bims-mascan 2022-03-13 papers

bims-mascan

Biomed News

on Mass spectrometry in cancer research

Issue of 2022–03–13
seventeen papers selected by
Giovanny Rodríguez Blanco, University of Edinburgh

The metabolomic landscape plays a critical role in glioma oncogenesis.
Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples.
Development of oxaalkyne and alkyne fatty acids as novel tracers to study fatty acid beta-oxidation pathways and intermediates.
Targeted Metabolomic Analysis in Alzheimer's Disease Plasma and Brain Tissue in Non-Hispanic Whites.
Comprehensive Metabolic Profiling of MYC-Amplified Medulloblastoma Tumors Reveals Key Dependencies on Amino Acid, Tricarboxylic Acid and Hexosamine Pathways.
Ultrasensitive Determination of Sugar Phosphates in Trace Samples by Stable Isotope Chemical Labeling Combined with RPLC-MS.
Development and Validation of a High-Resolving Power Absolute Quantitative PFAS method Incorporating Skyline Data Processing.
Targeting glutamine utilization to block metabolic adaptation of tumor cells under the stress of carboxyamidotriazole-induced nutrients unavailability.
Metabolic tricks of cancer cells.
Targeting metabolism to overcome cancer drug resistance: A promising therapeutic strategy for diffuse large B cell lymphoma.
p53-driven lipidome influences non-cell-autonomous lysophospholipids in pancreatic cancer.
Site-Specific Photochemical Reaction for Improved C=C Location Analysis of Unsaturated Lipids by Ultraviolet Photodissociation.
Lipid metabolism of cancer stem cells.
Lysophosphatidylethanolamine Affects Lipid Accumulation and Metabolism in a Human Liver-Derived Cell Line.
Faecal microbiome and metabolic signatures in rectal neuroendocrine tumors.
An Optimized Workflow for the Analysis of Metabolic Fluxes in Cancer Spheroids Using Seahorse Technology.
mTOR-Mediated Regulation of Immune Responses in Cancer and Tumor Microenvironment.

Cancer Sci. 2022 Mar 10.

The metabolomic landscape plays a critical role in glioma oncogenesis.

Kenta Masui, Webster K Cavenee, Paul S Mischel, Noriyuki Shibata.

  Cancer cells depend on metabolic reprogramming for survival, undergoing profound shifts in nutrient-sensing, nutrient uptake and flux through anabolic pathways, in order to drive nucleotide, lipid, and protein synthesis and provide key intermediates needed for those pathways. Although metabolic enzymes themselves can be mutated, including to generate oncometabolites, this is a relatively rare event in cancer. Usually, gene amplification, overexpression, and/or downstream signal transduction upregulate rate-limiting metabolic enzymes and limit feedback loops, to drive persistent tumor growth. Recent molecular genetic advances revealed discrete links between oncogenotypes and the resultant metabolic phenotypes. However, more comprehensive approaches are needed to unravel the dynamic spatio-temporal regulatory map of enzymes and metabolites that enable cancer cells to adapt to their microenvironment to maximize tumor growth. Proteomic and metabolomic analyses are powerful tools for analyzing a repertoire of metabolic enzymes as well as intermediary metabolites, and in conjunction with other omic approaches could provide critical information in this regard. Here, we provide an overview of cancer metabolism, especially from an "omics" perspective and with a particular focus on the genomically well-characterized malignant tumor, glioblastoma. We further discuss how metabolomics could be leveraged to improve the management of patients, by linking cancer cell genotype, epigenotype and phenotype through metabolic reprogramming.

Keywords:  OMICS; epigenetics; glioblastoma; mTOR complex; metabolome

DOI:  https://doi.org/10.1111/cas.15325
Biosystems. 2022 Mar 02. pii: S0303-2647(22)00053-3. [Epub ahead of print]215-216 104661

Assessing normalization methods in mass spectrometry-based proteome profiling of clinical samples.

Etienne Dubois, Antonio Núñez Galindo, Loïc Dayon, Ornella Cominetti.

   BACKGROUND: Large-scale proteomic studies have to deal with unwanted variability, especially when samples originate from different centers and multiple analytical batches are needed. Such variability is typically added throughout all the steps of a clinical research study, from human biological sample collection and storage, sample preparation, spectral data acquisition, to peptide and protein quantification. In order to remove such diverse and unwanted variability, normalization of the protein data is performed. There have been already several published reviews comparing normalization methods in the -omics field, but reports focusing on proteomic data generated with mass spectrometry (MS) are much fewer. Additionally, most of these reports have only dealt with small datasets.
RESULTS: As a case study, here we focused on the normalization of a large MS-based proteomic dataset obtained from an overweight and obese pan-European cohort, where different normalization methods were evaluated, namely: center standardize, quantile protein, quantile sample, global standardization, ComBat, median centering, mean centering, single standard and removal of unwanted variation (RUV); some of these are generic normalization methods while others have been specifically created to deal with genomic or metabolomic data. We checked how relationships between proteins and clinical variables (e.g., gender, levels of triglycerides or cholesterol) were improved after normalizing the data with the different methods.
CONCLUSIONS: Some normalization methods were better adapted for this particular large-scale shotgun proteomic dataset of human plasma samples labeled with isobaric tags and analyzed with liquid chromatography-tandem MS. In particular, quantile sample normalization, RUV, mean and median centering showed very good performances, while quantile protein normalization provided worse results than those obtained with unnormalized data.

Keywords:  Mass spectrometry; Normalization; Obesity; Protein; Proteomics; Quantification; Tandem mass tags

DOI:  https://doi.org/10.1016/j.biosystems.2022.104661
J Lipid Res. 2022 Mar 02. pii: S0022-2275(22)00021-9. [Epub ahead of print] 100188

Development of oxaalkyne and alkyne fatty acids as novel tracers to study fatty acid beta-oxidation pathways and intermediates.

Lars Kuerschner, Philipp Leyendecker, Kristina Klizaite, Maria Fiedler, Jennifer Saam, Christoph Thiele.

  Fatty acid beta-oxidation is a key process in mammalian lipid catabolism. Disturbance of this process results in severe clinical symptoms, including dysfunction of the liver, a major beta-oxidizing tissue. For a thorough understanding of this process, a comprehensive analysis of involved fatty acid and acyl-carnitine intermediates is desired, but capable methods are lacking. Here, we introduce oxaalkyne and alkyne fatty acids as novel tracers to study the beta-oxidation of long- and medium-chain fatty acids in liver lysates and primary hepatocytes. Combining these new tracer tools with highly sensitive chromatography and mass spectrometry analyses, this study confirms differences in metabolic handling of fatty acids of different chain length. Unlike longer chains, we found that medium-chain fatty acids that were activated inside or outside of mitochondria by different acyl-CoA synthetases could enter mitochondria in the form of free fatty acids or as carnitine esters. Upon mitochondrial beta-oxidation, shortened acyl-carnitine metabolites were then produced and released from mitochondria. In addition, we show that hepatocytes ultimately also secreted these shortened acyl chains into their surroundings. Furthermore, when mitochondrial beta-oxidation was hindered, we show that peroxisomal beta-oxidation likely acts as a salvage pathway, thereby maintaining the levels of shortened fatty acid secretion. Taken together, we conclude that this new method based on oxaalkyne and alkyne fatty acids allows for metabolic tracing of the beta-oxidation pathway in tissue lysate and in living cells with unique coverage of metabolic intermediates and at unprecedented detail.

Keywords:  CPT; click; fatty acid metabolism; lipid oxidation; lipid tracer; lipidomics; mid-chain fatty acid; mitochondria; peroxisomes; β-oxidation

DOI:  https://doi.org/10.1016/j.jlr.2022.100188
J Alzheimers Dis. 2022 Feb 28.

Targeted Metabolomic Analysis in Alzheimer's Disease Plasma and Brain Tissue in Non-Hispanic Whites.

Karel Kalecký, Dwight C German, Albert A Montillo, Teodoro Bottiglieri.

   BACKGROUND: Metabolites are biological compounds reflecting the functional activity of organs and tissues. Understanding metabolic changes in Alzheimer's disease (AD) can provide insight into potential risk factors in this multifactorial disease and suggest new intervention strategies or improve non-invasive diagnosis.
OBJECTIVE: In this study, we searched for changes in AD metabolism in plasma and frontal brain cortex tissue samples and evaluated the performance of plasma measurements as biomarkers.
METHODS: This is a case-control study with two tissue cohorts: 158 plasma samples (94 AD, 64 controls; Texas Alzheimer's Research and Care Consortium - TARCC) and 71 postmortem cortex samples (35 AD, 36 controls; Banner Sun Health Research Institute brain bank). We performed targeted mass spectrometry analysis of 630 compounds (106 small molecules: UHPLC-MS/MS, 524 lipids: FIA-MS/MS) and 232 calculated metabolic indicators with a metabolomic kit (Biocrates MxP® Quant 500).
RESULTS: We discovered disturbances (FDR≤0.05) in multiple metabolic pathways in AD in both cohorts including microbiome-related metabolites with pro-toxic changes, methylhistidine metabolism, polyamines, corticosteroids, omega-3 fatty acids, acylcarnitines, ceramides, and diglycerides. In AD, plasma reveals elevated triglycerides, and cortex shows altered amino acid metabolism. A cross-validated diagnostic prediction model from plasma achieves AUC = 82% (CI95 = 75-88%); for females specifically, AUC = 88% (CI95 = 80-95%). A reduced model using 20 features achieves AUC = 79% (CI95 = 71-85%); for females AUC = 84% (CI95 = 74-92%).
CONCLUSION: Our findings support the involvement of gut environment in AD and encourage targeting multiple metabolic areas in the design of intervention strategies, including microbiome composition, hormonal balance, nutrients, and muscle homeostasis.

Keywords:  Alzheimer’s disease; antioxidants; bacterial toxins; biomarkers; human microbiome; hyperlipidemia; lipidomics; metabolic pathways; metabolomics; polyamines

DOI:  https://doi.org/10.3233/JAD-215448
Cancers (Basel). 2022 Mar 03. pii: 1311. [Epub ahead of print]14(5):

Comprehensive Metabolic Profiling of MYC-Amplified Medulloblastoma Tumors Reveals Key Dependencies on Amino Acid, Tricarboxylic Acid and Hexosamine Pathways.

Khoa Pham, Allison R Hanaford, Brad A Poore, Micah J Maxwell, Heather Sweeney, Akhila Parthasarathy, Jesse Alt, Rana Rais, Barbara S Slusher, Charles G Eberhart, Eric H Raabe.

  Reprograming of cellular metabolism is a hallmark of cancer. Altering metabolism allows cancer cells to overcome unfavorable microenvironment conditions and to proliferate and invade. Medulloblastoma is the most common malignant brain tumor of children. Genomic amplification of MYC defines a subset of poor-prognosis medulloblastoma. We performed comprehensive metabolic studies of human MYC-amplified medulloblastoma by comparing the metabolic profiles of tumor cells in three different conditions-in vitro, in flank xenografts and in orthotopic xenografts in the cerebellum. Principal component analysis showed that the metabolic profiles of brain and flank high-MYC medulloblastoma tumors clustered closely together and separated away from normal brain and in vitro MYC-amplified cells. Compared to normal brain, MYC-amplified medulloblastoma orthotopic xenograft tumors showed upregulation of the TCA cycle as well as the synthesis of nucleotides, hexosamines, amino acids and glutathione. There was significantly higher glucose uptake and usage in orthotopic xenograft tumors compared to flank xenograft tumors and cells in culture. In orthotopic tumors, glucose was the main carbon source for the de novo synthesis of glutamate, glutamine and glutathione through the TCA cycle. In vivo, the glutaminase II pathway was the main pathway utilizing glutamine. Glutathione was the most abundant upregulated metabolite in orthotopic tumors compared to normal brain. Glutamine-derived glutathione was synthesized through the glutamine transaminase K (GTK) enzyme in vivo. In conclusion, high MYC medulloblastoma cells have different metabolic profiles in vitro compared to in vivo, and key vulnerabilities may be missed by not performing in vivo metabolic analyses.

Keywords:  Warburg effect; cancer metabolism; isotope labeling; mass spectrometry; pediatric brain tumor

DOI:  https://doi.org/10.3390/cancers14051311
Anal Chem. 2022 Mar 11.

Ultrasensitive Determination of Sugar Phosphates in Trace Samples by Stable Isotope Chemical Labeling Combined with RPLC-MS.

Sha Li, Fei-Long Liu, Zheng Zhang, Xiao-Ming Yin, Tian-Tian Ye, Bi-Feng Yuan, Yu-Qi Feng.

Sugar phosphates are important metabolic intermediates in organisms and play a vital role in energy and central carbon metabolism. Profiling of sugar phosphates is of great significance but full of challenges due to their high structural similarity and low sensitivities in liquid chromatography (LC)-mass spectrometry (MS). In this study, we developed a novel stable isotope chemical labeling combined with the reversed-phase (RP)LC-MS method for ultrasensitive determination of sugar phosphates at the single-cell level. By chemical derivatization with 2-(diazo-methyl)-N-methyl-N-phenyl-benzamide (2-DMBA) and d5-2-DMBA, sugar phosphate isomers can obtain better separation and identification, and the detection sensitivities of sugar phosphates increased by 3.5-147 folds. The obtained limits of detection of sugar phosphates ranged from 5 to 16 pg/mL. Using this method, we achieved ultrasensitive and accurate quantification of 12 sugar phosphates in different trace biological samples. Benefiting from the improved separation and detection sensitivity, we successfully quantified five sugar phosphates (d-glucose 1-phosphate, d-mannose 6-phosphate, d-fructose 6-phosphate, d-glucose 6-phosphate, and seduheptulose 7-phosphate) in a single protoplast of Arabidopsis thaliana.

DOI: https://doi.org/10.1021/acs.analchem.2c00346
Rapid Commun Mass Spectrom. 2022 Mar 11. e9295

Development and Validation of a High-Resolving Power Absolute Quantitative PFAS method Incorporating Skyline Data Processing.

Jeffrey R Enders, Rebecca A Weed, Emily Griffith, David C Muddiman.

RATIONALE: The ability to perform absolute quantitation and non-targeted analysis on a single mass spectrometry instrument would be advantageous to many researchers studying PFAS. High resolution accurate mass (HRAM) instrumentation (typically deployed for non-targeted work) carries several advantages over traditional triple quadrupole workflows when performing absolute quantitation. Processing this data using a vendor-neutral software would promote collaboration for these environmental studies.
METHODS: LC-MS (Orbitrap Exploris 240) was used for absolute quantitation of 45 PFAS using precursor (MS1) peak areas for quantitation while isotope pattern matching and fragmentation (MS2) pattern matching were used for qualitative identification. Additionally, a fluorinated chromatographic column provided superior separation compared to the typical C18 columns typically used in PFAS analyses. This method is validated across 8 different chemical classes using recommended guidelines found in EPA Method 537.1 and Skyline data processing software.
RESULTS: The validated limits of all 45 compounds are reported as well as metrics or accuracy and reproducibility. Most compounds achieved limits of quantitation in the range of 2-50 ng/L. Also validated were four newly released Chemours-specific compounds (PEPA, PFO3OA, PFO4DA, and PFO5DoA). Aspects of data analysis specific to high resolving power absolute quantitation are reviewed as are the details of processing this data via Skyline.
CONCLUSIONS: This method demonstrates the feasibility of performing reproducible absolute quantitation of PFAS on an HRAM platform and does so using an open-source vendor-neutral data processing software to facilitate sharing of data across labs and institutions.

DOI: https://doi.org/10.1002/rcm.9295
Acta Pharm Sin B. 2022 Feb;12(2): 759-773

Targeting glutamine utilization to block metabolic adaptation of tumor cells under the stress of carboxyamidotriazole-induced nutrients unavailability.

Jing Shi, Rui Ju, Hongting Gao, Yuqing Huang, Lei Guo, Dechang Zhang.

  Tumor cells have unique metabolic programming that is biologically distinct from that of corresponding normal cells. Resetting tumor metabolic programming is a promising strategy to ameliorate drug resistance and improve the tumor microenvironment. Here, we show that carboxyamidotriazole (CAI), an anticancer drug, can function as a metabolic modulator that decreases glucose and lipid metabolism and increases the dependency of colon cancer cells on glutamine metabolism. CAI suppressed glucose and lipid metabolism utilization, causing inhibition of mitochondrial respiratory chain complex I, thus producing reactive oxygen species (ROS). In parallel, activation of the aryl hydrocarbon receptor (AhR) increased glutamine uptake via the transporter SLC1A5, which could activate the ROS-scavenging enzyme glutathione peroxidase. As a result, combined use of inhibitors of GLS/GDH1, CAI could effectively restrict colorectal cancer (CRC) energy metabolism. These data illuminate a new antitumor mechanism of CAI, suggesting a new strategy for CRC metabolic reprogramming treatment.

Keywords:  2-NBDG, glucalogue 2-(N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-2-deoxyglucose; ATP, adenosine triphosphate; AhR; AhR, aryl hydrocarbon receptor; CAI; CAI, carboxyamidotriazole; CHIP, chromatin immunoprecipitation; CRC, colorectal cancer; Colorectal cancer metabolism; DMF, 3′,4′-dimethoxyflavone; DNA, deoxyribonucleic acid; ECAR, extracellular acidification rate; FACS, flow cytometry; GDH1, glutamate dehydrogenase 1; GLS, glutaminase; GPx, glutathione peroxidase; GSH, glutathione; GSSG, oxidized glutathione; Glutamine metabolism; Glutaminolysis; Kyn, kynurenine; MT, mito-TEMPO; Metabolic reprogramming; Mito-Q, mitoquinone mesylate; Mitochondrial oxidative stress; OCR, oxygen consumption rate; Redox homeostasis; TCA, tricarboxylic acid; α-KG, α-ketoglutarate

DOI:  https://doi.org/10.1016/j.apsb.2021.07.008
Biochim Biophys Acta Rev Cancer. 2022 Mar 08. pii: S0304-419X(22)00030-0. [Epub ahead of print] 188705

Metabolic tricks of cancer cells.

Katerina Hönigova, Jiri Navratil, Barbora Peltanova, Hana Holcova Polanska, Martina Raudenska, Michal Masarik.

  One of the characteristics of cancer cells important for tumorigenesis is their metabolic plasticity. Indeed, in various stress conditions, cancer cells can reshape their metabolic pathways to support the increased energy request due to continuous growth and rapid proliferation. Moreover, selective pressures in the tumor microenvironment, such as hypoxia, acidosis, and competition for resources, force cancer cells to adapt by complete reorganization of their metabolism. In this review, we highlight the characteristics of cancer metabolism and discuss its clinical significance, since overcoming metabolic plasticity of cancer cells is a key objective of modern cancer therapeutics and a better understanding of metabolic reprogramming may lead to the identification of possible targets for cancer therapy.

Keywords:  Cancer metabolism; Cell death; Glutaminolysis; Metabolic symbiosis; Mitochondrial bioenergetics; Warburg effect

DOI:  https://doi.org/10.1016/j.bbcan.2022.188705
Drug Resist Updat. 2022 Mar;pii: S1368-7646(22)00021-8. [Epub ahead of print]61 100822

Targeting metabolism to overcome cancer drug resistance: A promising therapeutic strategy for diffuse large B cell lymphoma.

Manfei Pi, Huixian Kuang, Chunyan Yue, Qixuan Yang, Anqin Wu, Yuhua Li, Yehuda G Assaraf, Dong-Hua Yang, Shaojie Wu.

  Cancer cell metabolism including aerobic glycolysis, amino acid and fatty acid metabolism, has been extensively studied. Metabolic reprogramming is a major hallmark of cancer, which promotes cancer cell proliferation, progression and metastasis, as well as provokes resistance to chemotherapeutic drugs. Several signal transduction pathways, such as BCR, MEK/ERK, Notch, NF-κB and PI3K/AKT/mTOR, regulate tumor metabolism, hence promoting tumor cell growth, proliferation and progression. Therefore, targeting metabolic enzymes, metabolites or their signal transduction pathways may constitute a promising therapeutic strategy to enhance cancer treatment efficacy. Diffuse large B-cell lymphoma (DLBCL) is the most aggressive form of non-Hodgkin lymphoma (NHL), and one-third of DLBCL patients suffer from relapsed/refractory disease after chemotherapy. The mechanisms underlying drug resistance are complex, including target gene mutations, metabolic reprogramming, aberrant signal transduction pathways, enhanced drug efflux via overexpression of multidrug efflux transporters like P-glycoprotein, upregulation of anti-apoptotic proteins, drug sequestration and enhanced DND repair. This review delineates the distinct metabolic reprogramming patterns and the association between metabolism and anticancer drug resistance in DLBCL as well as the emerging strategies to surmount chemoresistance in DLBCL.

Keywords:  cancer drug resistance; diffuse large B cell lymphoma; tumor metabolism

DOI:  https://doi.org/10.1016/j.drup.2022.100822
Biol Direct. 2022 Mar 08. 17(1): 6

p53-driven lipidome influences non-cell-autonomous lysophospholipids in pancreatic cancer.

Alessio Butera, Micaela Roy, Carlotta Zampieri, Eleonora Mammarella, Emanuele Panatta, Gerry Melino, Angelo D'Alessandro, Ivano Amelio.

  Adaptation of the lipid metabolism participates in cancer pathogenesis, facilitating energy storage and influencing cell fate and control of molecular signalling. The tumour suppressor protein p53 is a molecular hub of cell metabolism, supporting antioxidant capabilities and counteracting oncogene-induced metabolic switch. Despite extensive work has described the p53-dependent metabolic pathways, a global profiling of p53 lipidome is still missing. By high-throughput untargeted lipidomic analysis of pancreatic ductal adenocarcinoma (PDAC) cells, we profile the p53-dependent lipidome, revealing intracellular and secreted lysophospholipids as one of the most affected class. Lysophospholipids are hydrolysed forms of phospholipids that results from phospholipase activity, which can function as signalling molecules, exerting non-cell-autonomous effects and instructing cancer microenvironment and immunity. Here, we reveal that p53 depletion reduces abundance of intracellular lysophosphatidyl-choline, -ethanolamine and -serine and their secretion in the extracellular environment. By integrating this with genomic and transcriptomic studies from in vitro models and human PDAC patients, we identified potential clinically relevant candidate p53-dependent phospholipases. In particular PLD3, PLCB4 and PLCD4 expression is regulated by p53 and chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) indicates a direct transcriptional control on their chromatin accessible genomic loci. Consistently, PLD3, PLCB4 and PLCD4 expression correlates with p53 mutational status in PDAC patients, and these genes display prognostic significance. Overall, our data provide insights into lipidome rewiring driven by p53 loss and identify alterations of lysophospholipids as a potential molecular mechanism for p53-mediated non-cell-autonomous molecular signalling that instructs cancer microenvironment and immunity during PDAC pathogenesis.

Keywords:  Lipid metabolism; Pancreatic cancer; Phospholipase; p53

DOI:  https://doi.org/10.1186/s13062-022-00319-9
Research (Wash D C). 2022 ;2022 9783602

Site-Specific Photochemical Reaction for Improved C=C Location Analysis of Unsaturated Lipids by Ultraviolet Photodissociation.

Hai-Fang Li, Jing Zhao, Wenbo Cao, Wenpeng Zhang, Yu Xia, Zheng Ouyang.

Unraveling the complexity of the lipidome requires the development of novel approaches to facilitate structural identification and characterization of lipid species with isomer-level discrimination. Ultraviolet photodissociation tandem mass spectrometry (UVPD MS/MS) is a promising tool for structure determination of lipids. The sensitivity of UVPD for lipid analysis however is limited mainly due to weak absorption of UV photons by a C=C. Herein, a C=C site-specific derivatization, the Paternò-Büchi (PB) reaction, was used to incorporate a chromophore to the C=C moiety in fatty acyls, leading to significantly improved UVPD efficiency and sensitivity for pinpointing C=C locations. The wavelength-dependent photodissociation of the PB products demonstrated 4-CF3-benzophenone as the best reagent for UVPD in terms of the efficiency of generating C=C diagnostic fragments and simplicity for C=C location assignments. We demonstrated the effectiveness of this approach for the shotgun profiling of C=C location isomers in different lipid classes from complex lipid extracts, highlighting its potential to advancing the identification of the C=C bond locations in unsaturated lipids.

DOI: https://doi.org/10.34133/2022/9783602
Oncol Lett. 2022 Apr;23(4): 119

Lipid metabolism of cancer stem cells.

Huihui Liu, Zhengyang Zhang, Lian Song, Jie Gao, Yanfang Liu.

  Cancer stem cells (CSCs), also termed cancer-initiating cells, are a special subset of cells with high self-replicating and self-renewing abilities that can differentiate into various cell types under certain conditions. A number of studies have demonstrated that CSCs have distinct metabolic properties. The reprogramming of energy metabolism enables CSCs to meet the needs of self-renewal and stemness maintenance. Increasing evidence supports the view that alterations in lipid metabolism, including an increase in fatty acid (FA) uptake, de novo lipogenesis, formation of lipid droplets and mitochondrial FA oxidation, are involved in CSC regulation. In the present review, the metabolic characteristics of CSCs, particularly in lipid metabolism, were summarized. In addition, the potential mechanisms of CSC lipid metabolism in treatment resistance were discussed. Given their significance in cancer biology, targeting CSC metabolism may serve an important role in future cancer treatment.

Keywords:  cancer stem cells; key modulators; lipid metabolism; metabolic reprogramming; resistant to therapy

DOI:  https://doi.org/10.3892/ol.2022.13239
Nutrients. 2022 Jan 28. pii: 579. [Epub ahead of print]14(3):

Lysophosphatidylethanolamine Affects Lipid Accumulation and Metabolism in a Human Liver-Derived Cell Line.

Yusuke Yamamoto, Toshihiro Sakurai, Zhen Chen, Nao Inoue, Hitoshi Chiba, Shu-Ping Hui.

  The physiological functions of lysophosphatidylethanolamine (lysoPE) have not been fully elucidated. In this study, the effects of lysoPE on lipogenesis and lipolysis were investigated in a cultured human liver-derived cell line. The intracellular lipid profile was investigated in detail using liquid chromatography-tandem mass spectrometry (LC-MS/MS) to better understand the underlying mechanism. The expression of genes related to lipid metabolism and catabolism was analyzed using real-time PCR. LysoPE supplementation induced cellular lipid droplet formation and altered triacylglycerol (TAG) profiles. Furthermore, lysoPE downregulated expression of the TAG hydrolyzation regulation factor ATGL, and reduced the expression of fatty acid biosynthesis-related genes SREBP1 and SCD1. LC-MS/MS-based lipidomic profiling revealed that the addition of lysoPE 18:2 increased the PE species containing linoleic acyl, as well as the CE 18:2 species, likely due to the incorporation of linoleic acyl from lysoPE 18:2. Collectively, these findings suggest that lysoPE 18:2 is involved in lipid droplet formation by suppressing lipolysis and fatty acid biosynthesis. Thus, lysoPE might play a pathological role in the induction of fatty liver disease.

Keywords:  LC-MS/MS; adipose tissue triglyceride lipase; catabolism; lipid droplets; triacylglycerol

DOI:  https://doi.org/10.3390/nu14030579
Theranostics. 2022 ;12(5): 2015-2027

Faecal microbiome and metabolic signatures in rectal neuroendocrine tumors.

Wei Hu, Ze Min Chen, Xia Xi Li, Lan Lu, Gen Hua Yang, Zheng Xia Lei, Li Juan You, Xiao Bing Cui, Si Cun Lu, Zhi Yong Zhai, Zhi Yu Zeng, Ye Chen, Si Lin Huang, Wei Gong.

  Background: The prevalence of rectal neuroendocrine tumors (RNET) has increased substantially over the past decades. Little is known on mechanistic alteration in the pathogenesis of such disease. We postulate that perturbations of human gut microbiome-metabolome interface influentially affect the development of RNET. The study aims to characterize the composition and function of faecal microbiome and metabolites in RNET individuals. Methods: We performed deep shotgun metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomic profiling of faecal samples from the discovery cohort (18 RNET patients, 40 controls), and validated the microbiome and metabolite-based classifiers in an independent cohort (15 RNET participants, 19 controls). Results: We uncovered a dysbiotic gut ecological microenvironment in RNET patients, characterized by aberrant depletion and attenuated connection of microbial species, and abnormally aggregated lipids and lipid-like molecules. Functional characterization based on our in-house and Human Project Unified Metabolic Analysis Network 2 (HUMAnN2) pipelines further indicated a nutrient deficient gut microenvironment in RNET individuals, evidenced by diminished activities such as energy metabolism, vitamin biosynthesis and transportation. By integrating these data, we revealed 291 robust associations between representative differentially abundant taxonomic species and metabolites, indicating a tight interaction of gut microbiome with metabolites in RNET pathogenesis. Finally, we identified a cluster of gut microbiome and metabolite-based signatures, and replicated them in an independent cohort, showing accurate prediction of such neoplasm from healthy people. Conclusions: Our current study is the first to comprehensively characterize the perturbed interface of gut microbiome and metabolites in RNET patients, which may provide promising targets for microbiome-based diagnostics and therapies for this disorder.

Keywords:  Gut microbiota; Metabolite; Rectal neuroendocrine tumor; Shotgun metagenomic sequencing; Untargeted liquid chromatography-mass spectrometry (LC-MS) metabolomics.

DOI:  https://doi.org/10.7150/thno.66464
Cells. 2022 Mar 02. pii: 866. [Epub ahead of print]11(5):

An Optimized Workflow for the Analysis of Metabolic Fluxes in Cancer Spheroids Using Seahorse Technology.

Gloria Campioni, Valentina Pasquale, Stefano Busti, Giacomo Ducci, Elena Sacco, Marco Vanoni.

  Three-dimensional cancer models, such as spheroids, are increasingly being used to study cancer metabolism because they can better recapitulate the molecular and physiological aspects of the tumor architecture than conventional monolayer cultures. Although Agilent Seahorse XFe96 (Agilent Technologies, Santa Clara, CA, United States) is a valuable technology for studying metabolic alterations occurring in cancer cells, its application to three-dimensional cultures is still poorly optimized. We present a reliable and reproducible workflow for the Seahorse metabolic analysis of three-dimensional cultures. An optimized protocol enables the formation of spheroids highly regular in shape and homogenous in size, reducing variability in metabolic parameters among the experimental replicates, both under basal and drug treatment conditions. High-resolution imaging allows the calculation of the number of viable cells in each spheroid, the normalization of metabolic parameters on a per-cell basis, and grouping of the spheroids as a function of their size. Multivariate statistical tests on metabolic parameters determined by the Mito Stress test on two breast cancer cell lines show that metabolic differences among the studied spheroids are mostly related to the cell line rather than to the size of the spheroid. The optimized workflow allows high-resolution metabolic characterization of three-dimensional cultures, their comparison with monolayer cultures, and may aid in the design and interpretation of (multi)drug protocols.

Keywords:  3D cultures; bioenergetics; cancer metabolism; high-throughput quantitative live-cell confocal imaging; mitochondrial respiration

DOI:  https://doi.org/10.3390/cells11050866
Front Immunol. 2021 ;12 774103

mTOR-Mediated Regulation of Immune Responses in Cancer and Tumor Microenvironment.

Sahar Mafi, Behzad Mansoori, Shahram Taeb, Hossein Sadeghi, Reza Abbasi, William C Cho, Davoud Rostamzadeh.

  The mechanistic/mammalian target of rapamycin (mTOR) is a downstream mediator in the phosphatidylinositol 3-kinase (PI3K)/Akt signaling pathways, which plays a pivotal role in regulating numerous cellular functions including cell growth, proliferation, survival, and metabolism by integrating a variety of extracellular and intracellular signals in the tumor microenvironment (TME). Dysregulation of the mTOR pathway is frequently reported in many types of human tumors, and targeting the PI3K/Akt/mTOR signaling pathway has been considered an attractive potential therapeutic target in cancer. The PI3K/Akt/mTOR signaling transduction pathway is important not only in the development and progression of cancers but also for its critical regulatory role in the tumor microenvironment. Immunologically, mTOR is emerging as a key regulator of immune responses. The mTOR signaling pathway plays an essential regulatory role in the differentiation and function of both innate and adaptive immune cells. Considering the central role of mTOR in metabolic and translational reprogramming, it can affect tumor-associated immune cells to undergo phenotypic and functional reprogramming in TME. The mTOR-mediated inflammatory response can also promote the recruitment of immune cells to TME, resulting in exerting the anti-tumor functions or promoting cancer cell growth, progression, and metastasis. Thus, deregulated mTOR signaling in cancer can modulate the TME, thereby affecting the tumor immune microenvironment. Here, we review the current knowledge regarding the crucial role of the PI3K/Akt/mTOR pathway in controlling and shaping the immune responses in TME.

Keywords:  PI3K/Akt/mTOR signaling pathway; T cell; Tumor microenvironment; cancer; immune response; mTOR

DOI:  https://doi.org/10.3389/fimmu.2021.774103