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Notomi R, Sasaki S, Taniguchi Y. Novel strategy for activating gene expression through triplex DNA formation targeting epigenetically suppressed genes. RSC Chem Biol 2024; 5:884-890. [PMID: 39211471 PMCID: PMC11353075 DOI: 10.1039/d4cb00134f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024] Open
Abstract
Triplex DNA formation is a useful genomic targeting tool that is expected to have a wide range of applications, including the antigene method; however, there are fundamental limitations in its forming sequence. We recently extended the triplex DNA-forming sequence to methylated DNA sequences containing 5mCG base pairs by developing guanidino-dN, which is capable of recognizing a 5mCG base pair with high affinity. We herein investigated the effect of triplex DNA formation using TFOs with guanidino-dN on methylated DNA sequences at the promoter of the RASSF1A gene, whose expression is epigenetically suppressed by DNA methylation in MCF-7 cells, on gene expression. Interestingly, triplex DNA formation increased the expression of the RASSF1A gene at the transcript and protein levels. Furthermore, RASSF1A-activated MCF-7 cells exhibited cell growth suppressing activity. Changes in the expression of various genes associated with the promotion of apoptosis and breast cancer survival accompanied the activation of RASSF1A in cells exhibited antiproliferative activity. These results suggest the potential of increases in gene expression through triplex DNA formation as a new genomic targeting tool.
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Affiliation(s)
- Ryotaro Notomi
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
| | - Shigeki Sasaki
- Graduate School of Pharmaceutical Sciences, Nagasaki International University 22825-7 Huis Ten Bosch Machi Sasebo city Nagasaki 859-3298 Japan
| | - Yosuke Taniguchi
- Faculty of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University 1-1-1 Tsushima-naka Kita-ku Okayama 700-8530 Japan
- Graduate School of Pharmaceutical Sciences, Kyushu University 3-1-1 Maidashi Higashi-ku Fukuoka 812-8582 Japan
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Salla M, Guo J, Joshi H, Gordon M, Dooky H, Lai J, Capicio S, Armstrong H, Valcheva R, Dyck JRB, Thiesen A, Wine E, Dieleman LA, Baksh S. Novel Biomarkers for Inflammatory Bowel Disease and Colorectal Cancer: An Interplay between Metabolic Dysregulation and Excessive Inflammation. Int J Mol Sci 2023; 24:ijms24065967. [PMID: 36983040 PMCID: PMC10055751 DOI: 10.3390/ijms24065967] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Persistent inflammation can trigger altered epigenetic, inflammatory, and bioenergetic states. Inflammatory bowel disease (IBD) is an idiopathic disease characterized by chronic inflammation of the gastrointestinal tract, with evidence of subsequent metabolic syndrome disorder. Studies have demonstrated that as many as 42% of patients with ulcerative colitis (UC) who are found to have high-grade dysplasia, either already had colorectal cancer (CRC) or develop it within a short time. The presence of low-grade dysplasia is also predictive of CRC. Many signaling pathways are shared among IBD and CRC, including cell survival, cell proliferation, angiogenesis, and inflammatory signaling pathways. Current IBD therapeutics target a small subset of molecular drivers of IBD, with many focused on the inflammatory aspect of the pathways. Thus, there is a great need to identify biomarkers of both IBD and CRC, that can be predictive of therapeutic efficacy, disease severity, and predisposition to CRC. In this study, we explored the changes in biomarkers specific for inflammatory, metabolic, and proliferative pathways, to help determine the relevance to both IBD and CRC. Our analysis demonstrated, for the first time in IBD, the loss of the tumor suppressor protein Ras associated family protein 1A (RASSF1A), via epigenetic changes, the hyperactivation of the obligate kinase of the NOD2 pathogen recognition receptor (receptor interacting protein kinase 2 [RIPK2]), the loss of activation of the metabolic kinase, AMP activated protein kinase (AMPKα1), and, lastly, the activation of the transcription factor and kinase Yes associated protein (YAP) kinase, that is involved in proliferation of cells. The expression and activation status of these four elements are mirrored in IBD, CRC, and IBD-CRC patients and, importantly, in matched blood and biopsy samples. The latter would suggest that biomarker analysis can be performed non-invasively, to understand IBD and CRC, without the need for invasive and costly endoscopic analysis. This study, for the first time, illustrates the need to understand IBD or CRC beyond an inflammatory perspective and the value of therapeutics directed to reset altered proliferative and metabolic states within the colon. The use of such therapeutics may truly drive patients into remission.
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Mashayekhi M, Asadi M, Hashemzadeh S, Vahedi A, Shanehbandi D, Al-Omar AF, Akbari M, Raeisi M. Promoter methylation levels of RASSF1 and ATIC genes are associated with lung cancer in Iranian patients. Horm Mol Biol Clin Investig 2023:hmbci-2022-0007. [PMID: 36584330 DOI: 10.1515/hmbci-2022-0007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 12/11/2022] [Indexed: 12/31/2022]
Abstract
OBJECTIVES Epigenetic alterations like methylation of tumor suppressor genes or oncogenes, in respiratory epithelium have been associated with lung cancer. Hypermethylation of genes promoter is an epigenetic event, and is responsible to tumor suppressor genes inactivation as well as oncogenes activation. This study aimed to assess the role of methylation status in promoter of RASSF1 and ATIC genes their potential implication in the pathogenesis of lung tumor in Iranian patients. METHODS In this study, we collected 100 tissue samples (50 lung cancer tissues and 50 adjacent non-cancerous lung tissues) from Iranian lung cancer patients. The genomic DNA was extracted, and methylation status of both RASSF1 and ATIC genes was investigated by methylation-sensitive high-resolution melting (MS-HRM) assay technique and Real-Time PCR. Cancer Genome Atlas (TCGA) dataset was also analyzed for further validation of the gene's methylation. RESULTS Methylation of RASSF1 gene promoter was significantly higher in lung tumor tissues. However, promoter methylation levels of ATIC gene was significantly lower in lung tumor tissues. These results were additionally confirmed by TCGA analysis. Promoter methylation of both RASSF1 and ATIC genes was significantly associated with lymph node metastasis, and clinical stage of lung cancer. The receiver operating characteristic (ROC) curve analysis indicated a high accuracy of promoter methylation in these genes as a diagnostic biomarker for lung cancer. CONCLUSIONS Methylation levels of both RASSF1 and ATIC genes promoters were associated with lung cancer pathogenesis in Iranian population, and may be a suitable biomarker for diagnosis and prognosis of lung cancer in early stage of tumorigenesis.
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Affiliation(s)
- Mahsa Mashayekhi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Milad Asadi
- Department of Basic Oncology, Health Institute of Ege University, Izmir, Türkiye
| | - Shahriar Hashemzadeh
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Amir Vahedi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Dariush Shanehbandi
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ahmad Faris Al-Omar
- Department of Basic Oncology, Health Institute of Ege University, Izmir, Türkiye
| | - Morteza Akbari
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mortaza Raeisi
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Tognoli ML, Vlahov N, Steenbeek S, Grawenda AM, Eyres M, Cano‐Rodriguez D, Scrace S, Kartsonaki C, von Kriegsheim A, Willms E, Wood MJ, Rots MG, van Rheenen J, O'Neill E, Pankova D. RASSF1C oncogene elicits amoeboid invasion, cancer stemness, and extracellular vesicle release via a SRC/Rho axis. EMBO J 2021; 40:e107680. [PMID: 34532864 PMCID: PMC8521318 DOI: 10.15252/embj.2021107680] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 07/22/2021] [Accepted: 07/27/2021] [Indexed: 12/20/2022] Open
Abstract
Cell plasticity is a crucial hallmark leading to cancer metastasis. Upregulation of Rho/ROCK pathway drives actomyosin contractility, protrusive forces, and contributes to the occurrence of highly invasive amoeboid cells in tumors. Cancer stem cells are similarly associated with metastasis, but how these populations arise in tumors is not fully understood. Here, we show that the novel oncogene RASSF1C drives mesenchymal-to-amoeboid transition and stem cell attributes in breast cancer cells. Mechanistically, RASSF1C activates Rho/ROCK via SRC-mediated RhoGDI inhibition, resulting in generation of actomyosin contractility. Moreover, we demonstrate that RASSF1C-induced amoeboid cells display increased expression of cancer stem-like markers such as CD133, ALDH1, and Nanog, and are accompanied by higher invasive potential in vitro and in vivo. Further, RASSF1C-induced amoeboid cells employ extracellular vesicles to transfer the invasive phenotype to target cells and tissue. Importantly, the underlying RASSF1C-driven biological processes concur to explain clinical data: namely, methylation of the RASSF1C promoter correlates with better survival in early-stage breast cancer patients. Therefore, we propose the use of RASSF1 gene promoter methylation status as a biomarker for patient stratification.
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Affiliation(s)
| | | | - Sander Steenbeek
- Molecular PathologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | | | | | - David Cano‐Rodriguez
- University of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Simon Scrace
- Department of OncologyUniversity of OxfordOxfordUK
| | | | - Alex von Kriegsheim
- Cancer Research UK Edinburgh CentreMRC Institute of Genetics & Molecular MedicineThe University of EdinburghWestern General HospitalEdinburghUK
| | - Eduard Willms
- Department of Physiology, Anatomy and GeneticsUniversity of OxfordOxfordUK
- La Trobe Institute for Molecular ScienceLa Trobe UniversityMelbourneVic.Australia
| | | | - Marianne G Rots
- University of GroningenUniversity Medical Center GroningenGroningenThe Netherlands
| | - Jacco van Rheenen
- Molecular PathologyOncode InstituteThe Netherlands Cancer InstituteAmsterdamThe Netherlands
| | - Eric O'Neill
- Department of OncologyUniversity of OxfordOxfordUK
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Hofmann SR, Girschick L, Stein R, Schulze F. Immune modulating effects of receptor interacting protein 2 (RIP2) in autoinflammation and immunity. Clin Immunol 2020; 223:108648. [PMID: 33310070 DOI: 10.1016/j.clim.2020.108648] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 09/29/2020] [Accepted: 12/08/2020] [Indexed: 02/08/2023]
Abstract
Receptor-interacting protein 2 (RIP2) is a kinase that is involved in downstream signaling of nuclear oligomerization domain (NOD)-like receptors NOD1 and 2 sensing bacterial peptidoglycans. RIP2-deficiency or targeting of RIP2 by pharmaceutical inhibitors partially ameliorates inflammatory diseases by reducing pro-inflammatory signaling in response to peptidoglycans. However, RIP2 is widely expressed and interacts with several other proteins suggesting additional functions outside the NOD-signaling pathway. In this review, we discuss the immunological functions of RIP2 and its possible role in autoinflammation and immunity.
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Affiliation(s)
- Sigrun Ruth Hofmann
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany.
| | - Leonie Girschick
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Robert Stein
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Felix Schulze
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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Li N, Zeng Y, Huang J. Signaling pathways and clinical application of RASSF1A and SHOX2 in lung cancer. J Cancer Res Clin Oncol 2020; 146:1379-1393. [PMID: 32266538 DOI: 10.1007/s00432-020-03188-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 03/17/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND An increasing number of studies have focused on the early diagnostic value of the methylation of RASSF1A and SHOX2 in lung cancer. However, the intricate cellular events related to RASSF1A and SHOX2 in lung cancer are still a mystery. For researchers and clinicians aiming to more profoundly understand the diagnostic value of methylated RASSF1A and SHOX2 in lung cancer, this review will provide deeper insights into the molecular events of RASSF1A and SHOX2 in lung cancer. METHODOLOGY We searched for relevant publications in the PubMed and Google Scholar databases using the keywords "RASSF1A", "SHOX2" and "lung cancer" etc. First, we reviewed the RASSF1A and SHOX2 genes, from their family structures to the functions of their basic structural domains. Then we mainly focused on the roles of RASSF1A and SHOX2 in lung cancer, especially on their molecular events in recent decades. Finally, we compared the value of measuring RASSF1A and SHOX2 gene methylation with that of the common methods for the diagnosis of lung cancer patients. RESULTS The RASSF1A and SHOX2 genes were confirmed to be regulators or effectors of multiple cancer signaling pathways, driving tumorigenesis and lung cancer progression. The detection of RASSF1A and SHOX2 gene methylation has higher sensitivity and specificity than other commonly used methods for diagnosing lung cancer, especially in the early stage. CONCLUSIONS The RASSF1A and SHOX2 genes are critical for the processes of tumorigenesis, development, metastasis, drug resistance, and recurrence in lung cancer. The combined detection of RASSF1A and SHOX2 gene methylation was identified as an excellent method for the screening and surveillance of lung cancer that exhibits high sensitivity and specificity.
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Affiliation(s)
- Nanhong Li
- Department of Pathology, Guangdong Medical University, Zhanjiang, 524023, China
| | - Yu Zeng
- Department of Respiration, The Second Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524003, China
| | - Jian Huang
- Department of Pathology, Guangdong Medical University, Zhanjiang, 524023, China.
- Pathological Diagnosis and Research Center, Affiliated Hospital, Guangdong Medical University, Zhanjiang, 524001, China.
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Cojocneanu R, Braicu C, Raduly L, Jurj A, Zanoaga O, Magdo L, Irimie A, Muresan MS, Ionescu C, Grigorescu M, Berindan-Neagoe I. Plasma and Tissue Specific miRNA Expression Pattern and Functional Analysis Associated to Colorectal Cancer Patients. Cancers (Basel) 2020; 12:cancers12040843. [PMID: 32244548 PMCID: PMC7226631 DOI: 10.3390/cancers12040843] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 02/07/2023] Open
Abstract
An increasing number of studies suggest the implication of microRNAs (miRNAs) in colorectal (CRC) carcinogenesis and disease progression. Nevertheless, the basic mechanism is not yet clear. We determined plasma miRNA expression levels using Agilent microarray technology followed by overlapping with The Cancer Genome Atlas (TCGA) tissue data and a qRT-PCR validation step and analysis of the altered miRNA signatures to emphasize new mechanistic insights. For TGCA dataset, we identified 156 altered miRNAs (79 downregulated and 77 upregulated) in colorectal tissue samples versus normal tissue. The microarray experiment is based on 16 control samples, 38 CRC plasma samples from colorectal cancer patients who have not undergone chemotherapy, and 17 chemo-treated samples. In the case of the analysis of CRC cancer versus healthy control we identified 359 altered miRNAs (214 downregulated and 60 upregulated), considering as the cutoff value a fold-change of ±1.5 and p < 0.01. An additional microarray analysis was performed on plasma from untreated colorectal cancer (n = 38) and chemotherapy-treated colorectal cancer patients (n = 17), which revealed 15 downregulated miRNAs and 53 upregulated miRNAs, demonstrating that the plasma miRNA pattern is affected by chemotherapy and emphasizing important regulators of drug resistance mechanisms. For the validation of the microarray data, we selected a panel of 4 miRNAs from the common miRNA signatures for colon and rectal cancer (miR-642b-3p, miR-195-5p and miR-4741). At the tissue level, the expression levels were in agreement with those observed in colorectal plasma. miR-1228-3p, the top upregulated miRNA in CRC, was chosen to be validated on tissue and plasma samples, as it was demonstrated to be downregulated at tissue level in our patient cohort. This was confirmed by TCGA data and was one example of ta ranscript that has a different expression level between tumor tissue and plasma. Developing more efficient investigation methods will help explain the mechanisms responsible for miRNAs released in biofluids, which is the most upregulated transcript in colorectal plasma samples and which can function as a prediction tool within the oncological field.
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Affiliation(s)
- Roxana Cojocneanu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania; (R.C.); (L.R.); (A.J.); (O.Z.); (L.M.); (I.B.-N.)
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania; (R.C.); (L.R.); (A.J.); (O.Z.); (L.M.); (I.B.-N.)
- Correspondence: (C.B.); (C.I.)
| | - Lajos Raduly
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania; (R.C.); (L.R.); (A.J.); (O.Z.); (L.M.); (I.B.-N.)
| | - Ancuta Jurj
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania; (R.C.); (L.R.); (A.J.); (O.Z.); (L.M.); (I.B.-N.)
| | - Oana Zanoaga
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania; (R.C.); (L.R.); (A.J.); (O.Z.); (L.M.); (I.B.-N.)
| | - Lorand Magdo
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania; (R.C.); (L.R.); (A.J.); (O.Z.); (L.M.); (I.B.-N.)
| | - Alexandru Irimie
- Department of Surgery, The Oncology Institute “Prof. Dr. Ion Chiricuta”, 400015 Cluj-Napoca, Romania;
- Department of Surgical Oncology and Gynecological Oncology, University of Medicine and Pharmacy Iuliu Hatieganu, 400015 Cluj-Napoca, Romania
| | - Mihai-Stefan Muresan
- 5th Surgical Department, Municipal Hospital, 400139 Cluj-Napoca, Romania;
- Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania
| | - Calin Ionescu
- 5th Surgical Department, Municipal Hospital, 400139 Cluj-Napoca, Romania;
- Department of Surgery, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania
- Correspondence: (C.B.); (C.I.)
| | - Mircea Grigorescu
- Gastroenterology and Hepatology Department, 3rd Medical Clinic, Iuliu Hatieganu University of Medicine and Pharmacy, 400162 Cluj-Napoca, Romania;
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, 23 Marinescu Street, 400015 Cluj-Napoca, Romania; (R.C.); (L.R.); (A.J.); (O.Z.); (L.M.); (I.B.-N.)
- MEDFUTURE-Research Center for Advanced Medicine, University of Medicine and Pharmacy Iuliu Hatieganu, 23 Marinescu Street, 400015 Cluj-Napoca, Romania
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuta”, Republicii 34 Street, 400015 Cluj-Napoca, Romania
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Methylation Dynamics of RASSF1A and Its Impact on Cancer. Cancers (Basel) 2019; 11:cancers11070959. [PMID: 31323949 PMCID: PMC6678546 DOI: 10.3390/cancers11070959] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/03/2019] [Accepted: 07/08/2019] [Indexed: 01/15/2023] Open
Abstract
5-methyl cytosine (5mC) is a key epigenetic mark entwined with gene expression and the specification of cellular phenotypes. Its distribution around gene promoters sets a barrier for transcriptional enhancers or inhibitor proteins binding to their target sequences. As a result, an additional level of regulation is added to the signals that organize the access to the chromatin and its structural components. The tumor suppressor gene RASSF1A is a microtubule-associated and multitasking scaffold protein communicating with the RAS pathway, estrogen receptor signaling, and Hippo pathway. RASSF1A action stimulates mitotic arrest, DNA repair and apoptosis, and controls the cell cycle and cell migration. De novo methylation of the RASSF1A promoter has received much attention due to its increased frequency in most cancer types. RASSF1A methylation is preceded by histones modifications and could represent an early molecular event in cell transformation. Accordingly, RASSF1A methylation is proposed as an epigenetic candidate marker in many cancer types, even though an inverse correlation of methylation and expression remains to be fully ascertained. Some findings indicate that the epigenetic abrogation of RASSF1A can promote the alternative expression of the putative oncogenic isoform RASSF1C. Understanding the complexity and significance of RASSF1A methylation is instrumental for a more accurate determination of its biological and clinical role. The review covers the molecular events implicated in RASSF1A methylation and gene silencing and provides a deeper view into the significance of the RASSF1A methylation patterns in a number of gastrointestinal cancer types.
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Zare A, Petrova A, Agoumi M, Amstrong H, Bigras G, Tonkin K, Wine E, Baksh S. RIPK2: New Elements in Modulating Inflammatory Breast Cancer Pathogenesis. Cancers (Basel) 2018; 10:cancers10060184. [PMID: 29874851 PMCID: PMC6025367 DOI: 10.3390/cancers10060184] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/29/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022] Open
Abstract
Inflammatory breast cancer (IBC) is a rare and aggressive form of breast cancer that is associated with significantly high mortality. In spite of advances in IBC diagnoses, the prognosis is still poor compared to non-IBC. Due to the aggressive nature of the disease, we hypothesize that elevated levels of inflammatory mediators may drive tumorigenesis and metastasis in IBC patients. Utilizing IBC cell models and patient tumor samples, we can detect elevated NF-κB activity and hyperactivation of non-canonical drivers of NF-κB (nuclear factor kappaB)-directed inflammation such as tyrosine phosphorylated receptor-interacting protein kinase 2 (pY RIPK2), when compared to non-IBC cells or patients. Interestingly, elevated RIPK2 activity levels were present in a majority of pre-chemotherapy samples from IBC patients at the time of diagnosis to suggest that patients at diagnosis had molecular activation of NF-κB via RIPK2, a phenomenon we define as “molecular inflammation”. Surprisingly, chemotherapy did cause a significant increase in RIPK2 activity and thus molecular inflammation suggesting that chemotherapy does not resolve the molecular activation of NF-κB via RIPK2. This would impact on the metastatic potential of IBC cells. Indeed, we can demonstrate that RIPK2 activity correlated with advanced tumor, metastasis, and group stage as well as body mass index (BMI) to indicate that RIPK2 might be a useful prognostic marker for IBC and advanced stage breast cancer.
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Affiliation(s)
- Alaa Zare
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2E1, Canada.
| | - Alexandra Petrova
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2E1, Canada.
| | - Mehdi Agoumi
- Anatomic Pathologist at DynalifeDx, Diagnostic Laboratory Services; Department of Laboratory Medicine and Pathology, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2R3, Canada.
| | - Heather Amstrong
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2E1, Canada.
| | - Gilbert Bigras
- Cross Cancer Institute Department of Laboratory Medicine and Pathology, University of Alberta, 11560 University Ave, Edmonton, AB T6G 1Z2, Canada.
| | - Katia Tonkin
- Division of Medical Oncology, Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R7, Canada.
| | - Eytan Wine
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2E1, Canada.
| | - Shairaz Baksh
- Department of Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2E1, Canada.
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2E1, Canada.
- Division of Medical Oncology, Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2R7, Canada.
- Division of Experimental Oncology, Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 113 Street 87 Avenue, Edmonton, AB T6G 2E1, Canada.
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB T6G 2R7, Canada.
- Women and Children's Health Research Institute, Edmonton Clinic Health Academy (ECHA), University of Alberta, 4-081 11405 87 Avenue NW Edmonton, AB T6G 1C9, Canada.
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Voigt A, Nowick K, Almaas E. A composite network of conserved and tissue specific gene interactions reveals possible genetic interactions in glioma. PLoS Comput Biol 2017; 13:e1005739. [PMID: 28957313 PMCID: PMC5634634 DOI: 10.1371/journal.pcbi.1005739] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 10/10/2017] [Accepted: 08/24/2017] [Indexed: 02/08/2023] Open
Abstract
Differential co-expression network analyses have recently become an important step in the investigation of cellular differentiation and dysfunctional gene-regulation in cell and tissue disease-states. The resulting networks have been analyzed to identify and understand pathways associated with disorders, or to infer molecular interactions. However, existing methods for differential co-expression network analysis are unable to distinguish between various forms of differential co-expression. To close this gap, here we define the three different kinds (conserved, specific, and differentiated) of differential co-expression and present a systematic framework, CSD, for differential co-expression network analysis that incorporates these interactions on an equal footing. In addition, our method includes a subsampling strategy to estimate the variance of co-expressions. Our framework is applicable to a wide variety of cases, such as the study of differential co-expression networks between healthy and disease states, before and after treatments, or between species. Applying the CSD approach to a published gene-expression data set of cerebral cortex and basal ganglia samples from healthy individuals, we find that the resulting CSD network is enriched in genes associated with cognitive function, signaling pathways involving compounds with well-known roles in the central nervous system, as well as certain neurological diseases. From the CSD analysis, we identify a set of prominent hubs of differential co-expression, whose neighborhood contains a substantial number of genes associated with glioblastoma. The resulting gene-sets identified by our CSD analysis also contain many genes that so far have not been recognized as having a role in glioblastoma, but are good candidates for further studies. CSD may thus aid in hypothesis-generation for functional disease-associations.
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Affiliation(s)
- André Voigt
- Network Systems Biology Group, Department of Biotechnology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
| | - Katja Nowick
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany
- Bioinformatics, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
- Human Biology, Institute for Biology, Free University Berlin, Berlin, Germany
| | - Eivind Almaas
- Network Systems Biology Group, Department of Biotechnology, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and General Practice, NTNU - Norwegian University of Science and Technology, Trondheim, Norway
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Barnoud T, Schmidt ML, Donninger H, Clark GJ. The role of the NORE1A tumor suppressor in Oncogene-Induced Senescence. Cancer Lett 2017; 400:30-36. [PMID: 28455242 PMCID: PMC5502528 DOI: 10.1016/j.canlet.2017.04.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/18/2017] [Accepted: 04/19/2017] [Indexed: 12/14/2022]
Abstract
The Ras genes are the most frequently mutated oncogenes in human cancer. However, Ras biology is quite complex. While Ras promotes tumorigenesis by regulating numerous growth promoting pathways, activated Ras can paradoxically also lead to cell cycle arrest, death, and Oncogene-Induced Senescence (OIS). OIS is thought to be a critical pathway that serves to protect cells against aberrant Ras signaling. Multiple reports have highlighted the importance of the p53 and Rb tumor suppressors in Ras mediated OIS. However, until recently, the molecular mechanisms connecting Ras to these proteins remained unknown. The RASSF family of tumor suppressors has recently been identified as direct effectors of Ras. One of these members, NORE1A (RASSF5), may be the missing link between Ras-induced senescence and the regulation of p53 and Rb. This occurs both quantitatively, by promoting protein stability, as well as qualitatively via promoting critical pro-senescent post-translational modifications. Here we review the mechanisms by which NORE1A can activate OIS as a barrier against Ras-mediated transformation, and how this could lead to improved therapeutic strategies against cancers having lost NORE1A expression.
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Affiliation(s)
- Thibaut Barnoud
- Program in Molecular and Cellular Oncogenesis, The Wistar Institute, Philadelphia PA 19104, USA
| | - M Lee Schmidt
- Department of Pharmacology and Toxicology, University of Louisville, KY 40202, USA
| | | | - Geoffrey J Clark
- Department of Pharmacology and Toxicology, University of Louisville, KY 40202, USA.
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Motevaseli E, Dianatpour A, Ghafouri-Fard S. The Role of Probiotics in Cancer Treatment: Emphasis on their In Vivo and In Vitro Anti-metastatic Effects. INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2017; 6:66-76. [PMID: 28890883 PMCID: PMC5581548 DOI: 10.22088/acadpub.bums.6.2.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/21/2017] [Indexed: 12/12/2022]
Abstract
Probiotics are defined as live bacteria and yeasts that exert beneficial effects for health. Among their various effects, anti-cancer properties have been highlighted in recent years. Such effects include suppression of the growth of microbiota implicated in the production of mutagens and carcinogens, alteration in carcinogen metabolism and protection of DNA from oxidative damage as well as regulation of immune system. We performed a computerized search of the MEDLINE/PUBMED databases with key words: cancer, probiotics, lactobacilli, metastasis and invasion. Cell line studies as well as animal models and human studies have shown the therapeutic effects of probiotics in reduction of invasion and metastasis in cancer cells. These results support the beneficial effects of probiotics both in vitro and in vivo. However, pre-clinical or clinical studies are not enough to decide about their application.
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Affiliation(s)
- Elahe Motevaseli
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ali Dianatpour
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Analysis of the breast cancer methylome using formalin-fixed paraffin-embedded tumour. Breast Cancer Res Treat 2016; 160:173-180. [PMID: 27604360 DOI: 10.1007/s10549-016-3971-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/01/2016] [Indexed: 12/31/2022]
Abstract
PURPOSE Aberrant DNA methylation occurs frequently in breast carcinogenesis. Tools for translational epigenetic studies of breast cancer involving formalin-fixed paraffin-embedded (FFPE) human tissues have now been developed. Few studies have measured genome-wide methylation in DNA derived from paraffin-embedded tumour tissues and compared the DNA methylation in corresponding adjacent non-tumour ductal epithelium (ADJNT). These studies are technically challenging due to the spectrum of breast cancer pathologies, the variable suitability of DNA extracted from FFPE material and the difficulties in identifying ADJNT. We assessed the suitability of FFPE breast cancer material for genome-wide DNA methylation assessment of tumour and ADJNT. METHODS Twenty-one archival breast tumour tissues with paired ADJNT obtained from separate blocks and at least 2 cm from the tumour were sourced from The Melbourne Collaborative Cohort Study (MCCS). DNA was prepared from macrodissected tissue samples and assessed for genome-wide methylation using the Infinium HumanMethylation450 Beadchip (HM450K) array. RESULTS The 1000 most differentially methylated probes between tumour and ADJNT in this FFPE-derived dataset differentiated tumour and ADJNT in The Cancer Genome Atlas Network data (TCGA; derived from high molecular weight DNA using the same HM450K array). CONCLUSIONS Large-scale studies of genome-wide DNA methylation using FFPE breast cancer specimens offer the opportunity to further refine the pathological classification of tumours, to include subtypes that are underrepresented in the TCGA data and provide the capacity to further explore intra-tumoural heterogeneity.
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