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Zhang J, Li C, Sun L, Sun D, Zhao T. P53‑microRNA interactions regulate the response of colorectal tumor cells to oxaliplatin under normoxic and hypoxic conditions. Oncol Rep 2023; 50:219. [PMID: 37921068 PMCID: PMC10636723 DOI: 10.3892/or.2023.8656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2023] Open
Abstract
Oxaliplatin (OXA)‑containing regimens are used as first‑line chemotherapy in colorectal cancer (CRC). However, OXA resistance remains a major challenge in CRC treatment. CRC cells that adapt to hypoxia can potentially develop OXA resistance, and the underlying molecular mechanisms still need to be further investigated. In the current study, the OXA drug sensitivity of two CRC cell lines, HCT116 (TP53WT) and HT29 (TP53MT), was compared under both normoxic and hypoxic conditions. It was found that under normoxic condition, HCT116 cells showed significantly higher OXA sensitivity than HT29 cells. However, both cell lines showed remarkable OXA resistance under hypoxic conditions. It was also revealed that P53 levels were increased after OXA and hypoxia treatment in HCT116 cells but not in HT29 cells. Notably, knocking down P53WT decreased normoxic but increased hypoxic OXA sensitivity in HCT116 cells, which did not exist in HT29 cells. Molecular analysis indicated that P53WT activated microRNA (miR)‑26a and miR‑34a in OXA treatment and activated miR‑23a in hypoxia treatment. Cell proliferation experiments indicated that a high level of miR‑23a decreased OXA sensitivity and that a high level of miR‑26a or miR‑34a increased OXA sensitivity in HCT116 cells. Additionally, it was demonstrated that miR‑26a, miR‑34a and miR‑23a affect cell apoptosis through regulation of MCL‑1, EZH2, BCL‑2, SMAD 4 and STAT3. Taken together, the present findings revealed the dual function of P53 in regulating cellular chemo‑sensitivity and highlighted the role of P53‑miR interactions in the response of CRC cells to OXA chemotherapy under normoxic and hypoxic conditions.
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Affiliation(s)
- Jiayu Zhang
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Chenguang Li
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Luanbiao Sun
- Gastrointestinal Colorectal and Anal Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Denghua Sun
- Department of Breast Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Tiancheng Zhao
- Department of Endoscopy Center, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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2
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Przybyszewski J, Malawski M, Lichołai S. GraphTar: applying word2vec and graph neural networks to miRNA target prediction. BMC Bioinformatics 2023; 24:436. [PMID: 37978418 PMCID: PMC10657114 DOI: 10.1186/s12859-023-05564-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short, non-coding RNA molecules that regulate gene expression by binding to specific mRNAs, inhibiting their translation. They play a critical role in regulating various biological processes and are implicated in many diseases, including cardiovascular, oncological, gastrointestinal diseases, and viral infections. Computational methods that can identify potential miRNA-mRNA interactions from raw data use one-dimensional miRNA-mRNA duplex representations and simple sequence encoding techniques, which may limit their performance. RESULTS We have developed GraphTar, a new target prediction method that uses a novel graph-based representation to reflect the spatial structure of the miRNA-mRNA duplex. Unlike existing approaches, we use the word2vec method to accurately encode RNA sequence information. In conjunction with the novel encoding method, we use a graph neural network classifier that can accurately predict miRNA-mRNA interactions based on graph representation learning. As part of a comparative study, we evaluate three different node embedding approaches within the GraphTar framework and compare them with other state-of-the-art target prediction methods. The results show that the proposed method achieves similar performance to the best methods in the field and outperforms them on one of the datasets. CONCLUSIONS In this study, a novel miRNA target prediction approach called GraphTar is introduced. Results show that GraphTar is as effective as existing methods and even outperforms them in some cases, opening new avenues for further research. However, the expansion of available datasets is critical for advancing the field towards real-world applications.
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Affiliation(s)
- Jan Przybyszewski
- Sano Centre for Computational Medicine, Czarnowiejska 36, 30-054, Cracow, Poland.
| | - Maciej Malawski
- Sano Centre for Computational Medicine, Czarnowiejska 36, 30-054, Cracow, Poland
| | - Sabina Lichołai
- Division of Molecular Biology and Clinical Genetics, Faculty of Medicine, Jagiellonian University Medical College, Skawińska 8, 31-066, Cracow, Poland
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3
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Effects of TP53 Mutations and miRs on Immune Responses in the Tumor Microenvironment Important in Pancreatic Cancer Progression. Cells 2022; 11:cells11142155. [PMID: 35883598 PMCID: PMC9318640 DOI: 10.3390/cells11142155] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 01/27/2023] Open
Abstract
Approximately 90% of pancreatic cancers are pancreatic ductal adenocarcinomas (PDAC). PDAC is the fourth leading cause of cancer death world-wide. Therapies for PDAC are largely ineffective due to the dense desmoplastic tumor microenvironment which prevents chemotherapeutic drugs and small molecule inhibitors from exerting effective anti-cancer effects. In this review, we will discuss the roles of TP53 and miRs on the PDAC tumor microenvironment and how loss of the normal functions of TP53 promote tumor progression. The TP53 gene is mutated in approximately 50% of pancreatic cancers. Often, these TP53 mutations are point mutations which confer additional functions for the TP53 proteins. These are called gain of function (GOF) mutations (mut). Another class of TP53 mutations are deletions which result in loss of the TP53 protein; these are referred to TP53-null mutations. We have organized this review into various components/properties of the PDAC microenvironment and how they may be altered in the presence of mutant TP53 and loss of certain miR expression.
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4
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da Silva J, da Costa CC, de Farias Ramos I, Laus AC, Sussuchi L, Reis RM, Khayat AS, Cavalli LR, Pereira SR. Upregulated miRNAs on the TP53 and RB1 Binding Seedless Regions in High-Risk HPV-Associated Penile Cancer. Front Genet 2022; 13:875939. [PMID: 35812732 PMCID: PMC9263206 DOI: 10.3389/fgene.2022.875939] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 05/26/2022] [Indexed: 12/13/2022] Open
Abstract
Cancer development by the human papillomavirus (HPV) infection can occur through the canonical HPV/p53/RB1 pathway mediated by the E2/E6/E7 viral oncoproteins. During the transformation process, HPV inserts its genetic material into host Integration Sites (IS), affecting coding genes and miRNAs. In penile cancer (PeCa) there is limited data on the miRNAs that regulate mRNA targets associated with HPV, such as the TP53 and RB1 genes. Considering the high frequency of HPV infection in PeCa patients in Northeast Brazil, global miRNA expression profiling was performed in high-risk HPV-associated PeCa that presented with TP53 and RB1 mRNA downregulated expression. The miRNA expression profile of 22 PeCa tissue samples and five non-tumor penile tissues showed 507 differentially expressed miRNAs: 494 downregulated and 13 upregulated (let-7a-5p, miR-130a-3p, miR-142-3p, miR-15b-5p miR-16-5p, miR-200c-3p, miR-205-5p, miR-21-5p, miR-223-3p, miR-22-3p, miR-25-3p, miR-31-5p and miR-93-5p), of which 11 were identified to be in HPV16-IS and targeting TP53 and RB1 genes. One hundred and thirty-one and 490 miRNA binding sites were observed for TP53 and RB1, respectively, most of which were in seedless regions. These findings suggest that up-regulation of miRNA expression can directly repress TP53 and RB1 expression by their binding sites in the non-canonical seedless regions.
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Affiliation(s)
- Jenilson da Silva
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís, Brazil
| | - Carla Cutrim da Costa
- Degree in Biological Sciences, Department of Biology, Federal University of Maranhão, São Luís, Brazil
| | - Ingryd de Farias Ramos
- Postgraduate Program in Oncology and Medical Sciences, Federal University of Pará, Belém, Brazil
| | - Ana Carolina Laus
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Luciane Sussuchi
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - Rui Manuel Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | - André Salim Khayat
- Oncology Research Center, Federal University of Pará, Belém, Brazil
- Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | | | - Silma Regina Pereira
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís, Brazil
- *Correspondence: Silma Regina Pereira,
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5
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Han L, Huang Z, Liu Y, Ye L, Li D, Yao Z, Wang C, Zhang Y, Yang H, Tan Z, Tang J, Yang Z. MicroRNA-106a regulates autophagy-related cell death and EMT by targeting TP53INP1 in lung cancer with bone metastasis. Cell Death Dis 2021; 12:1037. [PMID: 34718338 PMCID: PMC8557209 DOI: 10.1038/s41419-021-04324-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 02/06/2023]
Abstract
Bone metastasis is one of the most serious complications in lung cancer patients. MicroRNAs (miRNAs) play important roles in tumour development, progression and metastasis. A previous study showed that miR-106a is highly expressed in the tissues of lung adenocarcinoma with bone metastasis, but its mechanism remains unclear. In this study, we showed that miR-106a expression is dramatically increased in lung cancer patients with bone metastasis (BM) by immunohistochemical analysis. MiR-106a promoted A549 and SPC-A1 cell proliferation, migration and invasion in vitro. The results of bioluminescence imaging (BLI), micro-CT and X-ray demonstrated that miR-106a promoted bone metastasis of lung adenocarcinoma in vivo. Mechanistic investigations revealed that miR-106a upregulation promoted metastasis by targeting tumour protein 53-induced nuclear protein 1 (TP53INP1)-mediated metastatic progression, including cell migration, autophagy-dependent death and epithelial-mesenchymal transition (EMT). Notably, autophagy partially attenuated the effects of miR-106a on promoting bone metastasis in lung adenocarcinoma. These findings demonstrated that restoring the expression of TP53INP1 by silencing miR-106a may be a novel therapeutic strategy for bone metastatic in lung adenocarcinoma.
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Affiliation(s)
- Lei Han
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Zeyong Huang
- Medical School, Kunming University of Science and Technology, Kunming, Yunnan, China
| | - Yan Liu
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Lijuan Ye
- Department of Pathology, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Dongqi Li
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Zhihong Yao
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Cao Wang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Ya Zhang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Hang Yang
- Department of Rehabilitation Medicine, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Zunxian Tan
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Jiadai Tang
- Department of Gastrointestinal Oncology, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China
| | - Zuozhang Yang
- Bone and Soft Tissue Tumors Research Center of Yunnan Province, Department of Orthopaedics, Yunnan Cancer Hospital, The Third Affiliated Hospital of Kunming Medical University, Yunnan Cancer Center, Kunming, Yunnan, China.
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6
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Fonseca A, Ramalhete SV, Mestre A, Pires das Neves R, Marreiros A, Castelo-Branco P, Roberto VP. Identification of colorectal cancer associated biomarkers: an integrated analysis of miRNA expression. Aging (Albany NY) 2021; 13:21991-22029. [PMID: 34547721 PMCID: PMC8507258 DOI: 10.18632/aging.203556] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/30/2021] [Indexed: 12/24/2022]
Abstract
Colorectal cancer is one of the leading causes of cancer-related deaths worldwide. This complex disease still holds severe problems concerning diagnosis due to the high invasiveness nature of colonoscopy and the low accuracy of the alternative diagnostic methods. Additionally, patient heterogeneity even within the same stage is not properly reflected in the current stratification system. This scenario highlights the need for new biomarkers to improve non-invasive screenings and clinical management of patients. MicroRNAs (miRNAs) have emerged as good candidate biomarkers in cancer as they are stable molecules, easily measurable and detected in body fluids thus allowing for non-invasive diagnosis and/or prognosis. In this study, we performed an integrated analysis first using 4 different datasets (discovery cohorts) to identify miRNAs associated with colorectal cancer development, unveil their role in this disease by identifying putative targets and regulatory networks and investigate their ability to serve as biomarkers. We have identified 26 differentially expressed miRNAs which interact with frequently deregulated genes known to participate in commonly altered pathways in colorectal cancer. Most of these miRNAs have high diagnostic power, and their prognostic potential is evidenced by panels of 5 miRNAs able to predict the outcome of stage II and III colorectal cancer patients. Notably, 8 miRNAs were validated in three additional independent cohorts (validation cohorts) including a plasma cohort thus reinforcing the value of miRNAs as non-invasive biomarkers.
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Affiliation(s)
- André Fonseca
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal
| | - Sara Ventura Ramalhete
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal.,Algarve Biomedical Center Research Institute (ABC-RI), Faro 8005-139, Portugal
| | - André Mestre
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal.,Algarve Biomedical Center Research Institute (ABC-RI), Faro 8005-139, Portugal
| | - Ricardo Pires das Neves
- CNC, Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, Coimbra 3004-517, Portugal.,IIIUC-Institute of Interdisciplinary Research, University of Coimbra, Coimbra 3030-789, Portugal
| | - Ana Marreiros
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal.,Algarve Biomedical Center Research Institute (ABC-RI), Faro 8005-139, Portugal
| | - Pedro Castelo-Branco
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal.,Algarve Biomedical Center Research Institute (ABC-RI), Faro 8005-139, Portugal.,Champalimaud Research Program, Champalimaud Center for the Unknown, Lisbon 1400-038, Portugal
| | - Vânia Palma Roberto
- Faculty of Medicine and Biomedical Sciences (FMCB), University of Algarve, Campus de Gambelas, Faro 8005-139, Portugal.,Algarve Biomedical Center Research Institute (ABC-RI), Faro 8005-139, Portugal.,Centre of Marine Sciences (CCMAR), University of Algarve, Faro 8005-139, Portugal
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7
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Zhang Y, Zhu L, Wang X. NEM-Tar: A Probabilistic Graphical Model for Cancer Regulatory Network Inference and Prioritization of Potential Therapeutic Targets From Multi-Omics Data. Front Genet 2021; 12:608042. [PMID: 33968127 PMCID: PMC8100334 DOI: 10.3389/fgene.2021.608042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Targeted therapy has been widely adopted as an effective treatment strategy to battle against cancer. However, cancers are not single disease entities, but comprising multiple molecularly distinct subtypes, and the heterogeneity nature prevents precise selection of patients for optimized therapy. Dissecting cancer subtype-specific signaling pathways is crucial to pinpointing dysregulated genes for the prioritization of novel therapeutic targets. Nested effects models (NEMs) are a group of graphical models that encode subset relations between observed downstream effects under perturbations to upstream signaling genes, providing a prototype for mapping the inner workings of the cell. In this study, we developed NEM-Tar, which extends the original NEMs to predict drug targets by incorporating causal information of (epi)genetic aberrations for signaling pathway inference. An information theory-based score, weighted information gain (WIG), was proposed to assess the impact of signaling genes on a specific downstream biological process of interest. Subsequently, we conducted simulation studies to compare three inference methods and found that the greedy hill-climbing algorithm demonstrated the highest accuracy and robustness to noise. Furthermore, two case studies were conducted using multi-omics data for colorectal cancer (CRC) and gastric cancer (GC) in the TCGA database. Using NEM-Tar, we inferred signaling networks driving the poor-prognosis subtypes of CRC and GC, respectively. Our model prioritized not only potential individual drug targets such as HER2, for which FDA-approved inhibitors are available but also the combinations of multiple targets potentially useful for the design of combination therapies.
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Affiliation(s)
- Yuchen Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Lina Zhu
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Xin Wang
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China.,Key Laboratory of Biochip Technology, Biotech and Health Centre, Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
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8
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Moghadamnia F, Ghoraeian P, Minaeian S, Talebi A, Farsi F, Akbari A. MicroRNA Expression and Correlation with mRNA Levels of Colorectal Cancer-Related Genes. J Gastrointest Cancer 2020; 51:271-279. [PMID: 31102171 DOI: 10.1007/s12029-019-00249-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION MicroRNAs (miRNAs), as a family of non-coding RNAs, have opened a new window in cancer biology and transcriptome. It has been revealed that miRNAs post-transcriptionally regulate the gene expression and involve in colorectal cancer (CRC) development and progression. Our aim was to examine the differential expression of miRNAs in a CRC and to correlate their expression levels with mRNA levels of CRC-related genes (K-ras, APC, p53). MATERIALS AND METHODS Seventy-two colorectal tumor tissues from patients with newly diagnosed CRC and 72 matched normal adjacent tissues were analyzed. Relative expression of seven CRC-related miRNAs (miR-21, miR-31, miR-20a, miR-133b, and miR-145, miR-135b and let-7g) and three CRC-related genes (K-ras, APC, p53) was detected using the SYBR Green quantitative real-time PCR technique. The correlation between gene expression levels and clinicopathological features was evaluated. RESULTS Our results showed a significant difference between the two groups for the expression level of miR-21, miR-31, miR-145, and miR-20a (P < 0.001). Also, a significant difference between the two groups for the expression level of K-ras was found (P < 0.001). Further analysis revealed an inverse significant correlation between miR-145 and K-ras (R2 = 0.662, P < 0.001), while a positive correlation was observed between miR-21 and K-ras (R2 = 0.732, P < 0.001). CONCLUSION Dysregulation of miRNAs and correlation with molecular signaling pathways designated a biological role for miRNAs in various cellular mechanisms underlying CRC. On the other hand, the pattern of miRNAs expression and its correlation with transcriptional status are helpful to discovery biomarkers and design therapeutics for CRC.
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Affiliation(s)
- Farahnaz Moghadamnia
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Pegah Ghoraeian
- Department of Genetics, Tehran Medical Sciences Branch, Islamic Azad University, Tehran, Iran
| | - Sara Minaeian
- Institute of Immunology and Infectious Diseases, Antimicrobial Resistance Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Atefeh Talebi
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Farnaz Farsi
- Department of Nutrition, School of Public Health, Iran University of Medical Sciences, Tehran, Iran
| | - Abolfazl Akbari
- Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran. .,Colorectal Research Center, Rasoul-e- Akram Hospital, Sattarkhan Ave, Niyayesh St, Tehran, Iran.
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9
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Angioregulatory microRNAs in Colorectal Cancer. Cancers (Basel) 2019; 12:cancers12010071. [PMID: 31887997 PMCID: PMC7016698 DOI: 10.3390/cancers12010071] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/21/2019] [Accepted: 12/23/2019] [Indexed: 12/14/2022] Open
Abstract
Colorectal cancer (CRC) is one of the leading causes of cancer mortality. Angiogenesis is a rate-determining step in CRC development and metastasis. The balance of angiogenic and antiangiogenic factors is crucial in this process. Angiogenesis-related genes can be regulated post-transcriptionally by microRNAs (miRNAs) and some miRNAs have been shown to shuttle between tumor cells and the tumor microenvironment (TME). MiRNAs have context-dependent actions and can promote or suppress angiogenesis dependent on the type of cancer. On the one hand, miRNAs downregulate anti-angiogenic targets and lead to angiogenesis induction. Tumor suppressor miRNAs, on the other hand, enhance anti-angiogenic response by targeting pro-angiogenic factors. Understanding the interaction between these miRNAs and their target mRNAs will help to unravel molecular mechanisms involved in CRC progression. The aim of this article is to review the current literature on angioregulatory miRNAs in CRC.
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Ge H, Yan Y, Guo L, Tian F, Wu D. Prognostic role of HSPs in human gastrointestinal cancer: a systematic review and meta-analysis. Onco Targets Ther 2018; 11:351-359. [PMID: 29391812 PMCID: PMC5774472 DOI: 10.2147/ott.s155816] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Background Heat shock proteins (HSPs) have been reported to be overexpressed in a wide range of human tumors. It has been shown that HSPs act as an oncogenic regulator and are involved in tumorigenesis. The clinical and prognostic significance of HSPs in gastrointestinal cancers (GICs) remains controversial. The aim of this study was to conduct a meta-analysis to assess the prognostic value of HSPs in GICs. Materials and methods A literature search was performed in PubMed, Cochrane Library, Web of Science, and Embase databases. Data on the relationship between expression of HSPs and survival outcomes were extracted. Pooled hazard ratios (HRs) with 95% CI were calculated. Results The expression of HSPs was not associated with the overall survival (OS) of GIC patients; however, it was significantly associated with worse OS for gastric cancer (GC) and colorectal cancer (CRC) patients. Conclusion Current evidence suggests that a high level of HSPs may not be a potential marker to predict the survival rate for every type of GICs. However, the expression of HSPs may predict a poor prognosis for GC and CRC patients.
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Affiliation(s)
- Hua Ge
- Department of Gastrointestinal Surgery
| | - Yan Yan
- Quality Control Department, The First People's Hospital of Zunyi, Zunyi Medical University, Huichuan, Zunyi, Guizhou, China
| | | | - Fei Tian
- Department of Gastrointestinal Surgery
| | - Di Wu
- Department of Gastrointestinal Surgery
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11
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Li W, Huang Y, Sargsyan D, Khor TO, Guo Y, Shu L, Yang AY, Zhang C, Paredes-Gonzalez X, Verzi M, Hart RP, Kong AN. Epigenetic alterations in TRAMP mice: epigenome DNA methylation profiling using MeDIP-seq. Cell Biosci 2018; 8:3. [PMID: 29344347 PMCID: PMC5767006 DOI: 10.1186/s13578-018-0201-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 01/05/2018] [Indexed: 01/15/2023] Open
Abstract
Purpose We investigated the genomic DNA methylation profile of prostate cancer in transgenic adenocarcinoma of the mouse prostate (TRAMP) cancer model and to analyze the crosstalk among targeted genes and the related functional pathways. Methods Prostate DNA samples from 24-week-old TRAMP and C57BL/6 male mice were isolated. The DNA methylation profiles were analyzed by methylated DNA immunoprecipitation (MeDIP) followed by next-generation sequencing (MeDIP-seq). Canonical pathways, diseases and function and network analyses of the different samples were then performed using the Ingenuity® Pathway Analysis (IPA) software. Some target genes with significant difference in methylation were selected for validation using methylation specific primers (MSP) and qPCR. Results TRAMP mice undergo extensive aberrant CpG hyper- and hypo-methylation. There were 2147 genes with a significant (log2-change ≥ 2) change in CpG methylation between the two groups, as mapped by the IPA software. Among these genes, the methylation of 1105 and 1042 genes was significantly decreased and increased, respectively, in TRAMP prostate tumors. The top associated disease identified by IPA was adenocarcinoma; however, the cAMP response element-binding protein (CREB)-, histone deacetylase 2 (HDAC2)-, glutathione S-transferase pi (GSTP1)- and polyubiquitin-C (UBC)-related pathways showed significantly altered methylation profiles based on the canonical pathway and network analyses. MSP and qPCR results of genes of interests corroborated with MeDIP-seq findings. Conclusions This is the first MeDIP-seq with IPA analysis of the TRAMP model to provide novel insight into the genome-wide methylation profile of prostate cancer. Studies on epigenetics, such as DNA methylation, will potentially provide novel avenues and strategies for further development of biomarkers targeted for treatment and prevention approaches for prostate cancer.
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Affiliation(s)
- Wenji Li
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Ying Huang
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Davit Sargsyan
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Tin Oo Khor
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Yue Guo
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Limin Shu
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
| | - Anne Yuqing Yang
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Chengyue Zhang
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ximena Paredes-Gonzalez
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA.,3Graduate Program in Pharmaceutical Sciences, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Michael Verzi
- 4Department of Genetics, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ronald P Hart
- 5Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ 08854 USA
| | - Ah-Ng Kong
- 1Center for Phytochemical Epigenome Studies, Ernest Mario School of Pharmacy, The State University of New Jersey, Piscataway, NJ 08854 USA.,2Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, 160 Frelinghuysen Road, Piscataway, NJ 08854 USA
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12
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Liu K, Chen W, Lei S, Xiong L, Zhao H, Liang D, Lei Z, Zhou N, Yao H, Liang Y. Wild-type and mutant p53 differentially modulate miR-124/iASPP feedback following pohotodynamic therapy in human colon cancer cell line. Cell Death Dis 2017; 8:e3096. [PMID: 29022915 PMCID: PMC5682646 DOI: 10.1038/cddis.2017.477] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 07/18/2017] [Accepted: 08/04/2017] [Indexed: 12/15/2022]
Abstract
Colorectal cancer (CRC) is a most common digestive system malignant tumor. p53 mutation has essential role in cancers and is frequently observed in CRC and presents a huge challenge. p53 mutation has been reported to attenuate the inhibitory effect of photofrin-based photodynamic therapy (PDT). p53 mutation-induced gain of function brings up the dysfunction of carcinogenic factors, including miRNAs. Our research found that PDT suppressed CRC cell viability, reduced the tumor size and prolonged the survival time, all of which could be attenuated by p53 mutation or deletion. After p53 mutation or deletion, several miRNA expression levels were downregulated, among which miR-124 was the most strongly downregulated, whereas iASPP expression was upregulated. p53 binds to the promoter of miR-124 to promote its expression and then inhibited iASPP expression, so as to amplify the inhibitory effect of PDT on wild-type p53 cells. In p53-mutant or -deleted cells, this binding no longer worked to promote miR-124 expression, and iASPP expression increased, finally resulted in promoted CRC cell viability upon PDT. The interactive modulation among miR and iASPP in p53-mutant or -deleted cells may serve as a crucial pathway, which mediates therapy resistance when p53 is mutated or deleted, in the process of PDT treatment of CRC.
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Affiliation(s)
- Kuijie Liu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Weidong Chen
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Sanlin Lei
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Li Xiong
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hua Zhao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Dong Liang
- The People's Hospital of Zhengzhou University (Henan Provincial People's Hospital), Zhengzhou 450003, China
| | - Zhendong Lei
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Nanjiang Zhou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Hongliang Yao
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Ying Liang
- Department of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, Hunan 410004, China
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13
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Du YY, Zhang QJ, Sun GP. Expression and Clinical Significance of Cytokeratin-19 and Thymidine Kinase-1 in Advanced Gastrointestinal Cancer. Chin Med J (Engl) 2017; 129:2168-72. [PMID: 27625087 PMCID: PMC5022336 DOI: 10.4103/0366-6999.189919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background: As the clinical value of cytokeratin-19 (CK19) and thymidine kinase-1 (TK1) in advanced gastrointestinal cancer remains controversial, we investigated their expression and clinical significance in this disease. Methods: A total of 171 advanced gastrointestinal cancer patients were prospectively enrolled in this study. The mRNA level of CK19 was detected using quantitative real-time reverse transcription-polymerase chain reaction (PCR) in all patients, along with a control group of fifty healthy individuals. Furthermore, detection of TK1 protein was carried out in 96 patients using a chemiluminescence dot blot assay. The primary endpoint was overall survival (OS) time. Results: Positive CK19 mRNA expression was detected in 74 (43.3%) of the 171 patients and positive TK1 expression was detected in 66 (68.8%) of the 96 patients. Furthermore, of the 96 patients, 36 (37.5%) were positive for both TK1 protein and CK19 mRNA, 30 (31.3%) were negative for TK1 protein, and 15 (15.6%) were negative for TK1 protein and positive for CK19 mRNA. The results indicated that patients who were positive for CK19 mRNA expression had significantly shorter OS times than those who were negative for it (median OS 7.7 vs. 9.7 months, respectively; P = 0.02). Moreover, patients who were positive for CK19 mRNA and TK1 protein expression had shorter OS times (median OS 6.1 months) than those who were positive for CK19 mRNA and negative for TK1 protein expression (median OS 9.1 months; P = 0.028). Positive CK19 mRNA expression was significantly associated with shorter OS in the univariate analysis (P = 0.027). Based on a multivariate Cox regression analysis, CK19 mRNA together with TK1 protein expression (P = 0.024) was an independent predictor for OS in gastrointestinal cancer patients. Conclusions: Our results suggest that positive expression of CK19 mRNA and TK1 protein is closely correlated with poor prognosis in advanced gastrointestinal cancer. Furthermore, both CK19 and TK1 are possible gastrointestinal cancer biomarkers.
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Affiliation(s)
- Ying-Ying Du
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Qiu-Jun Zhang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
| | - Guo-Ping Sun
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, China
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14
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Gan W, Zhao H, Li T, Liu K, Huang J. CDK1 interacts with iASPP to regulate colorectal cancer cell proliferation through p53 pathway. Oncotarget 2017; 8:71618-71629. [PMID: 29069733 PMCID: PMC5641076 DOI: 10.18632/oncotarget.17794] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 04/26/2017] [Indexed: 01/19/2023] Open
Abstract
CDK1 (cyclin-dependent kinase 1) is a critical regulator of the G2-M checkpoint. CDK1 is considered a possible target for cancer treatment. In addition to CDK1, iASPP plays essential role in maintaining cancer cell proliferation. In the present study, we monitored the expression of CDK1 and iASPP at mRNA and protein levels in CRC tissues and cell lines; we also predicted that iASPP protein might interact with CDK1 protein. By performing GST pull-down assay and Co-IP assay, we confirmed the interaction of CDK1 and iASPP protein. In CRC cell lines, CDK1 interacted with iASPP to affect CRC cell proliferation and apoptosis; moreover, the p53 apoptosis pathway was involved in this progression. Taken together, we revealed that CDK1 and iASPP was up-regulated in CRC tissues and cell lines; CDK1 protein interacted with iASPP protein to affect CRC cell proliferation and apoptosis through the p53 apoptosis pathway. CDK1 and iASPP might serve as not only promising targets in CRC treatment, but also efficient prognostic markers. From the perspective of protein interactions, we provided a novel theoretical basis for targeted therapy of CRC.
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Affiliation(s)
- Wei Gan
- Department of General Surgery, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Hua Zhao
- Department of General Surgery, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Tiegang Li
- Department of General Surgery, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Kuijie Liu
- Department of General Surgery, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
| | - Jiangsheng Huang
- Department of Minimally Invasive Surgery, the Second Xiangya Hospital, Central South University, Changsha 410011, Hunan, China
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15
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Zhao ZJ, Shen J. Circular RNA participates in the carcinogenesis and the malignant behavior of cancer. RNA Biol 2017; 14:514-521. [PMID: 26649774 PMCID: PMC5449088 DOI: 10.1080/15476286.2015.1122162] [Citation(s) in RCA: 328] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 11/02/2015] [Accepted: 11/16/2015] [Indexed: 01/01/2023] Open
Abstract
Circular RNAs (circRNAs) are long, non-coding RNAs that result from the non-canonical splicing of linear pre-mRNAs. However, the characteristics and the critical role of circRNA in co-/post-transcriptional regulation were not well recognized until the "microRNA sponge" function of circRNA is discovered. Recent studies have mainly been devoted to the function of the circular RNA sponge for miR-7 (ciRS-7) and sex-determining region Y (SRY) by targeting microRNA-7 (miR-7) and microRNA-138 (miR-138), respectively. In this review, we illustrate the specific role of circRNAs in a wide variety of cancers and in regulating the biological behavior of cancers via miR-7 or miR-138 regulation. Furthermore, circRNA, together with its gene silencing ability, also shows its potential in RNA interference (RNAi) therapy by binding to target RNAs, which provides a novel perspective in cancer treatment. Thus, this review concerns the biogenesis, biological function, oncogenesis, progression and possible therapies for cancer involving circRNAs.
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Affiliation(s)
- Zhen-Jun Zhao
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
| | - Jun Shen
- State Key Laboratory for Oncogenes and Related Genes, Key Laboratory of Gastroenterology & Hepatology, Ministry of Health, Division of Gastroenterology and Hepatology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai Cancer Institute, Shanghai Institute of Digestive Disease, Shanghai, China
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16
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Walter RFH, Vollbrecht C, Werner R, Wohlschlaeger J, Christoph DC, Schmid KW, Mairinger FD. microRNAs are differentially regulated between MDM2-positive and negative malignant pleural mesothelioma. Oncotarget 2017; 7:18713-21. [PMID: 26918730 PMCID: PMC4951323 DOI: 10.18632/oncotarget.7666] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/02/2016] [Indexed: 12/14/2022] Open
Abstract
Background Malignant pleural mesothelioma (MPM) is a highly aggressive tumour first-line treated with a combination of cisplatin and pemetrexed. MDM2 and P14/ARF (CDKN2A) are upstream regulators of TP53 and may contribute to its inactivation. In the present study, we now aimed to define the impact of miRNA expression on this mechanism. Material and Methods 24 formalin-fixed paraffin-embedded (FFPE) tumour specimens were used for miRNA expression analysis of the 800 most important miRNAs using the nCounter technique (NanoString). Significantly deregulated miRNAs were identified before a KEGG-pathway analysis was performed. Results 17 miRNAs regulating TP53, 18 miRNAs regulating MDM2, and 11 miRNAs directly regulating CDKN2A are significantly downregulated in MDM2-expressing mesotheliomas. TP53 is downregulated in MDM2-negative tumours through miRNAs with a miSVR prediction score of 11.67, RB1 with a prediction score of 8.02, MDM2 with a prediction score of 4.50 and CDKN2A with a prediction score of 1.27. Conclusion MDM2 expression seems to impact miRNA expression levels in MPM. Especially, miRNAs involved in TP53-signaling are strongly decreased in MDM2-positive mesotheliomas. A better understanding of its tumour biology may open the chance for new therapeutic approaches and thereby augment patients' outcome.
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Affiliation(s)
- Robert Fred Henry Walter
- Ruhrlandklinik, West German Lung Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Claudia Vollbrecht
- Institute of Pathology, University Hospital Cologne, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
| | - Robert Werner
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jeremias Wohlschlaeger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Daniel Christian Christoph
- Department of Medical Oncology, West German Cancer Centre, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kurt Werner Schmid
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Fabian Dominik Mairinger
- Institute of Pathology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.,Institute of Pathology, Division of Molecular Pathology, Charité, Berlin, Germany
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17
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Alhosin M, Omran Z, Zamzami MA, Al-Malki AL, Choudhry H, Mousli M, Bronner C. Signalling pathways in UHRF1-dependent regulation of tumor suppressor genes in cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2016; 35:174. [PMID: 27839516 PMCID: PMC5108085 DOI: 10.1186/s13046-016-0453-5] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/02/2016] [Indexed: 12/13/2022]
Abstract
Epigenetic silencing of tumor suppressor genes (TSGs) through DNA methylation and histone changes is a main hallmark of cancer. Ubiquitin-like with PHD and RING Finger domains 1 (UHRF1) is a potent oncogene overexpressed in various solid and haematological tumors and its high expression levels are associated with decreased expression of several TSGs including p16INK4A, BRCA1, PPARG and KiSS1. Using its several functional domains, UHRF1 creates a strong coordinated dialogue between DNA methylation and histone post-translation modification changes causing the epigenetic silencing of TSGs which allows cancer cells to escape apoptosis. To ensure the silencing of TSGs during cell division, UHRF1 recruits several enzymes including histone deacetylase 1 (HDAC1), DNA methyltransferase 1 (DNMT1) and histone lysine methyltransferases G9a and Suv39H1 to the right place at the right moment. Several in vitro and in vivo works have reported the direct implication of the epigenetic player UHRF1 in tumorigenesis through the repression of TSGs expression and suggested UHRF1 as a promising target for cancer treatment. This review describes the molecular mechanisms underlying UHRF1 regulation in cancer and discusses its importance as a therapeutic target to induce the reactivation of TSGs and subsequent apoptosis.
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Affiliation(s)
- Mahmoud Alhosin
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia. .,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia. .,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia. .,Biochemistry Department, Faculty of Sciences, Cancer and Mutagenesis Unit, King Fahd Centre for Medical Research, King Abdulaziz University, P. O. Box 80203, Jeddah, 21589, Saudi Arabia.
| | - Ziad Omran
- College of Pharmacy, Umm Al-Qura University, 21955, Makkah, Kingdom of Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdulrahman L Al-Malki
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hani Choudhry
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer Metabolism and Epigenetic Unit, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia.,Cancer and Mutagenesis Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia.,Center of Innovation in Personalized Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Marc Mousli
- Laboratoire de Biophotonique et Pharmacologie, UMR 7213 CNRS, Université de Strasbourg, Faculté de pharmacie, 74 route du Rhin, 67401, Illkirch, France
| | - Christian Bronner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964 CNRS UMR 7104, Université de Strasbourg, 1 rue Laurent Fries, 67404, Illkirch, France.
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18
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Loss-of-function screening to identify miRNAs involved in senescence: tumor suppressor activity of miRNA-335 and its new target CARF. Sci Rep 2016; 6:30185. [PMID: 27457128 PMCID: PMC4960484 DOI: 10.1038/srep30185] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/30/2016] [Indexed: 12/13/2022] Open
Abstract
Significance of microRNAs (miRs), small non-coding molecules, has been implicated in a variety of biological processes. Here, we recruited retroviral insertional mutagenesis to obtain induction of an arbitrary noncoding RNAs, and coupled it with a cell based loss-of-function (5-Aza-2′-deoxycytidine (5Aza-dC)-induced senescence bypass) screening system. Cells that escaped 5-Aza-dC-induced senescence were subjected to miR-microarray analysis with respect to the untreated control. We identified miR-335 as one of the upregulated miRs. In order to characterize the functional significance, we overexpressed miR-335 in human cancer cells and found that it caused growth suppression. We demonstrate that the latter accounted for inhibition of 5-Aza-dC incorporation into the cell genome, enabling them to escape from induction of senescence. We also report that CARF (Collaborator of ARF) is a new target of miR-335 that regulates its growth suppressor function by complex crosstalk with other proteins including p16INK4A, pRB, HDM2 and p21WAF1.
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19
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Abstract
Tumor suppresser gene TP53 is one of the most frequently deleted
or mutated genes in gastrointestinal cancers. As a transcription factor, p53
regulates a number of important protein coding genes to control cell cycle, cell
death, DNA damage/repair, stemness, differentiation and other key cellular
functions. In addition, p53 is also able to activate the expression of a number
of small non-coding microRNAs (miRNAs) through direct binding to the promoter
region of these miRNAs. Many miRNAs have been identified to be potential tumor
suppressors by regulating key effecter target mRNAs. Our understanding of the
regulatory network of p53 has recently expanded to include long non-coding RNAs
(lncRNAs). Like miRNA, lncRNAs have been found to play important roles in cancer
biology. With our increased understanding of the important functions of these
non-coding RNAs and their relationship with p53, we are gaining exciting new
insights into the biology and function of cells in response to various growth
environment changes. In this review we summarize the current understanding of
the ever expanding involvement of non-coding RNAs in the p53 regulatory network
and its implications for our understanding of gastrointestinal cancer.
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Affiliation(s)
- Andrew Fesler
- Translational Research Laboratory, Department of Pathology, Stony Brook University, Stony Brook, USA
| | - Ning Zhang
- Department of Pharmacy, Dalian Medical University, Dalian, China
| | - Jingfang Ju
- Translational Research Laboratory, Department of Pathology, Stony Brook University, Stony Brook, USA
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20
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Zhou E, Hui NA, Shu M, Wu B, Zhou J. Systematic analysis of the p53-related microRNAs in breast cancer revealing their essential roles in the cell cycle. Oncol Lett 2015; 10:3488-3494. [PMID: 26788155 PMCID: PMC4665839 DOI: 10.3892/ol.2015.3751] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 09/04/2015] [Indexed: 02/07/2023] Open
Abstract
Numerous miRNAs have been found to be involved in the regulation of the p53 signaling pathway. Conversely, p53 regulates the transcription or processing of microRNAs (miRNAs). Given that complexities in the association between p53 and miRNAs exist, and due to the rapidly increasing amount of literature regarding the interactions between p53 and miRNAs, the present study systematically analyzed the associations between miRNAs and p53 in breast cancer using a literature-based discovery approach, natural language processing. A total of 22 miRNAs were found to be associated with p53. Next, three popular online tools (PicTar, miRanda and TargetScan) were used to predict the targets of each miRNA, and certain targets were validated by experiments. Gene Ontology annotation and network analysis demonstrated that the majority of the targets of the p53-related miRNAs were enriched in the cell cycle process. These results suggest that, in addition to regulating the transcription of cell cycle-related genes, p53 also indirectly modulates the cell cycle via miRNAs.
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Affiliation(s)
- Enxiang Zhou
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - N A Hui
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Min Shu
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, P.R. China
| | - Baiping Wu
- Department of General Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, P.R. China
| | - Jianlin Zhou
- Key Laboratory of Protein Chemistry and Developmental Biology of the Ministry of Education, College of Life Science, Hunan Normal University, Changsha, Hunan 410081, P.R. China
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21
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Abstract
The Four-and-a-half LIM (FHL)-only protein is a subfamily of protein members under the LIM-only protein family. These proteins are identified by their characteristic four and a half cysteinerich LIM homeodomain. Five members have been categorized into the FHL subfamily, which are FHL1, FHL2, FHL3, FHL4 and activator of CREM in testis (ACT) in human. FHL2 is amongst the most examined members within the family. Fhl2, the gene that code for the protein, is transcriptionally regulated by diverse types of transcription factors, for example, p53, serum response factor (SRF), and specificity protein 1 (Sp1). The expression of FHL2 is found in different tissues and organs and has been reported as a critical participant influencing the wide types of cancer such as breast cancer, gastrointestinal (GI) cancers, liver cancer and prostate cancer. The expression profile of FHL2 appeared to have a significant functional role in the carcinogenesis of these cancers which are mediated by different types of transcription factor including both tumor suppressors and inducers. In this review, we will first describe the molecular network governing FHL2 expression, which focus on the transcription factors conveying FHL2-initiated responses. In the second part, FHL2-linked cancers and the underlying molecular machinery will be discussed. Factors other than transcriptional regulation which may involve the cancer progression such as mutations of fhl2 and posttranslational modifications of the protein will also be mentioned.
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Affiliation(s)
- Cyanne Ye Cao
- School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China
| | - Simon Wing-Fai Mok
- School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.
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22
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Hünten S, Kaller M, Drepper F, Oeljeklaus S, Bonfert T, Erhard F, Dueck A, Eichner N, Friedel CC, Meister G, Zimmer R, Warscheid B, Hermeking H. p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses. Mol Cell Proteomics 2015; 14:2609-29. [PMID: 26183718 DOI: 10.1074/mcp.m115.050237] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/20/2022] Open
Abstract
We determined the effect of p53 activation on de novo protein synthesis using quantitative proteomics (pulsed stable isotope labeling with amino acids in cell culture/pSILAC) in the colorectal cancer cell line SW480. This was combined with mRNA and noncoding RNA expression analyses by next generation sequencing (RNA-, miR-Seq). Furthermore, genome-wide DNA binding of p53 was analyzed by chromatin-immunoprecipitation (ChIP-Seq). Thereby, we identified differentially regulated proteins (542 up, 569 down), mRNAs (1258 up, 415 down), miRNAs (111 up, 95 down) and lncRNAs (270 up, 123 down). Changes in protein and mRNA expression levels showed a positive correlation (r = 0.50, p < 0.0001). In total, we detected 133 direct p53 target genes that were differentially expressed and displayed p53 occupancy in the vicinity of their promoter. More transcriptionally induced genes displayed occupied p53 binding sites (4.3% mRNAs, 7.2% miRNAs, 6.3% lncRNAs, 5.9% proteins) than repressed genes (2.4% mRNAs, 3.2% miRNAs, 0.8% lncRNAs, 1.9% proteins), suggesting indirect mechanisms of repression. Around 50% of the down-regulated proteins displayed seed-matching sequences of p53-induced miRNAs in the corresponding 3'-UTRs. Moreover, proteins repressed by p53 significantly overlapped with those previously shown to be repressed by miR-34a. We confirmed up-regulation of the novel direct p53 target genes LINC01021, MDFI, ST14 and miR-486 and showed that ectopic LINC01021 expression inhibits proliferation in SW480 cells. Furthermore, KLF12, HMGB1 and CIT mRNAs were confirmed as direct targets of the p53-induced miR-34a, miR-205 and miR-486-5p, respectively. In line with the loss of p53 function during tumor progression, elevated expression of KLF12, HMGB1 and CIT was detected in advanced stages of cancer. In conclusion, the integration of multiple omics methods allowed the comprehensive identification of direct and indirect effectors of p53 that provide new insights and leads into the mechanisms of p53-mediated tumor suppression.
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Affiliation(s)
- Sabine Hünten
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Markus Kaller
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany
| | - Friedel Drepper
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Silke Oeljeklaus
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Thomas Bonfert
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Florian Erhard
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Anne Dueck
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Norbert Eichner
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Caroline C Friedel
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Gunter Meister
- §§Biochemistry Center Regensburg (BZR), Laboratory for RNA Biology, University of Regensburg, 93053 Regensburg, Germany
| | - Ralf Zimmer
- ‡‡Institute for Informatics, Ludwig-Maximilians-University Munich, 80337 Munich, Germany
| | - Bettina Warscheid
- ‖Department of Biochemistry and Functional Proteomics, Faculty of Biology and BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; **Center for Biological Systems Analysis (ZBSA), University of Freiburg, 79104 Freiburg, Germany
| | - Heiko Hermeking
- From the ‡Experimental and Molecular Pathology, Institute of Pathology, Ludwig-Maximilians-University Munich, Thalkirchner Straβe 36, 80337 Munich, Germany; §German Cancer Consortium (DKTK), D-69120 Heidelberg, Germany; ¶German Cancer Research Center (DKFZ), D-69120 Heidelberg, Germany;
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MicroRNAs as Regulator of Signaling Networks in Metastatic Colon Cancer. BIOMED RESEARCH INTERNATIONAL 2015; 2015:823620. [PMID: 26064956 PMCID: PMC4438141 DOI: 10.1155/2015/823620] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/06/2015] [Accepted: 04/06/2015] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are a class of small, noncoding RNA molecules capable of regulating gene expression translationally and/or transcriptionally. A large number of evidence have demonstrated that miRNAs have a functional role in both physiological and pathological processes by regulating the expression of their target genes. Recently, the functionalities of miRNAs in the initiation, progression, angiogenesis, metastasis, and chemoresistance of tumors have gained increasing attentions. Particularly, the alteration of miRNA profiles has been correlated with the transformation and metastasis of various cancers, including colon cancer. This paper reports the latest findings on miRNAs involved in different signaling networks leading to colon cancer metastasis, mainly focusing on miRNA profiling and their roles in PTEN/PI3K, EGFR, TGFβ, and p53 signaling pathways of metastatic colon cancer. The potential of miRNAs used as biomarkers in the diagnosis, prognosis, and therapeutic targets in colon cancer is also discussed.
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Zhang G, An H, Fang X. MicroRNA-144 regulates proliferation, invasion, and apoptosis of cells in malignant solitary pulmonary nodule via zinc finger E-box-binding homeobox 1. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:5960-7. [PMID: 26191328 PMCID: PMC4503199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/30/2015] [Indexed: 06/04/2023]
Abstract
AIMS This study was to investigate the expression of microRNA (miR)-144 in malignant solitary pulmonary nodule (SPN) tissues and peripheral blood, as well as the biological function of miR-144 in the occurrence and development of lung cancer. METHODS In this study, 39 malignant and 30 benign SPN patients were included. The expression of miR-144 was examined using quantitative real-time polymerase chain reaction. Receiver operating characteristic (ROC) curve was used to identify the clinical value of miR-144 in the early diagnosis of malignant SPN. MTT assay was performed to determine A549 cell proliferation and Transwell assay was used to detect changes in A549 cell invasion and migration ability. Flow cytometry was performed to monitor cell apoptosis, while Western blotting assay was used to measure protein expression levels. At last, dual-luciferase reporter assay was employed to test whether miR-144 regulates zinc finger E-box-binding homeobox 1 (ZEB1) gene expression. RESULTS Expression of miR-144 was reduced in patients with malignant SPN. miR-144 had diagnostic value for malignant SPN. Proliferation of A549 cells was inhibited by miR-144. Invasion ability of A549 cells was reduced by miR-144. Apoptosis of A549 cells was promoted by miR-144. miR-144 induced A549 cell apoptosis by targeting ZEB1 protein. miR-144 regulated the expression of ZEB1 by interacting with its 3'-UTR region. CONCLUSIONS Expression of miR-144 is reduced in malignant SPN tissues and peripheral blood, being of clinical value in the diagnosis of malignant SPN. miR-144 promotes the apoptosis of lung cancer cells, and inhibits the proliferation, invasion and migration of lung cancer by regulating ZEB1 gene.
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Affiliation(s)
- Guizhi Zhang
- Department of Respiratory Medicine, General Hospital of Chinese People’s Liberation ArmyBeijing 100853, P. R. China
| | - Huaijie An
- Center of Basic Medical Sciences, Navy General Hospital of People’s Liberation ArmyBeijing 100048, P. R. China
| | - Xiangqun Fang
- Department of Respiratory Medicine, General Hospital of Chinese People’s Liberation ArmyBeijing 100853, P. R. China
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Zhang C, Liu J, Wang X, Feng Z. The regulation of the p53/MDM2 feedback loop by microRNAs. RNA & DISEASE 2015; 2:e502. [PMID: 25995995 DOI: 10.14800/rd.502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Tumor suppressor p53 and its signaling pathway play a central role in tumor prevention. The E3 ubiquitin ligase MDM2, which is a direct p53 transcriptional target and also the most critical negative regulator of p53, forms an autoregulatory negative feedback loop with p53 in the cell to tightly regulate the levels and activity of p53. MicroRNAs (miRNAs) are endogenously expressed small non-coding RNAs that play a critical role in the post-translational regulation of gene expression. Recent studies have revealed that miRNAs directly regulate the levels of p53 or MDM2 to modulate the p53 function in tumor suppression. Recently, we identified miR-339-5p as a new miRNA that directly represses MDM2 to activate p53 and enhance p53 function in tumor suppression. Thus, miRNAs have become a new but important component of the p53 signaling pathway through regulating the p53/MDM2 feedback loop.
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Affiliation(s)
- Cen Zhang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Juan Liu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Xiaolong Wang
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, State University of New Jersey, New Brunswick, NJ 08903, USA
| | - Zhaohui Feng
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey, Rutgers, State University of New Jersey, New Brunswick, NJ 08903, USA
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