bims-mascan Biomed News
on Mass spectrometry in cancer research
Issue of 2020‒09‒06
seventeen papers selected by
Giovanny Rodriguez Blanco
University of Edinburgh

  1. J Pharm Biomed Anal. 2020 Aug 15. pii: S0731-7085(20)31429-1. [Epub ahead of print]191 113543
      Polycystic ovary syndrome (PCOS) is a hormonal disorder common among women of reproductive age. Women with PCOS may have infrequent or prolonged menstrual periods or excess male hormone levels. Metabolomics provide information on early biochemical changes in patients. Our aim was to find potential biomarkers on metabolome level to notice PCOS in adolescents and propose treatment opportunities based on our findings on metabolome level. In this study, Q-TOF LC/MS based analysis of the plasma samples of 15 healthy adolescents as control group (Group C) were compared with the plasma samples of 15 adolescents having PCOS (Group T). Raw chromatograms were processed on XCMS using Isotopologue Parameter Optimization (IPO) to optimize XCMS parameters. Finally, 2288 peaks were found but 84 of them had fold changes >1.5 based on normalized peak areas and they were statistically different (p < 0.05) between the groups. These peaks were subjected to MetaboAnalyst 4.0 - MS Peaks to Pathways utility for putative identification. The final list based on putative identification were evaluated through a clinical perspective and the statistically proved variation on the metabolite profiles of Group T and Group C presented that PCOS directly affected the lipid metabolism in the body or occurred as a result of a deformation in the lipid metabolism. Lower amount of Gamma-Tocopherol and higher amount of Coenzyme Q9, which is a product of incomplete Coenzyme Q10 biosynthesis, in the plasma samples of adolescent PCOS patients encouraged us to suggest larger randomized placebo controlled studies for Gamma-Tocopherol and Coenzyme Q10 supplements on the disease situation since our findings on metabolome level were in an accordance with the previous clinical findings.
    Keywords:  Adolescents; MetaboAnalyst; Metabolomics; Polycystic ovary syndrome; Q-TOF LC/MS; XCMS
  2. Genes Dis. 2020 Sep;7(3): 299-307
      Metastasis and metabolism reprogramming are two major hallmarks of cancer. In the initiation and progression of cancer, tumor cells are known to undergo fundamental metabolic changes to sustain their development and progression. In recent years, much more attentions have been drawn to their important roles in facilitating cancer metastasis through regulating the biological properties. In this review, we summarized the recent progresses in the studies of metabolism reprogramming of cancer metastasis, particularly of primary liver cancer, and highlight their potential applications.
    Keywords:  Amino acid; Cancer metastasis; Cholesterol; Fatty acid; Glucose; Primary liver cancer; Tumor microenvironment
  3. Medicina (Kaunas). 2020 Aug 31. pii: E443. [Epub ahead of print]56(9):
      Searching for new cancer-related biomarkers is a key priority for the early detection of solid tumors, such as colorectal cancer (CRC), in clinically relevant biological fluids. The cell line and/or tumor tissue secretome represents a valuable resource for discovering novel protein markers secreted by cancer cells. The advantage of a secretome analysis is the reduction of the large dynamic range characterizing human plasma/serum, and the simultaneous enrichment of low abundance cancer-secreted proteins, thereby overcoming the technical limitations underlying the direct search in blood samples. In this review, we provided a comprehensive overview of recent studies on the CRC secretome for biomarker discovery, focusing both on methodological and technical aspects of secretome proteomic approaches and on biomarker-independent validation in CRC patient samples (blood and tissues). Secretome proteomics are mainly based on LC-MS/MS analyses for which secretome samples are either in-gel or in-solution trypsin-digested. Adequate numbers of biological and technical replicates are required to ensure high reproducibility and robustness of the secretome studies. Moreover, another major challenge is the accuracy of proteomic quantitative analysis performed by label-free or labeling methods. The analysis of differentially expressed proteins in the CRC secretome by using bioinformatic tools allowed the identification of potential biomarkers for early CRC detection. In this scenario, this review may help to follow-up the recent secretome studies in order to select promising circulating biomarkers to be validated in larger screenings, thereby contributing toward a complete translation in clinical practice.
    Keywords:  biomarker; cancer cell lines; colorectal cancer; mass spectrometry; proteomics; secretome
  4. Cancers (Basel). 2020 Aug 27. pii: E2428. [Epub ahead of print]12(9):
      Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.
    Keywords:  biomarkers; mass spectrometry; proteomics; serum
  5. Metabolites. 2020 Aug 31. pii: E356. [Epub ahead of print]10(9):
      The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection.
    Keywords:  SARS-CoV; cholesterol; lipid metabolism; lipidomics; membrane fusion; phosphatidylinositol; sphingolipids; ssRNA+ virus
  6. Proteomics. 2020 Sep 01. e1900058
      The important role of inducible cyclooxygenase-2 (COX-2) in inflammation-related diseases and cancer necessitates analytical tools that enable thorough understanding of its modulation. Analysis of a comprehensive pattern of oxylipins provides detailed information about changes in enzyme activities. In order to simultaneously monitor the gene expression levels, we developed a targeted proteomics method for human COX-2. With limits of detection and quantification down to 0.25 and 0.5 fmol (on column) the method enables sensitive quantitative analysis via LC-MS/MS within a linear range up to 2.5 pmol. Three housekeeping proteins were included in the method for data normalization. We describe a tiered approach for method development comprised of both in silico and experimental steps in order to choose unique peptides and selective and sensitive SRM transitions while avoiding isobaric interferences. This method combined with a well-established targeted oxylipin metabolomics method allowed us to investigate the role of COX-2 in the human colon carcinoma cell lines HCT-116, HT-29 and HCA-7. Moreover, the developed methodology was used to demonstrate the time-dependent prostanoid formation and COX-2 enzyme synthesis in LPS-stimulated human primary macrophages. The described approach is a helpful tool which will be further used as standard operation procedure, ultimately aiming at a comprehensive targeted proteomics / oxylipin metabolomics strategy to examine the entire arachidonic acid cascade. This article is protected by copyright. All rights reserved.
    Keywords:  LC-MS/MS, arachidonic acid cascade, eicosanoid, oxylipin; metabolomics, MRM/SRM, bottom-up proteomics, mass spectrometry
  7. Biomolecules. 2020 Aug 27. pii: E1242. [Epub ahead of print]10(9):
      The metabolic characteristics of metastatic and non-metastatic breast carcinomas remain poorly studied. In this work, untargeted Nuclear Magnetic Resonance (NMR) metabolomics was used to compare two medroxyprogesterone acetate (MPA)-induced mammary carcinomas lines with different metastatic abilities. Different metabolic signatures distinguished the non-metastatic (59-2-HI) and the metastatic (C7-2-HI) lines, with glucose, amino acid metabolism, nucleotide metabolism and lipid metabolism as the major affected pathways. Non-metastatic tumours appeared to be characterised by: (a) reduced glycolysis and tricarboxylic acid cycle (TCA) activities, possibly resulting in slower NADH biosynthesis and reduced mitochondrial transport chain activity and ATP synthesis; (b) glutamate accumulation possibly related to reduced glutathione activity and reduced mTORC1 activity; and (c) a clear shift to lower phosphoscholine/glycerophosphocholine ratios and sphingomyelin levels. Within each tumour line, metabolic profiles also differed significantly between tumours (i.e., mice). Metastatic tumours exhibited marked inter-tumour changes in polar compounds, some suggesting different glycolytic capacities. Such tumours also showed larger intra-tumour variations in metabolites involved in nucleotide and cholesterol/fatty acid metabolism, in tandem with less changes in TCA and phospholipid metabolism, compared to non-metastatic tumours. This study shows the valuable contribution of untargeted NMR metabolomics to characterise tumour metabolism, thus opening enticing opportunities to find metabolic markers related to metastatic ability in endocrine breast cancer.
    Keywords:  NMR; endocrine breast cancer; hormone-independent growth; medroxyprogesterone acetate; metabolism; metabolomics; metastatic potential; murine models
  8. Redox Biol. 2020 Jul 13. pii: S2213-2317(20)30848-X. [Epub ahead of print]36 101643
      Epithelial cells require attachment to a support, such as the extracellular matrix, for survival. During cancer progression and metastasis, cancerous epithelial cells must overcome their dependence on adhesion signals. Dependence on glucose metabolism is a hallmark of cancer cells, but the nutrient requirements of cancer cells under anchorage-deficient conditions remain uncharacterized. Here, we report that cancer cells prioritize glutamine-derived tricarboxylic acid cycle energy metabolism over glycolysis to sustain anchorage-independent survival. Moreover, glutamine-dependent metabolic reprogramming is required not only to maintain ATP levels but also to suppress excessive oxidative stress through interaction with cystine. Mechanistically, AMPK, a central regulator of cellular responses to metabolic stress, participates in the induction of the expression of ASCT2, a glutamine transporter, and enhances glutamine consumption. Most interestingly, AMPK activation induces Nrf2 and its target proteins, allowing cancer cells to maintain energy homeostasis and redox status through glutaminolysis. Treatment with an integrin inhibitor was used to mimic the alterations in cell morphology and metabolic reprogramming caused by detachment. Under these conditions, cells were vulnerable to glutamine starvation or glutamine metabolism inhibitors. The observed preference for glutamine over glucose was more pronounced in aggressive cancer cell lines, and treatment with the glutaminase inhibitor, CB839, and cystine transporter inhibitor, sulfasalazine, caused strong cytotoxicity. Our data clearly show that anchorage-independent survival of cancer cells is supported mainly by glutaminolysis via the AMPK-Nrf2 signal axis. The discovery of new vulnerabilities along this route could help slow or prevent cancer progression.
    Keywords:  Anoikis; Extracellular matrix detachment; Glutaminolysis; Metabolic reprogramming; Metastasis
  9. Proteomics. 2020 Aug 31. e2000116
      Analysis of tyrosine kinase signaling is critical for the development of targeted cancer therapy. Currently, immunoprecipitation (IP) of phosphotyrosine (pY) peptides prior to liquid chromatography-tandem mass spectrometry (LC-MS/MS) is used to profile tyrosine kinase substrates. A typical protocol requests 10 mg of total protein from ∼108 cells or 50-100 mg of tissue. Large sample requirements can be cost prohibitive or not feasible for certain experiments. Sample multiplexing using chemical labeling reduces the protein amount required for each sample, and newer approaches use a material-rich reference channel as a calibrator to trigger detection and quantification for smaller samples. Here, we demonstrate that the tandem mass tag (TMT) calibrator approach reduces the sample input for pY profiling 10-fold (to ∼1 mg total protein per sample from 107 cells grown in one plate), while maintaining the depth of pY proteome sampling and the biological content of the experiment. Data are available through PRIDE (PXD019764 for label free and PXD018952 for TMT). This strategy opens more opportunities for pY profiling of large sample cohorts and samples with limited protein quantity such as immune cells, xenograft models, and human tumors. This article is protected by copyright. All rights reserved.
    Keywords:  Cancer Signaling; Phosphotyrosine; Sample Reduction; TMT
  10. Cell Metab. 2020 Aug 31. pii: S1550-4131(20)30420-4. [Epub ahead of print]
      Skeletal muscle insulin resistance is the earliest defect in type 2 diabetes (T2D), preceding and predicting disease development. To what extent this reflects a primary defect or is secondary to tissue cross talk due to changes in hormones or circulating metabolites is unknown. To address this question, we have developed an in vitro disease-in-a-dish model using iPS cells from T2D patients differentiated into myoblasts (iMyos). We find that T2D iMyos in culture exhibit multiple defects mirroring human disease, including an altered insulin signaling, decreased insulin-stimulated glucose uptake, and reduced mitochondrial oxidation. More strikingly, global phosphoproteomic analysis reveals a multidimensional network of signaling defects in T2D iMyos going beyond the canonical insulin-signaling cascade, including proteins involved in regulation of Rho GTPases, mRNA splicing and/or processing, vesicular trafficking, gene transcription, and chromatin remodeling. These cell-autonomous defects and the dysregulated network of protein phosphorylation reveal a new dimension in the cellular mechanisms underlying the fundamental defects in T2D.
    Keywords:  chromatin remodeling; glucose transport; iPSC; insulin resistance; mRNA splicing; mitochondrial oxidation; phosphoproteomics; skeletal muscle; type 2 diabetes; vesicle trafficking
  11. Mol Cell Proteomics. 2020 Sep 03. pii: mcp.RA120.002260. [Epub ahead of print]
      Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, for example HexNAc(2)Hex(5) rather than man5. Even at this level, however, glycopeptide analysis poses challenges:  finding glycopeptide spectra when they are a tiny fraction of the total spectra; assigning spectra with unanticipated glycans, not in the initial glycan database; and finding, scoring, and labeling diagnostic peaks in tandem mass spectra.  Here we discuss recent improvements to Byonic, a glycoproteomics search program, that address these three issues. Byonic now supports filtering spectra by m/z peaks, so that the user can limit attention to spectra with diagnostic peaks, for example, at least two out of three of 204.087 for HexNAc, 274.092 for NeuAc (with water loss), and 366.139 for HexNAc-Hex, all within a set mass tolerance, for example, ± 0.01 Daltons. Also new is glycan "wildcard" search, which allows an unspecified mass within a user-set mass range to be applied to N- or O-linked glycans and enables assignment of spectra with unanticipated glycans. Finally the next release of Byonic supports user-specified peak annotations from user-defined posttranslational modifications. We demonstrate the utility of these new software features by finding previously unrecognized glycopeptides in publicly available data, including glycosylated neuropeptides from rat brain.
    Keywords:  Bioinformatics searching; Bioinformatics software; Byonic; Chemical biology; Glycoproteomics; Peptidomics; Post-translational modifications*; neuropeptide; prenylation
  12. J Pharm Biomed Anal. 2020 Aug 21. pii: S0731-7085(20)31464-3. [Epub ahead of print]190 113578
      When using Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) to quantify In Vivo samples, an internal standard (ISTD) is key in correcting for variability within the sample extraction process and injection volume. Just as important is the ability of the internal standard to identify any matrix effects, which can artificially suppress or enhance the signal of the compound of interest. To properly do this, the internal standard should co-elute with the compound. A common source of potential matrix effects with In Vivo studies is from the excipient(s) used to formulate the compound for dosing. In the world of high-throughput discovery bioanalysis, a lab can quantitate over a hundred compounds each week, many of which are evaluated once, and rarely is a stable-isotope labeled (SIL) internal standard available (the industry gold standard). Finding a suitable and easy-to-use alternative LC-MS/MS method is important to providing high quality data. To overcome this challenge, a homologous series of compounds was synthesized to improve the chromatographic range for co-eluting ISTD's. This novel mix of internal standards was shown to have key characteristics making it ideal for use as a near universal internal standard mix including but not limited to: they ionize in both positive and negative modes, they are susceptible to signal perturbation from common formulation excipients, and they cover a wide range of retention times.
    Keywords:  Bioanalysis; Formulation; In vivo quantitation; Internal standard; Ion suppression; Liquid chromatography-tandem mass spectrometry
  13. J Clin Invest. 2020 Sep 01. pii: 137552. [Epub ahead of print]
      Hypoxia-inducible factors (HIFs) and the HIF-dependent cancer hallmarks angiogenesis and metabolic rewiring are well-established drivers of breast cancer aggressiveness, therapy resistance, and poor prognosis. Targeting of HIF and its downstream targets in angiogenesis and metabolism has been unsuccessful so far in the breast cancer clinical setting, with major unresolved challenges residing in target selection, development of robust biomarkers for response prediction, and understanding and harnessing escape mechanisms. This Review discusses the pathophysiological role of HIFs, angiogenesis, and metabolism in breast cancer and the challenges of targeting these features in breast cancer patients. Rational therapeutic combinations, especially with immunotherapy and endocrine therapy, seem most promising in the clinical exploitation of the intricate interplay of HIFs, angiogenesis, and metabolism in breast cancer cells and the tumor microenvironment.
  14. Molecules. 2020 Aug 28. pii: E3935. [Epub ahead of print]25(17):
      In recent years, lipid metabolism has garnered significant attention as it provides the necessary building blocks required to sustain tumor growth and serves as an alternative fuel source for ATP generation. Fatty acid synthase (FASN) functions as a central regulator of lipid metabolism and plays a critical role in the growth and survival of tumors with lipogenic phenotypes. Accumulating evidence has shown that it is capable of rewiring tumor cells for greater energy flexibility to attain their high energy requirements. This multi-enzyme protein is capable of modulating the function of subcellular organelles for optimal function under different conditions. Apart from lipid metabolism, FASN has functional roles in other cellular processes such as glycolysis and amino acid metabolism. These pivotal roles of FASN in lipid metabolism make it an attractive target in the clinic with several new inhibitors currently being tested in early clinical trials. This article aims to present the current evidence on the emergence of FASN as a target in human malignancies.
    Keywords:  cancer; fatty acid synthase; lipid metabolism
  15. Metabolites. 2020 Aug 27. pii: E348. [Epub ahead of print]10(9):
      This mini-review aims to discuss the development and applications of mass spectrometry (MS)-based hybrid approaches in metabolomics. Several recently developed hybrid approaches are introduced. Then, the overall workflow, frequently used instruments, data handling strategies, and applications are compared and their pros and cons are summarized. Overall, the improved repeatability and quantitative capability in large-scale MS-based metabolomics studies are demonstrated, in comparison to either targeted or untargeted metabolomics approaches alone. In summary, we expect this review to serve as a first attempt to highlight the development and applications of emerging hybrid approaches in metabolomics, and we believe that hybrid metabolomics approaches could have great potential in many future studies.
    Keywords:  broad metabolite coverage; dynamic range; hybrid approaches; identification; metabolomics; quantitative analysis; repeatability
  16. Mol Biol Rep. 2020 Sep 03.
      The multipotent, self renewing "cancer stem cells" (CSCs), a small population within tumor microenvironment facilitates transformed cells to grow and propagate within the body. The CSCs are discovered as resistant to the chemotherapeutic drug with distinct immunological characteristics. In recent years, immunologically targeting CSCs have emerged as an integral part of effective and successful cancer therapy. CSCs notably exhibit dysregulation in conventional sub-cellular sphingolipid metabolism. Recently, ceramide decaying enzymes have been shown to activate alternative ceramide signaling pathways leading to reduction in efficacy of the chemotherapeutic drugs. Therefore, a control over ceramide mediated modulations of CSCs offers an attractive dimension of effective cancer treatment strategy in future. In this review, we focused on the recent findings on broad spectrum of ceramide mediated signaling in CSCs within the tumor niche and their role in potential cancer immunotherapy.
    Keywords:  Cancer stem cell; Ceramide; Glucosylceramide synthase; Hypoxia; Immunotherapy; Multidrug resistance
  17. Signal Transduct Target Ther. 2020 Sep 02. 5(1): 177
      Cancer cells are usually characterized by hyperactive glucose metabolism, which can often lead to glucose scarcity; thus, alternative pathways to rewire cancer metabolism are required. Here, we demonstrated that GLUT3 was highly expressed in colorectal cancer (CRC) and negatively linked to CRC patient outcomes, whereas GLUT1 was not associated with CRC prognosis. Under glucose-limiting conditions, GLUT3 expedited CRC cell growth by accelerating glucose input and fuelling nucleotide synthesis. Notably, GLUT3 had a greater impact on cell growth than GLUT1 under glucose-limiting stress. Mechanistically, low-glucose stress dramatically upregulated GLUT3 via the AMPK/CREB1 pathway. Furthermore, high GLUT3 expression remarkably increased the sensitivity of CRC cells to treatment with vitamin C and vitamin C-containing regimens. Together, the results of this study highlight the importance of the AMPK/CREB1/GLUT3 pathway for CRC cells to withstand glucose-limiting stress and underscore the therapeutic potential of vitamin C in CRC with high GLUT3 expression.