Identification and validation of N-acetylputrescine in combination with non-canonical clinical features as a Parkinson's disease biomarker panel

Parkinson's disease is a progressive neurodegenerative disorder in which loss of dopaminergic neurons in the substantia nigra results in a clinically heterogeneous group with variable motor and non-motor symptoms with a degree of misdiagnosis. Only 3-25% of sporadic Parkinson's patients present with genetic abnormalities that could represent a risk factor, thus environmental, metabolic, and other unknown causes contribute to the pathogenesis of Parkinson's disease, which highlights the critical need for biomarkers. In the present study, we prospectively collected and analyzed plasma samples from 194 Parkinson's disease patients and 197 age-matched non-diseased controls. N-acetyl putrescine (NAP) in combination with sense of smell (B-SIT), depression/anxiety (HADS), and acting out dreams (RBD1Q) clinical measurements demonstrated combined diagnostic utility. NAP was increased by 28% in Parkinsons disease patients and exhibited an AUC of 0.72 as well as an OR of 4.79. The clinical and NAP panel demonstrated an area under the curve, AUC = 0.9 and an OR of 20.4. The assessed diagnostic panel demonstrates combinatorial utility in diagnosing Parkinson's disease, allowing for an integrated interpretation of disease pathophysiology and highlighting the use of multi-tiered panels in neurological disease diagnosis.

Chronic exercise improves hepatic acylcarnitine handling

Exercise mediates tissue metabolic function through direct and indirect adaptations to acylcarnitine (AC) metabolism, but the exact mechanisms are unclear. We found that circulating medium-chain acylcarnitines (AC) (C12-C16) are lower in active/endurance trained human subjects compared to sedentary controls, and this is correlated with elevated cardiorespiratory fitness and reduced adiposity. In mice, exercise reduced serum AC and increased liver AC, and this was accompanied by a marked increase in expression of genes involved in hepatic AC metabolism and mitochondrial β-oxidation. Primary hepatocytes from high-fat fed, exercise trained mice had increased basal respiration compared to hepatocytes from high-fat fed sedentary mice, which may be attributed to increased Ca2+ cycling and lipid uptake into mitochondria. The addition of specific medium- and long-chain AC to sedentary hepatocytes increased mitochondrial respiration, mirroring the exercise phenotype. These data indicate that AC redistribution is an exercise-induced mechanism to improve hepatic function and metabolism.

Filamin A Is a Prognostic Serum Biomarker for Differentiating Benign Prostatic Hyperplasia from Prostate Cancer in Caucasian and African American Men

Prostate cancer represents a significant health risk to aging men, in which diagnostic challenges to the identification of aggressive cancers remain unmet. Prostate cancer screening is driven by the prostate-specific antigen (PSA); however, in men with benign prostatic hyperplasia (BPH) due to an enlarged prostate and elevated PSA, PSA's screening utility is diminished, resulting in many unnecessary biopsies. To address this issue, we previously identified a cleaved fragment of Filamin A (FLNA) protein (as measured with IP-MRM mass spectrometry assessment as a prognostic biomarker for stratifying BPH from prostate cancer and subsequently evaluated its expanded utility in Caucasian (CA) and African American (AA) men. All men had a negative digital rectal examination (DRE) and PSA between 4 and 10 ng/mL and underwent prostate biopsy. In AA men, FLNA serum levels exhibited diagnostic utility for stratifying BPH from patients with aggressive prostate cancer (0.71 AUC and 12.2 OR in 48 men with BPH and 60 men with PCa) and outperformed PSA (0.50 AUC, 2.2 OR). In CA men, FLNA serum levels also exhibited diagnostic utility for stratifying BPH from patients with aggressive prostate cancer (0.74 AUC and 19.4 OR in 191 men with BPH and 109 men with PCa) and outperformed PSA (0.46 AUC, 0.32 OR). Herein, we established FLNA alone as a serum biomarker for stratifying men with BPH vs. those with high Gleason (7-10) prostate cancers compared to the current diagnostic paradigm of using PSA. This approach demonstrates clinical actionability of FLNA alone without the requirement of prostate volume measurement as a test with utility in AA and CA men and represents a significant opportunity to decrease the number of unnecessary biopsies in aggressive prostate cancer diagnoses.

Residual Complex I activity and amphidirectional Complex II operation support glutamate catabolism through mtSLP in anoxia

Anoxia halts oxidative phosphorylation (OXPHOS) causing an accumulation of reduced compounds in the mitochondrial matrix which impedes dehydrogenases. By simultaneously measuring oxygen concentration, NADH autofluorescence, mitochondrial membrane potential and ubiquinone reduction extent in isolated mitochondria in real-time, we demonstrate that Complex I utilized endogenous quinones to oxidize NADH under acute anoxia. 13C metabolic tracing or untargeted analysis of metabolites extracted during anoxia in the presence or absence of site-specific inhibitors of the electron transfer system showed that NAD+ regenerated by Complex I is reduced by the 2-oxoglutarate dehydrogenase Complex yielding succinyl-CoA supporting mitochondrial substrate-level phosphorylation (mtSLP), releasing succinate. Complex II operated amphidirectionally during the anoxic event, providing quinones to Complex I and reducing fumarate to succinate. Our results highlight the importance of quinone provision to Complex I oxidizing NADH maintaining glutamate catabolism and mtSLP in the absence of OXPHOS.

ScreenDMT reveals linoleic acid diols replicably associate with BMI and stimulate adipocyte calcium fluxes

Activating brown adipose tissue (BAT) improves systemic metabolism, making it a promising target for metabolic syndrome. BAT is activated by 12, 13-dihydroxy-9Z-octadecenoic acid (12, 13-diHOME), which we previously identified to be inversely associated with BMI and which directly improves metabolism in multiple tissues. Here we profile plasma lipidomics from a cohort of 83 people and test which lipids' association with BMI replicates in a concordant direction using our novel tool ScreenDMT, whose power and validity we demonstrate via mathematical proofs and simulations. We find that the linoleic acid diols 12, 13-diHOME and 9, 10-diHOME both replicably inversely associate with BMI and mechanistically activate calcium fluxes in mouse brown and white adipocytes in vitro, which implicates this pathway and 9, 10-diHOME as candidate therapeutic targets. ScreenDMT can be applied to test directional mediation, directional replication, and qualitative interactions, such as identifying biomarkers whose association is shared (replication) or opposite (qualitative interaction) across diverse populations.

Exercise and ageing impact the kynurenine/tryptophan pathway and acylcarnitine metabolite pools in skeletal muscle of older adults

Exercise-induced perturbation of skeletal muscle metabolites is a probable mediator of long-term health benefits in older adults. Although specific metabolites have been identified to be impacted by age, physical activity and exercise, the depth of coverage of the muscle metabolome is still limited. Here, we investigated resting and exercise-induced metabolite distribution in muscle from well-phenotyped older adults who were active or sedentary, and a group of active young adults. Percutaneous biopsies of the vastus lateralis were obtained before, immediately after and 3 h following a bout of endurance cycling. Metabolite profile in muscle biopsies was determined by tandem mass spectrometry. Mitochondrial energetics in permeabilized fibre bundles was assessed by high resolution respirometry and fibre type proportion was assessed by immunohistology. We found that metabolites of the kynurenine/tryptophan pathway were impacted by age and activity. Specifically, kynurenine was elevated in muscle from older adults, whereas downstream metabolites of kynurenine (kynurenic acid and NAD⁺ ) were elevated in muscle from active adults and associated with cardiorespiratory fitness and muscle oxidative capacity. Acylcarnitines, a potential marker of impaired metabolic health, were elevated in muscle from physically active participants. Surprisingly, despite baseline group difference, acute exercise-induced alterations in whole-body substrate utilization, as well as muscle acylcarnitines and ketone bodies, were remarkably similar between groups. Our data identified novel muscle metabolite signatures that associate with the healthy ageing phenotype provoked by physical activity and reveal that the metabolic responsiveness of muscle to acute endurance exercise is retained [NB]:AUTHOR: Please ensure that the appropriate material has been provide for Table S2, as well as for Figures S1 to S7, as also cited in the text with age regardless of activity levels. KEY POINTS: Kynurenine/tryptophan pathway metabolites were impacted by age and physical activity in human muscle, with kynurenine elevated in older muscle, whereas downstream products kynurenic acid and NAD⁺ were elevated in exercise-trained muscle regardless of age. Acylcarnitines, a marker of impaired metabolic health when heightened in circulation, were elevated in exercise-trained muscle of young and older adults, suggesting that muscle act as a metabolic sink to reduce the circulating acylcarnitines observed with unhealthy ageing. Despite the phenotypic differences, the exercise-induced response of various muscle metabolite pools, including acylcarnitine and ketone bodies, was similar amongst the groups, suggesting that older adults can achieve the metabolic benefits of exercise seen in young counterparts.

Abstract 5321: BRG399: A novel potent small molecule modulator of UBE2K for the treatment of various cancers

The ubiquitin-proteasome system (UPS) plays an important role in cellular processes for protein quality control and homeostasis and indeed, dysregulation within the pathway has implications in numerous diseases, especially cancer. Here, we introduce BRG399, a novel modulator of UBE2K - a unique E2 conjugating enzyme of the UPS, that we previously identified as a potential therapeutic target using BERG’s Interrogative Biology® platform. The anticancer potential of UBE2K modulation was validated by gene manipulation using siRNA mediated knockdown of UBE2K in several cancer cell models. Knockdown of UBE2K resulted in a 50% decrease in cell number in MIA PaCa2 cells and a 30% decrease in cell number in SKHEP1 and HepG2 cells at 96h post transfection. This effect was the result of a robust G2/M cell cycle arrest associated with increased CyclinB1 expression. In addition, a modest increase in apoptosis/necrosis (6-8%) was observed in cells with UBE2K knockdown. Using Fragment-Based Ligand Discovery and structure-based drug design, BRG399 was developed as a new chemical entity (NCE) which binds to UBE2K, resulting in modulation of several established canonical functions and an anti-cancer phenotype. In a panel of 102 cancer cell lines, BRG399 exhibited an anti-cancer activity in all cell lines tested as evident by extrapolation of IC50 and %Max Effect values from the dose response curves. In all but one cell line, double to triple digit nanomolar potency was observed ranging from 17nM to 318 nM and viability of 76 cell lines was reduced by more than 70%. The anti-cancer potency of BRG399 was also established in a multi-tumor type panel of patient-derived organoids (PDO) of which 68% were highly or partially responsive to BRG399 as indicated by 37-73% decrease in PDO viability. Mechanistic studies demonstrated that BRG399’s anti-cancer effect was a result of a robust G2/M cell cycle arrest and apoptosis mediated cell death. Molecular events associated with G2/M arrest included stabilization of CyclinB1 and sustained activation of cyclin-dependent kinase CDK1, while those associated with apoptosis involved decreased expression of anti-apoptotic proteins Bcl-XL and Mcl-1 and increased expression of cleaved PARP (cPARP) and Capase 3. Together, these results support a novel role for UBE2K in the regulation of the cell cycle in cancer cells and demonstrate that its modulation by BRG399 influences phenotypic end-points consistent with an anti-cancer effect.

Citation Format: Maria-Dorothea Nastke, Marisa Permatteo, Pragalath Sundararajan, Shefali Sharma, Jacob Matson, Kaleigh Gray, Arcan Guven, Shiva Kazerounian, Anne Diers, Rangaprasad Sarangarajan, Niven R. Narain, Vivek K. Vishnudas, Stephane Gesta. BRG399: A novel potent small molecule modulator of UBE2K for the treatment of various cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5321.

Abstract 5320: BRG399, a small molecule modulator of UBE2K demonstrated dose-dependent anti-cancer efficacy in an in vivo model for gastric cancer

Gastric cancer is difficult to treat and exhibits poor survival with current therapies (five-year survival for all stages is 32% and 5% for metastatic gastric cancer) demonstrating a clear unmet clinical need. UBE2K was identified as a drug target from the BERG Interrogative Biology® Platform, from an Artificial Intelligence derived in vitro pan-cancer Bayesian network. UBE2K (also known as Huntington Interacting Protein 2 and E2-25K) is one of the ~40 E2 enzymes from the Ubiquitin Proteasome System and belongs to the Class II of E2 enzymes that preferentially catalyze the synthesis of Lys48-linked changes on monoubiquitinated substrates. Recently, high expression of UBE2K in tumors of gastric cancer patients has been shown to associate with poor prognosis. BERG has developed BRG399 as a candidate molecule to modulate UBE2K activity for use in oncology. Here, we evaluated the anti-cancer effect of BRG399 using Hs 746T, a human xenograft in vivo model for gastric cancer. In vitro evaluation of BRG399 potency revealed an IC50 of 44.3nM in Hs 746T cells. For determination of BRG399 potency in vivo, nude mice were inoculated subcutaneously with Hs 746T cell line and tumors were allowed to reach 120mm3. Animals were then randomized into four groups to receive oral administration of vehicle, 75, 100, or 150mg/kg of BRG399 twice per day for 15 days. The result revealed that BRG399 significantly decreased the growth of Hs 746T tumors in a dose-dependent manner. Statistical analysis using a mixed effect linear model of the tumor volumes on the last day of study demonstrated a tumor growth inhibition of 60.3, 71.2 and 85.3% at the three doses, respectively, without any significant effect on body weight. These results are well correlated with the dose-dependent increase of BRG399 in both plasma and tumor tissues. Anti-tumor effect of BRG399 appears to be the result of G2/M arrest, as indicated by a dose-dependent elevation of two cell cycle-dependent biomarkers, CNNB1 and pHH3, in tumor tissue. This is consistent with the role of UBE2K in regulating several components of cell cycle for dictating the precise timing of cell division. Mixed effect multivariable regression modeling was employed to identify the relationship between these two biomarkers and response. This analysis indicated that the level of plasma concentration of BRG399, together with the tumor levels of CNNB1 and pHH3, are significantly and negatively associated with tumor volume, allowing an inference that these biomarkers are indicative and/or involved in the tumor response of BRG399. In summary, these results signify the anti-cancer efficacy of BRG399 and support its potential as a drug candidate for treatment of gastric cancer.

Citation Format: Shiva Kazerounian, Mollie O'Hara, Arcan Guven, Kashni Grover, Nicole Pellegrino, Kayleigh Gray, Can Bruce, Gregory M. Miller, Maria-Dorothea Nastke, Michael A. Kiebish, Eric M. Grund, Rangaprasad Sarangarajan, Niven R. Narain, Stephane Gesta, Vivek K. Vishnudas. BRG399, a small molecule modulator of UBE2K demonstrated dose-dependent anti-cancer efficacy in an in vivo model for gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5320.

Abstract 5319: Treatment of K562 leukemia cells with an experimental UBE2K modifier identifies multi-omic changes associated with altered oncogenic processes

Ubiquitination is a conserved post translation modification involving covalent attachment of ubiquitin protein and is known to regulate many biological processes, including proteasomal degradation. Three major families of enzymes are involved in the regulation of ubiquitination, including activating enzyme E1, Ubiquitin conjugating enzyme E2 and ubiquitin ligase E3. UBE2K is an E2 conjugating ligase that was identified as an anti-cancer drug target from the BERG Interrogative Biology® platform, an artificial intelligence multi-omics analytical method employing Bayesian algorithms. Herein, we used proteomics, lipidomics and metabolomics to investigate the impact of the treatment of UBE2K small molecule ligand (BRG0451) on K562 leukemia cells. K562 cells were treated with 30, 100 and 300 nM concentrations for 24 hours with BRG0451 or Paclitaxel or 0.1% DMSO (Control). Cells were pelleted and analyzed using a multi-omics approach. Proteomic analysis was performed using Thermo Q-Exactive+ LC MS/MS analysis. Lipidomic analysis was performed using SCIEX TripleTOF MS/MS ALL shotgun workflow and metabolomics was performed using 3 different platforms (High resolution RP-LC-MS, HILIC QqQ LC-MS/MS and GC-TOF MS). Unsupervised clustering and differential analysis were used to investigate the impact of the treatments. Proteomic analysis identified and quantified 6930 proteins from K562 cells using TMT labelling with offline 24 fractions and LC-MS/MS. Structural lipidomics analysis evaluated 1980 lipid molecular species and metabolomics analysis identified over 700 metabolites using GC-MS, LC-MS and LC-MS/MS. Multiomics and regression analysis for 30 nM BRG0451 treatment revealed no distinct pattern of omics variables. However, treatment on K562 cells with 300 nM treatment demonstrated 97 differentially expressed proteins compared to control. Pathway analysis revealed chromatin remodeling, and more specifically, regulation of chromatin silencing and localization to nucleolus as major pathways impacted by differentially expressed proteins. Similar pathways were impacted by Paclitaxel and Nocodazole treatment compared to control. Additionally, metabolomic and lipidomic differentials were observed with 300 nM BRG0451 treatment. Structural lipidomics revealed dose -dependent changes in triacylglycerols and cholesterol esters, glycolipid monounsaturated species, and glycolipid medium carbon chain subgroups. Dose dependent impact on amino acids metabolism, purine metabolism, and pyrimidine metabolism was observed with a high degree of similarity for compared drugs. Herein, we demonstrated the use of multi-omics technology in deconvoluting the impact of BRG0451 on independent biological pathways, revealing the intricate mechanisms targeting cell cycle as well as ubiquitin regulator components in a leukemia cell line.

Citation Format: Punit Shah, Richard Searfoss, Valerie Bussberg, Bennett Greenwood, Shraddha Karmacharya, Allison MacDonald, Kennedy Ofori-Mensa, Vladimir Tolstikov, Pragalath Sundararajan, Maria-Dorothea Nastke, Eric M. Grund, Gregory M. Miller, Stephane Gesta, Rangaprasad Sarangarajan, Elder Granger, Niven R. Narain, Vivek K. Vishnudas, Michael A. Kiebish. Treatment of K562 leukemia cells with an experimental UBE2K modifier identifies multi-omic changes associated with altered oncogenic processes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5319.

Transplantation of Brown Adipose Tissue with the Ability of Converting Omega-6 to Omega-3 Polyunsaturated Fatty Acids Counteracts High-Fat-Induced Metabolic Abnormalities in Mice

A balanced omega (ω)-6/ω-3 polyunsaturated fatty acids (PUFAs) ratio has been linked to metabolic health and the prevention of chronic diseases. Brown adipose tissue (BAT) specializes in energy expenditure and secretes signaling molecules that regulate metabolism via inter-organ crosstalk. Recent studies have uncovered that BAT produces different PUFA species and circulating oxylipin levels are correlated with BAT-mediated energy expenditure in mice and humans. However, the impact of BAT ω-6/ω-3 PUFAs on metabolic phenotype has not been fully elucidated. The Fat-1 transgenic mice can convert ω-6 to ω-3 PUFAs. Here, we demonstrated that mice receiving Fat-1 BAT transplants displayed better glucose tolerance and higher energy expenditure. Expression of genes involved in thermogenesis and nutrient utilization was increased in the endogenous BAT of mice receiving Fat-1 BAT, suggesting that the transplants may activate recipients' BAT. Using targeted lipidomic analysis, we found that the levels of several ω-6 oxylipins were significantly reduced in the circulation of mice receiving Fat-1 BAT transplants than in mice with wild-type BAT transplants. The major altered oxylipins between the WT and Fat-1 BAT transplantation were ω-6 arachidonic acid-derived oxylipins via the lipoxygenase pathway. Taken together, these findings suggest an important role of BAT-derived oxylipins in combating obesity-related metabolic disorders.

Multiplexed LC-MS/MS analysis of methylsuccinic acid, ethylmalonic acid, and glutaric acid in plasma and urine

Low molecular-mass aliphatic carboxylic acids are critically important for intermediate metabolism and may serve as important biomarkers for metabolic homeostasis. Here in, we focused on multiplexed method development of aliphatic carboxylic analytes, including methylsuccinic acid (MSA), ethylmalonic acid (EMA), and glutaric acid (GA). Also assessed was their utility in a population's health as well as metabolic disease screening in both plasma and urine matrices. MSA, EMA, and GA are constitutional isomers of dicarboxylic acid with high polarity and poor ionization efficiency, resulting in such challenges as poor signal intensity and retention, particularly in reversed-phase liquid chromatography with electrospray mass spectrometry (RP-LC-ESI-MS/MS). Derivatization using n-butanol was performed in the sample preparation to enhance the signal intensity accompanied with a positive charge from ionization in complicated biomatrices as well as to improve the separation of these isomers with optimal retention. Fit-for-purpose method validation results demonstrated quantitative ranges for MSA/EMA/GA from 5/10/20 ng/mL to 400 ng/mL in plasma analysis, and 100/200/100 ng/mL to 5000/10000/5000 ng/mL in urine analysis. This validated method demonstrates future utility when exploring population health analysis and biomarker development in metabolic diseases.

Abstract P1-05-04: Novel breast cancer proteomic subtyping with connection to cell of origin

Introduction: In clinical practice, immunohistochemistry (IHC) is combined with clinicopathologic information to stratify patients into subtypes and guide treatment decisions. In our mass spectrometry study of 116 breast cancers (BrCAs), we identified 34 significant proteins which provide additional prognostic information. This novel proteomic subtyping, combining IHC with proteomics, separates HER2 negative (Her2-) BrCA patients into Luminal-like and TN-like subtypes. A novel subtype, luminal by IHC and TN-like by proteomics (L/T), is associated with unfavorable outcome compared with the luminal subtype (L/L) by both IHC and proteomics. These IHC-based Her2- subtypes are described as L/L, L/T, T/L and T/T subtypes. We investigated the cell-of-origin of our enhanced subtypes using gene set enrichment analysis with gene sets consisting of breast cancer cell-of-origin signatures. We further identified genes representing our 34 proteins in the significant gene sets and investigated their association with survival outcomes across The Cancer Genome Atlas (TCGA) pan-cancers. Method: The single-cell RNA-sequencing data analyses of health breast samples identified 23 breast cell-of-origin signatures (Bhat-Nakshatri et al., 2021) with 46 up and down-regulated gene sets based on the provided fold changes. Using our cohort, we performed differential analysis for each enhanced subtype (L/L, L/T, T/T) versus the other subtypes separately. Pre-ranked gene set enrichment analyses were used to identify significantly enriched gene sets. The significance of enriched gene sets was reported at FDR<0.05. We further identified genes of 34 biomarkers that overlapped in the identified significant gene sets and investigated the impact of the genes on survival across TCGA pan-cancers. Univariate overall survival (OS) and progression-free interval (PFI) analyses were performed on each cancer cohort and the significance of the association with survival outcome was reported by log-rank p-value <0.05. Results: Our signature was compared to the clusters from healthy tissues. We found up-regulated genes in L/L subtype were enriched in gene sets elevated in mature luminal annotated clusters (N8 and N12). Down-regulated genes in L/L subtype were enriched in the elevated genes in the N3 (luminal progenitor) and N9 (luminal progenitor/basal) clusters. Up-regulated genes in L/T subtype were enriched in the elevated genes in the N19 (luminal progenitor) and N11 (basal) clusters. Down-regulated genes in L/T were enriched in the elevated genes in the N8 (mature luminal) cluster and down-regulated genes in the N9 (luminal progenitor/basal) cluster. Up-regulated genes in T/T subtype were enriched in genes highly expressed in the luminal progenitor (N3) and luminal progenitor/basal (N9) clusters. Down-regulated genes in T/T subtype were enriched in the elevated genes in the mature luminal annotated clusters (N8, N12). One gene, KPNA2, was up-regulated in both the N9 (luminal progenitor/basal) cluster and the Basal-like (TN-like) subtype. The higher expression of this gene had significant association with worse OS outcomes in most of the cancers. Conclusions: T/T and L/T subtypes likely arise from progenitor and basal cells. The L/L subtype may arise from mature luminal cells. The novel L/T subtype appears to have characteristics that result in poorer survival. Disclaimers The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of USUHS, HJF, the DOD or the Departments of the Army, Navy, or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government.

Citation Format: Guisong Wang, Punit Shah, Rick Searfoss, J. Leigh Fantacone-Campbell, Jeffrey A. Hooke, Brenda Deyarmin, Rebecca N. Zingmark, Stella Somiari, Jianfang Liu, Leonid Kvecher, Lori A. Sturtz, Praveen-Kumar Raj-Kumar, Elder Granger, Linda Vahdat, Niven R. Narain, Mary L. Cutler, Rangaprasad Sarangarajan, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Craig D. Shriver. Novel breast cancer proteomic subtyping with connection to cell of origin [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P1-05-04.

Signaling Lipidomic Analysis of Thermogenic Adipocytes

Brown adipose tissue is a thermogenic organ that possesses anti-diabetic and anti-obesogenic potential. There has recently been growing interest on the secretory role of brown adipose tissue in regulating whole-body metabolism. Several signaling lipids, including 12-HEPE and 12,13-diHOME, have been shown to be secreted by brown adipose tissue and have demonstrated roles in regulating whole-body energy metabolism. Lipidomics platforms that broadly characterize the signaling lipidome can deconvolute the underlying biology of the lipid metabolites having a broad systemic impact on physiology. Herein, we describe how to perform and analyze LC-MS/MS signaling lipidomics on mature brown adipocytes.

Ubc1 turnover contributes to the spindle assembly checkpoint in Saccharomyces cerevisiae

The spindle assembly checkpoint protects the integrity of the genome by ensuring that chromosomes are properly attached to the mitotic spindle before they are segregated during anaphase. Activation of the spindle checkpoint results in inhibition of the Anaphase-Promoting Complex (APC), an E3 ubiquitin ligase that triggers the metaphase-anaphase transition. Here, we show that levels of Ubc1, an E2 enzyme that functions in complex with the APC, modulate the response to spindle checkpoint activation in Saccharomyces cerevisiae. Overexpression of Ubc1 increased resistance to microtubule poisons, whereas Ubc1 shut-off sensitized cells. We also found that Ubc1 levels are regulated by the spindle checkpoint. Checkpoint activation or direct APC inhibition led to a decrease in Ubc1 levels, charging, and half-life. Additionally, stabilization of Ubc1 prevented its down-regulation by the spindle checkpoint and increased resistance to checkpoint-activating drugs. These results suggest that down-regulation of Ubc1 in response to spindle checkpoint signaling is necessary for a robust cell cycle arrest.

Diagnostic Utility of Serum and Urinary Metabolite Analysis in Patients with Interstitial Cystitis/Painful Bladder Syndrome

OBJECTIVE

To identify the potential biomarkers of interstitial cystitis/painful bladder syndrome (IC), a chronic syndrome of bladder-centric pain with unknown etiology that has an adverse impact on quality of life, we analyzed the urine and serum metabolomes of a cohort of IC patients and non-disease controls (NC).

METHODS

Home collection of serum and urine samples was obtained from 19 IC and 20 NC females in the Veterans Affairs (VA) Health Care System. IC was diagnosed independently by thorough review of medical records using established criteria. Biostatistics and bioinformatics analyses, including univariate analysis, unsupervised clustering, random forest analysis, and metabolite set enrichment analysis (MSEA), were then utilized to identify potential IC biomarkers.

RESULTS

Metabolomics profiling revealed distinct expression patterns between NC and IC. Random forest analysis of urine samples suggested discriminators specific to IC; these include phenylalanine, purine, 5-oxoproline, and 5-hydroxyindoleacetic acid. When these urinary metabolomics-based analytes were combined into a single model, the AUC was 0.92, suggesting strong potential clinical value as a diagnostic signature. Serum-based metabolomics did not provide potential IC discriminators.

CONCLUSION

Analysis of serum and urine revealed that women with IC have distinct metabolomes, highlighting key metabolic pathways that may provide insight into the pathophysiology of IC. The findings from this pilot study suggest that integrated analyses of urinary metabolites, purine, phenylalanine, 5-oxoproline, and 5-HIAA, can lead to promising IC biomarkers for pathophysiology of IC. Validation of these results using a larger dataset is currently underway.

In-hospital use of ACE inhibitors/angiotensin receptor blockers associates with COVID-19 outcomes in African American patients

BACKGROUNDThe angiotensin-converting enzyme (ACE) D allele is more prevalent among African Americans compared with other races and ethnicities and has previously been associated with severe coronavirus disease 2019 (COVID-19) pathogenesis through excessive ACE1 activity. ACE inhibitors/angiotensin receptor blockers (ACE-I/ARB) may counteract this mechanism, but their association with COVID-19 outcomes has not been specifically tested in the African American population.METHODSWe identified 6218 patients who were admitted into Mount Sinai hospitals with COVID-19 between February 24 and May 31, 2020, in New York City. We evaluated whether the outpatient and in-hospital use of ACE-I/ARB is associated with COVID-19 in-hospital mortality in an African American compared with non-African American population.RESULTSOf the 6218 patients with COVID-19, 1138 (18.3%) were ACE-I/ARB users. In a multivariate logistic regression model, ACE-I/ARB use was independently associated with a reduced risk of in-hospital mortality in the entire population (OR, 0.655; 95% CI, 0.505-0.850; P = 0.001), African American population (OR, 0.44; 95% CI, 0.249-0.779; P = 0.005), and non-African American population (OR, 0.748, 95% CI, 0.553-1.012, P = 0.06). In the African American population, in-hospital use of ACE-I/ARB was associated with improved mortality (OR, 0.378; 95% CI, 0.188-0.766; P = 0.006), whereas outpatient use was not (OR, 0.889; 95% CI, 0.375-2.158; P = 0.812). When analyzing each medication class separately, ARB in-hospital use was significantly associated with reduced in-hospital mortality in the African American population (OR, 0.196; 95% CI, 0.074-0.516; P = 0.001), whereas ACE-I use was not associated with impact on mortality in any population.CONCLUSIONIn-hospital use of ARB was associated with a significant reduction in in-hospital mortality among COVID-19-positive African American patients.FUNDINGNone.

Abstract 2328: Interrogating the anti-cancer effects of co-enzyme Q10 (CoQ10) identifies metabolic and mitochondrial apoptotic responses as primary mechanisms in squamous cell carcinoma model

Targeting mitochondrial function as a therapeutic modality in cancer has been extensively investigated. BPM 31510 is a proprietary drug-lipid nanoconjugate formulation enabling delivery of supra-physiological concentrations of oxidized CoQ10 specifically into mitochondria. In this study, the anti-cancer properties of CoQ10 in squamous cell carcinoma (SCC) and its mechanism of action were investigated in in vivo xenograft and in vitro model systems. Nude mice were inoculated with a squamous carcinoma cell line isolated from tongue, SCC-25, and treated with a topical formulation containing 1.5% or 5% CoQ10. Treatment was associated with a dose-dependent delay in the detection of palatable tumors (14 ± 3 days vehicle control, 27 ± 7 days 1.5% cream, 39 ± 9 days 5% cream), (p<0.05). Histology and immunostaining analysis demonstrated a decrease in expression of VEGF in the treatment groups (p<0.05). The anti-cancer mechanism of action of CoQ10 was further investigated by interrogating the influence of CoQ10 exposure on molecular profiles using SCC-25 cells in vitro. Cell based assays, mRNA-based RT-PCR assays, and protein-based antibody chip microarrays confirmed an apoptotic response as a major anti-cancer effect in SCC-25 cells in response to CoQ10 exposure. The change in anti- and pro-apoptotic markers (Bcl-2 and caspase families) was independently confirmed by western blotting. In addition, global proteomic analysis revealed alterations in key metabolic proteins in the Pentose Phosphate Pathway (PPP). For example, expression of Transaldolase 1, an enzyme involved in the cellular protection against oxidative stress, resistance/susceptibility to apoptosis, and SCC tumor development and progression, was reduced 1.5 fold at both 6 and 24 hour time point in response to CoQ10 treatment. Together, the data suggests that CoQ10 influences cancer metabolism and redox pathway in activating apoptosis in SCC cancer model.

Citation Format: Niven R. Narain, Shiva Kazerounian, Shivani Khatu, Anne R. Diers, John McCook, Stephane Gesta, Robert S. Kirsner, Brian Berman, Rangaprasad Sarangarajan. Interrogating the anti-cancer effects of co-enzyme Q10 (CoQ10) identifies metabolic and mitochondrial apoptotic responses as primary mechanisms in squamous cell carcinoma model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2328.

Abstract 2342: Multidimensional metabolomic stratification of ER+/HER2- compared to ER-/HER2- breast tumors

Introduction: In the United States, breast cancer represents the leading cancer diagnosis among women and can readily be classified as a metabolic disease based on its distinct metabolic activity within the tumor microenvironment. Compared to other omics technologies, extensive lipidomic and metabolomic studies are lacking. Here in, we evaluated a cohort of 109 tumors characterized as ER+/HER2- and ER-/HER2- based on immunohistochemistry (IHC) and performed comprehensive structural lipidomic, signaling lipidomic, and global metabolomic analyses for an extensive characterization of the biophysical, signaling, and metabolic interplay between these tumors.

Methods: Clinical IHC subtyping of core biopsies was used to select a cohort of patients with ER+/HER2- or ER-/HER2- primary tumors from flash-frozen surgical samples. The positive/negative status of ER/PR/HER2 was defined using updated ASCO 2020 guidelines. Ki-67 status was determined using the 2011 St. Gallen's International Expert Consensus recommendations. ER low (1-10%) cases were excluded from this analysis. Structural lipidomic analysis was employed through the use of MS/MSALL high resolution shotgun lipidomics using a SCIEX 5600+ TripleTOF micro LC approach characterizing 23 lipid classes and over 1200 molecular species. Signaling lipids were analyzed using a SCIEX 6600 TripleTOF microLC platform characterizing 106 lipid analytes across octadecanoid, eicosanoid and docosanoid species. Metabolomics analysis was performed using LECO PEGASUS GC TOF, SCIEX 5500 HILIC LC MS/MS analysis, and SCIEX 6600 High resolution RP-LC-MS analysis detecting 450 metabolite Metabolomics data was further interpreted using MetaboAnalyst software.

Results/Conclusions: Compared to their ER+ counterparts, ER-/HER2- tumors exhibited a significant decrease in triacylglycerides, and a corresponding increase in cholesterol ester, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol species demonstrating a signature of biophysical and metabolic rewiring with alterations in Kennedy pathway lipid shuttling. One signaling lipid was decreased and six were increased (predominantly arachidonic species) in ER-/HER2- tumors compared to ER+/HER2- ones. Metabolomic analysis revealed distinct alterations in cysteine/methionine, arginine/proline, purine, butanoate, and tryptophan metabolism. Utilizing a multidimensional metabolic integration approach, we identified distinct biophysical, signaling, and biochemical alterations in ER+/HER2- compared to ER-/HER2- breast tumors, which may impact selection of therapy and outcome in the future.

Citation Format: Valerie Bussberg, Vladimir Tolstikov, Guisong Wang, Punit Shah, Rick Searfoss, Leigh Fantacone-Campbell, Jeffrey A. Hooke, Brenda Deyarmin, Rebecca N. Zingmark, Stella Somiari, Jianfang Liu, Leonid Kvecher, Bradley Mostoller, Lori Sturtz, Praveen-Kumar Raj-Kumar, Elder Granger, Linda Vahdat, Mary L. Cutler, Chas Bountra, Rangaprasad Sarangarajan, Hai Hu, Albert J. Kovatich, Michael A. Kiebish, Niven R. Narain, Craig D. Shriver. Multidimensional metabolomic stratification of ER+/HER2- compared to ER-/HER2- breast tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2342.

Abstract 1188: Reclassification of ER+ (luminal A/luminal B1 minus ER low)-like and ER- like breast tumors based on proteomic/gene and clinical outcome signatures

Introduction: Classification of breast cancer can incorporate immunohistochemical (IHC) detection of ER/PR/HER2/KI67 to stratify the subtypes. High throughput proteomics analysis allows for the expansion of biomarker discovery within the subtypes. We evaluated a cohort of 109 tumors characterized as ER+ (Luminal A and Luminal B1; HER2+ and ER low (1-10%) cases were excluded) compared to ER-/HER2- tumors. Utilizing an integrated bioinformatics approach, we developed a proteomic marker signature to reclassify tumors into ER+(like) and ER-(like) tumors. CPTAC (Proteomic)/TCGA (RNAseq) datasets and larger METBRIC and GSE96058 cohorts were used to validate this marker signature. The selected biomarkers demonstrated significant differences impacting survival outcome.

Methods: Clinical IHC subtyping of core biopsies was used to select a cohort of patients with ER+/HER2- and ER-/HER2- primary tumors from flash-frozen surgical samples. The positive/negative status of ER/PR/HER2 was defined using updated ASCO 2020 guidelines. Ki-67 status was determined using the 2011 St. Gallen's International Expert Consensus recommendations. Proteomic analysis was performed using Thermo Q-Exactive+ LC MS/MS analysis. Differential analysis was applied to select the significantly altered proteins between ER+ and ER- cases, Univariate survival analysis was engaged to filter informative protein/genes using TCGA RNA-Seq data. Nearest centroid analysis was deployed to define the classifier to predict novel molecular subtypes.

Results/Conclusions: We selected 34 proteins/genes from 164 significantly differentially expressed proteins for further analysis. The centroid model constructed with the 34 proteins defined 2 groups: ER+(like) and ER-(like). An additional 4 groups were defined across subtypes: luminal tumors classified both by IHC and marker signature (LL), luminal tumors classified by IHC but marker signature more like triple negative (LT), triple negative tumors classified by IHC but marker signature more like luminal (TL), and triple negative classified by both IHC and marker signature (TT). This marker signature segregated close to 5000 tumors across CPTAC, TCGA, METABRIC and GSE96058 cohorts. Survival analysis in these groups of patients revealed differences in radiation, hormone/radiation, hormone therapy, and hormone/radiation/chemotherapy treatments. In summary using proteomics data we identified a 34 gene/protein marker signature, validated in large external cohorts and exhibited impact on survival and response to therapy. Further, this signature was enriched in metabolism and microenvironmental associated factors that could represent novel targets or development combination strategies based on this signature.

Citation Format: Guisong Wang, Punit Shah, Rick Searfoss, Leigh Fantacone-Campbell, Jeffrey A. Hooke, Brenda Deyarmin, Rebecca N. Zingmark, Stella Somiari, Jianfang Liu, Leonid Kvecher, Bradley Mostoller, Lori A. Sturtz, Praven-Kumar Raj-Kumar, Elder Granger, Linda Vahdat, Mary L. Cutler, Chas Bountra, Rangaprasad Sarangarajan, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Niven R. Narain, Craig D. Shriver. Reclassification of ER+ (luminal A/luminal B1 minus ER low)-like and ER- like breast tumors based on proteomic/gene and clinical outcome signatures [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1188.

The influence of low-carbohydrate diets on the metabolic response to androgen-deprivation therapy in prostate cancer

BACKGROUND

Prostate cancer (PC) is the second most lethal cancer for men. For metastatic PC, standard first-line treatment is androgen deprivation therapy (ADT). While effective, ADT has many metabolic side effects. Previously, we found in serum metabolome analysis that ADT reduced androsterone sulfate, 3-hydroxybutyric acid, acyl-carnitines but increased serum glucose. Since ADT reduced ketogenesis, we speculate that low-carbohydrate diets (LCD) may reverse many ADT-induced metabolic abnormalities in animals and humans.

METHODS

In a multicenter trial of patients with PC initiating ADT randomized to no diet change (control) or LCD, we previously showed that LCD intervention led to significant weight loss, reduced fat mass, improved insulin resistance, and lipid profiles. To determine whether and how LCD affects ADT-induced metabolic changes, we analyzed serum metabolites after 3-, and 6-months of ADT on LCD versus control.

RESULTS

We found androsterone sulfate was most consistently reduced by ADT and was slightly further reduced in the LCD arm. Contrastingly, LCD intervention increased 3-hydroxybutyric acid and various acyl-carnitines, counteracting their reduction during ADT. LCD also reversed the ADT-reduced lactic acid, alanine, and S-adenosyl methionine (SAM), elevating glycolysis metabolites and alanine. While the degree of androsterone reduction by ADT was strongly correlated with glucose and indole-3-carboxaldehyde, LCD disrupted such correlations.

CONCLUSIONS

Together, LCD intervention significantly reversed many ADT-induced metabolic changes while slightly enhancing androgen reduction. Future research is needed to confirm these findings and determine whether LCD can mitigate ADT-linked comorbidities and possibly delaying disease progression by further lowering androgens.

Abstract 2982: Utility of S. cerevisiae genetic interactions in the mechanistic validation and therapeutic potential of highly conserved targets for drug discovery

Use of chemo-genetic interaction mediated synthetic lethality represents a strategy for mechanistic validation of targets and gene-based patient stratification for clinical development. Given that core pathways supporting cancer development and progression (cell cycle regulation, genome integrity, metabolism) are highly conserved, orthogonal model organisms represent powerful systems in which to identify synthetic lethal pairs for highly conserved human drug targets. BPM42522 is an enzyme in the ubiquitin proteasome system whose anti-cancer potential has been validated through genetic and pharmacologic modulation. The S. cerevisiae homolog of BPM42522 (yBPM42522) is a critical cell cycle-regulatory gene with 273 genetic interactions affecting fitness (Costanzo 2016). Negative genetic interactors regulate cellular processes validated for therapeutic intervention in oncology such as DNA replication and repair, protein turnover, and mitosis. Thus, mapping yBPM42522 negative genetic interactors to their human homologs and curating tumors in which they are altered may aid in identification of clinical contexts more susceptible to pharmacologic inhibition of BPM42522. To this end, conservation analysis of genetic interactors of yBPM42522 was performed, and coding mutations and deletion events were then characterized using The Cancer Genome Atlas (TCGA) tumor data. The most frequently altered genetic interactors across human tumors were reviewed for the direction and strength of the genetic interaction between their yeast homologs and yBPM42522, and mutations were curated by their likelihood to result in a loss of function. Those with strong negative genetic interactions with yBPM42522 and frequent mutation or deletion in its human homolog were prioritized. The resulting candidates included tumor suppressors (FBXW7, NF1), cell cycle regulators (CCNB1, CCNB3, BUB1B), and the NIMA kinase and GTPase-activating protein families (NEK3, NEK4, RASA1, RASAL2). TCGA database was used to determine if alterations in these candidate genes were prevalent in specific tumor types and whether they co-occurred with alterations in established cancer driver genes. Several candidate genetic interactors identified were frequently mutated or deleted in specific tumor types including uterine carcinosarcoma, uterine corpus endometrial carcinoma, ovarian serous cystadenocarcinoma, and mesothelioma. Moreover, these alterations were mutually exclusive with 96 reported cancer driver genes. Validation of the candidate genetic interactors for synthetic lethality with BPM42522 and their role in specific cancer types highlights the approach for rapid identification of synthetic lethality and its potential use to stratify patient populations most likely to benefit from therapeutic agents targeting highly conserved drug targets.

Citation Format: Anne R. Diers, Kris Richardson, Leonardo O. Rodrigues, Rangaprasad Sarangarajan, Niven R. Narain, Jennifer A. Benanti, Stephane Gesta. Utility of S. cerevisiae genetic interactions in the mechanistic validation and therapeutic potential of highly conserved targets for drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2982.

CRISPR-engineered human brown-like adipocytes prevent diet-induced obesity and ameliorate metabolic syndrome in mice

Brown and brown-like beige/brite adipocytes dissipate energy and have been proposed as therapeutic targets to combat metabolic disorders. However, the therapeutic effects of cell-based therapy in humans remain unclear. Here, we created human brown-like (HUMBLE) cells by engineering human white preadipocytes using CRISPR-Cas9-SAM-gRNA to activate endogenous uncoupling protein 1 expression. Obese mice that received HUMBLE cell transplants showed a sustained improvement in glucose tolerance and insulin sensitivity, as well as increased energy expenditure. Mechanistically, increased arginine/nitric oxide (NO) metabolism in HUMBLE adipocytes promoted the production of NO that was carried by S-nitrosothiols and nitrite in red blood cells to activate endogenous brown fat and improved glucose homeostasis in recipient animals. Together, these data demonstrate the utility of using CRISPR-Cas9 technology to engineer human white adipocytes to display brown fat-like phenotypes and may open up cell-based therapeutic opportunities to combat obesity and diabetes.

Comprehensive molecular pharmacodynamic assessment identifies response markers of intermediary metabolism associated with BPM 31510-IV treatment in advanced glioblastoma multiforme patients

2059

Background: BPM 31510-IV is a drug-lipid conjugate nanodispersion containing oxidized Coenzyme Q10 (CoQ10) in clinical development for glioblastoma multiforme (GBM). In a recently concluded Phase 1 study of BPM 31510-IV (NCT03020602), in addition to safety and tolerability, longitudinal pharmacodynamic samples (20 samples/cycle of 28 days) were collected at various times in patient’s refractory to radiation, temozolomide, and bevacizumab. Methods: Comprehensive multi-omic (proteomic, lipidomic, metabolomic) profiles were generated from buffy coat (proteomics only), plasma, and urine matrices. These data were further analyzed using bAIcis, a Bayesian statistics based artificial intelligence (AI) software, creating causal networks linking clinical information and endpoints to molecular composition of diverse biomatrices of patients prior to, as well as during, treatment with BPM 31510-IV. Twelve subjects comprised the intent to treat population (ITT) which were stratified across days of treatment (DR1; ≤28 days; DLT period; n=6) and (DR2, OS; >28 days; n=6). Bayesian networks and regression analysis were performed on the outputs of the analysis. Molecular analyte panels (combination of proteins, lipids, and metabolites) descriptive of progression free survival (PFS), adverse events (possibly/probably related to BPM 31510-IV), and of overall survival (OS) were generated. Results: Significant alteration (p<0.05) of metabolically associated protein and critical metabolite drivers of intermediary metabolism were identified as causally related to PFS. Significant quantitative changes in levels of several proteins (buffy coat) and metabolites (urine) were identified with probable or possible associations to adverse events in BPM 31510-IV treated subjects. Conclusions: Overall, alterations in proteins and metabolites influencing mitochondrial function and intermediary metabolism that differentiated responders versus non-responders and identified potential markers of adverse events associated with BPM 31510-IV exposure were identified and will be further explored for complementary diagnostic utility.

Elevated levels of mitochondrial CoQ10 induce ROS-mediated apoptosis in pancreatic cancer

Reactive oxygen species (ROS) are implicated in triggering cell signalling events and pathways to promote and maintain tumorigenicity. Chemotherapy and radiation can induce ROS to elicit cell death allows for targeting ROS pathways for effective anti-cancer therapeutics. Coenzyme Q10 is a critical cofactor in the electron transport chain with complex biological functions that extend beyond mitochondrial respiration. This study demonstrates that delivery of oxidized Coenzyme Q10 (ubidecarenone) to increase mitochondrial Q-pool is associated with an increase in ROS generation, effectuating anti-cancer effects in a pancreatic cancer model. Consequent activation of cell death was observed in vitro in pancreatic cancer cells, and both human patient-derived organoids and tumour xenografts. The study is a first to demonstrate the effectiveness of oxidized ubidecarenone in targeting mitochondrial function resulting in an anti-cancer effect. Furthermore, these findings support the clinical development of proprietary formulation, BPM31510, for treatment of cancers with high ROS burden with potential sensitivity to ubidecarenone.

Abstract PS5-34: Identification of proteomics-based biomarkers for ER+/HER2- breast cancer stratification: Implications on clinical outcome

Introduction: Improving stratification of breast cancer (BC) patients based on molecular signatures for treatment responses and clinical outcomes is a critical unmet need. Currently, endocrine therapy is first-line for hormone receptor positive (HR+) BC. Chemotherapy is added to patients with high-risk luminal BC. In practice, levels of Ki-67 are used to distinguish luminal tumors as low-risk luminal A (LA) and high-risk luminal B (LB) for adjuvant therapy decisions. Herein, proteomic tumor assessment from ER-positive HER2-negative (ER+/HER2-) BC patients was utilized to define molecular subtyping, estimate congruency between proteomic subtyping and traditionally used Ki67 marker, and define a new set of potential predictive and prognostic therapeutic biomarkers for ER+/HER2- BC patients.

Method/Result: Clinical immunohistochemistry (IHC) subtyping of core biopsies was used to select a cohort of 86 BC patients with ER+/HER2- primary tumors from flash-frozen surgical samples. The positive/negative status of ER/PR/HER2 was defined using updated ASCO 2020 guidelines. Ki-67 status was determined using the 2011 St. Gallen’s International Expert Consensus recommendations. The cohort includes 28 LA (Ki67 &lt; 14%) cases and 58 LB1 (Ki67 &gt;= 14%) cases. Integrated consensus clustering algorithms with the most varying proteins in our cohort were applied to identify proteomic subtypes. Two distinct separations were observed from the analysis, resulting in one cluster enriched with LA (40 cases) and the other enriched with LB1 (46 cases) called by Fisher’s exact test. These clusters matched 100% with the clusters generated using 900+ proteins common to the 1500+ proteins used in the CPTAC-BC proteomics-based subtyping analysis (Mertins et al. Nature 2016). The differential analyses demonstrated that there is no significant difference between Ki67-defined subtypes and proteomics-defined subtypes (LA-enriched vs. LA cases, LB1-enriched vs. LB1 cases),indicating they are consistent in the molecular profile. Differential analysis was performed to compare LB1-enriched versus LA-enriched cases, resulting in 672 significantly differentially expressed proteins defined at false discovery rate (FDR) &lt; 0.05 and |log2(fold change)|&gt;1. 353 of the 672 proteins were correlated with mRNA at Pearson correlation &gt; 0.39 as reported in the CPTAC-BC study or cBioPortal for Cancer Genome, and their coding genes were used for progression free interval (PFI) analysis based on TCGA RNA-seq data in the TCGA ER+/HER2- cases (662 cases, c.f. Huo et al. JAMA Oncology 2017). 90 of the 353 coding genes significantly associated with PFI were detected at p-value&lt;0.05. Unsupervised hierarchical clustering method and principal component analysis (PCA) of the 90 genes were applied to our cohort to investigate the clustering performance and 94.2% of the cases were clustered correctly using support vector machine (SVM) method after PCA analysis. Biological process and molecular function GO term over-representation analyses of the 90 coding genes were performed separately. Some significant and biologically meaningful GO terms were identified at FDR&lt;0.05.

Conclusions: We identified a set of biomarkers that can be potentially employed as proteomic or gene signatures to stratify ER+/HER2- BC into low risk and high-risk groups.

Disclaimers The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions, or policies of Uniformed Services University of the Health Sciences, The Henry M Jackson Foundation for the Advancement of Military Medicine Inc., the Department of Defense or the Departments of the Army, Navy or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government.

Citation Format: Guisong Wang, Punit Shah, Rick Searfoss, J. Leigh Fantacone Campbell, Jeffrey A. Hooke, Brenda Deyarmin, Rebecca N. Zingmark, Stella Somiari, Jianfang Liu, Leonid Kvecher, Lori A. Sturtz, Praveen-Kumar Raj-Kumar, Elder Granger, Linda Vahdat, Mary L. Cutler, Rangaprasad Sarangarajan, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Niven R. Narain, Craig D. Shriver. Identification of proteomics-based biomarkers for ER+/HER2- breast cancer stratification: Implications on clinical outcome [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-34.

Abstract PS18-38: Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples

Background: Proteomic studies are typically conducted using flash-frozen (FF) samples utilizing tandem mass spectrometry. However, FF samples are comprised of multiple cell types, making it difficult to ascertain the proteomic profiles of specific cells. Conversely, OCT-embedded (Optimal Cutting Temperature compound) specimens can undergo laser microdissection (LMD) to capture and study specific cell types separately from the cell mixture. In the current study, we compared proteomic data obtained from FF and OCT samples to determine if samples that are stored and processed differently produce comparable results. Methods: Proteins were extracted from FF and OCT-embedded invasive breast tumors from 5 female patients. FF samples were lysed via homogenization (FF/HOM) while OCT-embedded specimens underwent LMD to collect only tumor cells (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS) followed by incubation at 37°C. Proteins were extracted using the illustra triplePrep kit and then trypsin-digested, TMT-labeled, and processed by two-dimensional liquid chromatography-tandem mass spectrometry (2D LC-MS/MS). Proteins were identified and quantified with Proteome Discoverer v1.4 and comparative analyses performed to identify proteins that were significantly differentially expressed amongst the different processing methods. Results: Among 4,950 proteins consistently quantified across all samples, 216 and 171 proteins were significantly differentially expressed (adjusted p-value &lt; 0.05; |log2 FC| &gt; 1) between FF/HOM vs. OCT/LMD-T and FF/HOM vs. OCT/LMD-TS, respectively, with most proteins being more highly abundant in the FF/HOM samples. PCA and unsupervised hierarchical clustering analysis with these 216 and 171 proteins were able to distinguish FF/HOM from OCT/LMD-T and OCT/LMD-TS samples, respectively. Likewise, PCA analysis and unsupervised clustering analysis using the 402 and 60 significantly differentially enriched GO terms (adjusted p-value (BH) &lt; 0.2) in the FF/HOM vs. OCT/LMD-T and FF/HOM vs OCT/LMD-TS comparisons, respectively, not only distinguished OCT/LMD from FF/HOM samples but also separated LA and LB1 breast cancer subtypes within each storage/preparation method from one another. Although FF/HOM appears to be more similar to OCT/LMD-TS than OCT/LMD-T based on the number of differentially enriched proteins (216 vs. 171; p=0.022) and GO terms (402 vs. 60; p &lt; 2.2 x 10-16), FF/HOM shows no greater similarity to OCT/LMD-TS than OCT/LMD-T based on PCA analysis with either proteins or GO terms ( based on weighted distance for pairwise samples, p = 0.97 from paired t-test). No significantly differentially enriched proteins or GO terms were detected between the OCT/LMD-T and OCT/LMD-TS samples but trended differences were detected. Conclusions: The proteomic profiles of the OCT/LMD-TS samples were more similar to those from OCT/LMD-T samples than FF/HOM samples, suggesting a strong influence from the sample processing methods. These results indicate that in LC-MS/MS proteomic studies, FF/HOM samples exhibit different protein profiles from OCT/LMD samples and thus, results from these two different methods cannot be directly compared. Our study also provides preliminary data for designing new studies to explore why OCT/LMD-TS samples are more similar to OCT/LMD-T than to FF/HOM samples, and to separate LA from LB1 samples. Disclaimer: The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of USUHS, HJF, the DOD or the Departments of the Army, Navy or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government.

Citation Format: Lori A. Sturtz, Guisong Wang, Punit Shah, Richard Searfoss, Praveen-Kumar Raj-Kumar, Jeffrey A. Hooke, J. Leigh Fantacone-Campbell, Brenda Deyarmin, Mary Lou Cutler, Rangaprasad Sarangarajan, Niven R. Narain, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Craig D. Shriver. Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS18-38.

Skeletal Muscle Energetics and Mitochondrial Function Are Impaired Following 10 Days of Bed Rest in Older Adults

Background

Older adults exposed to periods of inactivity during hospitalization, illness, or injury lose muscle mass and strength. This, in turn, predisposes poor recovery of physical function upon reambulation and represents a significant health risk for older adults. Bed rest (BR) results in altered skeletal muscle fuel metabolism and loss of oxidative capacity that have recently been linked to the muscle atrophy program. Our primary objective was to explore the effects of BR on mitochondrial energetics in muscle from older adults. A secondary objective was to examine the effect of β-hydroxy-β-methylbuturate (HMB) supplementation on mitochondrial energetics.

Methods

We studied 20 older adults before and after a 10-day BR intervention, who consumed a complete oral nutritional supplement (ONS) with HMB (3.0 g/d HMB, n = 11) or without HMB (CON, n = 9). Percutaneous biopsies of the vastus lateralis were obtained to determine mitochondrial respiration and H₂O₂ emission in permeabilized muscle fibers along with markers of content. RNA sequencing and lipidomics analyses were also conducted.

Results

We found a significant up-regulation of collagen synthesis and down-regulation of ribosome, oxidative metabolism and mitochondrial gene transcripts following BR in the CON group. Alterations to these gene transcripts were significantly blunted in the HMB group. Mitochondrial respiration and markers of content were both reduced and H₂O₂ emission was elevated in both groups following BR.

Conclusions

In summary, 10 days of BR in older adults causes a significant deterioration in mitochondrial energetics, while transcriptomic profiling revealed that some of these negative effects may be attenuated by an ONS containing HMB.

Brown Fat-Activating Lipokine 12,13-diHOME in Human Milk Is Associated With Infant Adiposity

CONTEXT

Little is known about the specific breastmilk components responsible for protective effects on infant obesity. Whether 12,13-dihydroxy-9Z-octadecenoic acid (12,13-diHOME), an oxidized linoleic acid metabolite and activator of brown fat metabolism, is present in human milk, or linked to infant adiposity, is unknown.

OBJECTIVE

To examine associations between concentrations of 12,13-diHOME in human milk and infant adiposity.

DESIGN

Prospective cohort study from 2015 to 2019, following participants from birth to 6 months of age.

SETTING

Academic medical centers.

PARTICIPANTS

Volunteer sample of 58 exclusively breastfeeding mother-infant pairs; exclusion criteria included smoking, gestational diabetes, and health conditions with the potential to influence maternal or infant weight gain.

MAIN OUTCOME MEASURES

Infant anthropometric measures including weight, length, body mass index (BMI), and body composition at birth and at 1, 3, and 6 months postpartum.

RESULTS

We report for the first time that 12,13-diHOME is present in human milk. Higher milk 12,13-diHOME level was associated with increased weight-for-length Z-score at birth (β = 0.5742, P = 0.0008), lower infant fat mass at 1 month (P = 0.021), and reduced gain in BMI Z-score from 0 to 6 months (β = -0.3997, P = 0.025). We observed similar associations between infant adiposity and milk abundance of related oxidized linoleic acid metabolites 12,13-Epoxy-9(Z)-octadecenoic acid (12,13-epOME) and 9,10-Dihydroxy-12-octadecenoic acid (9,10-diHOME), and metabolites linked to thermogenesis including succinate and lyso-phosphatidylglycerol 18:0. Milk abundance of 12,13-diHOME was not associated with maternal BMI, but was positively associated with maternal height, milk glucose concentration, and was significantly increased after a bout of moderate exercise.

CONCLUSIONS

We report novel associations between milk abundance of 12,13-diHOME and adiposity during infancy.

Endogenous Fatty Acid Synthesis Drives Brown Adipose Tissue Involution

Thermoneutral conditions typical for standard human living environments result in brown adipose tissue (BAT) involution, characterized by decreased mitochondrial mass and increased lipid deposition. Low BAT activity is associated with poor metabolic health, and BAT reactivation may confer therapeutic potential. However, the molecular drivers of this BAT adaptive process in response to thermoneutrality remain enigmatic. Using metabolic and lipidomic approaches, we show that endogenous fatty acid synthesis, regulated by carbohydrate-response element-binding protein (ChREBP), is the central regulator of BAT involution. By transcriptional control of lipogenesis-related enzymes, ChREBP determines the abundance and composition of both storage and membrane lipids known to regulate organelle turnover and function. Notably, ChREBP deficiency and pharmacological inhibition of lipogenesis during thermoneutral adaptation preserved mitochondrial mass and thermogenic capacity of BAT independently of mitochondrial biogenesis. In conclusion, we establish lipogenesis as a potential therapeutic target to prevent loss of BAT thermogenic capacity as seen in adult humans.

Schlein et al. show that carbohydrate-response element-binding protein (ChREBP) controls de novo lipogenesis (DNL) in brown adipose tissue (BAT) and determines BAT whitening in response to thermoneutral housing. ChREBP deficiency prevents enrichment of DNL-derived lipids and mitophagy during BAT involution, which is associated with higher thermogenic capacity.

A phase I safety study of topical calcitriol (BPM31543) for the prevention of chemotherapy-induced alopecia

PURPOSE

Chemotherapy-induced alopecia (CIA) negatively affects psychosocial health and quality of life (QoL). Currently, there are no approved pharmacologic agents to prevent CIA. Here, we evaluated the safety, tolerability, and potential signal of efficacy of topical calcitriol (BPM31543) on CIA prevention.

MATERIALS AND METHODS

This Phase 1 trial included 23 female patients with breast cancer, gynecologic cancer, or sarcomas receiving a taxane-based chemotherapy. Patients received a 3 + 3 dose-escalation regimen at 5, 10, 20, 40, 60, and 80 μg/mL, with 3-6 patients per group. Patients applied topical BPM31543 to the scalp twice a day for 2 weeks prior to chemotherapy and continued until chemotherapy treatment was completed. The maximum tolerated dose (MTD) during first 28 day application was determined. Adverse event (AE) monitoring, pharmacokinetics, blinded photographic assessments, and patient self-assessment were evaluated.

RESULTS

Out of 23 patients treated with BPM31543, 8 patients experienced at least 1 treatment-related adverse event (AE). The majority of AEs were mild to moderate in severity. Only 1 patient experienced SAEs (vomiting, nausea, fever, and flank pain) considered treatment related. Alopecia < 50% from baseline was observed in 8 patients at Week 7, and, of which 2 patients had < 50% alopecia maintained at Week 15. There were no detectable effects of topical BPM31543 on serum levels of calcitriol.

CONCLUSIONS

BPM31543 applied topically twice daily to the scalp is safe and well tolerated in patients receiving taxane-based chemotherapy. No DLT was observed at up to 80 µg/mL, and MTD was not reached. Based on the data from this trial, BPM31543 represents a promising therapy and warrants further investigation in Phase 2/3 trials.

Author Correction: Divergence in the metabolome between natural aging and Alzheimer's disease

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Comparative analysis of differentially abundant proteins quantified by LC-MS/MS between flash frozen and laser microdissected OCT-embedded breast tumor samples

Background

Proteomic studies are typically conducted using flash-frozen (FF) samples utilizing tandem mass spectrometry (MS). However, FF specimens are comprised of multiple cell types, making it difficult to ascertain the proteomic profiles of specific cells. Conversely, OCT-embedded (Optimal Cutting Temperature compound) specimens can undergo laser microdissection (LMD) to capture and study specific cell types separately from the cell mixture. In the current study, we compared proteomic data obtained from FF and OCT samples to determine if samples that are stored and processed differently produce comparable results.

Methods

Proteins were extracted from FF and OCT-embedded invasive breast tumors from 5 female patients. FF specimens were lysed via homogenization (FF/HOM) while OCT-embedded specimens underwent LMD to collect only tumor cells (OCT/LMD-T) or both tumor and stromal cells (OCT/LMD-TS) followed by incubation at 37 °C. Proteins were extracted using the illustra triplePrep kit and then trypsin-digested, TMT-labeled, and processed by two-dimensional liquid chromatography-tandem mass spectrometry (2D LC–MS/MS). Proteins were identified and quantified with Proteome Discoverer v1.4 and comparative analyses performed to identify proteins that were significantly differentially expressed amongst the different processing methods.

Results

Among the 4,950 proteins consistently quantified across all samples, 216 and 171 proteins were significantly differentially expressed (adjusted p-value < 0.05; |log₂ FC|> 1) between FF/HOM vs. OCT/LMD-T and FF/HOM vs. OCT/LMD-TS, respectively, with most proteins being more highly abundant in the FF/HOM samples. PCA and unsupervised hierarchical clustering analysis with these 216 and 171 proteins were able to distinguish FF/HOM from OCT/LMD-T and OCT/LMD-TS samples, respectively. Similar analyses using significantly differentially enriched GO terms also discriminated FF/HOM from OCT/LMD samples. No significantly differentially expressed proteins were detected between the OCT/LMD-T and OCT/LMD-TS samples but trended differences were detected.

Conclusions

The proteomic profiles of the OCT/LMD-TS samples were more similar to those from OCT/LMD-T samples than FF/HOM samples, suggesting a strong influence from the sample processing methods. These results indicate that in LC–MS/MS proteomic studies, FF/HOM samples exhibit different protein expression profiles from OCT/LMD samples and thus, results from these two different methods cannot be directly compared.

A Novel Endocrine Role for the BAT-Released Lipokine 12,13-diHOME to Mediate Cardiac Function

BACKGROUND

Brown adipose tissue (BAT) is an important tissue for thermogenesis, making it a potential target to decrease the risks of obesity, type 2 diabetes, and cardiovascular disease, and recent studies have also identified BAT as an endocrine organ. Although BAT has been implicated to be protective in cardiovascular disease, to this point there are no studies that identify a direct role for BAT to mediate cardiac function.

METHODS

To determine the role of BAT on cardiac function, we utilized a model of BAT transplantation. We then performed lipidomics and identified an increase in the lipokine 12,13-dihydroxy-9Z-octadecenoic acid (12,13-diHOME). We utilized a mouse model with sustained overexpression of 12,13-diHOME and investigated the role of 12,13-diHOME in a nitric oxide synthase type 1 deficient (NOS1^-/-) mouse and in isolated cardiomyocytes to determine effects on function and respiration. We also investigated 12,13-diHOME in a cohort of human patients with heart disease.

RESULTS

Here, we determined that transplantation of BAT (+BAT) improves cardiac function via the release of the lipokine 12,13-diHOME. Sustained overexpression of 12,13-diHOME using tissue nanotransfection negated the deleterious effects of a high-fat diet on cardiac function and remodeling, and acute injection of 12,13-diHOME increased cardiac hemodynamics via direct effects on the cardiomyocyte. Furthermore, incubation of cardiomyocytes with 12,13-diHOME increased mitochondrial respiration. The effects of 12,13-diHOME were absent in NOS1^-/- mice and cardiomyocytes. We also provide the first evidence that 12,13-diHOME is decreased in human patients with heart disease.

CONCLUSIONS

Our results identify an endocrine role for BAT to enhance cardiac function that is mediated by regulation of calcium cycling via 12,13-diHOME and NOS1.

Chronic stress and antidepressant treatment alter purine metabolism and beta oxidation within mouse brain and serum

Major depressive disorder (MDD) is a complex condition with unclear pathophysiology. Molecular disruptions within limbic brain regions and the periphery contribute to depression symptomatology and a more complete understanding the diversity of molecular changes that occur in these tissues may guide the development of more efficacious antidepressant treatments. Here, we utilized a mouse chronic social stress model for the study of MDD and performed metabolomic, lipidomic, and proteomic profiling on serum plus several brain regions (ventral hippocampus, nucleus accumbens, and medial prefrontal cortex) of susceptible, resilient, and unstressed control mice. To identify how commonly used tricyclic antidepressants impact the molecular composition in these tissues, we treated stress-exposed mice with imipramine and repeated our multi-OMIC analyses. Proteomic analysis identified three serum proteins reduced in susceptible animals; lipidomic analysis detected differences in lipid species between resilient and susceptible animals in serum and brain; and metabolomic analysis revealed dysfunction of purine metabolism, beta oxidation, and antioxidants, which were differentially associated with stress susceptibility vs resilience by brain region. Antidepressant treatment ameliorated stress-induced behavioral abnormalities and affected key metabolites within outlined networks, most dramatically in the ventral hippocampus. This work presents a resource for chronic social stress-induced, tissue-specific changes in proteins, lipids, and metabolites and illuminates how molecular dysfunctions contribute to individual differences in stress sensitivity.

High levels of ubidecarenone (oxidized CoQ10) delivered using a drug-lipid conjugate nanodispersion (BPM31510) differentially affect redox status and growth in malignant glioma versus non-tumor cells

Metabolic reprogramming in cancer cells, vs. non-cancer cells, elevates levels of reactive oxygen species (ROS) leading to higher oxidative stress. The elevated ROS levels suggest a vulnerability to excess prooxidant loads leading to selective cell death, a therapeutically exploitable difference. Co-enzyme Q₁₀ (CoQ₁₀) an endogenous mitochondrial resident molecule, plays an important role in mitochondrial redox homeostasis, membrane integrity, and energy production. BPM31510 is a lipid-drug conjugate nanodispersion specifically formulated for delivery of supraphysiological concentrations of ubidecarenone (oxidized CoQ₁₀) to the cell and mitochondria, in both in vitro and in vivo model systems. In this study, we sought to investigate the therapeutic potential of ubidecarenone in the highly treatment-refractory glioblastoma. Rodent (C6) and human (U251) glioma cell lines, and non-tumor human astrocytes (HA) and rodent NIH3T3 fibroblast cell lines were utilized for experiments. Tumor cell lines exhibited a marked increase in sensitivity to ubidecarenone vs. non-tumor cell lines. Further, elevated mitochondrial superoxide production was noted in tumor cells vs. non-tumor cells hours before any changes in proliferation or the cell cycle could be detected. In vitro co-culture experiments show ubidecarenone differentially affecting tumor cells vs. non-tumor cells, resulting in an equilibrated culture. In vivo activity in a highly aggressive orthotopic C6 glioma model demonstrated a greater than 25% long-term survival rate. Based on these findings we conclude that high levels of ubidecarenone delivered using BPM31510 provide an effective therapeutic modality targeting cancer-specific modulation of redox mechanisms for anti-cancer effects.

Abstract 2943: Interrogative Biology® platform identifies a novel target in the ubiquitin pathway and its utility in cancer is supported by small molecule modulators

Identification of novel therapeutic targets for the development of drugs with a large spectrum of applications in oncology is extremely difficult due, in part, to the complex and heterogenous etiology of the disease. To address this, we interrogated in vitro cancer models representative of multiple tumor types (HepG2, MIA PaCa2, SKMEL28, SCC-25, SkBr-3 MCF7, PC-3, and LnCAP) and compared them to non-tumorigenic and primary cells. Proteomic profiling of these models under various cancer relevant perturbations and analysis through a Bayesian Artificial Intelligence algorithm (Interrogative Biology® platform) allowed the generation of causal inference networks which identified BPM42522 as potential therapeutic target. The anticancer potential of BPM42522, an enzyme in the ubiquitin proteasomal system, was then validated through molecular and pharmacological modulation. siRNA mediated knockdown of BPM42522 resulted in a 50% decrease in cell number in MIA PaCa2 cells and a 30% decrease in cell number in SKHEP1 and HepG2 cells at 96h post transfection. This effect was the result of a robust G2/M cell cycle arrest associated with increased CyclinB1 expression. In addition, a modest increased in apoptosis/necrosis (6-8%) was observed in cells with BPM42522 knockdown. Using Fragment-Based Ligand Discovery, we developed a series of compounds modulating BPM42522 activity and exhibiting anti-cancer properties. A panel of cells lines (Oncolines™) was used to evaluate the potency of our optimized lead compounds. Of 102 cell lines, treatment with optimized lead molecules for 72h reduced the viability of 76 cells lines by more than 70% with an IC50 ranging from 17nM to 318nM. Additional studies on a selected panel of cancer cell lines, upon treatment with modulators, demonstrated that this effect was the result of a G2/M arrest occurring as early as 5h and significantly different by 24h. The accumulation of cells in G2/M was confirmed by increased expression of CyclinB1 and phospho-histone H3 in a dose dependent manner. Furthermore, this increase in G2/M arrest was followed by an increase in apoptosis which could be observed within 24h and progressed until 72h. Identification of BPM42522 as a target for cancer and development of small molecule modulators demonstrates the utility of BERG's Interrogative Biology® platform in elucidating fundamental biology to identify novel therapeutic targets, based on causality, with broad anti-cancer properties.

Citation Format: Stephane Gesta, Shefali Sharma, Pragalath Sundararajan, Mingshu Huang, Kayleigh Gray, Maria Nastke, Arcan Guven, Anne Diers, Shiva Kazerounian, Suwagmani Hazarika, Eric M. Grund, Vivek K. Vishnudas, Niven R. Narain, Rangaprasad Sarangarajan. Interrogative Biology® platform identifies a novel target in the ubiquitin pathway and its utility in cancer is supported by small molecule modulators [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2943.

Abstract 2968: BPM31510, a Coenzyme Q10 (CoQ10) containing lipid nanodispersion, enhances radiation effects to prolong survival in a rodent glioblastoma model

BPM31510 is a Coenzyme Q10 (CoQ10)-containing lipid nanodispersion in clinical development for the treatment of glioblastoma. Prior results demonstrate that high doses of CoQ10 delivered via BPM31510 differentially increases oxidative stress in glioblastoma relative to non-tumor cells in vitro and extends long-term survival (LTS) in an in vivo glioblastoma model. Since a primary consequences of tumor irradiation is induction of oxidative stress, we hypothesized that BPM31510 treatment would result in an enhanced radiation response and influence survival outcomes.1 x 106 luciferase labeled C6 cells were implanted into the right striatum of Sprague Dawley rats. 4 days post-implantation, rats were randomized into one of four groups: (i) Saline injection ip bid; (ii) BPM31510 50 mg/kg ip bid to continue up to 35 days; (iii) 12 Gy radiotherapy (RT) to be administered on Day 8 post-implant with saline injection; and (iv) BPM31510 + RT. Tumor-bearing rats were monitored until death or Day 50. Log rank survival analysis indicated a marked enhancement of median survival with the addition of BPM31510 to RT. While neither RT nor BPM31510 enhanced median survival relative to saline, the combination was markedly more effective (median survival of 17, 19, 24 and &gt;50 days for saline, BPM31510, RT and combination, respectively, p &lt; 0.001). This was also reflected in increase in frequency of LTS, which was over 70% (11 of 14 rats) in the combination group (p &lt; 0.01 compared to control). BPM31510 significantly enhanced the therapeutic efficacy of radiation in this model of glioblastoma. Effects on median survival and an enhancement of LTS with combination treatment were observed. While the mechanistic underpinnings are under investigation, the low toxicity profile of BPM31510 and its potential protective effects on normal cells may offer a unique strategy with which to enhance radiation.

Citation Format: Jiaxin Sun, Milton Merchant, Anne R. Diers, Shiva Kazerounian, Stephane Gesta, Niven R. Narain, Rangaprasad Sarangarajan, Seema Nagpal, Lawrence Recht. BPM31510, a Coenzyme Q10 (CoQ10) containing lipid nanodispersion, enhances radiation effects to prolong survival in a rodent glioblastoma model [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2968.

Abstract 5311: Integrated proteomic and informatic assessment of ER+/HER2- and ER-/HER2- breast tumors

Introduction

Emerging OMIC technologies enable the comprehensive molecular characterization of breast cancer to continually evolve. Published gene expression-based studies have differentiated ER-positive and ER-negative breast cancer. Herein, we have expanded these investigations utilizing a proteomics approach.

Methods

Clinical IHC subtyping on core biopsies was used to select available flash-frozen surgical samples for a cohort of 121 primary breast cancer patients. The cohort includes 103 ER+/HER2- and 18 ER-/PR-/HER2- cases. Mass spectrometry-based analyses were performed on these samples for proteomic, metabolomic, and lipidomic features. Comparative analysis was performed on proteomic data between the two groups of samples using Limma with stratified subsampling method and significance is reported at FDR&lt;0.05 and absolute FC&gt;1.5. PCA and hierarchical clustering analysis were applied on our training dataset and independent testing datasets using the identified significantly differentially expressed proteins as a signature to distinguish ER+/HER2- samples from ER-/PR-/HER2- samples. Euclidian distance was used as distance matrix and Ward was used as a linkage method in hierarchical clustering algorithm.

Results

The cohort was split into a training set (81 cases) and a testing set (40 cases) using stratification randomization. There were 171 differentially expressed proteins identified from the training dataset. 95% cases in our training dataset and 92.5% cases in our testing dataset were clustered correctly using hierarchical clustering method with the 171 proteins. Publicly available datasets from TCGA (RNA-seq, 846 cases) and CPTAC (proteomics, 57 cases) further validated the proteomic results from our cohort. 94.7% cases in CPTAC cohort and 93.2% cases in TCGA RNA-seq cohort were clustered correctly using the 171 proteins. KEGG pathway analysis using the differentially expressed proteins identified two significant pathways at FDR &lt; 0.05: DNA replication and cysteine and methionine metabolism. Independent metabolomic and lipidomic analysis identified profiles supporting our proteomic analysis. These results confirm that ER+/HER2- and ER-/PR-/HER2- tumors are molecularly distinct which can be separated by a panel of expressed proteins.

Disclaimers

The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of Uniformed Services University of the Health Sciences, The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., the Department of Defense, the Departments of the Army, Navy, or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government.

Citation Format: Guisong Wang, Punit Shah, Vladimir Tolstikov, Praveen-Kumar Raj-Kumar, Jianfang Liu, Lori A. Sturtz, J. Leigh Fantacone-Campbell, Rebecca Zingmark, Jeffrey A. Hooke, Mary L. Cutler, Kris Richardson, Leonardo Rodrigues, Valerie Bussberg, Rangaprasad Sarangarajan, Niven R. Narain, Hai Hu, Michael A. Kiebish, Albert J. Kovatich, Craig D. Shriver. Integrated proteomic and informatic assessment of ER+/HER2- and ER-/HER2- breast tumors [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5311.

Abstract 2860: Impact of hemolysis on multi-omic pancreatic cancer biomarker discovery: De-risking precision medicine biomarker development

Biomarker analysis is critically dependent on the quality of biofluid or tissue samples obtained from human research studies. Although proteomic, lipidomic, and metabolomic analyses can be dramatically impacted by the time of sample collection, fasting status, and participant demographics, the hemolysis status of plasma, serum or buffy coat samples is a poorly understood confounder of sample quality. Hemoglobin levels can range between 0 - 10 g/L in samples (referred to as 1-4 in plasma/serum and 0-4 level in buffy coat) as a marker of hemolysis severity and sample contamination by reticulocyte-derived analytes. In oncology clinical trials, patients can be more susceptible to hemolysis due to chemotherapy treatment, which can impact sample assessment and study results. Herein, we analyzed 941 plasma and 950 serum samples using comprehensive proteomics, structural lipidomics, signaling lipidomics, and metabolomics in a pancreatic cancer biomarker discovery program referred to as Project Survival as well as 951 buffy coat samples using only proteomic analysis. Project survival is a 7-year longitudinal pancreatic cancer biomarker discovery trial analyzing 400+ pancreatic cancer and at-risk patients using multi-omic and multiple biofluid assessment. To date this study yielded samples in plasma with 92.3% - #1, 6.5% - #2, 1.2% - #3, and 0% - #4 hemolysis, serum with 94.8% - #1, 3.8% - #2, 1.4% - #3, and 0% - #4 hemolysis and buffy coat 42.7% - #0, 25.6% - #1, 20.8% -#2, 10.4% - #3, and 0.5% - #4 hemolysis. Multi-omic and regression analysis of sample data for hemolysis status revealed a distinct pattern of OMIC variables correlated with the degree of hemolysis. Proteomics analysis was the greatest impacted in terms of the protein identification and quantitation. Additionally, pathway analysis revealed expected pathways associated with hemolysis and coagulation, but also unknown pathways and corresponding proteins that were differentially correlated with hemolysis state. Additionally, metabolomics and lipidomics analysis also revealed distinct differentials associated with hemolysis state. Herein, our analysis is the first to analyze thousands of samples using multi-omics revealing critically informative molecular differentials across OMIC technologies demonstrating that caution should be given to avoid these identified biomarkers for translational development.

Citation Format: Michael A. Kiebish, Punit Shah, Valerie Bussberg, Vladimir Tolstikov, Rick Searfoss, Kennedy Ofori-Mensa, Eric M. Grund, Abena Darkwah, Emily Y. Chen, Bennett Greenwood, Ellaine Adu Ntoso, Leonardo Rodrigues, Mia Liu, Elder Granger, Chas Bountra, Rangaprasad Sarangarajan, A J. Moser, Niven R. Narain. Impact of hemolysis on multi-omic pancreatic cancer biomarker discovery: De-risking precision medicine biomarker development [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2860.

Abstract 2929: Benchmarking targets from cancer models using causal inference based drug-target and phenotype identification (Interrogative Biology®) cross-validates “high-priority” targets identified in CRISPR-CAS9 screen

In 2018, the FDA set a record of 59 new drug approvals. However, the percentage of first-in-class drugs to date has not exceeded 50% since 2015. The advent of innovative and orthogonal technologies focused on biological and phenotypic outcomes provides opportunity for identification of novel disease specific target identification for drug discovery programs. The Interrogative Biology® platform deconstructs the drug discovery paradigm by comprehensive molecular capture of human derived disease models. Using high-throughput multi-omic (proteomic, lipidomic, metabolomic) profiling and the causal inference-based AI tool, bAIcis®, the BERG Interrogative Biology® platform, identifies new therapeutic targets and biomarkers, as well as provides de novo inference to mechanism of action. BERG's pan-cancer models were built using multiple normal/cancer model systems covering broad etiologies and mutational profiles. A recently published study, Behan FM et al. (Nature, 2019 Apr 10) combined 941 CRISPR - CAS9 (CC9) drop-out screens, from 324 human cancer cell lines, with genetic information to generate a list of 628 priority targets across 19 different tissues. The congruent gene-phenotype linkage of targets identified from BERG's multi-omics pan-cancer profiles to the gene based CC9 was identified from an in-silico data-set overlay. Approximately 80% of the priority targets identified in the CC9 study were found to be present in BERG's pan-cancer networks identified using Interrogative Biology® platform. Overlay of CC9 targets on BERG's pan-cancer models identified 159 (protein based) priority candidate targets. Of the top 46 targets, 15 had the same protein, gene, and cancer types in both BERG and CC9 study. These protein targets demonstrated dependencies to well defined oncogenes and represent “high confidence” targets for immediate next steps in development. The remaining 13 targets, highly ranked by both Behan's and BERG's methods, are “low risk” pan-cancer targets. A set of 113 other potential targets were ranked in the CC9 study, but not by BERG's approach, represent low priority targets, requiring additional validation prior to hit finding screens and druggability assessment. The identification of a high percentage of protein targets, from phenotypic biology-based pan-cancer models in a gene based CRISPr-CAS9 screen, exemplifies the robustness of multi-omics profiling and Bayesian AI analytics in identifying de novo therapeutic targets in a reliable and unbiased manner, for rapid validation and deployment into drug discovery programs.

Citation Format: Leonardo O. Rodrigues, Lixia Zhang, Poornima Tekumalla, Stephane Gesta, Vivek K. Vishnudas, Michael A. Kiebish, Niven R. Narain, Rangaprasad Sarangarajan. Benchmarking targets from cancer models using causal inference based drug-target and phenotype identification (Interrogative Biology®) cross-validates “high-priority” targets identified in CRISPR-CAS9 screen [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2929.

Divergence in the metabolome between natural aging and Alzheimer's disease

Alzheimer's disease (AD) is a progressive and debilitating neurodegenerative disorder and one of the leading causes of death in the United States. Although amyloid plaques and fibrillary tangles are hallmarks of AD, research suggests that pathology associated with AD often begins 20 or more years before symptoms appear. Therefore, it is essential to identify early-stage biomarkers in those at risk for AD and age-related cognitive decline (ARCD) in order to develop preventative treatments. Here, we used an untargeted metabolomics analysis to define system-level alterations following cognitive decline in aged and APP/PS1 (AD) mice. At 6, 12, and 24 months of age, both control (Ctrl) and AD mice were tested in a 3-shock contextual fear conditioning (CFC) paradigm to assess memory decline. AD mice exhibited memory deficits across age and these memory deficits were also seen in naturally aged mice. Prefrontal cortex (PFC), hippocampus (HPC), and spleen were then collected and analyzed for metabolomic alterations. A number of significant pathways were altered between Ctrl and AD mice and naturally aged mice. By identifying systems-level alterations following ARCD and AD, these data could provide insights into disease mechanisms and advance the development of biomarker panels.

Integrated metabolomics reveals altered lipid metabolism in adipose tissue in a model of extreme longevity

Adipose tissue plays an essential role in metabolic health. Ames dwarf mice are exceptionally long-lived and display metabolically beneficial phenotypes in their adipose tissue, providing an ideal model for studying the intersection between adipose tissue and longevity. To this end, we assessed the metabolome and lipidome of adipose tissue in Ames dwarf mice. We observed distinct lipid profiles in brown versus white adipose tissue of Ames dwarf mice that are consistent with increased thermogenesis and insulin sensitivity, such as increased cardiolipin and decreased ceramide concentrations. Moreover, we identified 5-hydroxyeicosapentaenoic acid (5-HEPE), an ω-3 fatty acid metabolite, to be increased in Ames dwarf brown adipose tissue (BAT), as well as in circulation. Importantly, 5-HEPE is increased in other models of BAT activation and is negatively correlated with body weight, insulin resistance, and circulating triglyceride concentrations in humans. Together, these data represent a novel lipid signature of adipose tissue in a mouse model of extreme longevity.

Older adults with sarcopenia have distinct skeletal muscle phosphodiester, phosphocreatine, and phospholipid profiles

The loss of skeletal muscle mass and function with age (sarcopenia) is a critical healthcare challenge for older adults. 31‐phosphorus magnetic resonance spectroscopy (³¹P‐MRS) is a powerful tool used to evaluate phosphorus metabolite levels in muscle. Here, we sought to determine which phosphorus metabolites were linked with reduced muscle mass and function in older adults. This investigation was conducted across two separate studies. Resting phosphorus metabolites in skeletal muscle were examined by ³¹P‐MRS. In the first study, fifty‐five older adults with obesity were enrolled and we found that resting phosphocreatine (PCr) was positively associated with muscle volume and knee extensor peak power, while a phosphodiester peak (PDE2) was negatively related to these variables. In the second study, we examined well‐phenotyped older adults that were classified as nonsarcopenic or sarcopenic based on sex‐specific criteria described by the European Working Group on Sarcopenia in Older People. PCr content was lower in muscle from older adults with sarcopenia compared to controls, while PDE2 was elevated. Percutaneous biopsy specimens of the vastus lateralis were obtained for metabolomic and lipidomic analyses. Lower PCr was related to higher muscle creatine. PDE2 was associated with glycerol‐phosphoethanolamine levels, a putative marker of phospholipid membrane damage. Lipidomic analyses revealed that the major phospholipids, (phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol) were elevated in sarcopenic muscle and were inversely related to muscle volume and peak power. These data suggest phosphorus metabolites and phospholipids are associated with the loss of skeletal muscle mass and function in older adults.

Current Status of Metabolomic Biomarker Discovery: Impact of Study Design and Demographic Characteristics

Widespread application of omic technologies is evolving our understanding of population health and holds promise in providing precise guidance for selection of therapeutic interventions based on patient biology. The opportunity to use hundreds of analytes for diagnostic assessment of human health compared to the current use of 10–20 analytes will provide greater accuracy in deconstructing the complexity of human biology in disease states. Conventional biochemical measurements like cholesterol, creatinine, and urea nitrogen are currently used to assess health status; however, metabolomics captures a comprehensive set of analytes characterizing the human phenotype and its complex metabolic processes in real-time. Unlike conventional clinical analytes, metabolomic profiles are dramatically influenced by demographic and environmental factors that affect the range of normal values and increase the risk of false biomarker discovery. This review addresses the challenges and opportunities created by the evolving field of clinical metabolomics and highlights features of study design and bioinformatics necessary to maximize the utility of metabolomics data across demographic groups.

Phase I study of BPM31510 and vitamin K in patients with high grade glioma recurrent after a bevacizumab-containing regimen

2543

Background: BPM31510 is an ubidecarenone-lipid conjugate nanodispersion in clinical development for advanced malignancies, including high grade glioma (HGG). BPM31510’s anti-cancer effect is mediated by induction of mitochondrial superoxide and activation of cell death in glioblastoma models. Herein, we present preliminary pharmaco-kinetic and dynamic data, and survival from a phase I study of BPM31510 + Vitamin K in HGG with progression after bevacizumab (BEV). Methods: This was an open-label phase I study of BPM31510 continuous infusion with Vitamin K (10mg IM qweek) using a mTPI design, starting at 110mg/kg 2X/week, allowing 2 dose escalations & 1 de-escalation. Patients had received ChemoRT and were in recurrence after BEV. Results: Of 12 patients treated with BPM31510, 9 completed the 28-day DLT period. 2 patients came off study for progressive disease; 1 patient after asymptomatic hemorrhage into tumor bed (G1). 10 patients had primary GB, 2 had AA. Median age was 54.5yo (27-67) and KPS 70 (60-90). On Day 1 of BPM31510, a dose dependent increase in Cmax was observed; Tmax values were similar for all doses. AUC was linear with dose escalation. For all doses, Day 4 Cmax values were higher compared to Day 1. In contrast there was variable decrease in Tmax (table). Of evaluable patients, 4 patients received the highest dose 171mg/kg, where a single patient experienced DLT: G3 AST & ALT. The most common grade 1/2 AEs were elevated AST, rash, and fatigue, each occurring in 4 patients. The mOS for 9 eligible/evaluable patients was 128 days (95% CI: 48-209) while PFS was 34 days (95% CI of mean 8.9). Two patients are currently alive >12 months. Conclusions: BPM31510 + vitamin K demonstrated a safe profile to maximum dose of 171mg/kg twice/week with potential therapeutic utility in treatment-refractory HGG patients. Multi-omic molecular profiles characterizing AE and response to be reported from the study will be investigated for next phase of clinical development. Clinical trial information: NCT03020602 . [Table: see text]

Metabolomic effects of androgen deprivation therapy treatment for prostate cancer

Androgen deprivation therapy (ADT) is the main treatment strategy for men with metastatic prostate cancer (PC). However, ADT is associated with various metabolic disturbances, including impaired glucose tolerance, insulin resistance and weight gain, increasing risk of diabetes and cardiovascular death. Much remains unknown about the metabolic pathways and disturbances altered by ADT and the mechanisms. We assessed the metabolomic effects of ADT in the serum of 20 men receiving ADT. Sera collected before (baseline), 3 and 6 months after initiation of ADT was used for the metabolomics and lipidomics analyses. The ADT‐associated metabolic changes were identified by univariable and multivariable statistical analysis, ANOVA, and Pearson correlation. We found multiple key changes. First, ADT treatments reduced the steroid synthesis as reflected by the lower androgen sulfate and other steroid hormones. Greater androgen reduction was correlated with higher serum glucose levels, supporting the diabetogenic role of ADT. Second, ADT consistently decreased the 3‐hydroxybutyric acid and ketogenesis. Third, many acyl‐carnitines were reduced, indicating the effects on the fatty acid metabolism. Fourth, ADT was associated with a corresponding reduction in 3‐formyl indole (a.k.a. indole‐3‐carboxaldehyde), a microbiota‐derived metabolite from the dietary tryptophan. Indole‐3‐carboxaldehyde is an agonist for the aryl hydrocarbon receptor and regulates the mucosal reactivity and inflammation. Together, these ADT‐associated metabolomic analyses identified reduction in steroid synthesis and ketogenesis as prominent features, suggesting therapeutic potential of restricted ketogenic diets, though this requires formal testing. ADT may also impact the microbial production of indoles related to the immune pathways. Future research is needed to determine the functional impact and underlying mechanisms to prevent ADT‐linked comorbidities and diabetes risk.

Phase II trial of BPM31510-IV plus gemcitabine in advanced pancreatic ductal adenocarcinomas (PDAC)

723

Background: BPM31510-IV is an Ubidecarenone (CoQ10) drug-lipid conjugate nanodispersion targeting metabolic machinery in cancer, shifting bioenergetics from lactate dependency towards mitochondrial OxPhos to generate ROS and activate apoptosis. An MTD of BPM31510-IV in combination with gemcitabine was established at 110mg/kg in a Phase I clinical trial, which determined the dose for the Phase 2 investigation. Methods: Eligible patients (aged ≥ 18 y) with relapsed/refractory PDAC to standard treatment (ST) and met inclusion/exclusion criteria were recruited. Patients received 110mg/kg IV BPM31510 in combination with gemcitabine in a 144-hour infusion. Tumor response was evaluated at week 10 and then every 8 weeks. Study endpoints assessed were Overall Response Rate (ORR), Overall Survival (OS), Progression-Free Survival (PFS), Time to Progression (TTP), Tumor Response using Adaptive Molecular Responses (multi-omic molecular profiling), changes in CA 19-9 levels and patient reported Quality of Life (QOL) using the validated FACT-HEP PRO. A comprehensive multi-omic profiling for identification of biomarkers for patient stratification was explored. Results: Of the 35 patients enrolled to receive therapy, 18 patients met criteria of an adequately treated cohort (ATC- received BPM31510-IV + gemcitabine for 30 days over 2 cycles and had a RECIST 1.1 evaluation) while remaining (n = 17) had progressive disease (PD). Half of the ATC population (n = 9/18, 50%) achieved best ORR of stable disease (SD); 10/18 (55 %) demonstrated SD as best response at target lesions and 8/18 demonstrated SD at end of Cycle 2. The mTTP was 121 days (70 – 147, 95% CI); PFS 118 days (70 – 131, 95% CI) and OS 218 days (131 – 228, 95% CI), respectively. Overall, BPM31510-IV was well tolerated; the most common AE’s were GI related. Conclusions: The efficacy signal observed in this heavily pretreated population in addition to the toxicity profile warrants further clinical investigation of BPM31510-IV + gemcitabine in advanced PDAC. Clinical trial information: NCT02650804 . [Table: see text]

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.