Methyl‐CpG binding column‐based identification of nine genes hypermethylated in colorectal cancer

Kober, Paulina; Bujko, Mateusz; Olędzki, Janusz; Tysarowski, Andrzej; Siedlecki, Janusz A.

doi:10.1002/mc.20763

Cited by 40 publications

(22 citation statements)

References 42 publications

(45 reference statements)

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“…The rationale was based on evidence that overexpression of different KLF transcription factors promote or inhibit neurite outgrowth of RGCs and other neurons (7), the role of EPHA5 in patterning RGC axon connectivity during early visual system development (33), and our previous identification of putativeKLF-bindingsitesassociatedwithdifferentialCpGmethylation within the EphA5 promoter in the nasal versus temporal retina (25). DNA hypermethylation is a well known epigenetic mechanism for gene silencing, and hypermethylation of the EPHA5 promoter (Ͼ70%) has been detected in prostate (24), colorectal (23), and breast cancers (22) and is highly correlated with transcriptional silencing of EPHA5. We previously showed that EphA5 promoter transactivation in luciferase assays is blocked by SssI methylation of all CpG dinucleotides and that transcription of the endogenous EphA5 gene in a mouse Müller glial cell line is silenced by hypermethylation (25).…”

Section: Regulation Of Epha5 Expression By Klfs and Dna Methylation-tmentioning

confidence: 99%

“…There is evidence for silencing of EphA5 expression by hypermethylation in cancer (22)(23)(24). We previously showed that total CpG methylation abolishes activity of mEphA5 promoter-reporter constructs in R28 retinal progenitor cells and that transcriptional silencing of the endogenous EphA5 gene in a mouse retinal cell line (ImM10) is reversed by genome-wide demethylation (25).…”

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confidence: 99%

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Novel Roles and Mechanism for Krüppel-like Factor 16 (KLF16) Regulation of Neurite Outgrowth and Ephrin Receptor A5 (EphA5) Expression in Retinal Ganglion Cells

Wang¹,

Galvão

Beach³

et al. 2016

Journal of Biological Chemistry

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Regenerative medicine holds great promise for the treatment of degenerative retinal disorders. Krüppel-like factors (KLFs) are transcription factors that have recently emerged as key tools in regenerative medicine because some of them can function as epigenetic reprogrammers in stem cell biology. Here, we show that KLF16, one of the least understood members of this family, is a POU4F2 independent transcription factor in retinal ganglion cells (RGCs) as early as embryonic day 15. When overexpressed, KLF16 inhibits RGC neurite outgrowth and enhances RGC growth cone collapse in response to exogenous ephrinA5 ligands. Ephrin/EPH signaling regulates RGC connectivity. The EphA5 promoter contains multiple GC-and GT-rich KLF-binding sites, which, as shown by ChIP-assays, bind KLF16 in vivo. In electrophoretic mobility shift assays, KLF16 binds specifically to a single KLF site near the EphA5 transcription start site that is required for KLF16 transactivation. Interestingly, methylation of only six of 98 CpG dinucleotides within the EphA5 promoter blocks its transactivation by KLF16 but enables transactivation by KLF2 and KLF15. These data demonstrate a role for KLF16 in regulation of RGC neurite outgrowth and as a methylation-sensitive transcriptional regulator of EphA5 expression. Together, these data identify differential low level methylation as a novel mechanism for regulating KLF16-mediated EphA5 expression across the retina. Because of the critical role of ephrin/EPH signaling in patterning RGC connectivity, understanding the role of KLFs in regulating neurite outgrowth and Eph receptor expression will be vital for successful restoration of functional vision through optic nerve regenerative therapies. Progressive loss of retinal ganglion cells (RGCs)2 leads to blindness in diseases such as glaucoma, the leading cause of irreversible bilateral blindness worldwide (1). Current treatments can slow progression but cannot restore lost vision. Recent advances in generating retinal cells from embryonic and induced pluripotent stem cells have stimulated interest in the potential for neuronal regeneration to treat blindness (2-4). For successful optic nerve regeneration, newly regenerated RGCs will need to extend axons considerable distances to reach the visual centers of the brain, where they must make the correct patterns of termination on post-synaptic neurons to reestablish retinotopic maps. Thus, it is critical to understand the mechanisms that regulate expression of molecules involved in axonal growth and connectivity.Krüppel-like factors (KLFs) are members of the SP/KLF family of transcription factors that are characterized by three zinc finger DNA binding domains near their C terminus (5). KLFs bind to GT-or GC-rich sequences and can function as either transcriptional activators or repressors, depending on the promoter context (6). At least 15 of the 17 members of the KLF transcription factor family are expressed in RGCs, and overexpression of different KLF transcription factors in RGCs, hippocampal neurons, or cor...

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Section: Regulation Of Epha5 Expression By Klfs and Dna Methylation-tmentioning

confidence: 99%

mentioning

confidence: 99%

Novel Roles and Mechanism for Krüppel-like Factor 16 (KLF16) Regulation of Neurite Outgrowth and Ephrin Receptor A5 (EphA5) Expression in Retinal Ganglion Cells

Wang¹,

Galvão

Beach³

et al. 2016

Journal of Biological Chemistry

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“…Here, EPHB1, EPHA5, and EPHA6 were the most frequently mutated Eph receptors, accounting for 63% of Eph mutations. EPHA5 has been associated with metastases in breast cancer, where promoter hypermethylation results in downregulation of expression (39,40). Although EphA6 expression was found strongly downregulated in colorectal cancer compared with normal colon, mutations have not previously been reported in CIN tumors (41).…”

Section: Discussionmentioning

confidence: 97%

Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer

et al. 2017

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The contribution of somatic mutations to metastasis of colorectal cancers is currently unknown. To find mutations involved in the colorectal cancer metastatic process, we performed deep mutational analysis of 676 genes in 107 stages II to IV primary colorectal cancer, of which half had metastasized. The mutation prevalence in the ephrin (EPH) family of tyrosine kinase receptors was 10-fold higher in primary tumors of metastatic colorectal than in nonmetastatic cases and preferentially occurred in stage III and IV tumors. Mutational analyses in situ confirmed expression of mutant EPH receptors. To enable functional studies of EPHB1 mutations, we demonstrated that DLD-1 colorectal cancer cells expressing EPHB1 form aggregates upon coculture with ephrin B1 expressing cells. When mutations in the fibronectin type III and kinase domains of EPHB1 were compared with wild-type EPHB1 in DLD-1 colorectal cancer cells, they decreased ephrin B1-induced compartmentalization. These observations provide a mechanistic link between EPHB receptor mutations and metastasis in colorectal cancer.

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“…EphA5 gene silenced by methylation has been demonstrated in breast cancer [14], prostate cancer [20], and colorectal cancer [21], implying that the hypermethylation of EphA5 might be of great importance during tumorigenesis and progression in cancer. Identification of hypermethylated EphA5 DNA in ovarian serous carcinoma will improve our understanding of the mechanisms leading to the downregulation of EphA5 expression in ovarian tumorigenesis and can serve as valuable diagnostic marker.…”

Section: Discussionmentioning

confidence: 99%

EphA5 protein, a potential marker for distinguishing histological grade and prognosis in ovarian serous carcinoma

et al. 2016

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BackgroundOvarian serous carcinoma (OSC) is the most common ovarian epithelial malignancy. Disregulation of Eph/ephrin signaling has been implicated in oncogenesis and tumor progression. EphA5 receptor is one of large families of Eph tyrosine kinase receptor and is documented in the development of nervous system. Till now, there is no published data about the role of EphA5 in ovarian epithelial neoplasmas.MethodsThis study aims to investigate the expression of EphA5 protein in ovarian serous carcinoma, and its relationship to clinical pathological characteristics. Sixty-one cases of ovarian serous carcinoma, 24 cases of benign ovarian serous tumors, 42 cases of serous borderline tumors and 20 cases of normal fallopian tubes were examined using immunohistochemical staining. The relationship between EphA5 expression and pathological parameters was analyzed. Kaplan-Meier survival function was used to analyze prognosis of patients.ResultsImmunostaining analysis demonstrated that the EphA5 protein was highly expressed in 100% (20/20) of normal fallopian tube samples, 100% (24/24) of benign epithelial ovarian tumors, 76% (32/42) of ovarian serous borderline tumors, and 31% (19/61) of ovarian serous carcinomas. Loss of EphA5expression was associated with tumor grade (P < 0.001) and FIGO stage (P = 0.005). The survival analysis showed that patients with negative or weak expression of EphA5 protein had a poor outcome than those with positive expression (P = 0.004).ConclusionsOur results show that EphA5 may be a potential biomarker for distinguishing high-and low-grade ovarian serous carcinoma and a potential prognostic marker.

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Methyl‐CpG binding column‐based identification of nine genes hypermethylated in colorectal cancer

Cited by 40 publications

References 42 publications

Novel Roles and Mechanism for Krüppel-like Factor 16 (KLF16) Regulation of Neurite Outgrowth and Ephrin Receptor A5 (EphA5) Expression in Retinal Ganglion Cells

Novel Roles and Mechanism for Krüppel-like Factor 16 (KLF16) Regulation of Neurite Outgrowth and Ephrin Receptor A5 (EphA5) Expression in Retinal Ganglion Cells

Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer

EphA5 protein, a potential marker for distinguishing histological grade and prognosis in ovarian serous carcinoma

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