1
|
Sanjeev D, George M, John L, Gopalakrishnan AP, Priyanka P, Mendon S, Yandigeri T, Nisar M, Nisar M, Kanekar S, Balaya RDA, Raju R. Tyr352 as a Predominant Phosphosite in the Understudied Kinase and Molecular Target, HIPK1: Implications for Cancer Therapy. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:111-124. [PMID: 38498023 DOI: 10.1089/omi.2023.0244] [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: 03/19/2024]
Abstract
Homeodomain-interacting protein kinase 1 (HIPK1) is majorly found in the nucleoplasm. HIPK1 is associated with cell proliferation, tumor necrosis factor-mediated cellular apoptosis, transcription regulation, and DNA damage response, and thought to play significant roles in health and common diseases such as cancer. Despite this, HIPK1 remains an understudied molecular target. In the present study, based on a systematic screening and mapping approach, we assembled 424 qualitative and 44 quantitative phosphoproteome datasets with 15 phosphosites in HIPK1 reported across multiple studies. These HIPK1 phosphosites were not currently attributed to any functions. Among them, Tyr352 within the kinase domain was identified as the predominant phosphosite modulated in 22 differential datasets. To analyze the functional association of HIPK1 Tyr352, we first employed a stringent criterion to derive its positively and negatively correlated protein phosphosites. Subsequently, we categorized the correlated phosphosites in known interactors, known/predicted kinases, and substrates of HIPK1, for their prioritized validation. Bioinformatics analysis identified their significant association with biological processes such as the regulation of RNA splicing, DNA-templated transcription, and cellular metabolic processes. HIPK1 Tyr352 was also identified to be upregulated in Her2+ cell lines and a subset of pancreatic and cholangiocarcinoma tissues. These data and the systems biology approach undertaken in the present study serve as a platform to explore the functional role of other phosphosites in HIPK1, and by extension, inform cancer drug discovery and oncotherapy innovation. In all, this study highlights the comprehensive phosphosite map of HIPK1 kinase and the first of its kind phosphosite-centric analysis of HIPK1 kinase based on global-level phosphoproteomics datasets derived from human cellular differential experiments across distinct experimental conditions.
Collapse
Affiliation(s)
- Diya Sanjeev
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | - Mejo George
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | - Levin John
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | | | - Pahal Priyanka
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | - Spoorthi Mendon
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | - Tanuja Yandigeri
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | - Mahammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | - Muhammad Nisar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | - Saptami Kanekar
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| | | | - Rajesh Raju
- Centre for Integrative Omics Data Science (CIODS), Yenepoya (Deemed-to-be University), Mangalore, Karnataka, India
| |
Collapse
|
2
|
Capaci V, Arrigoni G, Monasta L, Aloisio M, Rocca G, Di Lorenzo G, Licastro D, Romano F, Ricci G, Ura B. Phospho-DIGE Identified Phosphoproteins Involved in Pathways Related to Tumour Growth in Endometrial Cancer. Int J Mol Sci 2023; 24:11987. [PMID: 37569364 PMCID: PMC10419128 DOI: 10.3390/ijms241511987] [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: 07/05/2023] [Revised: 07/21/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Endometrial cancer (EC) is the most common gynecologic malignancy of the endometrium. This study focuses on EC and normal endometrium phosphoproteome to identify differentially phosphorylated proteins involved in tumorigenic signalling pathways which induce cancer growth. We obtained tissue samples from 8 types I EC at tumour stage 1 and 8 normal endometria. We analyzed the phosphoproteome by two-dimensional differential gel electrophoresis (2D-DIGE), combined with immobilized metal affinity chromatography (IMAC) and mass spectrometry for protein and phosphopeptide identification. Quantities of 34 phosphoproteins enriched by the IMAC approach were significantly different in the EC compared to the endometrium. Validation using Western blotting analysis on 13 patients with type I EC at tumour stage 1 and 13 endometria samples confirmed the altered abundance of HBB, CKB, LDHB, and HSPB1. Three EC samples were used for in-depth identification of phosphoproteins by LC-MS/MS analysis. Bioinformatic analysis revealed several tumorigenic signalling pathways. Our study highlights the involvement of the phosphoproteome in EC tumour growth. Further studies are needed to understand the role of phosphorylation in EC. Our data shed light on mechanisms that still need to be ascertained but could open the path to a new class of drugs that could hinder EC growth.
Collapse
Affiliation(s)
- Valeria Capaci
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (B.U.)
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (G.A.); (G.R.)
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
- CRIBI Biotechnology Center, University of Padova, 35131 Padova, Italy
| | - Lorenzo Monasta
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (B.U.)
| | - Michelangelo Aloisio
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (B.U.)
| | - Giulia Rocca
- Department of Biomedical Sciences, University of Padova, 35131 Padova, Italy; (G.A.); (G.R.)
- Proteomics Center, University of Padova and Azienda Ospedaliera di Padova, 35131 Padova, Italy
| | - Giovanni Di Lorenzo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (B.U.)
| | | | - Federico Romano
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (B.U.)
| | - Giuseppe Ricci
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (B.U.)
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34129 Trieste, Italy
| | - Blendi Ura
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, 34137 Trieste, Italy; (V.C.); (M.A.); (G.D.L.); (F.R.); (G.R.); (B.U.)
| |
Collapse
|
3
|
Li Y, Zhu J, Yu Z, Li H, Jin X. The role of Lamin B2 in human diseases. Gene 2023; 870:147423. [PMID: 37044185 DOI: 10.1016/j.gene.2023.147423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 04/14/2023]
Abstract
Lamin B2 (LMNB2), on the inner side of the nuclear envelope, constitutes the nuclear skeleton by connecting with other nuclear proteins. LMNB2 is involved in a wide range of nuclear functions, including DNA replication and stability, regulation of chromatin, and nuclear stiffness. Moreover, LMNB2 regulates several cellular processes, such as tissue development, cell cycle, cellular proliferation and apoptosis, chromatin localization and stability, and DNA methylation. Besides, the influence of abnormal expression and mutations of LMNB2 has been gradually discovered in cancers and laminopathies. Therefore, this review summarizes the recent advances of LMNB2-associated biological roles in physiological or pathological conditions, with a particular emphasis on cancers and laminopathies, as well as the potential mechanism of LMNB2 in related cancers.
Collapse
Affiliation(s)
- Yuxuan Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Jie Zhu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Zongdong Yu
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China
| | - Hong Li
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
| | - Xiaofeng Jin
- Department of Hepatobiliary and Pancreatic Surgery, Ningbo Medical Center of LiHuiLi Hospital, Ningbo University, Ningbo, Zhejiang 315040, P.R. China; Department of Biochemistry and Molecular Biology, Zhejiang Key Laboratory of Pathophysiology, Health Science Center, Ningbo University, Ningbo, Zhejiang 315211, P.R. China.
| |
Collapse
|
4
|
Kannan S, Souchelnytskyi S. The Exposure to Human Breast Cancer Cells Altered 14 Post-Translational Modifications of Human Serum Albumin. EJIFCC 2022; 33:295-308. [PMID: 36605305 PMCID: PMC9768621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Purpose Serum albumin is in contact with practically all cells in the human body, including tumor cells in cancer patients. The purpose of this study was to explore whether cancer cells affect post-translational modifications (PTMs) of albumin. Material and methods Mass spectrometry was used to identify the PTMs. Purified human serum albumin was incubated with human breast cancer cells MDA-MB-231, MDA-MB-468, MCF7, or kept in water or in cell culture media. PTMs which were affected upon exposure of the albumin to cancer cells were identified. Three-dimensional analysis was performed to locate PTMs in albumin. Results We report here that an exposure to human breast cancer cells affected post-translational modifications (PTMs) of 14 peptides of human serum albumin (HSA). PTMs at 8 peptides were observed upon exposure of HSA to metastatic MDA-MB-231 and MDA-MB-468 breast cancer cells. PTMs at another 6 peptides were lost in MDA-MB-231 and MDA-MB-468 cells, while these 6 PTMs were observed in HSA exposed to conditionally tumorigenic MCF7 cells, or in HSA kept in water or a cell culture medium. Cancer cell altered phosphorylation, deamidation followed by methylation, acetylation, myristylation, palmitoylation, methylation, cysteine persulfide, and S-6-FMN cysteine modifications were detected in HSA. These PTMs locate predominantly in IB and IIA domains of HSA. Three-dimensional analysis showed that this region corresponds to the lipid-binding site and Sudlow's site 1. Conclusion Data reported here show that 14 PTMs of human serum albumin can be modified upon its exposure to human breast cancer cells.
Collapse
Affiliation(s)
- Surya Kannan
- College of Medicine, QU Health, Qatar University, Doha, Qatar
| | - Serhiy Souchelnytskyi
- Oranta Cancer Diagnostics AB, Uppsala, Sweden,Lviv National University, Lviv, Ukraine,Corresponding author: Serhiy Souchelnytskyi Oranta Cancer Diagnostics AB Uppsala, 75263 Sweden E-mail:
| |
Collapse
|
5
|
Lanz TV, Brewer RC, Ho PP, Moon JS, Jude KM, Fernandez D, Fernandes RA, Gomez AM, Nadj GS, Bartley CM, Schubert RD, Hawes IA, Vazquez SE, Iyer M, Zuchero JB, Teegen B, Dunn JE, Lock CB, Kipp LB, Cotham VC, Ueberheide BM, Aftab BT, Anderson MS, DeRisi JL, Wilson MR, Bashford-Rogers RJ, Platten M, Garcia KC, Steinman L, Robinson WH. Clonally expanded B cells in multiple sclerosis bind EBV EBNA1 and GlialCAM. Nature 2022; 603:321-327. [PMID: 35073561 PMCID: PMC9382663 DOI: 10.1038/s41586-022-04432-7] [Citation(s) in RCA: 341] [Impact Index Per Article: 170.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 01/14/2022] [Indexed: 11/09/2022]
Abstract
Multiple sclerosis (MS) is a heterogenous autoimmune disease in which autoreactive lymphocytes attack the myelin sheath of the central nervous system. B lymphocytes in the cerebrospinal fluid (CSF) of patients with MS contribute to inflammation and secrete oligoclonal immunoglobulins1,2. Epstein-Barr virus (EBV) infection has been epidemiologically linked to MS, but its pathological role remains unclear3. Here we demonstrate high-affinity molecular mimicry between the EBV transcription factor EBV nuclear antigen 1 (EBNA1) and the central nervous system protein glial cell adhesion molecule (GlialCAM) and provide structural and in vivo functional evidence for its relevance. A cross-reactive CSF-derived antibody was initially identified by single-cell sequencing of the paired-chain B cell repertoire of MS blood and CSF, followed by protein microarray-based testing of recombinantly expressed CSF-derived antibodies against MS-associated viruses. Sequence analysis, affinity measurements and the crystal structure of the EBNA1-peptide epitope in complex with the autoreactive Fab fragment enabled tracking of the development of the naive EBNA1-restricted antibody to a mature EBNA1-GlialCAM cross-reactive antibody. Molecular mimicry is facilitated by a post-translational modification of GlialCAM. EBNA1 immunization exacerbates disease in a mouse model of MS, and anti-EBNA1 and anti-GlialCAM antibodies are prevalent in patients with MS. Our results provide a mechanistic link for the association between MS and EBV and could guide the development of new MS therapies.
Collapse
Affiliation(s)
- Tobias V. Lanz
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States,Department of Neurology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany,Department of Neurology and National Center for Tumor Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany
| | - R. Camille Brewer
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Peggy P. Ho
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Jae-Seung Moon
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Kevin M. Jude
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Daniel Fernandez
- Stanford ChEM-H Institute, Macromolecular Structure Knowledge Center, 290 Jane Stanford Way, Stanford, CA 94305, United States
| | - Ricardo A. Fernandes
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Alejandro M. Gomez
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Gabriel-Stefan Nadj
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States
| | - Christopher M. Bartley
- Hanna H. Gray Fellow, Howard Hughes Medical Institute, 4000 Jones Bridge Rd, Chevy Chase, MD 20815, United States,Weill Institute for Neurosciences, Department of Psychiatry and Behavioral Sciences, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Ryan D. Schubert
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Isobel A. Hawes
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Sara E. Vazquez
- Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, United States
| | - Manasi Iyer
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welsh Road, Stanford, CA, United States
| | - J. Bradley Zuchero
- Department of Neurosurgery, Stanford University School of Medicine, 1201 Welsh Road, Stanford, CA, United States
| | - Bianca Teegen
- Institute of Experimental Immunology, Euroimmun AG, Seekamp 31, 23560 Lübeck, Germany
| | - Jeffrey E. Dunn
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, 213 Quarry Road, Stanford, CA, United States
| | - Christopher B. Lock
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, 213 Quarry Road, Stanford, CA, United States
| | - Lucas B. Kipp
- Division of Neuroimmunology, Department of Neurology and Neurological Sciences, Stanford University School of Medicine, 213 Quarry Road, Stanford, CA, United States
| | - Victoria C. Cotham
- Department of Biochemistry and Molecular Pharmacology, NYU Perlmutter Cancer Center, and NYU Langone Health Proteomics Laboratory, Division of Advanced Research Technologies, NYU School of Medicine, 430 East 29th St, New York, NY, 10016, United States
| | - Beatrix M. Ueberheide
- Department of Biochemistry and Molecular Pharmacology, NYU Perlmutter Cancer Center, and NYU Langone Health Proteomics Laboratory, Division of Advanced Research Technologies, NYU School of Medicine, 430 East 29th St, New York, NY, 10016, United States
| | - Blake T. Aftab
- Preclinical Science and Translational Medicine, Atara Biotherapeutics, 611 Gateway Blvd South San Francisco, CA 94080, United States
| | - Mark S. Anderson
- Department of Medicine, Diabetes Center, University of California San Francisco, 513 Parnassus Ave, San Francisco, CA 94143, United States
| | - Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, United States,Chan Zuckerberg Biohub, University of California San Francisco, 499 Illinois Street, San Francisco, CA 94158, United States
| | - Michael R. Wilson
- Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, 675 Nelson Rising Ln San Francisco, CA 94158, San Francisco, United States
| | - Rachael J.M. Bashford-Rogers
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Dr, Headington, Oxford OX3 7BN, United Kingdom
| | - Michael Platten
- Department of Neurology, Mannheim Center for Translational Neurosciences (MCTN), Medical Faculty Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany,Department of Neurology and National Center for Tumor Diseases, University Hospital Heidelberg, Im Neuenheimer Feld 400, 69120 Heidelberg, Germany,DKTK Clinical Cooperation Unit Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - K. Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - Lawrence Steinman
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Beckman Center for Molecular Medicine, 279 Campus Drive, Stanford, CA 94305, United States
| | - William H. Robinson
- Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States, and the Geriatric Research, Education, and Clinical Centers (GRECC), VA Palo Alto Health Care System, 3801 Miranda Ave, Palo Alto, CA 94304, United States,Corresponding Author: William H. Robinson, Division of Immunology and Rheumatology, Department of Medicine, Stanford University School of Medicine, 269 Campus Drive, Stanford, CA 94305, United States,
| |
Collapse
|
6
|
Phosphorylated Osteopontin Secreted from Cancer Cells Induces Cancer Cell Motility. Biomolecules 2021; 11:biom11091323. [PMID: 34572536 PMCID: PMC8470647 DOI: 10.3390/biom11091323] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/30/2021] [Accepted: 09/04/2021] [Indexed: 12/22/2022] Open
Abstract
Osteopontin (OPN) plays a pivotal role in cancer cell invasion and metastasis. Although OPN has a large number of phosphorylation sites, the functional significance of OPN phosphorylation in cancer cell motility remains unclear. In this study, we attempted to investigate whether phosphorylated OPN secreted from cancer cells affect cancer cell migration. Quantitative PCR and Western blot analyses revealed that MDA-MB435S, A549, and H460 cells highly expressed OPN, whereas the OPN expression levels in H358, MIAPaca-2, and Panc-1 cells were quite low or were not detected. Compared with the cancer cell lines with a low OPN expression, the high OPN-expressing cancer cell lines displayed a higher cell migration, and the cell migration was suppressed by the anti-OPN antibody. This was confirmed by the OPN overexpression in H358 cancer cells with a low endogenous OPN. Phos-tag ELISA showed that phosphorylated OPN was abundant in the cell culture media of A549 and H460 cells, but not in those of MDA-MB435S cells. Moreover, the A549 and H460 cell culture media, as well as the MDA-MB435S cell culture media with a kinase treatment increased cancer cell motility, both of which were abrogated by phosphatase treatment or anti-OPN antibodies. These results suggest that phosphorylated OPN secreted from cancer cells regulates cancer cell motility.
Collapse
|
7
|
Shimakura K, Sato K, Mitsui S, Ono S, Otomo A, Hadano S. The N-terminal intrinsically disordered region mediates intracellular localization and self-oligomerization of ALS2. Biochem Biophys Res Commun 2021; 569:106-111. [PMID: 34243065 DOI: 10.1016/j.bbrc.2021.06.095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 12/31/2022]
Abstract
ALS2, a product of the causative gene for familial amyotrophic lateral sclerosis (ALS) type 2, plays a pivotal role in the regulation of endosome dynamics by activating small GTPase Rab5 via its intrinsic guanine nucleotide-exchange factor activity. Previously, we have reported that the N-terminal region of ALS2 has crucial roles in its endosomal localization and self-oligomerization, both of which are indispensable for the cellular function of ALS2. The N-terminus of ALS2 contains the regulator of chromosome condensation 1-like domain (RLD), which is predicted to form a seven-bladed β-propeller structure. Interestingly, the RLD is interrupted by the intrinsically disordered region (IDR), within which there are several amino acid residues which undergo phosphorylation. In this study, we sought to investigate as to whether and how the IDR as well as phosphorylation at either Ser483, Ser492 or Thr510 affect the intracellular localization and self-oligomerization of ALS2. All phospho- and dephospho-mimetic ALS2 mutants that were transiently expressed in HeLa cells were diffusely distributed throughout the cytosol with a partial localization to early endosomes. When expressed under Rac1-activating conditions, these mutants were localized to membrane ruffles as well as enlarged endosomes. Further, gel-filtration analysis revealed that these mutants primarily existed as a tetramer in cells. However, all these phenotypes were indistinguishable from those of wild-type ALS2. On the other hand, IDR-deleted ALS2 mutant was exclusively present in perinuclear aggregates colocalizing with the autophagy-related protein SQSTM1. Moreover, IDR-deleted ALS2 mutant formed an abnormally high molecular weight complex compared to wild-type ALS2. These results indicate that the IDR of ALS2 plays a crucial role not only in the regulation of intracellular localization but also in the self-oligomerization of ALS2 in cells, whereas phosphorylation of certain residues within the IDR exerts limited effects on such phenotypes.
Collapse
Affiliation(s)
- Kento Shimakura
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kai Sato
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Shun Mitsui
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Suzuka Ono
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Asako Otomo
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan; The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, 259-1193, Japan
| | - Shinji Hadano
- Molecular Neuropathobiology Laboratory, Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan; Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan; The Institute of Medical Sciences, Tokai University, Isehara, Kanagawa, 259-1193, Japan; Research Center for Brain and Nervous Diseases, Tokai University Graduate School of Medicine, Isehara, Kanagawa, 259-1193, Japan.
| |
Collapse
|
8
|
A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression. Cell Rep 2021; 35:109129. [PMID: 34010649 DOI: 10.1016/j.celrep.2021.109129] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 02/26/2021] [Accepted: 04/22/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondria are highly dynamic organelles subjected to fission and fusion events. During mitosis, mitochondrial fission ensures equal distribution of mitochondria to daughter cells. If and how this process can actively drive mitotic progression remains largely unknown. Here, we discover a pathway linking mitochondrial fission to mitotic progression in mammalian cells. The mitochondrial fission factor (MFF), the main mitochondrial receptor for the Dynamin-related protein 1 (DRP1), is directly phosphorylated by Protein Kinase D (PKD) specifically during mitosis. PKD-dependent MFF phosphorylation is required and sufficient for mitochondrial fission in mitotic but not in interphasic cells. Phosphorylation of MFF is crucial for chromosome segregation and promotes cell survival by inhibiting adaptation of the mitotic checkpoint. Thus, PKD/MFF-dependent mitochondrial fission is critical for the maintenance of genome integrity during cell division.
Collapse
|
9
|
Wang L, Sparks-Wallace A, Casteel JL, Howell MEA, Ning S. Algorithm-Based Meta-Analysis Reveals the Mechanistic Interaction of the Tumor Suppressor LIMD1 With Non-Small-Cell Lung Carcinoma. Front Oncol 2021; 11:632638. [PMID: 33869018 PMCID: PMC8044451 DOI: 10.3389/fonc.2021.632638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/15/2021] [Indexed: 12/25/2022] Open
Abstract
Non-small-cell lung carcinoma (NSCLC) is the major type of lung cancer, which is among the leading causes of cancer-related deaths worldwide. LIMD1 was previously identified as a tumor suppressor in lung cancer, but their detailed interaction in this setting remains unclear. In this study, we have carried out multiple genome-wide bioinformatic analyses for a comprehensive understanding of LIMD1 in NSCLC, using various online algorithm platforms that have been built for mega databases derived from both clinical and cell line samples. Our results indicate that LIMD1 expression level is significantly downregulated at both mRNA and protein levels in both lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC), with a considerable contribution from its promoter methylation rather than its gene mutations. The Limd1 gene undergoes mutation only at a low rate in NSCLC (0.712%). We have further identified LIMD1-associated molecular signatures in NSCLC, including its natural antisense long non-coding RNA LIMD1-AS1 and a pool of membrane trafficking regulators. We have also identified a subgroup of tumor-infiltrating lymphocytes, especially neutrophils, whose tumor infiltration levels significantly correlate with LIMD1 level in both LUAD and LUSC. However, a significant correlation of LIMD1 with a subset of immune regulatory molecules, such as IL6R and TAP1, was only found in LUAD. Regarding the clinical outcomes, LIMD1 expression level only significantly correlates with the survival of LUAD (p<0.01) but not with that of LUSC (p>0.1) patients. These findings indicate that LIMD1 plays a survival role in LUAD patients at least by acting as an immune regulatory protein. To further understand the mechanisms underlying the tumor-suppressing function of LIMD1 in NSCLC, we show that LIMD1 downregulation remarkably correlates with the deregulation of multiple pathways that play decisive roles in the oncogenesis of NSCLC, especially those mediated by EGFR, KRAS, PIK3CA, Keap1, and p63, in both LUAD and LUSC, and those mediated by p53 and CDKN2A only in LUAD. This study has disclosed that LIMD1 can serve as a survival prognostic marker for LUAD patients and provides mechanistic insights into the interaction of LIMD1 with NSCLC, which provide valuable information for clinical applications.
Collapse
Affiliation(s)
- Ling Wang
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Ayrianna Sparks-Wallace
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Jared L Casteel
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Mary E A Howell
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| | - Shunbin Ning
- Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States.,Center of Excellence for Inflammation, Infectious Diseases and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson City, TN, United States
| |
Collapse
|
10
|
Rezcallah MC, Al-Mazi T, Ammit AJ. Cataloguing the phosphorylation sites of tristetraprolin (TTP): Functional implications for inflammatory diseases. Cell Signal 2020; 78:109868. [PMID: 33276085 DOI: 10.1016/j.cellsig.2020.109868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/29/2020] [Accepted: 11/29/2020] [Indexed: 01/10/2023]
Abstract
Tristetraprolin (TTP) is a destabilizing mRNA binding protein known to regulate gene expression of a wide variety of targets, including those that control inflammation. TTP expression, regulation and function is controlled by phosphorylation. While the importance of key serine (S) sites (S52 and S178 in mice and S186 in humans) has been recognized, other sites on the hyperphosphorylated TTP protein have more recently emerged as playing an important role in regulating cellular signalling and downstream functions of TTP. In order to propel investigation of TTP and fully exploit its potential as a drug target in inflammatory disease, this review will catalogue TTP phosphorylation sites in both the murine and human TTP protein, the known and unknown roles and functions of these sites, the kinases and phosphatases that act upon TTP and overview methodological approaches to increase our knowledge of this important protein regulated by phosphorylation.
Collapse
Affiliation(s)
- Maria C Rezcallah
- Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, NSW, Australia; School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Trisha Al-Mazi
- Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, NSW, Australia; School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia
| | - Alaina J Ammit
- Woolcock Emphysema Centre, Woolcock Institute of Medical Research, University of Sydney, NSW, Australia; School of Life Sciences, Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia.
| |
Collapse
|
11
|
Creeden JF, Alganem K, Imami AS, Henkel ND, Brunicardi FC, Liu SH, Shukla R, Tomar T, Naji F, McCullumsmith RE. Emerging Kinase Therapeutic Targets in Pancreatic Ductal Adenocarcinoma and Pancreatic Cancer Desmoplasia. Int J Mol Sci 2020; 21:ijms21228823. [PMID: 33233470 PMCID: PMC7700673 DOI: 10.3390/ijms21228823] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
Kinase drug discovery represents an active area of therapeutic research, with previous pharmaceutical success improving patient outcomes across a wide variety of human diseases. In pancreatic ductal adenocarcinoma (PDAC), innovative pharmaceutical strategies such as kinase targeting have been unable to appreciably increase patient survival. This may be due, in part, to unchecked desmoplastic reactions to pancreatic tumors. Desmoplastic stroma enhances tumor development and progression while simultaneously restricting drug delivery to the tumor cells it protects. Emerging evidence indicates that many of the pathologic fibrotic processes directly or indirectly supporting desmoplasia may be driven by targetable protein tyrosine kinases such as Fyn-related kinase (FRK); B lymphoid kinase (BLK); hemopoietic cell kinase (HCK); ABL proto-oncogene 2 kinase (ABL2); discoidin domain receptor 1 kinase (DDR1); Lck/Yes-related novel kinase (LYN); ephrin receptor A8 kinase (EPHA8); FYN proto-oncogene kinase (FYN); lymphocyte cell-specific kinase (LCK); tec protein kinase (TEC). Herein, we review literature related to these kinases and posit signaling networks, mechanisms, and biochemical relationships by which this group may contribute to PDAC tumor growth and desmoplasia.
Collapse
Affiliation(s)
- Justin F. Creeden
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 6038, USA
- Correspondence: ; Tel.: +1-419-383-6474
| | - Khaled Alganem
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - Ali S. Imami
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - Nicholas D. Henkel
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - F. Charles Brunicardi
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 6038, USA
| | - Shi-He Liu
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 6038, USA
| | - Rammohan Shukla
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
| | - Tushar Tomar
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Faris Naji
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Robert E. McCullumsmith
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (N.D.H.); (R.S.); (R.E.M.)
- Neurosciences Institute, ProMedica, Toledo, OH 6038, USA
| |
Collapse
|
12
|
Creeden JF, Alganem K, Imami AS, Brunicardi FC, Liu SH, Shukla R, Tomar T, Naji F, McCullumsmith RE. Kinome Array Profiling of Patient-Derived Pancreatic Ductal Adenocarcinoma Identifies Differentially Active Protein Tyrosine Kinases. Int J Mol Sci 2020; 21:ijms21228679. [PMID: 33213062 PMCID: PMC7698519 DOI: 10.3390/ijms21228679] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 11/12/2020] [Accepted: 11/14/2020] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer remains one of the most difficult malignancies to treat. Minimal improvements in patient outcomes and persistently abysmal patient survival rates underscore the great need for new treatment strategies. Currently, there is intense interest in therapeutic strategies that target tyrosine protein kinases. Here, we employed kinome arrays and bioinformatic pipelines capable of identifying differentially active protein tyrosine kinases in different patient-derived pancreatic ductal adenocarcinoma (PDAC) cell lines and wild-type pancreatic tissue to investigate the unique kinomic networks of PDAC samples and posit novel target kinases for pancreatic cancer therapy. Consistent with previously described reports, the resultant peptide-based kinome array profiles identified increased protein tyrosine kinase activity in pancreatic cancer for the following kinases: epidermal growth factor receptor (EGFR), fms related receptor tyrosine kinase 4/vascular endothelial growth factor receptor 3 (FLT4/VEGFR-3), insulin receptor (INSR), ephrin receptor A2 (EPHA2), platelet derived growth factor receptor alpha (PDGFRA), SRC proto-oncogene kinase (SRC), and tyrosine kinase non receptor 2 (TNK2). Furthermore, this study identified increased activity for protein tyrosine kinases with limited prior evidence of differential activity in pancreatic cancer. These protein tyrosine kinases include B lymphoid kinase (BLK), Fyn-related kinase (FRK), Lck/Yes-related novel kinase (LYN), FYN proto-oncogene kinase (FYN), lymphocyte cell-specific kinase (LCK), tec protein kinase (TEC), hemopoietic cell kinase (HCK), ABL proto-oncogene 2 kinase (ABL2), discoidin domain receptor 1 kinase (DDR1), and ephrin receptor A8 kinase (EPHA8). Together, these results support the utility of peptide array kinomic analyses in the generation of potential candidate kinases for future pancreatic cancer therapeutic development.
Collapse
Affiliation(s)
- Justin F. Creeden
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
- Correspondence: ; Tel.: +1-419-383-6474
| | - Khaled Alganem
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - Ali S. Imami
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - F. Charles Brunicardi
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Shi-He Liu
- Department of Cancer Biology, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (F.C.B.); (S.-H.L.)
- Department of Surgery, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA
| | - Rammohan Shukla
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
| | - Tushar Tomar
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Faris Naji
- PamGene International BV, 5200 BJ’s-Hertogenbosch, The Netherlands; (T.T.); (F.N.)
| | - Robert E. McCullumsmith
- Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH 43614, USA; (K.A.); (A.S.I.); (R.S.); (R.E.M.)
- Neurosciences Institute, ProMedica, Toledo, OH 43606, USA
| |
Collapse
|
13
|
Park KC, Paluncic J, Kovacevic Z, Richardson DR. Pharmacological targeting and the diverse functions of the metastasis suppressor, NDRG1, in cancer. Free Radic Biol Med 2020; 157:154-175. [PMID: 31132412 DOI: 10.1016/j.freeradbiomed.2019.05.020] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/24/2019] [Accepted: 05/16/2019] [Indexed: 12/18/2022]
Abstract
N-myc downstream regulated gene-1 (NDRG1) is a potent metastasis suppressor that is regulated by hypoxia, metal ions including iron, the free radical nitric oxide (NO.), and various stress stimuli. This intriguing molecule exhibits diverse functions in cancer, inhibiting epithelial-mesenchymal transition (EMT), cell migration and angiogenesis by modulation of a plethora of oncogenes via cellular signaling. Thus, pharmacological targeting of NDRG1 signaling in cancer is a promising therapeutic strategy. Of note, novel anti-tumor agents of the di-2-pyridylketone thiosemicarbazone series, which exert the "double punch" mechanism by binding metal ions to form redox-active complexes, have been demonstrated to markedly up-regulate NDRG1 expression in cancer cells. This review describes the mechanisms underlying NDRG1 modulation by the thiosemicarbazones and the diverse effects NDRG1 exerts in cancer. As a major induction mechanism, iron depletion appears critical, with NO. also inducing NDRG1 through its ability to bind iron and generate dinitrosyl-dithiol iron complexes, which are then effluxed from cells. Apart from its potent anti-metastatic role, several studies have reported a pro-oncogenic role of NDRG1 in a number of cancer-types. Hence, it has been suggested that NDRG1 plays pleiotropic roles depending on the cancer-type. The molecular mechanism(s) underlying NDRG1 pleiotropy remain elusive, but are linked to differential regulation of WNT signaling and potentially differential interaction with the tumor suppressor, PTEN. This review discusses NDRG1 induction mechanisms by metal ions and NO. and both the anti- and possible pro-oncogenic functions of NDRG1 in multiple cancer-types and compares the opposite effects this protein exerts on cancer progression.
Collapse
Affiliation(s)
- Kyung Chan Park
- Molecular Pharmacology and Pathology Program, Discipline of Pathology and Bosch Institute, Medical Foundation Building (K25), The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Jasmina Paluncic
- Molecular Pharmacology and Pathology Program, Discipline of Pathology and Bosch Institute, Medical Foundation Building (K25), The University of Sydney, Sydney, New South Wales, 2006, Australia
| | - Zaklina Kovacevic
- Molecular Pharmacology and Pathology Program, Discipline of Pathology and Bosch Institute, Medical Foundation Building (K25), The University of Sydney, Sydney, New South Wales, 2006, Australia.
| | - Des R Richardson
- Molecular Pharmacology and Pathology Program, Discipline of Pathology and Bosch Institute, Medical Foundation Building (K25), The University of Sydney, Sydney, New South Wales, 2006, Australia.
| |
Collapse
|
14
|
Zmuda F, Chamberlain LH. Regulatory effects of post-translational modifications on zDHHC S-acyltransferases. J Biol Chem 2020; 295:14640-14652. [PMID: 32817054 PMCID: PMC7586229 DOI: 10.1074/jbc.rev120.014717] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/15/2020] [Indexed: 01/09/2023] Open
Abstract
The human zDHHC S-acyltransferase family comprises 23 enzymes that mediate the S-acylation of a multitude of cellular proteins, including channels, receptors, transporters, signaling molecules, scaffolds, and chaperones. This reversible post-transitional modification (PTM) involves the attachment of a fatty acyl chain, usually derived from palmitoyl-CoA, to specific cysteine residues on target proteins, which affects their stability, localization, and function. These outcomes are essential to control many processes, including synaptic transmission and plasticity, cell growth and differentiation, and infectivity of viruses and other pathogens. Given the physiological importance of S-acylation, it is unsurprising that perturbations in this process, including mutations in ZDHHC genes, have been linked to different neurological pathologies and cancers, and there is growing interest in zDHHC enzymes as novel drug targets. Although zDHHC enzymes control a diverse array of cellular processes and are associated with major disorders, our understanding of these enzymes is surprisingly incomplete, particularly with regard to the regulatory mechanisms controlling these enzymes. However, there is growing evidence highlighting the role of different PTMs in this process. In this review, we discuss how PTMs, including phosphorylation, S-acylation, and ubiquitination, affect the stability, localization, and function of zDHHC enzymes and speculate on possible effects of PTMs that have emerged from larger screening studies. Developing a better understanding of the regulatory effects of PTMs on zDHHC enzymes will provide new insight into the intracellular dynamics of S-acylation and may also highlight novel approaches to modulate S-acylation for clinical gain.
Collapse
Affiliation(s)
- Filip Zmuda
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
| | - Luke H Chamberlain
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, United Kingdom.
| |
Collapse
|
15
|
Meleady P, Abdul Rahman R, Henry M, Moriarty M, Clynes M. Proteomic analysis of pancreatic ductal adenocarcinoma. Expert Rev Proteomics 2020; 17:453-467. [PMID: 32755290 DOI: 10.1080/14789450.2020.1803743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Pancreatic ductal adenocarcinoma (PDAC), which represents approximately 80% of all pancreatic cancers, is a highly aggressive malignant disease and one of the most lethal among all cancers. Overall, the 5-year survival rate among all pancreatic cancer patients is less than 9%; these rates have shown little change over the past 30 years. A more comprehensive understanding of the molecular mechanisms underlying this complex disease is crucial to the development of new diagnostic tools for early detection and disease monitoring, as well as to identify new and more effective therapeutics to improve patient outcomes. AREA COVERED We summarize recent advances in proteomic strategies and mass spectrometry to identify new biomarkers for early detection and monitoring of disease progression, predict response to therapy, and to identify novel proteins that have the potential to be 'druggable' therapeutic targets. An overview of proteomic studies that have been conducted to further our mechanistic understanding of metastasis and chemotherapy resistance in PDAC disease progression will also be discussed. EXPERT COMMENTARY The results from these PDAC proteomic studies on a variety of PDAC sample types (e.g., blood, tissue, cell lines, exosomes, etc.) provide great promise of having a significant clinical impact and improving patient outcomes.
Collapse
Affiliation(s)
- Paula Meleady
- National Institute for Cellular Biotechnology, Dublin City University , Dublin, Ireland
| | - Rozana Abdul Rahman
- St. Vincent's University Hospital , Dublin, Ireland.,St. Luke's Hospital , Dublin, Ireland
| | - Michael Henry
- National Institute for Cellular Biotechnology, Dublin City University , Dublin, Ireland
| | - Michael Moriarty
- National Institute for Cellular Biotechnology, Dublin City University , Dublin, Ireland.,St. Luke's Hospital , Dublin, Ireland
| | - Martin Clynes
- National Institute for Cellular Biotechnology, Dublin City University , Dublin, Ireland
| |
Collapse
|
16
|
de Oliveira G, Paccielli Freire P, Santiloni Cury S, de Moraes D, Santos Oliveira J, Dal-Pai-Silva M, do Reis PP, Francisco Carvalho R. An Integrated Meta-Analysis of Secretome and Proteome Identify Potential Biomarkers of Pancreatic Ductal Adenocarcinoma. Cancers (Basel) 2020; 12:E716. [PMID: 32197468 PMCID: PMC7140071 DOI: 10.3390/cancers12030716] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/10/2020] [Accepted: 03/12/2020] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is extremely aggressive, has an unfavorable prognosis, and there are no biomarkers for early detection of the disease or identification of individuals at high risk for morbidity or mortality. The cellular and molecular complexity of PDAC leads to inconsistences in clinical validations of many proteins that have been evaluated as prognostic biomarkers of the disease. The tumor secretome, a potential source of biomarkers in PDAC, plays a crucial role in cell proliferation and metastasis, as well as in resistance to treatments, which together contribute to a worse clinical outcome. The massive amount of proteomic data from pancreatic cancer that has been generated from previous studies can be integrated and explored to uncover secreted proteins relevant to the diagnosis and prognosis of the disease. The present study aimed to perform an integrated meta-analysis of PDAC proteome and secretome public data to identify potential biomarkers of the disease. Our meta-analysis combined mass spectrometry data obtained from two systematic reviews of the pancreatic cancer literature, which independently selected 20 studies of the secretome and 35 of the proteome. Next, we predicted the secreted proteins using seven in silico tools or databases, which identified 39 secreted proteins shared between the secretome and proteome data. Notably, the expression of 31 genes of these secretome-related proteins was upregulated in PDAC samples from The Cancer Genome Atlas (TCGA) when compared to control samples from TCGA and The Genotype-Tissue Expression (GTEx). The prognostic value of these 39 secreted proteins in predicting survival outcome was confirmed using gene expression data from four PDAC datasets (validation set). The gene expression of these secreted proteins was able to distinguish high- and low-survival patients in nine additional tumor types from TCGA, demonstrating that deregulation of these secreted proteins may also contribute to the prognosis in multiple cancers types. Finally, we compared the prognostic value of the identified secreted proteins in PDAC biomarkers studies from the literature. This analysis revealed that our gene signature performed equally well or better than the signatures from these previous studies. In conclusion, our integrated meta-analysis of PDAC proteome and secretome identified 39 secreted proteins as potential biomarkers, and the tumor gene expression profile of these proteins in patients with PDAC is associated with worse overall survival.
Collapse
Affiliation(s)
- Grasieli de Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Paula Paccielli Freire
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Sarah Santiloni Cury
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Diogo de Moraes
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Jakeline Santos Oliveira
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Maeli Dal-Pai-Silva
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| | - Patrícia Pintor do Reis
- Department of Surgery and Orthopedics, Faculty of Medicine, São Paulo State University (UNESP), Botucatu 18618-687, São Paulo, Brazil;
- Experimental Research Unity, Faculty of Medicine, São Paulo State University, UNESP, Botucatu 18618-970, São Paulo, Brazil
| | - Robson Francisco Carvalho
- Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University (UNESP), Botucatu 18618-689, São Paulo, Brazil; (G.d.O.); (P.P.F.); (S.S.C.); (D.d.M.); (J.S.O.); (M.D.-P.-S.)
| |
Collapse
|
17
|
Santana-Codina N, Chandhoke AS, Yu Q, Małachowska B, Kuljanin M, Gikandi A, Stańczak M, Gableske S, Jedrychowski MP, Scott DA, Aguirre AJ, Fendler W, Gray NS, Mancias JD. Defining and Targeting Adaptations to Oncogenic KRASG12C Inhibition Using Quantitative Temporal Proteomics. Cell Rep 2020; 30:4584-4599.e4. [DOI: 10.1016/j.celrep.2020.03.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/04/2020] [Accepted: 03/07/2020] [Indexed: 02/07/2023] Open
|
18
|
Wong M, Newton LR, Hartmann J, Hennrich ML, Wachsmuth M, Ronchi P, Guzmán-Herrera A, Schwab Y, Gavin AC, Gilmour D. Dynamic Buffering of Extracellular Chemokine by a Dedicated Scavenger Pathway Enables Robust Adaptation during Directed Tissue Migration. Dev Cell 2020; 52:492-508.e10. [PMID: 32059773 DOI: 10.1016/j.devcel.2020.01.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 11/22/2019] [Accepted: 01/13/2020] [Indexed: 01/16/2023]
Abstract
How tissues migrate robustly through changing guidance landscapes is poorly understood. Here, quantitative imaging is combined with inducible perturbation experiments to investigate the mechanisms that ensure robust tissue migration in vivo. We show that tissues exposed to acute "chemokine floods" halt transiently before they perfectly adapt, i.e., return to the baseline migration behavior in the continued presence of elevated chemokine levels. A chemokine-triggered phosphorylation of the atypical chemokine receptor Cxcr7b reroutes it from constitutive ubiquitination-regulated degradation to plasma membrane recycling, thus coupling scavenging capacity to extracellular chemokine levels. Finally, tissues expressing phosphorylation-deficient Cxcr7b migrate normally in the presence of physiological chemokine levels but show delayed recovery when challenged with elevated chemokine concentrations. This work establishes that adaptation to chemokine fluctuations can be "outsourced" from canonical GPCR signaling to an autonomously acting scavenger receptor that both senses and dynamically buffers chemokine levels to increase the robustness of tissue migration.
Collapse
Affiliation(s)
- Mie Wong
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Lionel R Newton
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Jonas Hartmann
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Marco L Hennrich
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Malte Wachsmuth
- Luxendo GmbH, Kurfürsten-Anlage 58, 69115 Heidelberg, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Alejandra Guzmán-Herrera
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Yannick Schwab
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany; Electron Microscopy Core Facility, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Anne-Claude Gavin
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany; Department for Cell Physiology and Metabolism, University of Geneva, 1 rue Michel Servet, 1211 Geneva 4, Switzerland
| | - Darren Gilmour
- Department of Molecular Life Sciences, University of Zürich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| |
Collapse
|
19
|
Thompson A, Wölmer N, Koncarevic S, Selzer S, Böhm G, Legner H, Schmid P, Kienle S, Penning P, Höhle C, Berfelde A, Martinez-Pinna R, Farztdinov V, Jung S, Kuhn K, Pike I. TMTpro: Design, Synthesis, and Initial Evaluation of a Proline-Based Isobaric 16-Plex Tandem Mass Tag Reagent Set. Anal Chem 2019; 91:15941-15950. [DOI: 10.1021/acs.analchem.9b04474] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Andrew Thompson
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London WC1H 9BB, United Kingdom
| | - Nikolai Wölmer
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Sasa Koncarevic
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stefan Selzer
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Gitte Böhm
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Harald Legner
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Peter Schmid
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stefan Kienle
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Petra Penning
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Claudia Höhle
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Antje Berfelde
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Roxana Martinez-Pinna
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Vadim Farztdinov
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stephan Jung
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Karsten Kuhn
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Ian Pike
- Proteome Sciences Plc, Hamilton House, Mabledon Place, London WC1H 9BB, United Kingdom
| |
Collapse
|
20
|
Tian C, Clauser KR, Öhlund D, Rickelt S, Huang Y, Gupta M, Mani DR, Carr SA, Tuveson DA, Hynes RO. Proteomic analyses of ECM during pancreatic ductal adenocarcinoma progression reveal different contributions by tumor and stromal cells. Proc Natl Acad Sci U S A 2019; 116:19609-19618. [PMID: 31484774 PMCID: PMC6765243 DOI: 10.1073/pnas.1908626116] [Citation(s) in RCA: 238] [Impact Index Per Article: 47.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) has prominent extracellular matrix (ECM) that compromises treatments yet cannot be nonselectively disrupted without adverse consequences. ECM of PDAC, despite the recognition of its importance, has not been comprehensively studied in patients. In this study, we used quantitative mass spectrometry (MS)-based proteomics to characterize ECM proteins in normal pancreas and pancreatic intraepithelial neoplasia (PanIN)- and PDAC-bearing pancreas from both human patients and mouse genetic models, as well as chronic pancreatitis patient samples. We describe detailed changes in both abundance and complexity of matrisome proteins in the course of PDAC progression. We reveal an early up-regulated group of matrisome proteins in PanIN, which are further up-regulated in PDAC, and we uncover notable similarities in matrix changes between pancreatitis and PDAC. We further assigned cellular origins to matrisome proteins by performing MS on multiple lines of human-to-mouse xenograft tumors. We found that, although stromal cells produce over 90% of the ECM mass, elevated levels of ECM proteins derived from the tumor cells, but not those produced exclusively by stromal cells, tend to correlate with poor patient survival. Furthermore, distinct pathways were implicated in regulating expression of matrisome proteins in cancer cells and stromal cells. We suggest that, rather than global suppression of ECM production, more precise ECM manipulations, such as targeting tumor-promoting ECM proteins and their regulators in cancer cells, could be more effective therapeutically.
Collapse
Affiliation(s)
- Chenxi Tian
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | | | - Daniel Öhlund
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Department of Radiation Sciences, Umeå University, 901 87 Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, 901 85 Umeå, Sweden
| | - Steffen Rickelt
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ying Huang
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Mala Gupta
- New York University Winthrop Hospital, Mineola, NY 11501
| | - D R Mani
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | | | - Richard O Hynes
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139;
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| |
Collapse
|
21
|
Harding RJ, Loppnau P, Ackloo S, Lemak A, Hutchinson A, Hunt B, Holehouse AS, Ho JC, Fan L, Toledo-Sherman L, Seitova A, Arrowsmith CH. Design and characterization of mutant and wildtype huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems. J Biol Chem 2019; 294:6986-7001. [PMID: 30842263 PMCID: PMC6497952 DOI: 10.1074/jbc.ra118.007204] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/19/2019] [Indexed: 12/11/2022] Open
Abstract
The gene mutated in individuals with Huntington's disease (HD) encodes the 348-kDa huntingtin (HTT) protein. Pathogenic HD CAG-expansion mutations create a polyglutamine (polyQ) tract at the N terminus of HTT that expands above a critical threshold of ∼35 glutamine residues. The effect of these HD mutations on HTT is not well understood, in part because it is difficult to carry out biochemical, biophysical, and structural studies of this large protein. To facilitate such studies, here we have generated expression constructs for the scalable production of HTT in multiple eukaryotic expression systems. Our set of HTT expression clones comprised both N- and C-terminally FLAG-tagged HTT constructs with polyQ lengths representative of the general population, HD patients, and juvenile HD patients, as well as the more extreme polyQ expansions used in some HD tissue and animal models. Our expression system yielded milligram quantities of pure recombinant HTT protein, including many of the previously mapped post-translational modifications. We characterized both apo and HTT-HTT-associated protein 40 (HAP40) complex samples produced with this HD resource, demonstrating that this toolkit can be used to generate physiologically meaningful HTT complexes. We further demonstrate that these resources can produce sufficient material for protein-intensive experiments, such as small-angle X-ray scattering, providing biochemical insight into full-length HTT protein structure. The work outlined and the tools generated here lay a foundation for further biochemical and structural work on the HTT protein and for studying its functional interactions with other biomolecules.
Collapse
Affiliation(s)
- Rachel J Harding
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada,
| | - Peter Loppnau
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Suzanne Ackloo
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Alexander Lemak
- the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Ashley Hutchinson
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Brittany Hunt
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Alex S Holehouse
- the Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in Saint Louis, Saint Louis, Missouri 63130
| | - Jolene C Ho
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Lixin Fan
- the Basic Science Program, Frederick National Laboratory for Cancer Research, SAXS Core of NCI, National Institutes of Health, Frederick, Maryland 21701, and
| | | | - Alma Seitova
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada
| | - Cheryl H Arrowsmith
- From the Structural Genomics Consortium, University of Toronto, Ontario M5G 1L7, Canada,
- the Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| |
Collapse
|
22
|
Leskelä S, Takalo M, Marttinen M, Huber N, Paananen J, Mitra V, Rauramaa T, Mäkinen P, Leinonen V, Soininen H, Pike I, Remes AM, Hiltunen M, Haapasalo A. Interrelationship between the Levels of C9orf72 and Amyloid-β Protein Precursor and Amyloid-β in Human Cells and Brain Samples. J Alzheimers Dis 2019; 62:269-278. [PMID: 29439323 DOI: 10.3233/jad-170362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A subset of C9orf72 repeat expansion-carrying frontotemporal dementia patients display an Alzheimer-like decrease in cerebrospinal fluid amyloid-β (Aβ) biomarker levels. We report that downregulation of C9orf72 in non-neuronal human cells overexpressing amyloid-β protein precursor (AβPP) resulted in increased levels of secreted AβPP fragments and Aβ, while levels of AβPP or its C-terminal fragments (CTFs) remained unchanged. In neuronal cells, AβPP and C83 CTF levels were decreased upon C9orf72 knockdown, but those of secreted AβPP fragments or Aβ remained unchanged. C9orf72 protein levels significantly increased in human brain with advancing neurofibrillary pathology and positively correlated with brain Aβ42 levels. Our data suggest that altered C9orf72 levels may lead to cell-type specific alterations in AβPP processing, but warrant further studies to clarify the underlying mechanisms.
Collapse
Affiliation(s)
- Stina Leskelä
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mari Takalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Mikael Marttinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Nadine Huber
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Vikram Mitra
- Proteome Sciences plc, Coveham House, Cobham, Surrey, UK
| | - Tuomas Rauramaa
- Institute of Clinical Medicine - Pathology, University of Eastern Finland, Kuopio, Finland.,Department of Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Petra Mäkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Leinonen
- Neurosurgery of NeuroCenter, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland.,NeuroCenter, Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Ian Pike
- Proteome Sciences plc, Coveham House, Cobham, Surrey, UK
| | - Anne M Remes
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland.,NeuroCenter, Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.,Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland.,NeuroCenter, Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| | - Annakaisa Haapasalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland.,NeuroCenter, Neurology, Kuopio University Hospital and University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
23
|
Chandana S, Babiker HM, Mahadevan D. Therapeutic trends in pancreatic ductal adenocarcinoma (PDAC). Expert Opin Investig Drugs 2018; 28:161-177. [DOI: 10.1080/13543784.2019.1557145] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Sreenivasa Chandana
- Phase I program, START Midwest, Grand Rapids, MI, USA
- Department of Gastrointestinal Medical Oncology, Cancer and Hematology Centers of Western Michigan, Grand Rapids, MI, USA
- Department of Medicine, College of Human Medicine, Michigan State University, East Lansing, MI, USA
| | - Hani M. Babiker
- Early Phase Therapeutics Program, University of Arizona Cancer Center, Tucson, AZ, USA
| | - Daruka Mahadevan
- Early Phase Therapeutics Program, University of Arizona Cancer Center, Tucson, AZ, USA
| |
Collapse
|
24
|
Marttinen M, Paananen J, Neme A, Mitra V, Takalo M, Natunen T, Paldanius KMA, Mäkinen P, Bremang M, Kurki MI, Rauramaa T, Leinonen V, Soininen H, Haapasalo A, Pike I, Hiltunen M. A multiomic approach to characterize the temporal sequence in Alzheimer's disease-related pathology. Neurobiol Dis 2018; 124:454-468. [PMID: 30557660 DOI: 10.1016/j.nbd.2018.12.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 11/15/2018] [Accepted: 12/13/2018] [Indexed: 02/08/2023] Open
Abstract
No single-omic approach completely elucidates the multitude of alterations taking place in Alzheimer's disease (AD). Here, we coupled transcriptomic and phosphoproteomic approaches to determine the temporal sequence of changes in mRNA, protein, and phosphopeptide expression levels from human temporal cortical samples, with varying degree of AD-related pathology. This approach highlighted fluctuation in synaptic and mitochondrial function as the earliest pathological events in brain samples with AD-related pathology. Subsequently, increased expression of inflammation and extracellular matrix-associated gene products was observed. Interaction network assembly for the associated gene products, emphasized the complex interplay between these processes and the role of addressing post-translational modifications in the identification of key regulators. Additionally, we evaluate the use of decision trees and random forests in identifying potential biomarkers differentiating individuals with different degree of AD-related pathology. This multiomic and temporal sequence-based approach provides a better understanding of the sequence of events leading to AD.
Collapse
Affiliation(s)
- Mikael Marttinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Antonio Neme
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Vikram Mitra
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mari Takalo
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Kaisa M A Paldanius
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Petra Mäkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland
| | - Michael Bremang
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mitja I Kurki
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Psychiatry, Psychiatric and Neurodevelopmental Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Neurosurgery of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital and University of Eastern Finland, Kuopio 70029, Finland
| | - Ville Leinonen
- Neurosurgery of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland
| | - Hilkka Soininen
- Neurology of Neuro Center, Kuopio University Hospital, Kuopio 70029, Finland; Institute of Clinical Medicine/Neurology, University of Eastern Finland, Kuopio 70210, Finland
| | - Annakaisa Haapasalo
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Ian Pike
- Proteome Sciences plc, Cobham, London WC1H 9BB, United Kingdom
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio 70210, Finland.
| |
Collapse
|
25
|
Lin J, Wu YJ, Liang X, Ji M, Ying HM, Wang XY, Sun X, Shao CH, Zhan LX, Zhang Y. Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer. Mol Carcinog 2018; 58:206-218. [PMID: 30294829 DOI: 10.1002/mc.22920] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 08/31/2018] [Accepted: 10/03/2018] [Indexed: 12/30/2022]
Abstract
Pancreatic cancer is regarded as the most fatal and aggressive malignancy cancer due to its low 5-year survival rate and poor prognosis. The approaches of early diagnosis and treatment are limited, which makes it urgent to identify the complex mechanism of pancreatic oncogenesis. In this study, we used RNA-seq to investigate the transcriptomic (mRNA and miRNA) profiles of pancreatic cancer in paired tumor and normal pancreatic samples from ten patients. More than 1000 differentially expressed genes were identified, nearly half of which were also found to be differentially expressed in the majority of examined patients. Functional enrichment analysis revealed that these genes were significantly enriched in multicellular organismal and metabolic process, secretion, mineral transport, and intercellular communication. In addition, only 24 differentially expressed miRNAs were found, all of which have been reported to be associated with pancreatic cancer. Furthermore, an integrated miRNA-mRNA interaction network was generated using multiple resources. Based on the calculation of disease correlation scores developed here, several genes present in the largest connected subnetwork, such as albumin, ATPase H+ /K+ exchanging alpha polypeptide and carcinoembryonic antigen-related cell adhesion molecule 1, were considered as novel genes that play important roles in the development of pancreatic cancer. Overall, our data provide new insights into further understanding of key molecular mechanisms underlying pancreatic tumorigenesis.
Collapse
Affiliation(s)
- Jie Lin
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong Province, P. R. China.,Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yan-Jun Wu
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Xing Liang
- Department of Pancreatic-Biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
| | - Meng Ji
- Department of Pancreatic-Biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
| | - Hui-Min Ying
- Department of Endocrinology, Hangzhou Xixi Hospital, Hangzhou, Zhejiang, P. R. China
| | - Xin-Yu Wang
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Xia Sun
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Cheng-Hao Shao
- Department of Pancreatic-Biliary Surgery, Changzheng Hospital, Second Military Medical University, Shanghai, P. R. China
| | - Li-Xing Zhan
- Key Laboratory of Nutrition, Metabolism, and Food Safety, Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, P. R. China
| | - Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, Guangdong Province, P. R. China
| |
Collapse
|
26
|
Martiskainen H, Takalo M, Solomon A, Stančáková A, Marttinen M, Natunen T, Haapasalo A, Herukka SK, Kuusisto J, Soininen H, Kivipelto M, Laakso M, Hiltunen M. Decreased plasma C-reactive protein levels in APOE ε4 allele carriers. Ann Clin Transl Neurol 2018; 5:1229-1240. [PMID: 30349858 PMCID: PMC6186931 DOI: 10.1002/acn3.639] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 02/06/2023] Open
Abstract
Objective Apolipoprotein E (APOE) ε4 allele is a well‐established risk factor in Alzheimer's disease (AD). Here, we assessed the effects of APOE polymorphism on cardiovascular, metabolic, and inflammation‐related parameters in population‐based cohorts. Methods Association of cardiovascular, metabolic, and inflammation‐related parameters with the APOE polymorphism in a large Finnish Metabolic Syndrome in Men (METSIM) cohort and Finnish Geriatric Intervention study to prevent cognitive impairment and disability (FINGER) were investigated. Brain‐specific effects were addressed in postmortem brain samples. Results Individuals carrying the APOE ε4 allele displayed significantly elevated serum/plasma LDL cholesterol and apolipoprotein B levels. APOE ε3ε4 and ε4ε4 significantly associated with lower levels of plasma high‐sensitivity C‐reactive protein (hs‐CRP). Plasma amyloid‐β 42 (Aβ42) and reduced hs‐CRP levels showed an association independently of the APOE status. Interpretation These data suggest that the APOE ε4 allele associates with lower levels of hs‐CRP in individuals without dementia. Moreover, Aβ42 may encompass anti‐inflammatory effects reflected by reduced hs‐CRP levels.
Collapse
Affiliation(s)
- Henna Martiskainen
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland
| | - Mari Takalo
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Alina Solomon
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Division of Clinical Geriatrics Center for Alzheimer Research NVS, Karolinska Institutet Novum 5th floor Huddinge 14157 Sweden
| | - Alena Stančáková
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland
| | - Mikael Marttinen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Teemu Natunen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| | - Annakaisa Haapasalo
- A.I Virtanen Institute for Molecular Sciences University of Eastern Finland Neulaniementie 2 Kuopio 70211 Finland
| | - Sanna-Kaisa Herukka
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Neurocenter Neurology Kuopio University Hospital Kuopio Finland
| | - Johanna Kuusisto
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Kuopio University Hospital Kuopio Finland
| | - Hilkka Soininen
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Neurocenter Neurology Kuopio University Hospital Kuopio Finland
| | - Miia Kivipelto
- Department of Neurology Institute of Clinical Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Division of Clinical Geriatrics Center for Alzheimer Research NVS, Karolinska Institutet Novum 5th floor Huddinge 14157 Sweden.,Department of Public Health Solutions Public Health Promotion Unit National Institute for Health and Welfare PO Box 30 Helsinki 00271 Finland
| | - Markku Laakso
- Institute of Clinical Medicine Internal Medicine University of Eastern Finland P.O. Box 1627 Kuopio 70211 Finland.,Kuopio University Hospital Kuopio Finland
| | - Mikko Hiltunen
- Institute of Biomedicine University of Eastern Finland Yliopistonranta 1 E, P.O. Box 1627 Kuopio 70211 Finland
| |
Collapse
|
27
|
Signal-Targeted Therapies and Resistance Mechanisms in Pancreatic Cancer: Future Developments Reside in Proteomics. Cancers (Basel) 2018; 10:cancers10060174. [PMID: 29865155 PMCID: PMC6025626 DOI: 10.3390/cancers10060174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 05/29/2018] [Accepted: 05/30/2018] [Indexed: 12/18/2022] Open
Abstract
For patients with metastatic pancreatic cancer that are not eligible for surgery, signal-targeted therapies have so far failed to significantly improve survival. These therapeutic options have been tested in phase II/III clinical trials mostly in combination with the reference treatment gemcitabine. Innovative therapies aim to annihilate oncogenic dependency, or to normalize the tumoural stroma to allow immune cells to function and/or re-vascularisation to occur. Large scale transcriptomic and genomic analysis revealed that pancreatic cancers display great heterogeneity but failed to clearly delineate specific oncogene dependency, besides oncogenic Kras. Beyond these approaches, proteomics appears to be an appropriate approach to classify signal dependency and to identify specific alterations at the targetable level. However, due to difficulties in sampling, proteomic data for this pathology are scarce. In this review, we will discuss the current state of clinical trials for targeted therapies against pancreatic cancer. We will then highlight the most recent proteomic data for pancreatic tumours and their metastasis, which could help to identify major oncogenic signalling dependencies, as well as provide future leads to explain why pancreatic tumours are intrinsically resistant to signal-targeted therapies. We will finally discuss how studies on phosphatidylinositol-3-kinase (PI3K) signalling, as the paradigmatic pro-tumoural signal downstream of oncogenic Kras in pancreatic cancer, would benefit from exploratory proteomics to increase the efficiency of targeted therapies.
Collapse
|
28
|
Kwon Y, Ju S, Kaushal P, Lee JW, Lee C. Neutralizing the Detrimental Effect of an N-Hydroxysuccinimide Quenching Reagent on Phosphopeptide in Quantitative Proteomics. Anal Chem 2018; 90:3019-3023. [PMID: 29406695 DOI: 10.1021/acs.analchem.7b04678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the most common chemistries used to label primary amines utilizes N-hydroxysuccinimide (NHS), which is also structurally incorporated in various quantitative proteomic reagents such as isobaric tags for relative and absolute quantification (iTRAQ) and tandem mass tags (TMT). In this paper we report detrimental effect of hydroxylamine, a widely used quenching reagent for excess NHS, on phosphopeptides. We found an impairment in the degree of phosphopeptide identification when hydroxylamine-quenched TMT-labeled samples were vacuum-dried and desalted compared to the nondried (just diluted) and desalted ones prior to phosphoenrichment. We have also demonstrated that vacuum-drying in the presence of hydroxylamine promotes β-elimination of phosphate groups from phosphoserine and phosphothreonine while having a minimalistic effect on phosphotyrosine. Additionally, we herein report that this negative impact of hydroxylamine could be minimized by direct desalting after appropriate dilution of quenched samples. We also found a 1.6-fold increase in the number of phosphopeptide identifications after employing our optimized method. The above method was also successfully applied to human tumor tissues to quantify over 15000 phosphopeptides from 3 mg TMT 6-plex labeled-peptides.
Collapse
Affiliation(s)
- Yumi Kwon
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Shinyeong Ju
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Prashant Kaushal
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| | - Jin-Won Lee
- Department of Life Science and Research Institute for Natural Sciences , Hanyang University , Seoul 04763 , Korea
| | - Cheolju Lee
- Center for Theragnosis , Korea Institute of Science and Technology , Seoul 02792 , Korea.,Division of Bio-Medical Science and Technology, KIST School , Korea University of Science and Technology , Seoul 02792 , Korea
| |
Collapse
|
29
|
Kim H, Park J, Wang JI, Kim Y. Recent advances in proteomic profiling of pancreatic ductal adenocarcinoma and the road ahead. Expert Rev Proteomics 2017; 14:963-971. [PMID: 28926720 DOI: 10.1080/14789450.2017.1382356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide. However, there remain many unmet clinical needs, from diagnosis to treatment strategies. The inherent complexity of the molecular characteristics of PDAC has made it difficult to meet these challenges, rendering proteomic profiling of PDAC a critical area of research. Area covered: In this review, we present recent advances in mass spectrometry (MS) and its current application in proteomic studies on PDAC. In addition, we discuss future directions for research that can efficiently incorporate current MS-based technologies that address key issues of PDAC proteomics. Expert commentary: Compared with other cancer studies, little progress has been made in PDAC proteomics, perhaps attributed to the difficulty in performing in-depth and large-scale clinical studies on PDAC. However, recent advances in mass spectrometry can advance PDAC proteomics past the fundamental research stage.
Collapse
Affiliation(s)
- Hyunsoo Kim
- a Department of Biomedical Sciences , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,c Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Joonho Park
- b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Joseph I Wang
- b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| | - Youngsoo Kim
- a Department of Biomedical Sciences , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,b Department of Biomedical Engineering , Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea.,c Institute of Medical and Biological Engineering, Medical Research Center, Seoul National University College of Medicine , Yongon-Dong, Seoul 110-799 , Korea
| |
Collapse
|
30
|
Kanhaiya K, Czeizler E, Gratie C, Petre I. Controlling Directed Protein Interaction Networks in Cancer. Sci Rep 2017; 7:10327. [PMID: 28871116 PMCID: PMC5583175 DOI: 10.1038/s41598-017-10491-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 08/09/2017] [Indexed: 02/06/2023] Open
Abstract
Control theory is a well-established approach in network science, with applications in bio-medicine and cancer research. We build on recent results for structural controllability of directed networks, which identifies a set of driver nodes able to control an a-priori defined part of the network. We develop a novel and efficient approach for the (targeted) structural controllability of cancer networks and demonstrate it for the analysis of breast, pancreatic, and ovarian cancer. We build in each case a protein-protein interaction network and focus on the survivability-essential proteins specific to each cancer type. We show that these essential proteins are efficiently controllable from a relatively small computable set of driver nodes. Moreover, we adjust the method to find the driver nodes among FDA-approved drug-target nodes. We find that, while many of the drugs acting on the driver nodes are part of known cancer therapies, some of them are not used for the cancer types analyzed here; some drug-target driver nodes identified by our algorithms are not known to be used in any cancer therapy. Overall we show that a better understanding of the control dynamics of cancer through computational modelling can pave the way for new efficient therapeutic approaches and personalized medicine.
Collapse
Affiliation(s)
- Krishna Kanhaiya
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
| | - Eugen Czeizler
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
- National Institute for Research and Development for Biological Sciences, Bucharest, Romania
| | - Cristian Gratie
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland
| | - Ion Petre
- Computational Biomodeling Laboratory, Turku Centre for Computer Science, and Department of Computer Science, Åbo Akademi University, Turku, 20500, Finland.
| |
Collapse
|
31
|
Laser Capture Microdissection of Pancreatic Acinar Cells to Identify Proteomic Alterations in a Murine Model of Caerulein-Induced Pancreatitis. Clin Transl Gastroenterol 2017; 8:e89. [PMID: 28406494 PMCID: PMC5415897 DOI: 10.1038/ctg.2017.15] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 01/05/2017] [Indexed: 12/13/2022] Open
Abstract
Objectives: Chronic pancreatitis (CP) is characterized by inflammation and fibrosis of the pancreas, leading to pain, parenchymal damage, and loss of exocrine and endocrine function. There are currently no curative therapies; diagnosis remains difficult and aspects of pathogenesis remain unclear. Thus, there is a need to identify novel biomarkers to improve diagnosis and understand pathophysiology. We hypothesize that pancreatic acinar regions contain proteomic signatures relevant to disease processes, including secreted proteins that could be detected in biofluids. Methods: Acini from pancreata of mice injected with or without caerulein were collected using laser capture microdissection followed by mass spectrometry analysis. This protocol enabled high-throughput analysis that captured altered protein expression throughout the stages of CP. Results: Over 2,900 proteins were identified, whereas 331 were significantly changed ≥2-fold by mass spectrometry spectral count analysis. Consistent with pathogenesis, we observed increases in proteins related to fibrosis (e.g., collagen, P<0.001), several proteases (e.g., trypsin 1, P<0.001), and altered expression of proteins associated with diminished pancreas function (e.g., lipase, amylase, P<0.05). In comparison with proteomic data from a public data set of CP patients, a significant correlation was observed between proteomic changes in tissue from both the caerulein model and CP patients (r=0.725, P<0.001). CONCLUSIONS: This study illustrates the ability to characterize proteome changes of acinar cells isolated from pancreata of caerulein-treated mice and demonstrates a relationship between signatures from murine and human CP.
Collapse
|
32
|
Le Large TYS, Bijlsma MF, Kazemier G, van Laarhoven HWM, Giovannetti E, Jimenez CR. Key biological processes driving metastatic spread of pancreatic cancer as identified by multi-omics studies. Semin Cancer Biol 2017; 44:153-169. [PMID: 28366542 DOI: 10.1016/j.semcancer.2017.03.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 02/06/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is an extremely aggressive malignancy, characterized by a high metastatic burden, already at the time of diagnosis. The metastatic potential of PDAC is one of the main reasons for the poor outcome next to lack of significant improvement in effective treatments in the last decade. Key mutated driver genes, such as activating KRAS mutations, are concordantly expressed in primary and metastatic tumors. However, the biology behind the metastatic potential of PDAC is not fully understood. Recently, large-scale omic approaches have revealed new mechanisms by which PDAC cells gain their metastatic potency. In particular, genomic studies have shown that multiple heterogeneous subclones reside in the primary tumor with different metastatic potential. The development of metastases may be correlated to a more mesenchymal transcriptomic subtype. However, for cancer cells to survive in a distant organ, metastatic sites need to be modulated into pre-metastatic niches. Proteomic studies identified the influence of exosomes on the Kuppfer cells in the liver, which could function to prepare this tissue for metastatic colonization. Phosphoproteomics adds an extra layer to the established omic techniques by unravelling key functional signaling. Future studies integrating results from these large-scale omic approaches will hopefully improve PDAC prognosis through identification of new therapeutic targets and patient selection tools. In this article, we will review the current knowledge on the biology of PDAC metastasis unravelled by large scale multi-omic approaches.
Collapse
Affiliation(s)
- T Y S Le Large
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; Laboratory of Experimental Oncology and Radiobiology, Academic Medical Center, Amsterdam, The Netherlands; Department of Surgery, VU University Medical Center, Amsterdam, The Netherlands
| | - M F Bijlsma
- Laboratory of Experimental Oncology and Radiobiology, Academic Medical Center, Amsterdam, The Netherlands
| | - G Kazemier
- Department of Surgery, VU University Medical Center, Amsterdam, The Netherlands
| | - H W M van Laarhoven
- Department of Medical Oncology, Academic Medical Center, Amsterdam, The Netherlands
| | - E Giovannetti
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; Cancer Pharmacology Lab, AIRC Start Up Unit, University of Pisa, Pisa, Italy; CNR-Nano, Institute of Nanoscience and Nanotechnology, Pisa, Italy
| | - C R Jimenez
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands.
| |
Collapse
|
33
|
Casado P, Hijazi M, Britton D, Cutillas PR. Impact of phosphoproteomics in the translation of kinase-targeted therapies. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600235] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/29/2016] [Accepted: 10/20/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Pedro Casado
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - Maruan Hijazi
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - David Britton
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| | - Pedro R. Cutillas
- Cell Signalling and Proteomics Group; Centre for Haemato-Oncology; Barts Cancer Institute; Queen Mary University of London; UK
| |
Collapse
|
34
|
Coleman O, Henry M, McVey G, Clynes M, Moriarty M, Meleady P. Proteomic strategies in the search for novel pancreatic cancer biomarkers and drug targets: recent advances and clinical impact. Expert Rev Proteomics 2016; 13:383-94. [PMID: 26985644 DOI: 10.1586/14789450.2016.1167601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers; despite a low incidence rate it is the fourth leading cause of cancer-related death in the world. Improvement of the diagnosis, prognosis and treatment remains the main focus of pancreatic cancer research. Rapid developments in proteomic technologies has improved our understanding of the pancreatic cancer proteome. Here, the authors summarise the recent proteomic strategies undertaken in the search for: novel biomarkers for early diagnosis, pancreatic cancer-specific proteins which may be used for novel targeted therapies and proteins which may be useful for monitoring disease progression post-therapy. Recent advances and findings discussed here provide great promise of having a significant clinical impact and improving the outcome of patients with this malignancy.
Collapse
Affiliation(s)
- Orla Coleman
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
| | - Michael Henry
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
| | - Gerard McVey
- b St. Lukes Hospital , Rathgar , Dublin 6 , Ireland
| | - Martin Clynes
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
| | - Michael Moriarty
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland.,b St. Lukes Hospital , Rathgar , Dublin 6 , Ireland
| | - Paula Meleady
- a Department of Proteomics, National Institute for Cellular Biotechnology , Dublin City University , Glasnevin , Dublin 9 , Ireland
| |
Collapse
|
35
|
Abstract
Quantitative proteomics represents a powerful approach for the comprehensive analysis of proteins expressed under defined conditions. These properties have been used to investigate the proteome of disease states, including cancer. It has become a major subject of studies to apply proteomics for biomarker and therapeutic target identification. In the last decades, technical advances in mass spectrometry have increased the capacity of protein identification and quantification. Moreover, the analysis of posttranslational modification (PTM), especially phosphorylation, has allowed large-scale identification of biological mechanisms. Even so, increasing evidence indicates that global protein quantification is often insufficient for the explanation of biology and has shown to pose challenges in identifying new and robust biomarkers. As a consequence, to improve the accuracy of the discoveries made using proteomics in human tumors, it is necessary to combine (i) robust and reproducible methods for sample preparation allowing statistical comparison, (ii) PTM analyses in addition to global proteomics for additional levels of knowledge, and (iii) use of bioinformatics for decrypting protein list. Herein, we present technical specificities for samples preparation involving isobaric tag labeling, TiO2-based phosphopeptides enrichment and hydrazyde-based glycopeptides purification as well as the key points for the quantitative analysis and interpretation of the protein lists. The method is based on our experience with tumors analysis derived from hepatocellular carcinoma, chondrosarcoma, human embryonic intervertebral disk, and chordoma experiments.
Collapse
|
36
|
Identification of a novel serum biomarker for pancreatic cancer, C4b-binding protein α-chain (C4BPA) by quantitative proteomic analysis using tandem mass tags. Br J Cancer 2016; 115:949-956. [PMID: 27657339 PMCID: PMC5061912 DOI: 10.1038/bjc.2016.295] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/13/2016] [Accepted: 08/24/2016] [Indexed: 12/24/2022] Open
Abstract
Background: Pancreatic ductal adenocarcinoma (PDAC) remains a devastating disease due to the lack of specific early diagnostic markers. To improve the outcomes, proteomic approaches are being developed for the discovery of novel biomarkers of PDAC. Methods: Using tandem mass tag labelling and LC-MS/MS, we performed comparative analyses of pre- and postoperative sera from PDAC patients to identify specific serum biomarkers for PDAC. In validation studies, we evaluated the discriminatory power of candidate proteins. Results: Among the 302 proteins analysed, 20 were identified as potential biomarkers, with C4b-binding protein α-chain (C4BPA) and polymeric immunoglobulin receptor (PIGR) being selected for further analysis. The sera levels of C4BPA and PIGR were significantly higher in the preoperative PDAC patients than in the postoperative ones (P<0.008, P<0.036, respectively). In addition, serum C4BPA levels, but not PIGR, in patients with PDAC were significantly higher than those in healthy controls as well as in patients with pancreatitis and other malignancies including biliary tract cancers (BTC) (P<0.001). The respective area under the receiver operator characteristics (ROC) curve (AUC) was 0.860 for C4BPA, 0.846 for CA19-9 and 0.930 for the combination of C4BPA and CA19-9 in PDAC vs non-cancer individuals. The respective AUC was 0.912 for C4BPA, 0.737 for CA19-9 in Stages I and II of PDAC, 0.854 for C4BPA and 0.264 for CA19-9 in PDAC vs BTC. Conclusions: We have demonstrated that C4BPA is a novel serum biomarker for detecting early stage PDAC, as well as for distinguishing PDAC from other gastroenterological cancers. Further analysis in large cohort studies will warrant C4BPA as a promising biomarker of PDAC in clinical use.
Collapse
|
37
|
Mukherjee I, Powell B, Parianos M, Downs D, Ross SB. Available technologies and clinical applications of targeted chemotherapy in pancreatic cancer. Cancer Genet 2016; 209:582-591. [PMID: 27613576 DOI: 10.1016/j.cancergen.2016.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 08/01/2016] [Indexed: 02/08/2023]
Abstract
The incidence of pancreatic cancer, the fourth leading cause of cancer death in United States, is increasing worldwide. Even though the cure rate has doubled in 40 years, it is abysmally poor at 6-7%. As surgical resection remains the only curative treatment and less than 20% of the newly diagnosed cancers are resectable, the major burden of disease management lies in early diagnosis, good prognostication, and proper neo-adjuvant and/or adjuvant therapy. With advancing technologies and their ease of availability, researchers have better tools to understand pancreatic cancer. In the post-genetic era, proteomic, phosphoproteomic, metabolomic, and more have brought us to a multi-omics era. These newer avenues bring promises of better screening modalities, less invasive diagnostics and monitoring, subtyping of pancreatic cancer, and fine tuning the treatment modalities not only to the right stage of tumor but also to the right tumor biology. As the multitudes of technologies are generating extensive amounts of incongruous data, they are giving clinicians a lot of non-actionable information. In this paper, we wish to encompass the newer technologies, sub-classifications, and future treatment modalities in personalized care of patients with pancreatic cancer.
Collapse
Affiliation(s)
- Indraneil Mukherjee
- Southeastern Center for Digestive Disorders and Pancreatic Cancer, Florida Hospital Tampa, Tampa, FL, USA.
| | - Brett Powell
- Southeastern Center for Digestive Disorders and Pancreatic Cancer, Florida Hospital Tampa, Tampa, FL, USA
| | - Mary Parianos
- Southeastern Center for Digestive Disorders and Pancreatic Cancer, Florida Hospital Tampa, Tampa, FL, USA
| | - Darrell Downs
- Southeastern Center for Digestive Disorders and Pancreatic Cancer, Florida Hospital Tampa, Tampa, FL, USA
| | - Sharona B Ross
- Southeastern Center for Digestive Disorders and Pancreatic Cancer, Florida Hospital Tampa, Tampa, FL, USA
| |
Collapse
|
38
|
Humphrey ES, Su SP, Nagrial AM, Hochgräfe F, Pajic M, Lehrbach GM, Parton RG, Yap AS, Horvath LG, Chang DK, Biankin AV, Wu J, Daly RJ. Resolution of Novel Pancreatic Ductal Adenocarcinoma Subtypes by Global Phosphotyrosine Profiling. Mol Cell Proteomics 2016; 15:2671-85. [PMID: 27259358 PMCID: PMC4974343 DOI: 10.1074/mcp.m116.058313] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 05/11/2016] [Indexed: 12/20/2022] Open
Abstract
Comprehensive characterization of signaling in pancreatic ductal adenocarcinoma (PDAC) promises to enhance our understanding of the molecular aberrations driving this devastating disease, and may identify novel therapeutic targets as well as biomarkers that enable stratification of patients for optimal therapy. Here, we use immunoaffinity-coupled high-resolution mass spectrometry to characterize global tyrosine phosphorylation patterns across two large panels of human PDAC cell lines: the ATCC series (19 cell lines) and TKCC series (17 cell lines). This resulted in the identification and quantification of over 1800 class 1 tyrosine phosphorylation sites and the consistent segregation of both PDAC cell line series into three subtypes with distinct tyrosine phosphorylation profiles. Subtype-selective signaling networks were characterized by identification of subtype-enriched phosphosites together with pathway and network analyses. This revealed that the three subtypes characteristic of the ATCC series were associated with perturbations in signaling networks associated with cell-cell adhesion and epithelial-mesenchyme transition, mRNA metabolism, and receptor tyrosine kinase (RTK) signaling, respectively. Specifically, the third subtype exhibited enhanced tyrosine phosphorylation of multiple RTKs including the EGFR, ERBB3 and MET. Interestingly, a similar RTK-enriched subtype was identified in the TKCC series, and 'classifier' sites for each series identified using Random Forest models were able to predict the subtypes of the alternate series with high accuracy, highlighting the conservation of the three subtypes across the two series. Finally, RTK-enriched cell lines from both series exhibited enhanced sensitivity to the small molecule EGFR inhibitor erlotinib, indicating that their phosphosignature may provide a predictive biomarker for response to this targeted therapy. These studies highlight how resolution of subtype-selective signaling networks can provide a novel taxonomy for particular cancers, and provide insights into PDAC biology that can be exploited for improved patient management.
Collapse
Affiliation(s)
- Emily S Humphrey
- From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia
| | - Shih-Ping Su
- ¶Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, VIC 3800, Australia
| | - Adnan M Nagrial
- From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia
| | - Falko Hochgräfe
- ‖Competence Center Functional Genomics, University of Greifswald, F.-L-Jahnstr. 15, 17489 Greifswald, Germany
| | - Marina Pajic
- From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia
| | - Gillian M Lehrbach
- From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia
| | - Robert G Parton
- **Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane QLD 4072, Australia
| | - Alpha S Yap
- **Division of Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane QLD 4072, Australia
| | - Lisa G Horvath
- From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; ‡‡Chris O'Brien Lifehouse, Missenden Road, Camperdown, NSW 2050, Australia
| | - David K Chang
- §§Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK
| | - Andrew V Biankin
- §§Wolfson Wohl Cancer Research Centre, Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Bearsden, Glasgow G61 1BD, UK;
| | - Jianmin Wu
- ¶¶Key laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Center for Cancer Bioinformatics, Peking University Cancer Hospital & Institute, 52 Fu-Cheng Road, Hai-Dian District, Beijing 100142, China From the ‡Cancer Division and Kinghorn Cancer Centre, Garvan Institute of Medical Research, 384 Victoria St, Sydney, NSW 2010, Australia; §St Vincent's Hospital Clinical School, Faculty of Medicine, University of New South Wales, NSW 2052, Australia;
| | - Roger J Daly
- ¶Cancer Program, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Level 1, Building 77, Monash University, VIC 3800, Australia;
| |
Collapse
|
39
|
Timms JF, Hale OJ, Cramer R. Advances in mass spectrometry-based cancer research and analysis: from cancer proteomics to clinical diagnostics. Expert Rev Proteomics 2016; 13:593-607. [DOI: 10.1080/14789450.2016.1182431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
40
|
Abstract
Over the past decade, rapid advances in genomics, proteomics and functional genomics technologies that enable in-depth interrogation of cancer genomes and proteomes and high-throughput analysis of gene function have enabled characterization of the kinome 'at large' in human cancers, providing crucial insights into how members of the protein kinase superfamily are dysregulated in malignancy, the context-dependent functional role of specific kinases in cancer and how kinome remodelling modulates sensitivity to anticancer drugs. The power of these complementary approaches, and the insights gained from them, form the basis of this Analysis article.
Collapse
Affiliation(s)
- Emmy D G Fleuren
- Department of Medical Oncology, Radboud University Medical Centre, Geert Grooteplein-Zuid 10, 6525 GA Nijmegen, The Netherlands
| | - Luxi Zhang
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
- University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jianmin Wu
- Cancer Division, Kinghorn Cancer Centre, Garvan Institute of Medical Research, 370 Victoria Street, Sydney, New South Wales 2010, Australia
| | - Roger J Daly
- Cancer Program, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
41
|
Abstract
OBJECTIVES The aim of this study was to identify differentially expressed proteins among various stages of pancreatic ductal adenocarcinoma (PDAC) by shotgun proteomics using nano-liquid chromatography coupled tandem mass spectrometry and stable isotope dimethyl labeling. METHODS Differentially expressed proteins were identified and compared based on the mass spectral differences of their isotope-labeled peptide fragments generated from protease digestion. RESULTS Our quantitative proteomic analysis of the differentially expressed proteins with stable isotope (deuterium/hydrogen ratio, ≥ 2) identified a total of 353 proteins, with at least 5 protein biomarker proteins that were significantly differentially expressed between cancer and normal mice by at least a 2-fold alteration. These 5 protein biomarker candidates include α-enolase, α-catenin, 14-3-3 β, VDAC1, and calmodulin with high confidence levels. The expression levels were also found to be in agreement with those examined by Western blot and histochemical staining. CONCLUSIONS The systematic decrease or increase of these identified marker proteins may potentially reflect the morphological aberrations and diseased stages of pancreas carcinoma throughout progressive developments leading to PDAC. The results would form a firm foundation for future work concerning validation and clinical translation of some identified biomarkers into targeted diagnosis and therapy for various stages of PDAC.
Collapse
|
42
|
Quantitation of protein post-translational modifications using isobaric tandem mass tags. Bioanalysis 2015; 7:383-400. [PMID: 25697195 DOI: 10.4155/bio.14.296] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Post-translational modifications (PTMs) of proteins are known to modulate many cellular processes and their qualitative and quantitative evaluation is fundamental for understanding the mechanisms of biological events. Over the past decade, improvements in sample preparation techniques and enrichment strategies, the development of quantitative labeling strategies, the launch of a new generation of mass spectrometers and the creation of bioinformatics tools for the interrogation of ever larger datasets has established MS-based quantitative proteomics as a powerful workflow for global proteomics, PTM analysis and the elucidation of key biological mechanisms. With the advantage of their multiplexing capacity and the flexibility of an ever-growing family of different peptide-reactive groups, isobaric tandem mass tags facilitate quantitative proteomics and PTM experiments and enable higher sample throughput. In this review, we focus on the technical concept and utility of the isobaric tandem mass tag labeling approach to PTM analysis, including phosphorylation, glycosylation and S-nitrosylation.
Collapse
|
43
|
Zen Y, Britton D, Mitra V, Pike I, Heaton N, Quaglia A. A global proteomic study identifies distinct pathological features of IgG4-related and primary sclerosing cholangitis. Histopathology 2015; 68:796-809. [PMID: 26308372 DOI: 10.1111/his.12813] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2015] [Accepted: 08/15/2015] [Indexed: 02/06/2023]
Abstract
AIMS This combined proteomic and histopathological study was aimed to compare tissue characteristics of immunoglobulin (Ig)G4-related sclerosing cholangitis (ISC) and primary sclerosing cholangitis (PSC) in a global, non-biased manner. METHODS AND RESULTS Tissue proteomes and phosphorylomes of frozen large bile duct samples were analysed by a conventional liquid chromatography-tandem mass spectrometry (LC-MS/MS) protocol and additional phosphopeptide enrichment methods. The proteomic examination identified 23 373 peptides and 4870 proteins, including 4801 phosphopeptides and 1121 phosphoproteins. The expression profiles of phosphopeptides discriminated ISC from PSC more clearly than those of non-phosphopeptides. In the pathway analysis, ISC was found to have 11 more activated signal cascades, including three immunological pathways, all B cell- or immunoglobulin-related. On immunostaining, two immunological markers (FYN-binding protein and allograft inflammatory factor-1) up-regulated in ISC were expressed mainly in M2 macrophages, consistent with increased phagocytotic activity induced by the immunoglobulin (Ig)G-Fcγ receptor interaction. In contrast, PSC had two more activated signal pathways related to extracellular matrix (ECM) remodelling. Filamin-A involved in ECM remodelling was expressed aberrantly in injured bile ducts and associated cholangiocarcinomas in PSC, suggesting its possible roles in periductal fibrosis and carcinogenesis in PSC. CONCLUSIONS This study suggested crucial roles of B cells and macrophages in ISC, and more dynamic ECM remodelling in PSC.
Collapse
Affiliation(s)
- Yoh Zen
- Department of Diagnostic Pathology, Kobe University Graduate School of Medicine, Kobe, Japan.,Institute of Liver Studies, King's College Hospital, London, UK
| | | | | | - Ian Pike
- Proteome Sciences plc, Cobham, UK
| | - Nigel Heaton
- Institute of Liver Studies, King's College Hospital, London, UK
| | - Alberto Quaglia
- Institute of Liver Studies, King's College Hospital, London, UK
| |
Collapse
|
44
|
Böhm G, Prefot P, Jung S, Selzer S, Mitra V, Britton D, Kuhn K, Pike I, Thompson AH. Low-pH Solid-Phase Amino Labeling of Complex Peptide Digests with TMTs Improves Peptide Identification Rates for Multiplexed Global Phosphopeptide Analysis. J Proteome Res 2015; 14:2500-10. [DOI: 10.1021/acs.jproteome.5b00072] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Gitte Böhm
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Petra Prefot
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stephan Jung
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Stefan Selzer
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Vikram Mitra
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3E, United Kingdom
| | - David Britton
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3E, United Kingdom
| | - Karsten Kuhn
- Proteome Sciences R&D GmbH & Co. KG, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Ian Pike
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3E, United Kingdom
| | - Andrew H. Thompson
- Proteome Sciences plc, Coveham
House, Downside Bridge Road, Cobham KT11 3E, United Kingdom
| |
Collapse
|
45
|
Urayama S. Pancreatic cancer early detection: Expanding higher-risk group with clinical and metabolomics parameters. World J Gastroenterol 2015; 21:1707-1717. [PMID: 25684935 PMCID: PMC4323446 DOI: 10.3748/wjg.v21.i6.1707] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Revised: 10/01/2014] [Accepted: 01/08/2015] [Indexed: 02/06/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the fourth and fifth leading cause of cancer death for each gender in developed countries. With lack of effective treatment and screening scheme available for the general population, the mortality rate is expected to increase over the next several decades in contrast to the other major malignancies such as lung, breast, prostate and colorectal cancers. Endoscopic ultrasound, with its highest level of detection capacity of smaller pancreatic lesions, is the commonly employed and preferred clinical imaging-based PDAC detection method. Various molecular biomarkers have been investigated for characterization of the disease, but none are shown to be useful or validated for clinical utilization for early detection. As seen from studies of a small subset of familial or genetically high-risk PDAC groups, the higher yield and utility of imaging-based screening methods are demonstrated for these groups. Multiple recent studies on the unique cancer metabolism including PDAC, demonstrate the potential for utility of the metabolites as the discriminant markers for this disease. In order to generate an early PDAC detection screening strategy available for a wider population, we propose to expand the population of higher risk PDAC group with combination clinical and metabolomics parameters.
Collapse
|