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Nazir F, Munir I, Yesiloz G. A Microfluidics-Assisted Double-Barreled Nanobioconjugate Synthesis Introducing Aprotinin as a New Moonlight Nanocarrier Protein: Tested toward Physiologically Relevant 3D-Spheroid Models. ACS APPLIED MATERIALS & INTERFACES 2024; 16:18311-18326. [PMID: 38564228 DOI: 10.1021/acsami.3c16548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Proteins are promising substances for introducing new drug carriers with efficient blood circulation due to low possibilities of clearance by macrophages. However, such natural biopolymers have highly sophisticated molecular structures, preventing them from being assembled into nanoplatforms with manipulable payload release profiles. Here, we report a novel anticancer nanodrug carrier moonlighting protein, Aprotinin, to be used as a newly identified carrier for cytotoxic drugs. The Aprotinin-Doxorubicin (Apr-Dox) nanobioconjugate was prepared via a single-step microfluidics coflow mixing technique, a feasible and simple way to synthesize a carrier-based drug design with a double-barreled approach that can release and actuate two therapeutic agents simultaneously, i.e., Apr-Dox in 1:11 ratio (the antimetastatic carrier drug aprotinin and the chemotherapeutic drug DOX). With a significant stimuli-sensitive (i.e., pH) drug release ability, this nanobioconjugate achieves superior bioperformances, including high cellular uptake, efficient tumor penetration, and accumulation into the acidic tumor microenvironment, besides inhibiting further tumor growth by halting the urokinase plasminogen activator (uPA) involved in metastasis and tumor progression. Distinctly, in healthy human umbilical vein endothelial (HUVEC) cells, drastically lower cellular uptake of nanobioconjugates has been observed and validated compared to the anticancer agent Dox. Our findings demonstrate an enhanced cellular internalization of nanobioconjugates toward breast cancer, prostate cancer, and lung cancer both in vitro and in physiologically relevant biological 3D-spheroid models. Consequently, the designed nanobioconjugate shows a high potential for targeted drug delivery via a natural and biocompatible moonlighting protein, thus opening a new avenue for proving aprotinin in cancer therapy as both an antimetastatic and a drug-carrying agent.
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Affiliation(s)
- Faiqa Nazir
- National Nanotechnology Research Center (UNAM)- Bilkent University, 06800 Cankaya-Ankara, Türkiye
- Institute of Material Science and Nanotechnology, Bilkent University, 06800 Cankaya-Ankara, Türkiye
| | - Iqra Munir
- National Nanotechnology Research Center (UNAM)- Bilkent University, 06800 Cankaya-Ankara, Türkiye
| | - Gurkan Yesiloz
- National Nanotechnology Research Center (UNAM)- Bilkent University, 06800 Cankaya-Ankara, Türkiye
- Institute of Material Science and Nanotechnology, Bilkent University, 06800 Cankaya-Ankara, Türkiye
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2
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Lin C, Yu M, Wu X, Wang H, Wei M, Zhang L. Targeting Moonlighting Enzymes in Cancer. Molecules 2024; 29:1573. [PMID: 38611852 PMCID: PMC11013064 DOI: 10.3390/molecules29071573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Moonlighting enzymes are multifunctional proteins that perform multiple functions beyond their primary role as catalytic enzymes. Extensive research and clinical practice have demonstrated their pivotal roles in the development and progression of cancer, making them promising targets for drug development. This article delves into multiple notable moonlighting enzymes, including GSK-3, GAPDH, and ENO1, and with a particular emphasis on an enigmatic phosphatase, PTP4A3. We scrutinize their distinct roles in cancer and the mechanisms that dictate their ability to switch roles. Lastly, we discuss the potential of an innovative approach to develop drugs targeting these moonlighting enzymes: target protein degradation. This strategy holds promise for effectively tackling moonlighting enzymes in the context of cancer therapy.
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Affiliation(s)
- Chunxu Lin
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Mingyang Yu
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Ximei Wu
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Hui Wang
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Min Wei
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Luyong Zhang
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
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3
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Du Q, Shen W. Research progress of plant-derived natural products in thyroid carcinoma. Front Chem 2024; 11:1279384. [PMID: 38268761 PMCID: PMC10806030 DOI: 10.3389/fchem.2023.1279384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Thyroid carcinoma (TC) is a prevalent malignancy of the endocrine system, with a notable rise in its detection rate in recent decades. The primary therapeutic approaches for TC now encompass thyroidectomy and radioactive iodine therapy, yielding favorable prognoses for the majority of patients. TC survivors may necessitate ongoing surveillance, remedial treatment, and thyroid hormone supplementation, while also enduring the adverse consequences of thyroid hormone fluctuations, surgical complications, or side effects linked to radioactive iodine administration, and encountering enduring physical, psychosocial, and economic hardships. In vitro and in vivo studies of natural products against TC are demonstrating the potential of these natural products as alternatives to the treatment of thyroid cancer. This therapy may offer greater convenience, affordability, and acceptability than traditional therapies. In the early screening of natural products, we mainly use a combination of database prediction and literature search. The pharmacological effects on TC of selected natural products (quercetin, genistein, apigenin, luteolin, chrysin, myricetin, resveratrol, curcumin and nobiletin), which hold promise for therapeutic applications in TC, are reviewed in detail in this article through most of the cell-level evidence, animal-level evidence, and a small amount of human-level evidence. In addition, this article explores possible issues, such as bioavailability, drug safety.
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Affiliation(s)
- Qiujing Du
- The Affiliated Jiangyin People’s Hospital of Nantong University, Jiangyin, China
- Third Hospital of Shanxi Medical University, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Taiyuan, China
| | - Weidong Shen
- The Affiliated Jiangyin People’s Hospital of Nantong University, Jiangyin, China
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4
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Deng J, Xu W, Jie Y, Chong Y. Subcellular localization and relevant mechanisms of human cancer-related micropeptides. FASEB J 2023; 37:e23270. [PMID: 37994683 DOI: 10.1096/fj.202301019rr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Revised: 09/17/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023]
Abstract
Rapid advances in high-quality sequencing and bioinformatics have invalidated the argument that noncoding RNAs (ncRNAs) are junk transcripts that do not encode proteins. Increasing evidence suggests that small open reading frames (sORFs) in ncRNAs can encode micropeptides and polypeptides within 100 amino acids in length. Several micropeptides have been characterized and proven to have various functions in human physiology and pathology, particularly in cancer. The present review mainly highlights the latest studies on ncRNA-encoded micropeptides in different cancers and categorizes them based on their subcellular localization, thereby providing a theoretical basis for micropeptide applications in the early diagnosis and prognosis of cancer and as therapeutic targets. However, considering the inherent characteristics of micropeptides and the limitations of the assay technology methods, more detailed information is warranted.
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Affiliation(s)
- Jing Deng
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenli Xu
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yusheng Jie
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yutian Chong
- Department of Infectious Diseases, the Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Dev A, Vachher M, Prasad CP. β-catenin inhibitors in cancer therapeutics: intricacies and way forward. Bioengineered 2023; 14:2251696. [PMID: 37655825 PMCID: PMC10478749 DOI: 10.1080/21655979.2023.2251696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 09/02/2023] Open
Abstract
β-catenin is an evolutionary conserved, quintessential, multifaceted protein that plays vital roles in cellular homeostasis, embryonic development, organogenesis, stem cell maintenance, cell proliferation, migration, differentiation, apoptosis, and pathogenesis of various human diseases including cancer. β-catenin manifests both signaling and adhesive features. It acts as a pivotal player in intracellular signaling as a component of versatile WNT signaling cascade involved in embryonic development, homeostasis as well as in carcinogenesis. It is also involved in Ca2+ dependent cell adhesion via interaction with E-cadherin at the adherens junctions. Aberrant β-catenin expression and its nuclear accumulation promote the transcription of various oncogenes including c-Myc and cyclinD1, thereby contributing to tumor initiation, development, and progression. β-catenin's expression is closely regulated at various levels including its stability, sub-cellular localization, as well as transcriptional activity. Understanding the molecular mechanisms of regulation of β-catenin and its atypical expression will provide researchers not only the novel insights into the pathogenesis and progression of cancer but also will help in deciphering new therapeutic avenues. In the present review, we have summarized the dual functions of β-catenin, its role in signaling, associated mutations as well as its role in carcinogenesis and tumor progression of various cancers. Additionally, we have discussed the challenges associated with targeting β-catenin molecule with the presently available drugs and suggested the possible way forward in designing new therapeutic alternatives against this oncogene.
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Affiliation(s)
- Arundhathi Dev
- Department of Medical Oncology (Laboratory), DR BRAIRCH, All India Institute of Medical Sciences, New Delhi, India
| | - Meenakshi Vachher
- Department of Biochemistry, Institute of Home Economics, University of Delhi, New Delhi, India
| | - Chandra Prakash Prasad
- Department of Medical Oncology (Laboratory), DR BRAIRCH, All India Institute of Medical Sciences, New Delhi, India
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6
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Mitrić A, Castellano I. Targeting gamma-glutamyl transpeptidase: A pleiotropic enzyme involved in glutathione metabolism and in the control of redox homeostasis. Free Radic Biol Med 2023; 208:672-683. [PMID: 37739139 DOI: 10.1016/j.freeradbiomed.2023.09.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 09/07/2023] [Accepted: 09/18/2023] [Indexed: 09/24/2023]
Abstract
Gamma-glutamyl transpeptidase (GGT) is an enzyme located on the outer membrane of the cells where it regulates the metabolism of glutathione (GSH), the most abundant intracellular antioxidant thiol. GGT plays a key role in the control of redox homeostasis, by hydrolyzing extracellular GSH and providing the cell with the recovery of cysteine, which is necessary for de novo intracellular GSH and protein biosynthesis. Therefore, the upregulation of GGT confers to the cell greater resistance to oxidative stress and the advantage of growing fast. Indeed, GGT is upregulated in inflammatory conditions and in the progression of various human tumors and it is involved in many physiological disorders related to oxidative stress, such as cardiovascular disease and diabetes. Currently, increased GGT expression is considered a marker of liver damage, cancer, and low-grade chronic inflammation. This review addresses the current knowledge on the structure-function relationship of GGT, focusing on human GGT, and provides information on the pleiotropic biological role and relevance of the enzyme as a target of drugs aimed at alleviating oxidative stress-related diseases. The development of new GGT inhibitors is critically discussed, as are the advantages and disadvantages of their potential use in clinics. Considering its pleiotropic activities and evolved functions, GGT is a potential "moonlighting protein".
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Affiliation(s)
- Aleksandra Mitrić
- Institute of Clinical and Molecular Virology, Friedrich-Alexander University Erlangen-Nürnberg, 91054, Erlangen, Germany
| | - Immacolata Castellano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131, Naples, Italy; Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy.
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7
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Gupta S, Westacott MJ, Ayers DG, Weiss SJ, Whitley P, Mueller C, Weaver DC, Schneider DJ, Karimpour-Fard A, Hunter LE, Drolet DW, Janjic N. Plasma proteome of growing tumors. Sci Rep 2023; 13:12195. [PMID: 37500700 PMCID: PMC10374562 DOI: 10.1038/s41598-023-38079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023] Open
Abstract
Early detection of cancer is vital for the best chance of successful treatment, but half of all cancers are diagnosed at an advanced stage. A simple and reliable blood screening test applied routinely would therefore address a major unmet medical need. To gain insight into the value of protein biomarkers in early detection and stratification of cancer we determined the time course of changes in the plasma proteome of mice carrying transplanted human lung, breast, colon, or ovarian tumors. For protein measurements we used an aptamer-based assay which simultaneously measures ~ 5000 proteins. Along with tumor lineage-specific biomarkers, we also found 15 markers shared among all cancer types that included the energy metabolism enzymes glyceraldehyde-3-phosphate dehydrogenase, glucose-6-phophate isomerase and dihydrolipoyl dehydrogenase as well as several important biomarkers for maintaining protein, lipid, nucleotide, or carbohydrate balance such as tryptophanyl t-RNA synthetase and nucleoside diphosphate kinase. Using significantly altered proteins in the tumor bearing mice, we developed models to stratify tumor types and to estimate the minimum detectable tumor volume. Finally, we identified significantly enriched common and unique biological pathways among the eight tumor cell lines tested.
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Affiliation(s)
- Shashi Gupta
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | | | - Deborah G Ayers
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | - Sophie J Weiss
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | - Penn Whitley
- Boulder BioConsulting, Inc., 325 S 68th St., Boulder, CO, 80303, USA
| | | | - Daniel C Weaver
- Boulder BioConsulting, Inc., 325 S 68th St., Boulder, CO, 80303, USA
| | | | - Anis Karimpour-Fard
- University of Colorado School of Medicine, Mailstop 8303, Aurora, CO, 80045, USA
| | - Lawrence E Hunter
- University of Colorado School of Medicine, Mailstop 8303, Aurora, CO, 80045, USA
| | - Daniel W Drolet
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA.
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8
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Zhou J, Lei Z, Chen J, Liao S, Chen Y, Liu C, Huang S, Li L, Zhang Y, Wang P, Huang Y, Li J, Liang H. Nuclear export of BATF2 enhances colorectal cancer proliferation through binding to CRM1. Clin Transl Med 2023; 13:e1260. [PMID: 37151195 PMCID: PMC10165233 DOI: 10.1002/ctm2.1260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/21/2023] [Accepted: 04/26/2023] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND During the tumourigenesis and development of colorectal cancer (CRC), the inactivation of tumour suppressor genes is closely involved, although detailed molecular mechanisms remain elusive. Accumulating studies, including ours, have demonstrated that basic leucine zipper transcription factor ATF (activating transcription factor)-like 2 (BATF2) is a capable tumour suppressor that localises in the nucleus. However, its different subcellular localisation, potential functions and underlying mechanisms are unclear. METHODS The translocation of BATF2 and its clinical relevance were detected using CRC samples, cell lines and xenograft nude mice. Candidate BATF2-binding proteins were screened using co-immunoprecipitation, quantitative label-free liquid chromatography-tandem mass spectrometry proteomic analysis, Western blotting and immunofluorescence. Recombinant plasmids, point mutations and siRNAs were applied to clarify the binding sites between BATF2 and chromosome region maintenance 1 (CRM1). RESULTS The present study found that BATF2 was mainly localised in the cytoplasm, rather than nucleus, of CRC cells in vitro and in vivo, while cytoplasmic BATF2 expression was inversely correlated with the prognosis of CRC patients. Furthermore, we identified the nuclear export and subsequent ubiquitin-mediated degradation of BATF2 in CRC cells. Mechanistically, a functional nuclear export sequence (any amino acid) was characterised in BATF2 protein, through which BATF2 bound to CRM1 and translocated out of nucleus, ultimately enhancing CRC growth via inducing activator protein 1 (AP-1)/cyclin D1/phosphorylated retinoblastoma protein (pRb) signalling pathway. Additionally, nuclear export of BATF2 can be retarded by the mutation of NES in BATF2 or the knockdown of CRM1, whereas CRM1 expression was negatively associated with nuclear BATF2 expression and the prognosis of CRC patients. CONCLUSION These findings revealed the biological effects and underlying mechanisms of cytoplasmic localisation of BATF2. Furthermore, suppressing nuclear export of BATF2 via mutating its NES region or inhibiting CRM1 expression may serve as a promising therapeutic strategy against CRC.
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Affiliation(s)
- Jie Zhou
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Zengjie Lei
- Department of Medical OncologyAffiliated Jinling HospitalMedical School of Nanjing UniversityNanjingChina
| | - Jianfang Chen
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Shengbo Liao
- Department of OtolaryngologyPeople's Hospital of Xishui CountyGuizhouChina
| | - Yanrong Chen
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Chengxiang Liu
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Shuo Huang
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Liuli Li
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Yan Zhang
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Pei Wang
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Yinghui Huang
- Department of NephrologyKey Laboratory for the Prevention and Treatment of Chronic Kidney Disease of ChongqingChongqing Clinical Research Center of Kidney and Urology DiseasesXinqiao HospitalArmy Medical UniversityChongqingChina
| | - Jianjun Li
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
| | - Houjie Liang
- Department of Oncology and Southwest Cancer CenterSouthwest HospitalArmy Medical University (Third Military Medical University)ChongqingChina
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9
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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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10
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Gao J, Wang S, Wan H, Lan J, Yan Y, Yin D, Zhou W, Hun S, He Q. Prognostic Value of Transglutaminase 2 in Patients with Solid Tumors: A Meta-analysis. Genet Test Mol Biomarkers 2023; 27:36-43. [PMID: 36809173 DOI: 10.1089/gtmb.2022.0088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
Background: Transglutaminase 2 (TG2), a member of the transglutaminase family, also known as tissue transglutaminase, plays a fundamental role in cancer growth and progression. In this study, we aimed to comprehensively review the evidence of TG2 as a prognostic biomarker in solid tumors. Methods: PubMed, Embase, and Cochrane databases were searched for human studies with clearly described cancer types if they presented the relationship between TG2 expression and prognostic indicators from inception to February 2022. Two authors independently screened the eligible studies and extracted the relevant data. The association between TG2 and overall survival (OS), disease-free survival (DFS), and relapse-free survival (RFS) were described as hazard ratios (HR) and their corresponding 95% confidence intervals (CIs). Statistical heterogeneity was assessed using Cochrane Q-test and Higgins I-squared statistic. A sensitivity analysis was conducted by sequentially omitting the impact of each study. Publication bias was assessed by Egger's funnel plot. Results: A total of 2864 patients with various cancers from 11 individual studies were enrolled. Results showed that elevated TG2 protein expression and mRNA expression predicted a shorter OS, with a combined HR of 1.93 (95% CI: 1.41-2.63) or HR of 1.95 (95% CI: 1.27-2.99), respectively. Moreover, data suggested that elevated TG2 protein expression was correlated with a shorter DFS (HR = 1.76, 95% CI: 1.36-2.29); whereas elevated TG2 mRNA expression was associated with a shorter DFS (HR = 1.71, 95% CI: 1.30-2.24). Conclusions: Our meta-analysis indicated that TG2 might serve as a promising biomarker of cancer prognosis.
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Affiliation(s)
- Jie Gao
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shengjiang Wang
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Haiyan Wan
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Jinfeng Lan
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yong Yan
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Dongmei Yin
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Wenjing Zhou
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Shouyong Hun
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qi He
- Department of Transfusion Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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11
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Ahandoust S, Li K, Sun X, Li BY, Yokota H, Na S. Intracellular and extracellular moesins differentially regulate Src activity and β-catenin translocation to the nucleus in breast cancer cells. Biochem Biophys Res Commun 2023; 639:62-69. [PMID: 36470073 DOI: 10.1016/j.bbrc.2022.11.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
It is increasingly recognized that a single protein can have multiple, sometimes paradoxical, roles in cell functions as well as pathological conditions depending on its cellular locations. Here we report that moesins (MSNs) in the intracellular and extracellular domains present opposing roles in pro-tumorigenic signaling in breast cancer cells. Using live cell imaging with fluorescence resonance energy transfer (FRET)- and green fluorescent protein (GFP)-based biosensors, we investigated the molecular mechanism underlying the cellular location-dependent effect of MSN on Src and β-catenin signaling in MDA-MB-231 breast cancer cells. Inhibition of intracellular MSN decreased the activities of Src and FAK, whereas overexpression of intracellular MSN increased them. By contrast, extracellular MSN decreased the activities of Src, FAK, and RhoA, as well as β-catenin translocation to the nucleus. Consistently, Western blotting and MTT-based analysis showed that overexpression of intracellular MSN elevated the expression of oncogenic genes, such as p-Src, β-catenin, Lrp5, MMP9, Runx2, and Snail, as well as cell viability, whereas extracellular MSN suppressed them. Conditioned medium derived from MSN-overexpressing mesenchymal stem cells or osteocytes showed the anti-tumor effects by inhibiting the Src activity and β-catenin translocation to the nucleus as well as the activities of FAK and RhoA and MTT-based cell viability. Conditioned medium derived from MSN-inhibited cells increased the Src activity, but it did not affect the activities of FAK and RhoA. Silencing CD44 and/or FN1 in MDA-MB-231 cells blocked the suppression of Src activity and β-catenin accumulation in the nucleus by extracellular MSN. Collectively, the results suggest that cellular location-specific MSN is a strong regulator of Src and β-catenin signaling in breast cancer cells, and that extracellular MSN exerts tumor-suppressive effects via its interaction with CD44 and FN1.
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Affiliation(s)
- Sina Ahandoust
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Kexin Li
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA; Department of Pharmacology, School of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xun Sun
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA; Department of Pharmacology, School of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Bai-Yan Li
- Department of Pharmacology, School of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Hiroki Yokota
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Sungsoo Na
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
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12
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Huerta M, Franco-Serrano L, Amela I, Perez-Pons JA, Piñol J, Mozo-Villarías A, Querol E, Cedano J. Role of Moonlighting Proteins in Disease: Analyzing the Contribution of Canonical and Moonlighting Functions in Disease Progression. Cells 2023; 12:cells12020235. [PMID: 36672169 PMCID: PMC9857295 DOI: 10.3390/cells12020235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
The term moonlighting proteins refers to those proteins that present alternative functions performed by a single polypeptide chain acquired throughout evolution (called canonical and moonlighting, respectively). Over 78% of moonlighting proteins are involved in human diseases, 48% are targeted by current drugs, and over 25% of them are involved in the virulence of pathogenic microorganisms. These facts encouraged us to study the link between the functions of moonlighting proteins and disease. We found a large number of moonlighting functions activated by pathological conditions that are highly involved in disease development and progression. The factors that activate some moonlighting functions take place only in pathological conditions, such as specific cellular translocations or changes in protein structure. Some moonlighting functions are involved in disease promotion while others are involved in curbing it. The disease-impairing moonlighting functions attempt to restore the homeostasis, or to reduce the damage linked to the imbalance caused by the disease. The disease-promoting moonlighting functions primarily involve the immune system, mesenchyme cross-talk, or excessive tissue proliferation. We often find moonlighting functions linked to the canonical function in a pathological context. Moonlighting functions are especially coordinated in inflammation and cancer. Wound healing and epithelial to mesenchymal transition are very representative. They involve multiple moonlighting proteins with a different role in each phase of the process, contributing to the current-phase phenotype or promoting a phase switch, mitigating the damage or intensifying the remodeling. All of this implies a new level of complexity in the study of pathology genesis, progression, and treatment. The specific protein function involved in a patient's progress or that is affected by a drug must be elucidated for the correct treatment of diseases.
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Feng Y, Liu S, Zha R, Sun X, Li K, Wu D, Aryal UK, Koch M, Li BY, Yokota H. Prostate cancer-associated urinary proteomes differ before and after prostatectomy. Ther Adv Med Oncol 2022; 14:17588359221131532. [PMID: 36324734 PMCID: PMC9618752 DOI: 10.1177/17588359221131532] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND A wide range of disorders can be detected in the urine. Tumor-modifying proteins in the urine may serve as a diagnostic tool for cancer patients and the alterations in their profiles may indicate efficacies of chemotherapy, radiotherapy, and surgery. METHODS We focused on urinary proteomes of patients with prostate cancer and identified tumor-modifying proteins in the samples before and after prostatectomy. Protein array analysis was conducted to evaluate a differential profile of tumor-promoting cytokines, while mass spectrometry-based global proteomics was conducted to identify tumor-suppressing proteins. RESULTS The result revealed striking differences by prostatectomy. Notably, the urine from the post-prostatectomy significantly decreased the tumorigenic behaviors of prostate tumor cells as well as breast cancer cells. We observed that angiogenin, a stimulator of blood vessel formation, was reduced in the post-prostatectomy urine. By contrast, the levels of three cell-membrane proteins such as prostasin (PRSS8), nectin 2 (PVRL2), and nidogen 1 (NID1) were elevated and they acted as extracellular tumor-suppressing proteins. These three proteins, given extracellularly, downregulated tumorigenic genes such as Runx2, Snail, and transforming growth factor beta and induced apoptosis of tumor cells. However, the role of NID1 differed depending on the location, and intracellular NID1 was tumorigenic and reduced the percent survival. CONCLUSIONS This study demonstrated that prostatectomy remarkably altered the profile of urinary proteomes, and the post-prostatectomy urine provided tumor-suppressive proteomes. The result sheds novel light on the dynamic nature of the urinary proteomes and a unique strategy for predicting tumor suppressors.
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Affiliation(s)
| | | | - Rongrong Zha
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China,Department of Biomedical Engineering, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Xun Sun
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China,Department of Biomedical Engineering, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Kexin Li
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China,Department of Biomedical Engineering, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Di Wu
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, Harbin, China,Department of Biomedical Engineering, Indiana University Purdue University Indianapolis, Indianapolis, IN, USA
| | - Uma K. Aryal
- Department of Comparative Pathobiology, Purdue University, West Lafayette, IN, USA
| | - Michael Koch
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Bai-Yan Li
- Department of Pharmacology, College of Pharmacy, Harbin Medical University, #157 Baojian Road, Harbin, Heilongjiang 150081, China
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14
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Mei H, Gu Q, Wang W, Meng Y, Jiang L, Liu J. CRISPR-surfaceome: An online tool for designing highly efficient sgRNAs targeting cell surface proteins. Comput Struct Biotechnol J 2022; 20:3833-3838. [PMID: 35891797 PMCID: PMC9307495 DOI: 10.1016/j.csbj.2022.07.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 11/17/2022] Open
Abstract
CRISPR-based genome-editing tools have emerged as an efficient tool for functional genomics studies. Online tools and databases have been developed to facilitate the design and selection of CRISPR single guide RNA (sgRNA) for gene modifications. However, to the best of our knowledge, none of these tools or database are designated to cell surface proteins. In a previous study, we described the development and application of surfaceome CRISPR libraries targeting to cell surface proteins on human cells. Here, we present the design and construction of an online tool and database (https://crispr-surfaceome.siais.shanghaitech.edu.cn/home), named CRISPR-Surfaceome, for the design of highly efficient sgRNA targeting to the surface proteins on human cells. To show case and validate the efficiencies of sgRNAs designed by this online tool, we chose ICAM-1 gene for knockout studies and found that all the 10 designed ICAM-1 sgRNAs could efficiently generate knockout cells, with more than 80% gene disruption rates. These ICAM-1 knockout cells were found to be resistant to the infection of rhinovirus (RV), which utilizes ICAM-1 as the receptor. Therefore, CRISPR-Surfaceome can serve the research community for the functional genomics studies on cell surface proteins, such as identification of pathogen receptors and discovery of drug targets.
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Affiliation(s)
- Hong Mei
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Qian Gu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Wang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Yu Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lichun Jiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- Corresponding authors at: Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
| | - Jia Liu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Shanghai Clinical Research and Trial Center, Shanghai 201210, China
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, 201210, China
- Corresponding authors at: Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
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15
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Mendik P, Kerestély M, Kamp S, Deritei D, Kunšič N, Vassy Z, Csermely P, Veres DV. Translocating proteins compartment-specifically alter the fate of epithelial-mesenchymal transition in a compartmentalized Boolean network model. NPJ Syst Biol Appl 2022; 8:19. [PMID: 35680961 PMCID: PMC9184490 DOI: 10.1038/s41540-022-00228-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 05/20/2022] [Indexed: 11/13/2022] Open
Abstract
Regulation of translocating proteins is crucial in defining cellular behaviour. Epithelial-mesenchymal transition (EMT) is important in cellular processes, such as cancer progression. Several orchestrators of EMT, such as key transcription factors, are known to translocate. We show that translocating proteins become enriched in EMT-signalling. To simulate the compartment-specific functions of translocating proteins we created a compartmentalized Boolean network model. This model successfully reproduced known biological traits of EMT and as a novel feature it also captured organelle-specific functions of proteins. Our results predicted that glycogen synthase kinase-3 beta (GSK3B) compartment-specifically alters the fate of EMT, amongst others the activation of nuclear GSK3B halts transforming growth factor beta-1 (TGFB) induced EMT. Moreover, our results recapitulated that the nuclear activation of glioma associated oncogene transcription factors (GLI) is needed to achieve a complete EMT. Compartmentalized network models will be useful to uncover novel control mechanisms of biological processes. Our algorithmic procedures can be automatically rerun on the https://translocaboole.linkgroup.hu website, which provides a framework for similar future studies.
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Affiliation(s)
- Péter Mendik
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Márk Kerestély
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | | | - Dávid Deritei
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Nina Kunšič
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Zsolt Vassy
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Péter Csermely
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary
| | - Daniel V Veres
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, Hungary. .,Turbine Ltd, Budapest, Hungary.
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16
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Yang L, Vander Steen T, Espinoza I, Cuyàs E, Verdura S, Menendez JA, Lupu R. Nuclear moonlighting of the secreted growth factor heregulin drives endocrine-resistant breast cancer independently of HER2/HER3 signaling. Am J Cancer Res 2022; 12:2173-2188. [PMID: 35693067 PMCID: PMC9185626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/03/2022] [Indexed: 06/15/2023] Open
Abstract
The HER3/4 ligand heregulin-β2 (HRG) is a secreted growth factor that transactivates the ligand-less receptor HER2 to promote aggressive phenotypes in breast cancer. HRG can also localize to the nucleus of breast cancer cells, but both the nuclear translocation mechanism and the physiological role of nuclear HRG remain elusive. Here we show that nucleolin-driven nuclear moonlighting of HRG uncouples its role as a driver of endocrine resistance from its canonical HER network-activating role in breast cancer. Tandem affinity purification coupled to mass spectrometry identified the intracellular transporter nucleolin as a major HRG-binding protein. HRG interacts with nucleolin via a nuclear localization signal motif located at the N-terminal extracellular domain of HRG. Nucleolin interacts with HRG via aspartate/glutamate-rich acidic stretches located at the N-terminal domain of nucleolin. Depletion of nucleolin abolishes HRG nuclear translocation and decreases HRG mRNA and protein expression. Isolated deficiency of nuclear HRG abolishes the HRG-driven endocrine resistance phenotype in vitro and in mouse xenograft models, while preserving its capacity to activate the HRG/HER/MAPK autocrine signaling axis. Conversely, isolated deficiency of secreted HRG to bind HER2/3 receptors does not impair endocrine resistance. The discovery that the functions of dual compartment-resident HRG do not depend on the same effector (i.e., activation of HER2/3 receptors) establishes a new paradigm for the functional and therapeutic relevance of nuclear HRG in breast cancer.
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Affiliation(s)
- Lin Yang
- Precision Cancer Therapeutics Program, Center for Individualized Medicine, Mayo ClinicRochester, MN, USA
| | - Travis Vander Steen
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo ClinicRochester, MN, USA
| | - Ingrid Espinoza
- Department of Preventive Medicine, John D. Bower School of Population Health, University of Mississippi Medical CenterJackson, MS, USA
- Cancer Institute, School of Medicine, University of Mississippi Medical CenterJackson, MS, USA
| | - Elisabet Cuyàs
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of OncologyGirona, Spain
- Girona Biomedical Research InstituteSalt, Girona, Spain
| | - Sara Verdura
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of OncologyGirona, Spain
- Girona Biomedical Research InstituteSalt, Girona, Spain
| | - Javier A Menendez
- Program Against Cancer Therapeutic Resistance (ProCURE), Metabolism and Cancer Group, Catalan Institute of OncologyGirona, Spain
- Girona Biomedical Research InstituteSalt, Girona, Spain
| | - Ruth Lupu
- Department of Laboratory Medicine and Pathology, Division of Experimental Pathology, Mayo ClinicRochester, MN, USA
- Department of Biochemistry and Molecular Biology Laboratory, Mayo Clinic MinnesotaRochester, MN, USA
- Mayo Clinic Cancer CenterRochester, MN, USA
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17
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Watson J, Smith M, Francavilla C, Schwartz JM. SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment. Nucleic Acids Res 2022; 50:W718-W725. [PMID: 35536291 PMCID: PMC9252817 DOI: 10.1093/nar/gkac336] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/10/2022] [Accepted: 05/09/2022] [Indexed: 12/16/2022] Open
Abstract
Cells contain intracellular compartments, including membrane-bound organelles and the nucleus, and are surrounded by a plasma membrane. Proteins are localised to one or more of these cellular compartments; the correct localisation of proteins is crucial for their correct processing and function. Moreover, proteins and the cellular processes they partake in are regulated by relocalisation in response to various cellular stimuli. High-throughput ‘omics experiments result in a list of proteins or genes of interest; one way in which their functional role can be understood is through the knowledge of their subcellular localisation, as deduced through statistical enrichment for Gene Ontology Cellular Component (GOCC) annotations or similar. We have designed a bioinformatics tool, named SubcellulaRVis, that compellingly visualises the results of GOCC enrichment for quick interpretation of the localisation of a group of proteins (rather than single proteins). We demonstrate that SubcellulaRVis precisely describes the subcellular localisation of gene lists whose locations have been previously ascertained. SubcellulaRVis can be accessed via the web (http://phenome.manchester.ac.uk/subcellular/) or as a stand-alone app (https://github.com/JoWatson2011/subcellularvis). SubcellulaRVis will be useful for experimental biologists with limited bioinformatics expertise who want to analyse data related to protein (re)localisation and location-specific modules within the intracellular protein network.
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Affiliation(s)
- Joanne Watson
- Division of Evolution, Infection & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, UK.,Division of Molecular & Cell Biology, School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, UK
| | - Michael Smith
- Division of Molecular & Cell Biology, School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, UK
| | - Chiara Francavilla
- Division of Molecular & Cell Biology, School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, UK.,Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, M139PT, Manchester, UK
| | - Jean-Marc Schwartz
- Division of Evolution, Infection & Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine & Health, University of Manchester, Manchester M13 9PT, UK
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18
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Mulvey CM, Breckels LM, Crook OM, Sanders DJ, Ribeiro ALR, Geladaki A, Christoforou A, Britovšek NK, Hurrell T, Deery MJ, Gatto L, Smith AM, Lilley KS. Spatiotemporal proteomic profiling of the pro-inflammatory response to lipopolysaccharide in the THP-1 human leukaemia cell line. Nat Commun 2021; 12:5773. [PMID: 34599159 PMCID: PMC8486773 DOI: 10.1038/s41467-021-26000-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Protein localisation and translocation between intracellular compartments underlie almost all physiological processes. The hyperLOPIT proteomics platform combines mass spectrometry with state-of-the-art machine learning to map the subcellular location of thousands of proteins simultaneously. We combine global proteome analysis with hyperLOPIT in a fully Bayesian framework to elucidate spatiotemporal proteomic changes during a lipopolysaccharide (LPS)-induced inflammatory response. We report a highly dynamic proteome in terms of both protein abundance and subcellular localisation, with alterations in the interferon response, endo-lysosomal system, plasma membrane reorganisation and cell migration. Proteins not previously associated with an LPS response were found to relocalise upon stimulation, the functional consequences of which are still unclear. By quantifying proteome-wide uncertainty through Bayesian modelling, a necessary role for protein relocalisation and the importance of taking a holistic overview of the LPS-driven immune response has been revealed. The data are showcased as an interactive application freely available for the scientific community.
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Affiliation(s)
- Claire M Mulvey
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Oliver M Crook
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- MRC Biostatistics Unit, Cambridge Institute for Public Health, Forvie Site, Robinson Way, Cambridge, CB2 0SR, UK
| | - David J Sanders
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Andre L R Ribeiro
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | | | - Nina Kočevar Britovšek
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- Lek d.d., Kolodvorska 27, Mengeš, 1234, Slovenia
| | - Tracey Hurrell
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Michael J Deery
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK
- de Duve Institute, UCLouvain, Avenue Hippocrate 75, Brussels, 1200, Belgium
| | - Andrew M Smith
- Department of Microbial Diseases, Eastman Dental Institute, University College London, Royal Free Campus, Rowland Hill Street, London, NW3 2PF, UK.
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Cambridge Systems Biology Centre and Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QR, UK.
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19
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Das S, Amin SA, Jha T. Insight into the structural requirement of aryl sulphonamide based gelatinases (MMP-2 and MMP-9) inhibitors - Part I: 2D-QSAR, 3D-QSAR topomer CoMFA and Naïve Bayes studies - First report of 3D-QSAR Topomer CoMFA analysis for MMP-9 inhibitors and jointly inhibitors of gelatinases together. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:655-687. [PMID: 34355614 DOI: 10.1080/1062936x.2021.1955414] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 07/11/2021] [Indexed: 06/13/2023]
Abstract
Gelatinases [gelatinase A - matrix metalloproteinase-2 (MMP-2), gelatinase B - matrix metalloproteinase-9 (MMP-9)] play key roles in many disease conditions including cancer. Despite some research work on gelatinases inhibitors both jointly and individually had been reported, challenges still exist in achieving potency as well as selectivity. Here in part I of a series of work, we have reported the structural requirement of some arylsulfonamides. In particular, regression-based 2D-QSARs, topomer CoMFA (comparative molecular field analysis) and Bayesian classification models were constructed to refine structural features for attaining better gelatinase inhibitory activity. The 2D-QSAR models exhibited good statistical significance. The descriptors nsssN, SHBint6, SHBint7, PubchemFP629 were directly correlated with the MMP-2 binding affinities whereas nsssN, SHBint10 and AATS2i were directly proportional to MMP-9 binding affinities. The topomer CoMFA results indicated that the steric and electrostatic fields play key roles in gelatinase inhibition. The established Naïve Bayes prediction models were evaluated by fivefold cross validation and an external test set. Furthermore, important molecular descriptors related to MMP-2 and MMP-9 binding affinities and some active/inactive fragments were identified. Thus, these observations may be helpful for further work of aryl sulphonamide based gelatinase inhibitors in future.
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Affiliation(s)
- S Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - S A Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - T Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
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20
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Mills A, Gago F. On the Need to Tell Apart Fraternal Twins eEF1A1 and eEF1A2, and Their Respective Outfits. Int J Mol Sci 2021; 22:6973. [PMID: 34203525 PMCID: PMC8268798 DOI: 10.3390/ijms22136973] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 01/03/2023] Open
Abstract
eEF1A1 and eEF1A2 are paralogous proteins whose presence in most normal eukaryotic cells is mutually exclusive and developmentally regulated. Often described in the scientific literature under the collective name eEF1A, which stands for eukaryotic elongation factor 1A, their best known activity (in a monomeric, GTP-bound conformation) is to bind aminoacyl-tRNAs and deliver them to the A-site of the 80S ribosome. However, both eEF1A1 and eEF1A2 are endowed with multitasking abilities (sometimes performed by homo- and heterodimers) and can be located in different subcellular compartments, from the plasma membrane to the nucleus. Given the high sequence identity of these two sister proteins and the large number of post-translational modifications they can undergo, we are often confronted with the dilemma of discerning which is the particular proteoform that is actually responsible for the ascribed biochemical or cellular effects. We argue in this review that acquiring this knowledge is essential to help clarify, in molecular and structural terms, the mechanistic involvement of these two ancestral and abundant G proteins in a variety of fundamental cellular processes other than translation elongation. Of particular importance for this special issue is the fact that several de novo heterozygous missense mutations in the human EEF1A2 gene are associated with a subset of rare but severe neurological syndromes and cardiomyopathies.
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Affiliation(s)
| | - Federico Gago
- Department of Biomedical Sciences & “Unidad Asociada IQM-CSIC”, School of Medicine and Health Sciences, University of Alcalá, E-28805 Alcalá de Henares, Spain;
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21
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Quercetin Induces Anticancer Activity by Upregulating Pro-NAG-1/GDF15 in Differentiated Thyroid Cancer Cells. Cancers (Basel) 2021; 13:cancers13123022. [PMID: 34208730 PMCID: PMC8233818 DOI: 10.3390/cancers13123022] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/12/2021] [Accepted: 06/14/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Thyroid cancer is one of the most common cancers worldwide, and its incidence has increased over the last few decades. It is difficult to diagnose different types of thyroid cancer. Tumor tissues from papillary thyroid cancer patient showed higher expression of mature NAG-1, whereas adjacent normal tissues showed higher expression of pro-NAG-1. Several anti-cancer compounds increased pro-NAG-1 expression in thyroid cancer cell line. Quercetin (3,3’,4’,5,7-pentahydroxyflavone) is a flavonoid that is a major component of various plants, including raspberries, grapes, and onions. Quercetin induced apoptosis by inducing only pro-NAG-1 expression, but not mature NAG-1, mediated by the transcription factor C/EBP. This study indicates that pro-NAG-1 could be used as a useful biomarker for thyroid cancer and also provides a potential therapeutic target for the treatment of thyroid cancer with quercetin. Abstract Although the treatment of thyroid cancer has improved, unnecessary surgeries are performed due to a lack of specific diagnostic and prognostic markers. Therefore, the identification of novel biomarkers should be considered in the diagnosis and treatment of thyroid cancer. In this study, antibody arrays were performed using tumor and adjacent normal tissues of patients with papillary thyroid cancer, and several potential biomarkers were identified. Among the candidate proteins chosen based on the antibody array data, mature NAG-1 exhibited increased expression in tumor tissues compared to adjacent normal tissues. In contrast, pro-NAG-1 expression increased in normal tissues, as assessed by western blot analysis. Furthermore, pro-NAG-1 expression was increased when the thyroid cancer cells were treated with phytochemicals and nonsteroidal anti-inflammatory drugs in a dose-dependent manner. In particular, quercetin highly induced the expression of pro-NAG-1 but not that of mature NAG-1, with enhanced anticancer activity, including apoptosis induction and cell cycle arrest. Examination of the NAG-1 promoter activity showed that p53, C/EBPα, or C/EBPδ played a role in quercetin-induced NAG-1 expression. Overall, our study indicated that NAG-1 may serve as a novel biomarker for thyroid cancer prognosis and may be used as a therapeutic target for thyroid cancers.
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22
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Adamo A, Frusteri C, Pallotta MT, Pirali T, Sartoris S, Ugel S. Moonlighting Proteins Are Important Players in Cancer Immunology. Front Immunol 2021; 11:613069. [PMID: 33584695 PMCID: PMC7873856 DOI: 10.3389/fimmu.2020.613069] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/30/2020] [Indexed: 12/21/2022] Open
Abstract
Plasticity and adaptation to environmental stress are the main features that tumor and immune system share. Except for intrinsic and high-defined properties, cancer and immune cells need to overcome the opponent's defenses by activating more effective signaling networks, based on common elements such as transcriptional factors, protein-based complexes and receptors. Interestingly, growing evidence point to an increasing number of proteins capable of performing diverse and unpredictable functions. These multifunctional proteins are defined as moonlighting proteins. During cancer progression, several moonlighting proteins are involved in promoting an immunosuppressive microenvironment by reprogramming immune cells to support tumor growth and metastatic spread. Conversely, other moonlighting proteins support tumor antigen presentation and lymphocytes activation, leading to several anti-cancer immunological responses. In this light, moonlighting proteins could be used as promising new potential targets for improving current cancer therapies. In this review, we describe in details 12 unprecedented moonlighting proteins that during cancer progression play a decisive role in guiding cancer-associated immunomodulation by shaping innate or adaptive immune response.
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Affiliation(s)
- Annalisa Adamo
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | - Cristina Frusteri
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | | | - Tracey Pirali
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Novara, Italy
| | - Silvia Sartoris
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
| | - Stefano Ugel
- Section of Immunology, Department of Medicine, University of Verona, Verona, Italy
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23
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Abstract
Drug metabolizing enzymes catalyze the biotransformation of many of drugs and chemicals. The drug metabolizing enzymes are distributed among several evolutionary families and catalyze a range of detoxication reactions, including oxidation/reduction, conjugative, and hydrolytic reactions that serve to detoxify potentially toxic compounds. This detoxication function requires that drug metabolizing enzymes exhibit substrate promiscuity. In addition to their catalytic functions, many drug metabolizing enzymes possess functions unrelated to or in addition to catalysis. Such proteins are termed 'moonlighting proteins' and are defined as proteins with multiple biochemical or biophysical functions that reside in a single protein. This review discusses the diverse moonlighting functions of drug metabolizing enzymes and the roles they play in physiological functions relating to reproduction, vision, cell signaling, cancer, and transport. Further research will likely reveal new examples of moonlighting functions of drug metabolizing enzymes.
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Affiliation(s)
- Philip G Board
- John Curtin School of Medical Research, ANU College of Health and Medicine, The Australian National University, Canberra, ACT, Australia
| | - M W Anders
- Department of Pharmacology and Physiology, University of Rochester Medical Center, New York, NY, USA
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24
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Carriles AA, Mills A, Muñoz-Alonso MJ, Gutiérrez D, Domínguez JM, Hermoso JA, Gago F. Structural Cues for Understanding eEF1A2 Moonlighting. Chembiochem 2020; 22:374-391. [PMID: 32875694 DOI: 10.1002/cbic.202000516] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/01/2020] [Indexed: 12/16/2022]
Abstract
Spontaneous mutations in the EEF1A2 gene cause epilepsy and severe neurological disabilities in children. The crystal structure of eEF1A2 protein purified from rabbit skeletal muscle reveals a post-translationally modified dimer that provides information about the sites of interaction with numerous binding partners, including itself, and maps these mutations onto the dimer and tetramer interfaces. The spatial locations of the side chain carboxylates of Glu301 and Glu374, to which phosphatidylethanolamine is uniquely attached via an amide bond, define the anchoring points of eEF1A2 to cellular membranes and interorganellar membrane contact sites. Additional bioinformatic and molecular modeling results provide novel structural insight into the demonstrated binding of eEF1A2 to SH3 domains, the common MAPK docking groove, filamentous actin, and phosphatidylinositol-4 kinase IIIβ. In this new light, the role of eEF1A2 as an ancient, multifaceted, and articulated G protein at the crossroads of autophagy, oncogenesis and viral replication appears very distant from the "canonical" one of delivering aminoacyl-tRNAs to the ribosome that has dominated the scene and much of the thinking for many decades.
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Affiliation(s)
- Alejandra A Carriles
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano" CSIC, 28006, Madrid, Spain.,Biocrystallography Unit, Division of Immunology, Transplantation, and Infectious Diseases, IRCCS Scientific Institute San Raffaele, 20132, Milan, Italy
| | - Alberto Mills
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain
| | - María-José Muñoz-Alonso
- Department of Cell Biology and Pharmacogenomics, PharmaMar S.A.U., 28770, Colmenar Viejo, Madrid, Spain
| | - Dolores Gutiérrez
- Proteomics Unit, Faculty of Pharmacy, Complutense University, 28040, Madrid, Spain
| | - Juan M Domínguez
- Department of Cell Biology and Pharmacogenomics, PharmaMar S.A.U., 28770, Colmenar Viejo, Madrid, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano" CSIC, 28006, Madrid, Spain
| | - Federico Gago
- Department of Biomedical Sciences and "Unidad Asociada IQM-CSIC", School of Medicine and Health Sciences, University of Alcalá, 28805, Alcalá de Henares, Madrid, Spain
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25
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Pantouris G, Khurana L, Ma A, Skeens E, Reiss K, Batista VS, Lisi GP, Lolis EJ. Regulation of MIF Enzymatic Activity by an Allosteric Site at the Central Solvent Channel. Cell Chem Biol 2020; 27:740-750.e5. [PMID: 32433911 DOI: 10.1016/j.chembiol.2020.05.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/18/2020] [Accepted: 04/30/2020] [Indexed: 12/18/2022]
Abstract
In proteins with multiple functions, such as macrophage migration inhibitory factor (MIF), the study of its intramolecular dynamic network can offer a unique opportunity to understand how a single protein is able to carry out several nonoverlapping functions. A dynamic mechanism that controls the MIF-induced activation of CD74 was recently discovered. In this study, the regulation of tautomerase activity was explored. The catalytic base Pro1 is found to form dynamic communications with the same allosteric node that regulates CD74 activation. Signal transmission between the allosteric and catalytic sites take place through intramolecular aromatic interactions and a hydrogen bond network that involves residues and water molecules of the MIF solvent channel. Once thought to be a consequence of trimerization, a regulatory function for the solvent channel is now defined. These results provide mechanistic insights into the regulation of catalytic activity and the role of solvent channel water molecules in MIF catalysis.
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Affiliation(s)
- Georgios Pantouris
- Department of Chemistry, University of the Pacific, Stockton, CA 95211, USA.
| | - Leepakshi Khurana
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Anthony Ma
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06510, USA
| | - Erin Skeens
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, USA
| | - Krystle Reiss
- Department of Chemistry, Yale University, New Haven, CT 06510, USA
| | - Victor S Batista
- Department of Chemistry, Yale University, New Haven, CT 06510, USA
| | - George P Lisi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02903, USA.
| | - Elias J Lolis
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06510, USA; Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA.
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26
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Clark DJ, Schnaubelt M, Hoti N, Hu Y, Zhou Y, Gooya M, Zhang H. Impact of Increased FUT8 Expression on the Extracellular Vesicle Proteome in Prostate Cancer Cells. J Proteome Res 2020; 19:2195-2205. [PMID: 32378902 DOI: 10.1021/acs.jproteome.9b00578] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Extracellular vesicles (EVs) are involved in intercellular communication, transporting proteins and nucleic acids to proximal and distal regions. There is evidence of glycosylation influencing protein routing into EVs; however, the impact of aberrant cellular glycotransferase expression on EV protein profiles has yet to be evaluated. In this study, we paired extracellular vesicle characterization and quantitative proteomics to determine the systemic impact of altered α(1,6)fucosyltranferase (FUT8) expression on prostate cancer-derived EVs. Our results showed that increased cellular expression of FUT8 could reduce the number of vesicles secreted by prostate cancer cells as well as increase the abundance of proteins associated with cell motility and prostate cancer metastasis. In addition, overexpression of FUT8 resulted in altered glycans on select EV-derived glycoproteins. This study presents the first evidence of altered cellular glycosylation impacting EV protein profiles and provides further rationale for exploring the functional role of glycosylation in EV biogenesis and biology.
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Affiliation(s)
- David J Clark
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Michael Schnaubelt
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Naseruddin Hoti
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Yingwei Hu
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Yangying Zhou
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Mahta Gooya
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
| | - Hui Zhang
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore 21231, Maryland, United States
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27
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Uzdensky AB. Multifunctional Proteins. Biophysics (Nagoya-shi) 2020. [DOI: 10.1134/s0006350920030227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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28
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Nwamba OC. Membranes as the third genetic code. Mol Biol Rep 2020; 47:4093-4097. [PMID: 32279211 DOI: 10.1007/s11033-020-05437-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/03/2020] [Indexed: 02/07/2023]
Abstract
Biological membranes and their compositions influence cellular function, age and disease states of organisms. They achieve this by effecting the outcome of bound enzymes/proteins and carbohydrate moieties. While the membrane-bound carbohydrates give rise to antigenicity, membranes impact the eventual outcome of protein structures that would function even outside their enclosure. This is achieved by membrane modulation of translational and post-translational protein folding. Thus, the eventual 3D structures and functions of proteins might not be solely dependent on their primary amino acid sequences and surrounding environments. The 3D protein structures would also depend on enclosing membrane properties such as fluidity, other intrinsic and extrinsic proteins and carbohydrate functionalities. Also, membranes moderate DNA activities with consequences on gene activation-inactivation mechanisms. Consequently, membranes are almost indispensable to the functioning of other cell compositions and serve to modulate these other components. Besides, membrane lipid compositions are also moderated by nutrition and diets and the converse is true. Thus, it could be argued that membranes are the third genetic codes. Suggestively, membranes are at the center of the interplay between nature and nurture in health and disease states.
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29
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Dey A, Sen S, Uversky VN, Maulik U. Structural facets of POU2F1 in light of the functional annotations and sequence-structure patterns. J Biomol Struct Dyn 2020; 39:1093-1105. [PMID: 32081083 DOI: 10.1080/07391102.2020.1733092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
POU domain class 2 homebox 1 or POU2F1 is broadly known as an important transcription factor. Due to its association with different types of malignancies, POU2F1 became one of the key factors in pancancer analysis. However, in spite of considering this protein as a potential drug target, none of the drug targeting POU2F1 has been designed as of yet due to the extreme structural flexibility of this protein. In this article, we have proposed a three-level comprehensive framework for understanding the structural conservation and co-variation of POU2F1. First, a gene regulatory network based on the normal and pathological functions of POU2F1 has been created for better understanding the strong association between POU2F1 deregulation and cancers. After that, based on the evolutionary sequence space analysis, the comparative sequence dynamics of the protein members of POU domain family has been studied mostly between non-human and human species. Subsequently, the reciprocity effect of the residual co-variation has been identified through direct coupling analysis. Along with that, the structure of POU2F1 has been analyzed depending on quality assessment and normal mode-based structure network. Comparing the sequence and structure space information, the most significant set of residues viz., 3, 9, 13, 17, 20, 21, 28, 35, and 36 have been identified as structural facet for function. This study demonstrates that the structural malleability of POU2F1 serves as one of the prime reason behind its functional multiplicity in terms of protein moonlighting. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashmita Dey
- Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Sagnik Sen
- Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India
| | - Vladimir N Uversky
- Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences", Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, Russia.,Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Ujjwal Maulik
- Computer Science and Engineering, Jadavpur University, Kolkata, West Bengal, India
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30
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Liu J, Tuo W, Wu X, Xiong J, Yu E, Yin C, Ma Z, Liu L. Immunoproteomic and mass spectrometric analysis of Eimeria acervulina antigens recognized by antisera from chickens infected with E. acervulina, E. tenella or E. necatrix. Parasit Vectors 2020; 13:93. [PMID: 32085718 PMCID: PMC7035704 DOI: 10.1186/s13071-020-3965-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Background Coccidiosis is caused by Eimeria spp. and can result in severe economic losses to the global poultry industry. Due to anticoccidial drug resistance rapidly developing in the parasites and drug residues in poultry products, efficacious and safe alternative coccidia control measures are needed. The objective of the present study was to identify common protective antigens which may be used as vaccine candidates in the development of subunit, multivalent, cross-protective vaccines against most of the economically important Eimeria species. Methods Whole sporozoite proteins of Eimeria acervulina were prepared and analyzed by 2-dimensional gel electrophoresis (2-DE) followed by western blotting using immune sera specific to E. tenella, E. acervulina, or E. necatrix. The protein spots detected by all three immune sera were then excised from the preparative gel and protein ID was performed by MALDI-TOF-MS/MS. Results Approximately 620 E. acervulina sporozoite protein spots were demonstrated by 2-DE with silver staining, among which 23 protein spots were recognized by immune sera specific to all three Eimeria species. The results showed that 21 putative E. acervulina proteins were identified, which include proteins with known enzymatic properties, and those which are involved in protein translation, transport and trafficking, and ribosomal biogenesis and functions. There is one protein which may be involved in transcription and one heat-shock protein. Two proteins contain predicted domains, but with no apparent functions known. There were 2 protein spots which had no detectable proteins. None of the proteins has a predicted signal peptide or a transmembrane domain; however, 6 of the 21 putative proteins were predicted to be potentially secretory through the non-classical pathway. Conclusions Our study identified a diverse group of antigens immunologically common to all three Eimeria species, none of which was previously characterized and tested as a vaccine candidate. Further research on immunogenicity and cross-protective potential of these individual proteins as vaccine candidates will aid the development of vaccines against the most common and pathogenic Eimeria spp.![]()
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Affiliation(s)
- Jin Liu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, 20705, USA
| | - Xiangdong Wu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Jiaming Xiong
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Enchao Yu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Chao Yin
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Zhiwu Ma
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China
| | - Liheng Liu
- Jiangxi Provincial Key Laboratory for Animal Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, 330045, Jiangxi, People's Republic of China.
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31
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Liu X, Xu Y, Wang R, Liu S, Wang J, Luo Y, Leung KS, Cheng L. A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis. Brief Bioinform 2020; 22:581-588. [PMID: 32003790 DOI: 10.1093/bib/bbz154] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/26/2019] [Accepted: 11/01/2019] [Indexed: 12/26/2022] Open
Abstract
Moonlighting proteins provide more options for cells to execute multiple functions without increasing the genome and transcriptome complexity. Although there have long been calls for computational methods for the prediction of moonlighting proteins, no method has been designed for determining moonlighting long noncoding ribonucleicacidz (RNAs) (mlncRNAs). Previously, we developed an algorithm MoonFinder for the identification of mlncRNAs at the genome level based on the functional annotation and interactome data of lncRNAs and proteins. Here, we update MoonFinder to MoonFinder v2.0 by providing an extensive framework for the detection of protein modules and the establishment of RNA-module associations in human. A novel measure, moonlighting coefficient, was also proposed to assess the confidence of an ncRNA acting in a moonlighting manner. Moreover, we explored the expression characteristics of mlncRNAs in sepsis, in which we found that mlncRNAs tend to be upregulated and differentially expressed. Interestingly, the mlncRNAs are mutually exclusive in terms of coexpression when compared to the other lncRNAs. Overall, MoonFinder v2.0 is dedicated to the prediction of human mlncRNAs and thus bears great promise to serve as a valuable R package for worldwide research communities (https://cran.r-project.org/web/packages/MoonFinder/index.html). Also, our analyses provide the first attempt to characterize mlncRNA expression and coexpression properties in adult sepsis patients, which will facilitate the understanding of the interaction and expression patterns of mlncRNAs.
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Affiliation(s)
- Xueyan Liu
- Critical Care Medici at Shenzhen People's Hospital
| | | | - Ran Wang
- Computer Science at The Chinese University of Hong Kong
| | | | | | | | - Kwong-Sak Leung
- Computer Science at the Chinese University of Hong Kong, Hong Kong, China
| | - Lixin Cheng
- Bioinformatics at Shenzhen People's Hospital, China
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32
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Foyer CH, Baker A, Wright M, Sparkes IA, Mhamdi A, Schippers JHM, Van Breusegem F. On the move: redox-dependent protein relocation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:620-631. [PMID: 31421053 DOI: 10.1093/jxb/erz330] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/01/2019] [Indexed: 05/04/2023]
Abstract
Compartmentation of proteins and processes is a defining feature of eukaryotic cells. The growth and development of organisms is critically dependent on the accurate sorting of proteins within cells. The mechanisms by which cytosol-synthesized proteins are delivered to the membranes and membrane compartments have been extensively characterized. However, the protein complement of any given compartment is not precisely fixed and some proteins can move between compartments in response to metabolic or environmental triggers. The mechanisms and processes that mediate such relocation events are largely uncharacterized. Many proteins can in addition perform multiple functions, catalysing alternative reactions or performing structural, non-enzymatic functions. These alternative functions can be equally important functions in each cellular compartment. Such proteins are generally not dual-targeted proteins in the classic sense of having targeting sequences that direct de novo synthesized proteins to specific cellular locations. We propose that redox post-translational modifications (PTMs) can control the compartmentation of many such proteins, including antioxidant and/or redox-associated enzymes.
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Affiliation(s)
- Christine H Foyer
- School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Edgbaston, UK
- School of Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Alison Baker
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, UK
- Centre for Plant Sciences, University of Leeds, Leeds, UK
| | - Megan Wright
- The Astbury Centre for Structural Biology, University of Leeds, Leeds, UK
- School of Chemistry, University of Leeds, Leeds, UK
| | - Imogen A Sparkes
- School of Biological Sciences, University of Bristol, Bristol, UK
| | - Amna Mhamdi
- VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Jos H M Schippers
- Institute of Biology I, RWTH Aachen University, Aachen, Germany
- Department of Molecular Genetics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Frank Van Breusegem
- VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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33
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Griffiths SG, Ezrin A, Jackson E, Dewey L, Doucette AA. A robust strategy for proteomic identification of biomarkers of invasive phenotype complexed with extracellular heat shock proteins. Cell Stress Chaperones 2019; 24:1197-1209. [PMID: 31650515 PMCID: PMC6882979 DOI: 10.1007/s12192-019-01041-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/03/2019] [Accepted: 10/09/2019] [Indexed: 12/17/2022] Open
Abstract
As an extension of their orchestration of intracellular pathways, secretion of extracellular heat shock proteins (HSPs) is an emerging paradigm of homeostasis imperative to multicellular organization. Extracellular HSP is axiomatic to the survival of cells during tumorigenesis; proportional representation of specific HSP family members is indicative of invasive potential and prognosis. Further significance has been added by the knowledge that all cancer-derived exosomes have surface-exposed HSPs that reflect the membrane topology of cells that secrete them. Extracellular HSPs are also characteristic of chronic inflammation and sepsis. Accordingly, interrogation of extracellular HSPs secreted from cell culture models may represent a facile means of identifying translational biomarker signatures for targeting in situ. In the current study, we evaluated a simple peptide-based multivalent HSP affinity approach using the Vn96 peptide for low speed pelleting of HSP complexes from bioreactor cultures of cell lines with varying invasive phenotype in xenotransplant models: U87 (glioblastoma multiforme; invasive); HELA (choriocarcinoma; minimally invasive); HEK293T (virally transformed immortalized; embryonic). Proteomic profiling by bottom-up mass spectrometry revealed a comprehensive range of candidate biomarkers including primary HSP ligands. HSP complexes were associated with additional chaperones of prognostic significance such as protein disulfide isomerases, as well as pleiotropic metabolic enzymes, established as proportionally reflective of invasive phenotype. Biomarkers of inflammatory and mechanotransductive phenotype were restricted to the most invasive cell model U87, including chitinase CHI3L1, lamin C, amyloid derivatives, and histone isoforms.
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Affiliation(s)
| | - Alan Ezrin
- NX Development Corporation, Louisville, KY, USA
| | - Emily Jackson
- David H. Murdock Research Institute, Kannapolis, NC, USA
| | - Lisa Dewey
- David H. Murdock Research Institute, Kannapolis, NC, USA
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34
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Delgado-Carreño C, Méndez-Callejas G. Topological properties and in vitro identification of essential nodes of the Paclitaxel and Vincristine interactomes in PC-3 cells. Biomed J 2019; 42:307-316. [PMID: 31783991 PMCID: PMC6888721 DOI: 10.1016/j.bj.2019.04.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 12/20/2022] Open
Abstract
Background Microtubule-targeting agents (MTAs) disrupt microtubule dynamics, thereby inducing apoptosis via mitochondrial pathway activation through the modulation in the expression of the Bcl-2 family. Methods To describe topological features of the MTAs networks associated to intrinsic apoptosis induction in p53-null prostate cancer cells, we predicted and compared the interactomes and topological properties of Paclitaxel and Vincristine, and thus, the essential nodes corresponding with the pro- and anti-apoptotic proteins and their kinetics were subjected to experimental analysis in PC-3 cell line. Results The essential nodes of the apoptotic pathways, TP53, and CASP3, were identified in both, Paclitaxel and Vincristine networks, but the intrinsic pathway markers BCL2, BAX, and BCL2L1 were identified as hub nodes only in the Paclitaxel network. An in vitro analysis demonstrated an increase in BimEL and the cleaved-caspase-3 proteins in PC-3 cells exposed to both treatments. Immunoprecipitation analysis showed that treatments induced the releasing of Bax from the anti-apoptotic complex with Bcl-2 protein and the role of BimEL as a de-repressor from sequestering complexes, in addition, new protein complexes were identified between BimEL or Bcl-2 and cleaved-caspase-3, contributing data to the Vincristine network for p53-null cells in response to MTAs. Conclusion The differences in sensitivities, protein profiles, and protein complex kinetics observed between the drugs confirmed that the selectivity and stimulation of the apoptotic system vary depending on the cell's genotype, the drug used and its exposure period.
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Affiliation(s)
- Claudia Delgado-Carreño
- Group of Biomedical Research and Applied Human Genetics, Laboratory of Cellular and Molecular Biology, School of Medicine, University of Applied and Environmental Sciences, U.D.C.A, Bogota, Colombia; Department of Chemistry, Faculty of Science, Javeriana University, Bogota, Colombia
| | - Gina Méndez-Callejas
- Group of Biomedical Research and Applied Human Genetics, Laboratory of Cellular and Molecular Biology, School of Medicine, University of Applied and Environmental Sciences, U.D.C.A, Bogota, Colombia.
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35
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Harvey KL, Jarocki VM, Charles IG, Djordjevic SP. The Diverse Functional Roles of Elongation Factor Tu (EF-Tu) in Microbial Pathogenesis. Front Microbiol 2019; 10:2351. [PMID: 31708880 PMCID: PMC6822514 DOI: 10.3389/fmicb.2019.02351] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/27/2019] [Indexed: 12/25/2022] Open
Abstract
Elongation factor thermal unstable Tu (EF-Tu) is a G protein that catalyzes the binding of aminoacyl-tRNA to the A-site of the ribosome inside living cells. Structural and biochemical studies have described the complex interactions needed to effect canonical function. However, EF-Tu has evolved the capacity to execute diverse functions on the extracellular surface of both eukaryote and prokaryote cells. EF-Tu can traffic to, and is retained on, cell surfaces where can interact with membrane receptors and with extracellular matrix on the surface of plant and animal cells. Our structural studies indicate that short linear motifs (SLiMs) in surface exposed, non-conserved regions of the molecule may play a key role in the moonlighting functions ascribed to this ancient, highly abundant protein. Here we explore the diverse moonlighting functions relating to pathogenesis of EF-Tu in bacteria and examine putative SLiMs on surface-exposed regions of the molecule.
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Affiliation(s)
- Kate L Harvey
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Veronica M Jarocki
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
| | - Ian G Charles
- Quadram Institute, Norwich, United Kingdom.,Norwich Medical School, Norwich, United Kingdom
| | - Steven P Djordjevic
- The ithree Institute, University of Technology Sydney, Ultimo, NSW, Australia
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36
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Targeting a moonlighting function of aldolase induces apoptosis in cancer cells. Cell Death Dis 2019; 10:712. [PMID: 31558701 PMCID: PMC6763475 DOI: 10.1038/s41419-019-1968-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/18/2019] [Accepted: 09/09/2019] [Indexed: 02/07/2023]
Abstract
Muscle fructose-1,6-bisphosphate aldolase (ALDOA) is among the most abundant glycolytic enzymes in all cancer cells. Here, we show that the enzyme plays a previously unknown and critical role in a cancer cell survival. Simultaneous inhibition of ALDOA activity and interaction with F-actin cytoskeleton using ALDOA slow-binding inhibitor UM0112176 leads to a rapid cofilin-dependent loss of F-actin stress fibers which is associated with elevated ROS production, inhibition of ATP synthesis, increase in calcium levels, caspase activation and arrested cellular proliferation. These effects can be reproduced by silencing of ALDOA. The mechanism of pharmacological action is, however, independent of the catalytic function of the enzyme, specific to cancer cells, and is most deleterious to cells undergoing the epithelial–mesenchymal transition, a process facilitating cancer cell invasion. Our results demonstrate that the overabundance of ALDOA in cancer cells is associated with its moonlighting rather than catalytic functions. This may have significant implications for development of novel broad-based anti-cancer therapies.
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The Yin and Yang of cancer genes. Gene 2019; 704:121-133. [DOI: 10.1016/j.gene.2019.04.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/21/2019] [Accepted: 04/08/2019] [Indexed: 12/31/2022]
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Ha T, Lee J, Lou Z, Lee B, Kim C, Lee S. Identification of epithelial‐specific ETS‐1 (ESE‐1) as a tumor suppressor and molecular target of green tea compound, EGCG. Mol Carcinog 2019; 58:922-932. [DOI: 10.1002/mc.22981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/18/2019] [Accepted: 01/21/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Taekyu Ha
- Department of Nutrition and Food ScienceCollege of Agriculture and Natural ResourcesUniversity of MarylandCollege ParkMaryland
| | - Jihye Lee
- Department of Nutrition and Food ScienceCollege of Agriculture and Natural ResourcesUniversity of MarylandCollege ParkMaryland
| | - Zhiyuan Lou
- Department of Nutrition and Food ScienceCollege of Agriculture and Natural ResourcesUniversity of MarylandCollege ParkMaryland
| | - Bok‐Soon Lee
- Department of OtolaryngologySchool of MedicineAjou UniversitySuwonRepublic of Korea
| | - Chul‐Ho Kim
- Department of OtolaryngologySchool of MedicineAjou UniversitySuwonRepublic of Korea
| | - Seong‐Ho Lee
- Department of Nutrition and Food ScienceCollege of Agriculture and Natural ResourcesUniversity of MarylandCollege ParkMaryland
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Baek SJ, Eling T. Growth differentiation factor 15 (GDF15): A survival protein with therapeutic potential in metabolic diseases. Pharmacol Ther 2019; 198:46-58. [PMID: 30790643 DOI: 10.1016/j.pharmthera.2019.02.008] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/14/2019] [Indexed: 12/18/2022]
Abstract
Growth Differentiation Factor 15 (GDF15), also known as NSAID activated gene-1 (NAG-1), is associated with a large number of biological processes and diseases, including cancer and obesity. GDF15 is synthesized as pro-GDF15, is dimerized, and is cleaved and secreted into the circulation as a mature dimer GDF15. Both the intracellular GDF15 and the circulating mature GDF15 are implicated in biological processes, such as energy homeostasis and body weight regulation. Although there have been many studies on GDF15, GFRAL, a member of the glial-derived neurotropic factor receptor α family, has only been recently identified as a receptor for mature GDF15. In this review, we focused on cancer and energy homeostasis along with obesity and body weight, and the effect of the identification of the GDF15 receptor in these investigations. In addition, the therapeutic potential of GDF15 as a pharmacological agent in obesity and other metabolic diseases was discussed.
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Affiliation(s)
- Seung Joon Baek
- Bldg 81 Rm 413, Laboratory of Signal Transduction, College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea..
| | - Thomas Eling
- Scientist Emeritus, NIEHS/NIH, 111 TW Alexander Dr. Bldg. 101 F-095, Research Triangle Park, NC 27709, United States.
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Byeon HK, Ku M, Yang J. Beyond EGFR inhibition: multilateral combat strategies to stop the progression of head and neck cancer. Exp Mol Med 2019; 51:1-14. [PMID: 30700700 PMCID: PMC6353966 DOI: 10.1038/s12276-018-0202-2] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/03/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) overexpression is common in head and neck squamous cell carcinoma. Targeted therapy specifically directed towards EGFR has been an area of keen interest in head and neck cancer research, as EGFR is potentially an integration point for convergent signaling. Despite the latest advancements in cancer diagnostics and therapeutics against EGFR, the survival rates of patients with advanced head and neck cancer remain disappointing due to anti-EGFR resistance. This review article will discuss recent multilateral efforts to discover and validate actionable strategies that involve signaling pathways in heterogenous head and neck cancer and to overcome anti-EGFR resistance in the era of precision medicine. Particularly, this review will discuss in detail the issue of cancer metabolism, which has recently emerged as a novel mechanism by which head and neck cancer may be successfully controlled according to different perspectives. South Korean researchers propose novel combination strategies for overcoming drug resistance and halting the progression of head and neck cancer (HNC). Although high levels of epidermal growth factor receptor (EGFR) protein in HNC correlate with reduced survival, patients’ response to the EGFR inhibitor cetuximab often declines rapidly after a short period of effectiveness. Hyung Kwon Byeon at Korea University College of Medicine in Seoul and colleagues review current knowledge of the mechanisms underlying cetuximab resistance. They suggest that evaluating a patient’s genetic profile and combining cetuximab with drugs that enhance the effects of inhibiting EGFR signaling pathways (with inhibitors of other EGFR family members or proteins that mediate EGFR entry to the cell nucleus, for example) as well as with agents that inhibit cancer cell metabolism could be a more effective approach for treating HNC.
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Affiliation(s)
- Hyung Kwon Byeon
- Department of Otorhinolaryngology-Head and Neck Surgery, Soonchunhyang University College of Medicine, Seoul, Republic of Korea. .,Systems Molecular Oncology for Head and Neck Cancer, Seoul, Republic of Korea. .,Systems Molecular Radiology at Yonsei, Seoul, Republic of Korea.
| | - Minhee Ku
- Systems Molecular Radiology at Yonsei, Seoul, Republic of Korea.,Department of Radiology, Yonsei University College of Medicine, Seoul, Republic of Korea.,Research Institute of Radiological Science, Yonsei University, Seoul, Republic of Korea
| | - Jaemoon Yang
- Systems Molecular Radiology at Yonsei, Seoul, Republic of Korea. .,Department of Radiology, Yonsei University College of Medicine, Seoul, Republic of Korea. .,Research Institute of Radiological Science, Yonsei University, Seoul, Republic of Korea.
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Jaén RI, Prieto P, Casado M, Martín-Sanz P, Boscá L. Post-translational modifications of prostaglandin-endoperoxide synthase 2 in colorectal cancer: An update. World J Gastroenterol 2018; 24:5454-5461. [PMID: 30622375 PMCID: PMC6319129 DOI: 10.3748/wjg.v24.i48.5454] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 02/06/2023] Open
Abstract
The biosynthesis of prostanoids is involved in both physiological and pathological processes. The expression of prostaglandin-endoperoxide synthase 2 (PTGS2; also known as COX-2) has been traditionally associated to the onset of several pathologies, from inflammation to cardiovascular, gastrointestinal and oncologic events. For this reason, the search of selective PTGS2 inhibitors has been a focus for therapeutic interventions. In addition to the classic non-steroidal anti-inflammatory drugs, selective and specific PTGS2 inhibitors, termed coxibs, have been generated and widely used. PTGS2 activity is less restrictive in terms of substrate specificity than the homeostatic counterpart PTGS1, and it accounts for the elevated prostanoid synthesis that accompanies several pathologies. The main regulation of PTGS2 occurs at the transcription level. In addition to this, the stability of the mRNA is finely regulated through the interaction with several cytoplasmic elements, ranging from specific microRNAs to proteins that control mRNA degradation. Moreover, the protein has been recognized to be the substrate for several post-translational modifications that affect both the enzyme activity and the targeting for degradation via proteasomal and non-proteasomal mechanisms. Among these modifications, phosphorylation, glycosylation and covalent modifications by reactive lipidic intermediates and by free radicals associated to the pro-inflammatory condition appear to be the main changes. Identification of these post-translational modifications is relevant to better understand the role of PTGS2 in several pathologies and to establish a correct analysis of the potential function of this protein in diseases progress. Finally, these modifications can be used as biomarkers to establish correlations with other parameters, including the immunomodulation dependent on molecular pathological epidemiology determinants, which may provide a better frame for potential therapeutic interventions.
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Affiliation(s)
- Rafael I Jaén
- Department of Metabolism and Physiopathology of Inflammatory Diseases, Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid 28029, Spain
| | - Patricia Prieto
- Department of Metabolism and Physiopathology of Inflammatory Diseases, Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid 28029, Spain
| | - Marta Casado
- Department of Biomedicine, Instituto de Biomedicina de Valencia (CSIC), Valencia 46010, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, y Hepáticas y Digestivas, ISCIII, Madrid 28029, Spain
| | - Paloma Martín-Sanz
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, y Hepáticas y Digestivas, ISCIII, Madrid 28029, Spain
- Unidad Asociada IIBM-ULPGC, Universidad de las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria 35001, Spain
| | - Lisardo Boscá
- Department of Metabolism and Physiopathology of Inflammatory Diseases, Instituto de Investigaciones Biomédicas Alberto Sols (CSIC-UAM), Madrid 28029, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares, y Hepáticas y Digestivas, ISCIII, Madrid 28029, Spain
- Unidad Asociada IIBM-ULPGC, Universidad de las Palmas de Gran Canaria (ULPGC), Las Palmas de Gran Canaria 35001, Spain
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Zhao Q, Yang W, Qin T, Huang Z. Moonlighting Phosphatase Activity of Klenow DNA Polymerase in the Presence of RNA. Biochemistry 2018; 57:5127-5135. [PMID: 30059615 DOI: 10.1021/acs.biochem.8b00688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
RNA is a key player in the cellular central dogma, including RNA transcription and protein synthesis. However, it is unknown whether RNA can directly interfere with DNA synthesis. Recently, we have found in vitro that while binding to DNA polymerase nonspecifically, RNA can transform DNA polymerase to display a moonlighting activity, dNTP phosphatase, in turn interfering with DNA synthesis. This phosphatase activity removes the γ-phosphate from dNTPs (generating dNDPs) and subsequently removes the β-phosphate from the formed dNDPs (generating dNMPs), confirmed by the noncleavable α,β-CH2-dGTP and β,γ-CH2-dGTP analogues. We also found that dGTP is the best substrate for the phosphatase, and the dNTP phosphatase activity is sensitive to the reaction medium. In addition, we have revealed that RNA can tune the activity of closely related proteins and give rise to new catalytic functions with subtle differences. Moreover, we have demonstrated in vitro that at the lower dNTP level, this phosphatase can directly inhibit DNA synthesis by dNTP depletion, though the phosphatase activity is 690-fold slower than the polymerase activity. Our observation in vitro suggests a plausible strategy for RNA to directly interfere with DNA polymerase and DNA synthesis in vivo.
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Affiliation(s)
- Qianwei Zhao
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Wen Yang
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Tong Qin
- College of Life Sciences , Sichuan University , Chengdu , China
| | - Zhen Huang
- College of Life Sciences , Sichuan University , Chengdu , China.,Department of Chemistry , Georgia State University , Atlanta , Georgia 30303 , United States
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Rumjanek FD. Osmolyte Induced Tumorigenesis and Metastasis: Interactions With Intrinsically Disordered Proteins. Front Oncol 2018; 8:353. [PMID: 30234016 PMCID: PMC6127622 DOI: 10.3389/fonc.2018.00353] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/10/2018] [Indexed: 01/05/2023] Open
Abstract
In spite of a great deal of work, the biochemical mechanisms underlying tumorigenesis and metastasis are not yet fully understood. Specifically regarding metastasis many authors consider that malignancy is caused by the accumulation of mutations. However, evidence is gathering to show that tumors are composed of heterogeneous cell populations subjected to selective pressures. In this micro evolutionary scenario, intra- and extra-cellular selective pressures will determine which subpopulations of tumor cells will thrive and be able to dissociate from the tumor as autonomous metastatic cells. We propose here that alteration of conformations of transcription factors confer novel non-canonical functions that may induce oncogenesis and metastasis in a mutation independent manner. We argue that the functional plasticity of transcription factors is due to intrinsically disordered domains (IDRs) of proteins. IDRs prevent spontaneous folding of proteins into well-defined three-dimensional structures. Because most transcription factors contain IDRs, each could potentially interact with many ligands. This high degree of functional pleiotropy would then be ultimately responsible for the metastatic phenotype. The conformations of proteins can be altered by chemical chaperones collectively known as osmolytes. Osmolytes are small organic molecules permeable through biological membranes that can accumulate in cells, increase the thermodynamic stability of proteins, modulate enzyme activity and prevent protein aggregation. Thus, by modifying IDRs, osmolytes could subvert the homeostatic regulatory network of cells. Untargeted metabolomic analysis of oral cancer cells showed that those with the greatest metastatic potential contained several osmolytes that were absent in the non-metastatic cells. We hypothesize that high concentrations of osmolytes might promote conformational alterations of transcription factors that favor metastatic behavior. This hypothesis is eminently testable by investigating whether: (a) the intracellular microenvironment of metastatic cells differs from non-metastatic cells and whether osmolytes are responsible for this change and (b) high intracellular concentrations of osmolytes are sufficient to induce structural modifications in regulatory protein so as to establish novel interactive networks that will constitute the metastatic phenotype. Synthetic cell penetrating peptides mimicking IDRs could act as sensitive probes. By exposing the peptides to the microenvironments of living tumor and metastatic tumor cells one should be able to compare the chemical shifts as revealed by spectra obtained by nuclear magnetic resonance (NMR).
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Affiliation(s)
- Franklin D Rumjanek
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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Liu D, Skomorovska Y, Song J, Bowler E, Harris R, Ravasz M, Bai S, Ayati M, Tamai K, Koyuturk M, Yuan X, Wang Z, Wang Y, Ewing R. ELF3 is an antagonist of oncogenic-signalling-induced expression of EMT-TF ZEB1. Cancer Biol Ther 2018; 20:90-100. [PMID: 30148686 PMCID: PMC6292503 DOI: 10.1080/15384047.2018.1507256] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 06/22/2018] [Accepted: 07/29/2018] [Indexed: 12/23/2022] Open
Abstract
Background: Epithelial-to-mesenchymal transition (EMT) is a key step in the transformation of epithelial cells into migratory and invasive tumour cells. Intricate positive and negative regulatory processes regulate EMT. Many oncogenic signalling pathways can induce EMT, but the specific mechanisms of how this occurs, and how this process is controlled are not fully understood. Methods: RNA-Seq analysis, computational analysis of protein networks and large-scale cancer genomics datasets were used to identify ELF3 as a negative regulator of the expression of EMT markers. Western blotting coupled to siRNA as well as analysis of tumour/normal colorectal cancer panels was used to investigate the expression and function of ELF3. Results: RNA-Seq analysis of colorectal cancer cells expressing mutant and wild-type β-catenin and analysis of colorectal cancer cells expressing inducible mutant RAS showed that ELF3 expression is reduced in response to oncogenic signalling and antagonizes Wnt and RAS oncogenic signalling pathways. Analysis of gene-expression patterns across The Cancer Genome Atlas (TCGA) and protein localization in colorectal cancer tumour panels showed that ELF3 expression is anti-correlated with β-catenin and markers of EMT and correlates with better clinical prognosis. Conclusions: ELF3 is a negative regulator of the EMT transcription factor (EMT-TF) ZEB1 through its function as an antagonist of oncogenic signalling.
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Affiliation(s)
- D Liu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Y Skomorovska
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - J Song
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - E Bowler
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - R Harris
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - M Ravasz
- School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - S Bai
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - M Ayati
- Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - K Tamai
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - M Koyuturk
- Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, Ohio, USA
| | - X Yuan
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Z Wang
- School of Medicine, Case Western Reserve University, Cleveland, Ohio, USA
| | - Y Wang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
| | - R.M. Ewing
- School of Biological Sciences, Faculty of Natural and Environmental Sciences, University of Southampton, Southampton, UK
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Abstract
Moonlighting proteins exhibit multiple activities in different cellular compartments, and their abnormal regulation could play an important role in many diseases. To date, many proteins have been identified with moonlighting activity, and more such proteins are being gradually identified. Among the proteins that possess moonlighting activity, several secreted proteins exhibit multiple activities in different cellular locations, such as the extracellular matrix, nucleus, and cytoplasm. While acute inflammation starts rapidly and generally disappears in a few days, chronic inflammation can last for months or years. This is generally because of the failure to eliminate the cause of inflammation, along with repeated exposure to the inflammatory agent. Chronic inflammation is now considered as an overwhelming burden to the general wellbeing of patients and noted as an underlying cause of several diseases. Moonlighting proteins can contribute to the process of chronic inflammation; therefore, it is imperative to overview some proteins that exhibit multiple functions in inflammatory diseases. In this review, we will focus on inflammation, particularly unravelling several well-known secreted proteins with multiple functions in different cellular locations.
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Affiliation(s)
- Joo Heon Yoon
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Korea
| | - Junsun Ryu
- Department of Otolaryngology-Head and Neck Surgery, Center for Thyroid Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Seung Joon Baek
- Laboratory of Signal Transduction, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea.
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Pramanik KK, Nagini S, Singh AK, Mishra P, Kashyap T, Nath N, Alam M, Rana A, Mishra R. Glycogen synthase kinase-3β mediated regulation of matrix metalloproteinase-9 and its involvement in oral squamous cell carcinoma progression and invasion. Cell Oncol (Dordr) 2017; 41:47-60. [PMID: 29134466 DOI: 10.1007/s13402-017-0358-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2017] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Oral squamous cell carcinoma (OSCC)-related deaths mainly result from invasion of the tumor cells into local cervical lymph nodes. It has been reported that progressive basement membrane loss promotes the metastatic and invasive capacities of OSCCs. Matrix metalloproteinase-9 (MMP-9) is known to play a central role in tumor progression and invasion. However, the role of MMP-9 in OSCC invasion has so far remained paradoxical and little is known about its regulation. Here, we aimed to assess MMP-9 expression regulation and its activation by glycogen synthase kinase-3β during human OSCC progression and invasion. METHODS In the present study, 178 human OSCC samples, including 118 fresh samples (18 adjacent normal, 42 noninvasive and 58 invasive tumor samples) and 60 archival human tissue microarray (TMA) tongue cancer samples, were included. mRNA expression, protein expression, MMP-9/-2 activity, protein-protein interaction and Snail, c-Myc, β-catenin and TIMP1 expression were assessed using RT-PCR, immunohistochemistry, Western blotting, co-immunoprecipitation and gelatin zymography analyses, respectively. Wnt5a and LPA mediated MMP-9 regulation was assessed in OCSCC-derived SCC-9 cells exogenously expressing GSK3β (WT) or non phosphoryable GSK3β (S9A). RESULTS We observed a progressive up-regulation/activation of MMP-9 at various stages of oral tumor progression/invasion. Positive correlations were observed between MMP-9 and c-Myc expression, MMP-9 and MMP-2 activity, MMP-9 and TIMP1 expression and MMP-9 activity and TIMP1-MMP-9 interaction. In contrast, a negative correlation between phosphorylated β-catenin and MMP-9 expression was observed. Conversely, we found that in oral tongue SCC MMP-9 expression was positively correlated with inactivation of GSK3 signaling. Finally, we found that Wnt5a and LPA mediated increased MMP-9 and decreased GSK3β activities in tongue SCC-derived SCC-9 cells. MMP-9 regulation by GSK3β was confirmed by using phosphoryable/regulatory GSK3β (WT construct) and not by non-phosphoryable GSK3β (S9A construct). CONCLUSIONS Collectively, our results show that MMP-9 overexpression and activation are important events occurring during OSCC progression/invasion and that this overexpression/activation is regulated by c-Myc, active MMP-2 and inactive GSK3β mediated pathways.
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Affiliation(s)
- Kamdeo K Pramanik
- Centre for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, Jharkhand, -835205, India
| | - Siddavaram Nagini
- Department of Biochemistry and Biotechnology, Faculty of Science, Annamalai University, Annamalainagar, Tamil Nadu, -608 002, India
| | - Abhay K Singh
- Centre for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, Jharkhand, -835205, India
| | - Prajna Mishra
- Centre for Applied Chemistry, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, Jharkhand, -835205, India
| | - Tanushree Kashyap
- Centre for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, Jharkhand, -835205, India
| | - Nidhi Nath
- Centre for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, Jharkhand, -835205, India
| | - Manzar Alam
- Centre for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, Jharkhand, -835205, India
| | - Ajay Rana
- Division of Surgical Oncology, Department of Surgery, College of Medicine, The University of Illinois at Chicago, 840 S. Wood Street, Suite 601 Clinical Sciences Building, MC 958, Chicago, IL, 60612, USA
| | - Rajakishore Mishra
- Centre for Life Sciences, School of Natural Sciences, Central University of Jharkhand, Ratu-Lohardaga Road, Brambe, Ranchi, Jharkhand, -835205, India.
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Extracellular Cytosolic Aspartate Aminotransferase Promotes Axonal Growth and Object Recognition Memory. Neurochem Res 2017; 42:3465-3473. [PMID: 28852933 DOI: 10.1007/s11064-017-2394-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/14/2017] [Accepted: 08/23/2017] [Indexed: 12/12/2022]
Abstract
Previous proteome analysis studies from other groups have shown that cAST might be secreted from neurons and that cAST was detected in human cerebrospinal fluid. However, none of these studies focused on its role or significance. We therefore investigated the role of extracellular cAST for neurons. cAST was detected in conditioned medium from cultured cortical neurons, but not in fresh medium. Recombinant cAST treatment of cortical neurons significantly extended axonal length. Continuous intracerebroventricular administration of recombinant cAST in normal mice for 14 days significantly enhanced object recognition ability. In the brains of those mice, axonal densities and c-Fos expression levels were enhanced, especially in the perirhinal cortex, which mainly relates to object recognition memory. The present study found, for the first time, that extracellular cAST promoted axonal growth function in neurons and activated memory function. These findings indicate a new function of extracellular cAST and may drive the establishment of new therapeutic strategies for cognitive dysfunction. The present study found, for the first time, that extracellular cAST promotes axonal growth in neurons.
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León-Del-Río A, Valadez-Graham V, Gravel RA. Holocarboxylase Synthetase: A Moonlighting Transcriptional Coregulator of Gene Expression and a Cytosolic Regulator of Biotin Utilization. Annu Rev Nutr 2017; 37:207-223. [DOI: 10.1146/annurev-nutr-042617-104653] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Alfonso León-Del-Río
- Programa de Investigación de Cáncer de Mama y Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de Mexico 04500, México
| | - Viviana Valadez-Graham
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos 62250, México
| | - Roy A. Gravel
- Department of Biochemistry & Molecular Biology, the University of Calgary and the Alberta Children's Hospital Research Institute for Child and Maternal Health, Calgary, Alberta T2N 4N1, Canada
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Nasir B, Fatima H, Ahmed M, Phull AR, Ihsan-ul-Haq. Cannabis: A Prehistoric Remedy for the Deficits of Existing and Emerging Anticancer Therapies. JOURNAL OF EXPLORATORY RESEARCH IN PHARMACOLOGY 2017; 2:82-93. [DOI: 10.14218/jerp.2017.00012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Thul PJ, Åkesson L, Wiking M, Mahdessian D, Geladaki A, Ait Blal H, Alm T, Asplund A, Björk L, Breckels LM, Bäckström A, Danielsson F, Fagerberg L, Fall J, Gatto L, Gnann C, Hober S, Hjelmare M, Johansson F, Lee S, Lindskog C, Mulder J, Mulvey CM, Nilsson P, Oksvold P, Rockberg J, Schutten R, Schwenk JM, Sivertsson Å, Sjöstedt E, Skogs M, Stadler C, Sullivan DP, Tegel H, Winsnes C, Zhang C, Zwahlen M, Mardinoglu A, Pontén F, von Feilitzen K, Lilley KS, Uhlén M, Lundberg E. A subcellular map of the human proteome. Science 2017; 356:science.aal3321. [PMID: 28495876 DOI: 10.1126/science.aal3321] [Citation(s) in RCA: 1668] [Impact Index Per Article: 238.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 03/31/2017] [Indexed: 12/13/2022]
Abstract
Resolving the spatial distribution of the human proteome at a subcellular level can greatly increase our understanding of human biology and disease. Here we present a comprehensive image-based map of subcellular protein distribution, the Cell Atlas, built by integrating transcriptomics and antibody-based immunofluorescence microscopy with validation by mass spectrometry. Mapping the in situ localization of 12,003 human proteins at a single-cell level to 30 subcellular structures enabled the definition of the proteomes of 13 major organelles. Exploration of the proteomes revealed single-cell variations in abundance or spatial distribution and localization of about half of the proteins to multiple compartments. This subcellular map can be used to refine existing protein-protein interaction networks and provides an important resource to deconvolute the highly complex architecture of the human cell.
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Affiliation(s)
- Peter J Thul
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lovisa Åkesson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Mikaela Wiking
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Diana Mahdessian
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Aikaterini Geladaki
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Hammou Ait Blal
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Tove Alm
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Anna Asplund
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Lars Björk
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Lisa M Breckels
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Anna Bäckström
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Frida Danielsson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Linn Fagerberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jenny Fall
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Laurent Gatto
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
- Computational Proteomics Unit, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Christian Gnann
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Sophia Hober
- Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Martin Hjelmare
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredric Johansson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Sunjae Lee
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Cecilia Lindskog
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Jan Mulder
- Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden
| | - Claire M Mulvey
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Peter Nilsson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Per Oksvold
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Johan Rockberg
- Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Rutger Schutten
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Jochen M Schwenk
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Åsa Sivertsson
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Evelina Sjöstedt
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Marie Skogs
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Charlotte Stadler
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Devin P Sullivan
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Hanna Tegel
- Department of Proteomics, School of Biotechnology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Casper Winsnes
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Martin Zwahlen
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Adil Mardinoglu
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden
| | - Kalle von Feilitzen
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden
| | - Kathryn S Lilley
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Mathias Uhlén
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden.
| | - Emma Lundberg
- Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-171 21 Stockholm, Sweden.
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