cells.

Citation Format: Katrin Panzitt, Ali Shojaie, Nagireddy Putluri, Sumanta Basu, Vasanta Putluri, Susmita Samanta, Michael Ittmann, Ismael Vergara, George Michailidis, Ganesh Palapattu, Arun Sreekumar. Integrative analysis of transcriptomic and metabolomic data reveals a critical role for aminosugar metabolism in prostate 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 5387. doi:10.1158/1538-7445.AM2013-5387