51
|
Gowthami J, Gururaj N, Mahalakshmi V, Sathya R, Sabarinath TR, Doss DM. Genetic predisposition and prediction protocol for epithelial neoplasms in disease-free individuals: A systematic review. J Oral Maxillofac Pathol 2020; 24:293-307. [PMID: 33456239 PMCID: PMC7802851 DOI: 10.4103/jomfp.jomfp_348_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 03/23/2020] [Accepted: 04/24/2020] [Indexed: 01/13/2023] Open
Abstract
Background Epithelial neoplasm is an important global health-care problem, with high morbidity and mortality rates. Early diagnosis and appropriate treatment are essential for increased life survival. Prediction of occurrence of malignancy in a disease-free individual by any means will be a great breakthrough for healthy living. Aims and Objectives The aims and objectives were to predict the genetic predisposition and propose a prediction protocol for epithelial malignancy of various systems in our body, in a disease-free individual. Methods We have searched databases both manually and electronically, published in English language in Cochrane group, Google search, MEDLINE and PubMed from 2000 to 2019. We have included all the published, peer-reviewed, narrative reviews; randomized controlled trials; case-control studies; and cohort studies and excluded the abstract-only articles and duplicates. Specific words such as "etiological factors," "pathology and mutations," "signs and symptoms," "genetics and IHC marker," and "treatment outcome" were used for the search. A total of 1032 citations were taken, and only 141 citations met the inclusion criteria and were analyzed. Results After analyzing various articles, the etiological factors, clinical signs and symptoms, genes and the pathology involved and the commonly used blood and tissue markers were analyzed. A basic investigation strategy using immunohistochemistry markers was established. Conclusion The set of proposed biomarkers should be studied in future to predict genetic predisposition in disease-free individuals.
Collapse
Affiliation(s)
- J Gowthami
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - N Gururaj
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - V Mahalakshmi
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - R Sathya
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - T R Sabarinath
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| | - Daffney Mano Doss
- Department of Oral and Maxillofacial Pathology and Microbiology, CSI College of Dental Sciences and Research, Madurai, Tamil Nadu, India
| |
Collapse
|
52
|
Ghasemi T, Khalaj-Kondori M, Hosseinpour Feizi MA, Asadi P. lncRNA-miRNA-mRNA interaction network for colorectal cancer; An in silico analysis. Comput Biol Chem 2020; 89:107370. [PMID: 32932199 DOI: 10.1016/j.compbiolchem.2020.107370] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 05/26/2020] [Accepted: 09/01/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most frequent and diagnosed diseases. Accumulating evidences showed that mRNAs and noncoding RNAs play important regulatory roles in tumorigenesis. Identification and determining the relationship between them can help diagnosis and treatment of cancer. METHODS Here we analyzed three microarray datasets; GSE110715, GSE32323 and GSE21510, to identify differentially expressed lncRNAs and mRNAs in CRC. The adjusted p-value ≤0.05 was considered statistically significant. Gene set enrichment analysis was carried out using DAVID tool. The miRCancer database was searched to obtain differentially expressed miRNAs in colorectal cancer, and the miRDB database was used to attain the targets of the obtained miRNAs. To predict the lncRNA-miRNA interactions we used DIANA-LncBase v2 and RegRNA 2.0. Finally the lncRNA-miRNA-mRNA-signaling pathway network was constructed using Cytoscape v3.1. RESULTS By analyzing the three datasets, a total of 21 mRNAs (15 up- and 6 down-regulated) and 24 lncRNAs (18 up- and 6 down-regulated) were identified as common differentially expressed genes between CRC tumor and marginal tissues. Nevertheless, the constructed lncRNA-miRNA-mRNA-signaling pathway network revealed a convergence on 6 lncRNAs (3 up- and 3 downregulated), 7 mRNAs (2 up- and 5 downregulated) and 6 miRNAs (3 up- and 3 downregulated). We found that dysregulation of lncRNAs such as PCBP1-AS1, UCA1 and SNHG16 could sequester several miRNAs such as hsa-miR-582-5p and hsa-miR-198 and promote the proliferation, invasion and drug resistance of colorectal cancer cells. CONCLUSIONS We introduced a set of lncRNAs, mRNAs and miRNAs differentially expressed in CRC which might be considered for further experimental research as potential biomarkers of CRC development.
Collapse
Affiliation(s)
- Tayyebeh Ghasemi
- Dept. of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | | | | | - Parviz Asadi
- Gastroenterology ward, Shahid Mahallati Hospital, Tabriz, Iran
| |
Collapse
|
53
|
Soleimani A, Farshchi HK, Mirzavi F, Zamani P, Ghaderi A, Amini Y, Khorrami S, Mashayekhi K, Jaafari MR. The therapeutic potential of targeting CD73 and CD73-derived adenosine in melanoma. Biochimie 2020; 176:21-30. [PMID: 32585229 DOI: 10.1016/j.biochi.2020.06.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/12/2020] [Accepted: 06/06/2020] [Indexed: 12/18/2022]
Abstract
The hypoxic environment of melanoma results in CD73 upregulation on the surface of various tumor microenvironment (TME) cells including tumor cells, stromal cells and infiltrated immune cells. Consequently, CD73 through both enzymatic and none enzymatic functions affect melanoma progression. Overaccumulation of CD73-derived adenosine through interaction with its four G coupled receptors (A1AR, A2AAR, A2BAR, and A3AR) mediate tumor growth, immune suppression, angiogenesis, and metastasis. This paper aims to comprehensively review the therapeutic potential of CD73 ectonucleotidase targeting in melanoma. To reach this goal, firstly, we summarize the structure, function, regulation, and clinical outcome of CD73 ectonucleotidase. Then, we depict the metabolism and signaling of CD73-derived adenosine along with its progressive role in development of melanoma. Furthermore, the therapeutic potentials of CD73 -adenosine axis targeting is assessed in both preclinical and clinical studies. Targeting CD73-derived adenosine via small molecule inhibitor or monoclonal antibodies studies especially in combination with immune checkpoint blockers including PD-1 and CTLA-4 have shown desirable results for management of melanoma in preclinical studies and several clinical trials have recently been started to evaluate the therapeutic potential of CD73-derived adenosine targeting in solid tumors. Indeed, targeting of CD73-derived adenosine signaling could be considered as a new therapeutic target in melanoma.
Collapse
Affiliation(s)
- Anvar Soleimani
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Helale Kaboli Farshchi
- Department of Horticulture, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Farshad Mirzavi
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Parvin Zamani
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medical Biotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Ghaderi
- Department of Addiction Studies, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Yousef Amini
- Infectious Diseases and Tropical Medicine Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Shadi Khorrami
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Kazem Mashayekhi
- Immuno-Biochemistry Lab, Immunology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mahmoud Reza Jaafari
- Nanotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Nanotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
54
|
Liu Z, Wan Y, Yang M, Qi X, Dong Z, Huang J, Xu J. Identification of methylation-driven genes related to the prognosis of papillary renal cell carcinoma: a study based on The Cancer Genome Atlas. Cancer Cell Int 2020; 20:235. [PMID: 32536823 PMCID: PMC7291558 DOI: 10.1186/s12935-020-01331-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Background Aberrant DNA methylation patterns are involved in the pathogenesis of papillary renal cell carcinoma (pRCC). This study aimed to investigate the potential of methylation-driven genes as biomarkers in determining the prognosis of pRCC by bioinformatics analysis. Methods DNA methylation and transcriptome profiling data were downloaded from The Cancer Genome Atlas database. Methylation-driven genes (MDGs) were obtained using MethylMix R package. A Cox regression model was used to screen for pRCC prognosis-related MDGs, and a linear risk model based on MDG methylation profiles was constructed. A combined methylation and gene expression survival analysis was performed to further explore the prognostic value of MDGs independently. Results A total of 31 MDGs were obtained. Univariate and multivariate Cox regression analysis identified eight genes (CASP1, CD68, HOXD3, HHLA2, HOXD9, HOXA10-AS, TMEM71, and PLA2G16), which were used to construct a predictive model associated with overall survival in pRCC patients. Combined DNA methylation and gene expression survival analysis revealed that C19orf33, GGT6, GIPC2, HHLA2, HOXD3, HSD17B14, PLA2G16, and TMEM71 were significantly associated with patients’ survival. Conclusion Through the analysis of MDGs in pRCC, this study identified potential biomarkers for precision treatment and prognosis prediction, and provided the basis for future research into the molecular mechanism of pRCC.
Collapse
Affiliation(s)
- Zeyu Liu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Yuxiang Wan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Ming Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Xuewei Qi
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Zhenzhen Dong
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Jinchang Huang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Jingnan Xu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| |
Collapse
|
55
|
Chava S, Gupta R. Identification of the Mutational Landscape of Gynecological Malignancies. J Cancer 2020; 11:4870-4883. [PMID: 32626534 PMCID: PMC7330690 DOI: 10.7150/jca.46174] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 05/30/2020] [Indexed: 12/15/2022] Open
Abstract
Background: Cancer is a complex disease that arises from the accumulation of multiple genetic and non-genetic changes. Advances in sequencing technologies have allowed unbiased and global analysis of patient-derived tumor samples and the discovery of genetic and transcriptional changes in key genes and oncogenic pathways. That in turn has facilitated a better understanding of the underlying causes of cancer initiation and progression, resulting in new therapeutic targets. Methods: In our study, we have analyzed the mutational landscape of gynecological malignancies using datasets from The Cancer Genome Atlas (TCGA). We have also analyzed Oncomine datasets to establish the impact of their alteration on disease recurrence and survival of patients. Results: In this study, we analyzed a series of different gynecological malignancies for commonly occurring genetic and non-genetic alterations. These studies show that white women have higher incidence of gynecological malignancies. Furthermore, our study identified 16 genes that are altered at a frequency >10% among all of the gynecological malignancies and tumor suppressor TP53 is the most altered gene in these malignancies (>50% of the cases). The top 16 genes fall into the categories of either tumor suppressor or oncogenes and a subset of these genes are associated with poor prognosis, some affecting recurrence and survival of ovarian cancer patients. Conclusion: In sum, our study identified 16 major genes that are broadly mutated in a large majority of gynecological malignancies and in some cases predict survival and recurrence in patients with gynecological malignancies. We predict that the functional studies will determine their relative role in the initiation and progression of gynecological malignancies and also establish if some of them represents drug targets for anti-cancer therapy.
Collapse
Affiliation(s)
| | - Romi Gupta
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| |
Collapse
|
56
|
Roperch JP, Hennion C. A novel ultra-sensitive method for the detection of FGFR3 mutations in urine of bladder cancer patients - Design of the Urodiag® PCR kit for surveillance of patients with non-muscle-invasive bladder cancer (NMIBC). BMC MEDICAL GENETICS 2020; 21:112. [PMID: 32448160 PMCID: PMC7247276 DOI: 10.1186/s12881-020-01050-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/14/2020] [Indexed: 01/15/2023]
Abstract
Background We have recently developed a highly accurate urine-based test, named Urodiag®, associating FGFR3 mutation and DNA methylation assays for recurrence surveillance in patients with low-, intermediate-, and high-risk NMIBC. Previously, the detection of four FGFR3 mutations (G372C, R248C, S249C and Y375C) required amplification steps and PCR products were analyzed by capillary electrophoresis (Allele Specific-PCR, AS-PCR), which was expensive and time-consuming. Here, we present the development a novel ultra-sensitive multiplex PCR assay as called “Mutated Allele Specific Oligonucleotide-PCR (MASO-PCR)”, generating a cost-effective, simple, fast and clinically applicable assay for the detection of FGFR3 mutations in voided urine. Methods Comparative clinical performances of MASO-PCR and AS-PCR technologies were performed from 263 urine DNA samples (87 FGFR3 mutated and 176 FGFR3 wild-type). In the development of Urodiag® PCR Kit, we studied the stability and reproducibility of each all-in-one PCR master mix (single reaction mixture including all the necessary PCR components) for MASO-PCR and QM-MSPCR (Quantitative Multiplex Methylation-Specific PCR to co-amplify SEPTIN9, HS3ST2 and SLIT2 methylated genes) assays. Results Complete concordance (100%) was observed between the MASO-PCR and AS-PCR results. Each PCR master mix displayed excellent reproducibility and stability after 12 months of storage at − 20 °C, with intra-assay standard deviations lower than 0.3 Ct and coefficient of variations (CV) lower than 1%. The limit of detection (LoD) of MASO-PCR was 5% mutant detection in a 95% of wild-type background. The limit of quantification (LoQ) of QM-MSPCR was 10 pg of bisulfite-converted DNA. Conclusions We developed and clinically validated the MASO-PCR assay, generating cost-effective, simple, fast and clinically applicable assay for the detection of FGFR3 mutations in urine. We also designed the Urodiag® PCR Kit, which includes the MASO-PCR and QM-MSPCR assays. Adapted to routine clinical laboratory (simplicity, accuracy), the kit will be a great help to urologists for recurrence surveillance in patients at low-, intermediate- and high-risk NMIBC. Reducing the number of unnecessary cystoscopies, it will have extremely beneficial effects for patients (painless) and for the healthcare systems (low cost).
Collapse
|
57
|
Ahmed AA, Adam Essa ME. Epigenetic alterations in female urogenital organs cancer: Premise, properties, and perspectives. SCIENTIFIC AFRICAN 2020. [DOI: 10.1016/j.sciaf.2020.e00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
|
58
|
Zi Z, Zhang Y, Zhang P, Ding Q, Chu M, Chen Y, Minna JD, Yu Y. A Proteomic Connectivity Map for Characterizing the Tumor Adaptive Response to Small Molecule Chemical Perturbagens. ACS Chem Biol 2020; 15:140-150. [PMID: 31846293 DOI: 10.1021/acschembio.9b00694] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A powerful means to understand the cellular function of corrupt oncogenic signaling programs requires perturbing the system and monitoring the downstream consequences. Here, using a unique pair of non-small cell lung cancer (NSCLC)/normal lung epithelial patient-derived cell lines (HCC4017/HBEC30KT), we systematically interrogated the remodeling of the NSCLC proteome upon treatment with 35 chemical perturbagens targeting a diverse array of mechanistic classes. HCC4017 and HBEC30KT cells differ significantly in their proteomic response to the same compound treatment. Using protein covariance analyses, we identified a large number of functional protein networks. For example, we found that a poorly studied protein, C5orf22, is a novel component of the WBP11/PQBP1 splicing complex. Depletion of C5orf22 leads to the aberrant splicing and expression of genes involved in cell growth and immunomodulation. In summary, we show that by systematically measuring the tumor adaptive responses at the proteomic level, an understanding could be generated that provides critical circuit-level biological insights for these pharmacologic perturbagens.
Collapse
Affiliation(s)
- Zhenzhen Zi
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Yajie Zhang
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Peng Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qing Ding
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Michael Chu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Yiwen Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, United States
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Departments of Internal Medicine and Pharmacology, Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| | - Yonghao Yu
- Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas 75390, United States
| |
Collapse
|
59
|
Finding relationships among biological entities. LOGIC AND CRITICAL THINKING IN THE BIOMEDICAL SCIENCES 2020. [PMCID: PMC7499094 DOI: 10.1016/b978-0-12-821364-3.00005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Confusion over the concepts of “relationships” and “similarities” lies at the heart of many battles over the direction and intent of research projects. Here is a short story that demonstrates the difference between the two concepts: You look up at the clouds, and you begin to see the shape of a lion. The cloud has a tail, like a lion’s tale, and a fluffy head, like a lion’s mane. With a little imagination the mouth of the lion seems to roar down from the sky. You have succeeded in finding similarities between the cloud and a lion. If you look at a cloud and you imagine a tea kettle producing a head of steam and you recognize that the physical forces that create a cloud and the physical forces that produced steam from a heated kettle are the same, then you have found a relationship. Most popular classification algorithms operate by grouping together data objects that have similar properties or values. In so doing, they may miss finding the true relationships among objects. Traditionally, relationships among data objects are discovered by an intellectual process. In this chapter, we will discuss the scientific gains that come when we classify biological entities by relationships, not by their similarities.
Collapse
|
60
|
Tu Y, Chen C, Fan G. Association between the expression of secreted phosphoprotein - related genes and prognosis of human cancer. BMC Cancer 2019; 19:1230. [PMID: 31849319 PMCID: PMC6918603 DOI: 10.1186/s12885-019-6441-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 12/08/2019] [Indexed: 12/15/2022] Open
Abstract
Background While many studies have assessed the predictive value of secreted phosphoprotein (SPP) genes in cancer, the findings have been inconsistent. To resolve these inconsistencies, we systematically analyzed the available data to determine whether SPP1 and SPP2 are prognostic markers in the context of human cancer. Methods The expression of SPP1 and SPP2 was assessed by Oncomine analysis. The PrognoScan database was used to assess the prognostic value of SPP1 and SPP2, with cBioPortal used to assess copy number variations. The STRING database was used to generate a Protein - Protein Interaction (PPI) network for SPP genes. Results SPP1 was more likely to be over-expressed in breast, bladder, colorectal, head, neck, liver, lung, and esophageal cancers. SPP2 was expressed at lower levels in colorectal cancer, leukemia, liver cancer and pancreatic cancer. In addition, SPP1 and SPP2 mutations mainly occurred in cutaneous melanoma and endometrial cancer. Conclusions Our results suggest that SPP1 and SPP2 may be effective therapeutic or diagnostic targets in certain cancers. Further research is required to confirm these results and verify the value of SPP1 and SPP2 as clinical markers of cancer prognosis.
Collapse
Affiliation(s)
- Yaqin Tu
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Cai Chen
- Department of Endocrinology, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Guorun Fan
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| |
Collapse
|
61
|
Paudel S, Mehtani D, Puri N. Mast Cells May Differentially Regulate Growth of Lymphoid Neoplasms by Opposite Modulation of Histamine Receptors. Front Oncol 2019; 9:1280. [PMID: 31824856 PMCID: PMC6881378 DOI: 10.3389/fonc.2019.01280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022] Open
Abstract
Cancer microenvironment is complex and consists of various immune cells. There is evidence for mast cell (MC) infiltration of tumors, but their role thereof is poorly understood. In this study, we explored the effects of mast cell and their mediators on the growth of hematological cancer cells. The affect is demonstrated using RBL-2H3 MCs, and YAC-1, EL4 and L1210 as hematological cancer cell lines. Direct contact with MCs or stimulation by their mediators caused growth inhibition of YAC-1 cells, growth enhancement of EL4 cells and no change in growth of L1210 cells. This effect was confirmed by cancer cell recovery, cell viability, mitochondrial health, and cell cycle analysis. MCs showed mediator release in direct contact with tumor cells. MC mediators' treatment to YAC-1 and EL4 yielded exactly opposite modulations of survival markers, Survivin and COX-2 and apoptosis markers, Caspase-3, Bcl-2, in the two cell lines. Histamine being an important MC mediator, effect of histamine on cell recovery, survival markers and expression of various histamine receptors and their modulation in cancer cells was studied. Again, YAC-1 and EL4 cells showed contrary histamine receptor expression modulation in response to MC mediators. Histamine receptor antagonist co-treatment with MC mediators to the cancer cells suggested a major involvement of H2 and H4 receptor in growth inhibition in YAC-1 cells, and contribution of H1, H2, and H4 receptors in cell growth enhancement in EL4 cells. L1210 showed changes in the histamine receptors' expression but no effect on treatment with receptor antagonists. It can be concluded that anti-cancerous action of MCs or their mediators may include direct growth inhibition, but their role may differ depending on the tumor.
Collapse
Affiliation(s)
- Sandeep Paudel
- Cellular and Molecular Immunology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Deeksha Mehtani
- Cellular and Molecular Immunology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Niti Puri
- Cellular and Molecular Immunology Lab, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| |
Collapse
|
62
|
Colleti C, Melo-Hanchuk TD, da Silva FRM, Saito Â, Kobarg J. Complex interactomes and post-translational modifications of the regulatory proteins HABP4 and SERBP1 suggest pleiotropic cellular functions. World J Biol Chem 2019; 10:44-64. [PMID: 31768228 PMCID: PMC6872977 DOI: 10.4331/wjbc.v10.i3.44] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/30/2019] [Accepted: 10/15/2019] [Indexed: 02/05/2023] Open
Abstract
The 57 kDa antigen recognized by the Ki-1 antibody, is also known as intracellular hyaluronic acid binding protein 4 and shares 40.7% identity and 67.4% similarity with serpin mRNA binding protein 1, which is also named CGI-55, or plasminogen activator inhibitor type-1-RNA binding protein-1, indicating that they might be paralog proteins, possibly with similar or redundant functions in human cells. Through the identification of their protein interactomes, both regulatory proteins have been functionally implicated in transcriptional regulation, mRNA metabolism, specifically RNA splicing, the regulation of mRNA stability, especially, in the context of the progesterone hormone response, and the DNA damage response. Both proteins also show a complex pattern of post-translational modifications, involving Ser/Thr phosphorylation, mainly through protein kinase C, arginine methylation and SUMOylation, suggesting that their functions and locations are highly regulated. Furthermore, they show a highly dynamic cellular localization pattern with localizations in both the cytoplasm and nucleus as well as punctuated localizations in both granular cytoplasmic protein bodies, upon stress, and nuclear splicing speckles. Several reports in the literature show altered expressions of both regulatory proteins in a series of cancers as well as mutations in their genes that may contribute to tumorigenesis. This review highlights important aspects of the structure, interactome, post-translational modifications, sub-cellular localization and function of both regulatory proteins and further discusses their possible functions and their potential as tumor markers in different cancer settings.
Collapse
Affiliation(s)
- Carolina Colleti
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Talita Diniz Melo-Hanchuk
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Flávia Regina Moraes da Silva
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| | - Ângela Saito
- Laboratório Nacional de Biociências, CNPEM, Campinas 13083-970, Brazil
| | - Jörg Kobarg
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
- Institute of Biology, Departament of Biochemistry and Tissue Biology, University of Campinas, Campinas 13083-862, Brazil
| |
Collapse
|
63
|
Huang S, Li R, Huang X, Zheng S, Wang L, Wen Z, Zou X, Wu J, Liu Y, Liu D, Wang Y, Dong S, Chen X, Zhu K, Du X, Zhou Z, Han Y, Ye X, Zeng C, Zhang B, Yang G, Jing C. Association Study Between Methylation in the Promoter Regions of cGAS, MAVS, and TRAF3 Genes and the Risk of Cervical Precancerous Lesions and Cervical Cancer in a Southern Chinese Population. Front Genet 2019; 10:1123. [PMID: 31803230 PMCID: PMC6868924 DOI: 10.3389/fgene.2019.01123] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 10/16/2019] [Indexed: 12/25/2022] Open
Abstract
A case-control study was used to explore the association between the methylation status in the promoter regions of the cGAS, MAVS, and TRAF3 genes and the diseases of cervical precancerous lesions (CPL) and cervical cancer (CC) in a Southern Chinese population, and to further explore their interaction effects with high-risk human papillomavirus (hrHPV) infection and environmental factors in these diseases. The study protocol was approved by the ethics committee of The First Affiliated Hospital of Jinan University, and this study was performed in 97 healthy controls, 75 patients with CPL and 33 patients with CC, while each participant has read and signed the informed consent forms before enrolment. The promoter methylation status genes were detected from the bisulfite-treated DNA by the bisulfite sequencing PCR (BSP) technique, which was carried out using MethPrimer. The cGAS, MAVS, and TRAF3 promoter methylation levels in CPL (CPL cGAS = 35.40%, CPL MAVS = 24.26%, and CPL TRAF3 = 96.76%) were significantly higher than those in the control (Control cGAS = 31.87%, Control MAVS = 21.16%, and Control TRAF3 = 96.26%, PcGAS < 0.001, PMAVS < 0.001, and PTRAF3 = 0.001); however, there was no significant differences between the CC and control. In the logistic regression model with adjusted covariates, compared with the individuals whose cGAS methylation levels were less than or equal to 31.87%, the women with the levels more than 31.87% increased the risk of CPL by 2.49 times (ORa = 2.49, 95% CI = 1.31-4.75, P a = 0.006). The women with MAVS methylation levels above 21.16% were 1.97 times more likely to have CPL than the those with the levels less than 21.16% (ORa = 1.97, 95% CI = 1.06-3.69, P a = 0.033). A synergistic interaction was found between hrHPV and gene promoter methylation levels of cGAS and MAVS in CPL; however, no potential interaction was observed in CC. The promoter methylation levels in cGAS, MAVS, and TRAF3 genes are higher in CPL than in control, indicating that hypermethylation might be an early event in the progression of cervical intraepithelial neoplasia (CIN). The interaction between the promoter methylation levels in cGAS and MAVS genes and hrHPV infection might play a role in the development of CPL.
Collapse
Affiliation(s)
- Shiqi Huang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Ruixin Li
- Department of Gynecologic Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiuxia Huang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Shaoling Zheng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Lijun Wang
- Department of Nutriology, School of Medicine, Jinan University, Guangzhou, China
| | - Zihao Wen
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaoqian Zou
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Jing Wu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Yumei Liu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Dandan Liu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Yao Wang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Shirui Dong
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaojing Chen
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Kehui Zhu
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiuben Du
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Zixing Zhou
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Yajing Han
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Xiaohong Ye
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Chengli Zeng
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Baohuan Zhang
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China
| | - Guang Yang
- Department of Pathogen Biology, School of Medicine, Jinan University, Guangzhou, China.,Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, China
| | - Chunxia Jing
- Department of Epidemiology, School of Medicine, Jinan University, Guangzhou, China.,Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou, China
| |
Collapse
|
64
|
The Alteration of CTNNBIP1 in Lung Cancer. Int J Mol Sci 2019; 20:ijms20225684. [PMID: 31766223 PMCID: PMC6888110 DOI: 10.3390/ijms20225684] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/07/2019] [Accepted: 11/12/2019] [Indexed: 12/13/2022] Open
Abstract
β-catenin is a major component of the Wnt/β-catenin signaling pathway, and is known to play a role in lung tumorigenesis. β-catenin-interacting protein 1 (CTNNBIP1) is a known repressor of β-catenin transactivation. However, little is known about the role of CTNNBIP1 in lung cancer. The aim of this study was to carry out a molecular analysis of CTNNBIP1 and its effect on β-catenin signaling, using samples from lung cancer patients and various lung cancer cell lines. Our results indicate a significant inverse correlation between the CTNNBIP1 mRNA expression levels and the CTNNBIP1 promoter hypermethylation, which suggests that the promoter hypermethylation is responsible for the low levels of CTNNBIP1 present in many lung cancer patient samples. The ectopic expression of CTNNBIP1 is able to reduce the β-catenin transactivation; this then brings about a decrease in the expression of β-catenin-targeted genes, such as matrix metalloproteinase 7 (MMP7). Conversely, CTNNBIP1 knockdown is able to increase β-catenin transactivation and the expression of MMP7. In agreement with these findings, a low level of CTNNBIP1 was found to be correlated with a high level of MMP7 when a publicly available microarray dataset for lung cancer was analyzed. Also, in agreement with the above, the ectopic expression of CTNNBIP1 inhibits the migration of lung cancer cells, whereas the CTNNBIP1 knockdown increases cancer cell migration. Our findings suggest that CTNNBIP1 is a suppressor of cancer migration, thus making it a potential prognostic predictor for lung cancer.
Collapse
|
65
|
Li R, Yang YE, Yin YH, Zhang MY, Li H, Qu YQ. Methylation and transcriptome analysis reveal lung adenocarcinoma-specific diagnostic biomarkers. J Transl Med 2019; 17:324. [PMID: 31558162 PMCID: PMC6764142 DOI: 10.1186/s12967-019-2068-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 09/14/2019] [Indexed: 02/07/2023] Open
Abstract
Background DNA methylation can regulate the role of long noncoding RNAs (lncRNAs) in the development of lung adenocarcinoma (LUAD). The present study aimed to identify methylation-driven lncRNAs and mRNAs as biomarkers in the prognosis of LUAD using bioinformatics analysis. Methods Differentially expressed RNAs were obtained using the edge R package from 535 LUAD tissues and 59 adjacent non-LUAD tissues. Differentially methylated genes were obtained using the limma R package from 475 LUAD tissues and 32 adjacent non-LUAD tissues. Methylation-driven mRNA and lncRNA were obtained using the MethylMix R package from 465 LUAD tissues with matched DNA methylation and RNA expression and 32 non-LUAD tissues with DNA methylation. Gene ontology and ConsensusPathDB pathway analysis were performed to identify functional enrichment of methylation-driven mRNAs. Univariate and multivariate Cox regression analyses were performed to identify the independent effect of each variable for predicting the prognosis of LUAD. Kaplan–Meier curve analysis of DNA methylation and gene expression might provide potential prognostic biomarkers for LUAD patients. Results A total of 99 methylation-driven mRNAs and 17 methylation-driven lncRNAs were obtained. Univariate and multivariate Cox regression analysis showed that 6 lncRNAs (FOXE1, HOXB13-AS1_2, VMO1, HIST1H3F, AJ003147.8, ASXL3) were retrieved to construct a predictive model associated with overall survival in LUAD patients. Combined DNA methylation and gene expression survival analysis revealed that 4 lncRNAs (AC023824.1, AF186192.1, LINC01354 and WASIR2) and 8 mRNAs (S1PR1, CCDC181, F2RL1, EFS, KLHDC9, MPV17L, GKN2, ITPRIPL1) might act as independent biomarkers for the prognosis of LUAD. Conclusions Methylation-driven lncRNA and mRNA contribute to the survival of LUAD, and 4 lncRNAs and 8 mRNAs might be potential biomarkers for the prognosis of LUAD.
Collapse
Affiliation(s)
- Rui Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Yi-E Yang
- Department of Clinical Laboratory, Qianfoshan Hospital of Shandong Province, Jinan, 250014, China
| | - Yun-Hong Yin
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Meng-Yu Zhang
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China
| | - Hao Li
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
| | - Yi-Qing Qu
- Department of Respiratory and Critical Care Medicine, Qilu Hospital of Shandong University, Jinan, 250012, China.
| |
Collapse
|
66
|
Reddy GP, Reddy LV, Kim S. CANCER BIOLOGY AND PATHOLOGY. Cancer 2019. [DOI: 10.1002/9781119645214.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
67
|
Abstract
Epigenetics is the study of heritable changes in DNA or its associated proteins except mutations in gene sequence. Epigenetic regulation plays fundamental roles in the processes of kidney cell biology through the action of DNA methylation, chromatin modifications via epigenetic regulators and interaction via transcription factors, and noncoding RNA species. Kidney diseases, including acute kidney injury, chronic kidney disease, nephritic and nephrotic syndromes, pyelonephritis and polycystic kidney diseases are driven by aberrant activity in numerous signaling pathways in even individual kidney cell. Epigenetic alterations, including DNA methylation, histone acetylation and methylation, noncoding RNAs, and protein posttranslational modifications, could disrupt essential pathways that protect the renal cells from uncontrolled growth, apoptosis and establishment of other renal associated syndromes, which have been recognized as one of the critical mechanisms for regulating functional changes that drive and maintain the kidney disease phenotype. In this chapter, we briefly summarize the epigenetic mechanisms in kidney cell biology and epigenetic basis of kidney development, and introduce epigenetic techniques that can be used in investigating the molecular mechanism of kidney cell biology and kidneys diseases, primarily focusing on the integration of DNA methylation and chromatin immunoprecipitation technologies into kidney disease associated studies. Future studies using these emerging technologies will elucidate how alterations in the renal cell epigenome cooperate with genetic aberrations for kidney disease initiation and progression. Incorporating epigenomic testing into the clinical research is essential to future studies with epigenetics biomarkers and precision medicine using emerging epigenetic therapies.
Collapse
Affiliation(s)
- Linda Xiaoyan Li
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Ewud Agborbesong
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Lu Zhang
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Xiaogang Li
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States; Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States.
| |
Collapse
|
68
|
Abstract
BACKGROUND Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the evolving topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time. In this paper, we consider the problem of identifying co-evolving subnetworks given a pair of temporal networks, which aim to capture the evolution of molecules and their interactions over time. Although this problem shares some characteristics of the well-known network alignment problems, it differs from existing network alignment formulations as it seeks a mapping of the two network topologies that is invariant to temporal evolution of the given networks. This is a computationally challenging problem as it requires capturing not only similar topologies between two networks but also their similar evolution patterns. RESULTS We present an efficient algorithm, Tempo, for solving identifying co-evolving subnetworks with two given temporal networks. We formally prove the correctness of our method. We experimentally demonstrate that Tempo scales efficiently with the size of network as well as the number of time points, and generates statistically significant alignments-even when evolution rates of given networks are high. Our results on a human aging dataset demonstrate that Tempo identifies novel genes contributing to the progression of Alzheimer's, Huntington's and Type II diabetes, while existing methods fail to do so. CONCLUSIONS Studying temporal networks in general and human aging specifically using Tempo enables us to identify age related genes from non age related genes successfully. More importantly, Tempo takes the network alignment problem one huge step forward by moving beyond the classical static network models.
Collapse
Affiliation(s)
- Rasha Elhesha
- University of Florida, CISE Department, Gainesville, Florida, 32611, US
| | - Aisharjya Sarkar
- University of Florida, CISE Department, Gainesville, Florida, 32611, US
| | - Christina Boucher
- University of Florida, CISE Department, Gainesville, Florida, 32611, US
| | - Tamer Kahveci
- University of Florida, CISE Department, Gainesville, Florida, 32611, US.
| |
Collapse
|
69
|
Mahmoudian RA, Bahadori B, Rad A, Abbaszadegan MR, Forghanifard MM. MEIS1 knockdown may promote differentiation of esophageal squamous carcinoma cell line KYSE-30. Mol Genet Genomic Med 2019; 7:e00746. [PMID: 31090196 PMCID: PMC6625128 DOI: 10.1002/mgg3.746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 04/01/2019] [Accepted: 04/27/2019] [Indexed: 12/11/2022] Open
Abstract
Background MEIS1 (Myeloid ecotropic viral integration site 1), as a homeobox (HOX) transcription factor, has a dual function in different types of cancer. Although numerous roles are proposed for MEIS1 in differentiation, stem cell function, gastrointestinal development and tumorigenesis, the involved molecular mechanisms are poor understood. Our aim in this study was to elucidate the functional correlation between MEIS1, as regulator of differentiation process, and the involved genes in cell differentiation in human esophageal squamous carcinoma (ESC) cell line KYSE‐30. Methods The KYSE‐30 cells were transduced using recombinant retroviral particles containing specific shRNA sequence against MEIS1 to knockdown MEIS1 gene expression. Following RNA extraction and cDNA synthesis, mRNA expression of MEIS1 and the selected genes including TWIST1, EGF, CDX2, and KRT4 was examined using relative comparative real‐time PCR. Results Retroviral transduction caused a significant underexpression of MEIS1 in GFP‐hMEIS1 compared to control GFP cells approximately 5.5‐fold. While knockdown of MEIS1 expression caused a significant decrease in EGF and TWIST1 mRNA expression, nearly ‐8‐ and ‐12‐fold respectively, it caused a significant increase in mRNA expression of differentiation markers including KRT4 and CDX2, approximately 34‐ and 1.14‐fold, correspondingly. Conclusion MEIS1 gene silencing in KYSE‐30 cells increased expression of epithelial markers and decreased expression of epithelial‐mesenchymal transition (EMT) marker TWIST1. It may highlight the role of MEIS1 in differentiation process of KYSE‐30 cells. These results may confirm that MEIS1 silencing promotes differentiation and decreases EMT capability of ESC cell line KYSE‐30.
Collapse
Affiliation(s)
| | - Bahareh Bahadori
- Department of Biology, Damghan Branch, Islamic Azad University, Damghan, Iran
| | - Abolfazl Rad
- Cellular and Molecular Research center, Sabzevar Univeristy of Medical Sciences, Sabzevar, Iran
| | | | | |
Collapse
|
70
|
Daum R, Brauchle EM, Berrio DAC, Jurkowski TP, Schenke-Layland K. Non-invasive detection of DNA methylation states in carcinoma and pluripotent stem cells using Raman microspectroscopy and imaging. Sci Rep 2019; 9:7014. [PMID: 31065074 PMCID: PMC6504883 DOI: 10.1038/s41598-019-43520-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 04/26/2019] [Indexed: 11/09/2022] Open
Abstract
DNA methylation plays a critical role in the regulation of gene expression. Global DNA methylation changes occur in carcinogenesis as well as early embryonic development. However, the current methods for studying global DNA methylation levels are invasive and require sample preparation. The present study was designed to investigate the potential of Raman microspectroscopy and Raman imaging as non-invasive, marker-independent and non-destructive tools for the detection of DNA methylation in living cells. To investigate global DNA methylation changes, human colon carcinoma HCT116 cells, which were hypomorphic for DNA methyltransferase 1, therefore showing a lower global DNA methylation (DNMT1−/− cells), were compared to HCT116 wildtype cells. As a model system for early embryogenesis, murine embryonic stem cells were adapted to serum-free 2i medium, leading to a significant decrease in DNA methylation. Subsequently, 2i medium -adapted cells were compared to cells cultured in serum-containing medium. Raman microspectroscopy and imaging revealed significant differences between high- and low-methylated cell types. Higher methylated cells demonstrated higher relative intensities of Raman peaks, which can be assigned to the nucleobases and 5-methylcytosine. Principal component analysis detected distinguishable populations of high- and low-methylated samples. Based on the provided data we conclude that Raman microspectroscopy and imaging are suitable tools for the real-time, marker-independent and artefact-free investigation of the DNA methylation states in living cells.
Collapse
Affiliation(s)
- Ruben Daum
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany.,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Eva M Brauchle
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany.,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany
| | - Daniel Alejandro Carvajal Berrio
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany
| | - Tomasz P Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Katja Schenke-Layland
- Department of Women's Health, Research Institute for Women's Health, Eberhard-Karls-University Tübingen, Silcherstr. 7/1, 72076, Tübingen, Germany. .,The Natural and Medical Sciences Institute (NMI) at the University of Tübingen, Markwiesenstr. 55, 72770, Reutlingen, Germany. .,Department of Medicine/Cardiology, Cardiovascular Research Laboratories, David Geffen School of Medicine at UCLA, 675 Charles E. Young Drive South, MRL 3645, Los Angeles, CA, USA.
| |
Collapse
|
71
|
Zeng XY, Xie H, Yuan J, Jiang XY, Yong JH, Zeng D, Dou YY, Xiao SS. M2-like tumor-associated macrophages-secreted EGF promotes epithelial ovarian cancer metastasis via activating EGFR-ERK signaling and suppressing lncRNA LIMT expression. Cancer Biol Ther 2019; 20:956-966. [PMID: 31062668 PMCID: PMC6606001 DOI: 10.1080/15384047.2018.1564567] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 12/07/2018] [Accepted: 12/25/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Ovarian cancer (OC) is the gynecologic malignant tumor with high mortality. Accumulating evidence indicates that M2-like tumor-associated macrophages (TAMs) can secret EGF to participate in ovarian cancer growth, migration, and metastasis. An EGF-downregulated lncRNA, LIMT (lncRNA inhibiting metastasis), was identified as a critical regulator of mammary cell migration and invasion. Nevertheless, whether EGF secreted from M2-like TAMs regulates LIMT expression in ovarian cancer progression remains largely unknown. Methods: The human OC cell lines OV90 and OVCA429 were recruited in this study. The differentiation of the human monocyte cell line THP-1 into M2-like TAMs was confirmed using flow cytometry within the application of phorbol 12-myristate 13-acetate (PMA). ELISA was performed to detect EGF concentration in co-culture system of M2-like TAMs and OC cell lines. Moreover, CCK-8, flow cytometry and immunofluorescence staining of Ki67 were performed to assess the capacity of cell proliferation. Besides, cell migration and invasion were determined by wound healing and transwell assays. Furthermore, the expression levels of epithelial-mesenchymal transition (EMT) markers and EGFR/ERK signals were analyzed by qRT-PCR and western blot. Female athymic nude mice (8-12 weeks of age; n = 8 for each group) were recruited for in vivo study. Results: In the present study, THP-1 cells exhibited the phenotype markers of M2-like TAMs with low proportion of CD14+ marker and high proportion of CD68+, CD204+, CD206+ markers within the application of PMA. After co-culturing with M2-like TAMs, EGF concentration in the supernatants was significantly increased in a time-dependent manner. Besides, OC cells presented better cell viability, higher cell proliferation, and stronger migration and invasion. The expression of EMT-related markers N-cadherin, Vimentin and EGFR/ERK signals were markedly up-regulated, while E-cadherin was significantly decreased. However, these effects induced by co-culture system were reversed by the application of AG1478 (an EGFR inhibitor) or LIMT overexpression. Furthermore, the endogenous expression of LIMT was decreased in OC cell lines compared with the control group. Also, the in vivo experiments verified that the inhibition of EGFR signaling by AG1478 or overexpression of LIMT effectively repressed the tumor growth. Conclusion: Taken together, we demonstrated that EGF secreted by M2-like TAMs might suppress LIMT expression via activating EGFR-ERK signaling pathway to promote the progression of OC.
Collapse
Affiliation(s)
- Xiang-Yang Zeng
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Hui Xie
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Jing Yuan
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Xiao-Yan Jiang
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Jia-Hui Yong
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Da Zeng
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Ying-Yu Dou
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| | - Song-Shu Xiao
- Department of Gynecology, The Third Xiangya Hospital of Central South University, Changsha, P.R. China
| |
Collapse
|
72
|
Toh TB, Lim JJ, Chow EKH. Epigenetics of hepatocellular carcinoma. Clin Transl Med 2019; 8:13. [PMID: 31056726 PMCID: PMC6500786 DOI: 10.1186/s40169-019-0230-0] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, large scale genomics and genome-wide studies using comprehensive genomic tools have reshaped our understanding of cancer evolution and heterogeneity. Hepatocellular carcinoma, being one of the most deadly cancers in the world has been well established as a disease of the genome that harbours a multitude of genetic and epigenetic aberrations during the process of liver carcinogenesis. As such, in depth understanding of the cancer epigenetics in cancer specimens and biopsy can be useful in clinical settings for molecular subclassification, prognosis, and prediction of therapeutic responses. In this review, we present a concise discussion on recent progress in the field of liver cancer epigenetics and some of the current works that contribute to the progress of liver cancer therapeutics.
Collapse
Affiliation(s)
- Tan Boon Toh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, MD6 #12-01, Singapore, 117599, Singapore
| | - Jhin Jieh Lim
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, MD6 #12-01, Singapore, 117599, Singapore
| | - Edward Kai-Hua Chow
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, MD6 #12-01, Singapore, 117599, Singapore. .,Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Level 5, Singapore, 117597, Singapore.
| |
Collapse
|
73
|
Liao Z, Chua D, Tan NS. Reactive oxygen species: a volatile driver of field cancerization and metastasis. Mol Cancer 2019; 18:65. [PMID: 30927919 PMCID: PMC6441160 DOI: 10.1186/s12943-019-0961-y] [Citation(s) in RCA: 142] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/20/2019] [Indexed: 12/24/2022] Open
Abstract
Field cancerization and metastasis are the leading causes for cancer recurrence and mortality in cancer patients. The formation of primary, secondary tumors or metastasis is greatly influenced by multifaceted tumor-stroma interactions, in which stromal components of the tumor microenvironment (TME) can affect the behavior of the cancer cells. Many studies have identified cytokines and growth factors as cell signaling molecules that aid cell to cell communication. However, the functional contribution of reactive oxygen species (ROS), a family of volatile chemicals, as communication molecules are less understood. Cancer cells and various tumor-associated stromal cells produce and secrete a copious amount of ROS into the TME. Intracellular ROS modulate cell signaling cascades that aid in the acquisition of several hallmarks of cancers. Extracellular ROS help to propagate, amplify, and effectively create a mutagenic and oncogenic field which facilitate the formation of multifoci tumors and act as a springboard for metastatic tumor cells. In this review, we summarize our current knowledge of ROS as atypical paracrine signaling molecules for field cancerization and metastasis. Field cancerization and metastasis are often discussed separately; we offer a model that placed these events with ROS as the focal instigating agent in a broader "seed-soil" hypothesis.
Collapse
Affiliation(s)
- Zehuan Liao
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore
- Department of Microbiology, Tumor, and Cell Biology (MTC), Karolinska Institutet, Biomedicum, Solnavägen 9, SE-17177, Stockholm, Sweden
| | - Damien Chua
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Nguan Soon Tan
- School of Biological Sciences, Nanyang Technological University Singapore, 60 Nanyang Drive, Singapore, 637551, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University Singapore, 11 Mandalay Road, Singapore, 308232, Singapore.
| |
Collapse
|
74
|
Kobets T, Iatropoulos MJ, Williams GM. Mechanisms of DNA-reactive and epigenetic chemical carcinogens: applications to carcinogenicity testing and risk assessment. Toxicol Res (Camb) 2019; 8:123-145. [PMID: 30997017 PMCID: PMC6417487 DOI: 10.1039/c8tx00250a] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/18/2018] [Indexed: 01/03/2023] Open
Abstract
Chemicals with carcinogenic activity in either animals or humans produce increases in neoplasia through diverse mechanisms. One mechanism is reaction with nuclear DNA. Other mechanisms consist of epigenetic effects involving either modifications of regulatory macromolecules or perturbation of cellular regulatory processes. The basis for distinguishing between carcinogens that have either DNA reactivity or an epigenetic activity as their primary mechanism of action is detailed in this review. In addition, important applications of information on these mechanisms of action to carcinogenicity testing and human risk assessment are discussed.
Collapse
Affiliation(s)
- Tetyana Kobets
- Department of Pathology , New York Medical College , Valhalla , NY 10595 , USA . ; ; Tel: +1 914-594-3105
| | - Michael J Iatropoulos
- Department of Pathology , New York Medical College , Valhalla , NY 10595 , USA . ; ; Tel: +1 914-594-3105
| | - Gary M Williams
- Department of Pathology , New York Medical College , Valhalla , NY 10595 , USA . ; ; Tel: +1 914-594-3105
| |
Collapse
|
75
|
Saleembhasha A, Mishra S. Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach. PeerJ 2019; 7:e6388. [PMID: 30809433 PMCID: PMC6387586 DOI: 10.7717/peerj.6388] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 01/04/2019] [Indexed: 12/18/2022] Open
Abstract
Despite years of research, we are still unraveling crucial stages of gene expression regulation in cancer. On the basis of major biological hallmarks, we hypothesized that there must be a uniform gene expression pattern and regulation across cancer types. Among non-coding genes, long non-coding RNAs (lncRNAs) are emerging as key gene regulators playing powerful roles in cancer. Using TCGA RNAseq data, we analyzed coding (mRNA) and non-coding (lncRNA) gene expression across 15 and 9 common cancer types, respectively. 70 significantly differentially expressed genes common to all 15 cancer types were enlisted. Correlating with protein expression levels from Human Protein Atlas, we observed 34 positively correlated gene sets which are enriched in gene expression, transcription from RNA Pol-II, regulation of transcription and mitotic cell cycle biological processes. Further, 24 lncRNAs were among common significantly differentially expressed non-coding genes. Using guilt-by-association method, we predicted lncRNAs to be involved in same biological processes. Combining RNA-RNA interaction prediction and transcription regulatory networks, we identified E2F1, FOXM1 and PVT1 regulatory path as recurring pan-cancer regulatory entity. PVT1 is predicted to interact with SYNE1 at 3′-UTR; DNAJC9, RNPS1 at 5′-UTR and ATXN2L, ALAD, FOXM1 and IRAK1 at CDS sites. The key findings are that through E2F1, FOXM1 and PVT1 regulatory axis and possible interactions with different coding genes, PVT1 may be playing a prominent role in pan-cancer development and progression.
Collapse
Affiliation(s)
- Asanigari Saleembhasha
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Seema Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| |
Collapse
|
76
|
Kothari C, Ouellette G, Labrie Y, Jacob S, Diorio C, Durocher F. Identification of a gene signature for different stages of breast cancer development that could be used for early diagnosis and specific therapy. Oncotarget 2018; 9:37407-37420. [PMID: 30647841 PMCID: PMC6324778 DOI: 10.18632/oncotarget.26448] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Accepted: 11/26/2018] [Indexed: 12/16/2022] Open
Abstract
Breast cancer (BC) is a heterogeneous disease where the survival rate of patients decreases with progression of the disease. BC usually has a linear progression, classified into normal/benign, atypical ductal hyperplasia (ADH), ductal carcinoma in situ (DCIS), and invasive ductal carcinoma (IDC). This study aimed to identify gene signature for each of these subgroups. We performed human transcriptome array analysis on 5 patient samples from each Normal, ADH, IDC and DCIS and 2 replicates of MCF10A cell line representative of each subgroup. We identified SFRP1 and snoRNAs (especially SNORD115 and SNORD114) as the initial regulators of cancer progression, accompanied by significant changes in extracellular matrix organization. Tumor progression to the IDC stage showed upregulation of tumor promoting genes responsible for increased invasion, inflammation, survival in stress environment and metastasis. The gene signatures identified in this study could represent potential biomarkers for each subgroup of breast cancer progression, which could assist in early diagnosis of breast cancer progression as well as treatment interventions. Moreover, these gene signatures could serve in discovery of specific targeted therapies for each subgroup.
Collapse
Affiliation(s)
- Charu Kothari
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, Canada
- Centre de recherche sur le cancer, Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Geneviève Ouellette
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, Canada
- Centre de recherche sur le cancer, Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Yvan Labrie
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, Canada
- Centre de recherche sur le cancer, Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| | - Simon Jacob
- Centre de recherche sur le cancer, Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
- Laboratoire de pathologie, Hôpital du Saint-Sacrement, CHU de Québec-Université Laval, Québec, Canada
| | - Caroline Diorio
- Centre de recherche sur le cancer, Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
- Département de médecine sociale et préventive, Faculté de médecine, Université Laval, Québec, Canada
| | - Francine Durocher
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, Canada
- Centre de recherche sur le cancer, Centre de recherche du CHU de Québec-Université Laval, Québec, Canada
| |
Collapse
|
77
|
Sajid M, Agrewala JN. Low prevalence of anti-xenobiotic antibodies among the occupationally exposed individuals is associated with a high risk of cancer. Cancer Med 2018; 8:246-260. [PMID: 30575301 PMCID: PMC6346253 DOI: 10.1002/cam4.1773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 12/13/2022] Open
Abstract
Cancer is one of the major health problem globally, responsible for high morbidity and mortality. Exposure of humans to xenobiotics is associated with the development of cancer. Further, these xenobiotics may combine with the body proteins and can act as a hapten and elicit an antibody response. In this study, we examined whether the regular exposer to xenobiotics evokes anti-xenobiotic antibodies and the presence of these antibodies have any correlation with the prevention of cancer. Interestingly, we noticed that the healthy household contacts showed significantly greater titers of anti-xenobiotic antibodies, as compared to cancer patients. Consequently, suggesting that the higher level of anti-xenobiotic antibodies may be responsible for neutralizing the effect of xenobiotics in the healthy subjects. Thereby, preventing the individuals from disease. In contrast, the presence of a significantly lower level of anti-xenobiotic antibodies in the cancer patients may be a causative factor for disease infliction. In conclusion, immunotherapy employing anti-xenobiotic antibodies may provide a prudent remedial measure to clear xenobiotics from the body of the individuals and thereby protecting from cancer.
Collapse
Affiliation(s)
- Mohammad Sajid
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Javed N Agrewala
- Immunology Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India.,Indian Institute of Technology, Ropar, India
| |
Collapse
|
78
|
Das P, Sedighi A, Krull UJ. Cancer biomarker determination by resonance energy transfer using functional fluorescent nanoprobes. Anal Chim Acta 2018; 1041:1-24. [DOI: 10.1016/j.aca.2018.07.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022]
|
79
|
He W, Ju D, Jie Z, Zhang A, Xing X, Yang Q. Aberrant CpG-methylation affects genes expression predicting survival in lung adenocarcinoma. Cancer Med 2018; 7:5716-5726. [PMID: 30353687 PMCID: PMC6246931 DOI: 10.1002/cam4.1834] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/09/2018] [Accepted: 09/24/2018] [Indexed: 12/18/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a common diagnosed disease with high-mortality rate, and its prognostic implications are under discovered. DNA methylation aberrations are not only an important event for dysregulation of gene expression during tumorigenesis but also a revolution in epigenetics by identifying key prognostic biomarkers for multiple cancers. In this study, we analyzed methylation status of 485 578 CpG sites and RNA-seq transcriptomes of 20 532 genes for 1095 LUAD samples in TCGA database. The association between DNA methylation and the prognostic value of the corresponding gene expression was identified as well. In total, ten aberrantly methylated and dysregulated genes (AURKA, BLK, CNTN2, HMGA1, PTTG1, TNS4, DAPK2, MFSD2A, THSD1, and WNT7A) were highlighted which were significantly correlated with overall survival of 492 LUAD patients, which were all reported as tumor-associated genes in other various cancers and worthy of further investigated and might be used as therapeutic targets for LUAD. Together, methylation aberrances regulate gene expression level during tumorigenesis and influence prognosis of LUAD patients. Integrating knowledge of epigenetics and expression of genes can be useful for an in-depth understanding of cancer mechanism and for the eventual purpose of precisely prognostic and therapeutic target verification.
Collapse
Affiliation(s)
- Wei He
- Department of Respiratory Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Dandan Ju
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Zhijun Jie
- Department of Respiratory Medicine, The Fifth People's Hospital of Shanghai, Fudan University, Shanghai, China
| | - Ai Zhang
- The People's Hospital of Shanghai Pudong District, Shanghai, China
| | - Xin Xing
- Department of Obstetrics and Gynecology, Fengxian Hospital, Shanghai, China
| | - Qin Yang
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Cancer Institute, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
80
|
Fattahi S, Golpour M, Amjadi-Moheb F, Sharifi-Pasandi M, Khodadadi P, Pilehchian-Langroudi M, Ashrafi GH, Akhavan-Niaki H. DNA methyltransferases and gastric cancer: insight into targeted therapy. Epigenomics 2018; 10:1477-1497. [PMID: 30325215 DOI: 10.2217/epi-2018-0096] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Gastric cancer is a major health problem worldwide occupying most frequent causes of cancer-related mortality. In addition to genetic modifications, epigenetic alterations catalyzed by DNA methyltransferases (DNMTs) are a well-characterized epigenetic hallmark in gastric cancer. The reversible nature of epigenetic alterations and central role of DNA methylation in diverse biological processes provides an opportunity for using DNMT inhibitors to enhance the efficacy of chemotherapeutics. In this review, we discussed key factors or mechanisms such as SNPs, infections and genetic modifications that trigger DNMTs level modification in gastric cancer, and their potential roles in cancer progression. Finally, we focused on how inhibitors of the DNMTs can most effectively be used for the treatment of gastric cancer with multidrug resistance.
Collapse
Affiliation(s)
- Sadegh Fattahi
- Cellular & Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, 4717647745, Babol, Iran.,North Research Center, Pasteur Institute, Amol, 4615885399, Iran
| | - Monireh Golpour
- Molecular & Cell Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Science, Sari, 4817844718, Iran
| | - Fatemeh Amjadi-Moheb
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, 4717647745, Babol, Iran
| | - Marzieh Sharifi-Pasandi
- Molecular & Cell Biology Research Center, Student Research Committee, Faculty of Medicine, Mazandaran University of Medical Science, Sari, 4817844718, Iran
| | - Parastesh Khodadadi
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, 4717647745, Babol, Iran
| | | | - Gholam Hossein Ashrafi
- School of Life Science, Pharmacy & Chemistry, SEC Faculty, Cancer Theme, Kingston University London, Kingston upon Thames, London KT1 2EE, UK
| | - Haleh Akhavan-Niaki
- Department of Genetics, Faculty of Medicine, Babol University of Medical Sciences, 4717647745, Babol, Iran
| |
Collapse
|
81
|
Takahashi T, Ogawa M, Sato A, Koyama Y. Translocated duplication of a targeted chromosomal segment enhances gene expression at the duplicated site and results in phenotypic changes in Aspergillus oryzae. Fungal Biol Biotechnol 2018; 5:17. [PMID: 30305913 PMCID: PMC6171174 DOI: 10.1186/s40694-018-0061-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 09/21/2018] [Indexed: 11/30/2022] Open
Abstract
Background Translocated chromosomal duplications occur spontaneously in many organisms; segmental duplications of large chromosomal regions are expected to result in phenotypic changes because of gene dosage effects. Therefore, experimentally generated segmental duplications in targeted chromosomal regions can be used to study phenotypic changes and determine the functions of unknown genes in these regions. Previously, we performed tandem duplication of a targeted chromosomal segment in Aspergillus oryzae. However, in tandem chromosomal duplication, duplication of chromosomal ends and multiple chromosomal duplication are difficult. In this study, we aimed to generate fungal strains with a translocated duplication or triplication of a targeted chromosomal region via break-induced replication. Results Double-strand breaks were introduced into chromosomes of parental strains by treating protoplast cells with I-SceI meganuclease. Subsequently, strains were generated by nonreciprocal translocation of a 1.4-Mb duplicated region of chromosome 2 to the end of chromosome 4. Another strain, containing a triplicated region of chromosome 2, was generated by translocating a 1.4-Mb region of chromosome 2 onto the ends of chromosomes 4 and 7. Phenotypic analyses of the strains containing segmental duplication or triplication of chromosome 2 showed remarkable increases in protease and amylase activities in solid-state cultures. Protease activity was further increased in strains containing the duplication and triplication after overexpression of the transcriptional activator of proteases prtT. This indicates that the gene-dosage effect and resulting phenotypes of the duplicated chromosomal region were enhanced by multiple duplications, and by the combination of the structural gene and its regulatory genes. Gene expression analysis, conducted using oligonucleotide microarrays, showed increased transcription of a large population of genes located in duplicated or triplicated chromosomal regions. Conclusion In this study, we performed translocated chromosomal duplications and triplications of a 1.4-Mb targeted region of chromosome 2. Strains containing a duplication of chromosome 2 showed significant increases in protease and amylase activities; these enzymatic activities were further increased in the strain containing a triplication of chromosome 2. This indicates that segmental duplications of chromosomes enhance gene-dosage effects, and that the resulting phenotypes play important phenotypic roles in A. oryzae. Electronic supplementary material The online version of this article (10.1186/s40694-018-0061-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Tadashi Takahashi
- Noda Institute for Scientific Research, 399 Noda, Noda City, Chiba Pref 278-0037 Japan
| | - Masahiro Ogawa
- Noda Institute for Scientific Research, 399 Noda, Noda City, Chiba Pref 278-0037 Japan
| | - Atsushi Sato
- Noda Institute for Scientific Research, 399 Noda, Noda City, Chiba Pref 278-0037 Japan
| | - Yasuji Koyama
- Noda Institute for Scientific Research, 399 Noda, Noda City, Chiba Pref 278-0037 Japan
| |
Collapse
|
82
|
Rhee JK, Kim SJ, Zhang BT. Identifying DNA Methylation Modules Associated with a Cancer by Probabilistic Evolutionary Learning. IEEE COMPUT INTELL M 2018. [DOI: 10.1109/mci.2018.2840659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
83
|
Jiménez G, Hackenberg M, Catalina P, Boulaiz H, Griñán-Lisón C, García MÁ, Perán M, López-Ruiz E, Ramírez A, Morata-Tarifa C, Carrasco E, Aguilera M, Marchal JA. Mesenchymal stem cell's secretome promotes selective enrichment of cancer stem-like cells with specific cytogenetic profile. Cancer Lett 2018; 429:78-88. [DOI: 10.1016/j.canlet.2018.04.042] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Revised: 04/27/2018] [Accepted: 04/27/2018] [Indexed: 12/15/2022]
|
84
|
Baliou S, Adamaki M, Kyriakopoulos AM, Spandidos DA, Panayiotidis M, Christodoulou I, Zoumpourlis V. CRISPR therapeutic tools for complex genetic disorders and cancer (Review). Int J Oncol 2018; 53:443-468. [PMID: 29901119 PMCID: PMC6017271 DOI: 10.3892/ijo.2018.4434] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/18/2018] [Indexed: 12/13/2022] Open
Abstract
One of the fundamental discoveries in the field of biology is the ability to modulate the genome and to monitor the functional outputs derived from genomic alterations. In order to unravel new therapeutic options, scientists had initially focused on inducing genetic alterations in primary cells, in established cancer cell lines and mouse models using either RNA interference or cDNA overexpression or various programmable nucleases [zinc finger nucleases (ZNF), transcription activator-like effector nucleases (TALEN)]. Even though a huge volume of data was produced, its use was neither cheap nor accurate. Therefore, the clustered regularly interspaced short palindromic repeats (CRISPR) system was evidenced to be the next step in genome engineering tools. CRISPR-associated protein 9 (Cas9)-mediated genetic perturbation is simple, precise and highly efficient, empowering researchers to apply this method to immortalized cancerous cell lines, primary cells derived from mouse and human origins, xenografts, induced pluripotent stem cells, organoid cultures, as well as the generation of genetically engineered animal models. In this review, we assess the development of the CRISPR system and its therapeutic applications to a wide range of complex diseases (particularly distinct tumors), aiming at personalized therapy. Special emphasis is given to organoids and CRISPR screens in the design of innovative therapeutic approaches. Overall, the CRISPR system is regarded as an eminent genome engineering tool in therapeutics. We envision a new era in cancer biology during which the CRISPR-based genome engineering toolbox will serve as the fundamental conduit between the bench and the bedside; nonetheless, certain obstacles need to be addressed, such as the eradication of side-effects, maximization of efficiency, the assurance of delivery and the elimination of immunogenicity.
Collapse
Affiliation(s)
- Stella Baliou
- National Hellenic Research Foundation, 11635 Athens, Greece
| | - Maria Adamaki
- National Hellenic Research Foundation, 11635 Athens, Greece
| | | | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, Heraklion 71003, Greece
| | - Mihalis Panayiotidis
- Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, NE1 8ST, UK
| | | | | |
Collapse
|
85
|
Ahmadi K, Soleimani A, Irani S, Kiani A, Ghanadi K, Noormohamadi Z, Sakinejad F. DNMT3B -579 G>T Promoter Polymorphism and the Risk of Gastric Cancer in the West of Iran. J Gastrointest Cancer 2018; 49:167-171. [PMID: 28220295 DOI: 10.1007/s12029-017-9928-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
BACKGROUND Many studies have suggested that modulation of DNMT3B function caused by single nucleotide polymorphisms of the DNMT3B promoter region may underlie the susceptibility to various cancers such as tumors of the digestive system. The aim of this study was to investigate the effect of -579 G>T polymorphism in the promoter of the DNMT3B gene on risk of gastric cancer in a population from West Iran. PATIENTS AND METHODS We conducted a case-control study in 100 gastric cancer patients and 112 cancer-free controls to assess the correlation between DNMT3B -579 G>T (rs1569686) polymorphism and the risk of gastric cancer. Detection of genotypes of DNMT3B G39179T polymorphism was analyzed by PCR-RFLP. RESULTS There was no significant difference in the distribution of DNMT3B -579 G>T genotypes between the cases and controls. However, in the stratified analysis by clinicopathological characteristic types, we found that statistically, the risk susceptibility to gastric cancer was significantly associated with tumor grade II and GT/TT genotype of patients, compared to patients having GG genotype, (OR = 5.4737, 95% CI = 1.4746. 20.3184, P = 0.01). CONCLUSIONS Our study suggested that the -579 T allele may increase the relative risk for the progression of clinicopathological characteristic of tumor grade of gastric cancer patients.
Collapse
Affiliation(s)
- Kulsom Ahmadi
- Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Azam Soleimani
- Razi Herbal Medicines Research Center, Lorestan University of Medical Sciences, Khorramabad, Iran.
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Kourosh Ghanadi
- Razi Herbal Medicines Research Center and Department of Internal Medicine, Lorestan University of Medical Sciences, Khorramabad, Iran
| | - Zahra Noormohamadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | |
Collapse
|
86
|
Li Y, Buckhaults P, Li S, Tollefsbol T. Temporal Efficacy of a Sulforaphane-Based Broccoli Sprout Diet in Prevention of Breast Cancer through Modulation of Epigenetic Mechanisms. Cancer Prev Res (Phila) 2018; 11:451-464. [PMID: 29764806 PMCID: PMC6072582 DOI: 10.1158/1940-6207.capr-17-0423] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Revised: 04/06/2018] [Accepted: 05/07/2018] [Indexed: 01/21/2023]
Abstract
Breast cancer is the most common cancer and the second leading cause of cancer-related death among women. An important risk factor for breast cancer is individual genetic background, which is initially generated early in human life, for example, during the processes of embryogenesis and fetal development in utero Bioactive dietary components such as sulforaphane (SFN), an isothiocyanate from cruciferous vegetables including broccoli sprouts (BSp), cabbage, and kale, has been shown to reduce the risk of developing many common cancers through regulation of epigenetic mechanisms. Our study indicates a prenatal/maternal BSp dietary treatment exhibited maximal preventive effects in inhibiting breast cancer development compared with postnatal early-life and adult BSp treatments in two transgenic mouse models that can develop breast cancer. Postnatal early-life BSp treatment starting prior to puberty onset showed protective effects in prevention of breast cancer but was not as effective as the prenatal/maternal BSp treatment. However, adulthood-administered BSp diet did not reduce mammary tumorigenesis. Our results suggest that the prenatal/maternal BSp bioactive natural plant product may impact early embryonic development by regulating global differential gene expression through affecting epigenetic profiles resulting in differential susceptibility to breast cancer later in life. These results suggest that a temporal exposure to epigenetic-modulating dietary components such as cruciferous vegetables could be a key factor for maximizing chemopreventive effects on human breast cancer. This study may lead to translational breast cancer chemopreventive potential by appropriate administration of key dietary components leading to early breast cancer prevention in humans. Cancer Prev Res; 11(8); 451-64. ©2018 AACR.
Collapse
Affiliation(s)
- Yuanyuan Li
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, Alabama. .,Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, Alabama
| | - Phillip Buckhaults
- Department of Drug Discovery and Biomedical Sciences, University of South Carolina, Columbia, South Carolina
| | - Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Trygve Tollefsbol
- Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, Alabama.,Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, Alabama.,Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama.,Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, Alabama
| |
Collapse
|
87
|
Cao X, Tang Q, Holland-Letz T, Gündert M, Cuk K, Schott S, Heil J, Golatta M, Sohn C, Schneeweiss A, Burwinkel B. Evaluation of Promoter Methylation of RASSF1A and ATM in Peripheral Blood of Breast Cancer Patients and Healthy Control Individuals. Int J Mol Sci 2018; 19:ijms19030900. [PMID: 29562656 PMCID: PMC5877761 DOI: 10.3390/ijms19030900] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 03/11/2018] [Accepted: 03/12/2018] [Indexed: 01/26/2023] Open
Abstract
Breast cancer (BC) is the most common cancer among women and has high mortality rates. Early detection is supposed to be critical for the patient’s prognosis. In recent years, several studies have investigated global DNA methylation profiles and gene-specific DNA methylation in blood-based DNA to develop putative screening markers for cancer. However, most of the studies have not yet been validated. In our study, we analyzed the promoter methylation of RASSF1A and ATM in peripheral blood DNA of 229 sporadic patients and 151 healthy controls by the MassARRAY EpiTYPER assay. There were no significant differences in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. Furthermore, we performed the Infinium HumanMethylation450 BeadChip (450K) array analysis using 48 sporadic BC cases and 48 healthy controls (cases and controls are the same from those of the MassARRAY EpiTYPER assay) and made a comparison with the published data. No significant differences were presented in DNA methylation levels of RASSF1A and ATM between the sporadic BC cases and the healthy controls. So far, the evidence for powerful blood-based methylation markers is still limited and the identified markers need to be further validated.
Collapse
Affiliation(s)
- Xue Cao
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Qiuqiong Tang
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Tim Holland-Letz
- Division of Biostatistics (C060), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Melanie Gündert
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Katarina Cuk
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| | - Sarah Schott
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Jörg Heil
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Michael Golatta
- Department of Gynecology and Obstetrics, University Women's Clinic, Heidelberg 69120, Germany.
| | - Christof Sohn
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
| | - Andreas Schneeweiss
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- National Centre for Tumor Diseases, Heidelberg 69120, Germany.
| | - Barbara Burwinkel
- Molecular Biology of Breast Cancer, Department of Gynecology and Obstetrics, University of Heidelberg, Heidelberg 69120, Germany.
- Division of Molecular Epidemiology (C080), German Cancer Research Center (DKFZ), Heidelberg 69120, Germany.
| |
Collapse
|
88
|
A functional variant at the miRNA binding site in HMGB1 gene is associated with risk of oral squamous cell carcinoma. Oncotarget 2018; 8:34630-34642. [PMID: 28423715 PMCID: PMC5470997 DOI: 10.18632/oncotarget.16120] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/15/2017] [Indexed: 12/12/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a common malignancy that has been causally associated with both hereditary and acquired factors. The high mobility group box 1 (HMGB1) gene plays an important role as a DNA chaperone to help maintain nuclear homeostasis. Altered expression of HMGB1 has been implicated in a wide range of pathological processes, including inflammation and cancer. The present study explores the impact of HMGB1 gene polymorphisms, combined with environmental risks regarding susceptibility to oral tumorigenesis. Four single-nucleotide polymorphisms (SNPs) of the HMGB1 gene, rs1412125, rs2249825, rs1045411, and rs1360485, were evaluated in 1,200 normal controls and 772 patients with OSCC. We found an association between the wild-type allele of rs1045411 and genotypes CT and CT/TT (AOR=0.754, 95% CI=0.582-0.978 and AOR=0.778, 95% CI=0.609-0.995, respectively). Additionally, bioinformatics analysis was used to characterize the functional relevance of these variants for the miRNA-505-5p binding site and transcriptional regulation by the HMGB1 3’-UTR and promoter regions. Moreover, in considering behavioral exposure to environmental carcinogens, the presence of the four HMGB1 SNPs, combined with/without betel quid chewing and smoking showed, profoundly synergistic effects on the risk of OSCC. In conclusion, we present a potential clinical relevance for HMGB1 variants in OSCC, as well as associations between HMGB1 polymorphisms, haplotypes and environmental risk factors. The finding may help in development of optimal therapeutic approaches for OSCC patients.
Collapse
|
89
|
Xu Y, So C, Lam HM, Fung MC, Tsang SY. Apoptosis Reversal Promotes Cancer Stem Cell-Like Cell Formation. Neoplasia 2018; 20:295-303. [PMID: 29476980 PMCID: PMC5883632 DOI: 10.1016/j.neo.2018.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 12/28/2017] [Accepted: 01/03/2018] [Indexed: 12/28/2022] Open
Abstract
It has long been a puzzle in cancer treatment that despite the initial appearance of apoptosis, the process could be reversed in some cancer cells and often results in more aggressive tumors and metastasis. The mechanism for this recurrence is yet unknown. Here we report that human mammary carcinoma cells induced to undergo apoptosis could recover with increased tumorigenicity in vitro and in vivo, and induced lymph node metastasis. Specifically, the reversed cells underwent epithelial-to-mesenchymal transitions in the primary tumors in situ, and mesenchymal-to-epithelial transitions in the metastatic cells. Flow cytometry confirmed an elevated percentage of cells carrying cancer stem cells (CSCs) markers (CD44+/CD24-) in the reversed breast cancer cell population, with hypomethylated CD44 promoters and hypermethylated CD24 promoters. More importantly, CSCs were generated anew from non-stem cancer cells after apoptosis reversal possibly through epigenetic modifications. The results from this study can open doors to discovering more effective cancer treatments by suppressing apoptosis reversal.
Collapse
Affiliation(s)
- Yiyue Xu
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR; State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR
| | - Chun So
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR
| | - Hon-Ming Lam
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR; State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR.
| | - Ming-Chiu Fung
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR; State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR.
| | - Suk-Ying Tsang
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR; State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong SAR; Key Laboratory for Regenerative Medicine, Ministry of Education, The Chinese University of Hong Kong, Hong Kong SAR; Centre for Novel Biomaterials, The Chinese University of Hong Kong, Hong Kong SAR.
| |
Collapse
|
90
|
Grunt TW. Interacting Cancer Machineries: Cell Signaling, Lipid Metabolism, and Epigenetics. Trends Endocrinol Metab 2018; 29:86-98. [PMID: 29203141 DOI: 10.1016/j.tem.2017.11.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/21/2022]
Abstract
Cancer-specific perturbations of signaling, metabolism, and epigenetics can be a cause and/or consequence of malignant transformation. Evidence indicates that these regulatory systems interact with each other to form highly flexible and robust cybernetic networks that promote malignant growth and confer treatment resistance. Deciphering these plexuses using holistic approaches known from systems biology can be instructive for the future design of novel anticancer strategies. In this review, I discuss novel findings elucidating the multiple molecular interdependence among cancer-specific signaling, cell metabolism, and epigenetics to provide an insightful understanding of how major cancer machineries interact with each other during cancer development and progression, and how this knowledge may be used for future co-targeting strategies.
Collapse
Affiliation(s)
- Thomas W Grunt
- Signaling Networks Program, Division of Oncology, Department of Medicine I, Medical University of Vienna, Vienna, Austria; Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria; Ludwig Boltzmann Cluster Oncology, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
91
|
Carter CA, Zeman K, Day RM, Richard P, Oronsky A, Oronsky N, Lybeck M, Scicinski J, Oronsky B. Addressing the elephant in the room, therapeutic resistance in non-small cell lung cancer, with epigenetic therapies. Oncotarget 2018; 7:40781-40791. [PMID: 27007055 PMCID: PMC5130044 DOI: 10.18632/oncotarget.8205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 03/07/2016] [Indexed: 12/15/2022] Open
Abstract
Like Chinese boxes nesting inside each other, the classification of non-small cell lung cancer (NSCLC) is subdivided into smaller and smaller subtypes on the basis of histological and molecular attributes. The latter characterizes NSCLC by its molecular alterations and the identification of inhibitors that target these cancer-specific "driver" mutations. Despite the initial promise of precision-guided therapies to inhibit a finer and finer array of molecular subcategories, despite even the curative potential of immunotherapeutic checkpoint blockade, in particular, casualties still abound and true clinical success stories are few and far between; the ever-present, if sometimes unmentioned, "elephant in the room", is the acquisition of resistance, which, sooner or later, rears its ugly head to undermine treatment success and shorten survival. Emerging data suggests that epigenetic therapies are able to reprogram the aberrant tumor-associated epigenome and 'tame the beast of resistance', thereby prolonging survival. This article reviews the role of epigenetic dysregulation in NSCLC, explores PFS2 as a possible surrogate endpoint, briefly mentions possible biomarkers and highlights combinatorial treatment epigenetic strategies to "prime" tumors and reverse resistance.
Collapse
Affiliation(s)
- Corey A Carter
- Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Karen Zeman
- National Naval Medical Center, Bethesda, MD, USA
| | - Regina M Day
- Uniformed Services University of The Health Sciences, Bethesda, MD, USA
| | - Patrick Richard
- Uniformed Services University of The Health Sciences, Bethesda, MD, USA
| | | | | | | | | | | |
Collapse
|
92
|
Mitochondrial UQCRB as a new molecular prognostic biomarker of human colorectal cancer. Exp Mol Med 2017; 49:e391. [PMID: 29147009 PMCID: PMC5704184 DOI: 10.1038/emm.2017.152] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/21/2017] [Accepted: 04/26/2017] [Indexed: 12/17/2022] Open
Abstract
Ubiquinol cytochrome c reductase binding protein (UQCRB) is important for mitochondrial complex III stability, electron transport, cellular oxygen sensing and angiogenesis. However, its potential as a prognostic marker in colorectal cancer (CRC) remains unclear. The aim of this study was to determine whether UQCRB can be used as a diagnostic molecular marker for CRC. The correlation between the expression of three genes (UQCRB, UQCRFS1 and MT-CYB) in the mitochondrial respiratory chain complex III and clinico-pathological features was determined. Compared to non-tumor tissues, UQCRB gene expression was upregulated in CRC tissues. Gene and protein expression of the genes were positively correlated. Copy number variation (CNV) differences in UQCRB were observed in CRC tissues (1.32-fold) compared to non-tumor tissues. The CNV of UQCRB in CRC tissues increased proportionally with gene expression and clinical stage. Single-nucleotide polymorphisms in the 3′-untranslated region of UQCRB (rs7836698 and rs10504961) were investigated, and the rs7836698 polymorphism was associated with CRC clinical stage. DNA methylation of the UQCRB promoter revealed that most CRC patients had high methylation levels (12/15 patients) in CRC tissues compared to non-tumor tissues. UQCRB overexpression and CNV gain were correlated with specific CRC clinico-pathological features, indicating clinical significance as a prognostic predictor in CRC. Gene structural factors may be more important than gene transcription repression factors with respect to DNA methylation in UQCRB overexpression. Our results provide novel insights into the critical role of UQCRB in regulating CRC, supporting UQCRB as a new candidate for the development of diagnostics for CRC patients.
Collapse
|
93
|
Sharma D, Koshy G, Gupta S, Sharma B, Grover S. Deciphering the Role of the Barr Body in Malignancy: An insight into head and neck cancer. Sultan Qaboos Univ Med J 2017; 17:e389-e397. [PMID: 29372079 PMCID: PMC5766293 DOI: 10.18295/squmj.2017.17.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 08/03/2017] [Accepted: 08/24/2017] [Indexed: 01/20/2023] Open
Abstract
X chromosome inactivation is the epitome of epigenetic regulation and long non-coding ribonucleic acid function. The differentiation status of cells has been ascribed to X chromosome activity, with two active X chromosomes generally only observed in undifferentiated or poorly differentiated cells. Recently, several studies have indicated that the reactivation of an inactive X chromosome or X chromosome multiplication correlates with the development of malignancy; however, this concept is still controversial. This review sought to shed light on the role of the X chromosome in cancer development. In particular, there is a need for further exploration of the expression patterns of X-linked genes in cancer cells, especially those in head and neck squamous cell carcinoma (HNSCC), in order to identify different prognostic subpopulations with distinct clinical implications. This article proposes a functional relationship between the loss of the Barr body and the disproportional expression of X-linked genes in HNSCC development.
Collapse
Affiliation(s)
- Deepti Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - George Koshy
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Shruti Gupta
- Department of Oral Anatomy, Postgraduate Institute of Dental Sciences, Rohtak, Haryana, India
| | - Bhushan Sharma
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| | - Sonal Grover
- Department of Oral & Maxillofacial Pathology, Christian Dental College, Ludhiana, Punjab, India
| |
Collapse
|
94
|
Farahmand S, Foroughmand-Araabi MH, Goliaei S, Razaghi-Moghadam Z. CytoGTA: A cytoscape plugin for identifying discriminative subnetwork markers using a game theoretic approach. PLoS One 2017; 12:e0185016. [PMID: 28968407 PMCID: PMC5624584 DOI: 10.1371/journal.pone.0185016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 09/04/2017] [Indexed: 01/07/2023] Open
Abstract
In recent years, analyzing genome-wide expression profiles to find genetic markers has received much attention as a challenging field of research aiming at unveiling biological mechanisms behind complex disorders. The identification of reliable and reproducible markers has lately been achieved by integrating genome-scale functional relationships and transcriptome datasets, and a number of algorithms have been developed to support this strategy. In this paper, we present a promising and easily applicable tool to accomplish this goal, namely CytoGTA, which is a Cytoscape plug-in that relies on an optimistic game theoretic approach (GTA) for identifying subnetwork markers. Given transcriptomic data of two phenotype classes and interactome data, this plug-in offers discriminative markers for the two classes. The high performance of CytoGTA would not have been achieved if the strategy of GTA was not implemented in Cytoscape. This plug-in provides a simple-to-use platform, convenient for biological researchers to interactively work with and visualize the structure of subnetwork markers. CytoGTA is one of the few available Cytoscape plug-ins for marker identification, which shows superior performance to existing methods.
Collapse
Affiliation(s)
- S. Farahmand
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
- College of Science and Mathematics, University of Massachusetts Boston, Boston, Massachusetts, United States of America
| | | | | | - Z. Razaghi-Moghadam
- Faculty of New Sciences and Technologies, University of Tehran, Tehran, Iran
- * E-mail:
| |
Collapse
|
95
|
Andrisic L, Dudzik D, Barbas C, Milkovic L, Grune T, Zarkovic N. Short overview on metabolomics approach to study pathophysiology of oxidative stress in cancer. Redox Biol 2017; 14:47-58. [PMID: 28866248 PMCID: PMC5583394 DOI: 10.1016/j.redox.2017.08.009] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 08/08/2017] [Indexed: 12/14/2022] Open
Abstract
Association of oxidative stress with carcinogenesis is well known, but not understood well, as is pathophysiology of oxidative stress generated during different types of anti-cancer treatments. Moreover, recent findings indicate that cancer associated lipid peroxidation might eventually help defending adjacent nonmalignant cells from cancer invasion. Therefore, untargeted metabolomics studies designed for advanced translational and clinical studies are needed to understand the existing paradoxes in oncology, including those related to controversial usage of antioxidants aiming to prevent or treat cancer. In this short review we have tried to put emphasis on the importance of pathophysiology of oxidative stress and lipid peroxidation in cancer development in relation to metabolic adaptation of particular types of cancer allowing us to conclude that adaptation to oxidative stress is one of the main driving forces of cancer pathophysiology. With the help of metabolomics many novel findings are being achieved thus encouraging further scientific breakthroughs. Combined with targeted qualitative and quantitative methods, especially immunochemistry, further research might reveal bio-signatures of individual patients and respective malignant diseases, leading to individualized treatment approach, according to the concepts of modern integrative medicine.
Collapse
Affiliation(s)
- Luka Andrisic
- CEMBIO (Centre for Metabolomics and Bioanalysis); Facultad de Farmacia; Universidad San Pablo CEU, Campus Montepríncipe, Madrid, Spain; Rudjer Boskovic Institute, Division of Molecular Medicine, Laboratory for Oxidative Stress, Zagreb, Croatia
| | - Danuta Dudzik
- CEMBIO (Centre for Metabolomics and Bioanalysis); Facultad de Farmacia; Universidad San Pablo CEU, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- CEMBIO (Centre for Metabolomics and Bioanalysis); Facultad de Farmacia; Universidad San Pablo CEU, Campus Montepríncipe, Madrid, Spain
| | - Lidija Milkovic
- Rudjer Boskovic Institute, Division of Molecular Medicine, Laboratory for Oxidative Stress, Zagreb, Croatia
| | - Tilman Grune
- German Institute of Human Nutrition, Potsdam-Rehbruecke, Nuthetal, Germany
| | - Neven Zarkovic
- Rudjer Boskovic Institute, Division of Molecular Medicine, Laboratory for Oxidative Stress, Zagreb, Croatia.
| |
Collapse
|
96
|
Karthi N, Karthiga A, Kalaiyarasu T, Stalin A, Manju V, Singh SK, Cyril R, Lee SM. Exploration of cell cycle regulation and modulation of the DNA methylation mechanism of pelargonidin: Insights from the molecular modeling approach. Comput Biol Chem 2017; 70:175-185. [PMID: 28950208 DOI: 10.1016/j.compbiolchem.2017.08.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/28/2017] [Accepted: 08/01/2017] [Indexed: 12/18/2022]
Abstract
Pelargonidin is an anthocyanidin isolated from plant resources. It shows strong cytotoxicity toward various cancer cell lines, even though the carcinogenesis-modulating pathway of pelargonidin is not yet known. One of our previous reports showed that pelargonidin arrests the cell cycle and induces apoptosis in HT29 cells. Flowcytometry and immunoblot analysis confirmed that pelargonidin specifically inhibits the activation of CDK1 and blocks the G2-M transition of the cell cycle. In addition, DNA fragmentation was observed along with induction of cytochrome c release-mediated apoptosis. Hence, the aim of the present study was to investigate the molecular mechanism of pelargonidin's action on cell cycle regulators CDK1, CDK4, and CDK6 as well as the substrate-binding domain of DNMT1 and DNMT3A, which regulate the epigenetic signals related to DNA methylation. The results of docking analysis, binding free energy calculation, and molecular dynamics simulation correlated with the experimental results, and pelargonidin showed a specific interaction with CDK1. In this context, pelargonidin may also inhibit the recognition of DNA and catalytic binding by DNMT1 and DNMT3A. The HOMO-LUMO analysis mapped the functional groups of pelargonidin. Prediction of pharmacological descriptors suggested that pelargonidin can serve as a multitarget inhibitor for cancer treatment.
Collapse
Affiliation(s)
- Natesan Karthi
- Department of Biochemistry, Periyar University, Salem 636011, Tamilnadu, India; Division of Biotechnology, Advanced Institute of Environment and Bioscience, Safety, Environment and Life Science Institute, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, South Korea
| | | | | | - Antony Stalin
- Center for Advanced Studies (CAS) in Botany, University of Madras, Guindy Campus, Chennai - 600 025. India
| | - Vaiyapuri Manju
- Department of Biochemistry, Periyar University, Salem 636011, Tamilnadu, India.
| | - Sanjeev Kumar Singh
- Computer Aided Drug Designing and Molecular Modeling Lab, Department of Bioinformatics, Alagappa University, Karaikudi 630 003, Tamil Nadu, India
| | - Ravi Cyril
- Department of Zoology, Thiagarajar College, Madurai 625009, Tamilnadu, India
| | - Sang-Myeong Lee
- Division of Biotechnology, Advanced Institute of Environment and Bioscience, Safety, Environment and Life Science Institute, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, South Korea.
| |
Collapse
|
97
|
Multiple endpoints to evaluate pristine and remediated titanium dioxide nanoparticles genotoxicity in lung epithelial A549 cells. Toxicol Lett 2017; 276:48-61. [DOI: 10.1016/j.toxlet.2017.05.016] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 05/05/2017] [Accepted: 05/15/2017] [Indexed: 12/14/2022]
|
98
|
Saeki Y, Abe M, Kono F, Nakazato A, Ishihara Y, Abe H. DNA methylation analysis of cancer-related genes from cell-free DNA of patients with cancer. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.pmu.2017.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
|
99
|
Pitfalls and Opportunities for Epigenomic Analyses Focused on Disease Diagnosis, Prognosis, and Therapy. Trends Pharmacol Sci 2017. [PMID: 28625497 DOI: 10.1016/j.tips.2017.05.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
100
|
Liou SH, Wu WT, Liao HY, Chen CY, Tsai CY, Jung WT, Lee HL. Global DNA methylation and oxidative stress biomarkers in workers exposed to metal oxide nanoparticles. JOURNAL OF HAZARDOUS MATERIALS 2017; 331:329-335. [PMID: 28273583 DOI: 10.1016/j.jhazmat.2017.02.042] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/11/2017] [Accepted: 02/22/2017] [Indexed: 06/06/2023]
Abstract
This is the first study to assess global methylation, oxidative DNA damage, and lipid peroxidation in workers with occupational exposure to metal oxide nanomaterials (NMs). Urinary and white blood cell (WBC) 8-hydroxydeoxyguanosine (8-OHdG), and exhaled breath condensate (EBC) 8-isoprostane were measured as oxidative stress biomarkers. WBC global methylation was measured as an epigenetic alteration. Exposure to TiO2, SiO2, and indium tin oxide (ITO) resulted in significantly higher oxidative biomarkers such as urinary 8-OHdG and EBC 8-isoprostane. However, significantly higher WBC 8-OHdG and lower global methylation were only observed in ITO handling workers. Significant positive correlations were noted between WBC and urinary 8-OHdG (Spearman correlation r=0.256, p=0.003). Furthermore, a significant negative correlation was found between WBC 8-OHdG and global methylation (r=-0.272, p=0.002). These results suggest that exposure to metal oxide NMs may lead to global methylation, DNA oxidative damage, and lipid peroxidation.
Collapse
Affiliation(s)
- Saou-Hsing Liou
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Wei-Te Wu
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Hui-Yi Liao
- National Institute of Environmental Health Sciences, National Health Research Institutes, Zhunan, Miaoli County, Taiwan
| | - Chao-Yu Chen
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Cheng-Yen Tsai
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Wei-Ting Jung
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Hui-Ling Lee
- Department of Chemistry, Fu Jen Catholic University, New Taipei City, Taiwan.
| |
Collapse
|