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Melanoma central nervous system metastases: An update to approaches, challenges, and opportunities

Karz, Alcida; Dimitrova, Maya; Kleffman, Kevin; Alvarez-Breckenridge, Christopher; Atkins, Michael B; Boire, Adrienne; Bosenberg, Marcus; Brastianos, Priscilla; Cahill, Daniel P; Chen, Qing; Ferguson, Sherise; Forsyth, Peter; Glitza Oliva, Isabella C; Goldberg, Sarah B; Holmen, Sheri L; Knisely, Jonathan P S; Merlino, Glenn; Nguyen, Don X; Pacold, Michael E; Perez-Guijarro, Eva; Smalley, Keiran S M; Tawbi, Hussein A; Wen, Patrick Y; Davies, Michael A; Kluger, Harriet M; Mehnert, Janice M; Hernando, Eva
Brain metastases are the most common brain malignancy. This review discusses the studies presented at the third annual meeting of the Melanoma Research Foundation in the context of other recent reports on the biology and treatment of melanoma brain metastases (MBM). Although symptomatic MBM patients were historically excluded from immunotherapy trials, efforts from clinicians and patient advocates have resulted in more inclusive and even dedicated clinical trials for MBM patients. The results of checkpoint inhibitor trials were discussed in conversation with current standards of care for MBM patients, including steroids, radiotherapy and targeted therapy. Advances in the basic scientific understanding of melanoma brain metastases, including the role of astrocytes and metabolic adaptations to the brain microenvironment are exposing new vulnerabilities which could be exploited for therapeutic purposes. Technical advances including single cell omics and multiplex imaging are expanding our understanding of the MBM ecosystem and its response to therapy. This unprecedented level of spatial and temporal resolution is expected to dramatically advance the field in coming years and render novel treatment approaches that might improve the MBM patient outcomes.
PMID: 35912544
ISSN: 1755-148x
CID: 5287832

Reversal of cancer gene expression identifies repurposed drugs for diffuse intrinsic pontine glioma

Zhao, Guisheng; Newbury, Patrick; Ishi, Yukitomo; Chekalin, Eugene; Zeng, Billy; Glicksberg, Benjamin S; Wen, Anita; Paithankar, Shreya; Sasaki, Takahiro; Suri, Amreena; Nazarian, Javad; Pacold, Michael E; Brat, Daniel J; Nicolaides, Theodore; Chen, Bin; Hashizume, Rintaro
Diffuse intrinsic pontine glioma (DIPG) is an aggressive incurable brainstem tumor that targets young children. Complete resection is not possible, and chemotherapy and radiotherapy are currently only palliative. This study aimed to identify potential therapeutic agents using a computational pipeline to perform an in silico screen for novel drugs. We then tested the identified drugs against a panel of patient-derived DIPG cell lines. Using a systematic computational approach with publicly available databases of gene signature in DIPG patients and cancer cell lines treated with a library of clinically available drugs, we identified drug hits with the ability to reverse a DIPG gene signature to one that matches normal tissue background. The biological and molecular effects of drug treatment was analyzed by cell viability assay and RNA sequence. In vivo DIPG mouse model survival studies were also conducted. As a result, two of three identified drugs showed potency against the DIPG cell lines Triptolide and mycophenolate mofetil (MMF) demonstrated significant inhibition of cell viability in DIPG cell lines. Guanosine rescued reduced cell viability induced by MMF. In vivo, MMF treatment significantly inhibited tumor growth in subcutaneous xenograft mice models. In conclusion, we identified clinically available drugs with the ability to reverse DIPG gene signatures and anti-DIPG activity in vitro and in vivo. This novel approach can repurpose drugs and significantly decrease the cost and time normally required in drug discovery.
PMID: 36274161
ISSN: 2051-5960
CID: 5352632

Resurrecting essential amino acid biosynthesis in mammalian cells

Trolle, Julie; McBee, Ross M; Kaufman, Andrew; Pinglay, Sudarshan; Berger, Henri; German, Sergei; Liu, Liyuan; Shen, Michael J; Guo, Xinyi; Martin, J Andrew; Pacold, Michael E; Jones, Drew R; Boeke, Jef D; Wang, Harris H
Major genomic deletions in independent eukaryotic lineages have led to repeated ancestral loss of biosynthesis pathways for nine of the twenty canonical amino acids1. While the evolutionary forces driving these polyphyletic deletion events are not well understood, the consequence is that extant metazoans are unable to produce nine essential amino acids (EAAs). Previous studies have highlighted that EAA biosynthesis tends to be more energetically costly2,3, raising the possibility that these pathways were lost from organisms with access to abundant EAAs in the environment4,5. It is unclear whether present-day metazoans can reaccept these pathways to resurrect biosynthetic capabilities that were lost long ago or whether evolution has rendered EAA pathways incompatible with metazoan metabolism. Here, we report progress on a large-scale synthetic genomics effort to reestablish EAA biosynthetic functionality in mammalian cells. We designed codon-optimized biosynthesis pathways based on genes mined from Escherichia coli. These pathways were de novo synthesized in 3 kilobase chunks, assembled in yeasto and genomically integrated into a Chinese Hamster Ovary (CHO) cell line. One synthetic pathway produced valine at a sufficient level for cell viability and proliferation, and thus represents a successful example of metazoan EAA biosynthesis restoration. This prototrophic CHO line grows in valine-free medium, and metabolomics using labeled precursors verified de novo biosynthesis of valine. RNA-seq profiling of the valine prototrophic CHO line showed that the synthetic pathway minimally disrupted the cellular transcriptome. Furthermore, valine prototrophic cells exhibited transcriptional signatures associated with rescue from nutritional starvation. 13C-tracing revealed build-up of pathway intermediate 2,3-dihydroxy-3-isovalerate in these cells. Increasing the dosage of downstream ilvD boosted pathway performance and allowed for long-term propagation of second-generation cells in valine-free medium at a consistent doubling time of 3.2 days. This work demonstrates that mammalian metabolism is amenable to restoration of ancient core pathways, paving a path for genome-scale efforts to synthetically restore metabolic functions to the metazoan lineage.
PMID: 36165439
ISSN: 2050-084x
CID: 5334162

The polar oxy-metabolome reveals the 4-hydroxymandelate CoQ10 synthesis pathway

Banh, Robert S; Kim, Esther S; Spillier, Quentin; Biancur, Douglas E; Yamamoto, Keisuke; Sohn, Albert S W; Shi, Guangbin; Jones, Drew R; Kimmelman, Alec C; Pacold, Michael E
Oxygen is critical for a multitude of metabolic processes that are essential for human life. Biological processes can be identified by treating cells with 18O2 or other isotopically labelled gases and systematically identifying biomolecules incorporating labeled atoms. Here we labelled cell lines of distinct tissue origins with 18O2 to identify the polar oxy-metabolome, defined as polar metabolites labelled with 18O under different physiological O2 tensions. The most highly 18O-labelled feature was 4-hydroxymandelate (4-HMA). We demonstrate that 4-HMA is produced by hydroxyphenylpyruvate dioxygenase-like (HPDL), a protein of previously unknown function in human cells. We identify 4-HMA as an intermediate involved in the biosynthesis of the coenzyme Q10 (CoQ10) headgroup in human cells. The connection of HPDL to CoQ10 biosynthesis provides crucial insights into the mechanisms underlying recently described neurological diseases related to HPDL deficiencies1-4 and cancers with HPDL overexpression5.
PMID: 34471290
ISSN: 1476-4687
CID: 4989322

Neurons Release Serine to Support mRNA Translation in Pancreatic Cancer

Banh, Robert S; Biancur, Douglas E; Yamamoto, Keisuke; Sohn, Albert S W; Walters, Beth; Kuljanin, Miljan; Gikandi, Ajami; Wang, Huamin; Mancias, Joseph D; Schneider, Robert J; Pacold, Michael E; Kimmelman, Alec C
Pancreatic ductal adenocarcinoma (PDAC) tumors have a nutrient-poor, desmoplastic, and highly innervated tumor microenvironment. Although neurons can release stimulatory factors to accelerate PDAC tumorigenesis, the metabolic contribution of peripheral axons has not been explored. We found that peripheral axons release serine (Ser) to support the growth of exogenous Ser (exSer)-dependent PDAC cells during Ser/Gly (glycine) deprivation. Ser deprivation resulted in ribosomal stalling on two of the six Ser codons, TCC and TCT, and allowed the selective translation and secretion of nerve growth factor (NGF) by PDAC cells to promote tumor innervation. Consistent with this, exSer-dependent PDAC tumors grew slower and displayed enhanced innervation in mice on a Ser/Gly-free diet. Blockade of compensatory neuronal innervation using LOXO-101, a Trk-NGF inhibitor, further decreased PDAC tumor growth. Our data indicate that axonal-cancer metabolic crosstalk is a critical adaptation to support PDAC growth in nutrient poor environments.
PMID: 33142117
ISSN: 1097-4172
CID: 4656002

Rapid purification and metabolomic profiling of synaptic vesicles from mammalian brain

Chantranupong, Lynne; Saulnier, Jessica L; Wang, Wengang; Jones, Drew R; Pacold, Michael E; Sabatini, Bernardo L
Neurons communicate by the activity-dependent release of small-molecule neurotransmitters packaged into synaptic vesicles (SVs). Although many molecules have been identified as neurotransmitters, technical limitations have precluded a full metabolomic analysis of synaptic vesicle content. Here, we present a workflow to rapidly isolate SVs and to interrogate their metabolic contents at high-resolution using mass spectrometry. We validated the enrichment of glutamate in SVs of primary cortical neurons using targeted polar metabolomics. Unbiased and extensive global profiling of SVs isolated from these neurons revealed that the only detectable polar metabolites they contain are the established neurotransmitters glutamate and GABA. In addition, we adapted the approach to enable quick capture of SVs directly from brain tissue and determined the neurotransmitter profiles of diverse brain regions in a cell-type specific manner. The speed, robustness, and precision of this method to interrogate SV contents will facilitate novel insights into the chemical basis of neurotransmission.
PMID: 33043885
ISSN: 2050-084x
CID: 4632432

Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition

Ngo, Bryan; Kim, Eugenie; Osorio-Vasquez, Victoria; Doll, Sophia; Bustraan, Sophia; Liang, Roger J; Luengo, Alba; Davidson, Shawn M; Ali, Ahmed; Ferraro, Gino B; Fischer, Grant M; Eskandari, Roozbeh; Kang, Diane S; Ni, Jing; Plasger, Ariana; Rajasekhar, Vinagolu K; Kastenhuber, Edward R; Bacha, Sarah; Sriram, Roshan K; Stein, Benjamin D; Bakhoum, Samuel F; Snuderl, Matija; Cotzia, Paolo; Healey, John H; Mainolfi, Nello; Suri, Vipin; Friedman, Adam; Manfredi, Mark; Sabatini, David M; Jones, Drew R; Yu, Min; Zhao, Jean J; Jain, Rakesh K; Keshari, Kayvan R; Davies, Michael A; Vander Heiden, Matthew G; Hernando, Eva; Mann, Matthias; Cantley, Lewis C; Pacold, Michael E
A hallmark of metastasis is the adaptation of tumor cells to new environments. Metabolic constraints imposed by the serine and glycine-limited brain environment restrict metastatic tumor growth. How brain metastases overcome these growth-prohibitive conditions is poorly understood. Here, we demonstrate that 3-phosphoglycerate dehydrogenase (PHGDH), which catalyzes the rate-limiting step of glucose-derived serine synthesis, is a major determinant of brain metastasis in multiple human cancer types and preclinical models. Enhanced serine synthesis proved important for nucleotide production and cell proliferation in highly aggressive brain metastatic cells. In vivo, genetic suppression and pharmacological inhibition of PHGDH attenuated brain metastasis, but not extracranial tumor growth, and improved overall survival in mice. These results reveal that extracellular amino acid availability determines serine synthesis pathway dependence, and suggests that PHGDH inhibitors may be useful in the treatment of brain metastasis.
PMID: 32571778
ISSN: 2159-8290
CID: 4492952

Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy

Wu, Lin; Hollinshead, Kate E R; Hao, Yuhan; Au, Christy; Kroehling, Lina; Ng, Charles; Lin, Woan-Yu; Li, Dayi; Silva, Hernandez Moura; Shin, Jong; Lafaille, Juan J; Possemato, Richard; Pacold, Michael E; Papagiannakopoulos, Thales; Kimmelman, Alec C; Satija, Rahul; Littman, Dan R
Targeting glycolysis has been considered therapeutically intractable owing to its essential housekeeping role. However, the context-dependent requirement for individual glycolytic steps has not been fully explored. We show that CRISPR-mediated targeting of glycolysis in T cells in mice results in global loss of Th17 cells, whereas deficiency of the glycolytic enzyme glucose phosphate isomerase (Gpi1) selectively eliminates inflammatory encephalitogenic and colitogenic Th17 cells, without substantially affecting homeostatic microbiota-specific Th17 cells. In homeostatic Th17 cells, partial blockade of glycolysis upon Gpi1 inactivation was compensated by pentose phosphate pathway flux and increased mitochondrial respiration. In contrast, inflammatory Th17 cells experience a hypoxic microenvironment known to limit mitochondrial respiration, which is incompatible with loss of Gpi1. Our study suggests that inhibiting glycolysis by targeting Gpi1 could be an effective therapeutic strategy with minimum toxicity for Th17-mediated autoimmune diseases, and, more generally, that metabolic redundancies can be exploited for selective targeting of disease processes.
PMID: 32615085
ISSN: 1097-4172
CID: 4504552

The uninhibited pathway is not worth studying

Pacold, Michael E
PMID: 32572257
ISSN: 1552-4469
CID: 4492962

WWOX somatic ablation in skeletal muscles alters glucose metabolism

Abu-Remaileh, Muhannad; Abu-Remaileh, Monther; Akkawi, Rania; Knani, Ibrahim; Udi, Shiran; Pacold, Micheal E; Tam, Joseph; Aqeilan, Rami I
OBJECTIVE:WWOX, a well-established tumor suppressor, is frequently lost in cancer and plays important roles in DNA damage response and cellular metabolism. METHODS:We re-analyzed several genome-wide association studies (GWAS) using the Type 2 Diabetes Knowledge Portal website to uncover WWOX's association with metabolic syndrome (MetS). Using several engineered mouse models, we studied the effect of somatic WWOX loss on glucose homeostasis. RESULTS:mice display reduced amounts of slow-twitch fibers, decreased mitochondrial quantity and activity, and lower glucose oxidation levels. Mechanistically, we found that WWOX physically interacts with the cellular energy sensor AMP-activated protein kinase (AMPK) and that its loss is associated with impaired activation of AMPK, and with significant accumulation of the hypoxia inducible factor 1 alpha (HIF1α) in SKM. CONCLUSIONS:Our studies uncover an unforeseen role of the tumor suppressor WWOX in whole-body glucose homeostasis and highlight the intimate relationship between cancer progression and metabolic disorders, particularly obesity and type-2 diabetes. SUBJECT AREAS/UNASSIGNED:Genetics, Metabolic Syndrome, Diabetes.
PMID: 30755385
ISSN: 2212-8778
CID: 3656252