bims-glucam 2023-07-23 papers

Issue of 2023‒07‒23
eleven papers selected by
Sreeparna Banerjee
Middle East Technical University

Am J Respir Cell Mol Biol. 2023 Jul 17.

Targeting Pulmonary Fibrosis by SLC1A5 Dependent Glutamine Transport Blockade.

Malay Choudhury, Kyle J Schaefbauer, Theodore J Kottom, Eunhee S Yi, Daniel J Tschumperlin, Andrew H Limper.

The neutral amino acid glutamine plays a central role in TGF-β-induced myofibroblast activation and differentiation. Cells take up glutamine mainly through a transporter expressed on the cell surface known as solute carrier SLC1A5. In this current work, we demonstrated that profibrotic actions of TGF-β are mediated, at least in part, through a metabolic maladaptation of SLC1A5 and targeting SLC1A5 abrogates multiple facets of fibroblast activation. This approach could thus represent a novel therapeutic strategy to treat fibroproliferative diseases. We found that SLC1A5 was highly expressed in fibrotic lung fibroblasts and fibroblasts isolated from IPF lungs. The expression of profibrotic targets, cell migration, and anchorage independent growth by TGF-β required the activity of SLC1A5. Loss or inhibition of SLC1A5 function enhanced fibroblast susceptibility to autophagy, suppressed mTOR, HIF, Myc signaling, and impaired mitochondrial function, ATP production and glycolysis. Pharmacological inhibition of SLC1A5 by small molecule inhibitor V-9302 shifted fibroblast transcriptional profiles from profibrotic to fibrosis resolving, and attenuated fibrosis in a bleomycin treated mouse model of lung fibrosis. This is the first study, to our knowledge, to demonstrate the utility of a pharmacological inhibitor of glutamine transport in fibrosis, laying a framework for new paradigm-shifting therapies targeting cellular metabolism for this devastating disease.

Keywords: TGF-β signaling; bleomycin; glutamine metabolism; pulmonary fibrosis; solute carrier protein

DOI: https://doi.org/10.1165/rcmb.2022-0339OC

Cell Death Dis. 2023 Jul 21. 14(7): 454

STAG2 inactivation reprograms glutamine metabolism of BRAF-mutant thyroid cancer cells.

Xinru Li, Yan Liu, Juan Liu, Wei Qiang, Jingjing Ma, Jingyi Xie, Pu Chen, Yubo Wang, Peng Hou, Meiju Ji.

STAG2, an important subunit in cohesion complex, is involved in the segregation of chromosomes during the late mitosis and the formation of sister chromatids. Mutational inactivation of STAG2 is a major cause of the resistance of BRAF-mutant melanomas to BRAF/MEK inhibitors. In the present study, we found that STAG2 was frequently down-regulated in thyroid cancers compared with control subjects. By a series of in vitro and in vivo studies, we demonstrated that STAG2 knockdown virtually had no effect on malignant phenotypes of BRAF-mutant thyroid cancer cells such as cell proliferation, colony formation and tumorigenic ability in nude mice compared with the control. In addition, unlike melanoma, STAG2 knockdown also did not affect the sensitivity of these cells to MEK inhibitor. However, we surprisingly found that STAG2-knockdown cells exhibited more sensitive to glutamine deprivation or glutaminase inhibitor BPTES compared with control cells. Mechanistically, knocking down STAG2 in BRAF-mutant thyroid cancer cells decreases the protein stability of c-Myc via the ERK/AKT/GSK3β feedback pathway, thereby impairing glutamine metabolism of thyroid cancer cells by down-regulating its downstream targets such as SCL1A5, GLS and GLS2. Our data, taken together, demonstrate that STAG2 inactivation reprograms glutamine metabolism of BRAF-mutant thyroid cancer cells, thereby improving their cellular response to glutaminase inhibitor. This study will provide a potential therapeutic strategy for BRAF-mutant thyroid cancers.

DOI: https://doi.org/10.1038/s41419-023-05981-z

Cancer Discov. 2023 Jul 21. OF1

Glutamine Influences Type-1 Conventional Dendritic Cell Antitumor Immunity.

Glutamine supplementation improves antitumor immunity and reduces tumor growth by restoring cDC1 function.

DOI: https://doi.org/10.1158/2159-8290.CD-RW2023-113

Cell Rep. 2023 Jul 19. pii: S2211-1247(23)00839-2. [Epub ahead of print]42(8): 112828

QUAS-R: An SLC1A5-mediated glutamine uptake assay with single-cell resolution reveals metabolic heterogeneity with immune populations.

Leonard R Pelgrom, Gavin M Davis, Simon O'Shaughnessy, Emilie J M Wezenberg, Sander I Van Kasteren, David K Finlay, Linda V Sinclair.

System-level analysis of single-cell data is rapidly transforming the field of immunometabolism. Given the competitive demand for nutrients in immune microenvironments, there is a need to understand how and when immune cells access these nutrients. Here, we describe a new approach for single-cell analysis of nutrient uptake where we use in-cell biorthogonal labeling of a functionalized amino acid after transport into the cell. In this manner, the bona fide active uptake of glutamine via SLC1A5/ASCT2 could be quantified. We used this assay to interrogate the transport capacity of complex immune subpopulations, both in vitro and in vivo. Taken together, our findings provide an easy sensitive single-cell assay to assess which cells support their function via SLC1A5-mediated uptake. This is a significant addition to the single-cell metabolic toolbox required to decode the metabolic landscape of complex immune microenvironments.

Keywords: CP: Immunology; CP: Metabolism; SLC1A5; amino acid transport; glutamine uptake; lymphocytes

DOI: https://doi.org/10.1016/j.celrep.2023.112828

Am J Physiol Cell Physiol. 2023 Jul 17.

The SLC38A5/SNAT5 amino acid transporter: from pathophysiology to pro-cancer roles in the tumor microenvironment.

Giuseppe Taurino, Martina Chiu, Massimiliano G Bianchi, Erika Griffini, Ovidio Bussolati.

SLC38A5/SNAT5 is a system N transporter that can mediate net inward or outward transmembrane fluxes of neutral amino acids coupled with Na+ (symport) and H+ (antiport). Its preferential substrates are amino acids with side chains containing amide (glutamine, and asparagine) or imidazole (histidine) groups, but also serine, glycine and alanine are transported by the carrier. Expressed in the pancreas, intestinal tract, brain, liver, bone marrow, and placenta, it is regulated at mRNA and protein levels by mTORC1 and WNT/β-catenin pathways, and it is sensitive to pH, nutritional stress, inflammation, and hypoxia. SNAT5 expression has been found to be altered in pathological conditions such as chronic inflammatory diseases, gestational complications, chronic metabolic acidosis and malnutrition. Growing experimental evidence shows that SNAT5 is overexpressed in several types of cancer cells. Moreover, recently published results indicate that SNAT5 expression in stromal cells can support the metabolic exchanges occurring in the tumor microenvironment of asparagine-auxotroph tumors. We review the functional role of the SNAT5 transporter in pathophysiology and propose that, due to its peculiar operational and regulatory features, SNAT5 may play important pro-cancer roles when expressed either in neoplastic or in stromal cells of glutamine-auxotroph tumors.

Keywords: Amino acid transport; Asparagine; Cancer; Glutamine; Metabolic diseases

DOI: https://doi.org/10.1152/ajpcell.00169.2023

Clin Transl Oncol. 2023 Jul 21.

Energy metabolism: a new target for gastric cancer treatment.

Jiangrong Liu, Xue Bai, Meilan Zhang, Shihua Wu, Juan Xiao, Xuemei Zeng, Yuwei Li, Zhiwei Zhang.

Gastric cancer is the fifth most common malignancy worldwide having the fourth highest mortality rate. Energy metabolism is key and closely linked to tumour development. Most important in the reprogramming of cancer metabolism is the Warburg effect, which suggests that tumour cells will utilise glycolysis even with normal oxygen levels. Various molecules exert their effects by acting on enzymes in the glycolytic pathway, integral to glycolysis. Second, mitochondrial abnormalities in the reprogramming of energy metabolism, with consequences for glutamine metabolism, the tricarboxylic acid cycle and oxidative phosphorylation, abnormal fatty acid oxidation and plasma lipoprotein metabolism are important components of tumour metabolism. Third, inflammation-induced oxidative stress is a danger signal for cancer. Fourth, patterns of signalling pathways involve all aspects of metabolic transduction, and many clinical drugs exert their anticancer effects through energy metabolic signalling. This review summarises research on energy metabolism genes, enzymes and proteins and transduction pathways associated with gastric cancer, and discusses the mechanisms affecting their effects on postoperative treatment resistance and prognoses of gastric cancer. We believe that an in-depth understanding of energy metabolism reprogramming will aid the diagnosis and subsequent treatment of gastric cancer.

Keywords: Energy metabolism; Enzyme; Gastric cancer; Noncoding RNA

DOI: https://doi.org/10.1007/s12094-023-03278-3

Elife. 2023 07 17. pii: e89825. [Epub ahead of print]12

How nearby nutrients shape tumor growth.

Nada Kalaany.

Studying the nutrient composition immediately surrounding pancreatic cancer cells provides new insights into their metabolic properties and how they can evade the immune system to promote disease progression.

Keywords: amino acid homeostasis; biochemistry; cancer; cancer biology; chemical biology; human; immunotherapy; metabolism; mouse; nutrient stress; tumor microenvironment

DOI: https://doi.org/10.7554/eLife.89825

ACS Med Chem Lett. 2023 Jul 13. 14(7): 920-928

Diselenide Covalent Allosteric Inhibitors of Glutaminase with Strong In Vivo Anticancer Activity.

Wei Hou, Zhao Chen, Chuqiao Pan, Maowei Ni, Haoqiang Ruan, Jun Song, Shiying Lu, Aman Bhasin, Benfang Helen Ruan.

Allosteric glutaminase inhibitors demonstrate inhibition of glutamine-dependent cancer cells with low general drug toxicity, but have issues with efficacy in vivo. Here, we designed a series of diselenide compounds with 6 atoms in the middle, aiming to target the allosteric site of kidney type glutaminase (KGA) with a covalent linkage to strengthen the interaction. Proteomic analysis demonstrated that the diselenide compounds cross-linked with the Lys320 residue at the KGA allosteric site; this was confirmed by the KGA K320A mutant which showed essentially no binding to the diselenide. Further, structure-activity relationship (SAR) analysis demonstrated that growth inhibition correlated well with KGA inhibition and was enhanced by thioredoxin reductase (TrxR) inhibition. Interestingly, diselenide compounds showed no inhibition of glutamate dehydrogenase (GDH), indicating some enzyme selectivity. Importantly, the designed novel diselenides are glutaminase allosteric inhibitors that showed in vivo efficacy and survival in the xenograft animal model.

DOI: https://doi.org/10.1021/acsmedchemlett.2c00470

Cancer Biol Ther. 2023 Dec 31. 24(1): 2237200

Identification of USP29 as a key regulator of nucleotide biosynthesis in neuroblastoma through integrative analysis of multi-omics data.

Ye Kang, Yahuan Yu, Yijia Liu, Yiwen Pan, Ru Zhang, Doudou Ren, Zeqiong Cai, Junpeng Ma, Xiaofan Xiong, Qi Zhang, Chengsheng Zhang, Rongfu Tu.

Cancer cells show enhanced nucleotide biosynthesis, which is essential for their unlimited proliferation, but the underlying mechanisms are not entirely clear. Ubiquitin specific peptidase 29 (USP29) was reported to sustain neuroblastoma progression by promoting glycolysis and glutamine catabolism; however, its potential role in regulating nucleotide biosynthesis in tumor cells remains unknown. In this study, we depleted endogenous USP29 in MYCN-amplified neuroblastoma SK-N-BE2 cells by sgRNAs and conducted metabolomic analysis in cells with or without USP29 depletion, we found that USP29 deficiency caused a disorder of intermediates involved in glycolysis and nucleotide biosynthesis. De novo nucleotide biosynthesis was analyzed using 13C6 glucose as a tracer under normoxia and hypoxia. The results indicated that USP29-depleted cells showed inhibition of nucleotide anabolic intermediates derived from glucose, and this inhibition was more significant under hypoxic conditions. Analysis of RNA sequencing data in SK-N-BE2 cells demonstrated that USP29 promoted the gene expression of metabolic enzymes involved in nucleotide anabolism, probably by regulating MYC and E2F downstream pathways. These findings indicated that USP29 is a key regulator of nucleotide biosynthesis in tumor cells.

Keywords: USP29; cancer metabolism; neuroblastoma; nucleotide biosynthesis

DOI: https://doi.org/10.1080/15384047.2023.2237200

bioRxiv. 2023 Jul 11. pii: 2023.07.07.548031. [Epub ahead of print]

Transcriptional regulation of amino acid metabolism by KDM2B, in the context of ncPRC1.1 and in concert with MYC and ATF4.

Evangelia Chavdoula, Vollter Anastas, Alessandro La Ferlita, Julian Aldana, Giuseppe Carota, Mariarita Spampinato, Burak Soysal, Ilaria Cosentini, Sameer Parashar, Anuvrat Sircar, Giovanni Nigita, Lalit Sehgal, Michael A Freitas, Philip N Tsichlis.

Introduction: KDM2B encodes a JmjC domain-containing histone lysine demethylase, which functions as an oncogene in several types of tumors, including TNBC. This study was initiated to address the cancer relevance of the results of our earlier work, which had shown that overexpression of KDM2B renders mouse embryonic fibroblasts (MEFs) resistant to oxidative stress by regulating antioxidant mechanisms.Methods: We mainly employed a multi-omics strategy consisting of RNA-Seq, quantitative TMT proteomics, Mass-spectrometry-based global metabolomics, ATAC-Seq and ChIP-seq, to explore the role of KDM2B in the resistance to oxidative stress and intermediary metabolism. These data and data from existing patient datasets were analyzed using bioinformatic tools, including exon-intron-split analysis (EISA), FLUFF and clustering analyses. The main genetic strategy we employed was gene silencing with shRNAs. ROS were measured by flow cytometry, following staining with CellROX and various metabolites were measured with biochemical assays, using commercially available kits. Gene expression was monitored with qRT-PCR and immunoblotting, as indicated.
Results: The knockdown of KDM2B in basal-like breast cancer cell lines lowers the levels of GSH and sensitizes the cells to ROS inducers, GSH targeting molecules, and DUB inhibitors. To address the mechanism of GSH regulation, we knocked down KDM2B in MDA-MB-231 cells and we examined the effects of the knockdown, using a multi-omics strategy. The results showed that KDM2B, functioning in the context of ncPRC1.1, regulates a network of epigenetic and transcription factors, which control a host of metabolic enzymes, including those involved in the SGOC, glutamate, and GSH metabolism. They also showed that KDM2B enhances the chromatin accessibility and expression of MYC and ATF4, and that it binds in concert with MYC and ATF4, the promoters of a large number of transcriptionally active genes, including many, encoding metabolic enzymes. Additionally, MYC and ATF4 binding sites were enriched in genes whose accessibility depends on KDM2B, and analysis of a cohort of TNBCs expressing high or low levels of KDM2B, but similar levels of MYC and ATF4 identified a subset of MYC targets, whose expression correlates with the expression of KDM2B. Further analyses of basal-like TNBCs in the same cohort, revealed that tumors expressing high levels of all three regulators exhibit a distinct metabolic signature that carries a poor prognosis.
Conclusions: The present study links KDM2B, ATF4, and MYC in a transcriptional network that regulates the expression of multiple metabolic enzymes, including those that control the interconnected SGOC, glutamate, and GSH metabolic pathways. The co-occupancy of the promoters of many transcriptionally active genes, by all three factors, the enrichment of MYC binding sites in genes whose chromatin accessibility depends on KDM2B, and the correlation of the levels of KDM2B with the expression of a subset of MYC target genes in tumors that express similar levels of MYC, suggest that KDM2B regulates both the expression and the transcriptional activity of MYC. Importantly, the concerted expression of all three factors also defines a distinct metabolic subset of TNBCs with poor prognosis. Overall, this study identifies novel mechanisms of SGOC regulation, suggests novel KDM2B-dependent metabolic vulnerabilities in TNBC, and provides new insights into the role of KDM2B in the epigenetic regulation of transcription.
Highlights: The knockdown of KDM2B in basal-like breast cancer cell lines lowers the levels of GSH and sensitizes the cells to ROS inducers, GSH targeting molecules, and DUB inhibitors.KDM2B regulates intermediary metabolism by targeting the expression of a host of metabolic enzymes, including those in the SGOC, glutamate, and GSH metabolism.KDM2B enhances chromatin accessibility of MYC and ATF4 and promotes their expression.MYC and ATF4 binding sites are enriched in the promoters of genes whose accessibility depends on KDM2B.KDM2B functioning in the context of ncPRC1.1, binds the promoters of transcriptionally active genes, including those encoding KDM2B-regulated metabolic enzymes, in concert with MYC and ATF4.Basal-like TNBCs expressing high levels of all three regulators, exhibit a distinct metabolic signature that is associated with poor prognosis.

DOI: https://doi.org/10.1101/2023.07.07.548031

NPJ Syst Biol Appl. 2023 Jul 15. 9(1): 32

Synthetic lethality in large-scale integrated metabolic and regulatory network models of human cells.

Naroa Barrena, Luis V Valcárcel, Danel Olaverri-Mendizabal, Iñigo Apaolaza, Francisco J Planes.

Synthetic lethality (SL) is a promising concept in cancer research. A wide array of computational tools has been developed to predict and exploit synthetic lethality for the identification of tumour-specific vulnerabilities. Previously, we introduced the concept of genetic Minimal Cut Sets (gMCSs), a theoretical approach to SL developed for genome-scale metabolic networks. The major challenge in our gMCS framework is to go beyond metabolic networks and extend existing algorithms to more complex protein-protein interactions. In this article, we take a step further and incorporate linear regulatory pathways into our gMCS approach. Extensive algorithmic modifications to compute gMCSs in integrated metabolic and regulatory models are presented in detail. Our extended approach is applied to calculate gMCSs in integrated models of human cells. In particular, we integrate the most recent genome-scale metabolic network, Human1, with 3 different regulatory network databases: Omnipath, Dorothea and TRRUST. Based on the computed gMCSs and transcriptomic data, we discovered new essential genes and their associated synthetic lethal for different cancer cell lines. The performance of the different integrated models is assessed with available large-scale in-vitro gene silencing data. Finally, we discuss the most relevant gene essentiality predictions based on published literature in cancer research.

DOI: https://doi.org/10.1038/s41540-023-00296-3