bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒11‒15
twenty-six papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh

  1. Cancers (Basel). 2020 Nov 06. pii: E3292. [Epub ahead of print]12(11):
      Cancer alters cell metabolism. How these changes are manifested in the metabolite cargo of cancer-derived extracellular vesicles (EVs) remains poorly understood. To explore these changes, EVs from prostate, cutaneous T-cell lymphoma (CTCL), colon cancer cell lines, and control EVs from their noncancerous counterparts were isolated by differential ultracentrifugation and analyzed by nanoparticle tracking analysis (NTA), electron microscopy (EM), Western blotting, and liquid chromatography-mass spectrometry (LC-MS). Although minor differences between the cancerous and non-cancerous cell-derived EVs were observed by NTA and Western blotting, the largest differences were detected in their metabolite cargo. Compared to EVs from noncancerous cells, cancer EVs contained elevated levels of soluble metabolites, e.g., amino acids and B vitamins. Two metabolites, proline and succinate, were elevated in the EV samples of all three cancer types. In addition, folate and creatinine were elevated in the EVs from prostate and CTCL cancer cell lines. In conclusion, we present the first evidence in vitro that the altered metabolism of different cancer cells is reflected in common metabolite changes in their EVs. These results warrant further studies on the significance and usability of this metabolic fingerprint in cancer.
    Keywords:  cancer metabolism; colon cancer; cutaneous T-cell lymphoma; extracellular vesicles; prostate cancer
  2. Methods Mol Biol. 2021 ;2234 271-295
      A method based on reversed phase high-performance liquid chromatography coupled with electrospray ionization high-resolution mass spectrometry (RP-HPLC-ESI-HRMS) for the comprehensive and reliable detection of secondary metabolites of Trichoderma reesei cultured in synthetic minimal liquid medium is presented. A stable isotope-assisted (SIA) workflow is used, which allows the automated, comprehensive extraction of truly fungal metabolite-derived LC-MS signals from the acquired chromatographic data. The subsequent statistical data analysis and a typical outcome of such a metabolomics data evaluation are shown by way of example in a previously published study on the influence of the pleiotropic regulator transcription factor Xylanase promoter binding protein 1 (Xpp1) in T. reesei on secondary metabolism.
    Keywords:  Liquid chromatography–high-resolution mass spectrometry; Metabolomics; Stable isotope-assisted workflow; Stable isotopic labeling
  3. Cells. 2020 Nov 10. pii: E2447. [Epub ahead of print]9(11):
      Fatty acid synthase (FAS) is a key enzyme involved in de novo lipogenesis that produces lipids that are necessary for cell growth and signal transduction, and it is known to be overexpressed, especially in cancer cells. Although lipid metabolism alteration is an important metabolic phenotype in cancer cells, the development of drugs targeting FAS to block lipid synthesis is hampered by the characteristics of cancer cells with metabolic flexibility leading to rapid adaptation and resistance. Therefore, to confirm the metabolic alterations at the cellular level during FAS inhibition, we treated LNCaP-LN3 prostate cancer cells with FAS inhibitors (Fasnall, GSK2194069, and TVB-3166). With untargeted metabolomics, we observed significant changes in a total of 56 metabolites in the drug-treated groups. Among the altered metabolites, 28 metabolites were significantly changed in all of the drug-treated groups. To our surprise, despite the inhibition of FAS, which is involved in palmitate production, the cells increase their fatty acids and glycerophospholipids contents endogenously. Also, some of the notable changes in the metabolic pathways include polyamine metabolism and energy metabolism. This is the first study to compare and elucidate the effect of FAS inhibition on cellular metabolic flexibility using three different FAS inhibitors through metabolomics. We believe that our results may provide key data for the development of future FAS-targeting drugs.
    Keywords:  enzyme inhibition; fatty acid synthase; glycerophospholipid metabolism; metabolic flexibility; metabolomics
  4. Cell Metab. 2020 Nov 06. pii: S1550-4131(20)30535-0. [Epub ahead of print]
      The emergence of cancer from diverse normal tissues has long been rationalized to represent a common set of fundamental processes. However, these processes are not fully defined. Here, we show that forced expression of glucose-6-phosphate dehydrogenase (G6PD) affords immortalized mouse and human cells anchorage-independent growth in vitro and tumorigenicity in animals. Mechanistically, G6PD augments the NADPH pool by stimulating NAD+ kinase-mediated NADP+ biosynthesis in addition to converting NADP+ to NADPH, bolstering antioxidant defense. G6PD also increases nucleotide precursor levels through the production of ribose and NADPH, promoting cell proliferation. Supplementation of antioxidants or nucleosides suffices to convert immortalized mouse and human cells into a tumorigenic state, and supplementation of both is required when their overlapping metabolic consequences are minimized. These results suggest that normal cells have a limited capacity for redox balance and nucleotide synthesis, and overcoming this limit might represent a key aspect of oncogenic transformation.
    Keywords:  G6PD; NAD kinase; NADPH; antioxidants; cancer metabolism; nucleosides; nucleotide synthesis; oncogenic transformation; pentose phosphate pathway; redox regulation
  5. J Proteome Res. 2020 Nov 11.
      Tandem mass tag (TMT)-based mass spectrometry (MS) enables deep proteomic profiling of more than 10,000 proteins in complex biological samples but requires up to 100 μg protein in starting materials during a standard analysis. Here, we present a streamlined protocol to quantify more than 9000 proteins with 0.5 μg protein per sample by 16-plex TMT coupled with two-dimensional liquid chromatography and tandem mass spectrometry (LC/LC-MS/MS). In this protocol, we optimized multiple conditions to reduce sample loss, including processing each sample in a single tube to minimize surface adsorption, increasing digestion enzymes to shorten proteolysis and function as carriers, eliminating a desalting step between digestion and TMT labeling, and developing miniaturized basic pH LC for prefractionation. By profiling 16 identical human brain tissue samples of Alzheimer's disease (AD), vascular dementia (VaD), and non-dementia controls, we directly compared this new microgram-scale protocol to the standard-scale protocol, quantifying 9116 and 10,869 proteins, respectively. Importantly, bioinformatics analysis indicated that the microgram-scale protocol had adequate sensitivity and reproducibility to detect differentially expressed proteins in disease-related pathways. Thus, this newly developed protocol is of general application for deep proteomics analysis of biological and clinical samples at sub-microgram levels.
    Keywords:  Alzheimer’s disease; TMT; isobaric labeling; liquid chromatography; mass spectrometry; nanoscale; proteome; proteomics; single cell proteomics; vascular dementia
  6. Biochim Biophys Acta Mol Cell Biol Lipids. 2020 Nov 04. pii: S1388-1981(20)30245-6. [Epub ahead of print] 158853
      BACKGROUND: Lipids participate in many important biological functions through energy storage, material transport, signal transduction, and molecular recognition processes. Studies have reported that asthmatic patients have abnormal lipid metabolism. However, there are limited studies on the characterization of lipid metabolism in asthmatic patients by lipidomics.METHODS: We characterized the plasma lipid profile of 28 healthy controls and 33 outpatients with asthma (18 mild, 15 moderate) by liquid chromatography mass spectrometry/mass spectrometry-based lipidomics.
    RESULTS: We determined 1338 individual lipid species in the plasma. Significant changes were identified in ten lipid species in asthmatic patients than in healthy controls (all P < 0.05). Phosphatidylethanolamine (PE) (18:1p/22:6), PE (20:0/18:1), PE (38:1), sphingomyelin (SM) (d18:1/18:1), and triglyceride (TG) (16:0/16:0/18:1) positively correlated with the severity of asthma (all P < 0.05). Phosphatidylinositol (PI) (16:0/20:4), TG (17:0/18:1/18:1), phosphatidylglycerol (PG) (44:0), ceramide (Cer) (d16:0/27:2), and lysophosphatidylcholine (LPC) (22:4) negatively correlated with the severity of asthma (all P < 0.05). Correlation analysis showed a significant correlation between all ten lipid species (all P < 0.05). From the area under the curve of the receiver operating characteristic curve analysis, PE (38:1) was the major lipid metabolite that distinguished asthmatic patients from healthy controls, and may be considered a potential lipid biomarker. PE (20:0/18:1) and TG (16:0/16:0/18:1) might be related to IgE levels in asthmatic patients.
    CONCLUSIONS: Our results indicated the presence of abnormal lipid metabolism, which correlated with the severity and IgE levels in asthmatic patients.
    Keywords:  Asthma; Biomarkers; Lipid metabolism; Lipidomics
  7. J Proteome Res. 2020 Nov 09.
      Mass spectrometry has greatly improved the analysis of phosphorylation events in complex biological systems and on a large scale. Despite considerable progress, the correct identification of phosphorylated sites, their quantification, and their interpretation regarding physiological relevance remain challenging. The MS Resource Pillar of the Human Proteome Organization (HUPO) Human Proteome Project (HPP) initiated the Phosphopeptide Challenge as a resource to help the community evaluate methods, learn procedures and data analysis routines, and establish their own workflows by comparing results obtained from a standard set of 94 phosphopeptides (serine, threonine, tyrosine) and their nonphosphorylated counterparts mixed at different ratios in a neat sample and a yeast background. Participants analyzed both samples with their method(s) of choice to report the identification and site localization of these peptides, determine their relative abundances, and enrich for the phosphorylated peptides in the yeast background. We discuss the results from 22 laboratories that used a range of different methods, instruments, and analysis software. We reanalyzed submitted data with a single software pipeline and highlight the successes and challenges in correct phosphosite localization. All of the data from this collaborative endeavor are shared as a resource to encourage the development of even better methods and tools for diverse phosphoproteomic applications. All submitted data and search results were uploaded to MassIVE ( as data set MSV000085932 with ProteomeXchange identifier PXD020801.
    Keywords:  Human Proteome Organization (HUPO); Human Proteome Project (HPP); MS Resource Pillar; Phosphopeptide Challenge; false identification rate; mass spectrometry; phospho site localization; phosphopeptide enrichment; phosphorylated peptides
  8. Cell Death Dis. 2020 Nov 11. 11(11): 964
      By targeting the tumor microenvironment to stimulate antitumor immunity, immunotherapies have revolutionized cancer treatment. However, many patients do not respond initially or develop secondary resistance. Based on the limited resources in the tumor microenvironment and competition between tumor and immune cells, the field of immune metabolism has produced extensive knowledge showing that targeting metabolism could help to modulate antitumor immunity. However, among all the different potentially targetable metabolic pathways, it remains unclear which have more potential to overcome resistance to immune checkpoint inhibitors. Here, we explore metabolic reprogramming in cancer cells, which might inhibit antitumor immunity, and strategies that can be used to favor the antitumor response.
  9. Prostaglandins Other Lipid Mediat. 2020 Oct 22. pii: S1098-8823(20)30073-3. [Epub ahead of print]152 106480
      Biologically active glutathione (GSH) conjugates of oxygenated fatty acids comprise a group of pro- and anti-inflammatory lipid mediators. While arachidonic acid (AA)-derived conjugates, as the cysteinyl leukotrienes (cys-LTs) and eoxins (EXs) have pro-inflammatory properties, conjugates in tissue regeneration (CTRs) biosynthesized from docosahexaenoic acid (DHA) exhibit pro-resolving activity. Human platelets express abundant amounts of platelet-type 12-lipoxygenase (pt12-LOX) and leukotriene C4 synthase (LTC4S). However, the only two described GSH conjugates formed by platelets are the AA-derived cys-LTs and the recently reported maresin CTRs (MCTRs). While cys-LTs are biosynthesized in a transcellular mechanism via the action of 5-LOX and LTC4S, MCTR1 is formed by 12-LOX and a yet unidentified GSH S-transferase (GST). Here, we present a novel GSH conjugate formed from AA via the 12-LOX pathway in human platelets. The 12-oxo-glutathione adduct, 12-oxo-10-glutathionyl-5,8,14-eicosatrienoic acid (TOG10), was identified by mass spectrometry using positive electrospray ionization. The structural proposal is supported by fragmentation data of the labeled metabolite obtained after incubation of deuterated AA (AA-d8). In platelets as well as in HEK293 cells stably expressing pt12-LOX, TOG10 biosynthesis was inhibited by the 12-LOX inhibitor ML-355 (5 μM), which confirms the involvement of pt12-LOX. Interestingly, TOG10 was formed independently of LTC4S in platelets. This is in accordance with the observation that the conjugate was also generated by AA-stimulated HEK_12-LOX cells in absence of LTC4S. Nevertheless, TOG10 can also be formed by LTC4S as the biosynthesis in HEK_12-LOX_LTC4S cells was reduced by the specific LTC4S inhibitor TK04a. In summary, TOG10 was identified as a new AA-derived GSH conjugate generated in human platelets via the action of pt12-LOX in combination with a GST.
    Keywords:  1,4 Michael addition; 12-Lipoxygenase; Glutathione conjugate; Platelets
  10. Amino Acids. 2020 Nov 11.
      Amino acids (AAs) play a crucial role in cancer cell metabolism. Levels of 22 plasma AAs at the time of diagnosis and after treatment were established among 39 pediatric cancer patients and 33 healthy children. Glutamic acid levels decreased and tryptophan levels increased during treatment. Cancer patients presented significantly lower levels of glutamine and leucine post-treatment while levels of 12 other AAs were higher comparing to controls. Results suggest that plasma free AA profile may serve as a prognostic biomarker.
    Keywords:  Amino acid profile; Cancer; Metabolomics; Tumor biomarkers
  11. Anal Chem. 2020 Nov 11.
      S-Nitrosylation is an important post-translational modification that occurs on cysteine amino acid and regulates signal transduction in diverse cell processes. Dysregulation of protein nitrosylation has shown close association with cardiovascular and neurological diseases, thus demanding further precise and in-depth understanding. Mass spectrometry-based proteomics has been the method of choice for analyzing S-nitrosylated (SNO-) proteins. However, due to their extremely low expression level and rapid turnover rate, quantitative analysis of the S-nitrosylation at the proteomic level remains challenging. Herein, we developed a novel approach termed FluoroTRAQ, which combined the fluorous solid-phase extraction of SNO-peptides and iTRAQ labeling for the quantitative analysis of the SNO-proteome with high sensitivity and specificity. This new analytical strategy was subsequently applied to examine the dynamic SNO-proteome changes of human umbilical vein endothelial cells upon in vitro S-nitrosoglutathione induction. Our data identified a number of novel SNO-proteins and revealed their temporal modulation as validated by biotin switch assay. Our study offered a practical approach for quantitative analysis of protein S-nitrosylation.
  12. Cell Metab. 2020 Nov 06. pii: S1550-4131(20)30545-3. [Epub ahead of print]
      Triple-negative breast cancer (TNBC) remains an unmet medical challenge. We investigated metabolic dysregulation in TNBCs by using our multi-omics database (n = 465, the largest to date). TNBC samples were classified into three heterogeneous metabolic-pathway-based subtypes (MPSs) with distinct metabolic features: MPS1, the lipogenic subtype with upregulated lipid metabolism; MPS2, the glycolytic subtype with upregulated carbohydrate and nucleotide metabolism; and MPS3, the mixed subtype with partial pathway dysregulation. These subtypes were validated by metabolomic profiling of 72 samples. These three subtypes had distinct prognoses, molecular subtype distributions, and genomic alterations. Moreover, MPS1 TNBCs were more sensitive to metabolic inhibitors targeting fatty acid synthesis, whereas MPS2 TNBCs showed higher sensitivity to inhibitors targeting glycolysis. Importantly, inhibition of lactate dehydrogenase could enhance tumor response to anti-PD-1 immunotherapy in MPS2 TNBCs. Collectively, our analysis demonstrated the metabolic heterogeneity of TNBCs and enabled the development of personalized therapies targeting unique tumor metabolic profiles.
    Keywords:  glycolysis; heterogeneity; immunotherapy; metabolic inhibitor; metabolic pathway; metabolism; subtype; survival; triple-negative breast cancer
  13. Biology (Basel). 2020 Nov 07. pii: E380. [Epub ahead of print]9(11):
      Tumors consist of a wide variety of cells, including immune cells, that affect tumor progression. Macrophages are abundant innate immune cells in the tumor microenvironment (TME) and are crucial in regulating tumorigenicity. Specific metabolic conditions in the TME can alter the phenotype of tumor-associated macrophages (TAMs) in a direction that supports their pro-tumor functions. One of these conditions is the accumulation of metabolites, also known as oncometabolites. Interactions of oncometabolites with TAMs can promote a pro-tumorigenic phenotype, thereby sustaining cancer cell growth and decreasing the chance of eradication. This review focuses on the metabolic cancer-macrophage crosstalk in the TME. We discuss how cancer cell metabolism and oncometabolites affect macrophage phenotype and function, and conversely how macrophage metabolism can impact tumor progression. Lastly, we propose tumor-secreted exosome-mediated metabolic signaling as a potential factor in tumorigenesis. Insight in these processes may contribute to the development of novel cancer therapies.
    Keywords:  TAM; cancer; macrophages; metabolism; oncometabolite; tumor; tumor-associated macrophage
  14. Mol Metab. 2020 Nov 10. pii: S2212-8778(20)30189-7. [Epub ahead of print] 101115
      BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is defined by the abundance of lipid droplets (LDs) in hepatocytes. While historically considered simply a depot for energy storage, LDs are increasingly recognized to impact a wide range of biological processes that influence cellular metabolism, signaling, and function. While progress has been made towards our understanding of factors leading to LD accumulation (i.e. steatosis) and its progression to advanced stages of NAFLD and/or systemic metabolic dysfunction, much remains to be resolved.SCOPE OF REVIEW: This review will cover many facets of LD biology. We will provide a brief overview of the major pathways of lipid accretion and degradation that contribute to steatosis, and how they are altered in NAFLD. The major focus will be on the relationship between LDs and cell function and the detailed mechanisms that couple or uncouple steatosis from severity and progression of NAFLD and systemic comorbidities. The importance of specific lipids and proteins within or on LDs as key components that determine whether LD accumulation is linked to cellular and metabolic dysfunction will be presented. Finally, we will discuss emerging areas of LD biology and future research directions that are needed to advance our understanding into the role of LDs in NAFLD etiology.
    MAJOR CONCLUSIONS: Impairments in LD breakdown appear to contribute to disease progression, but inefficient incorporation of fatty acids (FAs) into LD-containing triacylglycerol (TAG) and the consequential changes in FA partitioning also affect NAFLD etiology. Increased LD abundance in hepatocytes does not necessarily equate to cellular dysfunction. While LD accumulation is the commitment step for most NAFLD cases, the protein and lipid composition of LDs are critical factors in determining the progression from simple steatosis. Further defining the detailed molecular mechanisms linking LDs to metabolic dysfunction will be important for the design of effective therapeutic approaches targeting NAFLD and its comorbidities.
    Keywords:  Lipid droplets; Lipotoxicity; NAFLD; NASH; Perilipins
  15. Nat Commun. 2020 11 10. 11(1): 5698
      Changes to lipid metabolism are tightly associated with the onset and pathology of Alzheimer's disease (AD). Lipids are complex molecules comprising many isomeric and isobaric species, necessitating detailed analysis to enable interpretation of biological significance. Our expanded targeted lipidomics platform (569 species across 32 classes) allows for detailed lipid separation and characterisation. In this study we examined peripheral samples of two cohorts (AIBL, n = 1112 and ADNI, n = 800). We are able to identify concordant peripheral signatures associated with prevalent AD arising from lipid pathways including; ether lipids, sphingolipids (notably GM3 gangliosides) and lipid classes previously associated with cardiometabolic disease (phosphatidylethanolamine and triglycerides). We subsequently identified similar lipid signatures in both cohorts with future disease. Lastly, we developed multivariate lipid models that improved classification and prediction. Our results provide a holistic view between the lipidome and AD using a comprehensive approach, providing targets for further mechanistic investigation.
  16. Talanta. 2021 Jan 15. pii: S0039-9140(20)30970-X. [Epub ahead of print]222 121679
      The identification of new biomarkers (e.g., metabolic biomarkers) will facilitate not only the diagnosis of stroke but also the differentiation of stroke subtypes, especially the discrimination of ischaemic stroke from intracerebral hemorrhage. Herein, we develop for the first time an ultra-high-pressure liquid chromatography tandem mass spectrometry (UHPLC-MS)-based targeted metabolomic method to screen the metabolic biomarkers of stroke and identify the fatty acid metabolite 20-hydroxy-leukotriene B4 (20-OH-LTB4) and its key enzyme cytochrome P450 family 4 subfamily F member 2 (CYP4F2) as the potential biomarkers for differentiating healthy persons, acute ischemic stroke (AIS) patients, and intracerebral hemorrhage stroke (ICH) patients. We evaluated 158 fatty acids and their metabolites in 177 serum samples obtained from 65 healthy volunteers, 70 AIS patients and 42 ICH patients, and identified the potential biomarkers associated with ICH by using multivariate statistical analysis. We found that 20-OH-LTB4 and arachidonic acid can be used to discriminate ICH patients from healthy individuals, and 20-OH-LTB4 and 17, 18-epoxy-eicosatetraenoic acid (7,18-EpETE) can be used to differentiate the subtypes of ICH and AIS. Especially, 20-OH-LTB4 may function as a potential biomarker for ICH diagnosis and risk assessment, and it can discriminate ICH patients from healthy individuals and AIS patients. Moreover, we identified CYP4F2 protein as a potential biomarker of ICH for prevention and treatment assessment. This method may provide a powerful platform for ICH diagnosis, prevention, and treatment assessment.
    Keywords:  Biomarkers; Intracerebral hemorrhage stroke; Mass spectrometry; Metabolomics; Prediction
  17. Am J Pathol. 2020 Nov 04. pii: S0002-9440(20)30488-0. [Epub ahead of print]
      Utilization of proper preclinical models accelerates development of immunotherapeutic and the study of the interplay between human malignant cells and immune cells. Lysosomal acid lipase (LAL) is a critical lipid hydrolase that generates free fatty acids and cholesterol. Ablation of LAL suppresses immune-rejection and allows growth of human lung cancer cells in lal-/- mice. In the lal-/- lymph nodes, the percentages of both T regulatory and B regulatory cells (Tregs and Bregs) are increased with elevated expression of PD-L1, IL-10, and decreased expression of IFNγ. In Tregs and Bregs of the lal-/- lymph nodes, levels of enzymes in glucose and glutamine metabolic pathways are elevated. Pharmacologic inhibitor of pyruvate dehydrogenase (PDH), which controls the transition from glycolysis to the citric acid cycle, effectively reduces Treg and Breg elevation in the lal-/- lymph nodes. Blocking the mammalian target of rapamycin (mTOR) or reactivating peroxisome proliferator-activated receptor gamma (PPARγ), an LAL downstream effector, reduces lal-/- Treg and Breg elevation, PD-L1 expression in lal-/- Tregs and Bregs, and improves human cancer cell rejection. Treatment of PD-L1 antibody also reduces Treg and Breg elevation in the lal-/- lymph nodes and improves human cancer cell rejection. These observations conclude that LAL-regulated lipid metabolism is essential to maintain anti-tumor immunity.
    Keywords:  Bregs; PD-L1; PPARgamma; Tregs; human cancer cell-derived xenografts; lymph node; lysosomal acid lipase; mTOR; metabolic regulation; tumor animal models
  18. Int J Mol Sci. 2020 Nov 09. pii: E8387. [Epub ahead of print]21(21):
      Tumor suppressor p53 plays a key role in tumor suppression. In addition to tumor suppression, p53 is also involved in many other biological and pathological processes, such as immune response, maternal reproduction, tissue ischemia/reperfusion injuries and neurodegenerative diseases. While it has been widely accepted that the role of p53 in regulation of cell cycle arrest, senescence and apoptosis contributes greatly to the function of p53 in tumor suppression, emerging evidence has implicated that p53 also exerts its tumor suppressive function through regulation of many other cellular processes, such as metabolism, anti-oxidant defense and ferroptosis. Ferroptosis is a unique iron-dependent form of programmed cell death driven by lipid peroxidation in cells. Ferroptosis has been reported to be involved in cancer, tissue ischemia/reperfusion injuries and neurodegenerative diseases. Recent studies have shown that ferroptosis can be regulated by p53 and its signaling pathway as well as tumor-associated mutant p53. Interestingly, the regulation of ferroptosis by p53 appears to be highly context-dependent. In this review, we summarize recent advances in the regulation of ferroptosis by p53 and its signaling pathway. Further elucidation of the role and molecular mechanism of p53 in ferroptosis regulation will yield new therapeutic strategies for cancer and other diseases, including neurodegenerative diseases and tissue ischemia/reperfusion injuries.
    Keywords:  cancer; disease; ferroptosis; lipid peroxidation; metabolism; p53; tumor suppressor
  19. Methods Mol Biol. 2021 ;2248 251-258
      Detection of tumor necrosis factor-alpha (TNF-α) is usually performed in cell cultured medium or body fluids via measurement of its soluble extracellular form. However, depending on cellular condition, TNF-α might be transported through extracellular vesicles (EV) from donor cells to recipient cells. EV are small membrane-delimited structures (∼50 nm to 10 μm) that are spontaneously released from multiple cell types. In cancer, EV arise as important mediators in intercellular communication, and their molecular content may support tumor progression. This chapter describes methods to identify protein content in EV released from the tumor cell cultures. Through this protocol, we show first how to purify EV from in vitro cell culture by using differential centrifugation technique and then we demonstrate how to identify both membrane and soluble TNF-α forms in EV by Western blotting.
    Keywords:  Cancer; Differential centrifugation; Extracellular vesicles; TNF-α; Western blotting
  20. Methods Mol Biol. 2021 ;2185 159-179
      Leukemic stem cells are highly dynamic and heterogeneous. Analysis of leukemic stem cells at the single-cell level should provide a wealth of insights that would not be possible using bulk measurements. Mass spectrometry (MS)-based proteomic workflows can quantify hundreds or thousands of proteins from a biological sample and has proven invaluable for biomedical research, but samples comprising large numbers of cells are typically required due to limited sensitivity. Recent developments in sample processing, chromatographic separations, and MS instrumentation are now extending in-depth proteome profiling to single mammalian cells. Here, we describe specific techniques that increase the sensitivity of single-cell proteomics by orders of magnitude, enabling the promise of single-cell proteomics to become a reality. We anticipate such techniques can significantly advance the understanding of leukemic stem cells.
    Keywords:  Proteome mapping; Single-cell analysis; Single-cell proteomics; Small cell populations; Small sample; Ultrasensitive; nanoLC; nanoPOTS
  21. Metabolites. 2020 Nov 06. pii: E447. [Epub ahead of print]10(11):
      Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates' labeling patterns. As a result, MFA can tell the relative contributions of converging metabolic pathways only when these pathways make substrates in different labeling patterns for the shared product. This is the fundamental principle guiding the design of isotope labeling experiment for MFA including tracer selection. In addition, we will also discuss the basic biochemical assumptions of MFA, and we will show the flux-solving procedure and result evaluation. Finally, we will highlight the link between isotopically stationary and nonstationary flux analysis.
    Keywords:  MFA assumptions; metabolic flux analysis; non-steady-state versus steady-state; tracer selection
  22. Methods Mol Biol. 2021 ;2234 237-249
      Trichoderma reesei (T. reesei) is the workhorse for the production of industrial cellulolytic enzyme cocktails for cellulose hydrolysis. However, the current industrial process using enzyme cocktails is not efficient enough for the cost-effective generation of cellulosic sugar. Here, we describe a protocol for the application of a state-of-the-art LC-MS/MS-based proteomics method for studying the T. reesei secretome. A protein-free minimal chemically defined cell culture medium must be used for a successful secretome analysis. A lignocellulose substrate can be added to this minimal medium to stimulate the fungal secretion of enzymes specific to that substrate. The secretory proteins in the conditioned medium can be purified for quantitative proteomics profiling. T. reesei secretes several hundred enzymes including cellulases, hemicellulases, pectinases, proteases, oxidoreductases, and many putative proteins when it is stimulated with lignocellulose. By combining an understanding of the basic biomass hydrolytic mechanisms with the discovery of novel enzymes, more effective enzyme cocktails can be designed for a sustainable biochemical-based biorefinery.
    Keywords:  Cellulolytic enzymes; LC-MS/MS; Lignocellulose; Proteomics; Secretome; Trichoderma reesei
  23. J Chromatogr A. 2020 Oct 22. pii: S0021-9673(20)30908-0. [Epub ahead of print]1634 461634
      Lysophosphatidic acids (LPAs) are important bioactive phospholipids consisting of various species involved in a wide array of physiological and pathological processes. However, LPAs were rarely identified in untargeted lipidomics studies because of the incompatibility with analytical methods. Moreover, in targeted studies, the coverages of LPAs remained unsatisfactorily low due to the limitation of reference standards. Herein, a "modeling-prediction" workflow for deep profiling of LPAs by liquid chromatography-mass spectrometry was developed. Multiple linear regression models of qualitative and quantitative parameters were established according to features of fatty acyl tails of the commercial standards to predict the corresponding parameters for unknown LPAs. Then 72 multiple reaction monitoring (MRM) transitions were monitored simultaneously and species of LPA 14:0, LPA 16:1, LPA 18:3, LPA 20:3 and LPA 20:5 were firstly characterized and quantified in plasma. Finally, the workflow was applied to explore the changes of LPAs in plasma of breast cancer patients compared with healthy volunteers. Multi-LPAs indexes with strong diagnostic ability for breast cancer were identified successfully using Student's t- test, orthogona partial least-squares discrimination analysis (OPLS-DA) and logistic regression- receiver operating characteristic (ROC) curve analysis. The proposed workflow with high sensitivity, high accuracy, high coverage and reliable identification would be a powerful complement to untargeted lipidomics and shed a light on the analysis of other lipids.
    Keywords:  Breast cancer biomarker; Deep profiling; Lysophosphatidic acid; “Modeling−prediction” strategy
  24. Cancers (Basel). 2020 Nov 11. pii: E3339. [Epub ahead of print]12(11):
      De novo lipogenesis (DNL) is now considered as a hallmark of cancer. The overexpression of key enzymes of DNL is characteristic of both primary and advanced disease and may play an important role in resistance to therapies. Here, we showed that DNL is highly enhanced in castrate resistant prostate cancer (CRPC) cells compared to hormone sensitive and enzalutamide resistant cells. This observation suggests that this pathway plays an important role in the initiation of aggressive prostate cancer and in the development of enzalutamide resistance. Importantly, here we show that both prostate cancer cells sensitive and resistant to enzalutamide are dependent on DNL to proliferate. We next combined enzalutamide with an inhibitor of Stearoyl CoA Desaturase 1 (SCD1), an important enzyme in DNL, and observed significantly reduced tumor growth caused by the important change in tumoral lipid desaturation. Our findings suggest that the equilibrium between monounsaturated fatty acids and saturated fatty acids is essential in the establishment of the more aggressive prostate cancer phenotype and that the combination therapy induces a disruption of this equilibrium leading to an important decrease of cell proliferation. These findings provide new insights into the role of DNL in the progression of prostate cancer cells. The study also provides the rationale for the use of an inhibitor of SCD1 in combination with enzalutamide to improve response, delay enzalutamide resistance and improve disease free progression.
    Keywords:  cellular stress; combination therapy; de novo lipogenesis; lipid desaturation; prostate cancer therapy
  25. Talanta. 2021 Jan 15. pii: S0039-9140(20)30916-4. [Epub ahead of print]222 121625
      Data-driven engineering of microbes has been demonstrated for the sustainable production of high-performance chemicals. Metabolic profiling analysis is essential to increase the productivity of target compounds. However, improvement of comprehensive analysis methodologies is required for the high demands of metabolic engineering. Therefore, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) based methodology was designed and applied to cover a wide target range with high precision. Ion-pair free separation of metabolites on a pentafluorophenyl propyl column enabled high-precision quantification of 113 metabolites. The method was further evaluated for high reproducibility and robustness. Target analytes consisted of primary metabolites and intermediate metabolites for microbial production of high-performance chemicals. 95 metabolites could be detected with high reproducibility of peak area (intraday data: CV<15%), and 53 metabolites could be sensitively determined within a wide dynamic linear range (3-4 orders of magnitude). The developed system was further applied to the metabolomic analysis of various prokaryotic and eukaryotic microorganisms. Differences due to culture media and metabolic phenotypes could be observed when comparing the metabolomes of conventional and non-conventional yeast. Furthermore, almost all Kluyveromyces marxianus metabolites could be detected with moderate reproducibility (CV<40%, among independent extractions), where 41 metabolites were detected with very high reproducibility (CV<15%). In addition, the accuracy was validated via a spike-and-recovery test,and 78 metabolites were detected with analyte recovery in the 80-120% range. Together these results establish ion-pair free metabolic profiling as a comprehensive and precise tool for data-driven bioengineering applications.
    Keywords:  Ion-pair free; Liquid chromatography-tandem mass spectrometry; Metabolomics; Microbes; Pentafluorophenyl propyl column
  26. Cell Metab. 2020 Nov 03. pii: S1550-4131(20)30554-4. [Epub ahead of print]
      NAD+ metabolism is implicated in aging and cancer. However, its role in immune checkpoint regulation and immune evasion remains unclear. Here, we find nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme of the NAD+ biogenesis, drives interferon γ (IFNγ)-induced PD-L1 expression in multiple types of tumors and governs tumor immune evasion in a CD8+ T cell-dependent manner. Mechanistically, NAD+ metabolism maintains activity and expression of methylcytosine dioxygenase Tet1 via α-ketoglutarate (α-KG). IFNγ-activated Stat1 facilitates Tet1 binding to Irf1 to regulate Irf1 demethylation, leading to downstream PD-L1 expression on tumors. Importantly, high NAMPT-expressing tumors are more sensitive to anti-PD-L1 treatment and NAD+ augmentation enhances the efficacy of anti-PD-L1 antibody in immunotherapy-resistant tumors. Collectively, these data delineate an NAD+ metabolism-dependent epigenetic mechanism contributing to tumor immune evasion, and NAD+ replenishment combined with PD-(L)1 antibody provides a promising therapeutic strategy for immunotherapy-resistant tumors.
    Keywords:  NAD(+) metabolism; NAMPT; PD-L1; Tet1; cancer immune evasion; cancer immunotherapy; epigenetics; immune checkpoint blockade; interferon γ