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Bozoky B, Szekely L, Ernberg I, Savchenko A. AtlasGrabber: a software facilitating the high throughput analysis of the human protein atlas online database. BMC Bioinformatics 2022; 23:546. [PMID: 36526955 PMCID: PMC9758778 DOI: 10.1186/s12859-022-05097-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The human protein atlas (HPA) is an online database containing large sets of protein expression data in normal and cancerous tissues in image form from immunohistochemically (IHC) stained tissue microarrays. In these, the tissue architecture is preserved and thus provides information on the spatial distribution and localization of protein expression at the cellular and extracellular levels. The database is freely available online through the HPA website but currently without support for large-scale screening and analysis of the images in the database. Features like spatial information are typically lacking in gene expression datasets from homogenized tissues or single-cell analysis. To enable high throughput analysis of the HPA database, we developed the AtlasGrabber software. It is available freely under an open-source license. Based on a predefined gene list, the software fetches the images from the database and displays them for the user. Several filters for specific antibodies or images enable the user to customize her/his image analysis. Up to four images can be displayed simultaneously, which allows for the comparison of protein expression between different tissues and between normal and cancerous tissues. An additional feature is the XML parser that allows the extraction of a list of available antibodies, images, and genes for specific tissues or cancer types from the HPA's database file. RESULTS Compared to existing software designed for a similar purpose, ours provide more functionality and is easier to use. To demonstrate the software's usability, we identified six new markers of basal cells of the prostate. A comparison to prostate cancer showed that five of them are absent in prostate cancer. CONCLUSIONS The HPA is a uniquely valuable database. By facilitating its usefulness with the AtlasGrabber, we enable researchers to exploit its full capacity. The loss of basal cell markers is diagnostic for prostate cancer and can help refine the histopathological diagnosis of prostate cancer. As proof of concept, with the AtlasGrabber we identified five new potential biomarkers specific for prostate basal cells which are lost in prostate cancer and thus can be used for prostate cancer diagnostics.
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Affiliation(s)
- Benedek Bozoky
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum C8, Solnavägen 9, 171 65 Solna, Sweden
| | - Laszlo Szekely
- grid.4714.60000 0004 1937 0626Department of Laboratory Medicine, Karolinska Institutet, Alfred Nobels Allé 8, 171 77 Huddinge, Sweden
| | - Ingemar Ernberg
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum C8, Solnavägen 9, 171 65 Solna, Sweden
| | - Andrii Savchenko
- Department of Microbiology, Tumor and Cell Biology (MTC), Biomedicum C8, Solnavägen 9, 171 65 Solna, Sweden
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Yang Y, Cao X, Huang L, Yang A. RNF19a inhibits antiviral immune response to RNA viruses through degradation of TBK1. Mol Immunol 2022; 143:1-6. [PMID: 34990937 DOI: 10.1016/j.molimm.2021.12.021] [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: 07/22/2021] [Revised: 12/12/2021] [Accepted: 12/26/2021] [Indexed: 11/19/2022]
Abstract
TANK-binding kinase 1 (TBK1) plays a pivotal role in antiviral innate immunity. TBK1 mediates the activation of interferon regulatory factor (IRF) 3, leading to the induction of type I IFNs (IFN-α/β) and of NF-κB signal transduction following viral infections. TBK1 must be tightly regulated to effectively control viral infections and maintain immune homeostasis. Here, we found that E3 ubiquitin ligase RNF19a mediated K48-linked ubiquitination and proteasomal degradation of TBK1. Specifically, the silence of RNF19a enhanced the production of type I interferons and suppressed RNA viral replication. Our results uncover that RNF19a acts as a negative mediator in the RIG-I signaling pathway to attenuate antiviral immune responses and suggest RNF19a as a potential therapy target in clinical infectious and inflammatory diseases.
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Affiliation(s)
- Yingyun Yang
- Department of Gastroenterology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Beijing, 100730, China
| | - Xinyuan Cao
- Department of Gastroenterology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Beijing, 100730, China
| | - Lisong Huang
- Emergency Department, The Aerospace Central Hospital, Beijing, 100049, China
| | - Aiming Yang
- Department of Gastroenterology, Peking Union Medical College Hospital (PUMCH), Chinese Academy of Medical Sciences & Peking Union Medical College (CAMS & PUMC), Beijing, 100730, China.
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Identification and Validation of PLOD2 as an Adverse Prognostic Biomarker for Oral Squamous Cell Carcinoma. Biomolecules 2021; 11:biom11121842. [PMID: 34944486 PMCID: PMC8699216 DOI: 10.3390/biom11121842] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/03/2021] [Accepted: 12/04/2021] [Indexed: 02/06/2023] Open
Abstract
Background: Procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2 (PLOD2), a key enzyme that catalyzes the hydroxylation of lysine, plays a crucial role in the progression of several solid tumors. However, its spatial expression profile and prognostic significance in oral squamous cell carcinoma (OSCC) have not been revealed. Materials: Mass spectrometry was used to explore amino acid perturbations between OSCC tumor tissues and paired normal tissues of 28 patients. Then, PLOD2 mRNA and protein levels were assessed using several public databases and 18 pairs of OSCC patients’ tissues. Additionally, PLOD2 spatial expression profiles were investigated in 100 OSCC patients by immunohistochemistry and its diagnostic and prognostic values were also evaluated. Lastly, gene set enrichment analysis (GSEA) was used to investigate the potential functions of PLOD2 in OSCC. Results: Lysine was significantly elevated in OSCC tissues and could effectively distinguish tumor from normal tissues (AUC = 0.859, p = 0.0035). PLOD2 mRNA and protein levels were highly increased in tumor tissues of head and neck squamous cell carcinoma (HNSCC) (p < 0.001) and OSCC compared with those in nontumor tissues (p < 0.001). Histopathologically, PLOD2 was ubiquitously expressed in tumor cells (TCs) and fibroblast-like cells (FLCs) of OSCC patients but absent in tumor-infiltrating lymphocytes (TILs). Patients with highly expressed PLOD2 in TCs (PLOD2TCs) and FLCs (PLOD2FLCs) showed poor differentiation, a worse pattern of invasion (WPOI) and more lymph node metastasis (LNM), contributing to higher postoperative metastasis risk and poor survival time. However, PLOD2FLCs rather than PLOD2TCs was an independent risk factor for survival outcomes in OSCC patients. Molecularly, GSEA demonstrated highly expressed PLOD2 was mainly enriched in epithelial–mesenchymal transformation (EMT), TGF-beta signaling and hypoxia pathway, which are associated with poor clinical outcomes of OSCC patients. Conclusions: PLOD2 was a poor prognostic biomarker for OSCC patients and may affect the metastasis of OSCC through EMT pathway. These findings might shed novel sights for future research in PLOD2 targeted OSCC therapy.
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Zhu Q, Huang J, Huang H, Li H, Yi P, Kloeber JA, Yuan J, Chen Y, Deng M, Luo K, Gao M, Guo G, Tu X, Yin P, Zhang Y, Su J, Chen J, Lou Z. RNF19A-mediated ubiquitination of BARD1 prevents BRCA1/BARD1-dependent homologous recombination. Nat Commun 2021; 12:6653. [PMID: 34789768 PMCID: PMC8599684 DOI: 10.1038/s41467-021-27048-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 11/01/2021] [Indexed: 12/19/2022] Open
Abstract
BRCA1-BARD1 heterodimers act in multiple steps during homologous recombination (HR) to ensure the prompt repair of DNA double strand breaks. Dysfunction of the BRCA1 pathway enhances the therapeutic efficiency of poly-(ADP-ribose) polymerase inhibitors (PARPi) in cancers, but the molecular mechanisms underlying this sensitization to PARPi are not fully understood. Here, we show that cancer cell sensitivity to PARPi is promoted by the ring between ring fingers (RBR) protein RNF19A. We demonstrate that RNF19A suppresses HR by ubiquitinating BARD1, which leads to dissociation of BRCA1-BARD1 complex and exposure of a nuclear export sequence in BARD1 that is otherwise masked by BRCA1, resulting in the export of BARD1 to the cytoplasm. We provide evidence that high RNF19A expression in breast cancer compromises HR and increases sensitivity to PARPi. We propose that RNF19A modulates the cancer cell response to PARPi by negatively regulating the BRCA1-BARD1 complex and inhibiting HR-mediated DNA repair.
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Affiliation(s)
- Qian Zhu
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Hongyang Huang
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, 999077, China
| | - Huan Li
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Peiqiang Yi
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jake A Kloeber
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jian Yuan
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China
| | - Yuping Chen
- Research Center for Translational Medicine, East Hospital, Tongji University School of medicine, Shanghai, 200120, China
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Yong Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jun Su
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China
| | - Jiayi Chen
- Department of Radiation Oncology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, 200025, China.
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA.
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Crosas-Molist E, Samain R, Kohlhammer L, Orgaz J, George S, Maiques O, Barcelo J, Sanz-Moreno V. RhoGTPase Signalling in Cancer Progression and Dissemination. Physiol Rev 2021; 102:455-510. [PMID: 34541899 DOI: 10.1152/physrev.00045.2020] [Citation(s) in RCA: 95] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Rho GTPases are a family of small G proteins that regulate a wide array of cellular processes related to their key roles controlling the cytoskeleton. On the other hand, cancer is a multi-step disease caused by the accumulation of genetic mutations and epigenetic alterations, from the initial stages of cancer development when cells in normal tissues undergo transformation, to the acquisition of invasive and metastatic traits, responsible for a large number of cancer related deaths. In this review, we discuss the role of Rho GTPase signalling in cancer in every step of disease progression. Rho GTPases contribute to tumour initiation and progression, by regulating proliferation and apoptosis, but also metabolism, senescence and cell stemness. Rho GTPases play a major role in cell migration, and in the metastatic process. They are also involved in interactions with the tumour microenvironment and regulate inflammation, contributing to cancer progression. After years of intensive research, we highlight the importance of relevant models in the Rho GTPase field, and we reflect on the therapeutic opportunities arising for cancer patients.
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Affiliation(s)
- Eva Crosas-Molist
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Remi Samain
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Leonie Kohlhammer
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jose Orgaz
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom.,Instituto de Investigaciones Biomédicas 'Alberto Sols', CSIC-UAM, 28029, Madrid, Spain
| | - Samantha George
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Oscar Maiques
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Jaume Barcelo
- Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
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Zhou X, Barkley-Levenson AM, Montilla-Perez P, Telese F, Palmer AA. Functional validation of a finding from a mouse genome-wide association study shows that Azi2 influences the acute locomotor stimulant response to methamphetamine. GENES, BRAIN, AND BEHAVIOR 2021; 20:e12760. [PMID: 34173327 DOI: 10.1111/gbb.12760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 12/12/2022]
Abstract
In a previous genome-wide association study (GWAS) using outbred Carworth Farms White (CFW) mice, we identified a locus that influenced the stimulant response to methamphetamine and colocalized with an eQTL for Azi2. Based on those findings, we hypothesized that heritable differences in Azi2 expression were causally related to the differential response to methamphetamine. To test that hypothesis, we created a mutant Azi2 allele on an inbred C57BL/6J background. The mutant allele enhanced the locomotor response to methamphetamine. However, the GWAS had suggested that lower Azi2 would decrease the locomotor response to methamphetamine. We also sought to explore the mechanism by which Azi2 influenced methamphetamine sensitivity. A recent publication reported that the 3'UTR of Azi2 mRNA downregulates the expression of Slc6a3, which encodes the dopamine transporter, which is a key target of methamphetamine. We evaluated the relationship between Azi2, Azi2 3'UTR and Slc6a3 expression in the ventral tegmental area of wildtype, mutant Azi2 heterozygotes and mutant Azi2 homozygotes and in a new cohort of outbred CFW mice where both allele mapped in our prior GWAS were segregating. We did not observe any correlation between Azi2 and Slc6a3 in either cohort. However, RNA sequencing confirmed that the Azi2 mutation altered Azi2 expression and also revealed a number of potentially important genes and pathways that were regulated by Azi2, including the metabotropic glutamate receptor group III pathway and nicotinic acetylcholine receptor signaling pathway. Our results support a role for Azi2 in methamphetamine sensitivity; however, the exact mechanism does not appear to involve regulation of Slc6a3.
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Affiliation(s)
- Xinzhu Zhou
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, California, USA
| | | | | | - Francesca Telese
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Abraham A Palmer
- Department of Psychiatry, University of California San Diego, La Jolla, California, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, California, USA
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7
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Molecular subversion of Cdc42 signalling in cancer. Biochem Soc Trans 2021; 49:1425-1442. [PMID: 34196668 PMCID: PMC8412110 DOI: 10.1042/bst20200557] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/18/2021] [Accepted: 05/24/2021] [Indexed: 12/21/2022]
Abstract
Cdc42 is a member of the Rho family of small GTPases and a master regulator of the actin cytoskeleton, controlling cell motility, polarity and cell cycle progression. This small G protein and its regulators have been the subject of many years of fruitful investigation and the advent of functional genomics and proteomics has opened up new avenues of exploration including how it functions at specific locations in the cell. This has coincided with the introduction of new structural techniques with the ability to study small GTPases in the context of the membrane. The role of Cdc42 in cancer is well established but the molecular details of its action are still being uncovered. Here we review alterations found to Cdc42 itself and to key components of the signal transduction pathways it controls in cancer. Given the challenges encountered with targeting small G proteins directly therapeutically, it is arguably the regulators of Cdc42 and the effector signalling pathways downstream of the small G protein which will be the most tractable targets for therapeutic intervention. These will require interrogation in order to fully understand the global signalling contribution of Cdc42, unlock the potential for mapping new signalling axes and ultimately produce inhibitors of Cdc42 driven signalling.
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Lucken-Ardjomande Häsler S, Vallis Y, Pasche M, McMahon HT. GRAF2, WDR44, and MICAL1 mediate Rab8/10/11-dependent export of E-cadherin, MMP14, and CFTR ΔF508. J Cell Biol 2021; 219:151714. [PMID: 32344433 PMCID: PMC7199855 DOI: 10.1083/jcb.201811014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/07/2019] [Accepted: 02/26/2020] [Indexed: 02/07/2023] Open
Abstract
In addition to the classical pathway of secretion, some transmembrane proteins reach the plasma membrane through alternative routes. Several proteins transit through endosomes and are exported in a Rab8-, Rab10-, and/or Rab11-dependent manner. GRAFs are membrane-binding proteins associated with tubules and vesicles. We found extensive colocalization of GRAF1b/2 with Rab8a/b and partial with Rab10. We identified MICAL1 and WDR44 as direct GRAF-binding partners. MICAL1 links GRAF1b/2 to Rab8a/b and Rab10, and WDR44 binds Rab11. Endogenous WDR44 labels a subset of tubular endosomes, which are closely aligned with the ER via binding to VAPA/B. With its BAR domain, GRAF2 can tubulate membranes, and in its absence WDR44 tubules are not observed. We show that GRAF2 and WDR44 are essential for the export of neosynthesized E-cadherin, MMP14, and CFTR ΔF508, three proteins whose exocytosis is sensitive to ER stress. Overexpression of dominant negative mutants of GRAF1/2, WDR44, and MICAL1 also interferes with it, facilitating future studies of Rab8/10/11-dependent exocytic pathways of central importance in biology.
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Affiliation(s)
| | - Yvonne Vallis
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Mathias Pasche
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Harvey T McMahon
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
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9
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Lee YT, Tan YJ, Falasca M, Oon CE. Cancer-Associated Fibroblasts: Epigenetic Regulation and Therapeutic Intervention in Breast Cancer. Cancers (Basel) 2020; 12:E2949. [PMID: 33066013 PMCID: PMC7600259 DOI: 10.3390/cancers12102949] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 09/24/2020] [Accepted: 09/30/2020] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is the leading cause of cancer-related mortality in women worldwide. Cancer-associated fibroblasts (CAFs) are a heterogeneous population of cells in the solid tumour microenvironment. These cells are positively linked to breast cancer progression. Breast CAFs can be categorised into distinct subtypes according to their roles in breast carcinogenesis. Epigenetic modifications change gene expression patterns as a consequence of altered chromatin configuration and DNA accessibility to transcriptional machinery, without affecting the primary structure of DNA. Epigenetic dysregulation in breast CAFs may enhance breast cancer cell survival and ultimately lead to therapeutic resistance. A growing body of evidence has described epigenetic modulators that target histones, DNA, and miRNA as a promising approach to treat cancer. This review aims to summarise the current findings on the mechanisms involved in the epigenetic regulation in breast CAFs and discusses the potential therapeutic strategies via targeting these factors.
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Affiliation(s)
- Yeuan Ting Lee
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia; (Y.T.L.); (Y.J.T.)
| | - Yi Jer Tan
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia; (Y.T.L.); (Y.J.T.)
| | - Marco Falasca
- Metabolic Signalling Group, School of Pharmacy and Biomedical Sciences, Curtin Health Innovation Research Institute, Curtin University, Perth, WA 6102, Australia
| | - Chern Ein Oon
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang 11800, Malaysia; (Y.T.L.); (Y.J.T.)
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Wang P, Dai X, Jiang W, Li Y, Wei W. RBR E3 ubiquitin ligases in tumorigenesis. Semin Cancer Biol 2020; 67:131-144. [PMID: 32442483 DOI: 10.1016/j.semcancer.2020.05.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/28/2020] [Accepted: 05/04/2020] [Indexed: 02/06/2023]
Abstract
RING-in-between-RING (RBR) E3 ligases are one class of E3 ligases that is characterized by the unique RING-HECT hybrid mechanism to function with E2s to transfer ubiquitin to target proteins for degradation. Emerging evidence has demonstrated that RBR E3 ligases play essential roles in neurodegenerative diseases, infection, inflammation and cancer. Accumulated evidence has revealed that RBR E3 ligases exert their biological functions in various types of cancers by modulating the degradation of tumor promoters or suppressors. Hence, we summarize the differential functions of RBR E3 ligases in a variety of human cancers. In general, ARIH1, RNF14, RNF31, RNF144B, RNF216, and RBCK1 exhibit primarily oncogenic roles, whereas ARIH2, PARC and PARK2 mainly have tumor suppressive functions. Moreover, the underlying mechanisms by which different RBR E3 ligases are involved in tumorigenesis and progression are also described. We discuss the further investigation is required to comprehensively understand the critical role of RBR E3 ligases in carcinogenesis. We hope our review can stimulate the researchers to deeper explore the mechanism of RBR E3 ligases-mediated carcinogenesis and to develop useful inhibitors of these oncogenic E3 ligases for cancer therapy.
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Affiliation(s)
- Peter Wang
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China
| | - Xiaoming Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA
| | - Wenxiao Jiang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Yuyun Li
- School of Laboratory Medicine, Bengbu Medical College, Anhui, 233030, China.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Ave., Boston, MA, USA.
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The Gastrointestinal Tumor Microenvironment: An Updated Biological and Clinical Perspective. JOURNAL OF ONCOLOGY 2019; 2019:6240505. [PMID: 31885581 PMCID: PMC6893275 DOI: 10.1155/2019/6240505] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/30/2019] [Indexed: 12/24/2022]
Abstract
Gastrointestinal cancers are still responsible for high numbers of cancer-related deaths despite advances in therapy. Tumor-associated cells play a key role in tumor biology, by supporting or halting tumor development through the production of extracellular matrix, growth factors, cytokines, and extracellular vesicles. Here, we review the roles of these tumor-associated cells in the initiation, angiogenesis, immune modulation, and resistance to therapy of gastrointestinal cancers. We also discuss novel diagnostic and therapeutic strategies directed at tumor-associated cells and their potential benefits for the survival of these patients.
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12
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Chandler C, Liu T, Buckanovich R, Coffman LG. The double edge sword of fibrosis in cancer. Transl Res 2019; 209:55-67. [PMID: 30871956 PMCID: PMC6545239 DOI: 10.1016/j.trsl.2019.02.006] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/12/2019] [Accepted: 02/15/2019] [Indexed: 02/07/2023]
Abstract
Cancer-associated fibrosis is a critical component of the tumor microenvironment (TME) which significantly impacts cancer behavior. However, there is significant controversy regarding fibrosis as a predominantly tumor promoting or tumor suppressing factor. Cells essential to the generation of tissue fibrosis such as fibroblasts and mesenchymal stem cells (MSCs) have dual phenotypes dependent upon their independence or association with cancer cells. Cancer-associated fibroblasts and cancer-associated MSCs have unique molecular profiles which facilitate cancer cell cross talk, influence extracellular matrix deposition, and direct the immune system to generate a protumorigenic environment. In contrast, normal tissue fibroblasts and MSCs are important in restraining cancer initiation, influencing epithelial cell differentiation, and limiting cancer cell invasion. We propose this apparent dichotomy of function is due to (1) cancer mediated stromal reprogramming; (2) tissue stromal source; (3) unique subtypes of fibrosis; and (4) the impact of fibrosis on other TME elements. First, as cancer progresses, tumor cells influence their surrounding stroma to move from a cancer restraining phenotype into a cancer supportive role. Second, cancer has specific organ tropism, thus stroma derived from preferred metastatic organs support growth while less preferred metastatic tissues do not. Third, there are subtypes of fibrosis which have unique function to support or inhibit cancer growth. Fourth, depleting fibrosis influences other TME components which drive the cancer response. Collectively, this review highlights the complexity of cancer-associated fibrosis and supports a dual function of fibrosis which evolves during the continuum of cancer growth.
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Affiliation(s)
- Chelsea Chandler
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Tianshi Liu
- Department of Internal Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ronald Buckanovich
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Hematology Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Lan G Coffman
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Hematology Oncology, University of Pittsburgh, Pittsburgh, Pennsylvania.
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Masamune A, Hamada S, Yoshida N, Nabeshima T, Shimosegawa T. Pyruvate Kinase Isozyme M2 Plays a Critical Role in the Interactions Between Pancreatic Stellate Cells and Cancer Cells. Dig Dis Sci 2018; 63:1868-1877. [PMID: 29619774 DOI: 10.1007/s10620-018-5051-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 03/28/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND The interaction between pancreatic cancer cells and pancreatic stellate cells plays a pivotal role in the progression of pancreatic cancer. Pyruvate kinase isozyme M2 is a key enzyme in glycolysis. Previous studies have shown that pyruvate kinase isozyme M2 is overexpressed in pancreatic cancer and that it regulates the aggressive behaviors of pancreatic cancer cells. AIMS To clarify the role of pyruvate kinase isozyme M2 in the interactions between pancreatic cancer cells and pancreatic stellate cells. METHODS Pyruvate kinase isozyme M2-knockdown pancreatic cancer cells (Panc-1 and SUIT-2 cells) and pancreatic stellate cells were generated by the introduction of small interfering RNA-expressing vector against pyruvate kinase isozyme M2. Cell proliferation, migration, and epithelial-mesenchymal transition were examined in vitro. The impact of pyruvate kinase isozyme M2 knockdown on the growth of subcutaneous tumors was examined in nude mice in vivo. RESULTS Pyruvate kinase isozyme M2-kockdown pancreatic cancer cells and pancreatic stellate cells showed decreased proliferation and migration compared to their respective control cells. Pancreatic stellate cell-induced proliferation, migration, and epithelial-mesenchymal transition were inhibited when pyruvate kinase isozyme M2 expression was knocked down in pancreatic cancer cells. In vivo, co-injection of pancreatic stellate cells increased the size of the tumor developed by the control SUIT-2 cells, but the effects were less evident when pyruvate kinase isozyme M2 was knocked down in SUIT-2 cells or pancreatic stellate cells. CONCLUSIONS Our results suggested a critical role of pyruvate kinase isozyme M2 in the interaction between pancreatic cancer cells and pancreatic stellate cells.
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Affiliation(s)
- Atsushi Masamune
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan.
| | - Shin Hamada
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Naoki Yoshida
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Tatsuhide Nabeshima
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
| | - Tooru Shimosegawa
- Division of Gastroenterology, Tohoku University Graduate School of Medicine, 1-1 Seiryo-machi, Aoba-ku, Sendai, 980-8574, Japan
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14
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Qi Y, Xu R. Roles of PLODs in Collagen Synthesis and Cancer Progression. Front Cell Dev Biol 2018; 6:66. [PMID: 30003082 PMCID: PMC6031748 DOI: 10.3389/fcell.2018.00066] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/11/2018] [Indexed: 01/08/2023] Open
Abstract
Collagen is the major component of extracellular matrix. Collagen cross-link and deposition depend on lysyl hydroxylation, which is catalyzed by procollagen-lysine, 2-oxoglutarate 5-dioxygenase (PLOD). Aberrant lysyl hydroxylation and collagen cross-link contributes to the progression of many collagen-related diseases, such as fibrosis and cancer. Three lysyl hydroxylases (LH1, LH2, and LH3) are identified, encoded by PLOD1, PLOD2, and PLOD3 genes. Expression of PLODs is regulated by multiple cytokines, transcription factors and microRNAs. Dysregulation of PLODs promotes cancer progression and metastasis, suggesting that targeting PLODs is potential strategy for cancer treatment. Here, we summarize the recent progress in the investigation of function and regulation of PLODs in normal tissue development and disease progression, especially in cancer.
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Affiliation(s)
- Yifei Qi
- Markey Cancer Center, University of Kentucky, Lexington, KY, United States
| | - Ren Xu
- Markey Cancer Center, University of Kentucky, Lexington, KY, United States.,Department of Pharmacology and Nutritional Sciences, University of Kentucky, Lexington, KY, United States
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15
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Alkasalias T, Moyano-Galceran L, Arsenian-Henriksson M, Lehti K. Fibroblasts in the Tumor Microenvironment: Shield or Spear? Int J Mol Sci 2018; 19:ijms19051532. [PMID: 29883428 PMCID: PMC5983719 DOI: 10.3390/ijms19051532] [Citation(s) in RCA: 158] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/11/2022] Open
Abstract
Tumorigenesis is a complex process involving dynamic interactions between malignant cells and their surrounding stroma, including both the cellular and acellular components. Within the stroma, fibroblasts represent not only a predominant cell type, but also a major source of the acellular tissue microenvironment comprising the extracellular matrix (ECM) and soluble factors. Normal fibroblasts can exert diverse suppressive functions against cancer initiating and metastatic cells via direct cell-cell contact, paracrine signaling by soluble factors, and ECM integrity. The loss of such suppressive functions is an inherent step in tumor progression. A tumor cell-induced switch of normal fibroblasts into cancer-associated fibroblasts (CAFs), in turn, triggers a range of pro-tumorigenic signals accompanied by distraction of the normal tissue architecture, thus creating an optimal niche for cancer cells to grow extensively. To further support tumor progression and metastasis, CAFs secrete factors such as ECM remodeling enzymes that further modify the tumor microenvironment in combination with the altered adhesive forces and cell-cell interactions. These paradoxical tumor suppressive and promoting actions of fibroblasts are the focus of this review, highlighting the heterogenic molecular properties of both normal and cancer-associated fibroblasts, as well as their main mechanisms of action, including the emerging impact on immunomodulation and different therapy responses.
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Affiliation(s)
- Twana Alkasalias
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, Solnavägen 9, SE-17177 Stockholm, Sweden.
- Department of Biology, College of Science, Salahaddin University, Irbil 44002, Kurdistan-Iraq.
| | - Lidia Moyano-Galceran
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, Solnavägen 9, SE-17177 Stockholm, Sweden.
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, Solnavägen 9, SE-17177 Stockholm, Sweden.
| | - Kaisa Lehti
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, Solnavägen 9, SE-17177 Stockholm, Sweden.
- Research Programs Unit, Genome-Scale Biology and Medicum, University of Helsinki, and Helsinki University Hospital, P.O. Box 63, FI-00014 Helsinki, Finland.
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16
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Korcsmaros T, Schneider MV, Superti-Furga G. Next generation of network medicine: interdisciplinary signaling approaches. Integr Biol (Camb) 2017; 9:97-108. [PMID: 28106223 DOI: 10.1039/c6ib00215c] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the last decade, network approaches have transformed our understanding of biological systems. Network analyses and visualizations have allowed us to identify essential molecules and modules in biological systems, and improved our understanding of how changes in cellular processes can lead to complex diseases, such as cancer, infectious and neurodegenerative diseases. "Network medicine" involves unbiased large-scale network-based analyses of diverse data describing interactions between genes, diseases, phenotypes, drug targets, drug transport, drug side-effects, disease trajectories and more. In terms of drug discovery, network medicine exploits our understanding of the network connectivity and signaling system dynamics to help identify optimal, often novel, drug targets. Contrary to initial expectations, however, network approaches have not yet delivered a revolution in molecular medicine. In this review, we propose that a key reason for the limited impact, so far, of network medicine is a lack of quantitative multi-disciplinary studies involving scientists from different backgrounds. To support this argument, we present existing approaches from structural biology, 'omics' technologies (e.g., genomics, proteomics, lipidomics) and computational modeling that point towards how multi-disciplinary efforts allow for important new insights. We also highlight some breakthrough studies as examples of the potential of these approaches, and suggest ways to make greater use of the power of interdisciplinarity. This review reflects discussions held at an interdisciplinary signaling workshop which facilitated knowledge exchange from experts from several different fields, including in silico modelers, computational biologists, biochemists, geneticists, molecular and cell biologists as well as cancer biologists and pharmacologists.
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Affiliation(s)
- Tamas Korcsmaros
- Earlham Institute, Norwich Research Park, Norwich, UK. and Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, UK
| | | | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria and Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
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17
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Dourado MR, de Oliveira CE, Sawazaki-Calone I, Sundquist E, Coletta RD, Salo T. Clinicopathologic significance of ROCK2 expression in oral squamous cell carcinomas. J Oral Pathol Med 2017; 47:121-127. [PMID: 29052912 DOI: 10.1111/jop.12651] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/13/2017] [Indexed: 12/30/2022]
Abstract
BACKGROUND Rho-associated coiled-coil kinase 2 (ROCK2) is an oncoprotein that controls cytoskeleton organization and acts as prognostic marker in different types of solid tumors. ROCK2 overexpression is also observed in cancer-associated fibroblasts (CAF), which suggests its relevance within the tumor microenvironment. This study aimed to access the prognostic value of ROCK2 in oral squamous cell carcinomas (OSCCs) and its association with CAF density. METHODS Rho-associated coiled-coil kinase 2 immunohistochemical analysis was applied in 93 OSCC samples from 2 centers in Brazil and Finland. The samples were also stained for isoform α of smooth muscle actin (α-SMA) to characterize the presence of CAF in the tumor stroma. Clinicopathological associations were analyzed using Chi-squared test, survival curves were constructed according to the Kaplan-Meier method, and Cox proportional hazard model was applied for multivariate survival analysis. RESULTS Advanced clinical stage (P = .002) and increased density of CAF (P = .002) were significantly associated with high ROCK2 expression. The high expression of ROCK2 was also associated with shortened disease-specific survival (HR: 2.22, 95% CI: 1.15-4.38, P = .04), but the association did not withstand the Cox multivariate survival analysis. CONCLUSIONS The findings suggest that high ROCK2 expression in OSCC is associated with advanced disease and follows the increase in CAF density, which may be important for tumor progression.
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Affiliation(s)
- Mauricio R Dourado
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil.,Cancer and Translational Medicine Research Unit, Faculty of Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Carine E de Oliveira
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
| | - Iris Sawazaki-Calone
- Oral Pathology and Oral Medicine, School of Dentistry, Western Paraná State University, Cascavel, Brazil
| | - Elias Sundquist
- Cancer and Translational Medicine Research Unit, Faculty of Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Ricardo D Coletta
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil
| | - Tuula Salo
- Department of Oral Diagnosis, Piracicaba Dental School, University of Campinas, Piracicaba, Brazil.,Cancer and Translational Medicine Research Unit, Faculty of Medicine and Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.,Institute of Oral and Maxillofacial Disease, University of Helsinki, and HUSLAB, Department of Pathology, Helsinki University Hospital, Helsinki, Finland
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18
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PLOD2 in cancer research. Biomed Pharmacother 2017; 90:670-676. [PMID: 28415047 DOI: 10.1016/j.biopha.2017.04.023] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 03/31/2017] [Accepted: 04/10/2017] [Indexed: 12/22/2022] Open
Abstract
Collagen is not only the most abundant protein providing the scaffold for assembly of the extracellular matrix (ECM), but also considered to be the "highway" for cancer cell migration and invasion depending on the different collagen organizations. The accumulation of stabilized collagen is enhanced by different covalent collagen cross-links, lysyl hydroxylases 2 (encoded by the PLOD2 gene) is the key enzyme mediating the formation of the stabilized collagen cross-link. Interestingly, PLOD2 is overexpressed in different cancers and closely related to a poor prognosis. To the best of our knowledge, only the mechanisms of PLOD2 regulated by HIF-1α, TGF-β and microRNA-26a/b have been elaborated. In addition, several pharmacologic inhibitors of PLOD2 have been confirmed to have an anti-metastasis effect. However, there have been no reviews about PLOD2 in cancer research published thus far. In brief, this review about PLOD2 will describe the function, regulatory mechanism, and the inhibitors of PLOD2 in cancer, suggesting the credible clinical evaluation of a prognostic signature in pathological examination and the possible development of therapeutic strategies targeting PLOD2 in the future.
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19
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Oh HJ, Bae JM, Wen XY, Cho NY, Kim JH, Kang GH. Overexpression of POSTN in Tumor Stroma Is a Poor Prognostic Indicator of Colorectal Cancer. J Pathol Transl Med 2017; 51:306-313. [PMID: 28407462 PMCID: PMC5445202 DOI: 10.4132/jptm.2017.01.19] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/30/2016] [Accepted: 01/19/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Tumor microenvironment has recently drawn attention in that it is related with tumor prognosis. Cancer-associated fibroblast also plays a critical role in cancer invasiveness and progression in colorectal cancers. Periostin (POSTN), originally identified to be expressed in osteoblasts and osteoblast-derived cells, is expressed in cancer-associated fibroblasts in several tissue types of cancer. Recent studies suggest an association between stromal overexpression of POSTN and poor prognosis of cancer patients. METHODS We analyzed colorectal cancer cases for their expression status of POSTN in tumor stroma using immunohistochemistry and correlated the expression status with clinicopathological and molecular features. RESULTS High level of POSTN expression in tumor stroma was closely associated with tumor location in proximal colon, infiltrative growth pattern, undifferentiated histology, tumor budding, luminal necrosis, and higher TNM stage. High expression status of POSTN in tumor stroma was found to be an independent prognostic parameter implicating poor 5-year cancer-specific survival and 5-year progression-free survival. CONCLUSIONS Our findings suggest that POSTN overexpression in tumor stroma of colorectal cancers could be a possible candidate marker for predicting poor prognosis in patients with colorectal cancers.
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Affiliation(s)
- Hyeon Jeong Oh
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jeong Mo Bae
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea.,Department of Pathology, SMG-SNU Boramae Medical Center, Seoul, Korea
| | - Xian-Yu Wen
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Nam-Yun Cho
- Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Jung Ho Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Gyeong Hoon Kang
- Department of Pathology, Seoul National University College of Medicine, Seoul, Korea.,Laboratory of Epigenetics, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
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20
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RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo. Proc Natl Acad Sci U S A 2017; 114:E1413-E1421. [PMID: 28174275 DOI: 10.1073/pnas.1621161114] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Fibroblasts are a main player in the tumor-inhibitory microenvironment. Upon tumor initiation and progression, fibroblasts can lose their tumor-inhibitory capacity and promote tumor growth. The molecular mechanisms that underlie this switch have not been defined completely. Previously, we identified four proteins overexpressed in cancer-associated fibroblasts and linked to Rho GTPase signaling. Here, we show that knocking out the Ras homolog family member A (RhoA) gene in normal fibroblasts decreased their tumor-inhibitory capacity, as judged by neighbor suppression in vitro and accompanied by promotion of tumor growth in vivo. This also induced PC3 cancer cell motility and increased colony size in 2D cultures. RhoA knockout in fibroblasts induced vimentin intermediate filament reorganization, accompanied by reduced contractile force and increased stiffness of cells. There was also loss of wide F-actin stress fibers and large focal adhesions. In addition, we observed a significant loss of α-smooth muscle actin, which indicates a difference between RhoA knockout fibroblasts and classic cancer-associated fibroblasts. In 3D collagen matrix, RhoA knockout reduced fibroblast branching and meshwork formation and resulted in more compactly clustered tumor-cell colonies in coculture with PC3 cells, which might boost tumor stem-like properties. Coculturing RhoA knockout fibroblasts and PC3 cells induced expression of proinflammatory genes in both. Inflammatory mediators may induce tumor cell stemness. Network enrichment analysis of transcriptomic changes, however, revealed that the Rho signaling pathway per se was significantly triggered only after coculturing with tumor cells. Taken together, our findings in vivo and in vitro indicate that Rho signaling governs the inhibitory effects by fibroblasts on tumor-cell growth.
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21
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Csermely P, Korcsmáros T, Nussinov R. Intracellular and intercellular signaling networks in cancer initiation, development and precision anti-cancer therapy: RAS acts as contextual signaling hub. Semin Cell Dev Biol 2016; 58:55-9. [PMID: 27395026 PMCID: PMC5028272 DOI: 10.1016/j.semcdb.2016.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 07/05/2016] [Indexed: 12/31/2022]
Abstract
Cancer initiation and development are increasingly perceived as systems-level phenomena, where intra- and inter-cellular signaling networks of the ecosystem of cancer and stromal cells offer efficient methodologies for outcome prediction and intervention design. Within this framework, RAS emerges as a 'contextual signaling hub', i.e. the final result of RAS activation or inhibition is determined by the signaling network context. Current therapies often 'train' cancer cells shifting them to a novel attractor, which has increased metastatic potential and drug resistance. The few therapy-surviving cancer cells are surrounded by massive cell death triggering a primordial adaptive and reparative general wound healing response. Overall, dynamic analysis of patient- and disease-stage specific intracellular and intercellular signaling networks may open new areas of anticancer therapy using multitarget drugs, drugs combinations, edgetic drugs, as well as help design 'gentler', differentiation and maintenance therapies.
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Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 2, H-1428 Budapest, Hungary.
| | - Tamás Korcsmáros
- Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK; Earlham Institute/TGAC, The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, National Cancer Institute at Frederick, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
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22
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Bastos EP, Brentani H, Pereira CAB, Polpo A, Lima L, Puga RD, Pasini FS, Osorio CABT, Roela RA, Achatz MI, Trapé AP, Gonzalez-Angulo AM, Brentani MM. A Set of miRNAs, Their Gene and Protein Targets and Stromal Genes Distinguish Early from Late Onset ER Positive Breast Cancer. PLoS One 2016; 11:e0154325. [PMID: 27152840 PMCID: PMC4859528 DOI: 10.1371/journal.pone.0154325] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/12/2016] [Indexed: 01/16/2023] Open
Abstract
UNLABELLED Breast cancer (BC) in young adult patients (YA) has a more aggressive biological behavior and is associated with a worse prognosis than BC arising in middle aged patients (MA). We proposed that differentially expressed miRNAs could regulate genes and proteins underlying aggressive phenotypes of breast tumors in YA patients when compared to those arising in MA patients. OBJECTIVE Using integrated expression analyses of miRs, their mRNA and protein targets and stromal gene expression, we aimed to identify differentially expressed profiles between tumors from YA-BC and MA-BC. METHODOLOGY AND RESULTS Samples of ER+ invasive ductal breast carcinomas, divided into two groups: YA-BC (35 years or less) or MA-BC (50-65 years) were evaluated. Screening for BRCA1/2 status according to the BOADICEA program indicated low risk of patients being carriers of these mutations. Aggressive characteristics were more evident in YA-BC versus MA-BC. Performing qPCR, we identified eight miRs differentially expressed (miR-9, 18b, 33b, 106a, 106b, 210, 518a-3p and miR-372) between YA-BC and MA-BC tumors with high confidence statement, which were associated with aggressive clinicopathological characteristics. The expression profiles by microarray identified 602 predicted target genes associated to proliferation, cell cycle and development biological functions. Performing RPPA, 24 target proteins differed between both groups and 21 were interconnected within a network protein-protein interactions associated with proliferation, development and metabolism pathways over represented in YA-BC. Combination of eight mRNA targets or the combination of eight target proteins defined indicators able to classify individual samples into YA-BC or MA-BC groups. Fibroblast-enriched stroma expression profile analysis resulted in 308 stromal genes differentially expressed between YA-BC and MA-BC. CONCLUSION We defined a set of differentially expressed miRNAs, their mRNAs and protein targets and stromal genes that distinguish early onset from late onset ER positive breast cancers which may be involved with tumor aggressiveness of YA-BC.
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Affiliation(s)
- E. P. Bastos
- Oncology and Radiology Department, Laboratory of Medical Investigation 24 (LIM 24), University of Sao Paulo, Medical School, São Paulo, Brazil
| | - H. Brentani
- Laboratory of Medical Investigation 23 (LIM 23), Institute and Department of Psychiatry, University of Sao Paulo, Medical School, São Paulo, Brazil
| | - C. A. B. Pereira
- Mathematics and Statistic Institute, University of Sao Paulo, São Paulo, Brazil
| | - A. Polpo
- Department of Statistics, Federal University of Sao Carlos, São Paulo, Brazil
| | - L. Lima
- Laboratory of Medical Investigation 23 (LIM 23), Institute and Department of Psychiatry, University of Sao Paulo, Medical School, São Paulo, Brazil
| | | | - F. S. Pasini
- Oncology and Radiology Department, Laboratory of Medical Investigation 24 (LIM 24), University of Sao Paulo, Medical School, São Paulo, Brazil
| | - C. A. B. T. Osorio
- Department of Pathology of A.C. Camargo Cancer Center, São Paulo, Brazil
| | - R. A. Roela
- Oncology and Radiology Department, Laboratory of Medical Investigation 24 (LIM 24), University of Sao Paulo, Medical School, São Paulo, Brazil
| | - M. I. Achatz
- Department of Oncogenetics of A.C. Camargo Cancer Center, São Paulo, Brazil
| | - A. P. Trapé
- Department of Breast Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - A. M. Gonzalez-Angulo
- Department of Breast Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, United States of America
| | - M. M. Brentani
- Oncology and Radiology Department, Laboratory of Medical Investigation 24 (LIM 24), University of Sao Paulo, Medical School, São Paulo, Brazil
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23
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Suhovskih AV, Kashuba VI, Klein G, Grigorieva EV. Prostate cancer cells specifically reorganize epithelial cell-fibroblast communication through proteoglycan and junction pathways. Cell Adh Migr 2016; 11:39-53. [PMID: 27111714 DOI: 10.1080/19336918.2016.1182292] [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] [Indexed: 01/31/2023] Open
Abstract
Microenvironment and stromal fibroblasts are able to inhibit tumor cell proliferation both through secreted signaling molecules and direct cell-cell interactions but molecular mechanisms of these effects remain unclear. In this study, we investigated a role of cell-cell contact-related molecules (protein ECM components, proteoglycans (PGs) and junction-related molecules) in intercellular communications between the human TERT immortalized fibroblasts (BjTERT fibroblasts) and normal (PNT2) or cancer (LNCaP, PC3, DU145) prostate epithelial cells. It was shown that BjTERT-PNT2 cell coculture resulted in significant decrease of both BjTERT and PNT2 proliferation rates and reorganization of transcriptional activity of cell-cell contact-related genes in both cell types. Immunocytochemical staining revealed redistribution of DCN and LUM in PNT2 cells and significant increase of SDC1 at the intercellular contact zones between BjTERT and PNT2 cells, suggesting active involvement of the PGs in cell-cell contacts and contact inhibition of cell proliferation. Unlike to PNT2 cells, PC3 cells did not respond to BjTERT in terms of PGs expression, moderately increased transcriptional activity of junctions-related genes (especially tight junction) and failed to establish PC3-BjTERT contacts. At the same time, PC3 cells significantly down-regulated junctions-related genes (especially focal adhesions and adherens junctions) in BjTERT fibroblasts resulting in visible preference for homotypic PC3-PC3 over heterotypic PC3-BjTERT contacts and autonomous growth of PC3 clones. Taken together, the results demonstrate that an instructing role of fibroblasts to normal prostate epithelial cells is revoked by cancer cells through deregulation of proteoglycans and junction molecules expression and overall disorganization of fibroblast-cancer cell communication.
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Affiliation(s)
- Anastasia V Suhovskih
- a MTC, Karolinska Institute , Stockholm , Sweden.,b Institute of Molecular Biology and Biophysics , Novosibirsk , Russia
| | - Vladimir I Kashuba
- a MTC, Karolinska Institute , Stockholm , Sweden.,c Institute of Molecular Biology and Genetics , Kiev , Ukraine
| | - George Klein
- a MTC, Karolinska Institute , Stockholm , Sweden
| | - Elvira V Grigorieva
- a MTC, Karolinska Institute , Stockholm , Sweden.,b Institute of Molecular Biology and Biophysics , Novosibirsk , Russia
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24
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Gjaltema RAF, de Rond S, Rots MG, Bank RA. Procollagen Lysyl Hydroxylase 2 Expression Is Regulated by an Alternative Downstream Transforming Growth Factor β-1 Activation Mechanism. J Biol Chem 2015; 290:28465-28476. [PMID: 26432637 DOI: 10.1074/jbc.m114.634311] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Indexed: 11/06/2022] Open
Abstract
PLOD2 (procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2) hydroxylates lysine residues in collagen telopeptides and is essential for collagen pyridinoline cross-link formation. PLOD2 expression and subsequent pyridinoline cross-links are increased in fibrotic pathologies by transforming growth factor β-1 (TGFβ1). In this report we examined the molecular processes underlying TGFβ1-induced PLOD2 expression. We found that binding of the TGFβ1 pathway related transcription factors SMAD3 and SP1-mediated TGFβ1 enhanced PLOD2 expression and could be correlated to an increase of acetylated histone H3 and H4 at the PLOD2 promoter. Interestingly, the classical co-activators of SMAD3 complexes, p300 and CBP, were not responsible for the enhanced H3 and H4 acetylation. Depletion of SMAD3 reduced PLOD2 acetylated H3 and H4, indicating that another as of yet unidentified histone acetyltransferase binds to SMAD3 at PLOD2. Assessing histone methylation marks at the PLOD2 promoter depicted an increase of the active histone mark H3K79me2, a decrease of the repressive H4K20me3 mark, but no role for the generally strong transcription-related modifications: H3K4me3, H3K9me3 and H3K27me3. Collectively, our findings reveal that TGFβ1 induces a SP1- and SMAD3-dependent recruitment of histone modifying enzymes to the PLOD2 promoter other than the currently known TGFβ1 downstream co-activators and epigenetic modifications. This also suggests that additional activation strategies are used downstream of the TGFβ1 pathway, and hence their unraveling could be of great importance to fully understand TGFβ1 activation of genes.
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Affiliation(s)
- Rutger A F Gjaltema
- MATRIX Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands; Epigenetic Editing Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Saskia de Rond
- MATRIX Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Marianne G Rots
- Epigenetic Editing Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands
| | - Ruud A Bank
- MATRIX Research Group, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, 9713 GZ Groningen, The Netherlands.
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Alexeyenko A, Alkasalias T, Pavlova T, Szekely L, Kashuba V, Rundqvist H, Wiklund P, Egevad L, Csermely P, Korcsmaros T, Guven H, Klein G. Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:62. [PMID: 26081588 PMCID: PMC4472614 DOI: 10.1186/s13046-015-0178-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 06/02/2015] [Indexed: 12/24/2022]
Abstract
BACKGROUND There is growing evidence that emerging malignancies in solid tissues might be kept under control by physical intercellular contacts with normal fibroblasts. METHODS Here we characterize transcriptional landscapes of fibroblasts that confronted cancer cells. We studied four pairs of in vitro and ex vivo fibroblast lines which, within each pair, differed in their capacity to inhibit cancer cells. The natural process was modeled in vitro by confronting the fibroblasts with PC-3 cancer cells. Fibroblast transcriptomes were recorded by Affymetrix microarrays and then investigated using network analysis. RESULTS The network enrichment analysis allowed us to separate confrontation- and inhibition-specific components of the fibroblast transcriptional response. Confrontation-specific differences were stronger and were characterized by changes in a number of pathways, including Rho, the YAP/TAZ cascade, NF-kB, and TGF-beta signaling, as well as the transcription factor RELA. Inhibition-specific differences were more subtle and characterized by involvement of Rho signaling at the pathway level and by potential individual regulators such as IL6, MAPK8, MAP2K4, PRKCA, JUN, STAT3, and STAT5A. CONCLUSIONS We investigated the interaction between cancer cells and fibroblasts in order to shed light on the potential mechanisms and explain the differential inhibitory capacity of the latter, which enabled both a holistic view on the process and details at the gene/protein level. The combination of our methods pointed to proteins, such as members of the Rho pathway, pro-inflammatory signature and the YAP1/TAZ cascade, that warrant further investigation via tools of experimental perturbation. We also demonstrated functional congruence between the in vitro and ex vivo models. The microarray data are made available via the Gene Expression Omnibus as GSE57199.
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Affiliation(s)
- Andrey Alexeyenko
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden. .,Bioinformatics Infrastructure for Life Sciences, Science for Life Laboratory, Karolinska Institutet, Box 1031, 171 21, Solna, Sweden.
| | - Twana Alkasalias
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden. .,College of Science, Department of Biology, Salahaddin University, Erbil, Kurdistan-Iraq.
| | - Tatiana Pavlova
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
| | - Laszlo Szekely
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
| | - Vladimir Kashuba
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden. .,Institute of Molecular Biology and Genetics, UNAS, Kiev, Ukraine.
| | - Helene Rundqvist
- Department of Cell and Molecular Biology (CMB), Karolinska Institutet, Stockholm, Sweden.
| | - Peter Wiklund
- Department of Molecular Medicine and Surgery, section of Urology, Karolinska Institutet, Stockholm, Sweden.
| | - Lars Egevad
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
| | - Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444, Budapest 8, Hungary.
| | - Tamas Korcsmaros
- TGAC, The Genome Analysis Centre, Norwich Research Park, Norwich, UK. .,Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich, UK.
| | - Hayrettin Guven
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
| | - George Klein
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
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Das V, Bruzzese F, Konečný P, Iannelli F, Budillon A, Hajdúch M. Pathophysiologically relevant in vitro tumor models for drug screening. Drug Discov Today 2015; 20:848-55. [PMID: 25908576 DOI: 10.1016/j.drudis.2015.04.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/16/2015] [Accepted: 04/13/2015] [Indexed: 12/21/2022]
Abstract
The alarming rate of failure of clinical trials is a major hurdle in cancer therapy that partly results from the inadequate use of in vitro tumor models for the screening of promising hits and leads in preclinical studies. 2D cultures of cancer cell lines that are primarily used for drug screening do not adequately recapitulate tumor microenvironment (TME) complexities compared with 3D cancer cell cultures and tumor-derived primary cell cultures. In this review, we focus on the potential use of in vitro tumor models that reproduce in vivo tumor complexities for effective drug selection in the preclinical stages of drug development.
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Affiliation(s)
- Viswanath Das
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; EATRIS Headquarters, Giovanni Migliaccio, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands
| | - Francesca Bruzzese
- Experimental Pharmacology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori Fondazioni Giovanni Pascale - IRCCS, 80131 Naples, Italy; EATRIS Headquarters, Giovanni Migliaccio, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands
| | - Petr Konečný
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; EATRIS Headquarters, Giovanni Migliaccio, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands
| | - Federica Iannelli
- Experimental Pharmacology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori Fondazioni Giovanni Pascale - IRCCS, 80131 Naples, Italy; EATRIS Headquarters, Giovanni Migliaccio, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands
| | - Alfredo Budillon
- Experimental Pharmacology Unit, Istituto Nazionale per lo Studio e la Cura dei Tumori Fondazioni Giovanni Pascale - IRCCS, 80131 Naples, Italy; EATRIS Headquarters, Giovanni Migliaccio, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands
| | - Marián Hajdúch
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University Olomouc, Hněvotínská 5, 779 00 Olomouc, Czech Republic; EATRIS Headquarters, Giovanni Migliaccio, De Boelelaan 1118, 1081 HZ Amsterdam, The Netherlands.
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27
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Neri S, Ishii G, Hashimoto H, Kuwata T, Nagai K, Date H, Ochiai A. Podoplanin-expressing cancer-associated fibroblasts lead and enhance the local invasion of cancer cells in lung adenocarcinoma. Int J Cancer 2015; 137:784-96. [PMID: 25648219 DOI: 10.1002/ijc.29464] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 01/27/2015] [Indexed: 12/17/2022]
Abstract
Cancer-associated fibroblasts (CAFs) communicate with cancer cells and play important roles in cancer invasion. We previously reported that local invasion of cancer cells was frequently observed in lung adenocarcinoma patients with podoplanin (PDPN)-expressing CAFs. However, the underlying mechanisms of this phenomenon have remained unclear. In this study, we established a novel collagen invasion assay model in which cancer cells and CAFs were cocultured; we analyzed the mechanisms governing how cancer cell invasion was promoted by PDPN(+)CAFs. By observing the dynamic movement of both CAFs and cancer cells in the collagen matrix, we found that PDPN(+)CAFs invaded the matrix to a greater extent, with more cancer cells invading within the "tracks" created by the CAFs, compared with control CAFs. The knockdown of PDPN in CAFs decreased the invasion of both the CAFs and the cancer cells. PDPN(+)CAFs displayed a higher RhoA activity and treatment with a ROCK inhibitor cancelled the increased invasion ability of PDPN(+)CAFs and subsequently decreased the number of invaded cancer cells. After intravenous injection in the mouse tail vein, PDPN(+)CAFs invaded and promoted cancer cell invasion into the lung parenchyma, compared with control CAFs. Among the patients with lung adenocarcinoma, we observed some cases with PDPN(+)CAFs at the invasive front of the tumor. These cases predominantly exhibited pleural invasion of cancer cells, known as pathological invasiveness. Our results indicated that PDPN(+)CAFs were tumor-promoting CAFs that lead and enhance the local invasion of cancer cells, suggesting that the invasion activity of CAFs themselves could be rate-determining for cancer cell invasion.
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Affiliation(s)
- Shinya Neri
- Pathology Division, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan.,Division of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan.,Department of Thoracic Surgery, Graduate School of Medicine, Kyoto University, Sakyo-Ku, Kyoto, Japan
| | - Genichiro Ishii
- Pathology Division, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Hiroko Hashimoto
- Pathology Division, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Takeshi Kuwata
- Pathology Division, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Kanji Nagai
- Division of Thoracic Surgery, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
| | - Hiroshi Date
- Department of Thoracic Surgery, Graduate School of Medicine, Kyoto University, Sakyo-Ku, Kyoto, Japan
| | - Atsushi Ochiai
- Pathology Division, Research Center for Innovative Oncology, National Cancer Center Hospital East, Kashiwa, Chiba, Japan
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28
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Slany A, Meshcheryakova A, Beer A, Ankersmit HJ, Paulitschke V, Gerner C. Plasticity of fibroblasts demonstrated by tissue-specific and function-related proteome profiling. Clin Proteomics 2014; 11:41. [PMID: 26029019 PMCID: PMC4448269 DOI: 10.1186/1559-0275-11-41] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/17/2014] [Indexed: 01/15/2023] Open
Abstract
Background Fibroblasts are mesenchymal stromal cells which occur in all tissue types. While their main function is related to ECM production and physical support, they are also important players in wound healing, and have further been recognized to be able to modulate inflammatory processes and support tumor growth. Fibroblasts can display distinct phenotypes, depending on their tissue origin, as well as on their functional state. Results In order to contribute to the proteomic characterization of fibroblasts, we have isolated primary human fibroblasts from human skin, lung and bone marrow and generated proteome profiles of these cells by LC-MS/MS. Comparative proteome profiling revealed characteristic differences therein, which seemed to be related to the cell’s tissue origin. Furthermore, the cells were treated in vitro with the pro-inflammatory cytokine IL-1beta. While all fibroblasts induced the secretion of Interleukins IL-6 and IL-8 and the chemokine GRO-alpha, other inflammation-related proteins were up-regulated in an apparently tissue-dependent manner. Investigating fibroblasts from tumorous tissues of skin, lung and bone marrow with respect to such inflammation-related proteins revealed hardly any conformity but rather individual and tumor type-related variations. However, apparent up-regulation of IGF-II, PAI-1 and PLOD2 was observed in melanoma-, lung adenocarcinoma- and multiple myeloma-associated fibroblasts, as well as in hepatocellular carcinoma-associated fibroblasts. Conclusions Inflammation-related proteome alterations of primary human fibroblasts were determined by the analysis of IL-1beta treated cells. Tumor-associated fibroblasts from different tissue types hardly showed signs of acute inflammation but displayed characteristic functional aberrations potentially related to chronic inflammation. The present data suggest that the state of the tumor microenvironment is relevant for tumor progression and targeted treatment of tumor-associated fibroblasts may support anti-cancer strategies. Electronic supplementary material The online version of this article (doi:10.1186/1559-0275-11-41) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Astrid Slany
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria
| | - Anastasia Meshcheryakova
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
| | - Agnes Beer
- Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
| | - Hendrik Jan Ankersmit
- Department of Thoracic Surgery, Division of Surgery, Medical University Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
| | - Verena Paulitschke
- Department of Dermatology, Medical University of Vienna, Vienna, Austria
| | - Christopher Gerner
- Faculty of Chemistry, Department of Analytical Chemistry, University of Vienna, Vienna, Austria ; Department of Medicine I, Institute of Cancer Research, Medical University of Vienna, Vienna, Austria ; Christian Doppler Laboratory for the Diagnosis and Regeneration of Cardiac and Thoracic Diseases, Medical University Vienna, Vienna, Austria
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29
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Sajjadi SJ, Qian X, Zeng B, Adl AA. Network-Based Methods to Identify Highly Discriminating Subsets of Biomarkers. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:1029-1037. [PMID: 26357040 DOI: 10.1109/tcbb.2014.2325014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Complex diseases such as various types of cancer and diabetes are conjectured to be triggered and influenced by a combination of genetic and environmental factors. To integrate potential effects from interplay among underlying candidate factors, we propose a new network-based framework to identify effective biomarkers by searching for groups of synergistic risk factors with high predictive power to disease outcome. An interaction network is constructed with node weights representing individual predictive power of candidate factors and edge weights capturing pairwise synergistic interactions among factors. We then formulate this network-based biomarker identification problem as a novel graph optimization model to search for multiple cliques with maximum overall weight, which we denote as the Maximum Weighted Multiple Clique Problem (MWMCP). To achieve optimal or near optimal solutions, both an analytical algorithm based on column generation method and a fast heuristic for large-scale networks have been derived. Our algorithms for MWMCP have been implemented to analyze two biomedical data sets: a Type 1 Diabetes (T1D) data set from the Diabetes Prevention Trial-Type 1 (DPT-1) study, and a breast cancer genomics data set for metastasis prognosis. The results demonstrate that our network-based methods can identify important biomarkers with better prediction accuracy compared to the conventional feature selection that only considers individual effects.
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30
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Siani A, Tirelli N. Myofibroblast differentiation: main features, biomedical relevance, and the role of reactive oxygen species. Antioxid Redox Signal 2014; 21:768-85. [PMID: 24279926 DOI: 10.1089/ars.2013.5724] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
SIGNIFICANCE Myofibroblasts are prototypical fibrotic cells, which are involved in a number of more or less pathological conditions, from foreign body reactions to scarring, from liver, kidney, or lung fibrosis to neoplastic phenomena. The differentiation of precursor cells (not only of fibroblastic nature) is characterized by a complex interplay between soluble factors (growth factors such as transforming growth factor β1, reactive oxygen species [ROS]) and material properties (matrix stiffness). RECENT ADVANCES The last 15 years have seen very significant advances in the identification of appropriate differentiation markers, in the understanding of the differentiation mechanism, and above all, the involvement of ROS as causative and persistence factors. CRITICAL ISSUES The specific mechanisms of action of ROS remain largely unknown, although evidence suggests that both intracellular and extracellular phenomena play a role. FUTURE DIRECTIONS Approaches based on antioxidant (ROS-scavenging) principles and on the potentiation of nitric oxide signaling hold much promise in view of a pharmacological therapy of fibrotic phenomena. However, how to make the active principles available at the target sites is yet a largely neglected issue.
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Affiliation(s)
- Alessandro Siani
- 1 School of Pharmacy and Pharmaceutical Sciences, University of Manchester , Manchester, United Kingdom
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31
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Klein G. Evolutionary aspects of cancer resistance. Semin Cancer Biol 2014; 25:10-4. [DOI: 10.1016/j.semcancer.2014.01.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 12/19/2013] [Accepted: 01/05/2014] [Indexed: 02/01/2023]
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Bozoky B, Savchenko A, Guven H, Ponten F, Klein G, Szekely L. Decreased decorin expression in the tumor microenvironment. Cancer Med 2014; 3:485-91. [PMID: 24634138 PMCID: PMC4101739 DOI: 10.1002/cam4.231] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 01/27/2014] [Accepted: 02/21/2014] [Indexed: 12/20/2022] Open
Abstract
Decorin is a small leucine-rich proteoglycan, synthesized and deposited by fibroblasts in the stroma where it binds to collagen I. It sequesters several growth factors and antagonizes numerous members of the receptor tyrosine kinase family. In experimental murine systems, it acted as a potent tumor suppressor. Examining the Human Protein Atlas online database of immunostained tissue samples we have surveyed decorin expression in silico in several different tumor types, comparing them with corresponding normal tissues. We found that decorin is abundantly secreted and deposited in normal connective tissue but its expression is consistently decreased in the tumor microenvironment. We developed a software to quantitate the difference in expression. The presence of two closely related proteoglycans in the newly formed tumor stroma indicated that the decreased decorin expression was not caused by the delay in proteoglycan deposition in the newly formed connective tissue surrounding the tumor.
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Affiliation(s)
- Benedek Bozoky
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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Csermely P, Hódsági J, Korcsmáros T, Módos D, Perez-Lopez ÁR, Szalay K, Veres DV, Lenti K, Wu LY, Zhang XS. Cancer stem cells display extremely large evolvability: alternating plastic and rigid networks as a potential Mechanism: network models, novel therapeutic target strategies, and the contributions of hypoxia, inflammation and cellular senescence. Semin Cancer Biol 2014; 30:42-51. [PMID: 24412105 DOI: 10.1016/j.semcancer.2013.12.004] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 12/17/2013] [Accepted: 12/22/2013] [Indexed: 12/13/2022]
Abstract
Cancer is increasingly perceived as a systems-level, network phenomenon. The major trend of malignant transformation can be described as a two-phase process, where an initial increase of network plasticity is followed by a decrease of plasticity at late stages of tumor development. The fluctuating intensity of stress factors, like hypoxia, inflammation and the either cooperative or hostile interactions of tumor inter-cellular networks, all increase the adaptation potential of cancer cells. This may lead to the bypass of cellular senescence, and to the development of cancer stem cells. We propose that the central tenet of cancer stem cell definition lies exactly in the indefinability of cancer stem cells. Actual properties of cancer stem cells depend on the individual "stress-history" of the given tumor. Cancer stem cells are characterized by an extremely large evolvability (i.e. a capacity to generate heritable phenotypic variation), which corresponds well with the defining hallmarks of cancer stem cells: the possession of the capacity to self-renew and to repeatedly re-build the heterogeneous lineages of cancer cells that comprise a tumor in new environments. Cancer stem cells represent a cell population, which is adapted to adapt. We argue that the high evolvability of cancer stem cells is helped by their repeated transitions between plastic (proliferative, symmetrically dividing) and rigid (quiescent, asymmetrically dividing, often more invasive) phenotypes having plastic and rigid networks. Thus, cancer stem cells reverse and replay cancer development multiple times. We describe network models potentially explaining cancer stem cell-like behavior. Finally, we propose novel strategies including combination therapies and multi-target drugs to overcome the Nietzschean dilemma of cancer stem cell targeting: "what does not kill me makes me stronger".
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Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary.
| | - János Hódsági
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary
| | - Tamás Korcsmáros
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary
| | - Dezső Módos
- Department of Genetics, Eötvös Loránd University, Pázmány P. s. 1C, H-1117 Budapest, Hungary; Semmelweis University, Department of Morphology and Physiology, Faculty of Health Sciences, Vas u. 17, H-1088 Budapest, Hungary
| | - Áron R Perez-Lopez
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary
| | - Kristóf Szalay
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary
| | - Dániel V Veres
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary
| | - Katalin Lenti
- Semmelweis University, Department of Morphology and Physiology, Faculty of Health Sciences, Vas u. 17, H-1088 Budapest, Hungary
| | - Ling-Yun Wu
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, No. 55, Zhongguancun East Road, Beijing 100190, China
| | - Xiang-Sun Zhang
- Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, No. 55, Zhongguancun East Road, Beijing 100190, China
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Su Y, Li X, Ji W, Sun B, Xu C, Li Z, Qian G, Su C. Small molecule with big role: MicroRNAs in cancer metastatic microenvironments. Cancer Lett 2013; 344:147-56. [PMID: 24184826 DOI: 10.1016/j.canlet.2013.10.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 10/22/2013] [Accepted: 10/24/2013] [Indexed: 12/19/2022]
Abstract
Cancer metastasis is closely related to tumor cell microenvironments. Cancer cells and stromal cells interact with one another through extracellular matrix (ECM) and jointly participate in establishing the microenvironments. However, many questions remain to be addressed, in particular, a crucial question is which messengers mediate the mutual interaction and regulation between cancer cells and stromal cells. MicroRNAs (miRNAs), as oncogenic and oncosuppressor genes, regulate the expression and function of their related target genes to affect the biological behaviors of cancer cells and stromal cells, which may play an important role in cancer metastasis. Many miRNAs associated with cancer metastasis have been identified. The molecules of miRNAs are small and relatively easy to be secreted into extracellular microenvironments and devoured by nearby cells. As the regulatory messengers between cells, the secreted miRNAs function to regulate cancer cell proliferation, migration, intercellular communication and stromal modification, thereby helping cancer cells to establish their microenvironments for metastasis. In conclusion, miRNAs are small molecules, but they play a powerful role in regulating cancer metastatic ability by construction and modification of microenvironments.
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Affiliation(s)
- Yinghan Su
- Department of Biology, Xi'an Jiaotong-Liverpool University, Suzhou 215123, China
| | - Xiaoya Li
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital, Second Military Medical University, Shanghai 200438, China
| | - Weidan Ji
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital, Second Military Medical University, Shanghai 200438, China
| | - Bin Sun
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital, Second Military Medical University, Shanghai 200438, China
| | - Can Xu
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Zhaoshen Li
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai 200433, China
| | - Guojun Qian
- Department of Minimal Invasion Therapy, Eastern Hepatobiliary Surgical Hospital, Second Military Medical University, Shanghai 200438, China.
| | - Changqing Su
- Department of Molecular Oncology, Eastern Hepatobiliary Surgical Hospital, Second Military Medical University, Shanghai 200438, China.
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Nouraee N, Van Roosbroeck K, Vasei M, Semnani S, Samaei NM, Naghshvar F, Omidi AA, Calin GA, Mowla SJ. Expression, tissue distribution and function of miR-21 in esophageal squamous cell carcinoma. PLoS One 2013; 8:e73009. [PMID: 24039846 PMCID: PMC3769386 DOI: 10.1371/journal.pone.0073009] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 07/23/2013] [Indexed: 01/23/2023] Open
Abstract
Objective MiR-21 is an oncomir expressed by malignant cells and/or tumor microenvironment components. In this study we focused on understanding the effects of stromal miR-21 on esophageal malignant cells. Design MiR-21 expression was evaluated in formalin-fixed paraffin-embedded samples from patients with esophageal squamous-cell carcinoma (SCC) by quantitative RT-PCR. MiR-21 tissue distribution was visualized with in situ hybridization. A co-culture system of normal fibroblasts and esophageal cancer cells was used to determine the effects of fibroblasts on miR-21 expression levels, and on SCC cell migration and invasion. Results MiR-21 was overexpressed in SCCs, when compared to the adjacent non-tumor tissues (P = 0.0007), and was mainly localized in the cytoplasm of stromal cells adjacent to malignant cells. Accordingly, miR-21 expression was increased in tumors with high versus low stromal content (P = 0.04). When co-cultured with normal fibroblasts, miR-21 expression was elevated in SCC cells (KYSE-30), while its expression was restricted to fibroblasts when co-cultured with adenocarcinoma cells (OE-33 and FLO-1). MiR-21 was detected in conditioned media of cancer cell lines, illustrating the release of this miRNA into the environment. Co-culturing with normal fibroblasts or addition of fibroblast conditioned media caused a significant increase in cell migration and invasion potency of KYSE-30 cells (P<0.0001). In addition, co-culturing cancer cells with fibroblasts and expression of miR-21 induced the expression of the cancer associated fibroblast (CAF) marker S100A4. Conclusions MiR-21 expression is mostly confined to the SCC stroma and its release from fibroblasts influences the migration and invasion capacity of SCC cells. Moreover, miR-21 may be an important factor in “activating” fibroblasts to CAFs. These findings provide new insights into the role of CAFs and the extracellular matrix in tumor microenvironment formation and in tumor cell maintenance, and suggest miR-21 may contribute to cellular crosstalk in the tumor microenvironment.
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Affiliation(s)
- Nazila Nouraee
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
| | - Katrien Van Roosbroeck
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
| | - Mohammad Vasei
- Pathology Laboratory, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Shahriar Semnani
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nader Mansour Samaei
- Human Genetics Department, Golestan University of Medical Sciences, Gorgan, Iran
| | - Farshad Naghshvar
- Department of Pathology, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abbas Ali Omidi
- Department of Pathology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - George A. Calin
- Department of Experimental Therapeutics, MD Anderson Cancer Center, University of Texas, Houston, Texas, United States of America
- * E-mail: (GC); (SJM)
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail: (GC); (SJM)
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Csermely P, Korcsmáros T. Cancer-related networks: a help to understand, predict and change malignant transformation. Semin Cancer Biol 2013; 23:209-12. [PMID: 23831276 DOI: 10.1016/j.semcancer.2013.06.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Cancer is increasingly described as a systems-level, network phenomenon. Genetic methods, such as next generation sequencing and RNA interference uncovered the complexity tumor-specific mutation-induced effects and the identification of multiple target sets. Network analysis of cancer-specific metabolic and signaling pathways highlighted the structural features of cancer-related proteins and their complexes to develop next-generation protein kinase inhibitors, as well as the modulation of inflammatory and autophagic pathways in anti-cancer therapies. Importantly, malignant transformation can be described as a two-phase process, where an initial increase of system plasticity is followed by a decrease of plasticity at late stages of tumor development. Late-stage tumors should be attacked by an indirect network influence strategy. On the contrary, the attack of early-stage tumors may target central network nodes. Cancer stem cells need special diagnosis and targeting, since they potentially have an extremely high ability to change the rigidity/plasticity of their networks. The early warning signals of the activation of fast growing tumor cell clones are important in personalized diagnosis and therapy. Multi-target attacks are needed to perturb cancer-specific networks to exit from cancer attractors and re-enter a normal attractor. However, the dynamic non-genetic heterogeneity of cancer cell population induces the replenishment of the cancer attractor with surviving, non-responsive cells from neighboring abnormal attractors. The development of drug resistance is further complicated by interactions of tumor clones and their microenvironment. Network analysis of intercellular cooperation using game theory approaches may open new areas of understanding tumor complexity. In conclusion, the above applications of the network approach open up new, and highly promising avenues in anti-cancer drug design.
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Csermely P, Korcsmáros T, Kiss HJM, London G, Nussinov R. Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. Pharmacol Ther 2013; 138:333-408. [PMID: 23384594 PMCID: PMC3647006 DOI: 10.1016/j.pharmthera.2013.01.016] [Citation(s) in RCA: 512] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 01/22/2013] [Indexed: 02/02/2023]
Abstract
Despite considerable progress in genome- and proteome-based high-throughput screening methods and in rational drug design, the increase in approved drugs in the past decade did not match the increase of drug development costs. Network description and analysis not only give a systems-level understanding of drug action and disease complexity, but can also help to improve the efficiency of drug design. We give a comprehensive assessment of the analytical tools of network topology and dynamics. The state-of-the-art use of chemical similarity, protein structure, protein-protein interaction, signaling, genetic interaction and metabolic networks in the discovery of drug targets is summarized. We propose that network targeting follows two basic strategies. The "central hit strategy" selectively targets central nodes/edges of the flexible networks of infectious agents or cancer cells to kill them. The "network influence strategy" works against other diseases, where an efficient reconfiguration of rigid networks needs to be achieved by targeting the neighbors of central nodes/edges. It is shown how network techniques can help in the identification of single-target, edgetic, multi-target and allo-network drug target candidates. We review the recent boom in network methods helping hit identification, lead selection optimizing drug efficacy, as well as minimizing side-effects and drug toxicity. Successful network-based drug development strategies are shown through the examples of infections, cancer, metabolic diseases, neurodegenerative diseases and aging. Summarizing >1200 references we suggest an optimized protocol of network-aided drug development, and provide a list of systems-level hallmarks of drug quality. Finally, we highlight network-related drug development trends helping to achieve these hallmarks by a cohesive, global approach.
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Affiliation(s)
- Peter Csermely
- Department of Medical Chemistry, Semmelweis University, P.O. Box 260, H-1444 Budapest 8, Hungary.
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