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Kastana P, Ntenekou D, Mourkogianni E, Enake MK, Xanthopoulos A, Choleva E, Marazioti A, Nikou S, Akwii RG, Papadaki E, Gramage E, Herradón G, Stathopoulos GT, Mikelis CM, Papadimitriou E. Genetic deletion or tyrosine phosphatase inhibition of PTPRZ1 activates c-Met to up-regulate angiogenesis and lung adenocarcinoma growth. Int J Cancer 2023; 153:1051-1066. [PMID: 37260355 PMCID: PMC10524925 DOI: 10.1002/ijc.34564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 04/12/2023] [Accepted: 04/28/2023] [Indexed: 06/02/2023]
Abstract
Protein tyrosine phosphatase receptor zeta 1 (PTPRZ1) is a transmembrane tyrosine phosphatase (TP) expressed in endothelial cells and required for stimulation of cell migration by vascular endothelial growth factor A165 (VEGFA165 ) and pleiotrophin (PTN). It is also over or under-expressed in various tumor types. In this study, we used genetically engineered Ptprz1-/- and Ptprz1+/+ mice to study mechanistic aspects of PTPRZ1 involvement in angiogenesis and investigate its role in lung adenocarcinoma (LUAD) growth. Ptprz1-/- lung microvascular endothelial cells (LMVEC) have increased angiogenic features compared with Ptprz1+/+ LMVEC, in line with the increased lung angiogenesis and the enhanced chemically induced LUAD growth in Ptprz1-/- compared with Ptprz1+/+ mice. In LUAD cells isolated from the lungs of urethane-treated mice, PTPRZ1 TP inhibition also enhanced proliferation and migration. Expression of beta 3 (β3 ) integrin is decreased in Ptprz1-/- LMVEC, linked to enhanced VEGF receptor 2 (VEGFR2), c-Met tyrosine kinase (TK) and Akt kinase activities. However, only c-Met and Akt seem responsible for the enhanced endothelial cell activation in vitro and LUAD growth and angiogenesis in vivo in Ptprz1-/- mice. A selective PTPRZ1 TP inhibitor, VEGFA165 and PTN also activate c-Met and Akt in a PTPRZ1-dependent manner in endothelial cells, and their stimulatory effects are abolished by the c-Met TK inhibitor (TKI) crizotinib. Altogether, our data suggest that low PTPRZ1 expression is linked to worse LUAD prognosis and response to c-Met TKIs and uncover for the first time the role of PTPRZ1 in mediating c-Met activation by VEGFA and PTN.
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Affiliation(s)
- Pinelopi Kastana
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, Greece
| | - Despoina Ntenekou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, Greece
| | - Eleni Mourkogianni
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, Greece
| | - Michaela-Karina Enake
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, Greece
| | | | - Effrosyni Choleva
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, Greece
| | - Antonia Marazioti
- Laboratory of Molecular Respiratory Carcinogenesis, Department of Physiology, Faculty of Medicine, University of Patras, Greece
| | - Sophia Nikou
- Department of Anatomy, Faculty of Medicine, University of Patras, Greece
| | - Racheal G. Akwii
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Centre, Amarillo, TX, USA
| | - Eleni Papadaki
- Department of Anatomy, Faculty of Medicine, University of Patras, Greece
| | - Esther Gramage
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Gonzalo Herradón
- Departamento de Ciencias Farmacéuticas y de la Salud, Facultad de Farmacia, Universidad San Pablo-CEU, CEU Universities, Madrid, Spain
| | - Georgios T. Stathopoulos
- Laboratory of Molecular Respiratory Carcinogenesis, Department of Physiology, Faculty of Medicine, University of Patras, Greece
| | - Constantinos M. Mikelis
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, Greece
- Department of Pharmaceutical Sciences, School of Pharmacy, Texas Tech University Health Sciences Centre, Amarillo, TX, USA
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Gutierrez-Angulo M, Ayala-Madrigal MDLL, Moreno-Ortiz JM, Peregrina-Sandoval J, Garcia-Ayala FD. Microbiota composition and its impact on DNA methylation in colorectal cancer. Front Genet 2023; 14:1037406. [PMID: 37614819 PMCID: PMC10442805 DOI: 10.3389/fgene.2023.1037406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 07/20/2023] [Indexed: 08/25/2023] Open
Abstract
Colorectal cancer is a complex disease resulting from the interaction of genetics, epigenetics, and environmental factors. DNA methylation is frequently found in tumor suppressor genes to promote cancer development. Several factors are associated with changes in the DNA methylation pattern, and recently, the gastrointestinal microbiota could be associated with this epigenetic change. The predominant phyla in gut microbiota are Firmicutes and Bacteroidetes; however, an enrichment of Bacteroides fragilis, Fusobacterium nucleatum, and Streptococcus bovis, among others, has been reported in colorectal cancer, although the composition could be influenced by several factors, including diet, age, sex, and cancer stage. Fusobacterium nucleatum, a gram-negative anaerobic bacillus, is mainly associated with colorectal cancer patients positive for the CpG island methylator phenotype, although hypermethylation in genes such as MLH1, CDKN2A, MTSS1, RBM38, PKD1, PTPRT, and EYA4 has also been described. Moreover, Hungatella hathewayi, a gram-positive, rod-shaped bacterium, is related to hypermethylation in SOX11, THBD, SFRP2, GATA5, ESR1, EYA4, CDX2, and APC genes. The underlying epigenetic mechanism is unclear, although it could be implicated in the regulation of DNA methyltransferases, enzymes that catalyze the transfer of a methyl group on cytosine of CpG sites. Since DNA methylation is a reversible event, changes in gut microbiota could modulate the gene expression through DNA methylation and improve the colorectal cancer prognosis.
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Affiliation(s)
- Melva Gutierrez-Angulo
- Departamento de Ciencias de la Salud, Centro Universitario de los Altos, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Maria de la Luz Ayala-Madrigal
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Jose Miguel Moreno-Ortiz
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Jorge Peregrina-Sandoval
- Departamento de Biología Celular y Molecular, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Fernando Daniel Garcia-Ayala
- Doctorado en Genética Humana e Instituto de Genética Humana “Dr. Enrique Corona Rivera”, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud (CUCS), Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
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3
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Papadimitriou E, Kanellopoulou VK. Protein Tyrosine Phosphatase Receptor Zeta 1 as a Potential Target in Cancer Therapy and Diagnosis. Int J Mol Sci 2023; 24:ijms24098093. [PMID: 37175798 PMCID: PMC10178973 DOI: 10.3390/ijms24098093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/25/2023] [Accepted: 04/27/2023] [Indexed: 05/15/2023] Open
Abstract
Protein tyrosine phosphatase receptor zeta 1 (PTPRZ1) is a type V transmembrane tyrosine phosphatase that is highly expressed during embryonic development, while its expression during adulthood is limited. PTPRZ1 is highly detected in the central nervous system, affecting oligodendrocytes' survival and maturation. In gliomas, PTPRZ1 expression is significantly upregulated and is being studied as a potential cancer driver and as a target for therapy. PTPRZ1 expression is also increased in other cancer types, but there are no data on the potential functional significance of this finding. On the other hand, low PTPRZ1 expression seems to be related to a worse prognosis in some cancer types, suggesting that in some cases, it may act as a tumor-suppressor gene. These discrepancies may be due to our limited understanding of PTPRZ1 signaling and tumor microenvironments. In this review, we present evidence on the role of PTPRZ1 in angiogenesis and cancer and discuss the phenomenal differences among the different types of cancer, depending on the regulation of its tyrosine phosphatase activity or ligand binding. Clarifying the involved signaling pathways will lead to its efficient exploitation as a novel therapeutic target or as a biomarker, and the development of proper therapeutic approaches.
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Affiliation(s)
- Evangelia Papadimitriou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, 26504 Patras, Greece
| | - Vasiliki K Kanellopoulou
- Laboratory of Molecular Pharmacology, Department of Pharmacy, University of Patras, 26504 Patras, Greece
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Li Z, Fu Y, Hu Y, Zhu Y, Hu L, Shi C, Zhang Y, Zhang J, Zhou S. Low-dose arecoline regulates distinct core signaling pathways in oral submucous fibrosis and oral squamous cell carcinoma. BMC Oral Health 2023; 23:171. [PMID: 36966276 PMCID: PMC10039525 DOI: 10.1186/s12903-023-02887-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/15/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND Betel nut chewing plays a role in the pathogenesis of oral submucous fibrosis (OSF) and oral squamous cell carcinoma (OSCC). As the major active ingredient of the betel nut, the effect of arecoline and its underlying mechanism to OSF and OSCC pathogenesis remain unclear. METHODS Next-generation sequencing-based transcriptome and dRRBS analysis were performed on OSF and OSCC cells under low-dose arecoline exposure. Functional analyses were performed to compare the different roles of arecoline during OSF and OSCC pathogenesis, and key genes were identified. RESULTS In this study, we identified that low-dose arecoline promoted cell proliferation of both NFs and OSCC cells via the acceleration of cell cycle progression, while high-dose arecoline was cytotoxic to both NFs and OSCC cells. We performed for the first time the transcriptome and methylome landscapes of NFs and OSCC cells under low-dose arecoline exposure. We found distinct transcriptome and methylome profiles mediated by low-dose arecoline in OSF and OSCC cells, as well as specific genes and signaling pathways associated with metabolic disorders induced by low-dose arecoline exposure. Additionally, low-dose arecoline displayed different functions at different stages, participating in the modulation of the extracellular matrix via Wnt signaling in NFs and epigenetic regulation in OSCC cells. After exposure to low-dose arecoline, the node roles of FMOD in NFs and histone gene clusters in OSCC cells were found. Meanwhile, some key methylated genes induced by arecoline were also identified, like PTPRM and FOXD3 in NFs, SALL3 and IRF8 in OSCC cells, indicating early molecular events mediated by arecoline during OSF and OSCC pathogenesis. CONCLUSIONS This study elucidated the contribution of low-dose arecoline to OSF and OSCC pathogenesis and identified key molecular events that could be targeted for further functional studies and their potential as biomarkers.
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Affiliation(s)
- Zhenming Li
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - You Fu
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Yuhua Hu
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
- Department of Oral Pathology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Yun Zhu
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Longwei Hu
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Chaoji Shi
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Yi Zhang
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
- Department of Endodontics and Operative Dentistry, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
| | - Jianjun Zhang
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China
- National Center for Stomatology, Shanghai, 200011, China
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Shanghui Zhou
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.
- College of Stomatology, Shanghai Jiao Tong University, Shanghai, 200011, China.
- National Center for Stomatology, Shanghai, 200011, China.
- National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.
- Shanghai Key Laboratory of Stomatology, Shanghai, 200011, China.
- Shanghai Research Institute of Stomatology, Shanghai, 200011, China.
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5
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Hühns M, Ameziane N, Holzmann C, Al-Ali R, Prall F. Clonal and "Intrinsic" Heterogeneity of Somatic Variants in Microsatellite-Stable Colorectal Carcinomas and Their Metastases. J Transl Med 2023; 103:100132. [PMID: 36966951 DOI: 10.1016/j.labinv.2023.100132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/07/2023] [Accepted: 03/19/2023] [Indexed: 04/21/2023] Open
Abstract
To test the traditional model of tumor progression, Darwinian-type evolution, against the more recent Big Bang model, we selected 6 microsatellite-stable colorectal standard-type adenocarcinomas and their synchronous lymph node and liver metastases. Somatic genomic variants were identified by whole-exome sequencing (WES) of large tumor fragments from the primaries and 1 liver metastasis each, and used to design targeted resequencing next-generation sequencing (NGS) panels, 1 per case. Targeted deep resequencing (mean coverage, 2725; median, 2222) was performed with DNA from punch samples (1-mm tissue microarrayer needles) obtained from different regions of the primaries and their metastases. In total, 255 genomic variants were interrogated in 108 punch samples. Clonal heterogeneity was infrequent: a pattern of clonal heterogeneity consistent with a role in metastasis formation was observed only in 1 case in a single gene (p. Asp604Tyr of the PTPRT gene). However, when comparing variant allele frequencies (VAFs) of genomic variants in adjacent positions on chromosomes ("matched genomic variant loci") across punch samples, differences that exceeded 2 SD of the NGS assay variations (ad hoc dubbed VAF dysbalance) were observed in 7.1% of the punch samples (2.6%-12.0% per case), which indicates an intricate intermixing of mutated and nonmutated tumor cells ("intrinsic heterogeneity"). Additional OncoScan array analyses on a subset of the punch samples (31 in total) showed gross genomic aberrations as a possible explanation in only some (39.2%) of the matched genomic variant loci with VAF dysbalance. Our study provides a fairly direct (statistical model-free) view of the genomic states of microsatellite-stable colorectal carcinomas and their metastases, and suggests that Darwinian-type tumor evolution is not the key pathway of the metastasizing disease; instead, we recorded an "intrinsic" genomic heterogeneity, which may echo an initial Big Bang-like event.
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Affiliation(s)
- Maja Hühns
- Institute of Pathology, University Medicine of Rostock, Strempelstraße, Rostock, Germany
| | - Najim Ameziane
- Centogene AG, Am Strande, Rostock, Germany; Arcensus GmbH, Goethestraße, Rostock, Germany
| | - Carsten Holzmann
- Institute of Medical Genetics, Rostock University Medical Center, Ernst-Heydemann-Straße, Rostock, Germany
| | | | - Friedrich Prall
- Institute of Pathology, University Medicine of Rostock, Strempelstraße, Rostock, Germany.
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6
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Feng Y, Yao S, Pu Z, Cheng H, Fei B, Zou J, Huang Z. Identification of New Tumor-Related Gene Mutations in Chinese Gastrointestinal Stromal Tumors. Front Cell Dev Biol 2021; 9:764275. [PMID: 34805171 PMCID: PMC8595335 DOI: 10.3389/fcell.2021.764275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the gastrointestinal tract. As the main GIST drivers, gain-of-function mutations in KIT or PDGFRA are closely associated with not only tumor development and progression but also therapeutic response. In addition to the status of KIT and PDGFRA, little is known about other potential GIST-related genes. In this study, we identified the mutation profiles in 49 KIT-mutated GIST tumors using the whole exome sequencing (WES) method. Furthermore, some representative mutations were further validated in an independent GIST cohort using the SNaPshot SNP assay. We identified extensive and diverse mutations of KIT in GIST, including many undescribed variants. In addition, we revealed some new tumor-related gene mutations with unknown pathogenicity. By enrichment analyses of gene function and protein-protein interaction network construction, we showed that these genes were enriched in several important cancer- or metabolism-related signaling pathways, including PI3K-AKT,RTK-RAS, Notch, Wnt, Hippo, mTOR, AMPK, and insulin signaling. In particular, DNA repair-related genes, including MLH1, MSH6, BRCA1, BRCA2, and POLE, are frequently mutated in GISTs, suggesting that immune checkpoint blockade may have promising clinical applications for these GIST subpopulations. In conclusion, in addition to extensive and diverse mutations of KIT, some genes related to DNA-repair and cell metabolism may play important roles in the development, progression and therapeutic response of GIST.
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Affiliation(s)
- Yuyang Feng
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Surui Yao
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Zhening Pu
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Han Cheng
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
| | - Bojian Fei
- Department of Gastrointestinal Surgery, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jian Zou
- Center of Clinical Research, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Zhaohui Huang
- Wuxi Cancer Institute, Affiliated Hospital of Jiangnan University, Wuxi, China.,Laboratory of Cancer Epigenetics, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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7
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Wang JL, Wang Y, Ren GP. Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods . J Zhejiang Univ Sci B 2021; 21:246-255. [PMID: 32133801 DOI: 10.1631/jzus.b1900329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
To identify novel genes in castration-resistant prostate cancer (CRPC), we downloaded three microarray datasets containing CRPC and primary prostate cancer in Gene Expression Omnibus (GEO). R packages affy and limma were performed to identify differentially expressed genes (DEGs) between primary prostate cancer and CRPC. After that, we performed functional enrichment analysis including gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway. In addition, protein-protein interaction (PPI) analysis was used to search for hub genes. Finally, to validate the significance of these genes, we performed survival analysis. As a result, we identified 53 upregulated genes and 58 downregulated genes that changed in at least two datasets. Functional enrichment analysis showed significant changes in the positive regulation of osteoblast differentiation pathway and aldosterone-regulated sodium reabsorption pathway. PPI network identified hub genes like cortactin-binding protein 2 (CTTNBP2), Rho family guanosine triphosphatase (GTPase) 3 (RND3), protein tyrosine phosphatase receptor-type R (PTPRR), Jagged1 (JAG1), and lumican (LUM). Based on PPI network analysis and functional enrichment analysis, we identified two genes (PTPRR and JAG1) as key genes. Further survival analysis indicated a relationship between high expression of the two genes and poor prognosis of prostate cancer. In conclusion, PTPRR and JAG1 are key genes in the CRPC, which may serve as promising biomarkers of diagnosis and prognosis of CRPC.
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Affiliation(s)
- Ji-Li Wang
- Department of Pathology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Yan Wang
- Department of Pathology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Guo-Ping Ren
- Department of Pathology, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.,Department of Pathology and Pathophysiology, School of Medicine, Zhejiang University, Hangzhou 310058, China
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8
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Sen M, Kindsfather A, Danilova L, Zhang F, Colombo R, LaPorte MG, Kurland BF, Huryn DM, Wipf P, Herman JG. PTPRT epigenetic silencing defines lung cancer with STAT3 activation and can direct STAT3 targeted therapies. Epigenetics 2019; 15:604-617. [PMID: 31595832 DOI: 10.1080/15592294.2019.1676597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Signal Transducers and Activators of Transcription-3 (STAT3), a potent oncogenic transcription factor, is constitutively activated in lung cancer, but mutations in pathway genes are infrequent. Protein Tyrosine Phosphatase Receptor-T (PTPRT) is an endogenous inhibitor of STAT3 and PTPRT loss-of-function represents one potential mechanism of STAT3 hyperactivation as observed in other malignancies. We determined the role of PTPRT promoter methylation and sensitivity to STAT3 pathway inhibitors in non-small cell lung cancer (NSCLC). TCGA and Pittsburgh lung cancer cohort methylation data revealed hypermethylation of PTPRT associated with diminished mRNA expression in a subset of NSCLC patients. We report frequent hypermethylation of the PTPRT promoter which correlates with transcriptional silencing of PTPRT and increased STAT3 phosphorylation (Y705) as determined by methylation-specific PCR (MSP) and real time quantitative reverse transcription (RT)-PCR in NSCLC cell lines. Silencing of PTPRT using siRNA in H520 lung cancer cell line resulted in increased pSTAT3Tyr705 and upregulation of STAT3 target genes such as Cyclin D1 and Bcl-XL expression. We show this association of PRPRT methylation with upregulation of the STAT3 target genes Cyclin D1 and Bcl-XL in patient derived lung tumour samples. We further demonstrate that PTPRT promoter methylation associated with different levels of pSTAT3Ty705 in lung cancer cell lines had selective sensitivity to STAT3 pathway small molecule inhibitors (SID 864,669 and SID 4,248,543). Our data strongly suggest that silencing of PTPRT by promoter hypermethylation is an important mechanism of STAT3 hyperactivation and targeting STAT3 may be an effective approach for the development of new lung cancer therapeutics.
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Affiliation(s)
- Malabika Sen
- Department of Hematology/Oncology, UPMC Hillman Cancer Center , Pittsburgh, PA, USA
| | - Audrey Kindsfather
- Department of Hematology/Oncology, UPMC Hillman Cancer Center , Pittsburgh, PA, USA
| | - Ludmila Danilova
- Department of Oncology, Laboratory of Systems Biology and Computational Genetics, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine , Baltimore, MD, USA.,Vavilov Institute of General Genetics, Russian Academy of Sciences , Moscow, Russia
| | - Feng Zhang
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Raffaele Colombo
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Matthew G LaPorte
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Brenda F Kurland
- Department of Biostatistics, University of Pittsburgh , Pittsburgh, PA, USA
| | - Donna M Huryn
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - Peter Wipf
- Chemical Diversity Center, University of Pittsburgh , Pittsburgh, PA, USA
| | - James G Herman
- Department of Hematology/Oncology, UPMC Hillman Cancer Center , Pittsburgh, PA, USA
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9
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Luo Z, Mao X, Cui W. Circular RNA expression and circPTPRM promotes proliferation and migration in hepatocellular carcinoma. Med Oncol 2019; 36:86. [PMID: 31494761 DOI: 10.1007/s12032-019-1311-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/28/2019] [Indexed: 12/25/2022]
Abstract
Circular RNAs (circRNAs) play a critical role during hepatocellular carcinoma (HCC) development. CircRNA PTPRM (circPTPRM) has not been reported to cause disease and its role in HCC is unclear. This study explored circRNA expression and the function of circPTPRM in HCC. RNA sequencing (RNA-seq) was performed on 3 randomly selected pairs of HCC tissues and their corresponding adjacent non-tumor tissues. Three differentially expressed circRNAs, circPTPRM, circSMAD2 and circPTBP3 were selected and verified by real-time quantitative reverse transcription-polymerase chain reactions in 30 pairs of tissue samples, In vitro cultured hepatoma cells, and normal liver cells. Clinical data analysis was performed to select target circRNAs. Anti-target circRNA siRNAs were transfected into hepatoma cell lines, and the biological behavior of hepatoma cells following silencing of the target circRNA were detected by cell proliferation, plate cloning, and transwell assays. There were 86 differentially expressed circRNAs from RNA-seq, of which 53 were significantly upregulated and 33 were significantly downregulated in HCC. CircPTPRM expression was significantly upregulated in HCC tissue (p = 0.023) based on the analysis of 30 paired samples. CircPTPRM expression positively correlated with HCC recurrence and metastasis (p = 0.039). CircPTPRM silencing reduced HCC cell proliferation, migration and invasion. CircRNAs were differentially expressed in HCC samples. CircPTPRM was significantly upregulated in HCC and may function during the tumorigenesis and metastasis of HCC.
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Affiliation(s)
- Zhun Luo
- Department of Infectious Diseases, The First Affiliated Hospital, China Medical University, Shenyang, China.,Department of Infectious Diseases, Yueyang Second People's Hospital, Yueyang, China
| | - Xuelan Mao
- Department of Infectious Diseases, The First Affiliated Hospital, China Medical University, Shenyang, China
| | - Wei Cui
- Department of Infectious Diseases, The First Affiliated Hospital, China Medical University, Shenyang, China.
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10
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Wang R, Zhang H, Li L, Yue F, Jiang Y, Li S, Liu R. Prenatal detection of interstitial 18p11.31-p11.22 microduplications: Phenotypic diversity and literature review. Prenat Diagn 2019; 39:1120-1126. [PMID: 31461790 DOI: 10.1002/pd.5553] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 08/20/2019] [Accepted: 08/20/2019] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Pure duplication of chromosome 18p is rare, with clinical phenotypes ranging from normal or slight abnormalities to various degrees of mental retardation. It remains difficult to establish a clear genotype-phenotype correlation. METHODS Chromosomal karyotyping analysis was performed on cultured amniotic fluid cells from three cases. Single nucleotide polymorphism (SNP) array analysis was carried out using the Illumina Human CytoSNP-12 BeadChip. We also carried out a review of the literature regarding 18p11 microduplication. RESULTS G-banding analysis showed that the three cases had normal karyotypes. SNP array results showed 0.48- to 1.6-Mb microduplications of 18p11.31-p11.22 (chr18: 6995739-8713088) in these cases, encompassing different degrees of LAMA1 duplication. Follow-up analysis showed that the parents of both cases 1 and 2 chose termination of pregnancy. Case 3 presented with normal growth and physical development. Currently, there is not enough evidence supporting the pathogenicity of LAMA1 triplosensitivity. CONCLUSION We described three prenatal cases with 18p11.31-p11.22 microduplications involving part of the LAMA1 locus. There might be phenotypic diversity associated with 18p11.31-p11.22 microduplications. To avoid unnecessary abortions for pregnancies such as these, comprehensive genetic counseling should be offered.
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Affiliation(s)
- Ruixue Wang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Leilei Li
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Fagui Yue
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Yuting Jiang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China.,Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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11
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Barazeghi E, Hellman P, Westin G, Stålberg P. PTPRM, a candidate tumor suppressor gene in small intestinal neuroendocrine tumors. Endocr Connect 2019; 8:1126-1135. [PMID: 31349215 PMCID: PMC6687034 DOI: 10.1530/ec-19-0279] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 07/09/2019] [Indexed: 12/27/2022]
Abstract
Small intestinal neuroendocrine tumors (SI-NETs) are small, slow growing neoplasms with loss of one copy of chromosome 18 as a common event. Frequently mutated genes on chromosome 18 or elsewhere have not been found so far. The aim of this study was to investigate a possible tumor suppressor role of the transmembrane receptor type tyrosine phosphatase PTPµ (PTPRM at 18p11) in SI-NETs. Immunohistochemistry, quantitative RT-PCR, colony formation assay and quantitative CpG methylation analysis by pyrosequencing were performed. Undetectable/very low levels of PTPRM or aberrant pattern of immunostaining, with both negative and positive areas, were detected in the majority of tumors (33/40), and a significantly reduced mRNA expression in metastases compared to primary tumors was observed. Both the DNA methylation inhibitor 5-aza-2'-deoxycytidine and the S-adenosylhomocysteine hydrolase inhibitor 3-deazaneplanocin A (DZNep) induced PTPRM expression in CNDT2.5 and KRJ-I SI-NET cells. CpG methylation of upstream regulatory regions, the promoter region and the exon 1/intron 1 boundary was detected by pyrosequencing analysis of the two cell lines and not in the analyzed SI-NETs. Overexpression of PTPRM in the SI-NET cell lines reduced cell growth and cell proliferation and induced apoptosis. The tyrosine phosphatase activity of PTPRM was not involved in cell growth inhibition. The results support a role for PTPRM as a dysregulated candidate tumor suppressor gene in SI-NETs and further analyses of the involved mechanisms are warranted.
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Affiliation(s)
- Elham Barazeghi
- Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, Rudbeck Laboratory, Uppsala, Sweden
- Correspondence should be addressed to E Barazeghi or P Stålberg: or
| | - Per Hellman
- Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, Rudbeck Laboratory, Uppsala, Sweden
| | - Gunnar Westin
- Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, Rudbeck Laboratory, Uppsala, Sweden
| | - Peter Stålberg
- Department of Surgical Sciences, Uppsala University, Uppsala University Hospital, Rudbeck Laboratory, Uppsala, Sweden
- Correspondence should be addressed to E Barazeghi or P Stålberg: or
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12
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Kober P, Boresowicz J, Rusetska N, Maksymowicz M, Goryca K, Kunicki J, Bonicki W, Siedlecki JA, Bujko M. DNA methylation profiling in nonfunctioning pituitary adenomas. Mol Cell Endocrinol 2018; 473:194-204. [PMID: 29410024 DOI: 10.1016/j.mce.2018.01.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 12/21/2017] [Accepted: 01/29/2018] [Indexed: 01/08/2023]
Abstract
Nonfunctioning pituitary adenomas (NFPAs) are among the most frequent intracranial tumors but their molecular background, including changes in epigenetic regulation, remains poorly understood. We performed genome-wide DNA methylation profiling of 34 NFPAs and normal pituitary samples. Methylation status of the selected genomic regions and expression level of corresponding genes were assessed in a group of 75 patients. NFPAs exhibited distinct global methylation profile as compared to normal pituitary. Aberrant DNA methylation appears to contribute to deregulation of the cancer-related pathways as shown by preliminary functional analysis. Promoter hypermethylation and decreased expression level of SFN, STAT5A, DUSP1, PTPRE and FGFR2 was confirmed in the enlarged group of NFPAs. Difference in the methylation profiles between invasive and non-invasive NFPAs is very slight. Nevertheless, invasiveness-related aberrant epigenetic deregulation of the particular genes was found including upregulation of ITPKB and downregulation CNKSR1 in invasive tumors.
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Affiliation(s)
- Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland; Faculty of Chemistry, Warsaw University of Technology, Warsaw, Poland; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Nataliia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Krzysztof Goryca
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Janusz Aleksander Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland.
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13
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Davis TB, Yang M, Schell MJ, Wang H, Ma L, Pledger WJ, Yeatman TJ. PTPRS Regulates Colorectal Cancer RAS Pathway Activity by Inactivating Erk and Preventing Its Nuclear Translocation. Sci Rep 2018; 8:9296. [PMID: 29915291 PMCID: PMC6006154 DOI: 10.1038/s41598-018-27584-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/26/2018] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) growth and progression is frequently driven by RAS pathway activation through upstream growth factor receptor activation or through mutational activation of KRAS or BRAF. Here we describe an additional mechanism by which the RAS pathway may be modulated in CRC. PTPRS, a receptor-type protein tyrosine phosphatase, appears to regulate RAS pathway activation through ERK. PTPRS modulates ERK phosphorylation and subsequent translocation to the nucleus. Native mutations in PTPRS, present in ~10% of CRC, may reduce its phosphatase activity while increasing ERK activation and downstream transcriptional signaling.
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Affiliation(s)
- Thomas B Davis
- Gibbs Cancer Center & Research Institute, 380 Serpentine Drive, Spartanburg, SC, 29303, USA
| | - Mingli Yang
- Gibbs Cancer Center & Research Institute, 380 Serpentine Drive, Spartanburg, SC, 29303, USA
| | - Michael J Schell
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center & Research Institute, 12902 Magnolia Drive, Tampa, FL, 33612, USA
| | - Heiman Wang
- Gibbs Cancer Center & Research Institute, 380 Serpentine Drive, Spartanburg, SC, 29303, USA
| | - Le Ma
- Gibbs Cancer Center & Research Institute, 380 Serpentine Drive, Spartanburg, SC, 29303, USA
| | - W Jack Pledger
- Gibbs Cancer Center & Research Institute, 380 Serpentine Drive, Spartanburg, SC, 29303, USA
- Department of Molecular Medicine, VCOM, 350 Howard Street, Spartanburg, SC, 29303, USA
| | - Timothy J Yeatman
- Gibbs Cancer Center & Research Institute, 380 Serpentine Drive, Spartanburg, SC, 29303, USA.
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14
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Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PÉ, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JHA, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. eFORGE: A Tool for Identifying Cell Type-Specific Signal in Epigenomic Data. Cell Rep 2017; 17:2137-2150. [PMID: 27851974 PMCID: PMC5120369 DOI: 10.1016/j.celrep.2016.10.059] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 08/25/2016] [Accepted: 09/30/2016] [Indexed: 12/14/2022] Open
Abstract
Epigenome-wide association studies (EWAS) provide an alternative approach for studying human disease through consideration of non-genetic variants such as altered DNA methylation. To advance the complex interpretation of EWAS, we developed eFORGE (http://eforge.cs.ucl.ac.uk/), a new standalone and web-based tool for the analysis and interpretation of EWAS data. eFORGE determines the cell type-specific regulatory component of a set of EWAS-identified differentially methylated positions. This is achieved by detecting enrichment of overlap with DNase I hypersensitive sites across 454 samples (tissues, primary cell types, and cell lines) from the ENCODE, Roadmap Epigenomics, and BLUEPRINT projects. Application of eFORGE to 20 publicly available EWAS datasets identified disease-relevant cell types for several common diseases, a stem cell-like signature in cancer, and demonstrated the ability to detect cell-composition effects for EWAS performed on heterogeneous tissues. Our approach bridges the gap between large-scale epigenomics data and EWAS-derived target selection to yield insight into disease etiology.
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Affiliation(s)
- Charles E Breeze
- UCL Cancer Institute, University College London, London WC1E 6BT, UK.
| | - Dirk S Paul
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit Amsterdam, 1081BT Amsterdam, the Netherlands
| | - Lee M Butcher
- UCL Cancer Institute, University College London, London WC1E 6BT, UK; Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| | - John C Ambrose
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - James E Barrett
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Robert Lowe
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT London, UK
| | - Vardhman K Rakyan
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, E1 2AT London, UK
| | - Valentina Iotchkova
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0QQ, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Willem H Ouwehand
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0QQ, UK
| | - Jonathan Laperle
- Département d'Informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Pierre-Étienne Jacques
- Département d'Informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Centre de recherche du Centre hospitalier universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC H3G 1Y6, Canada; Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Anke K Bergmann
- Institute of Human Genetics, Christian Albrechts University, 24105 Kiel, Germany; Department of Pediatrics, Christian-Albrechts-University Kiel & University Hospital Schleswig-Holstein, 24105 Kiel, Germany
| | - Reiner Siebert
- Institute of Human Genetics, Christian Albrechts University, 24105 Kiel, Germany; Institute of Human Genetics, University of Ulm, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Edo Vellenga
- Department of Hematology, University of Groningen and University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, the Netherlands
| | - Sadia Saeed
- Department of Biochemistry, PMAS Arid Agriculture University Rawalpindi, 46300 Rawalpindi, Pakistan; Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, the Netherlands
| | | | - Javier Herrero
- UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ian Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Stephan Beck
- UCL Cancer Institute, University College London, London WC1E 6BT, UK.
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15
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Meeusen B, Janssens V. Tumor suppressive protein phosphatases in human cancer: Emerging targets for therapeutic intervention and tumor stratification. Int J Biochem Cell Biol 2017; 96:98-134. [PMID: 29031806 DOI: 10.1016/j.biocel.2017.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 10/04/2017] [Accepted: 10/05/2017] [Indexed: 02/06/2023]
Abstract
Aberrant protein phosphorylation is one of the hallmarks of cancer cells, and in many cases a prerequisite to sustain tumor development and progression. Like protein kinases, protein phosphatases are key regulators of cell signaling. However, their contribution to aberrant signaling in cancer cells is overall less well appreciated, and therefore, their clinical potential remains largely unexploited. In this review, we provide an overview of tumor suppressive protein phosphatases in human cancer. Along their mechanisms of inactivation in defined cancer contexts, we give an overview of their functional roles in diverse signaling pathways that contribute to their tumor suppressive abilities. Finally, we discuss their emerging roles as predictive or prognostic markers, their potential as synthetic lethality targets, and the current feasibility of their reactivation with pharmacologic compounds as promising new cancer therapies. We conclude that their inclusion in clinical practice has obvious potential to significantly improve therapeutic outcome in various ways, and should now definitely be pushed forward.
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Affiliation(s)
- Bob Meeusen
- Laboratory of Protein Phosphorylation & Proteomics, Dept. of Cellular & Molecular Medicine, Faculty of Medicine, KU Leuven & Leuven Cancer Institute (LKI), KU Leuven, Belgium
| | - Veerle Janssens
- Laboratory of Protein Phosphorylation & Proteomics, Dept. of Cellular & Molecular Medicine, Faculty of Medicine, KU Leuven & Leuven Cancer Institute (LKI), KU Leuven, Belgium.
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16
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Bujko M, Kober P, Statkiewicz M, Mikula M, Grecka E, Rusetska N, Ligaj M, Ostrowski J, Siedlecki JA. Downregulation of PTPRH (Sap-1) in colorectal tumors. Int J Oncol 2017; 51:841-850. [PMID: 28713969 DOI: 10.3892/ijo.2017.4068] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 06/13/2017] [Indexed: 11/05/2022] Open
Abstract
Tyrosine phosphorylation is one of the basic mechanisms for signal transduction in the cell. Receptors exhibiting tyrosine kinase activity are widely involved in carcinogenesis and are negatively regulated by receptor protein tyrosine phosphatases (RPTP). Genes encoding different RPTPs are affected by aberrant epigenetic regulation in cancer. PTPRH (SAP-1) has been previously described to be overexpressed in colorectal cancer (CRC) and classified as an oncogenic factor. Previous microarray-based mRNA expression comparison of colorectal adenomas (AD), CRC and normal mucosa samples (NM) demonstrated that PTPRH tumor expression is the most reduced of all RPTP genes. qRT-PCR validation revealed gene downregulation for CRC (7.6-fold-change; P<0.0001) and AD (3.4-fold-change; P<0.0001) compared to NM. This was confirmed by immunohistochemical staining of tumor and NM sections as pronounced decrease of protein expression was observed in CRCs compared to the corresponding normal tissue. DNA methylation of two PTPRH promoter fragments was analyzed by pyrosequencing in a group of CRC, and AD patients as well as NM samples and CRC cell lines. The mean DNA methylation levels of these two regions were significantly higher in CRC than in NM. Both regions were highly methylated in SW480 and HCT116 cell lines contrary to unmethylated HT29 and COLO205. Cell lines with highly methylated promoters notably showed lower PTPRH expression levels, lower RNA II polymerase concentrations and higher levels of H3K27 trimethylation in the promoter and gene body, measured by chromatin immunoprecipitation. Cells were cultured with 5-aza-deoxycitidine and an increase in PTPRH expression was observed in SW480 and HCT116, whereas this was unchanged in the unmethylated cell lines. The results indicate that PTPRH is downregulated in colorectal tumors and its expression is epigenetically regulated via DNA methylation and chromatin modifications.
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Affiliation(s)
- Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Małgorzata Statkiewicz
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Emilia Grecka
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Nataliia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Marcin Ligaj
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
| | - Janusz Aleksander Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of Oncology, Warsaw, Poland
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17
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Nikitina AS, Sharova EI, Danilenko SA, Butusova TB, Vasiliev AO, Govorov AV, Prilepskaya EA, Pushkar DY, Kostryukova ES. Novel RNA biomarkers of prostate cancer revealed by RNA-seq analysis of formalin-fixed samples obtained from Russian patients. Oncotarget 2017; 8:32990-33001. [PMID: 28380430 PMCID: PMC5464844 DOI: 10.18632/oncotarget.16518] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 03/15/2017] [Indexed: 01/23/2023] Open
Abstract
Due to heterogeneous multifocal nature of prostate cancer (PCa), there is currently a lack of biomarkers that stably distinguish it from benign prostatic hyperplasia (BPH), predict clinical outcome and guide the choice of optimal treatment. In this study RNA-seq analysis was applied to formalin-fixed paraffin-embedded (FFPE) tumor and matched normal tissue samples collected from Russian patients with PCa and BPH. We identified 3384 genes differentially expressed (DE) (FDR < 0.05) between tumor tissue of PCa patients and adjacent normal tissue as well as both tissue types from BPH patients. Overexpression of four of the discovered genes (ANKRD34B, NEK5, KCNG3, and PTPRT) was validated by RT-qPCR. Furthermore, the enrichment analysis of overrepresented microRNA and transcription factor (TF) recognition sites within DE genes revealed common regulatory elements of which 13 microRNAs and 53 TFs were thus linked to PCa for the first time. Moreover, 8 of these TFs (FOXJ2, GATA6, NFE2L1, NFIL3, PRRX2, TEF, EBF2 and ZBTB18) were found to be differentially expressed in this study making them not only candidate biomarkers of prostate cancer but also potential therapeutic targets.
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Affiliation(s)
- Anastasia S. Nikitina
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
| | - Elena I. Sharova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | | | - Tatiana B. Butusova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - Alexandr O. Vasiliev
- Department of Urology, Moscow State Medical Stomatological University, Moscow, Russia
| | - Alexandr V. Govorov
- Department of Urology, Moscow State Medical Stomatological University, Moscow, Russia
| | - Elena A. Prilepskaya
- Department of Urology, Moscow State Medical Stomatological University, Moscow, Russia
| | - Dmitry Y. Pushkar
- Department of Urology, Moscow State Medical Stomatological University, Moscow, Russia
| | - Elena S. Kostryukova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
- Moscow Institute of Physics and Technology, Dolgoprudnyi, Russia
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18
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Laczmanska I, Skiba P, Karpinski P, Bebenek M, Sasiadek MM. Customized Array Comparative Genomic Hybridization Analysis of 25 Phosphatase-encoding Genes in Colorectal Cancer Tissues. Cancer Genomics Proteomics 2017; 14:69-74. [PMID: 28031238 DOI: 10.21873/cgp.20019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/05/2016] [Accepted: 12/06/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND/AIM Molecular mechanisms of alterations in protein tyrosine phosphatases (PTPs) genes in cancer have been previously described and include chromosomal aberrations, gene mutations, and epigenetic silencing. However, little is known about small intragenic gains and losses that may lead to either changes in expression or enzyme activity and even loss of protein function. MATERIALS AND METHODS The aim of this study was to investigate 25 phosphatase genes using customized array comparative genomic hybridization in 16 sporadic colorectal cancer tissues. RESULTS The analysis revealed two unique small alterations: of 2 kb in PTPN14 intron 1 and of 1 kb in PTPRJ intron 1. We also found gains and losses of whole PTPs gene sequences covered by large chromosome aberrations. CONCLUSION In our preliminary studies using high-resolution custom microarray we confirmed that PTPs are frequently subjected to whole-gene rearrangements in colorectal cancer, and we revealed that non-polymorphic intragenic changes are rare.
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Affiliation(s)
| | - Pawel Skiba
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - Pawel Karpinski
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - Marek Bebenek
- 1st Department of Surgical Oncology, Lower Silesian Oncology Center, Wroclaw, Poland
| | - Maria M Sasiadek
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
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19
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Zhou R, Zhou X, Yin Z, Guo J, Hu T, Jiang S, Liu L, Dong X, Zhang S, Wu G. MicroRNA-574-5p promotes metastasis of non-small cell lung cancer by targeting PTPRU. Sci Rep 2016; 6:35714. [PMID: 27761023 PMCID: PMC5071770 DOI: 10.1038/srep35714] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/04/2016] [Indexed: 02/06/2023] Open
Abstract
Dysregulation of microRNAs (miRNAs) has been associated with malignant behavior in a variety of cancers. Our previous study demonstrated that miRNA expression profiles are predictors for patients with advanced non-small cell lung cancer (NSCLC). We also showed that miRNAs are involved in small-cell lung cancer metastasis. Here, we used qRT-PCR to re-analyze our previous microarray results using serum samples from 75 patients with NSCLC. Surprisingly, we found that miR-574-5p and miR-874 were overexpressed in patients with metastatic advanced NSCLC but not in patients with non-metastatic advanced NSCLC. Additionally, miR-574-5p expression was correlated between matched serum and tissue samples from 68 patients. However, these 2 miRNAs are not prognostic factors for NSCLC. Transwell and wound-healing assays showed that miR-574-5p promotes the migration and invasion of NSCLC cells. Furthermore, miR-574-5p enhanced the tyrosine phosphorylation of β-catenin by repressing PTPRU expression in vitro. In conclusion, this study explored the expression of miR-574-5p in clinical samples and its molecular mechanisms in the metastasis of advanced NSCLC.
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Affiliation(s)
- Rui Zhou
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Xiaoshu Zhou
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Zhongyuan Yin
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Jing Guo
- Department of Oncology of the Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ting Hu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Shun Jiang
- Department of Oncology, Second Xiangya Hospital of Central South University, Changsha, China
| | - Li Liu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Xiaorong Dong
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Sheng Zhang
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
| | - Gang Wu
- Cancer Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, China
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20
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Sokolova V, Crippa E, Gariboldi M. Integration of genome scale data for identifying new players in colorectal cancer. World J Gastroenterol 2016; 22:534-45. [PMID: 26811605 PMCID: PMC4716057 DOI: 10.3748/wjg.v22.i2.534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 10/13/2015] [Accepted: 11/09/2015] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancers (CRCs) display a wide variety of genomic aberrations that may be either causally linked to their development and progression, or might serve as biomarkers for their presence. Recent advances in rapid high-throughput genetic and genomic analysis have helped to identify a plethora of alterations that can potentially serve as new cancer biomarkers, and thus help to improve CRC diagnosis, prognosis, and treatment. Each distinct data type (copy number variations, gene and microRNAs expression, CpG island methylation) provides an investigator with a different, partially independent, and complementary view of the entire genome. However, elucidation of gene function will require more information than can be provided by analyzing a single type of data. The integration of knowledge obtained from different sources is becoming increasingly essential for obtaining an interdisciplinary view of large amounts of information, and also for cross-validating experimental results. The integration of numerous types of genetic and genomic data derived from public sources, and via the use of ad-hoc bioinformatics tools and statistical methods facilitates the discovery and validation of novel, informative biomarkers. This combinatory approach will also enable researchers to more accurately and comprehensively understand the associations between different biologic pathways, mechanisms, and phenomena, and gain new insights into the etiology of CRC.
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21
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Peyser ND, Freilino M, Wang L, Zeng Y, Li H, Johnson DE, Grandis JR. Frequent promoter hypermethylation of PTPRT increases STAT3 activation and sensitivity to STAT3 inhibition in head and neck cancer. Oncogene 2015; 35:1163-9. [PMID: 25982282 PMCID: PMC4651851 DOI: 10.1038/onc.2015.171] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/02/2015] [Accepted: 03/06/2015] [Indexed: 11/29/2022]
Abstract
STAT3 overactivation is a common event in many cancers, including head and neck squamous cell carcinoma (HNSCC), where STAT3 represents a promising therapeutic target. HNSCC is not characterized by frequent kinase mutations, in contrast to some malignancies where mutational activation of kinases upstream of STAT3 is common. Instead, STAT3 may be activated by loss-of-function (LOF) of negative regulators of STAT3, including by promoter hypermethylation of PTPRT. Here we first analyzed The Cancer Genome Atlas (TCGA) data and determined that the PTPRT promoter is frequently hypermethylated in several cancers, including HNSCC (60.1% of tumors analyzed) in association with downregulation of PTPRT mRNA expression and upregulation of pSTAT3 expression. These findings were confirmed in an independent cohort of HNSCC tumors by methylation-specific PCR (MSP) and immunohistochemistry. We demonstrate that PTPRT promoter methylation and gene silencing is reversible in HNSCC cells, leading to PTPRT-specific downregulation of pSTAT3 expression. We further show that PTPRT promoter methylation is significantly associated with sensitivity to STAT3 inhibition in HNSCC cells, suggesting that PTPRT promoter methylation may serve as a predictive biomarker for responsiveness to STAT3 inhibitors in clinical development.
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Affiliation(s)
- N D Peyser
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - M Freilino
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - L Wang
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Y Zeng
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - H Li
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - D E Johnson
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.,Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - J R Grandis
- Department of Otolaryngology, University of California, San Francisco, CA, USA
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22
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Duś-Szachniewicz K, Woźniak M, Nelke K, Gamian E, Gerber H, Ziółkowski P. Protein tyrosine phosphatase receptor R and Z1 expression as independent prognostic indicators in oral squamous cell carcinoma. Head Neck 2015; 37:1816-22. [DOI: 10.1002/hed.23835] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2014] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Marta Woźniak
- Department of Pathology; Wrocław Medical University; Wrocław Poland
| | - Kamil Nelke
- Department of Maxillo-Facial Surgery; Wrocław Medical University; Wrocław Poland
| | - Elżbieta Gamian
- Department of Pathology; Wrocław Medical University; Wrocław Poland
| | - Hanna Gerber
- Department of Maxillo-Facial Surgery; Wrocław Medical University; Wrocław Poland
| | - Piotr Ziółkowski
- Department of Pathology; Wrocław Medical University; Wrocław Poland
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23
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Aberrant methylation of ERBB pathway genes in sporadic colorectal cancer. J Appl Genet 2014; 56:185-92. [PMID: 25366420 PMCID: PMC4412553 DOI: 10.1007/s13353-014-0253-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 10/09/2014] [Accepted: 10/14/2014] [Indexed: 12/22/2022]
Abstract
The ErbB signalling network plays a crucial role in the growth and progression of several cancers, including colorectal cancer (CRC), and includes potentially drug-targetable genes. Oncogenic activation of the ErbB pathway by mutations and focal amplifications have emerged recently as an important predictive marker of the prognosis of CRC patients. However, in contrast to genetic events, little is known about epigenetic alternations of ErbB-associated genes and their impact on gene expression. Genome-wide methylation in sporadic CRCs (n = 12) paired with adjacent normal tissues have been previously analysed by Illumina Infinium HumanMethylation27 (HM27) at 27,578 CpG sites. For confirmation of our initial genome-wide analysis, we used a published HM27 dataset (GSE25062). Subsequently, CpG island methylation of selected ErbB pathway-associated genes was assessed on 233 CRC samples using methylation-sensitive polymerase chain reaction (MS-PCR) and analysed along with various genetic factors associated with CRC [epigenotype, BRAF and KRAS mutations, microsatellite instability (MSI)]. Methylation and expression integration was performed using published datasets including 25 pairs of CRC and normal colon tissues (GSE25062 and GSE25070), and confirmed with real-time PCR. Our previous microarray-based genome-wide DNA methylation analysis of 12 CRCs revealed that four ErbB-associated genes (PIK3CD, PKCΒ, ERBB4, ) were differentially methylated in CRCs. This was further confirmed by statistical re-analysis of an HM27 dataset (GSE25062). Frequent methylation at these loci in tumours was subsequently confirmed by MS-PCR (63 %, 43 %, 43 % and 92 %, respectively). Hypermethylation of PKCΒ associated with KRAS mutation (p = 0.04), whereas hypermethylation of ERBB4 associated with high-methylation epigenotypes (HME), BRAF mutation and MSI (p = 0.001, 0.002 and 0.0002, respectively). One of the four analysed genes (PKCΒ) was significantly downregulated in CRC tissue, as revealed by real-time PCR and re-analysis of the GSE25062 and GSE25070 datasets. After careful re-analysis of published methylation and expression data, we conclude that methylation of ERBB4, PAK7 and PIK3CD has no functional role in CRC carcinogenesis. In contrast, methylation seems to have a potential impact on the biology of colorectal tumours by negatively modulating the expression of PKCΒ. Importantly, the relationship between DNA methylation of PKCΒ and gene expression may warrant further attention in the context of colon cancer chemoprevention and anti-cancer therapy.
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24
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Du Y, Grandis JR. Receptor-type protein tyrosine phosphatases in cancer. CHINESE JOURNAL OF CANCER 2014; 34:61-9. [PMID: 25322863 PMCID: PMC4360074 DOI: 10.5732/cjc.014.10146] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play an important role in regulating cell signaling events in coordination with tyrosine kinases to control cell proliferation, apoptosis, survival, migration, and invasion. Receptor-type protein tyrosine phosphatases (PTPRs) are a subgroup of PTPs that share a transmembrane domain with resulting similarities in function and target specificity. In this review, we summarize genetic and epigenetic alterations including mutation, deletion, amplification, and promoter methylation of PTPRs in cancer and consider the consequences of PTPR alterations in different types of cancers. We also summarize recent developments using PTPRs as prognostic or predictive biomarkers and/or direct targets. Increased understanding of the role of PTPRs in cancer may provide opportunities to improve therapeutic approaches.
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Affiliation(s)
- Yu Du
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA.
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25
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Zhao S, Sedwick D, Wang Z. Genetic alterations of protein tyrosine phosphatases in human cancers. Oncogene 2014; 34:3885-94. [PMID: 25263441 PMCID: PMC4377308 DOI: 10.1038/onc.2014.326] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Revised: 08/20/2014] [Accepted: 08/21/2014] [Indexed: 12/12/2022]
Abstract
Protein tyrosine phosphatases (PTPs) are enzymes that remove phosphate from tyrosine residues in proteins. Recent whole-exome sequencing of human cancer genomes reveals that many PTPs are frequently mutated in a variety of cancers. Among these mutated PTPs, protein tyrosine phosphatase T (PTPRT) appears to be the most frequently mutated PTP in human cancers. Beside PTPN11 which functions as an oncogene in leukemia, genetic and functional studies indicate that most of mutant PTPs are tumor suppressor genes. Identification of the substrates and corresponding kinases of the mutant PTPs may provide novel therapeutic targets for cancers harboring these mutant PTPs.
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Affiliation(s)
- S Zhao
- 1] Division of Gastroenterology and Hepatology and Shanghai Institution of Digestive Disease, Shanghai Jiao-Tong University School of Medicine Renji Hospital, Shanghai, China [2] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [3] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - D Sedwick
- 1] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA [2] Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Z Wang
- 1] Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, USA [2] Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
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26
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Craig SEL, Brady-Kalnay SM. Regulation of development and cancer by the R2B subfamily of RPTPs and the implications of proteolysis. Semin Cell Dev Biol 2014; 37:108-18. [PMID: 25223585 DOI: 10.1016/j.semcdb.2014.09.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Revised: 09/04/2014] [Accepted: 09/05/2014] [Indexed: 01/04/2023]
Abstract
The initial cloning of receptor protein tyrosine phosphatases (RPTPs) was met with excitement because of their hypothesized function in counterbalancing receptor tyrosine kinase signaling. In recent years, members of a subfamily of RPTPs with homophilic cell-cell adhesion capabilities, known as the R2B subfamily, have been shown to have functions beyond that of counteracting tyrosine kinase activity, by independently influencing cell signaling in their own right and by regulating cell adhesion. The R2B subfamily is composed of four members: PTPmu (PTPRM), PTPrho (PTPRT), PTPkappa (PTPRK), and PCP-2 (PTPRU). The effects of this small subfamily of RPTPs is far reaching, influencing several developmental processes and cancer. In fact, R2B RPTPs are predicted to be tumor suppressors and are among the most frequently mutated protein tyrosine phosphatases (PTPs) in cancer. Confounding these conclusions are more recent studies suggesting that proteolysis of the full-length R2B RPTPs result in oncogenic extracellular and intracellular protein fragments. This review discusses the current knowledge of the role of R2B RPTPs in development and cancer, with special detail given to the mechanisms and implications that proteolysis has on R2B RPTP function. We also touch upon the concept of exploiting R2B proteolysis to develop cancer imaging tools, and consider the effects of R2B proteolysis on axon guidance, perineural invasion and collective cell migration.
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Affiliation(s)
- Sonya E L Craig
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4960, USA
| | - Susann M Brady-Kalnay
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4960, USA; Department of Neurosciences, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
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27
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Laczmanska I, Karpinski P, Kozlowska J, Bebenek M, Ramsey D, Sedziak T, Ziolkowski P, Sasiadek MM. Copy number alterations of chromosomal regions enclosing protein tyrosine phosphatase receptor-like genes in colorectal cancer. Pathol Res Pract 2014; 210:893-6. [PMID: 25169130 DOI: 10.1016/j.prp.2014.07.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 06/13/2014] [Accepted: 07/25/2014] [Indexed: 10/24/2022]
Abstract
Protein tyrosine phosphatases that act in different cellular pathways are described most commonly as tumor suppressors, but also as oncogenes. Their role has previously been described in colorectal cancer, as well as in gastric, breast, thyroid, prostate, ovarian, pancreatic, glioma, liver, leukemia and many other cancers. In a previous study, we have described protein tyrosine phosphatase receptor type T, M, Z1 and Q genes (PTPRT, PTPRM, PTPRZ1 and PTPRQ) hypermethylated in sporadic colorectal cancer. Thus, in this study, we examined the relation of unbalanced chromosomal alterations within regions covering these four protein tyrosine phosphatase genes with this cancer. One hundred and two cancer tissues were molecularly characterized, including analysis of the BRAF and K-ras mutations and methylator phenotype. The analysis of chromosomal aberrations was performed using Comparative Genomic Hybridization. We observed amplification of three regions containing genes coding for PTPs, such as PTPRZ1 (7q31.3, amplified in 23.5% of cases), PTPRQ (12q21.2, amplified in 5.9% of cases), PTPRT (20q12, amplified in 29.4% of cases), along with deletions in the region of PTPRM (18p11.2, deleted in 21.6% of cases). These data may suggest that in sporadic colorectal cancer PTPRZ1, PTPRT, PTPRQ probably act as oncogenes, while PTPRM acts as a tumor suppressor gene. Our study also revealed that gains on chromosome 20q12 and losses on chromosome 18p11.2 are connected with the absence of the BRAF mutation and the conventional adenocarcinoma pathway.
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Affiliation(s)
| | - Pawel Karpinski
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - Joanna Kozlowska
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
| | - Marek Bebenek
- 1st Department of Surgical Oncology, Lower Silesian Oncology Center, Poland
| | - David Ramsey
- Department of Computer Science and Management, Wroclaw University of Technology, Poland
| | - Tomasz Sedziak
- 1st Department of Surgical Oncology, Lower Silesian Oncology Center, Poland
| | | | - Maria M Sasiadek
- Genetics Department, Wroclaw Medical University, Wroclaw, Poland
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Xu E, Gu J, Hawk ET, Wang KK, Lai M, Huang M, Ajani J, Wu X. Genome-wide methylation analysis shows similar patterns in Barrett's esophagus and esophageal adenocarcinoma. Carcinogenesis 2013; 34:2750-6. [PMID: 23996928 DOI: 10.1093/carcin/bgt286] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Barrett's esophagus (BE) is a precursor of esophageal adenocarcinoma (EAC). To identify novel tumor suppressors involved in esophageal carcinogenesis and potential biomarkers for the malignant progression of BE, we performed a genome-wide methylation profiling of BE and EAC tissues. Using Illumina's Infinium HumanMethylation27 BeadChip microarray, we examined the methylation status of 27 578 CpG sites in 94 normal esophageal (NE), 77 BE and 117 EAC tissue samples. The overall methylation of CpG sites within the CpG islands was higher, but outside of the CpG islands was lower in BE and EAC tissues than in NE tissues. Hierarchical clustering analysis showed an excellent separation of NE tissues from BE and EAC tissues; however, the clustering of BE and EAC tissues was less clear, suggesting that methylation occurs early during the progression of EAC. We confirmed many previously reported hypermethylated genes and identified a large number of novel hypermethylated genes in BE and EAC tissues, particularly genes encoding ADAM (A Disintegrin And Metalloproteinase) peptidase proteins, cadherins and protocadherins, and potassium voltage-gated channels. Pathway analysis showed that a number of channel and transporter activities were enriched for hypermethylated genes. We used pyrosequencing to validate selected candidate genes and found high correlations between the array and pyrosequencing data (rho > 0.8 for each validated gene). The differentially methylated genes and pathways may provide biological insights into the development and progression of BE and become potential biomarkers for the prediction and early detection of EAC.
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Affiliation(s)
- Enping Xu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Peyser ND, Grandis JR. Critical analysis of the potential for targeting STAT3 in human malignancy. Onco Targets Ther 2013; 6:999-1010. [PMID: 23935373 PMCID: PMC3735336 DOI: 10.2147/ott.s47903] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The signal transducer and activator of transcription (STAT) family of proteins was originally discovered in the context of normal cell biology where they function to transduce intracellular and extracellular signals to the nucleus, ultimately leading to transcription of specific target genes and downstream phenotypic effects. It was quickly appreciated that the STATs, especially STAT3, play a fundamental role in human malignancy. In contrast to normal biology in which transient STAT3 signaling is strictly regulated by a tightly coordinated network of activators and deactivators, STAT3 is constitutively activated in human malignancies. Constitutive STAT3 signaling has been associated with many cancerous phenotypes across nearly all human cancers, including the upregulation of cell growth, proliferation, survival, and motility, among others. Studies involving candidate preclinical STAT3 inhibitors have further demonstrated that the reversal of these phenotypes results from pharmacologic or genetic inhibition of STAT3, suggesting that STAT3 may be a promising target for clinical interventions. Indeed, a Phase 0 clinical trial involving a STAT3 decoy oligonucleotide demonstrated that STAT3 is a drug-gable target in human tumors. Because of the ubiquity of overactive STAT3 in cancer, its role in promoting a wide variety of cancerous phenotypes, and the strong clinical and preclinical studies performed to date, STAT3 represents a promising target for the development of inhibitors for the treatment of human cancers.
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Affiliation(s)
- Noah D Peyser
- Departments of Otolaryngology and Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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30
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PTPN12 inhibits oral squamous epithelial carcinoma cell proliferation and invasion and can be used as a prognostic marker. Med Oncol 2013; 30:618. [DOI: 10.1007/s12032-013-0618-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2013] [Accepted: 05/23/2013] [Indexed: 01/24/2023]
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