Aggressive-variant prostate cancers (AVPCs) respond poorly to anti-androgen therapy but show sensitivity to taxane-platinum chemotherapy, though outcomes remain poor. We conducted a phase 2 trial testing induction cabazitaxel plus carboplatin (CabCarb) followed by olaparib maintenance versus observation in men with AVPC. The primary endpoint of improved progression-free survival (PFS) was not met, likely due to the study being underpowered after 38.5% of patients experienced early progression (ChemoPD) prior to randomization. No genomic alterations predicted ChemoPD; however, transcriptomic analysis revealed the enrichment of metabolic pathways, including arginine metabolism, in ChemoPD tumors. These findings were supported by metabolomics data from preclinical models. In AVPC models, arginine depletion with ADI-PEG20 enhanced CabCarb efficacy in vitro and in vivo. Together, these results provide insight into the heterogeneity of AVPCs and establish a rationale for novel combination treatment strategies to overcome chemotherapy resistance.

Abstract Triple negative breast cancer (TNBC) is an aggressive breast cancer subtype in which neoadjuvant chemotherapy (NACT) is the backbone of standard of care. Unfortunately, ∼45% of patients have residual tumor burden following NACT, which is strongly associated with poor prognoses. Our group previously demonstrated that mitochondrial oxidative phosphorylation is upregulated and is a therapeutic vulnerability of chemo-refractory TNBC. We used metabolomic flux tracing to show a heightened contribution of glucose oxidation to the tricarboxylic acid (TCA) cycle in residual human TNBC cells surviving several conventional chemotherapies. We found significantly elevated abundance of citrate and acetyl-coA (AcCoA) in residual cells. Further, glucose, but not palmitate, glutamine, or acetate, derived heavy carbon was more strongly incorporated into citrate and AcCoA in residual relative to naïve cells. Concomitantly, we observed drastic lipidomic remodeling, largely characterized by elevation of triglycerides, long chain fatty acids, and poly unsaturated fatty acids (PUFAs) in cultured TNBC cells and orthotopic patient-derived xenograft (PDX) tumors following chemotherapy relative to their treatment naïve counterparts. This was accompanied by a significant increase in the number of lipid droplets (LDs) in residual cells. Together, these data suggest glucose oxidation supports fatty acid synthesis (FAS) and storage in chemoresistant TNBC. Our analyses of human TNBC proteomic and transcriptomic data affirmed the significant association of fatty acid metabolism with TNBC chemoresistance, as well as its upregulation in chemotherapy-treated tumors relative to their pre-treated counterparts. Mining those data led us to ATP citrate lyase (ACLY), the rate limiting enzyme for cytosolic AcCoA production from citrate. We hypothesized that ACLY converts excess citrate, generated by heightened TCA cycling, to AcCoA to promote FAS and storage in chemoresistant TNBC. We found elevated protein levels of ACLY and an activating phosphorylation mark in TNBC cells surviving treatment with conventional chemotherapies doxorubicin and carboplatin. ACLY knockdown or inhibition potently reduced chemotherapy-induced accumulation of AcCoA and LDs and elicited lipidomic rewiring largely characterized by increased PUFAs. Notably, combining ACLY inhibition or KD with conventional chemotherapy treatments provided significant improvement of tumor cell growth inhibition. These data indicate that NACT can cause accumulation of citrate, AcCoA, LDs, and overall lipidomic rewiring through ACLY. ACLY is a novel functional dependency of chemo-refractory TNBC and should be further explored as a potential therapeutic target. We posit that TNBC cells adapt to the stress of NACT by upregulating lipid synthesis and storage in conjunction with glucose catabolism, enhancing metabolic flexibility and cell survival. Citation Format: Katherine E. Pendelton, Mokryun L. Baek, Mariah J. Berner-Wu, Steven W. Wall, Audra Lane, Jonathan T. Lei, Iqbal Mahmud, Lin Tan, Lacey E. Dobrolecki, Philip L. Lorenzi, Michael T. Lewis, Blake R. Rushing, Gloria V. Echeverria. ATP citrate lyase fuels lipid storage to support triple negative breast cancer chemoresistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 2027.

Abstract Pancreatic ductal adenocarcinoma (PDAC) is characterized by high resistance to anticancer therapies, which is caused in part by hypovascularization and dysfunctional vessels that inefficiently deliver chemotherapy. Exercise has been shown to improve tumor vascular function and chemotherapy efficacy in preclinical models. Uncovering the mechanism by which exercise modifies tumor vasculature could help identify potential strategies to improve drug delivery. In this study, we evaluated surgically resected PDAC from patients who exercised during neoadjuvant chemotherapy to demonstrate that exercise remodeled PDAC vasculature and improved tumor vascular function in patients. In mice bearing orthotopic PDAC and treadmill exercise, tumor vascular remodeling was dependent on sphingosine-1-phosphate receptor 1 (S1PR1) signaling in endothelial cells, and S1PR1 was necessary for improved chemotherapy efficacy by exercise. Exercise activated S1PR1 in tumor endothelium, improved tumor vascular function, and increased gemcitabine (Gem) delivery and efficacy. Mice with an endothelial cell–specific S1PR1 deletion did not display exercise-induced improvements in tumor vascular function or Gem efficacy. These findings demonstrate that exercise increases chemotherapy delivery and efficacy by improving vascular function, defining S1PR1 as a necessary mediator of exercise-induced vascular remodeling. Significance: Aerobic exercise induces tumor vasculature remodeling via endothelial S1PR1 to enhance drug delivery and suppress pancreatic cancer progression, supporting discovery of exercise efficacy biomarkers and therapeutic strategies for patients unable to exercise.

High-throughput proteomic profiling provides a comprehensive analysis of systemic cancer effects and tumor microenvironment interactions. Characterizing soluble proteins driving inflammation in acute myeloid leukemia (AML) offers insight into inflammatory diseases like differentiation syndrome related to AML therapies like menin inhibitors. We present our application of nucleic acid-linked immuno-sandwich assay, a novel technology leveraging next-generation sequencing for high throughput, ultrasensitive characterization of secreted inflammatory proteins in plasma or serum. Here, we report its use to identify dynamic soluble protein changes during treatment and at the time of suspected differentiation syndrome in pediatric AML patients treated with the menin inhibitor revumenib (NCT04065399 and NCT05360160).

Neutropenic fever (NF) is often the first sign of infection in patients with hematologic malignancies, but its cause is frequently unknown, leading to broad-spectrum antibiotic use without confirmed infections. Although research links gut microbiome disruptions to treatment-related infections, it typically examines NF as the outcome, leaving a gap in understanding how the microbiome and metabolic factors distinguish infectious from non-infectious cases. Stool samples from acute myeloid leukemia patients were analyzed to characterize gut microbiome composition and fecal metabolites at baseline and at fever onset. Machine learning models, network analyses, and functional profiling were used to differentiate infectious NF vs non-infectious NF at baseline and at fever onset. The baseline model (area under the receiver operating characteristic [AUROC] = 0.769) identified higher levels of Akkermansia, Enterobacter, Escherichia-Shigella, and Flavonifractor as predictors of infectious NF, while Collinsella, Lachnospiraceae, Coprococcus, and acetic acid were linked to non-infectious cases. At fever onset, Enterococcus was enriched in infectious NF, whereas Gemella, Butyrate, Lachnospiraceae, Ruminococcaceae, and Eisenbergiella abundances favored non-infectious NF outcomes (AUROC = 0.752). Network analyses also revealed greater functional diversity and microbiome-metabolome connectivity in non-infectious cases at fever onset. This study suggests that gut microbiota and metabolites may serve as biomarkers for distinguishing infectious from non-infectious neutropenic fever, warranting further validation in larger cohorts. IMPORTANCE:Our study tackles the challenge of managing neutropenic fever (NF) in immunocompromised patients whose numbers have increased due to various immunodeficiencies and treatments that suppress immune function. Fever is often the only sign of a serious infection in these patients, yet there are neither clear patterns linking risk factors to infection nor biomarkers reliable for ruling out non-infectious causes. As a result, febrile patients are typically empirically treated for major pathogens, even in the absence of confirmed infections, which propagates antimicrobial resistance and gut dysbiosis. Our research utilizes gut microbiome and targeted metabolomic profiling from two cohorts of patients with acute myeloid leukemia undergoing chemotherapy and employs a machine learning framework to distinguish between infectious and non-infectious NFs at baseline and upon fever onset.

BACKGROUND:Atherothrombosis, which underlies most acute coronary syndromes and is driven by intraplaque thrombosis, preferentially occurs in regions of disturbed blood flow (d-flow). Although LATS1/2 (large tumor suppressor kinases 1 and 2) are known regulators of endothelial mechanotransduction, the mechanisms by which d-flow connects endothelial senescence, proliferation, and intraplaque thrombosis remain poorly understood. METHODS:We investigated endothelial cell (EC)-specific roles of Lats1/2 using inducible EC-specific knockout mice in a partial carotid ligation model. Spatial multiomics of human and mouse plaques was performed using imaging mass cytometry, COMET sequential immunofluorescence, and spatial metabolomics. RESULTS:Tamoxifen-induced deletion of both Lats1 and Lats2 (homozygous) in ECs caused fatal edema and increased vascular permeability. In contrast, Lats1het(±)/Lats2 homo(-/-)-EC-specific knockout mice survived and developed spontaneous atherothrombotic plaques with neovascularization. Spatial proteomics revealed that LATS1/2 loss induced a senescence-associated stemness phenotype driven by CD38 upregulation. Spatial metabolomics showed sulfite and taurine accumulation, indicating SUOX (sulfite oxidase) deficiency. CD38 suppressed SUOX, demonstrated a switch into the reverse mode of mitochondrial complex V, increased succinate dehydrogenase activity, and promoted ATP consumption. Despite ATP depletion, glutamate metabolism and the citric acid cycle flux increased, sustaining EC proliferation under energetic stress. This senescence-associated stemness state promoted both proliferation and senescence, leading to fragile, leaky neovessels and intraplaque thrombotic lesions. Pharmacological CD38 inhibition attenuated these phenotypes. Similar EC states were observed in human plaques. CONCLUSIONS:Loss of Lats1/2 in ECs induces a CD38-associated senescence-associated stemness-like phenotype that promotes intraplaque thrombosis through mitochondrial metabolic reprogramming, including changes consistent with reverse-mode operation of mitochondrial complex V. These findings define a mechanistic link between disturbed flow, endothelial metabolic reprogramming, and intraplaque thrombosis and hemorrhage.

Primers, gRNA sequences, and antibodies used

PURPOSE:Magnetic resonance imaging using hyperpolarized (HP) [1-13C]-pyruvate enables assessment of pyruvate metabolism in vivo and offers new insight into metabolic changes in response to cancer therapy. Widely used semi-quantitative metrics of pyruvate metabolism can be affected by physiological factors that are extrinsic to intracellular metabolism. A validated pharmacokinetic (PK) model for analysis of intracellular pyruvate metabolism is needed to enhance the accuracy of quantitative metrics and clinical translation of metabolic MRI using HP pyruvate. METHODS:A PK model with two physical compartments and two chemical pools was developed to analyze the conversion of labeled pyruvate into lactate in vitro. Cells exposed to [U-13C3]-pyruvate were analyzed using pseudo-dynamic ion-coupled mass spectrometry (IC-MS) while cells exposed to HP [1-13C]-pyruvate were analyzed using dynamic NMR. The model was extended to incorporate a third physical compartment for vascular delivery, and quantification of changes in pyruvate metabolism in a patient with ATC was compared against semi-quantitative metrics. RESULTS:Good correspondence between complementary quantitative measures of pyruvate metabolism using IC-MS and NMR support the use of this framework as a foundation for quantitative analysis of HP pyruvate metabolism in vitro and in vivo. The three-compartment model identified changes in vascular delivery separately from changes in intracellular pyruvate metabolism, revealed greater heterogeneity in metabolic activity, and identified areas of persistent high metabolic activity against an overall reduction in tumor metabolism after 8 days of treatment. CONCLUSION:This framework for analysis provides a validated approach and demonstrates feasibility for quantitative evaluation of HP pyruvate metabolism in vivo.

Mass spectrometry (MS) is indispensable for high-throughput quantitation of protein expression. But protein function is regulated by factors beyond abundance alone. Here, we evaluate two supercharging reagents, dimethyl sulfoxide (DMSO) and m-nitrobenzyl alcohol (mNBA), in narrow-window data-independent acquisition (nDIA)-MS. DMSO markedly enhances MS signal and protein identification, whereas mNBA primarily increases peptide identifications. Optimizating nDIA-MS with 3

Rapid and comprehensive analysis of complex proteomes across large sample sets is vital for unlocking the potential of systems biology. We present a high-throughput mass spectrometry (MS) proteomics method that integrates narrow-window data-independent acquisition (nDIA) with short-gradient micro-flow chromatography, enabling profiling of >240 samples per day. This optimized MS approach identifies 6,201 and 7,466 human proteins with 1- and 2-min gradients, respectively. As a practical application, we analyzed 507 samples composed of 13 different tissues from mice treated with the enzyme-drug L-asparaginase (ASNase) or its glutaminase-free Q59L mutant, generating a quantitative profile of 11,472 proteins following drug treatment. The MS results confirmed the impact of ASNase on amino acid metabolism in solid tissues. Further analysis revealed broad suppression of anticoagulants and cholesterol metabolism and uncovered numerous tissue-specific dysregulated pathways. In summary, the optimized high-throughput proteomics method accelerates systems-level analysis of a preclinical model to generate biological insights and clinically actionable hypotheses.

BACKGROUND:Metabolic adaptation and maladaptation are hallmarks of the failing heart and may be a target for therapeutic interventions. For example, sustained glucose oxidation during cardiac stress is associated with increased activity and abundance of ACL (ATP-dependent citrate lyase, Acly), which produces acetyl-coenzyme A (CoA) from citrate and CoA and supports de novo lipid synthesis. However, our understanding of how ACL supports cardiac metabolic adaptation and its potential to modulate disease pathophysiology has not yet been investigated. METHODS:We used human heart tissue samples from healthy donors and patients with nonischemic cardiomyopathy. Next, we used CRISPR (clustered, regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated 9) gene editing to inactivate Acly in cardiomyocytes of Myh6-Cas9 mice. In vivo positron emission tomography and ex vivo stable isotope tracer labeling were used to quantify metabolic flux changes in response to Acly knockdown. We conducted a multi-omics analysis using RNA sequencing and mass spectrometry-based metabolomics and proteomics. Experimental data were integrated into computational modeling using the metabolic network CardioNet to identify significantly dysregulated metabolic processes at a systems level. RESULTS:We observed reduced ACL abundance and activity in human heart tissue samples from patients with nonischemic cardiomyopathy, which correlated with decreased abundance of Krebs cycle intermediates. Using CRISPR/Cas9 gene editing, we found that cardiac-specific loss of ACL reduces acetyl-CoA synthesis, leading to altered cardiac metabolism characterized by increased glucose uptake and oxidation, impaired energy flux, and elevated AMP to ATP ratios, which collectively promote left ventricular dysfunction. Transcriptomic and mass spectrometry-based metabolomics, as well as proteomic data, reveal compensatory cardiac lipid remodeling and reduced histone 3 acetylation. This metabolic stress promotes activation of AMPK (AMP kinase) and PKA (protein kinase A), which in turn mediates YAP (Yes-associated protein) inhibition through phosphorylation. Stable isotope tracer studies combined with CardioNet simulations demonstrated that increased IDH1 (isocitrate dehydrogenase 1) activity prevents allosteric inhibition of glycolysis from cytosolic citrate accumulation. AAV9-mediated cardiac Idh1 deletion improved cardiac function and energy provision, reducing YAP phosphorylation and restoring downstream YAP signaling. CONCLUSIONS:Our findings suggest that ACL plays a pivotal role in cardiac metabolism through regulating lipid synthesis and cardiac function. Exploiting compensatory pathways of citrate metabolism may improve cardiac function during heart failure.