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Young N, Gui Z, Mustafa S, Papa K, Jessop E, Ruddell E, Bevington L, Quinlan RA, Benham AM, Goldberg MW, Obara B, Karakesisoglou I. Inhibition of PDIs Downregulates Core LINC Complex Proteins, Promoting the Invasiveness of MDA-MB-231 Breast Cancer Cells in Confined Spaces In Vitro. Cells 2024; 13:906. [PMID: 38891038 PMCID: PMC11172124 DOI: 10.3390/cells13110906] [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: 04/17/2024] [Revised: 05/17/2024] [Accepted: 05/18/2024] [Indexed: 06/20/2024] Open
Abstract
Eukaryotic cells tether the nucleoskeleton to the cytoskeleton via a conserved molecular bridge, called the LINC complex. The core of the LINC complex comprises SUN-domain and KASH-domain proteins that directly associate within the nuclear envelope lumen. Intra- and inter-chain disulphide bonds, along with KASH-domain protein interactions, both contribute to the tertiary and quaternary structure of vertebrate SUN-domain proteins. The significance of these bonds and the role of PDIs (protein disulphide isomerases) in LINC complex biology remains unclear. Reducing and non-reducing SDS-PAGE analyses revealed a prevalence of SUN2 homodimers in non-tumorigenic breast epithelia MCF10A cells, but not in the invasive triple-negative breast cancer MDA-MB-231 cell line. Furthermore, super-resolution microscopy revealed SUN2 staining alterations in MCF10A, but not in MDA-MB-231 nuclei, upon reducing agent exposure. While PDIA1 levels were similar in both cell lines, pharmacological inhibition of PDI activity in MDA-MB-231 cells led to SUN-domain protein down-regulation, as well as Nesprin-2 displacement from the nucleus. This inhibition also caused changes in perinuclear cytoskeletal architecture and lamin downregulation, and increased the invasiveness of PDI-inhibited MDA-MB-231 cells in space-restrictive in vitro environments, compared to untreated cells. These results emphasise the key roles of PDIs in regulating LINC complex biology, cellular architecture, biomechanics, and invasion.
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Affiliation(s)
- Natalie Young
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Zizhao Gui
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Suleiman Mustafa
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK; (S.M.); (B.O.)
| | - Kleopatra Papa
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Emily Jessop
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Elizabeth Ruddell
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Laura Bevington
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Roy A. Quinlan
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Adam M. Benham
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Martin W. Goldberg
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
| | - Boguslaw Obara
- School of Computing, Newcastle University, Newcastle upon Tyne NE4 5TG, UK; (S.M.); (B.O.)
| | - Iakowos Karakesisoglou
- Department of Biosciences, Durham University, Durham DH1 3LE, UK; (N.Y.); (Z.G.); (K.P.); (E.J.); (E.R.); (L.B.); (R.A.Q.); (A.M.B.); (M.W.G.)
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Nechanitzky R, Ramachandran P, Nechanitzky D, Li WY, Wakeham AC, Haight J, Saunders ME, Epelman S, Mak TW. CaSSiDI: novel single-cell "Cluster Similarity Scoring and Distinction Index" reveals critical functions for PirB and context-dependent Cebpb repression. Cell Death Differ 2024; 31:265-279. [PMID: 38383888 PMCID: PMC10923835 DOI: 10.1038/s41418-024-01268-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 01/15/2024] [Accepted: 02/07/2024] [Indexed: 02/23/2024] Open
Abstract
PirB is an inhibitory cell surface receptor particularly prominent on myeloid cells. PirB curtails the phenotypes of activated macrophages during inflammation or tumorigenesis, but its functions in macrophage homeostasis are obscure. To elucidate PirB-related functions in macrophages at steady-state, we generated and compared single-cell RNA-sequencing (scRNAseq) datasets obtained from myeloid cell subsets of wild type (WT) and PirB-deficient knockout (PirB KO) mice. To facilitate this analysis, we developed a novel approach to clustering parameter optimization called "Cluster Similarity Scoring and Distinction Index" (CaSSiDI). We demonstrate that CaSSiDI is an adaptable computational framework that facilitates tandem analysis of two scRNAseq datasets by optimizing clustering parameters. We further show that CaSSiDI offers more advantages than a standard Seurat analysis because it allows direct comparison of two or more independently clustered datasets, thereby alleviating the need for batch-correction while identifying the most similar and different clusters. Using CaSSiDI, we found that PirB is a novel regulator of Cebpb expression that controls the generation of Ly6Clo patrolling monocytes and the expansion properties of peritoneal macrophages. PirB's effect on Cebpb is tissue-specific since it was not observed in splenic red pulp macrophages (RPMs). However, CaSSiDI revealed a segregation of the WT RPM population into a CD68loIrf8+ "neuronal-primed" subset and an CD68hiFtl1+ "iron-loaded" subset. Our results establish the utility of CaSSiDI for single-cell assay analyses and the determination of optimal clustering parameters. Our application of CaSSiDI in this study has revealed previously unknown roles for PirB in myeloid cell populations. In particular, we have discovered homeostatic functions for PirB that are related to Cebpb expression in distinct macrophage subsets.
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Affiliation(s)
- Robert Nechanitzky
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.
- Providence Therapeutics Holdings Inc., Calgary, AB, Canada.
| | - Parameswaran Ramachandran
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Duygu Nechanitzky
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Wanda Y Li
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China
| | - Andrew C Wakeham
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Jillian Haight
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Mary E Saunders
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
| | - Slava Epelman
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Ted Rogers Centre for Heart Research, Translational Biology and Engineering Program, Toronto, ON, Canada
- Peter Munk Cardiac Centre, UHN, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Departments of Immunology and Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Tak W Mak
- Princess Margaret Cancer Centre, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada.
- Centre for Oncology and Immunology, Hong Kong Science Park, Hong Kong SAR, China.
- Department of Pathology Department of Pathology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.
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3
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Wang Y, Hu Y, Wang M, Wang M, Xu Y. The Role of Breast Cancer Cells in Bone Metastasis: Suitable Seeds for Nourishing Soil. Curr Osteoporos Rep 2024; 22:28-43. [PMID: 38206556 DOI: 10.1007/s11914-023-00849-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
PURPOSE OF REVIEW The purpose of this review was to describe the characteristics of breast cancer cells prone to developing bone metastasis and determine how they are regulated by the bone microenvironment. RECENT FINDINGS The bone is a site of frequent breast cancer metastasis. Bone metastasis accounts for 70% of advanced breast cancer cases and remains incurable. It can lead to skeletal-related events, such as bone fracture and pain, and seriously affect the quality of life of patients. Breast cancer cells escape from the primary lesion and spread to the bone marrow in the early stages. They can then enter the dormant state and restore tumourigenicity after several years to develop overt metastasis. In the last few years, an increasing number of studies have reported on the factors promoting bone metastasis of breast cancer cells, both at the primary and metastatic sites. Identifying factors associated with bone metastasis aids in the early recognition of bone metastasis tendency. How to target these factors and minimize the side effects on the bone remains to be further explored.
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Affiliation(s)
- Yiou Wang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yue Hu
- Department of Outpatient, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Mozhi Wang
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China
| | - Mengshen Wang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yingying Xu
- Department of Breast Surgery, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning, China.
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Ren F, Jin Q, Liu T, Ren X, Zhan Y. Proteome-wide mendelian randomization study implicates therapeutic targets in common cancers. J Transl Med 2023; 21:646. [PMID: 37735436 PMCID: PMC10512580 DOI: 10.1186/s12967-023-04525-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 09/13/2023] [Indexed: 09/23/2023] Open
Abstract
BACKGROUND The interest in targeted cancer therapies has been growing rapidly. While numerous cancer biomarkers and targeted treatment strategies have been developed and employed, there are still significant limitations and challenges in the early diagnosis and targeted treatment of cancers. Accordingly, there is an urgent need to identify novel targets and develop new targeted drugs. METHODS The study was conducted using combined cis-Mendelian randomization (cis-MR) and colocalization analysis. We analyzed data from 732 plasma proteins to identify potential drug targets associated with eight site-specific cancers. These findings were further validated using the UK Biobank dataset. Then, a protein-protein interaction network was also constructed to examine the interplay between the identified proteins and the targets of existing cancer medications. RESULTS This MR analysis revealed associations between five plasma proteins and prostate cancer, five with breast cancer, and three with lung cancer. Subsequently, these proteins were classified into four distinct target groups, with a focus on tier 1 and 2 targets due to their higher potential to become drug targets. Our study indicatied that genetically predicted KDELC2 (OR: 0.89, 95% CI 0.86-0.93) and TNFRSF10B (OR: 0.74, 95% CI 0.65-0.83) are inversely associated with prostate cancer. Furthermore, we observed an inverse association between CPNE1 (OR: 0.96, 95% CI 0.94-0.98) and breast cancer, while PDIA3 (OR: 1.19, 95% CI 1.10-1.30) were found to be associated with the risk of breast cancer. In addition, we also propose that SPINT2 (OR: 1.05, 95% CI 1.03-1.06), GSTP1 (OR: 0.82, 95% CI 0.74-0.90), and CTSS (OR: 0.91, 95% CI 0.88-0.95) may serve as potential therapeutic targets in prostate cancer. Similarly, GDI2 (OR: 0.85, 95% CI 0.80-0.91), ISLR2 (OR: 0.87, 95% CI 0.82-0.93), and CTSF (OR: 1.14, 95% CI 1.08-1.21) could potentially be targets for breast cancer. Additionally, we identified SFTPB (OR: 0.93, 95% CI 0.91-0.95), ICAM5 (OR: 0.95, 95% CI 0.93-0.97), and FLRT3 (OR: 1.10, 95% CI 1.05-1.15) as potential targets for lung cancer. Notably, TNFRSF10B, GSTP1, and PDIA3 were found to interact with the target proteins of current medications used in prostate or breast cancer treatment. CONCLUSIONS This comprehensive analysis has highlighted thirteen plasma proteins with potential roles in three site-specific cancers. Continued research in this area may reveal their therapeutic potential, particularly KDELC2, TNFRSF10B, CPNE1, and PDIA3, paving the way for more effective cancer treatments.
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Affiliation(s)
- Feihong Ren
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
- Graduate School, Beijing University of Chinese Medicine, Beijing, 100029, China
| | - Qiubai Jin
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Tongtong Liu
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Xuelei Ren
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China
| | - Yongli Zhan
- Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing, 100053, China.
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Githaka JM, Pirayeshfard L, Goping IS. Cancer invasion and metastasis: Insights from murine pubertal mammary gland morphogenesis. Biochim Biophys Acta Gen Subj 2023; 1867:130375. [PMID: 37150225 DOI: 10.1016/j.bbagen.2023.130375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 04/20/2023] [Accepted: 05/02/2023] [Indexed: 05/09/2023]
Abstract
Cancer invasion and metastasis accounts for the majority of cancer related mortality. A better understanding of the players that drive the aberrant invasion and migration of tumors cells will provide critical targets to inhibit metastasis. Postnatal pubertal mammary gland morphogenesis is characterized by highly proliferative, invasive, and migratory normal epithelial cells. Identifying the molecular regulators of pubertal gland development is a promising strategy since tumorigenesis and metastasis is postulated to be a consequence of aberrant reactivation of developmental stages. In this review, we summarize the pubertal morphogenesis regulators that are involved in cancer metastasis and revisit pubertal mammary gland transcriptome profiling to uncover both known and unknown metastasis genes. Our updated list of pubertal morphogenesis regulators shows that most are implicated in invasion and metastasis. This review highlights molecular linkages between development and metastasis and provides a guide for exploring novel metastatic drivers.
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Affiliation(s)
- John Maringa Githaka
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada.
| | - Leila Pirayeshfard
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Ing Swie Goping
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; Department of Oncology, University of Alberta, Edmonton, AB T6G 2H7, Canada.
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Gelzinis JA, Szahaj MK, Bekendam RH, Wurl SE, Pantos MM, Verbetsky CA, Dufresne A, Shea M, Howard KC, Tsodikov OV, Garneau-Tsodikova S, Zwicker JI, Kennedy DR. Targeting thiol isomerase activity with zafirlukast to treat ovarian cancer from the bench to clinic. FASEB J 2023; 37:e22914. [PMID: 37043381 PMCID: PMC10360043 DOI: 10.1096/fj.202201952r] [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: 11/21/2022] [Revised: 03/06/2023] [Accepted: 03/29/2023] [Indexed: 04/13/2023]
Abstract
Thiol isomerases, including PDI, ERp57, ERp5, and ERp72, play important and distinct roles in cancer progression, cancer cell signaling, and metastasis. We recently discovered that zafirlukast, an FDA-approved medication for asthma, is a pan-thiol isomerase inhibitor. Zafirlukast inhibited the growth of multiple cancer cell lines with an IC50 in the low micromolar range, while also inhibiting cellular thiol isomerase activity, EGFR activation, and downstream phosphorylation of Gab1. Zafirlukast also blocked the procoagulant activity of OVCAR8 cells by inhibiting tissue factor-dependent Factor Xa generation. In an ovarian cancer xenograft model, statistically significant differences in tumor size between control vs treated groups were observed by Day 18. Zafirlukast also significantly reduced the number and size of metastatic tumors found within the lungs of the mock-treated controls. When added to a chemotherapeutic regimen, zafirlukast significantly reduced growth, by 38% compared with the mice receiving only the chemotherapeutic treatment, and by 83% over untreated controls. Finally, we conducted a pilot clinical trial in women with tumor marker-only (CA-125) relapsed ovarian cancer, where the rate of rise of CA-125 was significantly reduced following treatment with zafirlukast, while no severe adverse events were reported. Thiol isomerase inhibition with zafirlukast represents a novel, well-tolerated therapeutic in the treatment of ovarian cancer.
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Affiliation(s)
- Justine A. Gelzinis
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA
- Institute for Cardiovascular & Metabolic Research, School of Biological Sciences, University of Reading, UK
| | - Melanie K. Szahaj
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA
| | - Roelof H. Bekendam
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Sienna E. Wurl
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA
| | - Megan M. Pantos
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA
| | - Christina A. Verbetsky
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA
| | - Alexandre Dufresne
- Baystate Research Facility, Baystate Medical Center and UMass Chan Medical School, Springfield, MA
| | - Meghan Shea
- Division of Oncology, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
| | - Kaitlind C. Howard
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536
| | - Sylvie Garneau-Tsodikova
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, 789 S. Limestone St., Lexington, KY 40536
| | - Jeffrey I. Zwicker
- Division of Hemostasis and Thrombosis, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA
- These authors contributed equally
| | - Daniel R. Kennedy
- College of Pharmacy and Health Sciences, Western New England University, Springfield, MA
- Institute for Cardiovascular & Metabolic Research, School of Biological Sciences, University of Reading, UK
- Department of Medicine, UMass Chan Medical School-Baystate, Springfield, MA
- These authors contributed equally
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Germon A, Heesom KJ, Amoah R, Adams JC. Protein disulfide isomerase A3 activity promotes extracellular accumulation of proteins relevant to basal breast cancer outcomes in human MDA-MB-A231 breast cancer cells. Am J Physiol Cell Physiol 2023; 324:C113-C132. [PMID: 36374169 PMCID: PMC9799142 DOI: 10.1152/ajpcell.00445.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Metastasis and recurrence of breast cancer remain major causes of patient mortality, and there is an ongoing need to identify new therapeutic targets relevant to tumor invasion. Protein disulfide isomerase A3 (PDIA3) is a disulfide oxidoreductase and isomerase of the endoplasmic reticulum that has known extracellular substrates and has been correlated with aggressive breast cancers. We show that either prior PDIA3 inhibition by the disulfide isomerase inhibitor 16F16 or depletion of heparin-binding proteins strongly reduces the activity of conditioned medium (CM) of MDA-MB-231 human breast cancer cells to support promigratory cell spreading and F-actin organization by newly adherent MDA-MB-231 cells. Quantitative proteomics to investigate effects of 16F16 inhibition on heparin-binding proteins in the CM of MDA-MB-231 cells identified 80 proteins reproducibly decreased at least twofold (at q ≤ 0.05) after 16F16 treatment. By Gene Ontology analysis, many of these have roles in extracellular matrix (ECM) structure and function and cell adhesion; ribosomal proteins that also correlate with extracellular vesicles were also identified. Protein-protein interaction analysis showed that many of the extracellular proteins have known network interactions with each other. The predominant types of disulfide-bonded domains in the extracellular proteins contained β-hairpin folds, with the knottin fold the most common. From human breast cancer data sets, the extracellular proteins were found to correlate specifically with the basal subtype of breast cancer and their high expression in tumors correlated with reduced distant metastasis-free survival. These data provide new evidence that PDIA3 may be a relevant therapeutic target to alter properties of the ECM-associated microenvironment in basal breast cancer.
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Affiliation(s)
- Anna Germon
- 1School of Biochemistry, https://ror.org/0524sp257University of Bristol, Bristol, United Kingdom
| | - Kate J. Heesom
- 2University of Bristol Proteomics Facility, University of Bristol, Bristol, United Kingdom
| | - Reiss Amoah
- 1School of Biochemistry, https://ror.org/0524sp257University of Bristol, Bristol, United Kingdom
| | - Josephine C. Adams
- 1School of Biochemistry, https://ror.org/0524sp257University of Bristol, Bristol, United Kingdom
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Zhang H, Zhou Y, Cheng Q, Dai Z, Wang Z, Liu F, Fan F, Cui B, Cao H. PDIA3 correlates with clinical malignant features and immune signature in human gliomas. Aging (Albany NY) 2021; 12:15392-15413. [PMID: 32687065 PMCID: PMC7467394 DOI: 10.18632/aging.103601] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Accepted: 06/13/2020] [Indexed: 01/03/2023]
Abstract
Since therapeutic strategies are limited in gliomas, new molecules or biomarkers are essential for diagnosis and therapy. Here, we investigated expression of protein disulfide isomerase family A member 3 (PDIA3) in gliomas to evaluate its potential as a promising immune target or biomarker. Transcriptome level, genomic profiles and its association with clinical practice from TCGA and CGGA databases were analyzed. All statistical analyses were performed using R project. In gliomas with high PDIA3 expression, somatic mutations showed the correlation with loss of PTEN and amplification of EGFR; meanwhile, in PDIA3 low gliomas, mutations in isocitrate dehydrogenase (IDH) took 80%. Moreover, PDIA3 was found to positively correlate with ESTIMATE scores and diverse infiltrating immune and stromal cell types localizing in tumor microenvironment. PDIA3 was found to be highly correlated with macrophage and T cells based on single cell sequencing. Additionally, PDIA3 was also involved in suppression of anti-tumor immunity via multiple immune regulatory processes. Finally, PDIA3 was observed to correlate with other immune checkpoint inhibitors and associated with inflammation. Our findings identified the significance of PDIA3 in the process of gliomas and demonstrated the potential of PDIA3 as a molecular target in prognosis and immune related treatment of gliomas
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Affiliation(s)
- Hao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,Equal contribution
| | - Yulai Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Equal contribution
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Hunan, China
| | - Ziyu Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zeyu Wang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Fangkun Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Fan Fan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Biqi Cui
- Department of Neurology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Hui Cao
- Department of Psychiatry, The Second People’s Hospital of Hunan Province, The Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
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9
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Impairment of cell adhesion and migration by inhibition of protein disulphide isomerases in three breast cancer cell lines. Biosci Rep 2021; 40:226652. [PMID: 33095243 PMCID: PMC7584814 DOI: 10.1042/bsr20193271] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 09/25/2020] [Accepted: 10/05/2020] [Indexed: 12/30/2022] Open
Abstract
Protein disulphide isomerase A3 (PDIA3) is an endoplasmic reticulum (ER)-resident disulphide isomerase and oxidoreductase with known substrates that include some extracellular matrix (ECM) proteins. PDIA3 is up-regulated in invasive breast cancers and correlates in a mouse orthotopic xenograft model with breast cancer metastasis to bone. However, the underlying cellular mechanisms remain unclear. Here we investigated the function of protein disulphide isomerases in attachment, spreading and migration of three human breast cancer lines representative of luminal (MCF-7) or basal (MDA-MB-231 and HCC1937) tumour phenotypes. Pharmacological inhibition by 16F16 decreased initial cell spreading more effectively than inhibition by PACMA-31. Cells displayed diminished cortical F-actin projections, stress fibres and focal adhesions. Cell migration was reduced in a quantified ‘scratch wound’ assay. To examine whether these effects might result from alterations to secreted proteins in the absence of functional PDIA3, adhesion and migration were quantified in the above cells exposed to media conditioned by wildtype (WT) or Pdia3−/− mouse embryonic fibroblasts (MEFs). The conditioned medium (CM) of Pdia3−/− MEFs was less effective in promoting cell spreading and F-actin organisation or supporting ‘scratch wound’ closure. Similarly, ECM prepared from HCC1937 cells after 16F16 inhibition was less effective than control ECM to support spreading of untreated HCC1937 cells. Overall, these results advance the concept that protein disulphide isomerases including PDIA3 drive the production of secreted proteins that promote a microenvironment favourable to breast cancer cell adhesion and motility, characteristics that are integral to tumour invasion and metastasis. Inhibition of PDIA3 or related isomerases may have potential for anti-metastatic therapies.
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10
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Hua P, Zhang Y, Jin C, Zhang G, Wang B. Integration of gene profile to explore the hub genes of lung adenocarcinoma: A quasi-experimental study. Medicine (Baltimore) 2020; 99:e22727. [PMID: 33120770 PMCID: PMC7581154 DOI: 10.1097/md.0000000000022727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Lung cancer is a leading cause of morbidity diseases worldwide, but the key mechanisms of lung cancer remain elusive. This study aims to integrate of GSE 118370 and GSE 32863 profile and identify the key genes and pathway involved in human lung adenocarcinoma. METHODS R software (RStudio, Version info: R 3.2.3, Forrester, USA) were utilized to find the differentially expressed genes. All the differentially expressed genes were analyzed by gene ontology, kyoto encyclopedia of genes and genomes. Protein-protein interaction networks were constructed by STRING database and analyzed by Cytohubber and Module. The cancer genome atlas database was used to verification the expression of hub genes. Quantitative reverse transcription-PCR was used to verify the bio-information results. RESULTS Sixty-four lung adenocarcinoma and 64 adjacent normal tissues were used for integration analysis. Five hundred ninety-nine co-expression genes were locked. Biological processes mainly enriched in angiogenesis. Cellular component focused on extracellular exosome and molecular function aimed on protein disulfide isomerase activity. Cytohubber analysis showed that GNG11, FPR2, P4HB, PIK3R1, CDC20, ADCY4, TIMP1, IL6, CXC chemokine ligand (CXCL)12, and GAS6 acted as the hub genes during lung adenocarcinoma. Module analysis presented Chemokine signaling pathway was a key pathway. Quantitative reverse transcription-PCR showed that the expression level of GNG11, FPR2, PIK3R1, ADCY4, IL6, CXCL12, and GAS6 were significantly decreased and P4HB, CDC20 and TIMP1 were increased in human adenocarcinoma tissues (P < .05). The cancer genome atlas online analysis showed GNG11 was not associated with survival. CONCLUSIONS This study firstly reported GNG11 acting as a hub gene in adenocarcinoma. GNG11 could be used as a biomarker for human adenocarcinoma. Chemokine signaling pathway might play important roles in lung adenocarcinoma.
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11
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Machine learning and data mining frameworks for predicting drug response in cancer: An overview and a novel in silico screening process based on association rule mining. Pharmacol Ther 2019; 203:107395. [DOI: 10.1016/j.pharmthera.2019.107395] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 07/11/2019] [Indexed: 12/20/2022]
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12
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Plasma proteomic and autoantibody profiles reveal the proteomic characteristics involved in longevity families in Bama, China. Clin Proteomics 2019; 16:22. [PMID: 31139026 PMCID: PMC6526601 DOI: 10.1186/s12014-019-9242-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 05/15/2019] [Indexed: 12/23/2022] Open
Abstract
Background Chinese Bama Yao Autonomous County is a well-known longevity region in the world. In the past 30 years, population and genome studies were undertaken to investigate the secret of longevity and showed that longevity is the result of a combination of multiple factors, such as genetic, environmental and other causes. In this study, characteristics of the blood plasma proteomic and autoantibody profiles of people from Bama longevity family were investigated. Methods Sixty-six plasma donors from Chinese Bama longevity area were recruited in this study. Thirty-three offsprings of longevous families were selected as case studies (Longevous group) and 33 ABO (blood type), age, and gender-matched subjects from non-longevous families were selected as controls (Normal group). Each group contains 3 biological replicates. Tandem mass tag-based proteomic technique was used to investigate the differentially expressed plasma proteins between the two groups. The auto-reactive IgG antibody profiles of the 3 pooled samples in each group were revealed by human proteome microarrays with 17,000 recombinant human proteins. Results Firstly, 525 plasma proteins were quantified and 12 proteins were discovered differentially expressed between the two groups. Secondly, more than 500 proteins were recognized by plasma antibodies, 14 proteins ware differentially reacted with the autoantibodies in the two groups. Bioinformatics analysis showed some of the differential proteins and targeted autoantigens were involved in cancer, cardiovascular disease and immunity. Conclusions Proteomic and autoantibody profiles varied between the offspring of longevous and normal families which are from the same area and shared the same environmental factors. The identified differences were reported to be involved in several physiological and pathological pathways. The identified proteins will contribute to a better understanding of the proteomic characteristics of people from Bama longevous area and a revelation of the molecular mechanisms of longevity.
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13
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Würfel FM, Winterhalter C, Trenkwalder P, Wirtz RM, Würfel W. European Patent in Immunoncology: From Immunological Principles of Implantation to Cancer Treatment. Int J Mol Sci 2019; 20:ijms20081830. [PMID: 31013867 PMCID: PMC6514949 DOI: 10.3390/ijms20081830] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/09/2019] [Accepted: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
The granted European patent EP 2 561 890 describes a procedure for an immunological treatment of cancer. It is based on the principles of the HLA-supported communication of implantation and pregnancy. These principles ensure that the embryo is not rejected by the mother. In pregnancy, the placenta, more specifically the trophoblast, creates an “interface” between the embryo/fetus and the maternal immune system. Trophoblasts do not express the “original” HLA identification of the embryo/fetus (HLA-A to -DQ), but instead show the non-classical HLA groups E, F, and G. During interaction with specific receptors of NK cells (e.g., killer-immunoglobulin-like receptors (KIR)) and lymphocytes (lymphocyte-immunoglobulin-like receptors (LIL-R)), the non-classical HLA groups inhibit these immunocompetent cells outside pregnancy. However, tumors are known to be able to express these non-classical HLA groups and thus make use of an immuno-communication as in pregnancies. If this occurs, the prognosis usually worsens. This patent describes, in a first step, the profiling of the non-classical HLA groups in primary tumor tissue as well as metastases and recurrent tumors. The second step comprises tailored antibody therapies, which is the subject of this patent. In this review, we analyze the underlying mechanisms and describe the currently known differences between HLA-supported communication of implantation and that of tumors.
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Affiliation(s)
- Franziska M Würfel
- STRATIFYER Molecular Pathology GmbH, D-50935 Cologne, Werthmannstrasse 1c, 50935 Cologne, Germany.
| | | | | | - Ralph M Wirtz
- STRATIFYER Molecular Pathology GmbH, D-50935 Cologne, Werthmannstrasse 1c, 50935 Cologne, Germany.
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14
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Westbrook JA, Wood SL, Cairns DA, McMahon K, Gahlaut R, Thygesen H, Shires M, Roberts S, Marshall H, Oliva MR, Dunning MJ, Hanby AM, Selby PJ, Speirs V, Mavria G, Coleman RE, Brown JE. Identification and validation of DOCK4 as a potential biomarker for risk of bone metastasis development in patients with early breast cancer. J Pathol 2019; 247:381-391. [PMID: 30426503 PMCID: PMC6618075 DOI: 10.1002/path.5197] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 10/04/2018] [Accepted: 10/30/2018] [Indexed: 12/12/2022]
Abstract
Skeletal metastasis occurs in around 75% of advanced breast cancers, with the disease incurable once cancer cells disseminate to bone, but there remains an unmet need for biomarkers to identify patients at high risk of bone recurrence. This study aimed to identify such a biomarker and to assess its utility in predicting response to adjuvant zoledronic acid (zoledronate). We used quantitative proteomics (stable isotope labelling by amino acids in cell culture-mass spectrometry; SILAC-MS) to compare protein expression in a bone-homing variant (BM1) of the human breast cancer cell line MDA-MB-231 with parental non-bone-homing cells to identify novel biomarkers for risk of subsequent bone metastasis in early breast cancer. SILAC-MS showed that dedicator of cytokinesis protein 4 (DOCK4) was upregulated in bone-homing BM1 cells, confirmed by western blotting. BM1 cells also had enhanced invasive ability compared with parental cells, which could be reduced by DOCK4-shRNA. In a training tissue microarray (TMA) comprising 345 patients with early breast cancer, immunohistochemistry followed by Cox regression revealed that high DOCK4 expression correlated with histological grade (p = 0.004) but not oestrogen receptor status (p = 0.19) or lymph node involvement (p = 0.15). A clinical validation TMA used tissue samples and the clinical database from the large AZURE adjuvant study (n = 689). Adjusted Cox regression analyses showed that high DOCK4 expression in the control arm (no zoledronate) was significantly prognostic for first recurrence in bone (HR 2.13, 95%CI 1.06-4.30, p = 0.034). No corresponding association was found in patients who received zoledronate (HR 0.812, 95%CI 0.176-3.76, p = 0.790), suggesting that treatment with zoledronate may counteract the higher risk for bone relapse from high DOCK4-expressing tumours. High DOCK4 expression was not associated with metastasis to non-skeletal sites when these were assessed collectively. In conclusion, high DOCK4 in early breast cancer is significantly associated with aggressive disease and with future bone metastasis and is a potentially useful biomarker for subsequent bone metastasis risk. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Jules A Westbrook
- Department of Oncology and Metabolism, Academic Unit of Clinical OncologyUniversity of SheffieldSheffieldUK
- Clinical and Biomedical Proteomics GroupLeeds Institute of Cancer and Pathology, University of LeedsLeedsUK
| | - Steven L Wood
- Department of Oncology and Metabolism, Academic Unit of Clinical OncologyUniversity of SheffieldSheffieldUK
- Clinical and Biomedical Proteomics GroupLeeds Institute of Cancer and Pathology, University of LeedsLeedsUK
| | - David A Cairns
- Clinical and Biomedical Proteomics GroupLeeds Institute of Cancer and Pathology, University of LeedsLeedsUK
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials ResearchUniversity of LeedsLeedsUK
| | - Kathryn McMahon
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
| | - Renu Gahlaut
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
| | - Helene Thygesen
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
| | - Mike Shires
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
| | - Stephanie Roberts
- Clinical and Biomedical Proteomics GroupLeeds Institute of Cancer and Pathology, University of LeedsLeedsUK
| | - Helen Marshall
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials ResearchUniversity of LeedsLeedsUK
| | - Maria R Oliva
- Department of Oncology and Metabolism, Academic Unit of Clinical OncologyUniversity of SheffieldSheffieldUK
| | - Mark J Dunning
- Sheffield Institute of Translational NeuroscienceUniversity of SheffieldSheffieldUK
| | - Andrew M Hanby
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
| | - Peter J Selby
- Clinical and Biomedical Proteomics GroupLeeds Institute of Cancer and Pathology, University of LeedsLeedsUK
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
| | - Valerie Speirs
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
- Institute of Medical SciencesUniversity of AberdeenAberdeenUK
| | - Georgia Mavria
- Leeds Institute of Cancer and PathologyUniversity of LeedsLeedsUK
| | - Robert E Coleman
- Department of Oncology and Metabolism, Academic Unit of Clinical OncologyUniversity of SheffieldSheffieldUK
| | - Janet E Brown
- Department of Oncology and Metabolism, Academic Unit of Clinical OncologyUniversity of SheffieldSheffieldUK
- Clinical and Biomedical Proteomics GroupLeeds Institute of Cancer and Pathology, University of LeedsLeedsUK
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15
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Li S, Zhao X, Chang S, Li Y, Guo M, Guan Y. ERp57‑small interfering RNA silencing can enhance the sensitivity of drug‑resistant human ovarian cancer cells to paclitaxel. Int J Oncol 2018; 54:249-260. [PMID: 30431082 DOI: 10.3892/ijo.2018.4628] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Accepted: 10/08/2018] [Indexed: 11/05/2022] Open
Abstract
ERp57 has been identified to be associated with the chemoresistance of human ovarian cancer. However, its biological roles in the chemoresistance phenotype remain unclear. In the present study, the association of ERp57 with paclitaxel‑resistant cellular behavior was investigated and the sensitivity enhancement of chemoresistant human ovarian cancer cells to paclitaxel was examined using ERp57‑small interfering (si)RNA silencing. Cell viability, cell proliferation, cell apoptosis and cell migration were detected using an MTT assay, clonogenic assay, flow cytometry analysis and transwell assay. Furthermore, mRNA expression levels of ERp57 and protein expression levels of ERp57, STAT3, phosphorylated STAT3, PCNA, nucelolin, TUBB3, P-gp, vimentin, Bcl-2, Bax, Bcl-xl, p53, MMP1, MMP2 and MMP9 of paclitaxel-sensitive human SKOV3 ovarian cancer cells were compared with paclitaxel-resistant counterpart SKOV3/tax using the real-time PCR and western blot analysis. ERp57 was highly expressed in the paclitaxel‑resistant SKOV3/tax cells, and experimental results concluded that the paclitaxel‑resistance phenotype was due primarily to the activation of the STAT3 signaling pathway. ERp57 overexpression by lentiviral particle infection decreased the sensitivity of SKOV3 cells to paclitaxel. Furthermore, ERp57‑siRNA silencing restored paclitaxel sensitivity of SKOV3/tax cells. Notably, the IC50 value of ERp57‑siRNA silenced SKOV3/tax cells was reduced to the original level and colony survival was significantly decreased in comparison with that of SKOV3/tax cells. Additionally, co‑treatment of ERp57‑siRNA silencing and paclitaxel could inhibit the STAT3 signaling pathway and downregulate the expression levels of downstream proteins. Notably, ERp57‑siRNA and 100 nM paclitaxel co‑treatment downregulated Bcl‑2, Bcl‑xl, MMP2, MMP9, TUBB3 and P‑gp expression levels and upregulated the expression of Bax protein. Furthermore, co‑treatment promoted change of the isoform of p53 to p53/p47. Bioinformatics analyses supported the experimental observations that ERp57 was associated with drug resistance in ovarian cancer. The present study implies that ERp57 is a potential therapeutic target for the treatment of paclitaxel‑resistant human ovarian cancer.
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Affiliation(s)
- Shuo Li
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Xiaoyun Zhao
- Department of Microbiology and Cell Biology, Shenyang Pharmaceutical University, Shenyang, Liaoning 110016, P.R. China
| | - Shijie Chang
- Department of Biomedical Engineering, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yanqiu Li
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Min Guo
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110122, P.R. China
| | - Yifu Guan
- Department of Biochemistry and Molecular Biology, China Medical University, Shenyang, Liaoning 110122, P.R. China
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16
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Park S, Park JH, Jung HJ, Jang JH, Ahn S, Kim Y, Suh PG, Chae S, Yoon JH, Ryu SH, Hwang D. A secretome profile indicative of oleate-induced proliferation of HepG2 hepatocellular carcinoma cells. Exp Mol Med 2018; 50:1-14. [PMID: 30076294 PMCID: PMC6076227 DOI: 10.1038/s12276-018-0120-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Revised: 03/18/2018] [Accepted: 04/13/2018] [Indexed: 12/13/2022] Open
Abstract
Increased fatty acid (FA) is often observed in highly proliferative tumors. FAs have been shown to modulate the secretion of proteins from tumor cells, contributing to tumor survival. However, the secreted factors affected by FA have not been systematically explored. Here, we found that treatment of oleate, a monounsaturated omega-9 FA, promoted the proliferation of HepG2 cells. To examine the secreted factors associated with oleate-induced cell proliferation, we performed a comprehensive secretome profiling of oleate-treated and untreated HepG2 cells. A comparison of the secretomes identified 349 differentially secreted proteins (DSPs; 145 upregulated and 192 downregulated) in oleate-treated samples, compared to untreated samples. The functional enrichment and network analyses of the DSPs revealed that the 145 upregulated secreted proteins by oleate treatment were mainly associated with cell proliferation-related processes, such as lipid metabolism, inflammatory response, and ER stress. Based on the network models of the DSPs, we selected six DSPs (MIF, THBS1, PDIA3, APOA1, FASN, and EEF2) that can represent such processes related to cell proliferation. Thus, our results provided a secretome profile indicative of an oleate-induced proliferation of HepG2 cells. By exposing liver cancer cells to oleate, an unsaturated fatty acid, researchers have discovered a group of secreted proteins that may help explain why fatty acids increase proliferative capacity in tumors. Soyeon Park from Pohang University of Science and Technology in South Korea and coworkers treated liver cancer cells with oleate and then measured all the proteins released from the cells. Comparison with untreated cells revealed 145 proteins secreted at elevated levels—most of which were involved in metabolism, stress responses and other proliferation-related processes—and another 192 proteins secreted at reduced levels. The researchers ran additional biochemical analyses on six secreted proteins to validate the changes following exposure to oleate. The authors suggest that these validated proteins could now serve as biomarkers of tumor aggressiveness or as future drug targets.
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Affiliation(s)
- Soyeon Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, 37673, Republic of Korea
| | - Ji-Hwan Park
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Hee-Jung Jung
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Jin-Hyeok Jang
- Department of Brain and Cognitive Sciences, Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Republic of Korea
| | - Sanghyun Ahn
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Younah Kim
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Pann-Ghill Suh
- School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
| | - Sehyun Chae
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea
| | - Jong Hyuk Yoon
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, 37673, Republic of Korea. .,Department of Neural Development and Disease, Korea Brain Research Institute, Daegu, 41068, Republic of Korea.
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Kyungbuk, 37673, Republic of Korea.
| | - Daehee Hwang
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, 42988, Republic of Korea. .,Department of New Biology, DGIST, Daegu, 42988, Republic of Korea.
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17
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Gebhard C, Miller I, Hummel K, Neschi née Ondrovics M, Schlosser S, Walter I. Comparative proteome analysis of monolayer and spheroid culture of canine osteosarcoma cells. J Proteomics 2018; 177:124-136. [DOI: 10.1016/j.jprot.2018.01.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 12/20/2017] [Accepted: 01/04/2018] [Indexed: 12/13/2022]
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18
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Erin N, Ogan N, Yerlikaya A. Secretomes reveal several novel proteins as well as TGF-β1 as the top upstream regulator of metastatic process in breast cancer. Breast Cancer Res Treat 2018; 170:235-250. [PMID: 29557524 DOI: 10.1007/s10549-018-4752-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/13/2018] [Indexed: 12/11/2022]
Abstract
PURPOSE Metastatic breast cancer is resistant to many conventional treatments and novel therapeutic targets are needed. We previously isolated subsets of 4T1 murine breast cancer cells which metastasized to liver (4TLM), brain (4TBM), and heart (4THM). Among these cells, 4TLM is the most aggressive one, demonstrating mesenchymal phenotype. Here we compared secreted proteins from 4TLM, 4TBM, and 4THM cells and compared with that of hardly metastatic 67NR cells to detect differentially secreted factors involved in organ-specific metastasis. METHOD AND RESULTS Label-free LC-MS/MS proteomic technique was used to detect the differentially secreted proteins. Eighty-five of over 500 secreted proteins were significantly altered in metastatic breast cancer cells. Differential expression of several proteins such as fibulin-4, Bone Morphogenetic Protein 1, TGF-β1 MMP-3, MMP-9, and Thymic Stromal Lymphopoietin were further verified using ELISA or Western blotting. Many of these identified proteins were also present in human metastatic breast carcinomas. Annexin A1 and A5, laminin beta 1, Neutral alpha-glucosidase AB were commonly found at least in three out of six studies examined here. Ingenuity Pathway Analysis showed that proteins differentially secreted from metastatic cells are involved primarily in carcinogenesis and TGF-β1 is the top upstream regulator in all metastatic cells. CONCLUSIONS Cells metastasized to different organs displayed significant differences in several of secreted proteins. Proteins differentially altered were fibronectin, insulin-like growth factor-binding protein 7, and Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 1. On the other hand, many exosomal proteins were also common to all metastatic cells, demonstrating involvement of key universal factors in distant metastatic process.
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Affiliation(s)
- Nuray Erin
- Department of Medical Pharmacology, School of Medicine, Akdeniz University, B-blok kat 1, SBAUM/Immunoloji Lab, Antalya, Turkey.
| | - Nur Ogan
- Department of Medical Pharmacology, School of Medicine, Akdeniz University, B-blok kat 1, SBAUM/Immunoloji Lab, Antalya, Turkey
| | - Azmi Yerlikaya
- Department of Medical Biology, School of Medicine, Dumlupınar University, Kütahya, Turkey
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19
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Abstract
The protein disulfide isomerase (PDI) gene family is a protein family classically characterized by endoplasmic reticulum (ER) localization and isomerase and redox activity. ERp57, a prominent multifunctional member of the PDI family, is detected at various levels in multiple cellular localizations outside of the ER. ERp57 has been functionally linked to a host of physiological processes and numerous studies have demonstrated altered expression and aberrant functionality of ERp57 in association with diverse pathological states. Here, we summarize available knowledge of ERp57's functions in subcellular compartments and the roles of dysregulated ERp57 in various diseases toward an emphasis on the potential utility of therapeutic development of ERp57.
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Affiliation(s)
- Aubryanna Hettinghouse
- Department of Orthopaedic Surgery, New York University Medical Center, New York, NY 10003, USA
| | - Ronghan Liu
- Department of Orthopaedic Surgery, New York University Medical Center, New York, NY 10003, USA
| | - Chuan-Ju Liu
- Department of Orthopaedic Surgery, New York University Medical Center, New York, NY 10003, USA; Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA.
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20
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Protein disulfide isomerase a4 acts as a novel regulator of cancer growth through the procaspase pathway. Oncogene 2017; 36:5484-5496. [PMID: 28534513 DOI: 10.1038/onc.2017.156] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/21/2022]
Abstract
Protein disulfide isomerase a4 (PDIA4) is implicated in the growth and death of tumor cells; however, its molecular mechanism and therapeutic potential in cancer are unclear. Here, we found that PDIA4 expression was upregulated in a variety of tumor cell lines and human lung adenocarcinoma tissues. Knockdown and overexpression of PDIA4 in tumor cells showed that PDIA4 facilitated cell growth via the reduction of caspases 3 and 7 activity. Consistently, Lewis lung carcinoma cells overexpressing PDIA4 grew faster than did parental cells in tumor-bearing mice, as shown by a reduced survival rate, increased tumor size and metastasis, and decreased cell death and caspases 3 and 7 activity. PDIA4 knockdown resulted in opposite outcomes. Moreover, results obtained in mice with spontaneous hepatoma indicated that PDIA4 deficiency significantly reduced hepatic tumorigenesis and cyst formation and increased mouse survival, tumor death, and caspases 3 and 7 activity. Mechanistic studies illustrated that PDIA4 negatively regulated tumor cell death by inhibiting degradation and activation of procaspases 3 and 7 via their mutual interaction in a CGHC-dependent manner. Finally, we found that 1,2-dihydroxytrideca-5,7,9,11-tetrayne, a PDIA4 inhibitor, reduced tumor development via enhancement of caspase-mediated cell death in TSA tumor-bearing mice. These findings characterize PDIA4 as a negative regulator of cancer cell apoptosis and suggest that PDIA4 is a potential therapeutic target for cancer.
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21
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Yuan G, Hua B, Yang Y, Xu L, Cai T, Sun N, Yan Z, Lu C, Qian R. The Circadian Gene Clock Regulates Bone Formation Via PDIA3. J Bone Miner Res 2017; 32:861-871. [PMID: 27883226 DOI: 10.1002/jbmr.3046] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 11/11/2016] [Accepted: 11/19/2016] [Indexed: 11/10/2022]
Abstract
The expression patterns of clock-controlled genes (ccgs) are regulated by circadian rhythm, which is a major regulatory and physiological mechanism tied to the solar day. Disruptions in circadian rhythm contribute to the development of cardiovascular diseases, cancer, metabolic syndromes, and aging. It has been reported that bone remodeling is also regulated by circadian rhythm. However, the molecular mechanism by which the circadian gene Clock regulates bone remodeling has yet to be elucidated. Here, we show that Clock mutant mice exhibit a significant reduction in bone density as well as increased apoptosis. Protein disulfide isomerase family A member 3 (PDIA3) is a 1,25-dihydroxy-vitamin D3 [1α,25(OH)2D3] receptor that can regulate bone formation and apoptosis. Using luciferase and ChIP assays, we confirmed that Pdia3 is a ccg. Clock activates Pdia3 transcription by binding the E-box promoter, and transcription is decreased in ClockΔ19 mutant mice. Forced expression of Pdia3 or of Clock completely rescues the osteogenic disorders found in the mutant background and inhibits apoptosis in vivo and in vitro. Furthermore, ablation of PDIA3 via RNA interference completely blocks the compensatory effect of forced expression of Clock in osteoblasts. Our results demonstrate that the core circadian gene Clock regulates bone formation via transcriptional control of 1,2,5(OH)2D3 receptor PDIA3. © 2016 American Society for Bone and Mineral Research.
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Affiliation(s)
- Gongsheng Yuan
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Bingxuan Hua
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yang Yang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Lirong Xu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Tingting Cai
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Ning Sun
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China.,State Key Laboratory of Medical Neurobiology, Fudan University, Shanghai, China
| | - Zuoqin Yan
- Department of Orthopedics, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Chao Lu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
| | - Ruizhe Qian
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, China.,Research Center on Aging and Medicine, Fudan University, Shanghai, China
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22
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Depletion of Dicer promotes epithelial ovarian cancer progression by elevating PDIA3 expression. Tumour Biol 2016; 37:14009-14023. [PMID: 27492604 DOI: 10.1007/s13277-016-5218-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 07/14/2016] [Indexed: 10/21/2022] Open
Abstract
Dicer is an essential component of the microRNA (miRNA) processing machinery whose low expression is associated with advanced stage and poor clinical outcome in epithelial ovarian cancer. To investigate the functional relevance of Dicer in epithelial ovarian cancer and to identify its downstream effectors, two-dimensional gel electrophoresis combined with mass spectrometry was used for proteomic profiling. Dicer depletion promoted ovarian cancer cell proliferation and migration accompanied by a global upregulation of proteins. Twenty-six proteins, 7 upregulated and 19 downregulated, were identified. The functions of the identified proteins and their interactions were bioinformatically analyzed. Among them, protein disulfide-isomerase A3 (PDIA3) was considered to be a potential target protein of Dicer. PDIA3 repression by siRNA could significantly relieve the proliferation- and migration-promoting effect mediated by Dicer depletion in vitro and in vivo. Moreover, the miRNAs targeting PDIA3 were decreased in cells with Dicer depletion. In summary, low Dicer expression contributes to epithelial ovarian cancer progression by elevating PDIA3 expression.
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Zhao Z, Zhang Y, Gai F, Wang Y. Confirming an integrated pathology of diabetes and its complications by molecular biomarker-target network analysis. Mol Med Rep 2016; 14:2213-21. [PMID: 27430657 DOI: 10.3892/mmr.2016.5478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 05/27/2016] [Indexed: 11/06/2022] Open
Abstract
Despite ongoing research into diabetes and its complications, the underlying molecular associations remain to be elucidated. The systematic identification of molecular interactions in associated diseases may be approached using a network analysis strategy. The biomarker-target interrelated molecules associated with diabetes and its complications were identified via the Comparative Toxicogenomics Database (CTD); the Search Tool for Recurring Instances of Neighboring Genes was utilized for network construction. Functional enrichment analysis was performed with Database for Annotation, Visualization and Integrated Discovery software to investigate connections between diabetes and its complications. A total of 142 (including 122 biomarkers, 10 therapeutic targets and 10 overlapping molecules) biomarker-target interrelated molecules associated with diabetes and its complications were identified via the CTD database, and analysis of the network yielded 1,087 biological processes and fifteen Kyoto Encyclopedia of Genes and Genomes pathways with significant P‑values. Various critical aspects of the networks were examined in the present study: a) Intermolecular horizontal and vertical combinations in biomarkers and therapeutic targets associated with diabetes and its complicationb) network topology properties associated with molecular pathological responsec) contribution of key molecules to integrated regulation; and d) crosstalk between multiple pathways. Based on a multi-dimensional analysis, it was concluded that the integrated molecular pathological development of diabetes and its complications does not proceed randomly, which suggests a requirement for integrated, multi-target intervention.
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Affiliation(s)
- Zide Zhao
- Department of Neuro‑Ophthalmology, Eye Hospital, China Academy of Chinese Medical Sciences, Beijing 100040, P.R. China
| | - Yingying Zhang
- Laboratory of Pharmacology, Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, P.R. China
| | - Fengchun Gai
- Department of Infection Control, The Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin 130021, P.R. China
| | - Ying Wang
- Department of Neuro‑Ophthalmology, Eye Hospital, China Academy of Chinese Medical Sciences, Beijing 100040, P.R. China
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InteractoMIX: a suite of computational tools to exploit interactomes in biological and clinical research. Biochem Soc Trans 2016; 44:917-24. [DOI: 10.1042/bst20150001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 01/18/2023]
Abstract
Virtually all the biological processes that occur inside or outside cells are mediated by protein–protein interactions (PPIs). Hence, the charting and description of the PPI network, initially in organisms, the interactome, but more recently in specific tissues, is essential to fully understand cellular processes both in health and disease. The study of PPIs is also at the heart of renewed efforts in the medical and biotechnological arena in the quest of new therapeutic targets and drugs. Here, we present a mini review of 11 computational tools and resources tools developed by us to address different aspects of PPIs: from interactome level to their atomic 3D structural details. We provided details on each specific resource, aims and purpose and compare with equivalent tools in the literature. All the tools are presented in a centralized, one-stop, web site: InteractoMIX (http://interactomix.com).
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Basu A, Cajigas-Du Ross CK, Rios-Colon L, Mediavilla-Varela M, Daniels-Wells TR, Leoh LS, Rojas H, Banerjee H, Martinez SR, Acevedo-Martinez S, Casiano CA. LEDGF/p75 Overexpression Attenuates Oxidative Stress-Induced Necrosis and Upregulates the Oxidoreductase ERP57/PDIA3/GRP58 in Prostate Cancer. PLoS One 2016; 11:e0146549. [PMID: 26771192 PMCID: PMC4714844 DOI: 10.1371/journal.pone.0146549] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/19/2015] [Indexed: 12/22/2022] Open
Abstract
Prostate cancer (PCa) mortality is driven by highly aggressive tumors characterized by metastasis and resistance to therapy, and this aggressiveness is mediated by numerous factors, including activation of stress survival pathways in the pro-inflammatory tumor microenvironment. LEDGF/p75, also known as the DFS70 autoantigen, is a stress transcription co-activator implicated in cancer, HIV-AIDS, and autoimmunity. This protein is targeted by autoantibodies in certain subsets of patients with PCa and inflammatory conditions, as well as in some apparently healthy individuals. LEDGF/p75 is overexpressed in PCa and other cancers, and promotes resistance to chemotherapy-induced cell death via the transactivation of survival proteins. We report in this study that overexpression of LEDGF/p75 in PCa cells attenuates oxidative stress-induced necrosis but not staurosporine-induced apoptosis. This finding was consistent with the observation that while LEDGF/p75 was robustly cleaved in apoptotic cells into a p65 fragment that lacks stress survival activity, it remained relatively intact in necrotic cells. Overexpression of LEDGF/p75 in PCa cells led to the upregulation of transcript and protein levels of the thiol-oxidoreductase ERp57 (also known as GRP58 and PDIA3), whereas its depletion led to ERp57 transcript downregulation. Chromatin immunoprecipitation and transcription reporter assays showed LEDGF/p75 binding to and transactivating the ERp57 promoter, respectively. Immunohistochemical analysis revealed significantly elevated co-expression of these two proteins in clinical prostate tumor tissues. Our results suggest that LEDGF/p75 is not an inhibitor of apoptosis but rather an antagonist of oxidative stress-induced necrosis, and that its overexpression in PCa leads to ERp57 upregulation. These findings are of significance in clarifying the role of the LEDGF/p75 stress survival pathway in PCa.
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Affiliation(s)
- Anamika Basu
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
- * E-mail:
| | - Christina K. Cajigas-Du Ross
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Leslimar Rios-Colon
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Melanie Mediavilla-Varela
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Tracy R. Daniels-Wells
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Lai Sum Leoh
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Heather Rojas
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Hiya Banerjee
- Novartis Pharmaceutical Oncology, East Hanover, New Jersey 08807, United States of America
| | - Shannalee R. Martinez
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Stephanny Acevedo-Martinez
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
| | - Carlos A. Casiano
- Center for Health Disparities and Molecular Medicine, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
- Department of Medicine, Loma Linda University School of Medicine, Loma Linda, California 92350, United States of America
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Zeidán-Chuliá F, Gürsoy M, Neves de Oliveira BH, Özdemir V, Könönen E, Gürsoy UK. A Systems Biology Approach to Reveal Putative Host-Derived Biomarkers of Periodontitis by Network Topology Characterization of MMP-REDOX/NO and Apoptosis Integrated Pathways. Front Cell Infect Microbiol 2016; 5:102. [PMID: 26793622 PMCID: PMC4707239 DOI: 10.3389/fcimb.2015.00102] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/15/2015] [Indexed: 01/27/2023] Open
Abstract
Periodontitis, a formidable global health burden, is a common chronic disease that destroys tooth-supporting tissues. Biomarkers of the early phase of this progressive disease are of utmost importance for global health. In this context, saliva represents a non-invasive biosample. By using systems biology tools, we aimed to (1) identify an integrated interactome between matrix metalloproteinase (MMP)-REDOX/nitric oxide (NO) and apoptosis upstream pathways of periodontal inflammation, and (2) characterize the attendant topological network properties to uncover putative biomarkers to be tested in saliva from patients with periodontitis. Hence, we first generated a protein-protein network model of interactions ("BIOMARK" interactome) by using the STRING 10 database, a search tool for the retrieval of interacting genes/proteins, with "Experiments" and "Databases" as input options and a confidence score of 0.400. Second, we determined the centrality values (closeness, stress, degree or connectivity, and betweenness) for the "BIOMARK" members by using the Cytoscape software. We found Ubiquitin C (UBC), Jun proto-oncogene (JUN), and matrix metalloproteinase-14 (MMP14) as the most central hub- and non-hub-bottlenecks among the 211 genes/proteins of the whole interactome. We conclude that UBC, JUN, and MMP14 are likely an optimal candidate group of host-derived biomarkers, in combination with oral pathogenic bacteria-derived proteins, for detecting periodontitis at its early phase by using salivary samples from patients. These findings therefore have broader relevance for systems medicine in global health as well.
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Affiliation(s)
- Fares Zeidán-Chuliá
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do SulPorto Alegre, Brazil; Department of Periodontology, Institute of Dentistry, University of TurkuTurku, Finland
| | - Mervi Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku Turku, Finland
| | - Ben-Hur Neves de Oliveira
- Programa de Pós-Graduação em Ciências Biológicas: Bioquímica, Departamento de Bioquímica, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul Porto Alegre, Brazil
| | - Vural Özdemir
- Faculty of Communications and Office of the President, International Technology and Innovation Policy, Gaziantep UniversityGaziantep, Turkey; Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham (Amrita University)Kollam, India
| | - Eija Könönen
- Department of Periodontology, Institute of Dentistry, University of TurkuTurku, Finland; Oral Health Care, Welfare DivisionTurku, Finland
| | - Ulvi K Gürsoy
- Department of Periodontology, Institute of Dentistry, University of Turku Turku, Finland
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Choe MH, Min JW, Jeon HB, Cho DH, Oh JS, Lee HG, Hwang SG, An S, Han YH, Kim JS. ERp57 modulates STAT3 activity in radioresistant laryngeal cancer cells and serves as a prognostic marker for laryngeal cancer. Oncotarget 2015; 6:2654-66. [PMID: 25605256 PMCID: PMC4413608 DOI: 10.18632/oncotarget.3042] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 12/12/2014] [Indexed: 01/01/2023] Open
Abstract
Although targeting radioresistant tumor cells is essential for enhancing the efficacy of radiotherapy, the signals activated in resistant tumors are still unclear. This study shows that ERp57 contributes to radioresistance of laryngeal cancer by activating STAT3. Increased ERp57 was associated with the radioresistant phenotype of laryngeal cancer cells. Interestingly, increased interaction between ERp57 and STAT3 was observed in radioresistant cells, compared to the control cells. This physical complex is required for the activation of STAT3 in the radioresistant cells. Among STAT3-regulatory genes, Mcl-1 was predominantly regulated by ERp57. Inhibition of STAT3 activity with a chemical inhibitor or siRNA-mediated depletion of Mcl-1 sensitized radioresistant cells to irradiation, suggesting that the ERp57-STAT3-Mcl-1 axis regulates radioresistance of laryngeal cancer cells. Furthermore, we observed a positive correlation between ERp57 and phosphorylated STAT3 or Mcl-1 and in vivo interactions between ERp57 and STAT3 in human laryngeal cancer. Importantly, we also found that increased ERp57-STAT3 complex was associated with poor prognosis in human laryngeal cancer, indicating the prognostic role of ERp57-STAT3 regulation. Overall, our data suggest that ERp57-STAT3 regulation functions in radioresistance of laryngeal cancer, and targeting the ERp57-STAT3 pathway might be important for enhancing the efficacy of radiotherapy in human laryngeal cancer.
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Affiliation(s)
- Min Ho Choe
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Joong Won Min
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Hong Bae Jeon
- Biomedical Research Institute, MEDIPOST Co., Ltd., Seoul, Korea
| | - Dong-Hyung Cho
- Graduate School of East-West Medical Science, Kyung Hee University, Suwon, Korea
| | - Jeong Su Oh
- Department of Genetic Engineering, Sungkyunkwan University, Suwon, Korea
| | - Hyun Gyu Lee
- Department of Microbiology and Immunology, College of Medicine, Yonsei University, Seoul, Korea
| | - Sang-Gu Hwang
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Sungkwan An
- Molecular-Targeted Drug Research Center and Korea Institute for Skin and Clinical Sciences, Konkuk University, Seoul, Korea
| | - Young-Hoon Han
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jae-Sung Kim
- Division of Radiation Cancer Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
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28
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Kim BK, Yoo HI, Choi K, Yoon SK. miR-330-5p inhibits proliferation and migration of keratinocytes by targetingPdia3expression. FEBS J 2015; 282:4692-702. [DOI: 10.1111/febs.13523] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/11/2015] [Accepted: 09/21/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Bong-Kyu Kim
- Department of Medical Lifesciences; Catholic University of Korea; Seoul Korea
| | - Hye-In Yoo
- Department of Medical Lifesciences; Catholic University of Korea; Seoul Korea
| | - Keonwoo Choi
- Department of Medical Lifesciences; Catholic University of Korea; Seoul Korea
| | - Sungjoo Kim Yoon
- Department of Medical Lifesciences; Catholic University of Korea; Seoul Korea
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Wang LY, Liu J, Li Y, Li B, Zhang YY, Jing ZW, Yu YN, Li HX, Guo SS, Zhao YJ, Wang Z, Wang YY. Time-dependent variation of pathways and networks in a 24-hour window after cerebral ischemia-reperfusion injury. BMC SYSTEMS BIOLOGY 2015; 9:11. [PMID: 25884595 PMCID: PMC4355473 DOI: 10.1186/s12918-015-0152-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2014] [Accepted: 02/17/2015] [Indexed: 12/04/2022]
Abstract
Background Cerebral ischemia-reperfusion injury may simultaneously result in functional variation of multiple genes/pathways. However, most prior time-sequence studies on its pathomechanism only focused on a single gene or pathway. Our study aimed to systematically analyze the time-dependent variation in the expression of multiple pathways and networks within 24 h after cerebral ischemia-reperfusion injury. Results By uploading 374 ischemia-related genes into the MetaCore software, the variation in the expression of multiple pathways and networks in 3 h, 12 h, and 24 h after cerebral ischemia-reperfusion injury had been analyzed. The conserved TNFR1-signaling pathway, among the top 10 pathways, was consistently enriched in 3 h, 12 h, and 24 h groups. Three overlapping pathways were found between 3 h and 12 h groups; 2 between 12 h and 24 h groups; and 1 between 3 h and 24 h groups. Five, 4, and 6 non-overlapping pathways were observed in 3 h, 12 h, and 24 h groups, respectively. Apart from pathways reported by earlier studies, we identified a novel pathway related to the time-dependent development of cerebral ischemia pathogenesis. The process of apoptosis stimulation by external signals, among the top 10 processes, was consistently enriched in 3 h, 12 h, and 24 h groups; 2, 1, and 2 processes overlapped between 3 h and 12 h groups, 12 h and 24 h groups, and 3 h and 24 h groups, respectively. Four, 5, and 5 non-overlapping processes were found in 3 h, 12 h and 24 h groups, respectively. The presence of apoptotic processes was observed in all the 3 groups; while anti-apoptotic processes only existed in 3 h and 12 h groups. Additionally, according to node degree, network comparison identified 1, 8,and 5 important genes or proteins (e.g. Pyk2, PKC, E2F1, and VEGF-A) in 3 h, 12 h, and 24 h groups, respectively. The Jaccard similarity index revealed a higher level of similarity between 12 h and 24 h groups than that between 3 h and 12 h groups. Conclusion Time-dependent treatment can be utilized to reduce apoptosis, which may activate anti-apoptotic pathways within 12 h after cerebral ischemia-reperfusion injury. Pathway and network analyses may help identify novel pathways and genes implicated in disease pathogenesis. Electronic supplementary material The online version of this article (doi:10.1186/s12918-015-0152-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li-Ying Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Jun Liu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Yuan Li
- Beijing University of Chinese Medicine, No. 11 East Road, North of 3rd Ring Road, Beijing, 100029, China.
| | - Bing Li
- Institute of Information on Traditional Chinese Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Ying-Ying Zhang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Zhi-Wei Jing
- China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Ya-Nan Yu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Hai-Xia Li
- Guang'anmen Hospital, China Academy of China Medical Sciences, No.5 Beixiange, Beijing, 100053, China.
| | - Shan-Shan Guo
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Yi-Jun Zhao
- China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Zhong Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
| | - Yong-Yan Wang
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Dongzhimennei Nanxiaojie 16#, Beijing, 100700, China.
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30
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Guney E, Garcia-Garcia J, Oliva B. GUILDify: a web server for phenotypic characterization of genes through biological data integration and network-based prioritization algorithms. ACTA ACUST UNITED AC 2014; 30:1789-90. [PMID: 24532728 DOI: 10.1093/bioinformatics/btu092] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
SUMMARY Determining genetic factors underlying various phenotypes is hindered by the involvement of multiple genes acting cooperatively. Over the past years, disease-gene prioritization has been central to identify genes implicated in human disorders. Special attention has been paid on using physical interactions between the proteins encoded by the genes to link them with diseases. Such methods exploit the guilt-by-association principle in the protein interaction network to uncover novel disease-gene associations. These methods rely on the proximity of a gene in the network to the genes associated with a phenotype and require a set of initial associations. Here, we present GUILDify, an easy-to-use web server for the phenotypic characterization of genes. GUILDify offers a prioritization approach based on the protein-protein interaction network where the initial phenotype-gene associations are retrieved via free text search on biological databases. GUILDify web server does not restrict the prioritization to any predefined phenotype, supports multiple species and accepts user-specified genes. It also prioritizes drugs based on the ranking of their targets, unleashing opportunities for repurposing drugs for novel therapies. AVAILABILITY AND IMPLEMENTATION Available online at http://sbi.imim.es/GUILDify.php
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Affiliation(s)
- Emre Guney
- Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain
| | - Javier Garcia-Garcia
- Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain
| | - Baldo Oliva
- Departament de Ciencies Experimentals i de la Salut, Structural Bioinformatics Group (GRIB-IMIM), Universitat Pompeu Fabra, Barcelona, 08003 Catalonia, Spain
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