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Chen HY, Li XN, Yang L, Ye CX, Chen ZL, Wang ZJ. CircVMP1 promotes glycolysis and disease progression by upregulating HKDC1 in colorectal cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:1617-1630. [PMID: 38009649 DOI: 10.1002/tox.24061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 10/16/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND Circular RNAs (circRNAs) have been reported to play important roles in cancers. Here, we characterized circVMP1 (hsa_circ_0006508), an important circRNA which promoted glycolysis and disease progression in colorectal cancer (CRC). In this study, we aimed to explore the mechanism by which circVMP1 regulated tumor glycolysis and its related pathways in promoting CRC cell proliferation and metastasis. METHODS The expression level of circVMP1 in CRC tissues and adjacent normal tissues was detected using quantitative PCR. In vitro and in vivo functional experiments were used to evaluate the effects of circVMP1 in the regulation of CRC cell proliferation and migration. Mitochondrial stress tests and glycolysis stress tests were conducted to detect the effect of circVMP1 on oxidative phosphorylation and glycolysis. Dual-luciferase reporter and RNA immunoprecipitation assays were used to evaluate the interaction between circVMP1, miR-3167, and HKDC1. RESULTS We demonstrated that the level of circVMP1 was significantly upregulated in CRC tissues compared with normal tissues. In HCT116 and SW480 cells, overexpression of circVMP1 promoted proliferation, metastasis, and glycolysis. In vivo analysis indicated that circVMP1 accelerated the proliferation of xenograft tumors. As for the mechanism, overexpression of circVMP1 increased the levels of hexokinase domain component 1 (HKDC1) through competitive binding with miR-3167. CONCLUSION Our study reported that circVMP1 was one of the tumor driver genes that promoted CRC malignant progression and glycolysis by upregulating HKDC1. CircVMP1/miR-3167/HKDC1 was a signaling axis that might be a target for CRC therapy.
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Affiliation(s)
- Hong-Yu Chen
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Xiang-Nan Li
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Lei Yang
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
- Medical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Chun-Xiang Ye
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhi-Lei Chen
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
| | - Zhen-Jun Wang
- Department of General Surgery, Beijing Chao-Yang Hospital, Capital Medical University, Beijing, China
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Wang J, Jiang W, Liu S, Shi K, Zhang Y, Chen Y, Shan J, Wang Y, Xu X, Li C, Li X. Exosome-derived miR-182-5p promoted cholangiocarcinoma progression and vasculogenesis by regulating ADK/SEMA5a/PI3K pathway. Liver Int 2024; 44:370-388. [PMID: 37950359 DOI: 10.1111/liv.15773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 09/26/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND AND AIMS Increasing evidence suggested that miRNAs regulated the expression of pivotal genes involved in oncogenesis and malignant phenotype. In this project, the purpose was to make an inquiry to the effect and mechanism of miR-182-5p in the progression of cholangiocarcinoma. METHODS By analysing TCGA and GEO databases, combined with tissue expression levels, miR-182-5p was identified as one of the most valuable miRNAs for research. The function and relationships between miR-182-5p and downstream target genes were both verified by in vitro and in vivo experiments. Methylation-specific PCR and bisulphite sequencing were used to detect the methylation level changes of downstream gene promoter. RESULTS We found that miR-182-5p could be taken up by exosomes secreted from cholangiocarcinoma. Moreover, exosomal derived miR-182-5p promoted vascular endothelial cell proliferation and migration and induced angiogenesis by targeting ADK/SEMA5a. Subsequently, the PI3K/AKT/mTOR signalling pathway was activated and ultimately caused resistance to gemcitabine and cisplatin. CONCLUSIONS Our findings suggested that the miR-182-5p/ADK/SEMA5a axis might serve as a potential therapeutic target for cholangiocarcinoma.
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Affiliation(s)
- Jifei Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wangjie Jiang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Shuochen Liu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Kuangheng Shi
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yaodong Zhang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
- NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yananlan Chen
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jijun Shan
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Yuming Wang
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiao Xu
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Changxian Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
- NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiangcheng Li
- Hepatobiliary Center, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Key Laboratory of Liver Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
- NHC Key Laboratory of Living Donor Liver Transplantation, Nanjing Medical University, Nanjing, Jiangsu, China
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Weng YH, Yu WT, Luo YP, Liu C, Gu XX, Chen HY, Liu HB. Association between miR-365 polymorphism and ischemic stroke in a Chinese population. Front Neurol 2023; 14:1260230. [PMID: 37840919 PMCID: PMC10569467 DOI: 10.3389/fneur.2023.1260230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Background Ischemic stroke (IS) represents a major cause of morbidity and mortality across the globe. The aberrant expression of miR-365 has been found to be implicated in a wide array of human diseases, including atherosclerosis and cancer. Studies on single-nucleotide polymorphisms (SNPs) in miRNA genes can help gain insight into the susceptibility to the condition. This study aimed to examine the relationship between miR-365 SNPs and the risk of IS. Methods The study recruited 215 IS patients and 220 controls. The SNPscans genotyping was employed to genotype three polymorphic loci (rs121224, rs30230, and rs178553) of miR-365. The relative expression of miR-365 in peripheral blood mononuclear cells of the patients and controls was determined by using real-time quantitative PCR. Results The miR-365 rs30230 polymorphism exhibited a significant association with the risk of developing IS (TC vs. CC: adjusted OR = 0.55, 95% CI: 0.33-0.92, P = 0.022; TT vs. CC: adjusted OR = 0.34, 95% CI: 0.14-0.85, P = 0.021; TC +TT vs. CC: adjusted OR = 0.51, 95% CI: 0.31-0.83, P = 0.007; T vs. C: adjusted OR = 0.57, 95% CI: 0.39-0.83, P = 0.004). Haplotype analysis revealed that the C-T-G haplotype was associated with a decreased risk of IS (OR = 0.68, 95% CI: 0.46-1.00, P = 0.047). Furthermore, miR-365 expression was significantly higher in IS patients than in controls (P < 0.001). Interestingly, patients with rs30230 TC or TT genotypes had lower miR-365 levels compared to their counterparts with CC genotypes (P < 0.001). Conclusions The miR-365 rs30230 polymorphism might bear an association with IS susceptibility in the Chinese population, and the rs30230 TC/TT genotype might be a protective factor against IS.
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Affiliation(s)
- Yin-Hua Weng
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Wen-Tao Yu
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Yan-Ping Luo
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Chao Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Xi-Xi Gu
- School of Clinical Medicine, Guilin Medical University, Guilin, China
| | - Huo-Ying Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Hong-Bo Liu
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
- College of Medical Laboratory Science, Guilin Medical University, Guilin, China
- Guangxi Health Commission Key Laboratory of Glucose and Lipid Metabolism Disorders, Guangxi Key Laboratory of Metabolic Reprogramming and Intelligent Medical Engineering for Chronic Diseases, The Second Affiliated Hospital of Guilin Medical University, Guilin, China
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4
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Kalita A, Sikora-Skrabaka M, Nowakowska-Zajdel E. Role of Some microRNA/ADAM Proteins Axes in Gastrointestinal Cancers as a Novel Biomarkers and Potential Therapeutic Targets—A Review. Curr Issues Mol Biol 2023; 45:2917-2936. [PMID: 37185715 PMCID: PMC10136553 DOI: 10.3390/cimb45040191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 04/05/2023] Open
Abstract
Gastrointestinal (GI) cancers are some of the most common cancers in the world and their number is increasing. Their etiology and pathogenesis are still unclear. ADAM proteins are a family of transmembrane and secreted metalloproteinases that play a role in cancerogenesis, metastasis and neoangiogenesis. MicroRNAs are small single-stranded non-coding RNAs that take part in the post-transcriptional regulation of gene expression. Some ADAM proteins can be targets for microRNAs. In this review, we analyze the impact of microRNA/ADAM protein axes in GI cancers.
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Affiliation(s)
- Agnieszka Kalita
- Department of Nutrition-Related Disease Prevention, Department of Metabolic Disease Prevention, Faculty of Health Sciences in Bytom, Medical University of Silesia in Katowice, 40-055 Katowice, Poland
- Department of Clinical Oncology, No. 4 Provincial Specialist Hospital, 41-902 Bytom, Poland
| | - Magdalena Sikora-Skrabaka
- Department of Nutrition-Related Disease Prevention, Department of Metabolic Disease Prevention, Faculty of Health Sciences in Bytom, Medical University of Silesia in Katowice, 40-055 Katowice, Poland
- Department of Clinical Oncology, No. 4 Provincial Specialist Hospital, 41-902 Bytom, Poland
| | - Ewa Nowakowska-Zajdel
- Department of Nutrition-Related Disease Prevention, Department of Metabolic Disease Prevention, Faculty of Health Sciences in Bytom, Medical University of Silesia in Katowice, 40-055 Katowice, Poland
- Department of Clinical Oncology, No. 4 Provincial Specialist Hospital, 41-902 Bytom, Poland
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5
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Dinami R, Petti E, Porru M, Rizzo A, Ganci F, Sacconi A, Ostano P, Chiorino G, Trusolino L, Blandino G, Ciliberto G, Zizza P, Biroccio A. TRF2 cooperates with CTCF for controlling the oncomiR-193b-3p in colorectal cancer. Cancer Lett 2022; 533:215607. [PMID: 35240232 DOI: 10.1016/j.canlet.2022.215607] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 02/11/2022] [Accepted: 02/24/2022] [Indexed: 12/14/2022]
Abstract
The Telomeric Repeat binding Factor 2 (TRF2), a key protein involved in telomere integrity, is over-expressed in several human cancers and promotes tumor formation and progression. Recently, TRF2 has been also found outside telomeres where it can affect gene expression. Here we provide evidence that TRF2 is able to modulate the expression of microRNAs (miRNAs), small non-coding RNAs altered in human tumors. Among the miRNAs regulated by TRF2, we focused on miR-193b-3p, an oncomiRNA that positively correlates with TRF2 expression in human colorectal cancer patients from The Cancer Genome Atlas dataset. At the mechanistic level, the control of miR-193b-3p expression requires the cooperative activity between TRF2 and the chromatin organization factor CTCF. We found that CTCF physically interacts with TRF2, thus driving the proper positioning of TRF2 on a binding site located upstream the miR-193b-3p host-gene. The binding of TRF2 on the identified region is necessary for promoting the expression of miR-193b3p which, in turn, inhibits the translation of the onco-suppressive methyltransferase SUV39H1 and promotes tumor cell proliferation. The translational relevance of the oncogenic properties of miR-193b-3p was confirmed in patients, in whom the association between TRF2 and miR-193b-3p has a prognostic value.
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Affiliation(s)
- Roberto Dinami
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Eleonora Petti
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Manuela Porru
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Angela Rizzo
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Federica Ganci
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Andrea Sacconi
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Paola Ostano
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, via Malta 3, Biella, 13900, Italy
| | - Giovanna Chiorino
- Cancer Genomics Lab, Fondazione Edo ed Elvo Tempia, via Malta 3, Biella, 13900, Italy
| | - Livio Trusolino
- Department of Oncology, University of Torino, Strada Provinciale 142, Candiolo, TO, 10060, Italy; Laboratory of Translational Cancer Medicine, Candiolo Cancer Institute, FPO - IRCCS, Strada Provinciale 142, Candiolo, TO, 10060, Italy
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Gennaro Ciliberto
- Scientific Direction, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy
| | - Pasquale Zizza
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy.
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCCS - Regina Elena National Cancer Institute, via Elio Chianesi 53, Rome, 00144, Italy.
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6
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Liu C, Zou X, Song G, Fan X, Peng S, Zhang S, Geng X, zhou X, Wang T, Cheng W, Zhu W. Comprehensive analysis of negatively correlated miRNA-mRNA regulatory pairs associated with microsatellite instability in colorectal cancer. Cancer Biomark 2022; 34:471-483. [PMID: 35253734 DOI: 10.3233/cbm-210408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND: Several studies have demonstrated that microRNAs (miRNAs) and target mRNAs are associated with different frequencies of microsatellite instability. OBJECTIVE: The study aimed to elucidate the profiles of miRNAs and target mRNAs expression and their associations with the phenotypic hallmarks of microsatellite instability in colorectal cancers (CRC) by integrating transcriptomic, immunophenotype, methylation, mutation, and survival data. METHODS: Differentially expressed miRNAs (DEmiRNAs) and mRNAs (DEmRNAs) were screened out and then the miRNA-mRNA regulatory pairs were identified through two databases. We verified that the expression levels were detected in 40 microsatellite instable (MSI) and 40 microsatellite stable (MSS) CRC samples and used the logistic regression and the Cox regression method to evaluate the diagnostic and prognostic value of negative regulatory pairs respectively. RESULTS: The best diagnostic model that combines miR-31-5p, PLAGL2, miR-361-5p, and RAB27B, which were associated with immune microenvironment, tumor mutation burden (TMB), and overall DNA methylation, could significantly predict microsatellite instability in colon tissues. MiR-31-5p and RAB27B could also predict the overall survival of MSS CRCs. CONCLUSION: This study generated a predictive model of the combination of miRNAs and mRNAs to distinguish MSI versus MSS CRCs and elaborated their potential molecular mechanisms and biological functions.
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Affiliation(s)
- Cheng Liu
- Department of Gastroenterology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Xuan Zou
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Guoxin Song
- Department of Pathology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Xingchen Fan
- Department of Oncology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Shuang Peng
- Department of Oncology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Shiyu Zhang
- Department of Oncology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Xiangnan Geng
- Department of Clinical Engineer, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Xin zhou
- Department of Oncology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Tongshan Wang
- Department of Oncology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Wenfang Cheng
- Department of Gastroenterology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
| | - Wei Zhu
- Department of Oncology, Jiangsu Province People’s Hospital and Nanjing Medical University First Affiliated Hospital, Nanjing, Jiangsu, China
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Ionica E, Gaina G, Tica M, Chifiriuc MC, Gradisteanu-Pircalabioru G. Contribution of Epithelial and Gut Microbiome Inflammatory Biomarkers to the Improvement of Colorectal Cancer Patients’ Stratification. Front Oncol 2022; 11:811486. [PMID: 35198435 PMCID: PMC8859258 DOI: 10.3389/fonc.2021.811486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 12/20/2021] [Indexed: 12/24/2022] Open
Abstract
In order to ensure that primary endpoints of clinical studies are attained, the patients’ stratification is an important aspect. Selection criteria include age, gender, and also specific biomarkers, such as inflammation scores. These criteria are not sufficient to achieve a straightforward selection, however, in case of multifactorial diseases, with unknown or partially identified mechanisms, occasionally including host factors, and the microbiome. In these cases, the efficacy of interventions is difficult to predict, and as a result, the selection of subjects is often random. Colorectal cancer (CRC) is a highly heterogeneous disease, with variable clinical features, outcomes, and response to therapy; the CRC onset and progress involves multiple sequential steps with accumulation of genetic alterations, namely, mutations, gene amplification, and epigenetic changes. The gut microbes, either eubiotic or dysbiotic, could influence the CRC evolution through a complex and versatile crosstalk with the intestinal and immune cells, permanently changing the tumor microenvironment. There have been significant advances in the development of personalized approaches for CRC screening, treatment, and potential prevention. Advances in molecular techniques bring new criteria for patients’ stratification—mutational analysis at the time of diagnosis to guide treatment, for example. Gut microbiome has emerged as the main trigger of gut mucosal homeostasis. This may impact cancer susceptibility through maintenance of the epithelial/mucus barrier and production of protective metabolites, such as short-chain fatty acids (SCFAs) via interactions with the hosts’ diet and metabolism. Microbiome dysbiosis leads to the enrichment of cancer-promoting bacterial populations, loss of protective populations or maintaining an inflammatory chronic state, all of which contribute to the development and progression of CRC. Meanwhile, variations in patient responses to anti-cancer immuno- and chemotherapies were also linked to inter-individual differences in intestine microbiomes. The authors aim to highlight the contribution of epithelial and gut microbiome inflammatory biomarkers in the improvement of CRC patients’ stratification towards a personalized approach of early diagnosis and treatment.
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Affiliation(s)
- Elena Ionica
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- *Correspondence: Elena Ionica,
| | - Gisela Gaina
- Laboratory of Cell Biology, Neuroscience and Experimental Miology, Victor Babes National Institute of Pathology, Bucharest, Romania
| | - Mihaela Tica
- Bucharest Emergency University Hospital, Bucharest, Romania
| | - Mariana-Carmen Chifiriuc
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania
- Biological Science Division, Romanian Academy of Sciences, Bucharest, Romania
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8
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Chen Y, Liu H, Ning S, Wei C, Li J, Wei W, Zhang L. The High Ratio of the Plasma miR-96/miR-99b Correlated With Poor Prognosis in Patients With Metastatic Colorectal Cancer. Front Mol Biosci 2022; 8:799060. [PMID: 35047559 PMCID: PMC8762210 DOI: 10.3389/fmolb.2021.799060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/01/2021] [Indexed: 12/18/2022] Open
Abstract
Object: This study aims to clarify the expression of plasma miRNA in CRC patients, and to clarify the potential use of these miRNAs in diagnosis and prognosis, and to establish a prognostic model to initially explore its clinical value. Methods: We detected the expression of 6 miRNAs in normal colon epithelial cell lines and colorectal cancer cell lines by qRT-PCR and they were validated in the tissues of three subtypes: 20 healthy subjects, 41 pCRC and 49 mCRC patients. COX regression and ROC analyses use to evaluate the diagnostic and prognostic efficacy of candidate miRNAs. Subsequently, we initially established a nomogram prognostic model. MiRNA is also used to construct miRNA-mRNA interaction network and PPI network modules. Results: Five miRNAs showed significant differential expression in pCRC, mCRC patients and normal groups. ROC analysis showed that CEA, miR-96, miR-99b and miR-96/miR-99b are distinguishable from pCRC and mCRC patients, with AUC ranging from 0.65 to 0.91; among them, the ratio of miR-96/miR-99b is stronger than any diagnostic indicators, such as CEA and CA125. Multivariate survival analysis identified miR-96, miR-99b, N stage, M stage and clinical stage as independent prognostic indicators of mCRC. The nomogram based on these 5 characteristics has satisfactory prognostic values. Conclusion: Our data indicate that plasma miR-96/miR-99b can be used as a promising biomarker for early detection of mCRC patients; our nomogram has a promising evaluation value.
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Affiliation(s)
- Yi Chen
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Haizhou Liu
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Cancer Molecular Medicine Engineering Research Center, Nanning, China
| | - Shufang Ning
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Changhong Wei
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Jilin Li
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Wene Wei
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China
| | - Litu Zhang
- Department of Research, Guangxi Medical University Cancer Hospital, Nanning, China.,Guangxi Cancer Molecular Medicine Engineering Research Center, Nanning, China
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Moloudizargari M, Rahmani J, Asghari MH, Goel A. The prognostic role of miR-31 in colorectal cancer: the results of a meta-analysis of 4720 patients. Epigenomics 2021; 14:101-112. [PMID: 34894715 DOI: 10.2217/epi-2021-0277] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Aims: To study the association between miR-31 expression and clinical outcomes in colorectal cancer. Methods: A systematic search was performed and 16 studies were found eligible. To calculate the combined hazard ratio (HR), the DerSimonian and Laird random-effects model was used. Results: Pooled analysis revealed significant associations between high miR-31 expression and poor overall (HR: 0.68; 95% CI: 0.47-0.97; I2: 68.6%) and progression-free survival (HR: 0.49; 95% CI: 0.33-0.73; I2: 81.1%). High expressers were more likely to have a BRAF mutation. Therapeutic regimen and the mutational status significantly affected the observed associations. Conclusion: We identified that high miR-31 expression is associated with poor overall survival and progression-free survival and has a significant predictive value for anti-EGFR response.
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Affiliation(s)
- Milad Moloudizargari
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Jamal Rahmani
- Department of Community Nutrition, Faculty of Nutrition & Food Technology, National Nutrition & Food Technology Research Institute, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Hossein Asghari
- Department of Pharmacology & Toxicology, School of Medicine, Babol University of Medical Sciences, Babol, Iran
| | - Ajay Goel
- Department of Molecular Diagnostics & Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
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10
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Wang Y, Liu J, Ren F, Chu Y, Cui B. Identification and Validation of a Four-Long Non-coding RNA Signature Associated With Immune Infiltration and Prognosis in Colon Cancer. Front Genet 2021; 12:671128. [PMID: 34290738 PMCID: PMC8287327 DOI: 10.3389/fgene.2021.671128] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/07/2021] [Indexed: 01/05/2023] Open
Abstract
The emerging evidence has demonstrated the critical roles of long non-coding RNAs (lncRNAs) as regulators in the tumor immune microenvironment (TIME). However, the tumor immune infiltration-associated lncRNAs and their clinical significance in colon cancer have not yet been thoroughly investigated. This study performed an integrative analysis of lncRNA expression profiles and immune cell infiltration profiles and identified 258 immune infiltration-associated lncRNAs. Of them, four lncRNAs (AC008494.3, LINC00926, AC022034.1, and SNHG26) were significantly and independently associated with the patient’s overall survival. Finally, we developed a tumor immune infiltration-associated lncRNA signature (TIILncSig) comprising of these four lncRNAs, which can divide colon cancer patients of The Cancer Genome Atlas (TCGA) into high-risk and low-risk groups with a significantly different outcome [Hazard ratio (HR) = 2.718, 95% CI = 1.955–3.779, p < 0.001]. Prognostic performance of the TIILncSig was further validated in another independent colon cancer cohort (HR = 1.832, 95% CI = 1.045–3.21, p = 0.034). Results of multivariate Cox regression and stratification analysis demonstrated that the TIILncSig is an independent predictive factor from other clinical features (HR = 2.687, 95% CI = 1.912–3.776, p < 0.001 for TCGA cohort and HR = 1.837, 95% CI = 1.047–3.223, p = 0.034 for GSE17538 cohort). Literature analysis provided experimental evidence supporting roles of the TIILncSig in cancer carcinogenesis and progression and immune regulation. Summary, our study will help to understand the mechanisms of lncRNAs in immune regulation in the tumor microenvironment and provide novel biomarkers or targets for prognosis prediction and therapy decision-making for patients with colon cancer.
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Affiliation(s)
- Yanbo Wang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jing Liu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fenghai Ren
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yanjie Chu
- Department of Gastroenterology and Hepatology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Binbin Cui
- Department of Colorectal Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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11
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Microsatellite Instability in Colorectal Cancers: Carcinogenesis, Neo-Antigens, Immuno-Resistance and Emerging Therapies. Cancers (Basel) 2021; 13:cancers13123063. [PMID: 34205397 PMCID: PMC8235567 DOI: 10.3390/cancers13123063] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/15/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
Simple Summary A deficient mismatch repair system (dMMR) results in microsatellite instability (MSI). The MSI status of a tumor predicts the response to immune checkpoint inhibitors (ICI) that are now approved in patients with dMMR/MSI metastatic colorectal cancers. In addition to the mechanisms through which MSI can activate the immune system via particular neo-antigens, this review reports the clinical and pre-clinical strategies being developed in the case of resistance to ICI, including emerging therapies and new biomarkers. Abstract A defect in the DNA repair system through a deficient mismatch repair system (dMMR) leads to microsatellite instability (MSI). Microsatellites are located in both coding and non-coding sequences and dMMR/MSI tumors are associated with a high mutation burden. Some of these mutations occur in coding sequences and lead to the production of neo-antigens able to trigger an anti-tumoral immune response. This explains why non-metastatic MSI tumors are associated with high immune infiltrates and good prognosis. Metastatic MSI tumors result from tumor escape to the immune system and are associated with poor prognosis and chemoresistance. Consequently, immune checkpoint inhibitors (ICI) are highly effective and have recently been approved in dMMR/MSI metastatic colorectal cancers (mCRC). Nevertheless, some patients with dMMR/MSI mCRC have primary or secondary resistance to ICI. This review details carcinogenesis and the mechanisms through which MSI can activate the immune system. After which, we discuss mechanistic hypotheses in an attempt to explain primary and secondary resistances to ICI and emerging strategies being developed to overcome this phenomenon by targeting other immune checkpoints or through vaccination and modification of microbiota.
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12
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The Clinical Assessment of MicroRNA Diagnostic, Prognostic, and Theranostic Value in Colorectal Cancer. Cancers (Basel) 2021; 13:cancers13122916. [PMID: 34208056 PMCID: PMC8230660 DOI: 10.3390/cancers13122916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/29/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary MiRNAs are of great interest within colorectal cancers in diagnosis, prognosis, and within the field of personalized treatments; they are present within different biological fluids such as blood and can lead to specific information for daily clinical use. Herein, we review the current literature focusing on miRNAs as potential diagnostic and prognostic biomarkers in patients treated for colorectal cancers. Detection and analysis of miRNA expression are cost-effective and lead to high sensitivity and specificity rates. However, it is now necessary to highlight the most sensitive and specific miRNAs for each goal, either diagnostic, prognostic, or theranostic, thanks to multicentric prospective studies. Abstract MiRNAs have recently become a subject of great interest within cancers and especially colorectal cancers in diagnosis, prognosis, and therapy decisions; herein we review the current literature focusing on miRNAs in colorectal cancers, and we discuss future challenges to use this tool on a daily clinical basis. In liquid biopsies, miRNAs seem easily accessible and can give important information toward each step of the management of colorectal cancers. However, it is now necessary to highlight the most sensitive and specific miRNAs for each goal thanks to multicentric prospective studies. Conclusions: by their diversity and the feasibility of their use, miRNAs are getting part of the armamentarium of healthcare management of colorectal cancers.
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13
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Liu J, Wen Y, Liu Z, Liu S, Xu P, Xu Y, Deng S, Hu S, Luo R, Jiang J, Yu G. VPS33B modulates c-Myc/p53/miR-192-3p to target CCNB1 suppressing the growth of non-small cell lung cancer. MOLECULAR THERAPY. NUCLEIC ACIDS 2021; 23:324-335. [PMID: 33425490 PMCID: PMC7779536 DOI: 10.1016/j.omtn.2020.11.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 11/10/2020] [Indexed: 02/08/2023]
Abstract
VPS33B is reported to be a tumor suppressor in hepatocellular carcinoma, nasopharyngeal carcinoma, colon cancer, and lung adenocarcinoma. Here, we observed that reduced VPS33B protein level was an unfavorable factor that promoted the pathogenesis of non-small cell lung cancer (NSCLC) in clinical specimens. We achieved lentivirus-mediated stable overexpression of VPS33B in NSCLC cells. Increased VPS33B reduced cell cycle transition and cell proliferation of NSCLC cells in vivo and in vitro. Knocking down VPS33B restored cell growth. Mechanism analysis indicated that miR-192-3p was induced by VPS33B and acted as a tumor suppressor of cell growth in NSCLC. Further, c-Myc or p53 was identified as a transcription factor that bound to the miR-192-3p promoter and regulated its expression. miR-192-3p directly targeted cell cycle-promoted factor CCNB1 and suppressed NSCLC cell growth. VPS33B modulated c-Myc/p53/miR-192-3p signaling to target CCNB1 by reducing activation of the Ras/ERK pathway. Our study reveals a novel molecular basis for VPS33B as a tumor suppressor to participate in the pathogenesis of NSCLC.
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Affiliation(s)
- Jiahao Liu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yinghao Wen
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Zhen Liu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
- Key Laboratory of Protein Modification and Degradation, Basic School of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
| | - Shu Liu
- Department of Breast Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou, P.R. China
| | - Ping Xu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Yan Xu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Shuting Deng
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Shulu Hu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Rongcheng Luo
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
| | - Jingwen Jiang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
- Oncology Department, Hainan Province Hospital of Traditional Chinese Medicine, Haikou, Hainan, P.R. China
| | - Guifang Yu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, Guangzhou, Guangdong, P.R. China
- Oncology Department, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, P.R. China
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14
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Wang J, Wang T, Hu S, Li J, Ni C, Ye M. Hsa_circ_0043278 Inhibits Tumorigenesis and is Downregulated in Colorectal Cancer. Cancer Manag Res 2021; 13:965-975. [PMID: 33568942 PMCID: PMC7868253 DOI: 10.2147/cmar.s289775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/14/2021] [Indexed: 12/22/2022] Open
Abstract
Purpose Circular RNAs are novel endogenous RNAs, which are considered to play a role in tumorigenesis. Nevertheless, the role as well as clinical diagnostic value of most circular RNAs in colorectal cancer are still unclear. Materials and Methods We investigated the circular RNA microarray containing expression profiles in samples of colorectal cancer patients by bioinformatics. The consequence indicated that hsa_circ_0043278 was strongly downregulated. We then measured the expression level of hsa_circ_0043278 in tissue samples of colorectal cancer by quantitative real-time polymerase chain reaction. Besides, we also explored the expression condition of the circular RNA in colorectal cancer cell lines including HCT116, SW620, and SW480. Cell counting kit-8, colony formation, and transwell assays, as well as flow cytometry, were applied to detect changes in cell proliferation, migration, apoptosis, and cell cycle progression. Results We discovered that circular RNA hsa_circ_0043278 was significantly downregulated in tumor samples (P < 0.0001) as well as cell lines (P < 0.05). The value of the area under the receiver operating characteristic curve was 0.71, with a sensitivity of 0.72 and specificity of 0.70 (P = 0.0006). Moreover, we found that overexpression of hsa_circ_0043278 suppressed proliferation and migratory abilities while promoting apoptosis in colorectal cancer cells. Conclusion Our findings revealed that hsa_circ_0043278 inhibited the tumorigenesis of colorectal cancer and could be a potential biomarker for colorectal cancer diagnosis. Besides, it hopes to become a target for treatment.
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Affiliation(s)
- Jiali Wang
- Department of Oncology and Hematology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, People's Republic of China.,School of Medicine, Ningbo University, Ningbo, People's Republic of China
| | - Tiangong Wang
- School of Medicine, Ningbo University, Ningbo, People's Republic of China
| | - Shiyun Hu
- School of Medicine, Ningbo University, Ningbo, People's Republic of China
| | - Jinyun Li
- Department of Oncology and Hematology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, People's Republic of China
| | - Chao Ni
- Department of Oncology and Hematology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, People's Republic of China
| | - Meng Ye
- Department of Oncology and Hematology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, People's Republic of China
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15
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Li Y, Long X, Wang J, Peng J, Shen K. miRNA-128 modulates bone neoplasms cells proliferation and migration through the WNT/β-catenin and EMT signal pathways. J Orthop Surg Res 2021; 16:71. [PMID: 33472642 PMCID: PMC7816476 DOI: 10.1186/s13018-020-02164-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/17/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Bone neoplasms present poor prognosis due to recurrence and metastasis. Although the role microRNAs (miRNAs) in inhibiting growth and metastasis of bone neoplasms has been investigated, the underlying potential molecular mechanisms mediated by miRNA-128 (miR-218) for the invasiveness of bone neoplasms cells are still not completely understood. The purpose of this study was to identify the regulatory mechanisms of miR-218 in bone neoplasms cells. METHODS Western blotting, quantitative reverse transcription-polymerase chain reaction (qRT-PCR), Counting Kit-8 assay, terminal deoxynucleotidyl transferase-mediated dUTP nick end labeling (TUNEL) staining, luciferase activity assay immunofluorescence, and immunohistochemistry were used to analyze the regulatory effects of miR-218 on bone neoplasms cells. RESULTS Here, the results showed that transfection of miR-128 suppressed bone neoplasms cells proliferation, migration, and invasion. Genetic knockdown of miR-128 in bone neoplasms cells suppressed the activation of the Wnt/β-catenin and epithelial-mesenchymal transition (EMT) signaling pathways. Activation of Wnt or EMT blocked miR-128-inhibited cells proliferation and migration in bone neoplasms cells. Exogenously introduced miR-128 markedly inhibited tumor regeneration in bone neoplasms xenograft models. CONCLUSIONS These results define a tumor-regulated function for miR-128 in bone neoplasms by down-regulation of the Wnt/β-catenin and EMT signal pathways, which provided a potential target for bone neoplasms gene therapy.
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Affiliation(s)
- Yang Li
- Department of Orthopedics, Chongqing General Hospital, University of the Chinese Academy of Sciences, No. 312 Zhongshanyi Road, Yuzhong District, Chongqing, 400013, China
| | - Xiaotao Long
- Department of Orthopedics, Chongqing General Hospital, University of the Chinese Academy of Sciences, No. 312 Zhongshanyi Road, Yuzhong District, Chongqing, 400013, China
| | - Ji Wang
- Department of Orthopedics, Chongqing General Hospital, University of the Chinese Academy of Sciences, No. 312 Zhongshanyi Road, Yuzhong District, Chongqing, 400013, China
| | - Jing Peng
- Department of Orthopedics, Chongqing General Hospital, University of the Chinese Academy of Sciences, No. 312 Zhongshanyi Road, Yuzhong District, Chongqing, 400013, China
| | - Kai Shen
- Department of Orthopedics, Chongqing General Hospital, University of the Chinese Academy of Sciences, No. 312 Zhongshanyi Road, Yuzhong District, Chongqing, 400013, China.
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16
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Zhai H, Zhang X, Chen S, Fan M, Ma S, Sun X. RP5-1120P11.3 promotes hepatocellular carcinoma development via the miR-196b-5p–WIPF2 axis. Biochem Cell Biol 2020; 98:238-248. [PMID: 31299165 DOI: 10.1139/bcb-2019-0053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatocellular carcinoma (HCC) remains a huge threat to human health even though the diagnosis and treatment strategies have improved rapidly in the past few decades. Increasing evidence has illustrated the critical role noncoding RNA and their regulatory network play in the pathology of HCC. Here, we identified a novel long noncoding RNA, RP5-1120P11.3, that is ectopically expressed in HCC. Further characterization of RP5-1120P11.3 revealed that it promoted proliferation and invasion of HCC cells while inhibiting apoptosis. Importantly, our data revealed that miR-196b-5p interacted with and was regulated by RP5-1120P11.3 via a sponging mechanism. Inhibition of miR-196b-5p attenuated the phenotypes resulting from RP5-1120P11.3 inhibition. Moreover, our data showed that miR-196b-5p inhibited the expression of WIPF2 in HCC, illustrating a regulatory axis of RP5-1120P11.3–miR-196b-5p–WIPF2 that facilitated the progression of HCC. In addition, our data showed that RP5-1120P11.3 contributed to xenograft generation in vivo by regulating miR-196b-5p and WIPF2. These findings suggested that the RP5-1120P11.3–miR-196b-5p–WIPF2 axis is a potential target for treatment of HCC.
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Affiliation(s)
- Hongjun Zhai
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
| | - Xinwu Zhang
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
| | - Shuo Chen
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
| | - Meng Fan
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
| | - Shuangyu Ma
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
| | - Xiaoli Sun
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
- General Surgery Department, The Second Affiliated Hospital of Xi’an Jiaotong University, 157 Xinwu Road, Xincheng District, Xi’an, Shaanxi Province, 710032, China
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17
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MiR-4435 is an UQCRB-related circulating miRNA in human colorectal cancer. Sci Rep 2020; 10:2833. [PMID: 32071343 PMCID: PMC7029028 DOI: 10.1038/s41598-020-59610-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/31/2020] [Indexed: 11/08/2022] Open
Abstract
Ubiquinol-cytochrome c reductase (UQCRB), a subunit of the mitochondrial complex III, is highly expressed in tissues from colorectal cancer patients. Since UQCRB is highly expressed in colorectal cancer, we investigated miRNAs from mutant UQCRB-expressing cell lines to identify new miRNA biomarkers. After sequencing miRNAs in the mutant UQCRB-expressing cell lines, miR-4435 was selected as a potential biomarker candidate from the six up-regulated miRNAs. The expression level of miR-4435 in the mutant UQCRB-expressing cell lines and colon cancer was increased. Notably, the expression level of miR-4435 was increased in exosomes isolated from cell culture medium, suggesting that miR-4435 is closely related to colon cancer and that large amounts of miR-4435 may be secreted outside of the cells through exosomes. Additionally, exosomes extracted from the serum samples of colorectal cancer patients showed increased miR-4435 levels depending on the cancer progression stage. Moreover, analyses of a miRNA database and mRNA-sequencing data of the mutant UQCRB-expressing cell lines revealed that TIMP3, a tumor suppressor, could be a target of miR-4435. Additionally, the expression of miR-4435 was suppressed by UQCRB inhibitor treatment whereas TIMP3 was up-regulated. Upregulation of TIMP3 decreased proliferation of the mutant UQCRB-expressing cell lines and a colorectal cancer cell line. TIMP3 was also upregulated in response to miR-4435 inhibitor and UQCRB inhibitor treatments. Furthermore, these findings suggest that miR-4435 is related to an oncogenic function in UQCRB related disease, CRC, and that effects migration and invasion on mutant UQCRB-expressing cell lines and colorectal cancer cell. In conclusion, our results identified miR-4435 as a potential circulating miRNA biomarker of colorectal cancer associated with UQCRB.
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18
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Bardin P, Foussignière T, Rousselet N, Rebeyrol C, Porter JC, Corvol H, Tabary O. miR-636: A Newly-Identified Actor for the Regulation of Pulmonary Inflammation in Cystic Fibrosis. Front Immunol 2019; 10:2643. [PMID: 31803183 PMCID: PMC6874100 DOI: 10.3389/fimmu.2019.02643] [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: 08/20/2019] [Accepted: 10/24/2019] [Indexed: 12/21/2022] Open
Abstract
Cystic fibrosis (CF) results from deficient CF transmembrane conductance regulator (CFTR) protein activity leading to defective epithelial ion transport. Pulmonary degradation due to excessive inflammation is the main cause of morbidity and mortality in CF patients. By analysing miRNAs (small RNAseq) in human primary air-liquid interface cell cultures, we measured the overexpression of miR-636 in CF patients compared to non-CF controls. We validated these results in explant biopsies and determined that the mechanism underlying miR-636 overexpression is linked to inflammation. To identify specific targets, we used bioinformatics analysis to predict whether miR-636 targets the 3′-UTR mRNA regions of IL1R1 and RANK (two pro-inflammatory cytokine receptors), IKBKB (a major protein in the NF-κB pathway), and FAM13A (a modifier gene of CF lung phenotype implicated in epithelial remodelling). Using bronchial epithelial cells from CF patients to conduct a functional analysis, we showed a direct interaction between miR-636 and IL1R1, RANK, and IKBKB, but not with FAM13A. These interactions led to a decrease in IL1R1 and IKKβ protein expression levels, while we observed an increase in RANK protein expression levels following the overexpression of miR-636. Moreover, NF-κB activity and IL-8 and IL-6 secretions decreased following the transfection of miR-636 mimics in CF cells. Similar but opposite effects were found after transfection with an antagomiR-636 in the same cells. Furthermore, we demonstrated that miR-636 was not regulated by Pseudomonas aeruginosa in our model. We went on to show that miR-636 is raised in the blood neutrophils, but not in the plasma, of CF patients and may have potential as a novel biomarker. Collectively, our findings reveal a novel actor for the regulation of inflammation in CF, miR-636, which is able to reduce constitutive NF-κB pathway activation when it is overexpressed.
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Affiliation(s)
- Pauline Bardin
- Faculté des Sciences, Sorbonne Université, Paris, France.,Inserm, Centre de Recherche Saint-Antoine, Paris, France
| | | | | | - Carine Rebeyrol
- UCL Respiratory, University College London, Hospitals NHS Foundation Trust, London, United Kingdom
| | - Joanna C Porter
- UCL Respiratory, University College London, Hospitals NHS Foundation Trust, London, United Kingdom
| | - Harriet Corvol
- Faculté des Sciences, Sorbonne Université, Paris, France.,Inserm, Centre de Recherche Saint-Antoine, Paris, France.,Département de Pédiatrie Respiratoire, Hôpital Trousseau, AP-HP, Paris, France
| | - Olivier Tabary
- Faculté des Sciences, Sorbonne Université, Paris, France.,Inserm, Centre de Recherche Saint-Antoine, Paris, France
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Mjelle R, Sjursen W, Thommesen L, Sætrom P, Hofsli E. Small RNA expression from viruses, bacteria and human miRNAs in colon cancer tissue and its association with microsatellite instability and tumor location. BMC Cancer 2019; 19:161. [PMID: 30786859 PMCID: PMC6381638 DOI: 10.1186/s12885-019-5330-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/29/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNA) and other small RNAs are frequently dysregulated in cancer and are promising biomarkers for colon cancer. Here we profile human, virus and bacteria small RNAs in normal and tumor tissue from early stage colon cancer and correlate the expression with clinical parameters. METHODS Small RNAs from colon cancer tissue and adjacent normal mucosa of 48 patients were sequenced using Illumina high-throughput sequencing. Clinical parameters were correlated with the small RNA expression data using linear models. We performed a meta-analysis by comparing publicly available small RNA sequencing datasets with our original sequencing data to confirm the main findings. RESULTS We identified 331 differentially expressed miRNAs between tumor and normal samples. We found that the major changes in miRNA expression between left and right colon are due to miRNAs located within the Hox-developmental genes, including miR-10b, miR-196b and miR-615. Further, we identified new miRNAs associated with microsatellite instability (MSI), including miR-335, miR-26 and miR-625. We performed a meta-analysis on all publicly available miRNA-seq datasets and identified 117 common miRNAs that were differentially expressed between tumor and normal tissue. The miRNAs miR-135b and miR-31 were the most significant upregulated miRNA in tumor across all datasets. The miRNA miR-133a was the most strongly downregulated miRNA in our dataset and also showed consistent downregulation in the other datasets. The miRNAs associated with MSI and tumor location in our data showed similar changes in the other datasets. Finally, we show that small RNAs from Epstein-Barr virus and Fusobacterium nucleatum are differentially expressed between tumor and normal adjacent tissue. CONCLUSIONS Small RNA profiling in colon cancer tissue revealed novel RNAs associated with MSI and tumor location. We show that Fusobacterium nucleatum are detectable at the RNA-level in colon tissue, and that both Fusobacterium nucleatum and Epstein-Barr virus separate tumor and normal tissue.
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Affiliation(s)
- Robin Mjelle
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Medical Genetics, St Olavs Hospital, Trondheim Norway, Erling Skjalgssons gt 1, 7030, Trondheim, Norway
| | - Liv Thommesen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Biomedical Laboratory Science, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,Department of Computer and Information Science, Norwegian University of Science and Technology, NTNU, Sem Sælandsvei 9, 7491, Trondheim, Norway.,Bioinformatics core facility-BioCore, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway.,K.G. Jebsen Center for Genetic Epidemiology, Norwegian University of Science and Technology, NTNU, 7491, Trondheim, Norway
| | - Eva Hofsli
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, NTNU, Erling Skjalgssons gt 1, 7030, Trondheim, Norway.,The Cancer Clinic, St. Olav's Hospital, Trondheim University Hospital, Trondheim, Norway
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20
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Stevens JR, Herrick JS, Wolff RK, Slattery ML. Power in pairs: assessing the statistical value of paired samples in tests for differential expression. BMC Genomics 2018; 19:953. [PMID: 30572829 PMCID: PMC6302489 DOI: 10.1186/s12864-018-5236-2] [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] [Accepted: 11/09/2018] [Indexed: 12/19/2022] Open
Abstract
Background When genomics researchers design a high-throughput study to test for differential expression, some biological systems and research questions provide opportunities to use paired samples from subjects, and researchers can plan for a certain proportion of subjects to have paired samples. We consider the effect of this paired samples proportion on the statistical power of the study, using characteristics of both count (RNA-Seq) and continuous (microarray) expression data from a colorectal cancer study. Results We demonstrate that a higher proportion of subjects with paired samples yields higher statistical power, for various total numbers of samples, and for various strengths of subject-level confounding factors. In the design scenarios considered, the statistical power in a fully-paired design is substantially (and in many cases several times) greater than in an unpaired design. Conclusions For the many biological systems and research questions where paired samples are feasible and relevant, substantial statistical power gains can be achieved at the study design stage when genomics researchers plan on using paired samples from the largest possible proportion of subjects. Any cost savings in a study design with unpaired samples are likely accompanied by underpowered and possibly biased results. Electronic supplementary material The online version of this article (10.1186/s12864-018-5236-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, UT, USA.
| | - Jennifer S Herrick
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
| | - Martha L Slattery
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, UT, USA
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Kanth P, Hazel MW, Boucher KM, Yang Z, Wang L, Bronner MP, Boylan KE, Burt RW, Westover M, Neklason DW, Delker DA. Small RNA sequencing of sessile serrated polyps identifies microRNA profile associated with colon cancer. Genes Chromosomes Cancer 2018; 58:23-33. [PMID: 30265426 DOI: 10.1002/gcc.22686] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 09/21/2018] [Accepted: 09/21/2018] [Indexed: 12/21/2022] Open
Abstract
Sessile serrated adenoma/polyps (SSA/Ps) of the colon account for 20-30% of all colon cancers. Small non-coding RNAs, including microRNAs (miRNAs), may function as oncogenes or tumor suppressor genes involved in cancer development. Small RNA sequencing (RNA-seq) was used to characterize miRNA profiles in SSA/Ps, hyperplastic polyps (HPs), adenomatous polyps and paired uninvolved colon. Our 108 small RNA-seq samples' results were compared to small RNA-seq data from 212 colon cancers from the Cancer Genome Atlas. Twenty-three and six miRNAs were differentially expressed in SSA/Ps compared to paired uninvolved colon and HPs, respectively. Differential expression of MIR31-5p, MIR135B-5p and MIR378A-5p was confirmed by RT-qPCR. SSA/P-specific miRNAs are similarly expressed in colon cancers containing genomic aberrations described in serrated cancers. Correlation of miRNA expression with consensus molecular subtypes suggests more than one subtype is associated with the serrated neoplasia pathway. Canonical pathway analysis suggests many of these miRNAs target growth factor signaling pathways.
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Affiliation(s)
- Priyanka Kanth
- Division of Gastroenterology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Huntsman Cancer Institute, Salt Lake City, Utah
| | - Mark W Hazel
- Division of Gastroenterology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Kenneth M Boucher
- Huntsman Cancer Institute, Salt Lake City, Utah.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Zhihong Yang
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut
| | - Li Wang
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, Connecticut.,Veterans Affairs Connecticut Healthcare System, West Haven, Connecticut.,Department of Internal Medicine, Section of Digestive Diseases, Yale University, New Haven, Connecticut
| | - Mary P Bronner
- Huntsman Cancer Institute, Salt Lake City, Utah.,Department of Pathology, University of Utah, Salt Lake City, Utah
| | | | - Randall W Burt
- Division of Gastroenterology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah.,Huntsman Cancer Institute, Salt Lake City, Utah
| | | | - Deborah W Neklason
- Huntsman Cancer Institute, Salt Lake City, Utah.,Division of Epidemiology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
| | - Don A Delker
- Division of Gastroenterology, Department of Internal Medicine, University of Utah, Salt Lake City, Utah
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Yuan G, Chen T, Zhang H, Cao Q, Qiu Y, Que B, Peng S, Chen M, Ji W. Comprehensive analysis of differential circular RNA expression in a mouse model of colitis-induced colon carcinoma. Mol Carcinog 2018; 57:1825-1834. [PMID: 30182433 DOI: 10.1002/mc.22900] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/24/2018] [Accepted: 08/31/2018] [Indexed: 02/06/2023]
Abstract
Circular RNAs (circRNAs) have received increasing attention for their involvement in the pathogenesis of cancer; however, the characterization and function of circRNAs in colitis-induced colon carcinoma remains largely unknown. A colitis-induced colon carcinoma model was established in mice treated with azoxymethane-dextran sodium sulfate (AOM-DSS), and the circRNA profile was screened by next generation sequencing. Bioinformatic tools, including Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and network analysis were used to predict the functions of differentially expressed circRNAs and potentially coexpressed target genes. Among the detected candidate 3069 circRNA genes, 126 circRNAs were upregulated, and 108 circRNAs were down regulated in colon tissues from AOM/DSS mice compared to those from control mice. A total of six of these candidate circRNAs were validated by RT-PCR. GO analysis revealed that numerous target genes including most microRNAs were involved in the Ras-Raf-MAPK pathway, actin cytoskeleton, focal adhesion, and additional biological processes. Our study revealed a comprehensive expression and functional profile for differentially expressed circRNAs in AOM/DSS induced colon carcinogenesis, indicating possible involvement of these dysregulated circRNAs in the development of colitis-induced colon carcinoma. The mmu-circ-001226/mmu-circ-000287-miRNA-mRNA network may provide a potential mechanism for colitis-associated colorectal cancer.
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Affiliation(s)
- Gang Yuan
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Tingjia Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haiqing Zhang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qinghua Cao
- Department of Pathology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yun Qiu
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Biao Que
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sui Peng
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Minhu Chen
- Department of Gastroenterology, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Weidong Ji
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Clinical, Pathological, and Molecular Characteristics of CpG Island Methylator Phenotype in Colorectal Cancer: A Systematic Review and Meta-analysis. Transl Oncol 2018; 11:1188-1201. [PMID: 30071442 PMCID: PMC6080640 DOI: 10.1016/j.tranon.2018.07.008] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND: CpG island methylator phenotype (CIMP) tumors, comprising 20% of colorectal cancers, are associated with female sex, age, right-sided location, and BRAF mutations. However, other factors potentially associated with CIMP have not been robustly examined. This meta-analysis provides a comprehensive assessment of the clinical, pathologic, and molecular characteristics that define CIMP tumors. METHODS: We conducted a comprehensive search of the literature from January 1999 through April 2018 and identified 122 articles, on which comprehensive data abstraction was performed on the clinical, pathologic, molecular, and mutational characteristics of CIMP subgroups, classified based on the extent of DNA methylation of tumor suppressor genes assessed using a variety of laboratory methods. Associations of CIMP with outcome parameters were estimated using pooled odds ratio or standardized mean differences using random-effects model. RESULTS: We confirmed prior associations including female sex, older age, right-sided tumor location, poor differentiation, and microsatellite instability. In addition to the recognized association with BRAF mutations, CIMP was also associated with PIK3CA mutations and lack of mutations in KRAS and TP53. Evidence of an activated immune response was seen with high rates of tumor-infiltrating lymphocytes (but not peritumoral lymphocytes), Crohn-like infiltrates, and infiltration with Fusobacterium nucleatum bacteria. Additionally, CIMP tumors were associated with advance T-stage and presence of perineural and lymphovascular invasion. CONCLUSION: The meta-analysis highlights key features distinguishing CIMP in colorectal cancer, including molecular characteristics of an active immune response. Improved understanding of this unique molecular subtype of colorectal cancer may provide insights into prevention and treatment.
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MicroRNA-29b-2-5p inhibits cell proliferation by directly targeting Cbl-b in pancreatic ductal adenocarcinoma. BMC Cancer 2018; 18:681. [PMID: 29940895 PMCID: PMC6019739 DOI: 10.1186/s12885-018-4526-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 05/18/2018] [Indexed: 01/19/2023] Open
Abstract
Background MicroRNAs can be used in the prognosis of malignancies; however, their regulatory mechanisms are unknown, especially in pancreatic ductal adenocarcinoma (PDAC). Methods In 120 PDAC specimens, miRNA levels were assessed by quantitative real time polymerase chain reaction (qRT-PCR). Then, the role of miR-29b-2-5p in cell proliferation was evaluated both in vitro (Trypan blue staining and cell cycle analysis in the two PDAC cell lines SW1990 and Capan-2) and in vivo using a xenograft mouse model. Next, bioinformatics methods, a luciferase reporter assay, Western blot, and immunohistochemistry (IHC) were applied to assess the biological effects of Cbl-b inhibition by miR-29b-2-5p. Moreover, the relationship between Cbl-b and p53 was evaluated by immunoprecipitation (IP), Western blot, and immunofluorescence. Results From the 120 PDAC patients who underwent surgical resection, ten patients with longest survival and ten with shortest survival were selected. We found that high miR-29b-2-5p expression was associated with good prognosis (p = 0.02). The validation cohort confirmed miR-29b-2-5p as an independent prognostic factor in PDAC (n = 100, 95% CI = 0.305–0.756, p = 0.002). Furthermore, miR-29b-2-5p inhibited cell proliferation, induced cell cycle arrest, and promoted apoptosis both in vivo and in vitro. Interestingly, miR-29b-2-5p directly bound the Cbl-b gene, down-regulating its expression and reducing Cbl-b-mediated degradation of p53. Meanwhile, miR-29b-2-5p expression was negatively correlated with Cbl-b in PDAC tissues (r = − 0.33, p = 0.001). Conclusions Taken together, these findings indicated that miR-29b-2-5p improves prognosis in PDAC by targeting Cbl-b to promote p53 expression, and would constitute an important prognostic factor in PDAC. Electronic supplementary material The online version of this article (10.1186/s12885-018-4526-z) contains supplementary material, which is available to authorized users.
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Slattery ML, Mullany LE, Wolff RK, Sakoda LC, Samowitz WS, Herrick JS. The p53-signaling pathway and colorectal cancer: Interactions between downstream p53 target genes and miRNAs. Genomics 2018; 111:762-771. [PMID: 29860032 DOI: 10.1016/j.ygeno.2018.05.006] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 12/12/2022]
Abstract
INTRODUCTION We examined expression of genes in the p53-signaling pathway. We determine if genes that have significantly different expression in carcinoma tissue compared to normal mucosa also have significantly differentially expressed miRNAs. We utilize a sample of 217 CRC cases. METHODS We focused on fold change (FC) > 1.50 or <0.67 for genes and miRNAs, that were statistically significant after adjustment for multiple comparisons. We evaluated the linear association between the differential expression of miRNA and mRNA. miRNA:mRNA seed-region matches also were determined. RESULTS Eleven dysregulated genes were associated with 37 dysregulated miRNAs; all were down-stream from the TP53 gene. MiR-150-5p (HR = 0.82) and miR-196b-5p (HR 0.73) significantly reduced the likelihood of dying from CRC when miRNA expression increased in rectal tumors. CONCLUSIONS Our data suggest that activation of p53 from cellular stress, could target downstream genes that in turn could influence cell cycle arrest, apoptosis, and angiogenesis through mRNA:miRNA interactions.
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Affiliation(s)
- Martha L Slattery
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, UT, United States.
| | - Lila E Mullany
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, UT, United States
| | - Roger K Wolff
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, UT, United States
| | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, United States
| | - Wade S Samowitz
- Department of Pathology, University of Utah, Salt Lake City, UT, United States
| | - Jennifer S Herrick
- Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, UT, United States
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26
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Steviol, a natural product inhibits proliferation of the gastrointestinal cancer cells intensively. Oncotarget 2018; 9:26299-26308. [PMID: 29899860 PMCID: PMC5995179 DOI: 10.18632/oncotarget.25233] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 03/24/2018] [Indexed: 12/19/2022] Open
Abstract
New anticancer agents with lower toxicity have been always urged because of drug resistance associated with overused chemotherapy agents. In this study, steviol, a colonic metabolite of natural sweetener and also a component in leaves of stevia rebaudiana bertoni, was found to possess intensive anticancer activity on the human gastrointestinal cancer cells. Steviol inhibited six human gastrointestinal cancer cells intensively as 5-fluorouracil did at 100 μg/mL. The inhibition mechanism follows mitochondrial apoptotic pathway that was evidenced by increase of Bax/Bcl-2 ratio, activation of p21 and p53; and caspase 3-independent mechanism was also involved. These results are consistent with the miRNA expression analysis. The most regulated miRNAs in the steviol treated gastrointestinal cancer cells were miR-203a-3p (log2 =1.32) and miR-6088 (log2 =-2.54) in HCT-116, miR-1268b (log2 =19.85) and miR-23c (log2 =-2.05) in MKN-45. In view of the metabolic characteristics of steviol and its cytotoxicity on the cancer cells, steviol could be a chemotherapy agent potentially for cancer treatment.
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Site-specific associations between miRNA expression and survival in colorectal cancer cases. Oncotarget 2018; 7:60193-60205. [PMID: 27517623 PMCID: PMC5312378 DOI: 10.18632/oncotarget.11173] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 07/23/2016] [Indexed: 12/15/2022] Open
Abstract
Background MicroRNAs (miRNA) are small non-coding RNA involved in cellular processes, including cell proliferation and angiogenesis. Thus, miRNA expression may alter survival after diagnosis with colorectal cancer (CRC). Results Individuals diagnosed with stage 1 or stage 2 rectal cancer had worse survival than colon cancer cases diagnosed at stage 1 or stage 2. After adjustment for multiple comparisons, no miRNAs were significantly associated with disease stage. Two miRNAs infrequently expressed in the population and not previously reported were associated with survival after diagnosis with colon cancer (miR-1 HR 2.17 95% CI 1.41, 3.36; and miR-101-3p HR 3.51 95% CI 1.72, 7.15). Among those diagnosed with rectal cancer, 201 miRNAs were associated with survival when the FDR q value was < 0.05. Assessment of 105 previously reported miRNAs associated with prognosis showed that four miRNAs influenced colon cancer survival and 17 influenced survival after a diagnosis with rectal cancer when raw p values were considered. Patients and Methods This study includes data from population-based studies of CRC conducted in Utah and the Kaiser Permanente Medical Care Program. A total of 1893 carcinoma and normal paired colorectal mucosa tissue samples were run using the Agilent Human miRNA Microarray V19.0. We assessed miRNA differential expression between paired carcinoma and normal colonic mucosa tissue with CRC- specific survival evaluating stage and site-specific associations after adjusting for age, sex, microsatellite instability tumor status, and AJCC stage. Conclusions MiRNAs dysregulated for both colon and rectal cancer had a greater impact on survival after a diagnosis with rectal cancer.
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Small non-coding RNA profiling in human biofluids and surrogate tissues from healthy individuals: description of the diverse and most represented species. Oncotarget 2017; 9:3097-3111. [PMID: 29423032 PMCID: PMC5790449 DOI: 10.18632/oncotarget.23203] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/15/2017] [Indexed: 12/14/2022] Open
Abstract
The role of non-coding RNAs in different biological processes and diseases is continuously expanding. Next-generation sequencing together with the parallel improvement of bioinformatics analyses allows the accurate detection and quantification of an increasing number of RNA species. With the aim of exploring new potential biomarkers for disease classification, a clear overview of the expression levels of common/unique small RNA species among different biospecimens is necessary. However, except for miRNAs in plasma, there are no substantial indications about the pattern of expression of various small RNAs in multiple specimens among healthy humans. By analysing small RNA-sequencing data from 243 samples, we have identified and compared the most abundantly and uniformly expressed miRNAs and non-miRNA species of comparable size with the library preparation in four different specimens (plasma exosomes, stool, urine, and cervical scrapes). Eleven miRNAs were commonly detected among all different specimens while 231 miRNAs were globally unique across them. Classification analysis using these miRNAs provided an accuracy of 99.6% to recognize the sample types. piRNAs and tRNAs were the most represented non-miRNA small RNAs detected in all specimen types that were analysed, particularly in urine samples. With the present data, the most uniformly expressed small RNAs in each sample type were also identified. A signature of small RNAs for each specimen could represent a reference gene set in validation studies by RT-qPCR. Overall, the data reported hereby provide an insight of the constitution of the human miRNome and of other small non-coding RNAs in various specimens of healthy individuals.
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Stevens JR, Herrick JS, Wolff RK, Slattery ML. Identifying factors associated with the direction and significance of microRNA tumor-normal expression differences in colorectal cancer. BMC Cancer 2017; 17:707. [PMID: 29084506 PMCID: PMC5663119 DOI: 10.1186/s12885-017-3690-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023] Open
Abstract
Background microRNAs are small non-protein-coding RNA molecules that regulate gene expression, and have a potential epigenetic role in disease progression and survival of colorectal cancer. In terms of tumor-normal expression differences, many microRNAs exhibit evidence of being up-regulated in some subjects but down-regulated in others, or are dysregulated only for a subset of the population. We present and implement an approach to identify factors (lifestyle, tumor molecular phenotype, and survival-related) that are associated with the direction and/or significance of these microRNAs’ tumor-normal expression differences in colorectal cancer. Methods Using expression data for 1394 microRNAs and 1836 colorectal cancer subjects (each with both tumor and normal samples), we perform a dip test to identify microRNAs with multimodal distributions of tumor-normal expression differences. For proximal, distal, and rectal tumor sites separately, these microRNAs are tested for tumor-normal differential expression using a signed rank test, both overall and within levels of each lifestyle, tumor molecular phenotype, and survival-related factor. Appropriate adjustments are made to control the overall FDR. Results We identify hundreds of microRNAs whose direction and/or significance of tumor-normal differential expression is associated with one or more lifestyle, tumor molecular phenotype, or survival-related factors. Conclusions The results of this study demonstrate the benefit to colorectal cancer researchers to consider multiple subject-level factors when studying dysregulation of microRNAs, whose tumor-related changes in expression can be associated with multiple factors. Our results will serve as a publicly-available resource to provide clarifying information about various factors associated with the direction and significance of tumor-normal differential expression of microRNAs in colorectal cancer. Electronic supplementary material The online version of this article (10.1186/s12885-017-3690-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, USA.
| | - Jennifer S Herrick
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Logan, USA
| | - Roger K Wolff
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Logan, USA
| | - Martha L Slattery
- Division of Epidemiology, Department of Internal Medicine, University of Utah, Logan, USA
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MiR-107 suppresses cell proliferation and tube formation of Ewing sarcoma cells partly by targeting HIF-1β. Hum Cell 2017; 31:42-49. [DOI: 10.1007/s13577-017-0183-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Accepted: 08/29/2017] [Indexed: 12/12/2022]
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Slattery ML, Lee FY, Pellatt AJ, Mullany LE, Stevens JR, Samowitz WS, Wolff RK, Herrick JS. Infrequently expressed miRNAs in colorectal cancer tissue and tumor molecular phenotype. Mod Pathol 2017; 30:1152-1169. [PMID: 28548123 PMCID: PMC5537006 DOI: 10.1038/modpathol.2017.38] [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: 02/13/2017] [Revised: 03/23/2017] [Accepted: 03/23/2017] [Indexed: 12/16/2022]
Abstract
We have previously shown that commonly expressed miRNAs influenced tumor molecular phenotype in colorectal cancer. We hypothesize that infrequently expressed miRNAs, when showing higher levels of expression, help to define tumor molecular phenotype. In this study, we examine 304 miRNAs expressed in at least 30 individuals, but in <50% of the population and with a mean level of expression above 1.0 relative florescent unit. We examine associations in 1893 individuals who have the tumor molecular phenotype data as well as miRNA expression levels for both carcinoma and normal colorectal tissue. We compare miRNAs uniquely associated with tumor molecular phenotype to the RNAseq data to identify genes associated with these miRNAs. This information is used to further identify unique pathways associated with tumor molecular phenotypes of TP53-mutated, KRAS-mutated, CpG island methylator phenotype and microsatellite instability tumors. Thirty-seven miRNAs were uniquely associated with TP53-mutated tumors; 30 of these miRNAs had higher level of expression in TP53-mutated tumors, while seven had lower levels of expression. Of the 34 miRNAs associated with CpG island methylator phenotype-high tumors, 16 were more likely to have a CpG island methylator phenotype-high tumor and 19 were less likely to be CpG island methylator phenotype-high. For microsatellite instability, 13 of the 22 infrequently expressed miRNAs were significantly less likely to be expressed in microsatellite unstable tumors. KRAS-mutated tumors were not associated with any miRNAs after adjustment for multiple comparisons. Of the dysregulated miRNAs, 17 were more likely to be TP53-mutated tumors while simultaneously being less likely to be CpG island methylator phenotype-high and/or microsatellite instability tumors. Genes regulated by these miRNAs were involved in numerous functions and pathways that influence cancer risk and progression. In summary, some infrequently expressed miRNAs, when expressed at higher levels, appear to have significant biological meaning in terms of tumor molecular phenotype and gene expression profiles.
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Affiliation(s)
- Martha L Slattery
- Department of Medicine, University of Utah, Salt Lake City, UT, USA,Department of Medicine, University of Utah, 383 Colorow, Salt Lake City, UT 84108, USA. E-mail:
| | | | | | - Lila E Mullany
- Department of Medicine, University of Utah, Salt Lake City, UT, USA
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, UT, USA
| | - Wade S Samowitz
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Roger K Wolff
- Department of Medicine, University of Utah, Salt Lake City, UT, USA
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Slattery ML, Herrick JS, Stevens JR, Wolff RK, Mullany LE. An Assessment of Database-Validated microRNA Target Genes in Normal Colonic Mucosa: Implications for Pathway Analysis. Cancer Inform 2017; 16:1176935117716405. [PMID: 28690395 PMCID: PMC5484592 DOI: 10.1177/1176935117716405] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/28/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Determination of functional pathways regulated by microRNAs (miRNAs), while an essential step in developing therapeutics, is challenging. Some miRNAs have been studied extensively; others have limited information. In this study, we focus on 254 miRNAs previously identified as being associated with colorectal cancer and their database-identified validated target genes. METHODS We use RNA-Seq data to evaluate messenger RNA (mRNA) expression for 157 subjects who also had miRNA expression data. In the replication phase of the study, we replicated associations between 254 miRNAs associated with colorectal cancer and mRNA expression of database-identified target genes in normal colonic mucosa. In the discovery phase of the study, we evaluated expression of 18 miR-NAs (those with 20 or fewer database-identified target genes along with miR-21-5p, miR-215-5p, and miR-124-3p which have more than 500 database-identified target genes) with expression of 17 434 mRNAs to identify new targets in colon tissue. Seed region matches between miRNA and newly identified targeted mRNA were used to help determine direct miRNA-mRNA associations. RESULTS From the replication of the 121 miRNAs that had at least 1 database-identified target gene using mRNA expression methods, 97.9% were expressed in normal colonic mucosa. Of the 8622 target miRNA-mRNA associations identified in the database, 2658 (30.2%) were associated with gene expression in normal colonic mucosa after adjusting for multiple comparisons. Of the 133 miRNAs with database-identified target genes by non-mRNA expression methods, 97.2% were expressed in normal colonic mucosa. After adjustment for multiple comparisons, 2416 miRNA-mRNA associations remained significant (19.8%). Results from the discovery phase based on detailed examination of 18 miRNAs identified more than 80 000 miRNA-mRNA associations that had not previously linked to the miRNA. Of these miRNA-mRNA associations, 15.6% and 14.8% had seed matches for CRCh38 and CRCh37, respectively. CONCLUSIONS Our data suggest that miRNA target gene databases are incomplete; pathways derived from these databases have similar deficiencies. Although we know a lot about several miRNAs, little is known about other miRNAs in terms of their targeted genes. We encourage others to use their data to continue to further identify and validate miRNA-targeted genes.
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Affiliation(s)
- Martha L Slattery
- Department of Internal Medicine, The University of Utah, Salt Lake City, UT, USA
| | - Jennifer S Herrick
- Department of Internal Medicine, The University of Utah, Salt Lake City, UT, USA
| | - John R Stevens
- Department of Mathematics & Statistics, Utah State University, Logan, UT, USA
| | - Roger K Wolff
- Department of Internal Medicine, The University of Utah, Salt Lake City, UT, USA
| | - Lila E Mullany
- Department of Internal Medicine, The University of Utah, Salt Lake City, UT, USA
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Slattery ML, Herrick JS, Wolff RK, Mullany LE, Stevens JR, Samowitz W. The miRNA landscape of colorectal polyps. Genes Chromosomes Cancer 2017; 56:347-353. [PMID: 27925331 PMCID: PMC5357145 DOI: 10.1002/gcc.22436] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/22/2022] Open
Abstract
The genomic landscape of adenomas and polyps may help define disease pathways. Expression of miRNAs in adenomas and polyps may importantly contribute to these pathways. We evaluated miRNA expression in 293 polyp-normal colorectal mucosa pairs. Polyps were classified as either adenomatous polyp (AD), hyperplastic polyp (HP), or sessile serrated polyp (SSP). We compared these miRNA expression profiles in polyps to miRNA expression in microsatellite unstable (MSI) and stable (MSS) tumors. A False Discovery Rate of 0.05 based on Benjamini and Hochberg was used to adjust for multiple comparisons. There were 70 miRNAs with differential expression by polyp type with a fold change <0.75 or >1.34 after adjusting for multiple comparisons. The major differences in miRNA expression were observed between AD and SSP and AD and HP, with few differences in expression noted for SSP and HP. AD polyps were more likely to be upregulated from normal colonic mucosa, while SSP and HP were more likely to be downregulated from normal colonic mucosa. MiRNA expression in the SSP and HP tumors almost uniformly go in opposite directions from the MSS tumor miRNA expression and was mixed with MSI tumors. We conclude that different types of polyps have unique miRNA expression profiles. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Martha L Slattery
- Department of Medicine, University of Utah, Salt Lake City, UT, 84108
| | | | - Roger K Wolff
- Department of Medicine, University of Utah, Salt Lake City, UT, 84108
| | - Lila E Mullany
- Department of Medicine, University of Utah, Salt Lake City, UT, 84108
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, UT, 84322 3900
| | - Wade Samowitz
- Department of Pathology, University of Utah School, Salt Lake City, UT, 84108
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Kanno S, Nosho K, Ishigami K, Yamamoto I, Koide H, Kurihara H, Mitsuhashi K, Shitani M, Motoya M, Sasaki S, Tanuma T, Maguchi H, Hasegawa T, Kimura Y, Takemasa I, Shinomura Y, Nakase H. MicroRNA-196b is an independent prognostic biomarker in patients with pancreatic cancer. Carcinogenesis 2017; 38:425-431. [DOI: 10.1093/carcin/bgx013] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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