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Lippai Z, Péterfia B, Papp G, Dezső K, Bedics G, Pápai Z, Lamers MH, Kuin RC, Szuhai K, Sápi Z. A recurrent NTRK1 tyrosine kinase domain mutation pair is characteristic in a subset of dedifferentiated liposarcomas. Eur J Cancer 2024; 202:114005. [PMID: 38531265 DOI: 10.1016/j.ejca.2024.114005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/01/2024] [Accepted: 03/03/2024] [Indexed: 03/28/2024]
Abstract
INTRODUCTION Dedifferentiated liposarcoma (DDLPS) is a common form of liposarcoma with challenging treatment modalities. Pan-TRK immunopositivity can be often observed without NTRK gene fusion in soft tissue sarcomas with myogenic differentiation. Expression and the role of NTRK in DDLPS are under-studied. We sought to identify activating mutations of the NTRK genes. MATERIALS AND METHODS 131 DDLPS patients were selected for pan-TRK immunohistochemistry and positive cases were analyzed by Sanger sequencing for NTRK1, NTRK2 and NTRK3 genes. Functional assays were performed using a lentiviral transduction system to study the effect of NTRK variants in fibroblast, immortalized fibroblast, and dedifferentiated liposarcoma cell lines. RESULTS Out of the 131 DDLPS cases, 75 immunohistochemical staining positive cases, 46 were successfully Sanger sequenced. A recurrent somatic mutation pair in cis position (NGS) of the NTRK1 c.1810C>T (p.H604Y) and c.1838G>T (p.G613V) was identified in six cases (13%) that have never been reported in DDLPS. NTRK fusions were excluded in all six cases by FISH and NGS. The phospho-AKT immunopositivity among the six mutated cases suggested downstream activation of the NTRK signaling pathway. Functional assays showed no transforming effects, but resistance to first- and second-line TRK inhibitors of the p.G613V and p.H604Y variant. CONCLUSIONS We detected (de novo/somatic) missense mutation variants in cis position of the NTRK1 gene in a subset of DDLPS indicating modifying mutations that may contribute to tumorigenesis in a subset of DDLPS. These variants beget resistance to TRK inhibitors indicating an interesting biomarker for other studies with TRK inhibitors.
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Affiliation(s)
- Zoltán Lippai
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Hungary
| | - Gergő Papp
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Hungary
| | - Katalin Dezső
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Hungary
| | - Gábor Bedics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Hungary
| | - Zsuzsanna Pápai
- Department of Oncology, Medical Centre, Hungarian Defense Forces, Hungary
| | - Meindert H Lamers
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Rosan Cm Kuin
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands
| | - Károly Szuhai
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, the Netherlands.
| | - Zoltán Sápi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Hungary.
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Váncza L, Karászi K, Péterfia B, Turiák L, Dezső K, Sebestyén A, Reszegi A, Petővári G, Kiss A, Schaff Z, Baghy K, Kovalszky I. Corrigendum: SPOCK1 promotes the development of hepatocellular carcinoma. Front Oncol 2023; 13:1203745. [PMID: 37152016 PMCID: PMC10154680 DOI: 10.3389/fonc.2023.1203745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 04/12/2023] [Indexed: 05/09/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fonc.2022.819883.].
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Affiliation(s)
- Lóránd Váncza
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Katalin Karászi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, EötvösLoránd Research Network, Budapest, Hungary
| | - Katalin Dezső
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Anna Sebestyén
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Andrea Reszegi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Petővári
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Kiss
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Schaff
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Kornélia Baghy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- *Correspondence: Ilona Kovalszky, ;
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Sánta A, Czajlik A, Batta G, Péterfia B, Gáspári Z. Resonance assignment of the Shank1 PDZ domain. Biomol NMR Assign 2022; 16:121-127. [PMID: 35083656 PMCID: PMC9068651 DOI: 10.1007/s12104-022-10069-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Shank proteins are among the most abundant and well-studied postsynaptic scaffold proteins. Their PDZ domain has unique characteristics as one of its loop regions flanking the ligand-binding site is uniquely long and has also been implicated in the formation of PDZ dimers. Here we report the initial characterization of the Shank1 PDZ domain by solution NMR spectroscopy. The assigned chemical shifts are largely consistent with the common features of PDZ domains in general and the available Shank PDZ crystal structures in particular. Our analysis suggests that under the conditions investigated, the domain is monomeric and the unique loop harbors a short helical segment, observed in only one of the known X-ray structures so far. Our work stresses the importance of solution-state investigations to fully decipher the functional relevance of the structural and dynamical features unique to Shank PDZ domains.
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Affiliation(s)
- Anna Sánta
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
| | - András Czajlik
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
| | - Gyula Batta
- Faculty of Science and Technology, Institute of Chemistry, Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, 4032, Debrecen, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083, Budapest, Hungary.
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Váncza L, Karászi K, Péterfia B, Turiák L, Dezső K, Sebestyén A, Reszegi A, Petővári G, Kiss A, Schaff Z, Baghy K, Kovalszky I. SPOCK1 Promotes the Development of Hepatocellular Carcinoma. Front Oncol 2022; 12:819883. [PMID: 35186754 PMCID: PMC8853618 DOI: 10.3389/fonc.2022.819883] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022] Open
Abstract
The extracellular matrix proteoglycan SPOCK1 is increasingly recognized as a contributor to the development and progression of cancers. Here, we study how SPOCK1, which is present in non-tumorous hepatocytes at low concentrations, promotes the development and progression of malignant hepatocellular tumors. Although SPOCK1 is an extracellular matrix proteoglycan, its concentration increases in the cytoplasm of hepatocytes starting with very low expression in the normal cells and then appearing in much higher quantities in cells of cirrhotic human liver and hepatocellular carcinoma. This observation is similar to that observed after diethylnitrosamine induction of mouse hepatocarcinogenesis. Furthermore, syndecan-1, the major proteoglycan of the liver, and SPOCK1 are in inverse correlation in the course of these events. In hepatoma cell lines, the cytoplasmic SPOCK1 colocalized with mitochondrial markers, such as MitoTracker and TOMM20, a characteristic protein of the outer membrane of the mitochondrion and could be detected in the cell nucleus. SPOCK1 downregulation of hepatoma cell lines by siRNA inhibited cell proliferation, upregulated p21 and p27, and interfered with pAkt and CDK4 expression. A tyrosine kinase array revealed that inhibition of SPOCK1 in the liver cancer cells altered MAPK signaling and downregulated several members of the Sarc family, all related to the aggressivity of the hepatoma cell lines. These studies support the idea that SPOCK1 enhancement in the liver is an active contributor to human and rodent hepatocarcinogenesis and cancer progression. However, its mitochondrial localization raises the possibility that it has a currently unidentified physiological function in normal hepatocytes.
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Affiliation(s)
- Lóránd Váncza
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Katalin Karászi
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
| | - Lilla Turiák
- MS Proteomics Research Group, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary
| | - Katalin Dezső
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Anna Sebestyén
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Andrea Reszegi
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Gábor Petővári
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Kiss
- 2 Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Zsuzsanna Schaff
- 2 Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Kornélia Baghy
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ilona Kovalszky
- 1 Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- *Correspondence: Ilona Kovalszky, ;
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5
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Kiss-Tóth A, Dobson L, Péterfia B, Ángyán AF, Ligeti B, Lukács G, Gáspári Z. Occurrence of Ordered and Disordered Structural Elements in Postsynaptic Proteins Supports Optimization for Interaction Diversity. Entropy (Basel) 2019; 21:E761. [PMID: 33267475 PMCID: PMC7515291 DOI: 10.3390/e21080761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 07/30/2019] [Accepted: 08/02/2019] [Indexed: 12/15/2022]
Abstract
The human postsynaptic density is an elaborate network comprising thousands of proteins, playing a vital role in the molecular events of learning and the formation of memory. Despite our growing knowledge of specific proteins and their interactions, atomic-level details of their full three-dimensional structure and their rearrangements are mostly elusive. Advancements in structural bioinformatics enabled us to depict the characteristic features of proteins involved in different processes aiding neurotransmission. We show that postsynaptic protein-protein interactions are mediated through the delicate balance of intrinsically disordered regions and folded domains, and this duality is also imprinted in the amino acid sequence. We introduce Diversity of Potential Interactions (DPI), a structure and regulation based descriptor to assess the diversity of interactions. Our approach reveals that the postsynaptic proteome has its own characteristic features and these properties reliably discriminate them from other proteins of the human proteome. Our results suggest that postsynaptic proteins are especially susceptible to forming diverse interactions with each other, which might be key in the reorganization of the postsynaptic density (PSD) in molecular processes related to learning and memory.
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Affiliation(s)
- Annamária Kiss-Tóth
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
- 3in-PPCU Research Group, 2500 Esztergom, Hungary
| | - Laszlo Dobson
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Bálint Péterfia
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Annamária F. Ángyán
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Balázs Ligeti
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Gergely Lukács
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50A, 1083 Budapest, Hungary
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Péterfia B. Correction: Construction of a multiplex mutation hot spot PCR panel: the first step towards colorectal cancer genotyping on the GS Junior platform. J Cancer 2018; 9:2743. [PMID: 30087715 PMCID: PMC6072823 DOI: 10.7150/jca.27625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
[This corrects the article DOI: 10.7150/jca.16037.].
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Affiliation(s)
- Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary.,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
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7
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Molnár B, Galamb O, Péterfia B, Wichmann B, Csabai I, Bodor A, Kalmár A, Szigeti KA, Barták BK, Nagy ZB, Valcz G, Patai ÁV, Igaz P, Tulassay Z. Gene promoter and exon DNA methylation changes in colon cancer development - mRNA expression and tumor mutation alterations. BMC Cancer 2018; 18:695. [PMID: 29945573 PMCID: PMC6020382 DOI: 10.1186/s12885-018-4609-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 06/18/2018] [Indexed: 12/28/2022] Open
Abstract
Background DNA mutations occur randomly and sporadically in growth-related genes, mostly on cytosines. Demethylation of cytosines may lead to genetic instability through spontaneous deamination. Aims were whole genome methylation and targeted mutation analysis of colorectal cancer (CRC)-related genes and mRNA expression analysis of TP53 pathway genes. Methods Long interspersed nuclear element-1 (LINE-1) BS-PCR followed by pyrosequencing was performed for the estimation of global DNA metlyation levels along the colorectal normal-adenoma-carcinoma sequence. Methyl capture sequencing was done on 6 normal adjacent (NAT), 15 adenomatous (AD) and 9 CRC tissues. Overall quantitative methylation analysis, selection of top hyper/hypomethylated genes, methylation analysis on mutation regions and TP53 pathway gene promoters were performed. Mutations of 12 CRC-related genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53) were evaluated. mRNA expression of TP53 pathway genes was also analyzed. Results According to the LINE-1 methylation results, overall hypomethylation was observed along the normal-adenoma-carcinoma sequence. Within top50 differential methylated regions (DMRs), in AD-N comparison TP73, NGFR, PDGFRA genes were hypermethylated, FMN1, SLC16A7 genes were hypomethylated. In CRC-N comparison DKK2, SDC2, SOX1 genes showed hypermethylation, while ERBB4, CREB5, CNTN1 genes were hypomethylated. In certain mutation hot spot regions significant DNA methylation alterations were detected. The TP53 gene body was addressed by hypermethylation in adenomas. APC, TP53 and KRAS mutations were found in 30, 15, 21% of adenomas, and in 29, 53, 29% of CRCs, respectively. mRNA expression changes were observed in several TP53 pathway genes showing promoter methylation alterations. Conclusions DNA methylation with consecutive phenotypic effect can be observed in a high number of promoter and gene body regions through CRC development. Electronic supplementary material The online version of this article (10.1186/s12885-018-4609-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Béla Molnár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary. .,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, Budapest, H-1117, Hungary.,Institute of Mathematics and Informatics, Faculty of Sciences, University of Pécs, Ifjúság útja 6, Pécs, H-7624, Hungary
| | - Alexandra Kalmár
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Krisztina Andrea Szigeti
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Barbara Kinga Barták
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsófia Brigitta Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Péter Igaz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Szentkirályi str 46, Budapest, H-1088, Hungary.,2nd Department of Internal Medicine, Semmelweis University, Szentkirályi str 46, Budapest, H-1088, Hungary
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Ács OD, Péterfia B, Hollósi P, Haltrich I, Sallai Á, Luczay A, Buiting K, Horsthemke B, Török D, Szabó A, Fekete G. [Rapid first-tier genetic diagnosis in patients with Prader-Willi syndrome]. Orv Hetil 2018; 159:64-69. [PMID: 29307221 DOI: 10.1556/650.2018.30918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION According to the international literature, DNA methylation analysis of the promoter region of SNRPN locus is the most efficient way to start genetic investigation in patients with suspected Prader-Willi syndrome. AIM Our aim was to develop a simple, reliable first-tier diagnosis to confirm Prader-Willi syndrome, therefore to compare our self-designed simple, cost-efficient high-resolution melting analysis and the most commonly used methylation-specific multiplex ligation-dependent probe amplification to confirm Prader-Willi syndrome. METHOD We studied 17 clinically suspected Prader-Willi syndrome children and their DNA samples. With self-designed primers, bisulfite-sensitive polymerase chain reaction, high-resolution melting analysis and, as a control, methylation-specific multiplex ligation-dependent probe amplification were performed. RESULTS Prader-Willi syndrome was genetically confirmed in 6 out of 17 clinically suspected Prader-Willi syndrome patients. The results of high-resolution melting analysis and methylation-specific multiplex ligation-dependent probe amplification were equivalent in each case. CONCLUSION Using our self-designed primers and altered bisulfite-specific PCR conditions, high-resolution melting analysis appears to be a simple, fast, reliable and effective method for primarily proving or excluding clinically suspected Prade-Willi syndrome cases. Orv Hetil. 2018; 159(2): 64-69.
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Affiliation(s)
- Orsolya Dóra Ács
- II. Gyermekgyógyászati Klinika, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Tűzoltó u. 7-9., 1094
| | - Bálint Péterfia
- I. Patológiai és Kísérleti Rákkutató Intézet, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest
| | - Péter Hollósi
- I. Patológiai és Kísérleti Rákkutató Intézet, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest.,Daganatprogresszió Kutatócsoport, Magyar Tudományos Akadémia Budapest
| | - Irén Haltrich
- II. Gyermekgyógyászati Klinika, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Tűzoltó u. 7-9., 1094
| | - Ágnes Sallai
- II. Gyermekgyógyászati Klinika, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Tűzoltó u. 7-9., 1094
| | - Andrea Luczay
- II. Gyermekgyógyászati Klinika, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Tűzoltó u. 7-9., 1094
| | - Karin Buiting
- Institut für Humangenetik, Universität Duisburg-Essen Essen, Germany
| | | | - Dóra Török
- II. Gyermekgyógyászati Klinika, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Tűzoltó u. 7-9., 1094
| | - András Szabó
- II. Gyermekgyógyászati Klinika, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Tűzoltó u. 7-9., 1094
| | - György Fekete
- II. Gyermekgyógyászati Klinika, Semmelweis Egyetem, Általános Orvostudományi Kar Budapest, Tűzoltó u. 7-9., 1094
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Barták BK, Kalmár A, Péterfia B, Patai ÁV, Galamb O, Valcz G, Spisák S, Wichmann B, Nagy ZB, Tóth K, Tulassay Z, Igaz P, Molnár B. Colorectal adenoma and cancer detection based on altered methylation pattern of SFRP1, SFRP2, SDC2, and PRIMA1 in plasma samples. Epigenetics 2017; 12:751-763. [PMID: 28753106 DOI: 10.1080/15592294.2017.1356957] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aberrant methylation is one of the most frequent epigenetic alterations that can contribute to tumor formation. Cell-free DNA can originate from tumor tissue; therefore, the evaluation of methylation markers in cell-free DNA can be a promising method for cancer screening. Our aim was to develop a panel of biomarkers with altered methylation along the colorectal adenoma-carcinoma sequence in both colonic tissue and plasma. Methylation of selected CpG sites in healthy colonic (n = 15), adenoma (n = 15), and colorectal cancer (n = 15) tissues was analyzed by pyrosequencing. MethyLight PCR was applied to study the DNA methylation of SFRP1, SFRP2, SDC2, and PRIMA1 gene promoters in 121 plasma and 32 biopsy samples. The effect of altered promoter methylation on protein expression was examined by immunohistochemistry. Significantly higher (P < 0.05) DNA methylation levels were detected in the promoter regions of all 4 markers, both in CRC and adenoma tissues compared with healthy controls. Methylation of SFRP1, SFRP2, SDC2, and PRIMA1 promoter sequences was observed in 85.1%, 72.3%, 89.4%, and 80.9% of plasma samples from patients with CRC and 89.2%, 83.8%, 81.1% and 70.3% from adenoma patients, respectively. When applied as a panel, CRC patients could be distinguished from controls with 91.5% sensitivity and 97.3% specificity [area under the curve (AUC) = 0.978], while adenoma samples could be differentiated with 89.2% sensitivity and 86.5% specificity (AUC = 0.937). Immunohistochemical analysis indicated decreasing protein levels of all 4 markers along the colorectal adenoma-carcinoma sequence. Our findings suggest that this methylation biomarker panel allows non-invasive detection of colorectal adenoma and cancer from plasma samples.
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Affiliation(s)
- Barbara Kinga Barták
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary
| | - Alexandra Kalmár
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary
| | - Bálint Péterfia
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary
| | - Árpád V Patai
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary
| | - Orsolya Galamb
- b Molecular Medicine Research Group, Hungarian Academy of Sciences , H-1088 Budapest , Hungary
| | - Gábor Valcz
- b Molecular Medicine Research Group, Hungarian Academy of Sciences , H-1088 Budapest , Hungary
| | - Sándor Spisák
- c Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , Massachusetts , USA
| | - Barnabás Wichmann
- b Molecular Medicine Research Group, Hungarian Academy of Sciences , H-1088 Budapest , Hungary
| | - Zsófia Brigitta Nagy
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary
| | - Kinga Tóth
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary
| | - Zsolt Tulassay
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary.,b Molecular Medicine Research Group, Hungarian Academy of Sciences , H-1088 Budapest , Hungary
| | - Péter Igaz
- a 2nd Department of Internal Medicine , Semmelweis University , H-1088 Budapest , Hungary.,b Molecular Medicine Research Group, Hungarian Academy of Sciences , H-1088 Budapest , Hungary
| | - Béla Molnár
- b Molecular Medicine Research Group, Hungarian Academy of Sciences , H-1088 Budapest , Hungary
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10
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Péterfia B, Kalmár A, Patai ÁV, Csabai I, Bodor A, Micsik T, Wichmann B, Egedi K, Hollósi P, Kovalszky I, Tulassay Z, Molnár B. Construction of a multiplex mutation hot spot PCR panel: the first step towards colorectal cancer genotyping on the GS Junior platform. J Cancer 2017; 8:162-173. [PMID: 28243320 PMCID: PMC5327365 DOI: 10.7150/jca.16037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 09/04/2016] [Indexed: 12/15/2022] Open
Abstract
Background: To support cancer therapy, development of low cost library preparation techniques for targeted next generation sequencing (NGS) is needed. In this study we designed and tested a PCR-based library preparation panel with limited target area for sequencing the top 12 somatic mutation hot spots in colorectal cancer on the GS Junior instrument. Materials and Methods: A multiplex PCR panel was designed to amplify regions of mutation hot spots in 12 selected genes (APC, BRAF, CTNNB1, EGFR, FBXW7, KRAS, NRAS, MSH6, PIK3CA, SMAD2, SMAD4, TP53). Amplicons were sequenced on a GS Junior instrument using ligated and barcoded adaptors. Eight samples were sequenced in a single run. Colonic DNA samples (8 normal mucosa; 33 adenomas; 17 adenocarcinomas) as well as HT-29 and Caco-2 cell lines with known mutation profiles were analyzed. Variants found by the panel on APC, BRAF, KRAS and NRAS genes were validated by conventional sequencing. Results: In total, 34 kinds of mutations were detected including two novel mutations (FBXW7 c.1740:C>G and SMAD4 c.413C>G) that have not been recorded in mutation databases, and one potential germline mutation (APC). The most frequently mutated genes were APC, TP53 and KRAS with 30%, 15% and 21% frequencies in adenomas and 29%, 53% and 29% frequencies in carcinomas, respectively. In cell lines, all the expected mutations were detected except for one located in a homopolymer region. According to re-sequencing results sensitivity and specificity was 100% and 92% respectively. Conclusions: Our NGS-based screening panel denotes a promising step towards low cost colorectal cancer genotyping on the GS Junior instrument. Despite the relatively low coverage, we discovered two novel mutations and obtained mutation frequencies comparable to literature data. Additionally, as an advantage, this panel requires less template DNA than sequence capture colon cancer panels currently available for the GS Junior instrument.
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Affiliation(s)
- Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary;; Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - István Csabai
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - András Bodor
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary
| | - Tamás Micsik
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Krisztina Egedi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Péter Hollósi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary;; Tumor Progression Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary;; Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary;; Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
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11
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Ács O, Péterfia B, Hollósi P, Luczay A, Török D, Szabó A. Methylation Status of CYP27B1 and IGF2 Correlate to BMI SDS in Children with Obesity. Obes Facts 2017; 10:353-362. [PMID: 28787727 PMCID: PMC5644970 DOI: 10.1159/000477462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/02/2017] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Worldwide increasing childhood obesity is due to interactions between environmental and genetic factors, linked together by epigenetic mechanisms such as DNA methylation. METHODS 82 obese children (>95th BMI percentile , age: 3-18 years) were included. Anthropometric data, metabolic parameters, 25-OH vitamin D (25OHD), and pubertal status were recorded, 24-hour blood pressure monitoring was performed. BMI standard deviation score (SDS) was calculated. Using candidate gene approach, obesity- (insulin-like growth factor 2 (IGF2), proopiomelanocortin (POMC)) and vitamin D metabolism-related genes (1-alfa-hydroxylase (CYP27B1), VDR) regulated by DNA methylation were selected. After isolating DNA from peripheral blood, bisulfite conversion, bisulfite specific polymerase chain reaction (BS-PCR), and pyrosequencing were carried out. RESULTS No significant correlation between 25-OHD and metabolic parameters and DNA methylation status, but a tendency of positive correlation between VDR methylation status and 25-OHD (r = 0.2053,p = 0.066) were observed. Significant positive correlations between BMI SDS and CYP27B1 hypermethylation (r = 0.2371,p = 0.0342) and a significant negative correlation between IGF2 hypomethylation and BMI SDS (r = -0.305,p = 0.0059) were found. Conclusions Rate of obesity shows correlation with DNA methylation. Hypomethylation of IGF2 and hypermethylation of CYP27B1 genes might positively influence the rate of BMI observed in obese children.
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Affiliation(s)
- Orsolya Ács
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
- *Orsolya Dóra Ács, MD, 2nd Department of Pediatrics, Semmelweis University, 1094 Budapest, Tűzoltó utca 7–9, Hungary,
| | - Bálint Péterfia
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Péter Hollósi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Tumor Progression Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Andrea Luczay
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Dóra Török
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - András Szabó
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
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12
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Galamb O, Kalmár A, Péterfia B, Csabai I, Bodor A, Ribli D, Krenács T, Patai ÁV, Wichmann B, Barták BK, Tóth K, Valcz G, Spisák S, Tulassay Z, Molnár B. Aberrant DNA methylation of WNT pathway genes in the development and progression of CIMP-negative colorectal cancer. Epigenetics 2016; 11:588-602. [PMID: 27245242 DOI: 10.1080/15592294.2016.1190894] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The WNT signaling pathway has an essential role in colorectal carcinogenesis and progression, which involves a cascade of genetic and epigenetic changes. We aimed to analyze DNA methylation affecting the WNT pathway genes in colorectal carcinogenesis in promoter and gene body regions using whole methylome analysis in 9 colorectal cancer, 15 adenoma, and 6 normal tumor adjacent tissue (NAT) samples by methyl capture sequencing. Functional methylation was confirmed on 5-aza-2'-deoxycytidine-treated colorectal cancer cell line datasets. In parallel with the DNA methylation analysis, mutations of WNT pathway genes (APC, β-catenin/CTNNB1) were analyzed by 454 sequencing on GS Junior platform. Most differentially methylated CpG sites were localized in gene body regions (95% of WNT pathway genes). In the promoter regions, 33 of the 160 analyzed WNT pathway genes were differentially methylated in colorectal cancer vs. normal, including hypermethylated AXIN2, CHP1, PRICKLE1, SFRP1, SFRP2, SOX17, and hypomethylated CACYBP, CTNNB1, MYC; 44 genes in adenoma vs. NAT; and 41 genes in colorectal cancer vs. adenoma comparisons. Hypermethylation of AXIN2, DKK1, VANGL1, and WNT5A gene promoters was higher, while those of SOX17, PRICKLE1, DAAM2, and MYC was lower in colon carcinoma compared to adenoma. Inverse correlation between expression and methylation was confirmed in 23 genes, including APC, CHP1, PRICKLE1, PSEN1, and SFRP1. Differential methylation affected both canonical and noncanonical WNT pathway genes in colorectal normal-adenoma-carcinoma sequence. Aberrant DNA methylation appears already in adenomas as an early event of colorectal carcinogenesis.
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Affiliation(s)
- Orsolya Galamb
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Alexandra Kalmár
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Bálint Péterfia
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - István Csabai
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - András Bodor
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Dezső Ribli
- c Department of Physics of Complex Systems , Eötvös Loránd University , Budapest , Hungary
| | - Tibor Krenács
- d 1st Department of Pathology and Experimental Cancer Research , Semmelweis University , Budapest , Hungary.,e Tumor Progression Research Group , Hungarian Academy of Sciences - Semmelweis University , Budapest , Hungary
| | - Árpád V Patai
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Barnabás Wichmann
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Barbara Kinga Barták
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Kinga Tóth
- b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Gábor Valcz
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
| | - Sándor Spisák
- f Department of Medical Oncology , Dana-Farber Cancer Institute , Boston , MA , USA
| | - Zsolt Tulassay
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary.,b 2nd Department of Internal Medicine , Semmelweis University , Budapest , Hungary
| | - Béla Molnár
- a Molecular Medicine Research Group , Hungarian Academy of Sciences , Budapest , Hungary
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13
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Kalmár A, Péterfia B, Hollósi P, Galamb O, Spisák S, Wichmann B, Bodor A, Tóth K, Patai ÁV, Valcz G, Nagy ZB, Kubák V, Tulassay Z, Kovalszky I, Molnár B. DNA hypermethylation and decreased mRNA expression of MAL, PRIMA1, PTGDR and SFRP1 in colorectal adenoma and cancer. BMC Cancer 2015; 15:736. [PMID: 26482433 PMCID: PMC4612409 DOI: 10.1186/s12885-015-1687-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 10/07/2015] [Indexed: 12/18/2022] Open
Abstract
Background Colorectal cancer (CRC) development is accompanied by changes in expression for several genes; but the details of the underlying regulatory procesess remain unknown. Our aims were to assess the role of epigenetic processes in tumour formation and to identify characteristic DNA methylation and miRNA alterations in the colorectal adenoma-carcinoma sequence. Methods Whole genome expression profiling was performed on colonic biopsy samples (49 healthy normal, 49 colorectal adenoma (AD), 49 CRC); on laser capture microdissected (LCM) epithelial and stromal cells from 6 CRC-normal adjacent tissue (NAT) samples pairs, and on demethylated human CRC cell lines using HGU133 Plus 2.0 microarrays (Affymetrix). Methylation status of genes with gradually altering expression along the AD-CRC sequence was further analysed on 10–10 macrodissected and 5–5 LCM samples from healthy colon, from adenoma and from CRC biopsy samples using bisulfite-sequencing PCR (BS-PCR) followed by pyrosequencing. In silico miRNA prediction for the selected genes was performed with miRWALK algorithm, miRNA expression was analysed on 3 CRC-NAT sample pairs and 3 adenoma tissue samples using the Human Panel I + II (Exiqon). SFRP1 immunohistochemistry experiments were performed. Results A set of transcripts (18 genes including MAL, SFRP1, SULT1A1, PRIMA1, PTGDR) showed decreasing expression (p < 0.01) in the biopsy samples along the adenoma-carcinoma sequence. Three of those (COL1A2, SFRP2, SOCS3) showed hypermethylation and THBS2 showed hypomethylation both in AD and in CRC samples compared to NAT, while BCL2, PRIMA1 and PTGDR showed hypermethylation only in the CRC group. miR-21 was found to be significantly (p < 0.01) upregulated in adenoma and tumour samples compared to the healthy colonic tissue controls and could explain the altered expression of genes for which DNA methylation changes do not appear to play role (e.g. BCL2, MAL, PTGS2). Demethylation treatment could upregulate gene expression of genes that were found to be hypermethylated in human CRC tissue samples. Decreasing protein levels of SFRP1 was also observed along the adenoma-carcinoma sequence. Conclusion Hypermethylation of the selected markers (MAL, PRIMA1, PTGDR and SFRP1) can result in reduced gene expression and may contribute to the formation of colorectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1687-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Péter Hollósi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary. .,Tumour Progression Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Orsolya Galamb
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Sándor Spisák
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - András Bodor
- Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary.
| | - Kinga Tóth
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary.
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary.
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | | | - Vivien Kubák
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary.
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary. .,Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary.
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14
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Kalmár A, Péterfia B, Wichmann B, Patai ÁV, Barták BK, Nagy ZB, Furi I, Tulassay Z, Molnár B. Comparison of Automated and Manual DNA Isolation Methods for DNA Methylation Analysis of Biopsy, Fresh Frozen, and Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Samples. ACTA ACUST UNITED AC 2015; 20:642-51. [PMID: 25576093 DOI: 10.1177/2211068214565903] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Indexed: 12/18/2022]
Abstract
Automated DNA isolation can decrease hands-on time in routine pathology. Our aim was to apply automated DNA isolation and perform DNA methylation analyses. DNA isolation was performed manually from fresh frozen (CRC = 10, normal = 10) specimens and colonic biopsies (CRC = 10, healthy = 10) with QIAamp DNA Mini Kit and from FFPE blocks (CRC = 10, normal = 10) with QIAamp DNA FFPET Kit. Automated DNA isolation was performed with MagNA Pure DNA and Viral NA SV kit on MagNA Pure 96 system. DNA methylation of MAL, SFRP1, and SFRP2 were analyzed with methylation-specific high-resolution melting analysis. Yield of automatically isolated samples was equal in fresh frozens and significantly lower compared to manually isolated biopsy and FFPE samples. OD260/280 of fresh frozen and biopsy samples were similar after both isolations, automated isolation resulted in lower purity in FFPE samples. Both protocols resulted in similar OD260/230 from fresh frozens, automated isolation method was superior in biopsies and manual protocol in FFPE samples. DNA methylation of biopsies, fresh frozen samples were highly similar after both methods, results of automatically and manually isolated FFPE samples were different. Automated DNA isolation from fresh frozen samples can be suitable for high-throughput laboratories.
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Affiliation(s)
- Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád V Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Barbara K Barták
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Zsófia B Nagy
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - István Furi
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
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15
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Patai ÁV, Valcz G, Hollósi P, Kalmár A, Péterfia B, Patai Á, Wichmann B, Spisák S, Barták BK, Leiszter K, Tóth K, Sipos F, Kovalszky I, Péter Z, Miheller P, Tulassay Z, Molnár B. Comprehensive DNA Methylation Analysis Reveals a Common Ten-Gene Methylation Signature in Colorectal Adenomas and Carcinomas. PLoS One 2015; 10:e0133836. [PMID: 26291085 PMCID: PMC4546193 DOI: 10.1371/journal.pone.0133836] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/02/2015] [Indexed: 02/06/2023] Open
Abstract
Microarray analysis of promoter hypermethylation provides insight into the role and extent of DNA methylation in the development of colorectal cancer (CRC) and may be co-monitored with the appearance of driver mutations. Colonic biopsy samples were obtained endoscopically from 10 normal, 23 adenoma (17 low-grade (LGD) and 6 high-grade dysplasia (HGD)), and 8 ulcerative colitis (UC) patients (4 active and 4 inactive). CRC samples were obtained from 24 patients (17 primary, 7 metastatic (MCRC)), 7 of them with synchronous LGD. Field effects were analyzed in tissues 1 cm (n = 5) and 10 cm (n = 5) from the margin of CRC. Tissue materials were studied for DNA methylation status using a 96 gene panel and for KRAS and BRAF mutations. Expression levels were assayed using whole genomic mRNA arrays. SFRP1 was further examined by immunohistochemistry. HT29 cells were treated with 5-aza-2' deoxycytidine to analyze the reversal possibility of DNA methylation. More than 85% of tumor samples showed hypermethylation in 10 genes (SFRP1, SST, BNC1, MAL, SLIT2, SFRP2, SLIT3, ALDH1A3, TMEFF2, WIF1), whereas the frequency of examined mutations were below 25%. These genes distinguished precancerous and cancerous lesions from inflamed and healthy tissue. The mRNA alterations that might be caused by systematic methylation could be partly reversed by demethylation treatment. Systematic changes in methylation patterns were observed early in CRC carcinogenesis, occuring in precursor lesions and CRC. Thus we conclude that DNA hypermethylation is an early and systematic event in colorectal carcinogenesis, and it could be potentially reversed by systematic demethylation therapy, but it would need more in vitro and in vivo experiments to support this theory.
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Affiliation(s)
- Árpád V. Patai
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- * E-mail:
| | - Gábor Valcz
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Péter Hollósi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- Tumor Progression Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Alexandra Kalmár
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Bálint Péterfia
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád Patai
- Department of Gastroenterology and Medicine, Markusovszky University Teaching Hospital, Szombathely, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Sándor Spisák
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | | | - Katalin Leiszter
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Kinga Tóth
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Ferenc Sipos
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zoltán Péter
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Pál Miheller
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
| | - Béla Molnár
- 2nd Department of Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Hungarian Academy of Sciences, Budapest, Hungary
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16
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Fullár A, Baghy K, Deák F, Péterfia B, Zsák Y, Tátrai P, Schaff Z, Dudás J, Kiss I, Kovalszky I. Lack of Matrilin-2 favors liver tumor development via Erk1/2 and GSK-3β pathways in vivo. PLoS One 2014; 9:e93469. [PMID: 24691449 PMCID: PMC3972106 DOI: 10.1371/journal.pone.0093469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/06/2014] [Indexed: 11/19/2022] Open
Abstract
Matrilin-2 (Matn2) is a multidomain adaptor protein which plays a role in the assembly of extracellular matrix (ECM). It is produced by oval cells during stem cell-driven liver regeneration. In our study, the impact of Matn2 on hepatocarcinogenesis was investigated in Matn2(-/-) mice comparing them with wild-type (WT) mice in a diethylnitrosamine (DEN) model. The liver tissue was analyzed macroscopically, histologically and immunohistochemically, at protein level by Proteome Profiler Arrays and Western blot analysis. Matn2(-/-) mice exhibited higher susceptibility to hepatocarcinogenesis compared to wild-type mice. In the liver of Matn2(-/-) mice, spontaneous microscopic tumor foci were detected without DEN treatment. After 15 μg/g body weight DEN treatment, the liver of Matn2(-/-) mice contained macroscopic tumors of both larger number and size than the WT liver. In contrast with the WT liver, spontaneous phosphorylation of EGFR, Erk1/2 GSK-3α/β and retinoblastoma protein (p-Rb), decrease in p21/CIP1 level, and increase in β-Catenin protein expression were detected in Matn2(-/-) livers. Focal Ki-67 positivity of these samples provided additional support to our presumption that the lack of Matn2 drives the liver into a pro-proliferatory state, making it prone to tumor development. This enhanced proliferative capacity was further increased in the tumor nodules of DEN-treated Matn2(-/-) livers. Our study suggests that Matn2 functions as a tumor suppressor in hepatocarcinogenesis, and in this process activation of EGFR together with that of Erk1/2, as well as inactivation of GSK-3β, play strategic roles.
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Affiliation(s)
- Alexandra Fullár
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Kornélia Baghy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ferenc Deák
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Bálint Péterfia
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Yvonne Zsák
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Péter Tátrai
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zsuzsa Schaff
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - József Dudás
- Department of Otorhinolaryngology, Medical University Innsbruck, Innsbruck, Austria
| | - Ibolya Kiss
- Institute of Biochemistry, Biological Research Center, Hungarian Academy of Sciences, Szeged, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
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17
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Valcz G, Patai ÁV, Kalmár A, Péterfia B, Fűri I, Wichmann B, Műzes G, Sipos F, Krenács T, Mihály E, Spisák S, Molnár B, Tulassay Z. Myofibroblast-derived SFRP1 as potential inhibitor of colorectal carcinoma field effect. PLoS One 2014; 9:e106143. [PMID: 25405986 PMCID: PMC4236006 DOI: 10.1371/journal.pone.0106143] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Accepted: 07/28/2014] [Indexed: 02/05/2023] Open
Abstract
Epigenetic changes of stromal-epithelial interactions are of key importance in the regulation of colorectal carcinoma (CRC) cells and morphologically normal, but genetically and epigenetically altered epithelium in normal adjacent tumor (NAT) areas. Here we demonstrated retained protein expression of well-known Wnt inhibitor, secreted frizzled-related protein 1 (SFRP1) in stromal myofibroblasts and decreasing epithelial expression from NAT tissues towards the tumor. SFRP1 was unmethylated in laser microdissected myofibroblasts and partially hypermethylated in epithelial cells in these areas. In contrast, we found epigenetically silenced myofibroblast-derived SFRP1 in CRC stroma. Our results suggest that the myofibroblast-derived SFRP1 protein might be a paracrine inhibitor of epithelial proliferation in NAT areas and loss of this signal may support tumor proliferation in CRC.
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Affiliation(s)
- Gábor Valcz
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Árpád V. Patai
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- * E-mail:
| | - Alexandra Kalmár
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Bálint Péterfia
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - István Fűri
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Barnabás Wichmann
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
| | - Györgyi Műzes
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Tibor Krenács
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Emese Mihály
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Sándor Spisák
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Béla Molnár
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - Zsolt Tulassay
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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18
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Sipos F, Mũzes G, Patai AV, Fũri I, Péterfia B, Hollósi P, Molnár B, Tulassay Z. Genome-wide screening for understanding the role of DNA methylation in colorectal cancer. Epigenomics 2013; 5:569-81. [PMID: 24059802 DOI: 10.2217/epi.13.52] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA methylation analysis methods have undergone an impressive revolution over the past 15 years. Regarding colorectal cancer (CRC), the localization and distribution of several differently methylated genes have been determined by genome-wide DNA methylation assays. These genes do not just influence the pathogenesis of CRC, but can be used further as diagnostic or prognostic markers. Moreover, the identified four DNA methylation-based subgroups of CRC have important clinical and therapeutic merit. Since genome-wide DNA methylation analyzes result in a large amount of data, there is a need for complex bioinformatic and pathway analysis. Future challenges in epigenetic alterations of CRC include the demand for comprehensive identification and experimental validation of gene abnormalities. By introduction of genome-wide DNA methylation profiling into clinical practice not only the patients' risk stratification but development of targeted therapies will also be possible.
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Affiliation(s)
- Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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19
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Péterfia B, Füle T, Baghy K, Szabadkai K, Fullár A, Dobos K, Zong F, Dobra K, Hollósi P, Jeney A, Paku S, Kovalszky I. Syndecan-1 enhances proliferation, migration and metastasis of HT-1080 cells in cooperation with syndecan-2. PLoS One 2012; 7:e39474. [PMID: 22745764 PMCID: PMC3383727 DOI: 10.1371/journal.pone.0039474] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
Syndecans are transmembrane heparan sulphate proteoglycans. Their role in the development of the malignant phenotype is ambiguous and depends upon the particular type of cancer. Nevertheless, syndecans are promising targets in cancer therapy, and it is important to elucidate the mechanisms controlling their various cellular effects. According to earlier studies, both syndecan-1 and syndecan-2 promote malignancy of HT-1080 human fibrosarcoma cells, by increasing the proliferation rate and the metastatic potential and migratory ability, respectively. To better understand their tumour promoter role in this cell line, syndecan expression levels were modulated in HT-1080 cells and the growth rate, chemotaxis and invasion capacity were studied. For in vivo testing, syndecan-1 overexpressing cells were also inoculated into mice. Overexpression of full length or truncated syndecan-1 lacking the entire ectodomain but containing the four juxtamembrane amino acids promoted proliferation and chemotaxis. These effects were accompanied by a marked increase in syndecan-2 protein expression. The pro-migratory and pro-proliferative effects of truncated syndecan-1 were not observable when syndecan-2 was silenced. Antisense silencing of syndecan-2, but not that of syndecan-1, inhibited cell migration. In vivo, both full length and truncated syndecan-1 increased tumour growth and metastatic rate. Based on our in vitro results, we conclude that the tumour promoter role of syndecan-1 observed in HT-1080 cells is independent of its ectodomain; however, in vivo the presence of the ectodomain further increases tumour proliferation. The enhanced migratory ability induced by syndecan-1 overexpression is mediated by syndecan-2. Overexpression of syndecan-1 also leads to activation of IGF1R and increased expression of Ets-1. These changes were not evident when syndecan-2 was overexpressed. These findings suggest the involvement of IGF1R and Ets-1 in the induction of syndecan-2 synthesis and stimulation of proliferation by syndecan-1. This is the first report demonstrating that syndecan-1 enhances malignancy of a mesenchymal tumour cell line, via induction of syndecan-2 expression.
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Affiliation(s)
- Bálint Péterfia
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Tibor Füle
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Kornélia Baghy
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Krisztina Szabadkai
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Alexandra Fullár
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Katalin Dobos
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Fang Zong
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Katalin Dobra
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Péter Hollósi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - András Jeney
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sándor Paku
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Ilona Kovalszky
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
- * E-mail:
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20
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Spisák S, Kalmár A, Galamb O, Wichmann B, Sipos F, Péterfia B, Csabai I, Kovalszky I, Semsey S, Tulassay Z, Molnár B. Genome-wide screening of genes regulated by DNA methylation in colon cancer development. PLoS One 2012; 7:e46215. [PMID: 23049694 PMCID: PMC3462205 DOI: 10.1371/journal.pone.0046215] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Accepted: 08/28/2012] [Indexed: 02/05/2023] Open
Abstract
Tumorigenesis is accompanied by changes in the DNA methylation pattern. Our aim was to test a novel approach for identification of transcripts at whole transcript level which are regulated by DNA methylation. Our approach is based on comparison of data obtained from transcriptome profiling of primary human samples and in vitro cell culture models. Epithelial cells were collected by LCM from normal, adenoma, and tumorous colonic samples. Using gene expression analysis, we identified downregulated genes in the tumors compared to normal tissues. In parallel 3000 upregulated genes were determined in HT-29 colon adenocarcinoma cell culture model after DNA demethylation treatment. Of the 2533 transcripts showing reduced expression in the tumorous samples, 154 had increased expression as a result of DNA demethylation treatment. Approximately 2/3 of these genes had decreased expression already in the adenoma samples. Expression of five genes (GCG, NMES-1, LRMP, FAM161B and PTGDR), was validated using RT-PCR. PTGDR showed ambiguous results, therefore it was further studied to verify the extent of DNA methylation and its effect on the protein level. Results confirmed that our approach is suitable for genome-wide screening of genes which are regulated or inactivated by DNA methylation. Activity of these genes possibly interferes with tumor progression, therefore genes identified can be key factors in the formation and in the progression of the disease.
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Affiliation(s)
- Sándor Spisák
- Molecular Medicine Research Unit, Hungarian Academy of Sciences, Budapest, Hungary.
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21
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Baghy K, Dezső K, László V, Fullár A, Péterfia B, Paku S, Nagy P, Schaff Z, Iozzo RV, Kovalszky I. Ablation of the decorin gene enhances experimental hepatic fibrosis and impairs hepatic healing in mice. J Transl Med 2011; 91:439-51. [PMID: 20956977 PMCID: PMC5074558 DOI: 10.1038/labinvest.2010.172] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Accumulation of connective tissue is a typical feature of chronic liver diseases. Decorin, a small leucine-rich proteoglycan, regulates collagen fibrillogenesis during development, and by directly blocking the bioactivity of transforming growth factor-β1 (TGFβ1), it exerts a protective effect against fibrosis. However, no in vivo investigations on the role of decorin in liver have been performed before. In this study we used decorin-null (Dcn-/-) mice to establish the role of decorin in experimental liver fibrosis and repair. Not only the extent of experimentally induced liver fibrosis was more severe in Dcn-/- animals, but also the healing process was significantly delayed vis-à-vis wild-type mice. Collagen I, III, and IV mRNA levels in Dcn-/- livers were higher than those of wild-type livers only in the first 2 months, but no difference was observed after 4 months of fibrosis induction, suggesting that the elevation of these proteins reflects a specific impairment of their degradation. Gelatinase assays confirmed this hypothesis as we found decreased MMP-2 and MMP-9 activity and higher expression of TIMP-1 and PAI-1 mRNA in Dcn-/- livers. In contrast, at the end of the recovery phase increased production rather than impaired degradation was found to be responsible for the excessive connective tissue deposition in livers of Dcn-/- mice. Higher expression of TGFβ1-inducible early responsive gene in decorin-null livers indicated enhanced bioactivity of TGFβ1 known to upregulate TIMP-1 and PAI-1 as well. Moreover, two main axes of TGFβ1-evoked signaling pathways were affected by decorin deficiency, namely the Erk1/2 and Smad3 were activated in Dcn-/- samples, whereas no significant difference in phospho-Smad2 was observed between mice with different genotypes. Collectively, our results indicate that the lack of decorin favors the development of hepatic fibrosis and attenuates its subsequent healing process at least in part by affecting the bioactivity of TGFβ1.
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Affiliation(s)
- Kornélia Baghy
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Katalin Dezső
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Viktória László
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Alexandra Fullár
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Péterfia
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Sándor Paku
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Péter Nagy
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Zsuzsa Schaff
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Renato V Iozzo
- Department of Pathology, Anatomy, and Cell Biology, and the Cancer Cell Biology and Signaling Program, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Ilona Kovalszky
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary,Corresponding author. 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Ulloi ut 26., Budapest, Hungary 1085., Tel.: +36-1-459-1500, Ext. 54449, Fax.: +36-1-317-1074, (I. Kovalszky)
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22
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Németh A, Conesa A, Santoyo-Lopez J, Medina I, Montaner D, Péterfia B, Solovei I, Cremer T, Dopazo J, Längst G. Initial genomics of the human nucleolus. PLoS Genet 2010; 6:e1000889. [PMID: 20361057 PMCID: PMC2845662 DOI: 10.1371/journal.pgen.1000889] [Citation(s) in RCA: 293] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 03/01/2010] [Indexed: 12/28/2022] Open
Abstract
We report for the first time the genomics of a nuclear compartment of the eukaryotic cell. 454 sequencing and microarray analysis revealed the pattern of nucleolus-associated chromatin domains (NADs) in the linear human genome and identified different gene families and certain satellite repeats as the major building blocks of NADs, which constitute about 4% of the genome. Bioinformatic evaluation showed that NAD–localized genes take part in specific biological processes, like the response to other organisms, odor perception, and tissue development. 3D FISH and immunofluorescence experiments illustrated the spatial distribution of NAD–specific chromatin within interphase nuclei and its alteration upon transcriptional changes. Altogether, our findings describe the nature of DNA sequences associated with the human nucleolus and provide insights into the function of the nucleolus in genome organization and establishment of nuclear architecture. It is becoming increasingly clear that the nuclear organization and location of genes in metazoan organisms is not random. Functionally related genes are often found next to each other in the linear genome, and distant DNA elements or DNA regions residing on different chromosomes may reside in specific nuclear compartments. The largest nuclear compartment is the nucleolus with its shell of perinucleolar DNA. The nature of the nucleolus-associated DNA, the targeting mechanism, and the cellular function of this subset of genomic DNA are not known. In the present study we report for the first time the high-resolution analysis of a nuclear compartment by sequencing, microarray analysis, and single-cell analysis. We have characterized the nucleolus-associated DNA on sequence level and by 3D microscopy and have determined common elements and the molecular function of this compartment.
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Affiliation(s)
- Attila Németh
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Ana Conesa
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Javier Santoyo-Lopez
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Ignacio Medina
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - David Montaner
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Bálint Péterfia
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
| | - Irina Solovei
- Department of Biology II, Ludwig-Maximilians University of Munich, Planegg-Martinsried, Germany
| | - Thomas Cremer
- Department of Biology II, Ludwig-Maximilians University of Munich, Planegg-Martinsried, Germany
| | - Joaquin Dopazo
- Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Gernot Längst
- Department of Biochemistry III, University of Regensburg, Regensburg, Germany
- * E-mail:
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Zong F, Fthenou E, Castro J, Péterfia B, Kovalszky I, Szilák L, Tzanakakis G, Dobra K. Effect of syndecan-1 overexpression on mesenchymal tumour cell proliferation with focus on different functional domains. Cell Prolif 2009; 43:29-40. [PMID: 19840029 DOI: 10.1111/j.1365-2184.2009.00651.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVES Syndecan-1 is a transmembrane proteoglycan involved in various biological processes. Its extracellular, transmembrane and cytoplasmic domains may all participate in signal transduction. The aim of this study was to investigate the biological roles of these domains of syndecan-1. MATERIALS AND METHODS We transfected cells of two mesenchymal tumour cell lines with a full-length syndecan-1 construct and three truncated variants, namely 78 construct lacking the EC domain with exception of DRKE sequence; 77 construct lacking extracellular the whole domain and RMKKK corresponding to a short cytoplasmic motif. Subcellular distribution was revealed using confocal laser microscopy. Overexpression of the constructs was verified using real-time RT-PCR and by FACS analysis and effects of syndecan-1 on cell behaviour were explored. Cell cycle analysis allowed for dissection of mechanisms regulating cell proliferation. RESULTS Overexpression of syndecan-1 influenced expression profile of the other syndecan members, and decreased tumour cell proliferation significantly by two mechanisms, as follows: increased length of G0/G1 phase was the most evident change in RMKKK and 77 transfectants, whereas prolonged S phase was more obvious in full-length transfectants. Overexpression of syndecan-1 changed the tumour cell morphology in an epithelioid direction. CONCLUSIONS Both full-length and truncated syndecan-1 inhibited proliferation of the mesenchymal tumour cells, providing new insights into the importance for cancer growth of different functional domains of this proteoglycan.
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Affiliation(s)
- F Zong
- Department of Laboratory Medicine, Division of Pathology, Karolinska Institutet, Stockholm, Sweden.
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24
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Péterfia B, Hollósi P, Szilák L, Timár F, Paku S, Jeney A, Kovalszky I. [Role of syndecan-1 proteoglycan in the invasiveness of HT-1080 fibrosarcoma]. Magy Onkol 2006; 50:115-120. [PMID: 16888674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2006] [Accepted: 06/07/2006] [Indexed: 05/25/2023]
Abstract
Syndecan-1 is a transmembrane heparan sulfate proteoglycan which plays pivotal role in cell-cell and cell-extracellular matrix interactions. However, its implication in the establishment of malignant phenotype is still controversial. Its expression indicates differentiated phenotype in certain tumors, while it confers invasive nature for others. For the better understanding of the role of syndecan-1 in cancer we transfected HT-1080 fibrosarcoma cell line with the full and a truncated construct of syndecan-1 and established stable cell lines with them. We studied the in vitro and in vivo growth capacity and metastatic potential of the transfectants in comparison with the cell line bearing only the EGFP expression vector. Our results showed that the growth rate of syndecan transfectants increased and they developed more lung metastases than the control cells. As local growth of the full transfectant was faster than that of the 78sig we presume that the full protein and maybe the shedding is needed for the local development of the tumor, but the intracellular and transmembrane domain is sufficient to promote metastasis formation.
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Affiliation(s)
- Bálint Péterfia
- I. sz. Patológiai és Kísérleti Rákkutató Intézet, Semmelweis Egyetem, Budapest, Hungary
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