bims-prodis 2018-09-02 papers

Issue of 2018–09–02
five papers selected by
Nancy Gough, Bioserendipity

Cancer Lett. 2018 Aug 23. pii: S0304-3835(18)30526-3. [Epub ahead of print]

Integrated proteomic and phosphoproteomic analyses of cisplatin-sensitive and resistant bladder cancer cells reveal CDK2 network as a key therapeutic target.

Jae Hun Jung, Sungyong You, Jae Won Oh, Junhee Yoon, Austin Yeon, Muhammad Shahid, Eunho Cho, Vikram Sairam, Taeeun D Park, Kwang Pyo Kim, Jayoung Kim.

BACKGROUND: Cisplatin-based chemotherapy is currently part of the standard of care for bladder cancer (BC). Unfortunately, some patients respond poorly to chemotherapy and have acquired or developed resistance. The molecular mechanisms underlying this resistance remain unclear. Here, we introduce a multidimensional proteomic analysis of a cisplatin-resistant BC model that provides different levels of protein information, including that of the global proteome and phosphoproteome.
METHODS: To characterize the global proteome and phosphoproteome in cisplatin-resistant BC cells, liquid chromatography-mass spectrometry/mass spectrometry experiments combined with comprehensive bioinformatics analysis were performed. Perturbed expression and phosphorylation levels of key kinases associated with cisplatin resistance were further studied using various cell biology assays, including western blot analysis.
RESULTS: Analyses of protein expression and phosphorylation identified significantly altered proteins, which were also EGF-dependent and independent. This suggests that protein phosphorylation plays a significant role in cisplatin-resistant BC. Additional network analysis of significantly altered proteins revealed CDK2, CHEK1, and ERBB2 as central regulators mediating cisplatin resistance. In addition to this, we identified the CDK2 network, which consists of CDK2 and its 5 substrates, as being significantly associated with poor survival after cisplatin chemotherapy.
CONCLUSIONS: Collectively, these findings potentially provide a novel way of classifying higher-risk patients and may guide future research in developing therapeutic targets.

Keywords: Competing interests; biological network; bladder cancer; cisplatin resistance; global proteome; phosphoproteomics

DOI: https://doi.org/10.1016/j.canlet.2018.08.014

Adv Clin Chem. 2018 ;pii: S0065-2423(18)30034-9. [Epub ahead of print]86 179-210

The Proteome of Cataract Markers: Focus on Crystallins.

Keke Zhang, Xiangjia Zhu, Yi Lu.

Cataract is a major cause of blindness worldwide. It is characterized by lens opacification and is accompanied by extensive posttranslational modifications (PTMs) in various proteins. PTMs play an essential role in lens opacification. Several PTMs have been described in proteins isolated from relatively old human lenses, including phosphorylation, deamidation, racemization, truncation, acetylation, and methylation. An overwhelming majority of previous cataract proteomic studies have exclusively focused on crystallin proteins, which are the most abundant proteome components of the lens. To investigate the proteome of cataract markers, this chapter focuses on the proteomic research on the functional relevance of the major PTMs in crystallins of human cataractous lenses. Elucidating the role of these modifications in cataract formation has been a challenging task because they are among the most difficult PTMs to study analytically. The proteomic status of some amides presents similar properties in normal aged and cataractous lenses, whereas some may undergo greater PTMs in cataract. Therefore, it is of great importance to review the current proteomic research on crystallins, the major protein markers in different types of cataract, to elucidate the pathogenesis of this major human-blinding condition.

Keywords: Cataract; Crystallin; Lens; Posttranslational modification; Protein; Proteome; Proteomics

DOI: https://doi.org/10.1016/bs.acc.2018.05.005

Transl Res. 2018 Aug 01. pii: S1931-5244(18)30110-5. [Epub ahead of print]

Serum biomarkers for diagnosis and prediction of type 1 diabetes.

Lian Yi, Adam C Swensen, Wei-Jun Qian.

Type 1 diabetes (T1D) culminates in the autoimmune destruction of the pancreatic β cells, leading to insufficient production of insulin and development of hyperglycemia. Serum biomarkers including a combination of glucose, glycated molecules, c-peptide, and autoantibodies have been well established for the diagnosis of T1D. However, these molecules often mark a late stage of the disease when ∼90% of the pancreatic insulin-producing β-cells have already been lost. With the prevalence of T1D increasing worldwide and because of the physical and psychological burden induced by this disease, there is a great need for prognostic biomarkers to predict T1D development or progression. This would allow us to identify individuals at high risk for early prevention and intervention. Therefore, considerable efforts have been dedicated to the understanding of disease etiology and the discovery of novel biomarkers in the last few decades. The advent of high-throughput and sensitive "-omics" technologies for the study of proteins, nucleic acids, and metabolites have allowed large scale profiling of protein expression and gene changes in T1D patients relative to disease-free controls. In this review, we briefly discuss the classical diagnostic biomarkers of T1D but mainly focus on the novel biomarkers that are identified as markers of β-cell destruction and screened with the use of state-of-the-art "-omics" technologies.

DOI: https://doi.org/10.1016/j.trsl.2018.07.009

J Pharm Sci. 2018 Aug 23. pii: S0022-3549(18)30510-0. [Epub ahead of print]

Involvement of an orphan transporter, SLC22A18, in cell growth and drug resistance of human breast cancer MCF7 cells.

Shingo Ito, Yu Fujino, Seiryo Ogata, Mio Hirayama-Kurogi, Sumio Ohtsuki.

The SLC22A18 gene, which encodes an orphan transporter, is located at the 11p15.5 imprinted region, an important tumor-suppressor gene region. However, the role of SLC22A18 in tumor suppression remains unclear. Here, we investigated the involvement of SLC22A18 in cell growth, invasion and drug resistance of MCF7 human breast cancer cell line. Western blot analysis indicated that SLC22A18 is predominantly expressed at intracellular organelle membranes. Quantitative proteomics showed that knockdown of SLC22A18 significantly altered the expression of 578 (31.0%) out of 1867 proteins identified, including proteins related to malignancy and poor prognosis of breast cancer. SLC22A18 knockdown (1) increased MCF7 cell growth concomitantly with a >7-fold increase of annexin A8 (involved in cell growth and migration; a predictor of poor prognosis), (2) induced spherical morphology of MCF7 cells concomitantly with a nearly 3-fold increase of CD44 (involved in regulation of malignant phenotypes), and (3) increased chemosensitivity to vinca alkaloids concomitantly with a >80% reduction of doublecortin-like kinase 1 (DCLK1; involved in regulation of microtubule polymerization). Our results suggest that SLC22A18 may act as a tumor suppressor by regulating the expression levels of cell-growth-related proteins, and vinca alkaloids might show therapeutic efficacy against low-SLC22A18-expressing breast cancer.

Keywords: 2-HG; 2-hydroxyglutarate; Annexin A8; BME; BRCA1; Basement Membrane Extract; Breast cancer; CD44; DCLK1; ER; FBS; GOI; IDH; Orphan transporter; PR; Quantitative proteomics; SLC22A18; Short hairpin RNA; Vinca alkaloid; breast cancer susceptibility gene 1; doublecortin-like kinase 1; estrogen receptor; fetal bovine serum; gain-of-imprinting; isocitrate dehydrogenase; progesterone receptor; solute carrier family 22 member 18; α-ketoglutarate; αKG

DOI: https://doi.org/10.1016/j.xphs.2018.08.011

Autophagy. 2018 Aug 27.

Identification of compound CA-5f as a novel late-stage autophagy inhibitor with potent anti-tumor effect against non-small cell lung cancer.

Lu Zhang, PengFei Qiang, JingTing Yu, YiMing Miao, ZhiQiang Chen, Ju Qu, QianBing Zhao, Zhuo Chen, Yachao Liu, Xin Yao, Bin Liu, LiuQing Cui, HongJuan Jing, Gangchun Sun.

Currently, particular focus is placed on the implication of autophagy in a variety of human diseases, including cancer. Discovery of small-molecule modulators of autophagy as well as their potential use as anti-cancer therapeutic agents would be of great significance. To this end, a series of curcumin analogs previously synthesized in our laboratory were screened. Among these compounds, (3E,5E)-3-(3,4-dimethoxybenzylidene)-5-[(1H-indol-3-yl)methylene]-1-methylpiperidin-4-one (CA-5f) was identified as a potent late-stage macroautophagy/autophagy inhibitor via inhibiting autophagosome-lysosome fusion. We found that CA-5f neither impaired the hydrolytic function nor the quantity of lysosomes. Use of an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic screen in combination with bioinformatics analysis suggested that treatment of human umbilical vein endothelial cells (HUVECs) with CA-5f for 1 h suppressed the levels of cytoskeletal proteins and membrane traffic proteins. Subsequent studies showed that CA-5f exhibited strong cytotoxicity against A549 non-small cell lung cancer (NSCLC) cells, but low cytotoxicity to normal human umbilical vein endothelial cells (HUVECs), by increasing mitochondrial-derived reactive oxygen species (ROS) production. Moreover, CA-5f effectively suppressed the growth of A549 lung cancer xenograft as a single agent with an excellent tolerance in vivo. Results from western blot, immunofluorescence, and TdT-mediated dUTP nick end labeling (TUNEL) assays showed that CA-5f inhibited autophagic flux, induced apoptosis, and did not affect the level of CTSB (cathepsin B) and CTSD (cathepsin D) in vivo, which were consistent with the in vitro data. Collectively, these results demonstrated that CA-5f is a novel late-stage autophagy inhibitor with potential clinical application for NSCLC therapy.

Keywords: CA-5f; autophagy inhibitor; cell death; curcumin analogs; lysosome; non-small cell lung cancer

DOI: https://doi.org/10.1080/15548627.2018.1511503