Exogenous L-glutamine has preclinical antitumor activity although formal clinical translation has not been attempted. We conducted a single-arm phase 1 trial to assess the safety and preliminary efficacy of clinical-grade, US Food and Drug Administration-approved L-glutamine therapy with gemcitabine and nab-paclitaxel (GA) in participants with treatment-naive, advanced pancreatic cancer (n = 16). The primary endpoint was to determine the recommended phase 2 dose (RP2D) by adaptive Bayesian design across standard doses of GA and a dose range of 0.1-0.3 g kg-1 twice-daily oral L-glutamine. Secondary endpoints included safety and preliminary efficacy of the study combination. The primary endpoint was met with the RP2D reached at maximum doses of L-glutamine and GA. The grade ≥3 treatment-related adverse event rate was 66.7%, primarily from GA. Addition of L-glutamine to GA induced tumor shrinkage in 94% of subjects with a best overall response rate (ORR) of 44% (12.5% complete response). Median progression-free survival and overall survival (OS) were 8.5 months (95% confidence interval (CI) 6-not reached (NR)) and 22 months (95% CI 11-NR), respectively. L-Glutamine induced distinct metagenomic and metabolomic signatures on exploratory analyses in glutamine-treated subjects as a single agent, while the combination of L-glutamine and GA nearly doubled the ORR and tripled the OS compared to historical GA alone (ClinicalTrials.gov registration: NCT04634539 ).

Abstract Introduction Germinal center (GC) B cells and plasma cells strongly upregulate gene expression of SLC7A5, which is an amino acid antiporter that simultaneously mediates leucine uptake and glutamine export. While the importance of leucine uptake is established, the significance of glutamine export and its role in humoral immunity is unknown. Methods B-cell-specific Slc7a5-KO mice Results SLC7A5 was dispensable for B cell development. However, Slc7a5-/- GC-B cells failed to undergo IgG1 class switch and somatic hypermutation upon immunization. Moreover, Slc7a5-/- GC-B cells showed lower dark/light zone (DZ/LZ) cell ratio, cell cycle arrest in DZ, reduced AID expression, and impaired plasma cell differentiation and antibody production. In collagen induced arthritis model, Slc7a5 deletion decreased disease severity and reduced serum levels of anti-collagen IgG2a, IgG3, IgM, as well as IL6. To test whether impaired humoral immunity was caused by defective glutamine export, we created an alternative glutamine disposal route using 4-phenylbutyric acid (4-PBA). 4-PBA treatment significantly rescued IgG1 class switch of Slc7a5-/- cells ex vivo, supporting the critical role of glutamine export in GC-B cells. Metabolomics and isotope tracing revealed that Slc7a5-/- B-cells redirected glutamine from glutaminolysis to nucleotide salvage, prioritizing its role as nitrogen donor over carbon donor. We thus hypothesized that defective glutamine export led to cell defects by nitrogen (ammonia) accumulation. While only hepatic cells can use the urea cycle to detoxify ammonia, non-hepatic cells are known to transport ammonia to liver in the form of glutamine. To test if SLC7A5-mediated glutamine export indeed enables ammonia detoxification, we introduced the urea cycle enzyme CPS1 into Slc7a5-/- cells, which restored cell fitness, confirming the key role of SLC7A5-mediated glutamine export in ammonia detoxification. Conclusion SLC7A5-mediated glutamine export maintains humoral immunity by enabling ammonia detoxification. Funding Source n/a Topic Categories Immune Response Regulation: Molecular Mechanisms (IRM)

The kidney possesses a poor ability to robustly regenerate and repair after acute injury. We show that the ectonucleotidase ENPP1 (ectonucleotide pyrophosphatase/phosphodiesterase-1) is robustly expressed in diseased human kidneys and strongly correlates with clinical indices of renal dysfunction. Genetic targeting of Enpp1 in mice enhanced renal repair. A humanized monoclonal antibody, targeting human ENPP1 (hENPP1mAb), when administered in humanized mice, led to tubular cell proliferation, enhanced renal glomerular filtration rate, decreased fibrosis, and rescued renal function after kidney injury. hENPP1mAb augmented nucleotide metabolism and cellular energetics, enabling proliferation and rescuing cell cycle arrest. Single-cell transcriptomics demonstrated expanded signatures of effective repair with hENPP1mAb. In a good laboratory practice (GLP)-compliant dose escalation study, hENPP1mAb was found to be non-toxic and highly tolerated in non-human primates. Our findings identify ENPP1 as a central regulator of acute kidney injury and demonstrate the therapeutic benefit of targeting ENPP1 ectonucleotidase activity with a humanized monoclonal antibody.

Gliomas are lethal malignancies composed of heterogeneous and dynamic subpopulations of cellular states that resemble both normal neurodevelopmental cell types and adaptive responses to stress within the tumor microenvironment (TME). While cellular plasticity enables gliomas to survive environmental pressures, the mechanisms driving glioma state dynamics remain unclear. To explore how glioma state heterogeneity functionally and metabolically interacts with the brain TME, we conducted a multi-omic analysis across 392 glioma specimens, including patient tumors, orthotopic xenografts and gliomasphere cultures using bulk RNA/whole-exome sequencing and lipidomic profiling. Single-cell transcriptome sequencing of a diverse panel of glioma tumors (n = 21) integrated with bulk tumor transcriptome profiling revealed a spectrum of cellular identities associated with distinct lipidomic profiles. Comparison of matched patient and derived models showed that the non-native environments, such as gliomasphere culture, restricted glioma state diversity and enriched for states characterized by elevated de novo fatty acid synthesis. Across environmental contexts, glioma state plasticity was coupled to lipid metabolic plasticity, enabling tumors to concordantly remodel their state composition and lipid profiles in response to environmental constraints. Of note, certain tumors exhibited limited state and metabolic plasticity – specifically those enriched for states within oligodendroglial and neuronal lineages. These gliomas demonstrated reduced de novo lipid synthesis capacity, and a concordant increased reliance on exogenous lipid scavenging within the brain microenvironment for survival. Together, these results link glioma heterogeneity and plasticity to lipid metabolic reprogramming, and highlight how distinct cellular state profiles result in environment-dependent metabolic liabilities.

Genomic profiling often fails to predict therapeutic outcomes in cancer. This failure is, in part, due to a myriad of genetic alterations and the plasticity of cancer signaling networks. Functional profiling, which ascertains signaling dynamics, is an alternative method to anticipate drug responses. It is unclear whether integrating genomic and functional features of solid tumours can provide unique insight into therapeutic vulnerabilities. We perform combined molecular and functional characterization, via BH3 profiling of the intrinsic apoptotic machinery, in glioma patient samples and derivative models. We identify that standard-of-care therapy rapidly rewires apoptotic signaling in a genotype-specific manner, revealing targetable apoptotic vulnerabilities in gliomas containing specific molecular features (e.g., TP53 WT). However, integration of BH3 profiling reveals high mitochondrial priming is also required to induce glioma apoptosis. Accordingly, a machine-learning approach identifies a composite molecular and functional signature that best predicts responses of diverse intracranial glioma models to standard-of-care therapies combined with ABBV-155, a clinical drug targeting intrinsic apoptosis. This work demonstrates how complementary functional and molecular data can robustly predict therapy-induced cell death. Citation Format: Elizabeth G Fernandez, Wilson X Mai, Kai Song, Nicholas A Bayley, Andrew J. Souers, Jingyi Jessica Li, Thomas G. Graeber, Timothy F Cloughesy, David A. Nathanson. Integrated molecular and functional characterization of the intrinsic apoptotic machinery identifies therapeutic vulnerabilities in glioma [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Functional and Genomic Precision Medicine in Cancer: Different Perspectives, Common Goals; 2025 Mar 11-13; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2025;85(5 Suppl):Abstract nr A007.

SUMMARYNeuroendocrine prostate cancer (NEPC) arises primarily through neuroendocrine transdifferentiation (NEtD) as an adaptive mechanism of therapeutic resistance. Models to define the functional effects of putative drivers of this process on androgen receptor (AR) signaling and NE cancer lineage programs are lacking. We adapted a genetically defined strategy from the field of cellular reprogramming to directly convert AR-active prostate cancer (ARPC) to AR-independent NEPC using candidate factors. We delineated critical roles of the pioneer factors ASCL1 and NeuroD1 in NEtD and uncovered their abilities to silence AR expression and signaling by remodeling chromatin at the somatically acquired AR enhancer and global AR binding sites with enhancer activity. We also elucidated the dynamic temporal changes in the transcriptomic and epigenomic landscapes of cells undergoing acute lineage conversion from ARPC to NEPC which should inform future therapeutic development. Further, we distinguished the activities of ASCL1 and NeuroD1 from the inactivation of RE-1 silencing transcription factor (REST), a master suppressor of a major neuronal gene program, in establishing a NEPC lineage state and in modulating the expression of genes associated with major histocompatibility complex class I (MHC I) antigen processing and presentation. These findings provide important, clinically relevant insights into the biological processes driving NEtD of prostate cancer.

Phenotypic plasticity plays a pivotal role in cancer, enabling tumor cells to adapt to environmental pressures and evade therapeutic interventions by transitioning between distinct cellular states. However, the contribution of phenotypic plasticity to adaptive drug resistance in glioblastoma (GBM), one of the most lethal of all cancers, remains poorly understood. In this study, we identify that GBM tumor-initiating cells resembling normal radial glia (RG), which occupy the apex of normal neurodevelopment, are driven by aberrant epidermal growth factor receptor (EGFR) signaling. Using a suite of patient-derived GBM models, we demonstrate through global proteomics and single-cell RNA sequencing that pharmacological inhibition of EGFR triggers a lineage transition toward neuronal and oligodendrocyte progenitor (OPC)-like states. This shift is accompanied by activation of oncogenic RAS-MAPK signaling – despite robust and durable inhibition of EGFR activation – and is further modulated by brain microenvironmental cues, including synaptic and calcium-mediated signaling programs. Dual inhibition of EGFR and RAS-MAPK with novel, tumor-selective small molecules blocks these phenotypic transitions and enhances GBM cell death in EGFR-mutated GBM models. To determine the subpopulation dynamics of RAS-MAPK signaling within GBM neurodevelopmental lineages, we develop DENALI (Dual-Expression Nuclear reporter of ERK Activity and Lineage Identity) – a novel, high-complexity barcoded lentiviral vector and integrative fluorescence reporter system. Using DENALI, we investigate the clonal mechanisms driving lineage plasticity in GBM following oncogenic EGFR inhibition and couple adaptive RAS signaling programs to the emergence of neuronal and OPC-like states under EGFRi therapy. Together, our findings establish neurodevelopmental lineage plasticity as a key driver of adaptive resistance in GBM and support dual-inhibition strategies to improve therapeutic outcomes in patients with GBM tumors.

ABSTRACTMetabolites and metabolic co-factors can shape the innate immune response, though the pathways by which these molecules adjust inflammation remain incompletely understood. Here we show that the metabolic cofactor Coenzyme A (CoA) enhances IL-4 driven alternative macrophage activation [m(IL-4)]in vitroandin vivo. Unexpectedly, we found that perturbations in intracellular CoA metabolism did not influence m(IL-4) differentiation. Rather, we discovered that exogenous CoA provides a weak TLR4 signal which primes macrophages for increased receptivity to IL-4 signals and resolution of inflammation via MyD88. Mechanistic studies revealed MyD88-linked signals prime for IL-4 responsiveness, in part, by reshaping chromatin accessibility to enhance transcription of IL-4-linked genes. The results identify CoA as a host metabolic co-factor that influences macrophage function through an extrinsic TLR4-dependent mechanism, and suggests that damage-associated molecular patterns (DAMPs) can prime macrophages for alternative activation and resolution of inflammation.

Background and Significance: Oncogenic tyrosine kinases activate STAT5a and STAT5b to promote survival and proliferation in acute lymphoblastic leukemia (B-ALL). Counterintuitively, we found that high expression levels of negative STAT5-regulators (CISH and SOCS-family proteins) predict poor clinical outcomes for B-ALL patients. Likewise, our experiments based on genetic deletion of SOCS2 and SOCS3 showed that impaired STAT5 feedback inhibition resulted in loss of colony formation and cell death in B-ALL. While STAT5 functions as oncogenic driver in B-ALL, these results highlight a previously unrecognized role of STAT5-feedback inhibition in leukemia cells and suggest a “Goldilocks zone” to maintain optimal STAT5 signaling strength. Results: To assess STAT5 signaling thresholds in vivo, we modeled modest increases and decreases of STAT5-activity based on Stat5a gain- (GOF) and loss-of-function (LOF) point mutations. Stat5aGOF B-ALL cells showed increased cell mass, glycolysis (ECAR, lactate production) and accelerated proliferation. However, increased ER-stress and cellular senescence subverted colony formation and leukemia-initiation capacity of Stat5aGOF B-ALL cells. In contrast, Stat5aLOF leukemia cells were small and quiescent with 3.5-fold increased colony formation and a 21-fold increased the frequency of leukemia-initiating cells in transplant recipients. Studying Stat5aGOF- and Stat5aLOF-dependent transcriptional programs, we identified MYC- and BCL6-target genes as top-ranking gene sets. Metabolomic analyses revealed that Stat5aGOF increased 60 MYC-dependent metabolites across glycolysis, TCA cycle and amino acid metabolism pathways. In contrast, metabolomic and lipidomic analyses revealed that Stat5aLOF promoted BCL6-dependent phosphatidylethanolamine (PtdEtn) production, which is essential for autophagosome biogenesis. Stat5aLOF not only promoted PtdEtn synthesis but also increased autophagy (LC3B puncta formation and flux). Interestingly, defective autophagy, ER-stress, and senescence in Stat5aGOF B-ALL cells were largely mitigated by supplementation of PtdEtn. To leverage MYC and BCL6 as biomarker of increased and decreased STAT5-activity, respectively, we engineered patient-derived B-ALL xenografts (PDX) with N-terminal mNeonGreen-MYC and mScarlet-BCL6 fusion knockin-alleles by CRISPR and HDRT. Single-cell time-lapse experiments over 24 hours revealed that B-ALL cells with mutant JAK2 and BCR-ABL1 autonomously transitioned between cell states of high (MYC) and low (BCL6) STAT5-activity, with a period of four hours. Interestingly, inhibitors of JAK2 (ruxolitinib) and BCR-ABL1 (imatinib) suppressed STAT5 (MYC) activity and forced transition to a quiescent BCL6+ cell state. Conversely, treatment of B-ALL PDX carrying MYC- and BCL6-knockin fusions with the STAT5-agonist ABBV-CLS-484 had the opposite effect of imatinib, strongly activated STAT5 and forced transition of BCL6+ quiescent B-ALL cells into a MYC+ proliferative cell state. To assess potential therapeutic benefit of targeted STAT5-hyperactivation, we treated NSG mice bearing patient-derived BCR-ABL1 B-ALL xenografts with daily injections of 40 mg/kg ABBV-CLS-484 i.p. for two weeks. Recapitulating the effects of Stat5aGOF in murine B-ALL, ABBV-CLS-484 treatment subverted leukemia-initiation capacity and substantially prolonged survival of transplant recipient mice. Conclusions: The tyrosine kinase inhibition paradigm is based on the dependency of B-ALL cells on high-level STAT5-signaling and activation of MYC. Our findings reveal a previously unrecognized dependency of human B-ALL cells on negative STAT5-feedback regulation by CISH and SOCS and activation of BCL6. Every four hours, B-ALL cells transition between cell-states of higher (MYC) and lower (BCL6) STAT5 activity. While traditional tyrosine kinase inhibitors target the MYC-dependent cell proliferation, our findings support a rationale for targeting BCL6-dependent quiescence. The small molecule STAT5-agonist ABBV-CLS-484 was recently introduced in Phase 2 clinical trials as immunotherapy adjuvant to increase STAT5-activity in T-cells for enhanced T-cell antitumor immunity in patients with solid tumors (NCT04777994). Since ABBV-CLS-484 showed favorable safety and desirable activation of T-cell antitumor immunity, targeted STAT5-hyperactivation is amenable to near-term evaluation in patients with refractory B-ALL.

Comparing proteome changes during B-cell activation and transformation, we found strong induction of SLC7A5, which simultaneously mediates leucine uptake and glutamine export. However, the significance of glutamine export is unknown. Slc7a5 deletion in transformed B cells, but not primary resting B-cells, resulted in accumulated intracellular glutamine, impaired cell fitness, and prolonged survival of transplant recipients. Interestingly, glutamine deprivation, and pharmacological glutamine sequestration, partially rescued cell fitness, suggesting imbalanced amino acid pool due to abnormal accumulation of glutamine likely impedes B-cell activation and transformation. Isotope tracing of (15N)2-glutamine showed increased nitrogen flux from glutamine to purine synthesis upon Slc7a5 deletion, at the expense of glutathione, NAD+, and glucosamine synthesis. Chemogenomic screen with a selective SLC7A5 inhibitor revealed that deletion of genes involved in nucleotide metabolism led to synthetic lethality, whereas deletion of genes involved in protein translation rescued growth inhibition. Moreover, Slc7a5-deficient cells were more resistant to rapamycin and CHX treatment. Our findings suggest that bidirectional glutamine transport balances amino acid pool, which enables rapid protein synthesis and cell proliferation of activated and malignant B-cells. This is consistent with marked upregulation of SLC7A5 on plasma cells, which rely on massive protein synthesis for antibody secretion. Lymphocyte Differentiation and Peripheral Maintenance (LYM)

Abstract Malignant growth and survival of cancer is supported through reprogrammed lipid metabolism. In gliomas, genetic alterations can drive lipid metabolic dysregulation revealing therapeutic opportunities to exploit lipid metabolic vulnerabilities within genetically defined subsets of glioma tumors. However, it remains unclear whether inter- and intra-tumoral transcriptomic heterogeneity in gliomas relates to distinct lipid programs and potential dependencies. Here we set out to characterize pan-glioma lipid metabolic heterogeneity through genomic, transcriptomic, and lipidomic profiling of a large and diverse cohort of patient tumor samples. We define key axes of lipid metabolic variability across gliomas and identify relationships between lipid metabolic gene expression programs and glioma lipidomic profiles. Intriguingly, intersection of lipid gene expression signatures with single cell RNA sequencing revealed patterns of lipid metabolic heterogeneity that distinguish neurodevelopmental cellular states of gliomas, mirroring patterns of lipid metabolic diversity across cell types within the normal brain. Consequently, tumors with opposing cellular state enrichment have distinct lipid metabolism and environmental dependencies. Tumors enriched for Radial Glia-like states have high capacity for de novo fatty acid synthesis while tumors enriched for oligodendrocyte progenitor-like states are dependent on exogenous sources of lipids for survival and growth. These findings connect inter- and intra-tumoral heterogeneity of cellular states to variability in lipid metabolic reprogramming to reveal future avenues for precision medicine.

Myocardial infarction (MI) results in aberrant cardiac metabolism, but no therapeutics have been designed to target cardiac metabolism to enhance heart repair. We engineer a humanized monoclonal antibody against the ectonucleotidase ENPP1 (hENPP1mAb) that targets metabolic crosstalk in the infarcted heart. In mice expressing human ENPP1, systemic administration of hENPP1mAb metabolically reprograms myocytes and non-myocytes and leads to a significant rescue of post-MI heart dysfunction. Using metabolomics, single-nuclear transcriptomics, and cellular respiration studies, we show that the administration of the hENPP1mAb induces organ-wide metabolic and transcriptional reprogramming of the heart that enhances myocyte cellular respiration and decreases cell death and fibrosis in the infarcted heart. Biodistribution and safety studies showed specific organ-wide distribution with the antibody being well tolerated. In humanized animals, with drug clearance kinetics similar to humans, we demonstrate that a single “shot” of the hENPP1mAb after MI is sufficient to rescue cardiac dysfunction.

Abstract Gliomas are lethal malignancies comprised of heterogeneous and dynamic subpopulations of cell states resembling normal neurodevelopmental cell types (radial glia (RG), oligodendrocyte progenitor cell (OPC), neuron progenitor cell (NPC), neuron, etc). While both intrinsic (genetics) and extrinsic (brain environment) cues are coupled to glioma state identity, the functional programs governing glioma cell state and plasticity are unknown. Here we performed a multi-omic interrogation of a large library (n=392) of glioma patient tumors, in vivo orthotopic xenografts and in vitro gliomasphere cultures. Comparisons of matched glioma samples across environments revealed the non-native in vitro environment constrains glioma state diversity specifically enriching for stem-like glioma cell states (RG, immune, vascular). This enrichment was linked to lipid metabolic flexibility, enabling tumors enriched for stem-like states to adapt to various tumor microenvironments. By contrast, “lineage-committed” cell states (OPC, NPC, and neuron) demonstrate restricted lipid metabolism, consequently having a dependence on lipid scavenging from the brain microenvironment for survival. These results connect intra-tumoral heterogeneity and plasticity of glioma to lipid metabolism, leveraging the functional diversity of cellular states to reveal potential therapeutic opportunities.

Adenocarcinomas from multiple tissues can converge to treatment-resistant small cell neuroendocrine (SCN) cancers composed of ASCL1, POU2F3, NEUROD1, and YAP1 subtypes. We investigated how mitochondrial metabolism influences SCN cancer (SCNC) progression. Extensive bioinformatics analyses encompassing thousands of patient tumors and human cancer cell lines uncovered enhanced expression of proliferator-activatedreceptor gamma coactivator 1-alpha (PGC-1α), a potent regulator of mitochondrial oxidative phosphorylation (OXPHOS), across several SCNCs. PGC-1α correlated tightly with increased expression of the lineage marker Achaete-scute homolog 1, (ASCL1) through a positive feedback mechanism. Analyses using a human prostate tissue-based SCN transformation system showed that the ASCL1 subtype has heightened PGC-1α expression and OXPHOS activity. PGC-1α inhibition diminished OXPHOS, reduced SCNC cell proliferation, and blocked SCN prostate tumor formation. Conversely, PGC-1α overexpression enhanced OXPHOS, validated by small-animal Positron Emission Tomography mitochondrial imaging, tripled the SCN prostate tumor formation rate, and promoted commitment to the ASCL1 lineage. These results establish PGC-1α as a driver of SCNC progression and subtype determination, highlighting metabolic vulnerabilities in SCNCs across different tissues.

Abstract Phenotypic plasticity drives non-genetic tumor adaptation in response to various microenvironmental and therapeutic pressures, consequently promoting tumor heterogeneity and progression. In malignant gliomas, the intrinsic and extrinsic mechanisms underlying phenotypic lineage plasticity and its contribution to drug resistance remain unclear. The epidermal growth factor receptor (EGFR) is frequently altered in glioma and serves as a critical regulator of normal radial glia (RG) cells – multipotent progenitors that give rise to cortical neurons and glia in the developing brain. Here, through interrogation of a large panel of diverse glioblastoma (GBM) patient-derived gliomaspheres and orthotopic xenografts, we find that enrichment of RG-like cells is significantly correlated with responses to pharmacological ablation of EGFR, highlighting EGFR as a crucial lineage survival factor for a population of malignant RG-like cells in GBM. Single-cell RNA sequencing and quantitative proteomics reveal that adaptation to EGFR inhibition is linked to a temporal contraction in RG-like cells and concomitant increase in lineage-restricted neuronal and oligodendrocyte progenitor (NPC/OPC)-like states exclusively in the orthotopic brain environment. This lineage transition is coupled to heightened RAS signaling gene expression programs and sustained activation of MAPK signaling, despite robust and durable inhibition of EGFR activation. Furthermore, constitutively active MEK – but not AKT – is sufficient to rescue tumor proliferation under EGFRi, suggesting that the brain microenvironment modulates RAS-MAPK oncogenic signaling to drive lineage transitions following EGFR blockade. Collectively, these results highlight a critical link between oncogenic signaling and neurodevelopmental lineage plasticity in malignant gliomas, presenting a compelling therapeutic opportunity to block tumor cell state transitions for more durable tumor responses in the native glioma tumor microenvironment.

BackgroundPancreatic neuroendocrine tumors (pNETs) are genomically diverse tumors. The management of newly diagnosed well-differentiated pNETs is limited by a lack of sensitivity of existing biomarkers for prognostication. Our goal was to investigate the potential utility of genetic markers as a predictor of progression-free survival (PFS) and recurrence-free survival (RFS).MethodsWhole-exome sequencing of resected well-differentiated, low and intermediate-grade (G1 and G2) pNETs and normal adjacent tissue from patients who underwent resection from 2005 to 2015 was performed. Genetic alterations were classified using pan-genomic and oncogenic pathway classifications. Additional samples with genetic and clinicopathologic data available were obtained from the publicly available International Cancer Genome Consortium (ICGC) database and included in the analysis. The prognostic relevance of these genomic signatures on PFS and RFS was analyzed.ResultsThirty-one patients who underwent resection for pNET were identified. Genomic analysis of mutational, copy number, cytogenetic, and complex phenomena revealed similar patterns to prior studies of pNETs with relatively few somatic gene mutations but numerous instances of copy number changes. Analysis of genomic and clinicopathologic outcomes using the combined data from our study as well as the ICGC pNET cohort (n = 124 patients) revealed that the recurrent pattern of whole chromosome loss (RPCL) and metastatic disease were independently associated with disease progression. When evaluating patients with local disease at the time of resection, RPCL and alterations in the TGF beta oncogenic pathway were independently associated with the risk of recurrence.ConclusionsWell-differentiated pNETs are genomically diverse tumors. Pathway signatures may be prognostic for predicting disease progression and recurrence.

Purpose: High-grade complex karyotype sarcomas are a heterogeneous group of tumors with a uniformly poor prognosis. Within complex karyotype sarcomas, there are innumerable genetic changes but identifying those that are clinically relevant has been challenging.Experimental Design: To address this, we utilized a pooled genetic screening approach, informed by The Cancer Genome Atlas (TCGA) data, to identify key drivers and modifiers of sarcoma development that were validated in vivo.Results: YAP1 and wild-type KRAS were validated as drivers and transformed human mesenchymal stem cells into two distinct sarcoma subtypes, undifferentiated pleomorphic sarcoma and myxofibrosarcoma, respectively. A subset of tumors driven by CDK4 and PIK3CA reflected leiomyosarcoma and osteosarcoma demonstrating the plasticity of this approach and the potential to investigate sarcoma subtype heterogeneity. All generated tumors histologically reflected human sarcomas and had increased aneuploidy as compared to simple karyotype sarcomas. Comparing differential gene expression of TCGA samples to model data identified increased oxidative phosphorylation signaling in YAP1 tumors. Treatment of a panel of soft tissue sarcomas with a combination of YAP1 and oxidative phosphorylation inhibitors led to significantly decreased viability.Conclusions: Transcriptional co-analysis of TCGA patient samples to YAP1 and KRAS model tumors supports that these sarcoma subtypes lie along a spectrum of disease and adds guidance for further transcriptome-based refinement of sarcoma subtyping. This approach can be used to begin to understand pathways and mechanisms driving human sarcoma development, the relationship between sarcoma subtypes, and to identify and validate new therapeutic vulnerabilities for this aggressive and heterogeneous disease.

Genomic profiling often fails to predict therapeutic outcomes in cancer. This failure is, in part, due to a myriad of genetic alterations and the plasticity of cancer signaling networks. Functional profiling, which ascertains signaling dynamics, is an alternative method to anticipate drug responses. It is unclear whether integrating genomic and functional features of solid tumours can provide unique insight into therapeutic vulnerabilities. We perform combined molecular and functional characterization, via BH3 profiling of the intrinsic apoptotic machinery, in glioma patient samples and derivative models. We identify that standard-of-care therapy rapidly rewires apoptotic signaling in a genotype-specific manner, revealing targetable apoptotic vulnerabilities in gliomas containing specific molecular features (e.g., TP53 WT). However, integration of BH3 profiling reveals high mitochondrial priming is also required to induce glioma apoptosis. Accordingly, a machine-learning approach identifies a composite molecular and functional signature that best predicts responses of diverse intracranial glioma models to standard-of-care therapies combined with ABBV-155, a clinical drug targeting intrinsic apoptosis. This work demonstrates how complementary functional and molecular data can robustly predict therapy-induced cell death. Genomic profiling of tumours can help tailer treatments to the patient, however, it often fails to accurately predict therapeutic outcomes. Here, the authors combine molecular and functional characterisation via BH3 profiling to identify therapeutically targetable vulnerabilities in glioma.

Microphthalmia-associated transcription factor (MITF) is a master regulator of melanocyte function, development and plays a significant role in melanoma pathogenesis. MITF genomic amplification promotes melanoma development, and it can facilitate resistance to multiple therapies. Here, we show that MITF regulates a global antioxidant program that increases survival of melanoma cell lines by protecting the cells from reactive oxygen species (ROS)-induced damage. In addition, this redox program is correlated with MITF expression in human melanoma cell lines and patient-derived melanoma samples. Using a zebrafish melanoma model, we show that MITF decreases ROS-mediated DNA damage in vivo. Some of the MITF target genes involved, such as IDH1 and NNT, are regulated through direct MITF binding to canonical enhancer box (E-BOX) sequences proximal to their promoters. Utilizing functional experiments, we demonstrate the role of MITF and its target genes in reducing cytosolic and mitochondrial ROS. Collectively, our data identify MITF as a significant driver of the cellular antioxidant state.