bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒07‒26
twenty papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh


  1. J Proteome Res. 2020 Jul 22.
    You L, Fan Y, Liu X, Shao S, Guo L, Noreldeen HAA, Li Z, Ouyang Y, Li E, Pan X, Liu T, Tian X, Li X, Ye F, Xu G.
      Unclarified molecular mechanism and lack of practical diagnosis biomarkers hinder the effective treatment of non-small-cell lung cancer. Herein, we performed liquid chromatography-mass spectrometry-based nontargeted metabolomics analysis in 131 patients with their lung tissue pairs to study the metabolic characteristics and disordered metabolic pathways in lung tumor. 339 metabolites were identified in metabolic profiling. And 241 differential metabolites were found between lung carcinoma tissues (LCTs) and paired distal noncancerous tissues, amino acids, purine metabolites, fatty acids, phospholipids and most of lysophospholipids significantly increased in LCTs, while 3-phosphoglyceric acid, phosphoenolpyruvate, 6-phosphogluconate and citrate decreased. Additionally, pathway enrichment analysis revealed that energy, purine, amino acid, lipid, and glutathione metabolism are markedly disturbed in LCa. Using binary logistic regression, we further defined candidate biomarkers for different subtypes of lung tumor. Xanthine and PC 35:2 were selected as combinational biomarkers for distinguishing benign from malignant lung tumors with 0.886 area under curve (AUC) value, and creatine, myoinositol and LPE 16:0 were defined as combinational biomarkers for discriminating adenocarcinoma from squamous cell lung carcinoma with 0.934 AUC value. Overall, metabolic characterization and pathway disturbance demonstrated apparent metabolic reprogramming in LCa. The defined candidate metabolite marker panels are useful for subtyping of lung tumors to assist clinical diagnosis.
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00285
  2. Cell Oncol (Dordr). 2020 Jul 20.
    Ogrodzinski MP, Teoh ST, Lunt SY.
      PURPOSE: Breast cancer is a heterogeneous disease with several subtypes that currently do not have targeted therapeutic options. Metabolomics has the potential to uncover novel targeted treatment strategies by identifying metabolic pathways required for cancer cells to survive and proliferate.METHODS: The metabolic profiles of two histologically distinct breast cancer subtypes from a MMTV-Myc mouse model, epithelial-mesenchymal-transition (EMT) and papillary, were investigated using mass spectrometry-based metabolomics methods. Based on metabolic profiles, drugs most likely to be effective against each subtype were selected and tested.
    RESULTS: We found that the EMT and papillary subtypes display different metabolic preferences. Compared to the papillary subtype, the EMT subtype exhibited increased glutathione and TCA cycle metabolism, while the papillary subtype exhibited increased nucleotide biosynthesis compared to the EMT subtype. Targeting these distinct metabolic pathways effectively inhibited cancer cell proliferation in a subtype-specific manner.
    CONCLUSIONS: Our results demonstrate the feasibility of metabolic profiling to develop novel personalized therapy strategies for different subtypes of breast cancer. Schematic overview of the experimental design for drug selection based on breast cancer subtype-specific metabolism. The epithelial mesenchymal transition (EMT) and papillary tumors are histologically distinct mouse mammary tumor subtypes from the MMTV-Myc mouse model. Cell lines derived from tumors can be used to determine metabolic pathways that can be used to select drug candidates for each subtype.
    Keywords:  Breast cancer; Cancer subtypes; Mass spectrometry; Metabolic profile; Metabolomics; Targeted therapy
    DOI:  https://doi.org/10.1007/s13402-020-00545-1
  3. Anal Chem. 2020 Jul 22.
    Shi X, Xi B, Jasbi P, Turner C, Jin Y, Gu H.
      Metabolic flux analysis (MFA) is highly relevant to understanding metabolic mechanisms of various biological processes. While the pace of methodology development in MFA has been rapid, a major challenge the field continues to witness is limited metabolite coverage, often restricted to a small to moderate number of well-known compounds. In addition, isotopic peaks from an enriched metabolite tend to have low abundances, which makes liquid chromatography tandem mass spectrometry (LC-MS/MS) highly useful in MFA due to its high sensitivity and specificity. Previously we have built large-scale LC-MS/MS approaches that can be routinely used for measurement of up to ~1,900 metabolite/feature levels [Gu et al. Anal. Chem. 2015, 87, 12355-62; Shi et al. Anal. Chem. 2019, 91,13737-45]. In this study, we aim to expand our previous studies focused on metabolite level measurements to flux analysis and establish a novel comprehensive isotopic targeted mass spectrometry (CIT-MS) method for reliable MFA analysis with broad coverage. As a proof-of-principle, we have applied CIT-MS to compare the steady-state enrichment of metabolites between Myc(oncogene)-On and Myc-Off Tet21N human neuroblastoma cells cultured with U-13C6-glucose medium. CIT-MS is operationalized using multiple reaction monitoring (MRM) mode and is able to perform MFA of 310 identified metabolites (142 reliably detected, 46 kinetically profiled) selected from >35 metabolic pathways of strong biological significance. Further, we developed a novel concept of relative flux, which eliminates the requirement of absolute quantitation in traditional MFA and thus enables comparative MFA under the pseudosteady state. As a result, CIT-MS was shown to possess the advantages of broad coverage, easy implementation, fast throughput, and more importantly, high fidelity and accuracy in MFA. In principle, CIT-MS can be easily adapted to track the flux of other labeled tracers (such as 15N-tracers) in any metabolite detectable by LC-MS/MS and in various biological models (such as mice). Therefore, CIT-MS has great potential to bring new insights to both basic and clinical metabolism research.
    DOI:  https://doi.org/10.1021/acs.analchem.0c01767
  4. Metabolites. 2020 Jul 17. pii: E296. [Epub ahead of print]10(7):
    Jenkins B, Ronis M, Koulman A.
      Typical lipidomics methods incorporate a liquid-liquid extraction with LC-MS quantitation; however, the classic sample extraction methods are not high-throughput and do not perform well at extracting the full range of lipids especially, the relatively polar species (e.g., acyl-carnitines and glycosphingolipids). In this manuscript, we present a novel sample extraction protocol, which produces a single phase supernatant suitable for high-throughput applications that offers greater performance in extracting lipids across the full spectrum of species. We applied this lipidomics pipeline to a ruminant fat dose-response study to initially compare and validate the different extraction protocols but also to investigate complex lipid biomarkers of ruminant fat intake (adjoining onto simple odd chain fatty acid correlations). We have found 100 lipids species with a strong correlation with ruminant fat intake. This novel sample extraction along with the LC-MS pipeline have shown to be sensitive, robust and hugely informative (>450 lipids species semi-quantified): with a sample preparation throughput of over 100 tissue samples per day and an estimated ~1000 biological fluid samples per day. Thus, this work facilitating both the epidemiological involvement of ruminant fat, research into odd chain lipids and also streamlining the field of lipidomics (both by sample preparation methods and data presentation).
    Keywords:  Folch; lipid profiling; odd chain lipids; protein precipitation; relative lipid composition (Mol%); sample preparation
    DOI:  https://doi.org/10.3390/metabo10070296
  5. Elife. 2020 Jul 20. pii: e54166. [Epub ahead of print]9
    Nassar ZD, Mah CY, Dehairs J, Burvenich IJ, Irani S, Centenera MM, Helm M, Shrestha RK, Moldovan M, Don AS, Holst J, Scott AM, Horvath LG, Lynn DJ, Selth LA, Hoy AJ, Swinnen JV, Butler LM.
      Fatty acid β-oxidation (FAO) is the main bioenergetic pathway in human prostate cancer (PCa) and a promising novel therapeutic vulnerability. Here we demonstrate therapeutic efficacy of targeting FAO in clinical prostate tumors cultured ex vivo, and identify DECR1, encoding the rate-limiting enzyme for oxidation of polyunsaturated fatty acids (PUFAs), as robustly overexpressed in PCa tissues and associated with shorter relapse-free survival. DECR1 is a negatively-regulated androgen receptor (AR) target gene and, therefore, may promote PCa cell survival and resistance to AR targeting therapeutics. DECR1 knockdown selectively inhibited β-oxidation of PUFAs, inhibited proliferation and migration of PCa cells, including treatment resistant lines, and suppressed tumor cell proliferation and metastasis in mouse xenograft models. Mechanistically, targeting of DECR1 caused cellular accumulation of PUFAs, enhanced mitochondrial oxidative stress and lipid peroxidation, and induced ferroptosis. These findings implicate PUFA oxidation via DECR1 as an unexplored facet of FAO that promotes survival of PCa cells.
    Keywords:  cancer biology; human; mouse
    DOI:  https://doi.org/10.7554/eLife.54166
  6. Methods Mol Biol. 2020 ;2171 53-64
    Cheng CW, Yilmaz OH, Mihaylova MM.
      This protocol describes a multipronged approach that we have created to determine the transcriptional induction of fatty acid oxidation (FAO) genes in Lgr5high intestinal stem cells and a subsequent metabolomics-based approach for assessing fatty acid utilization in the mammalian intestinal crypt. More specifically, we describe methods for crypt isolation followed by a FACS-based purification of stem and progenitor populations and RNA-sequencing analysis. Using this workflow, we can determine both basal gene expression profiles of key metabolic genes as well as corresponding changes in response to altered metabolic states, such as fasting. Subsequently, we describe a complementary metabolomics-based approach that we have developed to assess fatty acid uptake and utilization in the crypt using 13C stable isotope tracing. Combining these approaches, one can gain a better understanding of substrate utilization and the preceding transcriptional changes that accommodate these reactions in physiologic states of low carbohydrate utilization or during overabundance of dietary lipids.
    Keywords:  Fatty acid oxidation; Metabolomics; RNA-sequencing; Stable isotope tracing; Stem cell metabolism
    DOI:  https://doi.org/10.1007/978-1-0716-0747-3_4
  7. Cells. 2020 Jul 18. pii: E1725. [Epub ahead of print]9(7):
    Aquila S, Santoro M, Caputo A, Panno ML, Pezzi V, De Amicis F.
      Recent studies conducted over the past 10 years evidence the intriguing role of the tumor suppressor gene Phosphatase and Tensin Homolog deleted on Chromosome 10 PTEN in the regulation of cellular energy expenditure, together with its capability to modulate proliferation and survival, thus expanding our knowledge of its physiological functions. Transgenic PTEN mice models are resistant to oncogenic transformation, present decreased adiposity and reduced cellular glucose and glutamine uptake, together with increased mitochondrial oxidative phosphorylation. These acquisitions led to a novel understanding regarding the role of PTEN to counteract cancer cell metabolic reprogramming. Particularly, PTEN drives an "anti-Warburg state" in which less glucose is taken up, but it is more efficiently directed to the mitochondrial Krebs cycle. The maintenance of cellular homeostasis together with reduction of metabolic stress are controlled by specific pathways among which autophagy, a catabolic process strictly governed by mTOR and PTEN. Besides, a role of PTEN in metabolic reprogramming and tumor/stroma interactions in cancer models, has recently been established. The genetic inactivation of PTEN in stromal fibroblasts of mouse mammary glands, accelerates breast cancer initiation and progression. This review will discuss our novel understanding in the molecular connection between cell metabolism and autophagy by PTEN, highlighting novel implications regarding tumor/stroma/immune system interplay. The newly discovered action of PTEN opens innovative avenues for investigations relevant to counteract cancer development and progression.
    Keywords:  Warburg state; cancer metabolism; immune system; stroma
    DOI:  https://doi.org/10.3390/cells9071725
  8. Metabolites. 2020 Jul 16. pii: E289. [Epub ahead of print]10(7):
    Chen X, Chen S, Yu D.
      Metabolic reprogramming is one of the hallmarks of tumors. Alterations of cellular metabolism not only contribute to tumor development, but also mediate the resistance of tumor cells to antitumor drugs. The metabolic response of tumor cells to various chemotherapy drugs can be analyzed by metabolomics. Although cancer cells have experienced metabolic reprogramming, the metabolism of drug resistant cancer cells has been further modified. Metabolic adaptations of drug resistant cells to chemotherapeutics involve redox, lipid metabolism, bioenergetics, glycolysis, polyamine synthesis and so on. The proposed metabolic mechanisms of drug resistance include the increase of glucose and glutamine demand, active pathways of glutaminolysis and glycolysis, promotion of NADPH from the pentose phosphate pathway, adaptive mitochondrial reprogramming, activation of fatty acid oxidation, and up-regulation of ornithine decarboxylase for polyamine production. Several genes are associated with metabolic reprogramming and drug resistance. Intervening regulatory points described above or targeting key genes in several important metabolic pathways may restore cell sensitivity to chemotherapy. This paper reviews the metabolic changes of tumor cells during the development of chemoresistance and discusses the potential of reversing chemoresistance by metabolic regulation.
    Keywords:  chemoresistance; drug resistance; metabolic regulation; metabolic reprogramming; reversal of chemoresistance
    DOI:  https://doi.org/10.3390/metabo10070289
  9. Autophagy. 2020 Jul 20.
    He A, Dean JM, Lu D, Chen Y, Lodhi IJ.
      Hepatic lipid homeostasis is controlled by a coordinated regulation of various metabolic pathways involved in de novo synthesis, uptake, storage, and catabolism of lipids. Disruption of this balance could lead to hepatic steatosis. Peroxisomes play an essential role in lipid metabolism, yet their importance is often overlooked. In a recent study, we demonstrated a role for hepatic peroxisomal β-oxidation in autophagic degradation of lipid droplets. ACOX1 (acyl-Coenzyme A oxidase 1, palmitoyl), the rate-limiting enzyme of peroxisomal β-oxidation, increases with fasting or high-fat diet (HFD). Liver-specific acox1 knockout (acox1-LKO) protects mice from hepatic steatosis induced by starvation or HFD via induction of lipophagy. Mechanistically, we showed that hepatic ACOX1 deficiency decreases the total cytosolic acetyl-CoA levels, which leads to reduced acetylation of RPTOR/RAPTOR, a component of MTORC1, which is a key regulator of macroautophagy/autophagy. These results identify peroxisome-derived acetyl-CoA as a critical metabolic regulator of autophagy that controls hepatic lipid homeostasis.
    Keywords:  ACOX1; MTORC1; NAFLD; autophagy; lipids; lipophagy; lysosome; peroxisome
    DOI:  https://doi.org/10.1080/15548627.2020.1797288
  10. J Chromatogr A. 2020 Aug 16. pii: S0021-9673(20)30511-2. [Epub ahead of print]1625 461233
    López-López Á, Godzien J, Soldevilla B, Gradillas A, López-Gonzálvez Á, Lens-Pardo A, La Salvia A, Del Carmen Riesco-Martínez M, García-Carbonero R, Barbas C.
      Untargeted metabolomics can be a great tool for exploring new scientific areas; however, wrong metabolite annotation questions the credibility and puts the success of the entire research at risk. Therefore, an effort should be made to improve the quality and robustness of the annotation despite of the challenges, especially when final identification with standards is not possible. Through non-targeted analysis of human plasma samples, from a large cancer cohort study using RP-LC-ESI-QTOF-MS/MS, we have resolved MS/MS annotation through spectral matching, directed to hydroxyeicosatetraenoic acids (HETEs) and, MS/MS structural elucidation for newly annotated oxidized lyso-phosphatidylcholines (oxLPCs). The annotation of unknowns is supported with structural information from fragmentation spectra as well as the fragmentation mechanisms involved, necessarily including data from both polarity modes and different collision energies. In this work, we present evidences that various oxidation products show significant differences between cancer patients and control individuals and we establish a workflow to help identify such modifications. We report here the upregulation of HETEs and oxLPCs in patients with neuroendocrine tumors (NETs). To our knowledge, this is the first attempt to determine HETEs in NETs and one of very few studies where oxLPCs are annotated. The obtained results provide an important insight regarding lipid oxidation in NETs, although their physiological functions still have to be established and require further research.
    Keywords:  Annotation; HETE; LC-ESI-QTOF-MS; Neuroendocrine tumors; Oxidized lipids; oxLPC
    DOI:  https://doi.org/10.1016/j.chroma.2020.461233
  11. Anal Bioanal Chem. 2020 Jul 22.
    Hellhake S, Meckelmann SW, Empl MT, Rentmeister K, Wißdorf W, Steinberg P, Schmitz OJ, Benter T, Schebb NH.
      Eicosanoids and other oxylipins play an important role in mediating inflammation as well as other biological processes. For the investigation of their biological role(s), comprehensive analytical methods are necessary, which are able to provide reliable identification and quantification of these compounds in biological matrices. Using charge-switch derivatization with AMPP (N-(4-aminomethylphenyl)pyridinium chloride) in combination with liquid chromatography ion mobility quadrupole time-of-flight mass spectrometry (LC-IM-QTOF-MS), we developed a non-target approach to analyze oxylipins in plasma, serum, and cells. The developed workflow makes use of an ion mobility resolved fragmentation to pinpoint derivatized molecules based on the cleavage of AMPP, which yields two specific fragment ions. This allows a reliable identification of known and unknown eicosanoids and other oxylipins. We characterized the workflow using 52 different oxylipins and investigated their fragmentation patterns and ion mobilities. Limits of detection ranged between 0.2 and 10.0 nM (1.0-50 pg on column), which is comparable with other state-of-the-art methods using LC triple quadrupole (QqQ) MS. Moreover, we applied this strategy to analyze oxylipins in different biologically relevant matrices, as cultured cells, human plasma, and serum. Graphical abstract.
    Keywords:  AMPP; DTIMS; Eicosanoids; Ion mobility-mass spectrometry; Lipidomics; Oxylipins
    DOI:  https://doi.org/10.1007/s00216-020-02795-2
  12. Metabolites. 2020 Jul 17. pii: E292. [Epub ahead of print]10(7):
    Sun X, Berger RS, Heinrich P, Marchiq I, Pouyssegur J, Renner K, Oefner PJ, Dettmer K.
      Glutathione (GSH) and glutathione disulfide (GSSG) are commonly used to assess the oxidative status of a biological system. Various protocols are available for the analysis of GSH and GSSG in biomedical specimens. In this study, we present an optimized protocol for the in situ derivatization of GSH with N-ethylmaleimide (NEM) to prevent GSH autooxidation, and thus to preserve the GSH/GSSG ratio during sample preparation. The protocol comprises the incubation of cells in NEM containing phosphate buffered saline (PBS), followed by metabolite extraction with 80% methanol. Further, to preserve the use of QTOF-MS, which may lack the linear dynamic range required for the simultaneous quantification of GSH and GSSG in non-targeted metabolomics, we combined liquid chromatographic separation with the online monitoring of UV absorbance of GS-NEM at 210 nm and the detection of GSSG and its corresponding stable isotope-labeled internal standard by QTOF-MS operated with a 10 Da Q1 window. The limit of detection (LOD) for GS-NEM was 7.81 µM and the linear range extended from 15.63 µM to 1000 µM with a squared correlation coefficient R2 of 0.9997. The LOD for GSSG was 0.001 µM, and the lower limit of quantification (LLOQ) was 0.01 µM, with the linear (R2 = 0.9994) range extending up to 10 µM. The method showed high repeatability with intra-run and inter-run coefficients of variation of 3.48% and 2.51% for GS-NEM, and 3.11% and 3.66% for GSSG, respectively. Mean recoveries of three different spike-in levels (low, medium, high) of GSSG and GS-NEM were above 92%. Finally, the method was applied to the determination of changes in the GSH/GSSG ratio either in response to oxidative stress in cells lacking one or both monocarboxylate transporters MCT1 and MCT4, or in adaptation to the NADPH (nicotinamide adenine dinucleotide phosphate) consuming production of D-2-hydroxyglutarate in cells carrying mutations in the isocitrate dehydrogenase genes IDH1 and IDH2.
    Keywords:  UV detection; cell culture; glutathione; glutathione disulfide; liquid chromatography; mass spectrometry
    DOI:  https://doi.org/10.3390/metabo10070292
  13. Biochim Biophys Acta Rev Cancer. 2020 Jul 19. pii: S0304-419X(20)30113-X. [Epub ahead of print] 188394
    Xu H, Zhou S, Tang Q, Xia H, Bi F.
      Cholesterol and its metabolites (precursors and derivatives) play an important role in cancer. In recent years, numerous studies have reported the functions of cholesterol metabolism in the regulation of tumor biological processes, especially oncogenic signaling pathways, ferroptosis, and tumor microenvironment. Preclinical studies have over the years indicated the inhibitory effects of blocking cholesterol synthesis and uptake on tumor formation and growth. Besides, some new cholesterol metabolic molecules such as SOAT1, SQLE, and NPC1 have recently emerged as promising drug targets for cancer treatment. Here, we systematically review the roles of cholesterol and its metabolites, and the latest advances in cancer therapy targeting cholesterol metabolism.
    Keywords:  Cancer treatment; Cholesterol; Functions; Metabolism
    DOI:  https://doi.org/10.1016/j.bbcan.2020.188394
  14. J Proteome Res. 2020 Jul 21.
    Liu J, Luo X, Guo R, Jing W, Lu H.
      Pancreatic cancer (PC) is becoming one of the deadliest cancers, with mortality among the highest worldwide because of its pathogenic latency and the lack of efficient drugs in the clinic. Considering that cancer cells undergo proliferation and differentiation at substantial metabolic costs, as indicated by dysregulated glycolysis and an abnormal TCA cycle induced by mitochondrial damage, we investigated the therapeutic capacity of berberine (BBR) in pancreatic cancer using a cell metabolomics method. A phenotypic assay revealed the significant inhibitory role of BBR on PC cell viability and metastasis. In addition, a precision-targeted metabolome assay showed that BBR profoundly dysregulated the energy metabolism of PC cells, and phenotypic observations based on imaging indicated that PC cell mitochondria were markedly damaged after BBR treatment. Notably, citrate metabolism and transportation in cell mitochondria were significantly influenced by BBR, which led to the blocked biosynthesis of the defined fatty acids (FAs) through the regulation of ACLY, ACO1 and SLC13A5. Therefore, the regulatory effects of FAs on PC cell proliferation and metastasis may be regulated by BBR through targeting citrate metabolism. Collectively, our in vitro data preliminarily reveals the therapeutic potential of BBR against pancreatic cancer by targeting citrate metabolism, citrate might be a new target for drug development and the treatment against PC, but further experimental verification will be required subsequently; Moreover, our study demonstrated cell metabolomics method pertains the capacity to rapidly explore biochemical function of natural products.
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00394
  15. Dev Cell. 2020 Jul 20. pii: S1534-5807(20)30544-X. [Epub ahead of print]54(2): 156-170
    Figlia G, Willnow P, Teleman AA.
      Metabolites affect cell growth in two different ways. First, they serve as building blocks for biomass accumulation. Second, metabolites regulate the activity of growth-relevant signaling pathways. They do so in part by covalently attaching to proteins, thereby generating post-translational modifications (PTMs) that affect protein function, the focus of this Perspective. Recent advances in mass spectrometry have revealed a wide variety of such metabolites, including lipids, amino acids, Coenzyme-A, acetate, malonate, and lactate to name a few. An active area of research is to understand which modifications affect protein function and how they do so. In many cases, the cellular levels of these metabolites affect the stoichiometry of the corresponding PTMs, providing a direct link between cell metabolism and the control of cell signaling, transcription, and cell growth.
    Keywords:  O-GlcNAc; YAP; acetylation; autophagy; crotonylation; glutathionylation; hippo; mTORC1; malonylation; methylation; palmitoylation
    DOI:  https://doi.org/10.1016/j.devcel.2020.06.036
  16. Methods Mol Biol. 2020 ;2141 819-833
    Valk E, Maljavin A, Loog M.
      Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) within proteins have attracted considerable attention in recent years. Several important biological signaling mechanisms including protein-protein interactions and post-translational modifications can be easily mediated by IDPs and IDRs due to their flexible structure. These regions can encode linear sequences that are indispensable in cell-signaling networks and circuits. For example, the linear multisite phosphorylation networks encoded in disordered protein sequences play a key role in cell-cycle regulation where the phosphorylation of proteins controls the orchestration of all major mechanisms. While elucidating a systems-level understanding of this process and other multisite phosphorylation processes, we extensively used mass-spectrometry and found it to be an ideal tool to identify, characterize, and quantify phosphorylation dynamics within IDPs. Here, we describe a quantitative proteomics method, together with a detailed protocol to analyze dynamic multisite phosphorylation processes within IDPs using an in vitro protein phosphorylation assay with "light" gamma-16O ATP and "heavy" gamma-18O ATP, combined with liquid chromatography mass spectrometry.
    Keywords:  IDPs; IDRs; Intrinsically disordered proteins; Phospho-proteomics; Protein phosphorylation; Quantitative mass spectrometry; Stable isotope labelling
    DOI:  https://doi.org/10.1007/978-1-0716-0524-0_42
  17. Clin Chim Acta. 2020 Jul 21. pii: S0009-8981(20)30363-6. [Epub ahead of print]
    Ge S, Zhang Q, Tian Y, Hao L, Duan J, Zhang B.
      BACKGROUND: Protein arginine methyltransferase 5 (PRMT5) belongs to a large family of protein arginine methyltransferases (PRMTs) that play essential role in gene transcription and regulate tumorigenesis. However, the role of PRMT5 in the regulation of cancer cell metabolism remains unclear.METHODS: Cell metabolomic analysis was performed on SW480 cells transfected with small interfering RNA (siRNA) specifically targeting PRMT5, followed by metabolomic pathway analysis.
    RESULTS: PRMT5 was overexpressed in colorectal cancer (CRC) tissues, and downregulation of PRMT5 suppressed CRC cell proliferation and the levels of PRMT5 and symmetric dimethylation of histone H3 (H3R8me2s). In addition, we found distinct differences in metabolite classification and function in PRMT5 knockdown SW480 cells compared to control SW480 cells. PRMT5 knockdown increased the levels of amino acids and carbohydrates, particularly related to the arginine metabolism such as glutamate, glutamine (Gln), proline, creatine, creatinine and phosphocreatine (PCr).
    CONCLUSIONS: These findings revealed a key role for PRMT5 as a regulator of CRC cell metabolism to mediate arginine methylation in CRC cells.
    Keywords:  (1)H-NMR; Colorectal cancer; Metabolomic profiling; PRMT5
    DOI:  https://doi.org/10.1016/j.cca.2020.07.039
  18. Pain. 2020 Jul 09.
    Domenichiello AF, Jensen JR, Zamora D, Horowitz M, Yuan ZX, Faurot K, Mann JD, Mannes AJ, Ramsden CE.
      Chronic Post Traumatic Headache (PTH) is among the most common and disabling sequelae of traumatic brain injury (TBI). Current PTH treatments are often only partially effective and have problematic side effects. We previously showed in a small randomized trial of patients with chronic non-traumatic headaches that manipulation of dietary fatty acids decreased headache frequency, severity, and pain medication use. Pain reduction was associated with alterations in oxylipins derived from n-3 and n-6 fatty acids, suggesting that oxylipins could potentially mediate clinical pain reduction. The objective of the present study was to investigate whether circulating oxylipins measured in the acute setting following TBI, could serve as prognostic biomarkers for developing chronic PTH. Participants enrolled in the Traumatic Head Injury Neuroimaging Classification Protocol provided serum within 3 days of TBI and were followed up at 90 days post-injury with a neurobehavioral symptom inventory (NSI) and satisfaction with-life-survey (SWLS). Liquid chromatography tandem mass spectrometry methods profiled 39 oxylipins derived from n-3 docosaheaxaenoic acid (DHA), and n-6 arachidonic acid (AA) and linoleic acid (LA).Statistical analyses assessed the association of oxylipins with headache severity (primary outcome, measured by headache question on NSI) as well as associations between oxylipins and total NSI or SWLS scores. Among oxylipins, 4-hydroxy-DHA and 19,20-epoxy-docosapentaenoate (DHA derivatives) were inversely associated with headache severity, and 11-hydroxy-9-epoxy-octadecenoate (an LA derivative) was positively associated with headache severity. These findings support a potential for DHA-derived oxylipins as prognostic biomarkers for development of chronic PTH.
    DOI:  https://doi.org/10.1097/j.pain.0000000000001983
  19. J Proteome Res. 2020 Jul 22.
    Waas M, Kislinger T.
      Cells exhibit a broad spectrum of functions driven by differences in molecular phenotype. Understanding the heterogeneity between and within cell types has led to advances in our ability to diagnose and manipulate biological systems. Heterogeneity within and between tumors still poses a challenge to the development and efficacy of therapeutics. In this 'Perspective' we review the toolkit of protein-level experimental approaches for investigating cellular heterogeneity. We describe how innovative approaches and technical developments have supported the advent of bottom-up single-cell proteomic analysis and present opportunities and challenges within cancer research. Finally, we introduce the concept of 'precision proteomics' and discuss how the advantages and limitations of various experimental approaches render them suitable for different biological systems and questions.
    DOI:  https://doi.org/10.1021/acs.jproteome.0c00338
  20. Cell Death Dis. 2020 Jul 24. 11(7): 580
    Zhang X, Wang L, Li H, Zhang L, Zheng X, Cheng W.
      Cancer progression including proliferation, metastasis, and chemoresistance has become a serious hindrance to cancer therapy. This phenomenon mainly derives from the innate insensitive or acquired resistance of cancer cells to apoptosis. Ferroptosis is a newly discovered mechanism of programmed cell death characterized by peroxidation of the lipid membrane induced by reactive oxygen species. Ferroptosis has been confirmed to eliminate cancer cells in an apoptosis-independent manner, however, the specific regulatory mechanism of ferroptosis is still unknown. The use of ferroptosis for overcoming cancer progression is limited. Noncoding RNAs have been found to play an important roles in cancer. They regulate gene expression to affect biological processes of cancer cells such as proliferation, cell cycle, and cell death. Thus far, the functions of ncRNAs in ferroptosis of cancer cells have been examined, and the specific mechanisms by which noncoding RNAs regulate ferroptosis have been partially discovered. However, there is no summary of ferroptosis associated noncoding RNAs and their functions in different cancer types. In this review, we discuss the roles of ferroptosis-associated noncoding RNAs in detail. Moreover, future work regarding the interaction between noncoding RNAs and ferroptosis is proposed, the possible obstacles are predicted and associated solutions are put forward. This review will deepen our understanding of the relationship between noncoding RNAs and ferroptosis, and provide new insights in targeting noncoding RNAs in ferroptosis associated therapeutic strategies.
    DOI:  https://doi.org/10.1038/s41419-020-02772-8