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Wei X, Shi S, Lu Z, Li C, Xu X, Chai J, Liu X, Hu T, Wang B. Elevated enteric putrescine suppresses differentiation of intestinal germinal center B cells. Int Immunopharmacol 2024; 128:111544. [PMID: 38266445 DOI: 10.1016/j.intimp.2024.111544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 01/11/2024] [Indexed: 01/26/2024]
Abstract
The dysregulation of B cell maturation and putrescine metabolism has been implicated in various diseases. However, the causal relationship between them and the underlying mechanisms remain unclear. In this study, we investigated the impact of exogenous putrescine on B cell differentiation in the intestinal microenvironment. Our results demonstrated that administration of exogenous putrescine significantly impaired the proportion of germinal center B (GC B) cells in Peyer's patches (PPs) and lamina propria. Through integration of bulk RNA sequencing and single-cell RNA sequencing (scRNA-seq), we identified putrescine-mediated changes in gene drivers, including those involved in the B cell receptor (BCR) signaling pathway and fatty acid oxidation. Furthermore, putrescine drinking disrupted T-B cell interactions and increased reactive oxygen species (ROS) production in B cells. In vitro activation of B cells confirmed the direct suppression of putrescine on GC B cells differentiation and ROS production. Additionally, we explored the Pearson correlations between putrescine biosynthesis activity and B cell infiltration in pan-cancers, revealing negative correlations in colon adenocarcinoma, stomach adenocarcinoma, and lung adenocarcinoma, but positive correlations in liver hepatocellular carcinoma, and breast invasive carcinoma. Our findings provided novel insights into the suppressive effects of elevated enteric putrescine on intestinal B cells differentiation and highlighted the complex and distinctive immunoregulatory role of putrescine in different microenvironments. These findings expand our understanding of the role of polyamines in B cell immunometabolism and related diseases.
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Affiliation(s)
- Xia Wei
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Shaojie Shi
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Zixuan Lu
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Chengyu Li
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Xiangping Xu
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Jinquan Chai
- Department of Immunology, Binzhou Medical University, Yantai, China
| | - Xiaofei Liu
- Breast and Thyroid Surgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China.
| | - Tao Hu
- Department of Immunology, Binzhou Medical University, Yantai, China.
| | - Bin Wang
- Department of Immunology, Binzhou Medical University, Yantai, China.
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2
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Lv W, Peng Y, Hu J, Zhu M, Mao Y, Wang L, Wang G, Xu Z, Wu W, Zuo B. Functional SNPs in SYISL promoter significantly affect muscle fiber density and muscle traits in pigs. Anim Genet 2024; 55:66-78. [PMID: 37881102 DOI: 10.1111/age.13370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/06/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
Our previous studies showed that SYISL is a negative regulator of muscle growth and regeneration in mice, pigs and humans. SYISL knockout resulted in an increase in the density of muscle fibers and muscle growth. However, it is unclear whether there are natural mutations in pig SYNPO2 intron sense-overlapping lncRNA (pSYISL) that affect the expression of pSYISL and muscle growth traits. In this study, three SNPs in exons and six SNPs within the promoter of pSYISL were identified. Association analysis showed that the two SNPs in exons are significantly associated with loin muscle area (p < 0.05); the six SNPs in the promoter that show complete linkage are significantly associated with live backfat thickness and live loin muscle area in American Large White pigs. Bioinformatics and luciferase reporter assays as well as in vitro binding experiments indicated that the mutation of SNP rs702045770 (g.539G>A) leads to the loss of YY1 binding to the promoter, thus affecting the expression level of pSYISL, and we found that Jiangshan Black pigs with genotype GG have a higher expression level of pSYISL than genotype AA individuals, but the muscle fiber density was significantly lower than in genotype AA individuals. Furthermore, the association analysis showed that the carcass backfat thickness of genotype GG of SNP rs702045770 was significantly higher than that of other genotypes in (Pietrain × Duroc) × (Landrace × Yorkshire) crossbred pigs (p < 0.05). The glycolytic potential of genotype GG was significantly higher than that of other genotypes (p < 0.05). These results provide novel insight into the identification of functional SNPs in non-coding genomic regions.
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Affiliation(s)
- Wei Lv
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yaxin Peng
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Hu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
| | - Mingfei Zhu
- The Tianpeng Group Co. Ltd, Jiangshan, China
| | | | - Litong Wang
- The Tianpeng Group Co. Ltd, Jiangshan, China
| | | | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Department of Basic Veterinary Medicine, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Wangjun Wu
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Agriculture Animal Genetics, Breeding and Reproduction of the Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
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3
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Zhou H, Hao X, Zhang P, He S. Noncoding RNA mutations in cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1812. [PMID: 37544928 DOI: 10.1002/wrna.1812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 07/14/2023] [Accepted: 07/17/2023] [Indexed: 08/08/2023]
Abstract
Cancer is driven by both germline and somatic genetic changes. Efforts have been devoted to characterizing essential genetic variations in cancer initiation and development. Most attention has been given to mutations in protein-coding genes and associated regulatory elements such as promoters and enhancers. The development of sequencing technologies and in silico and experimental methods has allowed further exploration of cancer predisposition variants and important somatic mutations in noncoding RNAs, mainly for long noncoding RNAs and microRNAs. Association studies including GWAS have revealed hereditary variations including SNPs and indels in lncRNA or miRNA genes and regulatory regions. These mutations altered RNA secondary structures, expression levels, and target recognition and then conferred cancer predisposition to carriers. Whole-exome/genome sequencing comparing cancer and normal tissues has revealed important somatic mutations in noncoding RNA genes. Mutation hotspots and somatic copy number alterations have been identified in various tumor-associated noncoding RNAs. Increasing focus and effort have been devoted to studying the noncoding region of the genome. The complex genetic network of cancer initiation is being unveiled. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Honghong Zhou
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xinpei Hao
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhang
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shunmin He
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Huang Y, Bao T, Zhang T, Ji G, Wang Y, Ling Z, Li W. Machine Learning Study of SNPs in Noncoding Regions to Predict Non-small Cell Lung Cancer Susceptibility. Clin Oncol (R Coll Radiol) 2023; 35:701-712. [PMID: 37689528 DOI: 10.1016/j.clon.2023.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/23/2023] [Accepted: 08/30/2023] [Indexed: 09/11/2023]
Abstract
Non-small cell lung cancer (NSCLC) is the most common pathological subtype of lung cancer. Both environmental and genetic factors have been reported to impact the lung cancer susceptibility. We conducted a genome-wide association study (GWAS) of 287 NSCLC patients and 467 healthy controls in a Chinese population using the Illumina Genome-Wide Asian Screening Array Chip on 712,095 SNPs (single nucleotide polymorphisms). Using logistic regression modeling, GWAS identified 17 new noncoding region SNP loci associated with the NSCLC risk, and the top three (rs80040741, rs9568547, rs6010259) were under a stringent p-value (<3.02e-6). Notably, rs80040741 and rs6010259 were annotated from the intron regions of MUC3A and MLC1, respectively. Together with another five SNPs previously reported in Chinese NSCLC patients and another four covariates (e.g., smoking status, age, low dose CT screening, sex), a predictive model by machine learning methods can separate the NSCLC from healthy controls with an accuracy of 86%. This is the first time to apply machine learning method in predicting the NSCLC susceptibility using both genetic and clinical characteristics. Our findings will provide a promising method in NSCLC early diagnosis and improve our understanding of applying machine learning methods in precision medicine.
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Affiliation(s)
- Y Huang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - T Bao
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - T Zhang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - G Ji
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Y Wang
- Health Management Center, General Practice Medical Center, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Z Ling
- Chengdu Genepre Technology Co., LTD, Chengdu, Sichuan, China
| | - W Li
- Institute of Respiratory Healthy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Healthy, Precision Medicine Key Laboratory of Sichuan Province, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China; The Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan 610041, China; State Key Laboratory of Respiratory Health and Multimorbidity, Chengdu, Sichuan 610041, West China Hospital, China.
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5
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Gautam N, Kaur M, Kashyap S. Meta-analysis of Genetic polymorphism of Enhancer of Zeste Homolog2 gene in cancer susceptibility. J Cancer Res Ther 2023; 19:1079-1092. [PMID: 37787267 DOI: 10.4103/jcrt.jcrt_1112_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The alteration in the expression of enhancer of zeste homolog-2 (EZH2) gene is very well known in the progression, severity, and aggressiveness of cancer. Hence, it is important to study the genomic variation of the EZH2 gene. Previously, many association-based studies investigated the association between rs2302427C>G and cancer susceptibility. However, the result had been inconsistent. Therefore, our meta-analysis aimed to identify the association between EZH2 rs2302427 and cancer risk. A systematic literature search was done for databases PubMed, Google Scholar, Science Direct, and Cochrane library up to September 2020 and statistical analysis was performed by RevMan v 5.3. A total of six studies comprised 1876 cases and 2555 controls were included in the current meta-analysis. The pooled analysis showed that overall, there is significant association of rs2302427 C>G change with reduced cancer risk (odds ratio = 0.60, 95% confidence interval [0.35-1.03], P = 0.07) but non-significantly. Further, the subgroup analysis also revealed that there is no significant difference between the Asian and European population, and both exhibit the protective nature of rs2302427 with cancer. The present meta-analysis indicated that EZH2 rs2302427 has an association with cancer in reducing the risk but for the Indian population studies are required as the Indian population comprises various sub-population genetically isolated for long.
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Affiliation(s)
- Nisha Gautam
- Department of Human Genetics, Punjabi University, Patiala, Punjab, India
| | - Mandeep Kaur
- Department of Human Genetics, Punjabi University, Patiala, Punjab, India
| | - Surender Kashyap
- Atal Medical and Research University, Mandi, Himachal Pradesh, India
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Aghiorghiesei O, Irimie AI, Braicu C, Raduly L, Nutu A, Balint E, Mehterov N, Vladimirov B, Sarafian V, Lucaciu O, Campian R, Berindan-Neagoe I. Epigenetic methylation changes: implication as biomarkers in oral and maxillofacial area cancers. Med Pharm Rep 2023; 96:310-317. [PMID: 37577021 PMCID: PMC10419680 DOI: 10.15386/mpr-2570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/07/2022] [Accepted: 10/21/2022] [Indexed: 08/15/2023] Open
Abstract
Background/Aim Squamous cell carcinoma (SCC) is the most frequent cancer of the head and neck area in the oral cavity. Epigenetic alterations in oral and maxillofacial area cancers are urgently needed to be investigated, as the observed changes might have crucial diagnostic value for personalized medicine. Methods Our study aimed to identify the most frequently hypermethylated tumor suppressor gene promoters in OSCC, followed by correlation analysis with the patients' survival. We evaluated the methylation status of the promoters in a panel of 22 tumor suppressor genes in Romanian (n=9) and Bulgarian (n=12) patient groups suffering from oral and maxillofacial area cancers. The extracted DNA was further digested through EpiTect Methyl II PCR Array System containing methylation-sensitive and methylation-dependent restriction enzymes, followed by specific amplification of the products obtained by qPCR and data analysis using the online platform provided by the producer. Results Different methylation patterns were observed in the tumor suppressor genes' promoters. Among them, the methylation profile of Cccnd2, Chd1, Cdh13, Cdkn1c, Neurog1, Gstp1, and Runx3 genes further correlated with overall survival rates. Conclusions Our data emphasize that epigenetic alterations are responsible for the clinical heterogeneity of oral and maxillofacial area cancers and significantly impact on patient survival. Additional investigation on a larger patient cohort should validate these potential biomarkers.
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Affiliation(s)
- Ovidiu Aghiorghiesei
- Department of Oral Health, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutics, Aesthetic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alexandra Iulia Irimie
- Department of Prosthetic Dentistry and Dental Materials, Division Dental Propaedeutics, Aesthetic, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cornelia Braicu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Lajos Raduly
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Andreea Nutu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Emilia Balint
- Faculty of Veterinary Medicine, University of Agronomic Sciences and Veterinary Medicine of Bucharest, Bucharest, Romania
| | - Nikolay Mehterov
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, Plovdiv, Bulgaria
- Clinic of Maxillofacial Surgery, University Hospital St. George, Plovdiv, Bulgaria
| | - Victoria Sarafian
- Department of Medical Biology, Faculty of Medicine, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Ondine Lucaciu
- Department of Preventive Dental Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu Campian
- Department of Oral Rehabilitation, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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7
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Aprile M, Costa V, Cimmino A, Calin GA. Emerging role of oncogenic long noncoding RNA as cancer biomarkers. Int J Cancer 2023; 152:822-834. [PMID: 36082440 DOI: 10.1002/ijc.34282] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 02/05/2023]
Abstract
The view of long noncoding RNAs as nonfunctional "garbage" has been definitely outdated by the large body of evidence indicating this class of ncRNAs as "golden junk", especially in precision oncology. Indeed, in light of their oncogenic role and the higher expression in multiple cancer types compared with paired adjacent tissues, the clinical interest for lncRNAs as diagnostic and/or prognostic biomarkers has been rapidly increasing. The emergence of large-scale sequencing technologies, their subsequent diffusion even in small research and clinical centers, the technological advances for the detection of low-copy lncRNAs in body fluids, coupled to the huge reduction of operating costs, have nowadays made possible to rapidly and comprehensively profile them in multiple tumors and large cohorts. In this review, we first summarize some relevant data about the oncogenic role of well-studied lncRNAs having a clinical relevance. Then, we focus on the description of their potential use as diagnostic/prognostic biomarkers, including an updated overview about licensed patents or clinical trials on lncRNAs in oncology.
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Affiliation(s)
- Marianna Aprile
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - Amelia Cimmino
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council (CNR), Naples, Italy
| | - George Adrian Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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8
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Jabraili M, Moniri-Javadhesari S, Pouladi N, Hosseinpour-Feizi MA. Evaluating the association of rs6983267 polymorphism of the CCAT2 gene with thyroid cancer susceptibility in the Iranian Azeri population. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2023; 12:127-131. [PMID: 37525664 PMCID: PMC10387174 DOI: 10.22099/mbrc.2023.47622.1839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Thyroid cancer is the most common malignancy of the endocrine system. LncRNAs play critical role in various cellular processes and are associated with several diseases. CCAT2 is a lncRNA molecule overexpressed in thyroid cancer. Single nucleotide polymorphisms in CCAT2 gene can cause changes in the structure and function of CCAT2 transcripts and susceptibility to several diseases. This study aimed to evaluate the association of rs6983267 in CCAT2 gene with thyroid cancer susceptibility in the Azeri population of Iran. In this "case-control" study, genomic DNA was extracted from peripheral blood of 102 individuals affected by thyroid cancer and 103 healthy individuals as controls. Genotyping was performed using TETRA-ARMS polymerase chain reaction. Statistical analysis showed no significant association between genotypes and/or alleles with the occurrence of thyroid cancer in the studied population, patients' gender, and tumor type. Nevertheless, we found that the allelic and genotypic distribution of this SNP was associated with the size of thyroid tumors in patients. It is assumed that investigating more individuals from both case and control group may further determine the genotypic and allelic frequencies of this SNP locus in Iranian-Azeri population.
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Affiliation(s)
- Masoud Jabraili
- Department of Cellular and Molecular Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Solmaz Moniri-Javadhesari
- Department of Cellular and Molecular Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Nasser Pouladi
- Department of Cellular and Molecular Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran
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Long non-coding RNA colon cancer-associated transcript 2: role and function in human cancers. Chin Med J (Engl) 2022; 135:2785-2797. [PMID: 36103972 PMCID: PMC9945556 DOI: 10.1097/cm9.0000000000002286] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Indexed: 01/03/2023] Open
Abstract
ABSTRACT Long non-coding RNAs (lncRNAs) are a family of non-protein-coding RNAs that span a length of over 200 nucleotides. Research reports have illustrated that lncRNAs are involved in various cellular processes and that their abnormal expression leads to the occurrence and development of various tumors. Colon cancer-associated transcript 2 (CCAT2) was first reported as an oncogene in colon cancer. LncRNA CCAT2 is abnormally expressed in hepatocellular carcinoma, cholangiocarcinoma, lung cancer, breast cancer, ovarian cancer, glioma, and other tumors. In tumor tissues, abnormally overexpressed CCAT2 can affect cell proliferation, migration, epithelial-mesenchymal transition, apoptosis, and other biological behaviors through endogenous RNAs mechanisms, various signaling pathways, transcriptional regulation, and other complex mechanisms. Additionally, the overexpression of CCAT2 is also closely related to the tumor size, tumor node metastasis (TNM) stage, survival time, and other prognostic factors, suggesting that it is a potential prognostic indicator. This article reviews the biological functions of CCAT2 and its mechanisms of action in tumors from previous studies. In this review, we attempt to provide a molecular basis for future clinical applications of lncRNA CCAT2.
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10
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Cao M, Wang Y, Lu G, Qi H, Li P, Dai X, Lu J. Classical Angiogenic Signaling Pathways and Novel Anti-Angiogenic Strategies for Colorectal Cancer. Curr Issues Mol Biol 2022; 44:4447-4471. [PMID: 36286020 PMCID: PMC9601273 DOI: 10.3390/cimb44100305] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/17/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Although productive progress has been made in colorectal cancer (CRC) researchs, CRC is the second most frequent type of malignancy and the major cause of cancer-related death among gastrointestinal cancers. As angiogenesis constitutes an important point in the control of CRC progression and metastasis, understanding the key signaling pathways that regulate CRC angiogenesis is critical in elucidating ways to inhibit CRC. Herein, we comprehensively summarized the angiogenesis-related pathways of CRC, including vascular endothelial growth factor (VEGF), nuclear factor-kappa B (NF-κB), Janus kinase (JAK)/signal transducer and activator of transcription (STAT), Wingless and int-1 (Wnt), and Notch signaling pathways. We divided the factors influencing the specific pathway into promoters and inhibitors. Among these, some drugs or natural compounds that have antiangiogenic effects were emphasized. Furthermore, the interactions of these pathways in angiogenesis were discussed. The current review provides a comprehensive overview of the key signaling pathways that are involved in the angiogenesis of CRC and contributes to the new anti-angiogenic strategies for CRC.
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Affiliation(s)
- Mengyuan Cao
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yunmeng Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Guige Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Haoran Qi
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Peiyu Li
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaoshuo Dai
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jing Lu
- Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
- Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou University, Zhengzhou 450001, China
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou 450052, China
- Correspondence:
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11
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Drula R, Iluta S, Gulei D, Iuga C, Dima D, Ghiaur G, Buzoianu AD, Ciechanover A, Tomuleasa C. Exploiting the ubiquitin system in myeloid malignancies. From basic research to drug discovery in MDS and AML. Blood Rev 2022; 56:100971. [PMID: 35595613 DOI: 10.1016/j.blre.2022.100971] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 12/19/2022]
Abstract
The ubiquitin-proteasome system is the crucial homeostatic mechanism responsible for the degradation and turnover of proteins. As such, alterations at this level are often associated with oncogenic processes, either through accumulation of undegraded pathway effectors or, conversely, excessive degradation of tumor-suppressing factors. Therefore, investigation of the ubiquitin- proteasome system has gained much attraction in recent years, especially in the context of hematological malignancies, giving rise to efficient therapeutics such as bortezomib for multiple myeloma. Current investigations are now focused on manipulating protein degradation via fine-tuning of the ubiquitination process through inhibition of deubiquitinating enzymes or development of PROTAC systems for stimulation of ubiquitination and protein degradation. On the other hand, the efficiency of Thalidomide derivates in myelodysplastic syndromes (MDS), such as Lenalidomide, acted as the starting point for the development of targeted leukemia-associated protein degradation molecules. These novel molecules display high efficiency in overcoming the limitations of current therapeutic regimens, such as refractory diseases. Therefore, in this manuscript we will address the therapeutic opportunities and strategies based on the ubiquitin-proteasome system, ranging from the modulation of deubiquitinating enzymes and, conversely, describing the potential of modern targeted protein degrading molecules and their progress into clinical implementation.
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Affiliation(s)
- Rares Drula
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Sabina Iluta
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Diana Gulei
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Cristina Iuga
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Pharmaceutical Analysis, Faculty of Pharmacy, Iuliu Hațieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Delia Dima
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Gabriel Ghiaur
- Department of Oncology, The Johns Hopkins Hospital, Johns Hopkins Medicine, Baltimore, MD, United States
| | - Anca Dana Buzoianu
- Department of Pharmacology, Toxicology and Clinical Pharmacology, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Aaron Ciechanover
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Rappaport Technion Integrated Cancer Center, Technion-Israel Institute of Technology, Haifa 3109601, Israel; Rappaport Faculty of Medicine and Research Institute, Technion-Israel Institute of Technology, Haifa 3109601, Israel
| | - Ciprian Tomuleasa
- Research Center for Advanced Medicine - MedFUTURE, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania; Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania.
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12
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Targeting non-coding RNAs to overcome cancer therapy resistance. Signal Transduct Target Ther 2022; 7:121. [PMID: 35418578 PMCID: PMC9008121 DOI: 10.1038/s41392-022-00975-3] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 02/07/2023] Open
Abstract
It is now well known that non-coding RNAs (ncRNAs), rather than protein-coding transcripts, are the preponderant RNA transcripts. NcRNAs, particularly microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), are widely appreciated as pervasive regulators of multiple cancer hallmarks such as proliferation, apoptosis, invasion, metastasis, and genomic instability. Despite recent discoveries in cancer therapy, resistance to chemotherapy, radiotherapy, targeted therapy, and immunotherapy continue to be a major setback. Recent studies have shown that ncRNAs also play a major role in resistance to different cancer therapies by rewiring essential signaling pathways. In this review, we present the intricate mechanisms through which dysregulated ncRNAs control resistance to the four major types of cancer therapies. We will focus on the current clinical implications of ncRNAs as biomarkers to predict treatment response (intrinsic resistance) and to detect resistance to therapy after the start of treatment (acquired resistance). Furthermore, we will present the potential of targeting ncRNA to overcome cancer treatment resistance, and we will discuss the challenges of ncRNA-targeted therapy—especially the development of delivery systems.
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13
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Alsheikh AJ, Wollenhaupt S, King EA, Reeb J, Ghosh S, Stolzenburg LR, Tamim S, Lazar J, Davis JW, Jacob HJ. The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases. BMC Med Genomics 2022; 15:74. [PMID: 35365203 PMCID: PMC8973751 DOI: 10.1186/s12920-022-01216-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/17/2022] [Indexed: 02/08/2023] Open
Abstract
Background The remarkable growth of genome-wide association studies (GWAS) has created a critical need to experimentally validate the disease-associated variants, 90% of which involve non-coding variants. Methods To determine how the field is addressing this urgent need, we performed a comprehensive literature review identifying 36,676 articles. These were reduced to 1454 articles through a set of filters using natural language processing and ontology-based text-mining. This was followed by manual curation and cross-referencing against the GWAS catalog, yielding a final set of 286 articles. Results We identified 309 experimentally validated non-coding GWAS variants, regulating 252 genes across 130 human disease traits. These variants covered a variety of regulatory mechanisms. Interestingly, 70% (215/309) acted through cis-regulatory elements, with the remaining through promoters (22%, 70/309) or non-coding RNAs (8%, 24/309). Several validation approaches were utilized in these studies, including gene expression (n = 272), transcription factor binding (n = 175), reporter assays (n = 171), in vivo models (n = 104), genome editing (n = 96) and chromatin interaction (n = 33). Conclusions This review of the literature is the first to systematically evaluate the status and the landscape of experimentation being used to validate non-coding GWAS-identified variants. Our results clearly underscore the multifaceted approach needed for experimental validation, have practical implications on variant prioritization and considerations of target gene nomination. While the field has a long way to go to validate the thousands of GWAS associations, we show that progress is being made and provide exemplars of validation studies covering a wide variety of mechanisms, target genes, and disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01216-w.
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Affiliation(s)
- Ammar J Alsheikh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA.
| | - Sabrina Wollenhaupt
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Emily A King
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jonas Reeb
- Information Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany
| | - Sujana Ghosh
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | | | - Saleh Tamim
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Jozef Lazar
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - J Wade Davis
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
| | - Howard J Jacob
- Genomics Research Center, AbbVie Inc, North Chicago, Illinois, 60064, USA
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14
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Ghanam AR, Bryant WB, Miano JM. Of mice and human-specific long noncoding RNAs. Mamm Genome 2022; 33:281-292. [PMID: 35106622 PMCID: PMC8806012 DOI: 10.1007/s00335-022-09943-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/10/2022] [Indexed: 01/05/2023]
Abstract
The number of human LncRNAs has now exceeded all known protein-coding genes. Most studies of human LncRNAs have been conducted in cell culture systems where various mechanisms of action have been worked out. On the other hand, efforts to elucidate the function of human LncRNAs in an in vivo setting have been limited. In this brief review, we highlight some strengths and weaknesses of studying human LncRNAs in the mouse. Special consideration is given to bacterial artificial chromosome transgenesis and genome editing. The integration of these technical innovations offers an unprecedented opportunity to complement and extend the expansive literature of cell culture models for the study of human LncRNAs. Two different examples of how BAC transgenesis and genome editing can be leveraged to gain insight into human LncRNA regulation and function in mice are presented: the random integration of a vascular cell-enriched LncRNA and a targeted approach for a new LncRNA immediately upstream of the ACE2 gene, which encodes the receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent underlying the coronavirus disease-19 (COVID-19) pandemic.
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Affiliation(s)
- Amr R Ghanam
- Vascular Biology Center, Department of Medicine, Medical College of Georgia at Augusta University, 1460 Laney Walker Blvd, CL-3060, Augusta, GA, 30912, USA
| | - William B Bryant
- Vascular Biology Center, Department of Medicine, Medical College of Georgia at Augusta University, 1460 Laney Walker Blvd, CL-3060, Augusta, GA, 30912, USA
| | - Joseph M Miano
- Vascular Biology Center, Department of Medicine, Medical College of Georgia at Augusta University, 1460 Laney Walker Blvd, CL-3060, Augusta, GA, 30912, USA.
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15
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The Roles of the Colon Cancer Associated Transcript 2 (CCAT2) Long Non-Coding RNA in Cancer: A Comprehensive Characterization of the Tumorigenic and Molecular Functions. Int J Mol Sci 2021; 22:ijms222212491. [PMID: 34830370 PMCID: PMC8620102 DOI: 10.3390/ijms222212491] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/17/2021] [Accepted: 11/17/2021] [Indexed: 12/12/2022] Open
Abstract
Colon cancer-associated transcript 2 (CCAT2) is an intensively studied lncRNA with important regulatory roles in cancer. As such, cumulative studies indicate that CCAT2 displays a high functional versatility due to its direct interaction with multiple RNA binding proteins, transcription factors, and other species of non-coding RNA, especially microRNA. The definitory mechanisms of CCAT2 are its role as a regulator of the TCF7L2 transcription factor, enhancer of MYC expression, and activator of the WNT/β-catenin pathway, as well as a role in promoting and maintaining chromosome instability through the BOP1–AURKB pathway. Additionally, we highlight how the encompassing rs6983267 SNP has been shown to confer CCAT2 with allele-specific functional and structural particularities, such as the allelic-specific reprogramming of glutamine metabolism. Additionally, we emphasize CCAT2’s role as a competitive endogenous RNA (ceRNA) for multiple tumor suppressor miRNAs, such as miR-4496, miR-493, miR-424, miR-216b, miR-23b, miR-34a, miR-145, miR-200b, and miR-143 and the pro-tumorigenic role of the altered regulatory axis. Additionally, due to its upregulation in tumor tissues, wide distribution across cancer types, and presence in serum samples, we outline CCAT2’s potential as a biomarker and disease indicator and its implications for the development of resistance against current cancer therapy regiments and metastasis.
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16
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Shi J, Guo C, Ma J. CCAT2 enhances autophagy-related invasion and metastasis via regulating miR-4496 and ELAVL1 in hepatocellular carcinoma. J Cell Mol Med 2021; 25:8985-8996. [PMID: 34409736 PMCID: PMC8435435 DOI: 10.1111/jcmm.16859] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 07/07/2021] [Accepted: 07/31/2021] [Indexed: 12/14/2022] Open
Abstract
Autophagy is thought to contribute to the pathogenesis of many diseases, including cancer. Long non‐coding RNA (lncRNA) CCAT2 functions as an oncogene in a variety of tumours. However, it is still unknown whether CCAT2 is involved in autophagy and metastasis of hepatocellular carcinoma (HCC). In our study, we found that lncRNA CCAT2 expression was significantly increased in HCC tissue and was correlated with advanced stage and venous invasion. Further experiments revealed that CCAT2 induced autophagy and promoted migration and invasion in vitro and in vivo. Mechanistic investigations found that CCAT2 involved in HCC by regulating miR‐4496/Atg5 in cytoplasm. In nucleus, CCAT2 bound with ELAVL1/HuR to facilitate HCC progression. Our findings suggest that CCAT2 is an oncogenic factor in the progression of HCC with different regulatory mechanisms and may serve as a target for HCC therapy.
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Affiliation(s)
- Jing Shi
- Affiliated Hospital of Jining Medical University, Jining, China
| | - Cao Guo
- Institute of Medical Sciences, Xiangya Hospital, Central South University, Changsha, China
| | - Junli Ma
- Affiliated Hospital of Jining Medical University, Jining, China
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17
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Pardini B, Dragomir MP. SCIRT lncRNA Blocks the Shot of Breast Cancer Cells Self-Renewal Mechanism. Cancer Res 2021; 81:535-536. [PMID: 33526468 DOI: 10.1158/0008-5472.can-20-3903] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 11/16/2022]
Abstract
The study by Zagorac and colleagues represents an important step forward in the field of breast cancer, explaining a novel molecular mechanism of transition from slowly multiplying tumor-initiating cells (TIC) into their more differentiated version characterized by high proliferation. The mechanism involves the transcription factors SOX2 and EZH2, which directly repress transcription of cell-cycle genes and activate self-renewal genes in breast cancer cells. This mechanism is further controlled by a negative feedback loop mediated by a long noncoding RNA, SCIRT, not described previously, which is upregulated in tumorspheres and inhibits SOX2 and EZH2. SCIRT is an atypical tumor suppressor in breast cancer, being upregulated in cancer cells, but counteracting their aggressive phenotype. At the molecular level, by direct interaction with EZH2, SCIRT inhibits the transcriptional activity of EZH2 and "blocks the shot" of cancer cells' self-renewal. From a translational perspective, activating SCIRT or induction of SCIRT mimetics in breast cancer cells may lead to the dedifferentiation of TICs toward a less protumorigenic phenotype and a therapy-fragile state that could open new therapeutic avenues.See related article by Zagorac et al., p. 580.
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Affiliation(s)
- Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), Candiolo, Turin, Italy.,Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Turin, Italy
| | - Mihnea P Dragomir
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.
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18
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Genetic variant rs10251977 (G>A) in EGFR-AS1 modulates the expression of EGFR isoforms A and D. Sci Rep 2021; 11:8808. [PMID: 33888812 PMCID: PMC8062556 DOI: 10.1038/s41598-021-88161-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Accepted: 03/30/2021] [Indexed: 02/02/2023] Open
Abstract
Tyrosine kinase inhibitor is an effective chemo-therapeutic drug against tumors with deregulated EGFR pathway. Recently, a genetic variant rs10251977 (G>A) in exon 20 of EGFR reported to act as a prognostic marker for HNSCC. Genotyping of this polymorphism in oral cancer patients showed a similar frequency in cases and controls. EGFR-AS1 expressed significantly high level in tumors and EGFR-A isoform expression showed significant positive correlation (r = 0.6464, p < 0.0001) with reference to EGFR-AS1 expression levels, consistent with larger TCGA HNSCC tumor dataset. Our bioinformatic analysis showed enrichment of alternative splicing marks H3K36me3 and presence of intronic polyA sites spanning around exon 15a and 15b of EGFR facilitates skipping of exon 15b, thereby promoting the splicing of EGFR-A isoform. In addition, high level expression of PTBP1 and its binding site in EGFR and EGFR-AS1 enhances the expression of EGFR-A isoform (r = 0.7404, p < 0.0001) suggesting that EGFR-AS1 expression modulates the EGFR-A and D isoforms through alternative splicing. In addition, this polymorphism creates a binding site for miR-891b in EGFR-AS1 and may negatively regulate the EGFR-A. Collectively, our results suggested the presence of genetic variant in EGFR-AS1 modulates the expression of EGFR-D and A isoforms.
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19
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Karimi F, Amiri-Moghaddam SM, Bagheri Z, Bahrami AR, Goshayeshi L, Allahyari A, Mirsadraee M, Fanipakdel A, Bari A, Emadi-Torghabeh A, Kerachian MA, Rahimi H, Matin MM. Investigating the association between rs6983267 polymorphism and susceptibility to gastrointestinal cancers in Iranian population. Mol Biol Rep 2021; 48:2273-2284. [PMID: 33713253 DOI: 10.1007/s11033-021-06249-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 02/24/2021] [Indexed: 11/28/2022]
Abstract
Genome-wide association studies have revealed that some single nucleotide polymorphisms at 8q24, such as rs6983267, might be effective in susceptibility to various cancers in different populations. Therefore, rs6983267 might be useful as a marker for multiple cancers. In this study, we considered a population, including 478 gastrointestinal cancer cases from the Iranian population, to investigate the association between rs6983267 and susceptibility to gastrointestinal cancers. The samples were genotyped using the TaqMan real-time PCR method while 10% of them were also confirmed by sequencing. Higher frequency of G allele was associated with higher grades of tumors in esophageal cancer and the tumors located in the lower portion of the esophagus (OR 3.56; 95% CI 1.13-11.24; P = 0.03) and cardia (OR 5.24; 95% CI 1.26-21.83; P = 0.02), which both locations are involved in esophageal adenocarcinomas with poor prognosis. The results indicated that in the male subgroup, the rs6983267 GG genotype significantly enhanced the gastric cancer susceptibility (OR 4.76; 95% CI 1.57-14.45; P = 0.01). GG genotype also increased the risk of intestinal-type gastric cancer, located in non-cardia (OR 4.62; 95% CI 1.25-17.04; P = 0.02). Moreover, gastric cancer cases and controls with a family history of gastrointestinal tumors were mostly genotyped with the G allele (OR 3.61; 95% CI = 1.09-12.01; P = 0.04). There were no remarkable associations between rs6983267 and susceptibility to esophageal and colon cancers in the Iranian population. However, different genotypes of rs6983267 had significant correlations with tumor grade, cancer type, and family history of gastrointestinal cancers. Further investigations in a larger population and other ethnicities are required to confirm these results.
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Affiliation(s)
- Farzaneh Karimi
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | | | - Zakieh Bagheri
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ahmad Reza Bahrami
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.,Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran
| | - Ladan Goshayeshi
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abolghasem Allahyari
- Hematology and Oncology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Azar Fanipakdel
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Bari
- Hematology and Oncology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Emadi-Torghabeh
- Cancer Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.,Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
| | - Hossein Rahimi
- Hematology and Oncology Department, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Maryam M Matin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran. .,Novel Diagnostics and Therapeutics Research Group, Institute of Biotechnology, Ferdowsi University of Mashhad, Mashhad, Iran.
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20
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Li HN, Deng N, Zhao X, Liu J, He T, Ding XW. Contributions of HOTAIR polymorphisms to the susceptibility of cancer. Int J Clin Oncol 2021; 26:1022-1038. [PMID: 33634340 DOI: 10.1007/s10147-021-01884-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/04/2021] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Hox transcript antisense intergenic RNA (HOTAIR), a lncRNA, functions as a critical regulator in cancer development. A plenty of case-control studies were conducted to assess the actual relationship of HOTAIR gene generic variants on cancer susceptibility, yet conflicting conclusions remain. Herein, we carried out this up-to-date meta-analysis to get a better understanding of such relationship by incorporating all eligible case-control studies. MATERIALS AND METHODS Six widely investigated polymorphisms were included in this meta-analysis: rs920778, rs4759314, rs7958904, rs874945, rs1899663, and rs12826786. We retrieved relevant studies from databases PubMed, EMBASE, Medline, CNKI and Wanfang update to June 2020. We applied odds ratios (ORs) and 95% confidence intervals (CIs) to estimate the relationship strengths. RESULTS Our findings indicate that rs920778, rs4759314, rs874945, rs12826786 polymorphism significantly increased with susceptibility to overall cancer. However, rs7958904, rs1899663 under any five genetic models could not impact susceptibility to overall cancer. Furthermore, altered cancer risk was detected when the data were stratified by cancer type, ethnicity, the source of controls, and HWE in all the SNPs. CONCLUSIONS These findings of the meta-analysis suggest that HOTAIR polymorphisms may predispose to cancer susceptibility.
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Affiliation(s)
- Hu-Nian Li
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, No. 37 Chaoyang Middle Road, Shiyan, 442000, Hubei, China
| | - Na Deng
- Children's Medical Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xu Zhao
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, No. 37 Chaoyang Middle Road, Shiyan, 442000, Hubei, China
| | - Jie Liu
- Emergency and Critical Care Center, Renmin Hospital, Hubei University of Medicine, No. 37 Chaoyang Middle Road, Shiyan, 442000, Hubei, China
| | - Ting He
- Department of Neurology, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
| | - Xi-Wei Ding
- Children's Medical Center, Renmin Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
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21
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Wilson C, Kanhere A. 8q24.21 Locus: A Paradigm to Link Non-Coding RNAs, Genome Polymorphisms and Cancer. Int J Mol Sci 2021; 22:1094. [PMID: 33499210 PMCID: PMC7865353 DOI: 10.3390/ijms22031094] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 01/17/2023] Open
Abstract
The majority of the human genome is comprised of non-protein-coding genes, but the relevance of non-coding RNAs in complex diseases has yet to be fully elucidated. One class of non-coding RNAs is long non-coding RNAs or lncRNAs, many of which have been identified to play a range of roles in transcription and translation. While the clinical importance of the majority of lncRNAs have yet to be identified, it is puzzling that a large number of disease-associated genetic variations are seen in lncRNA genes. The 8q24.21 locus is rich in lncRNAs and very few protein-coding genes are located in this region. Interestingly, the 8q24.21 region is also a hot spot for genetic variants associated with an increased risk of cancer. Research focusing on the lncRNAs in this area of the genome has indicated clinical relevance of lncRNAs in different cancers. In this review, we summarise the lncRNAs in the 8q24.21 region with respect to their role in cancer and discuss the potential impact of cancer-associated genetic polymorphisms on the function of lncRNAs in initiation and progression of cancer.
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Affiliation(s)
| | - Aditi Kanhere
- Department of Molecular Physiology and Cell Signalling, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 3BX, UK;
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22
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Torsin LI, Petrescu GED, Sabo AA, Chen B, Brehar FM, Dragomir MP, Calin GA. Editing and Chemical Modifications on Non-Coding RNAs in Cancer: A New Tale with Clinical Significance. Int J Mol Sci 2021; 22:ijms22020581. [PMID: 33430133 PMCID: PMC7827606 DOI: 10.3390/ijms22020581] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/11/2022] Open
Abstract
Currently, for seemingly every type of cancer, dysregulated levels of non-coding RNAs (ncRNAs) are reported and non-coding transcripts are expected to be the next class of diagnostic and therapeutic tools in oncology. Recently, alterations to the ncRNAs transcriptome have emerged as a novel hallmark of cancer. Historically, ncRNAs were characterized mainly as regulators and little attention was paid to the mechanisms that regulate them. The role of modifications, which can control the function of ncRNAs post-transcriptionally, only recently began to emerge. Typically, these modifications can be divided into reversible (i.e., chemical modifications: m5C, hm5C, m6A, m1A, and pseudouridine) and non-reversible (i.e., editing: ADAR dependent, APOBEC dependent and ADAR/APOBEC independent). The first research papers showed that levels of these modifications are altered in cancer and can be part of the tumorigenic process. Hence, the aim of this review paper is to describe the most common regulatory modifications (editing and chemical modifications) of the traditionally considered “non-functional” ncRNAs (i.e., microRNAs, long non-coding RNAs and circular RNAs) in the context of malignant disease. We consider that only by understanding this extra regulatory layer it is possible to translate the knowledge about ncRNAs and their modifications into clinical practice.
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Affiliation(s)
- Ligia I. Torsin
- Department of Anesthesiology and Critical Care, Elias Clinical Emergency Hospital, 011461 Bucharest, Romania;
| | - George E. D. Petrescu
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (G.E.D.P.); (F.M.B.)
- Department of Neurosurgery, Bagdasar-Arseni Clinical Emergency Hospital, 041915 Bucharest, Romania
| | - Alexandru A. Sabo
- Zentrum für Kinder, Jugend und Frauenmedizin, Pediatrics 2 (General and Special Pediatrics), Klinikum Stuttgart, Olgahospital, 70174 Stuttgart, Germany;
| | - Baoqing Chen
- State Key Laboratory of Oncology in South China, Department of Radiation Oncology, Collaborative Innovation Center of Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou 510060, China;
- Guangdong Esophageal Cancer Research Institute, Guangzhou 510060, China
| | - Felix M. Brehar
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (G.E.D.P.); (F.M.B.)
- Department of Neurosurgery, Bagdasar-Arseni Clinical Emergency Hospital, 041915 Bucharest, Romania
| | - Mihnea P. Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
- Correspondence: or (M.P.D.); (G.A.C.); Tel.: +40-254-219-493 (M.P.D.); +1-713-792-5461 (G.A.C.)
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Correspondence: or (M.P.D.); (G.A.C.); Tel.: +40-254-219-493 (M.P.D.); +1-713-792-5461 (G.A.C.)
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23
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Chen B, Dragomir MP, Fabris L, Bayraktar R, Knutsen E, Liu X, Tang C, Li Y, Shimura T, Ivkovic TC, De los Santos MC, Anfossi S, Shimizu M, Shah MY, Ling H, Shen P, Multani AS, Pardini B, Burks JK, Katayama H, Reineke LC, Huo L, Syed M, Song S, Ferracin M, Oki E, Fromm B, Ivan C, Bhuvaneshwar K, Gusev Y, Mimori K, Menter D, Sen S, Matsuyama T, Uetake H, Vasilescu C, Kopetz S, Parker-Thornburg J, Taguchi A, Hanash SM, Girnita L, Slaby O, Goel A, Varani G, Gagea M, Li C, Ajani JA, Calin GA. The Long Noncoding RNA CCAT2 Induces Chromosomal Instability Through BOP1-AURKB Signaling. Gastroenterology 2020; 159:2146-2162.e33. [PMID: 32805281 PMCID: PMC7725986 DOI: 10.1053/j.gastro.2020.08.018] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Chromosomal instability (CIN) is a carcinogenesis event that promotes metastasis and resistance to therapy by unclear mechanisms. Expression of the colon cancer-associated transcript 2 gene (CCAT2), which encodes a long noncoding RNA (lncRNA), associates with CIN, but little is known about how CCAT2 lncRNA regulates this cancer enabling characteristic. METHODS We performed cytogenetic analysis of colorectal cancer (CRC) cell lines (HCT116, KM12C/SM, and HT29) overexpressing CCAT2 and colon organoids from C57BL/6N mice with the CCAT2 transgene and without (controls). CRC cells were also analyzed by immunofluorescence microscopy, γ-H2AX, and senescence assays. CCAT2 transgene and control mice were given azoxymethane and dextran sulfate sodium to induce colon tumors. We performed gene expression array and mass spectrometry to detect downstream targets of CCAT2 lncRNA. We characterized interactions between CCAT2 with downstream proteins using MS2 pull-down, RNA immunoprecipitation, and selective 2'-hydroxyl acylation analyzed by primer extension analyses. Downstream proteins were overexpressed in CRC cells and analyzed for CIN. Gene expression levels were measured in CRC and non-tumor tissues from 5 cohorts, comprising more than 900 patients. RESULTS High expression of CCAT2 induced CIN in CRC cell lines and increased resistance to 5-fluorouracil and oxaliplatin. Mice that expressed the CCAT2 transgene developed chromosome abnormalities, and colon organoids derived from crypt cells of these mice had a higher percentage of chromosome abnormalities compared with organoids from control mice. The transgenic mice given azoxymethane and dextran sulfate sodium developed more and larger colon polyps than control mice given these agents. Microarray analysis and mass spectrometry indicated that expression of CCAT2 increased expression of genes involved in ribosome biogenesis and protein synthesis. CCAT2 lncRNA interacted directly with and stabilized BOP1 ribosomal biogenesis factor (BOP1). CCAT2 also increased expression of MYC, which activated expression of BOP1. Overexpression of BOP1 in CRC cell lines resulted in chromosomal missegregation errors, and increased colony formation, and invasiveness, whereas BOP1 knockdown reduced viability. BOP1 promoted CIN by increasing the active form of aurora kinase B, which regulates chromosomal segregation. BOP1 was overexpressed in polyp tissues from CCAT2 transgenic mice compared with healthy tissue. CCAT2 lncRNA and BOP1 mRNA or protein were all increased in microsatellite stable tumors (characterized by CIN), but not in tumors with microsatellite instability compared with nontumor tissues. Increased levels of CCAT2 lncRNA and BOP1 mRNA correlated with each other and with shorter survival times of patients. CONCLUSIONS We found that overexpression of CCAT2 in colon cells promotes CIN and carcinogenesis by stabilizing and inducing expression of BOP1 an activator of aurora kinase B. Strategies to target this pathway might be developed for treatment of patients with microsatellite stable colorectal tumors.
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Affiliation(s)
- Baoqing Chen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Radiation Oncology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, Guangdong, China,Department of Thoracic Oncology, Cancer Center and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania
| | - Linda Fabris
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Xu Liu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Thoracic Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Yongfeng Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tadanobu Shimura
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA
| | - Tina Catela Ivkovic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mireia Cruz De los Santos
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Masayoshi Shimizu
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maitri Y. Shah
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Peng Shen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Department of Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Asha S. Multani
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,present address: Italian Institute for Genomic Medicine (IIGM), Candiolo, Italy.,present address: Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Jared K. Burks
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucas C. Reineke
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
| | - Longfei Huo
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Muddassir Syed
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Manuela Ferracin
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna, 40126 Bologna, Italy
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Bastian Fromm
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden,Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Krithika Bhuvaneshwar
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Yuriy Gusev
- Innovation Center for Biomedical Informatics, Georgetown University, Washington, DC, USA
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Japan
| | - David Menter
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Subrata Sen
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Takatoshi Matsuyama
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Hiroyuki Uetake
- Department of Specialized Surgeries, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan
| | - Catalin Vasilescu
- Department of General Surgery, Fundeni Clinical Hospital, Carol Davila University of Medicine and Pharmacy, Bucharest, Romania.,“Carol Davila University of Medicine and Pharmacy”, Bucharest, Romania
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jan Parker-Thornburg
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ayumu Taguchi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Samir M. Hanash
- Department of Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Leonard Girnita
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institute and Karolinska University Hospital, SE-171 647 Stockholm, Sweden
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research; Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, USA.,present address: Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope Comprehensive Cancer Center, Duarte, CA
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Mihai Gagea
- Department of Veterinary Medicine and Surgery, The University of Texas MD Anderson Cancer Center, Houston Texas 77030, USA
| | - Chunlai Li
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Jaffer A. Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Center for RNA Interference and Non-coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Lead Contact
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Aznaourova M, Schmerer N, Schmeck B, Schulte LN. Disease-Causing Mutations and Rearrangements in Long Non-coding RNA Gene Loci. Front Genet 2020; 11:527484. [PMID: 33329688 PMCID: PMC7735109 DOI: 10.3389/fgene.2020.527484] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 11/02/2020] [Indexed: 12/12/2022] Open
Abstract
The classic understanding of molecular disease-mechanisms is largely based on protein-centric models. During the past decade however, genetic studies have identified numerous disease-loci in the human genome that do not encode proteins. Such non-coding DNA variants increasingly gain attention in diagnostics and personalized medicine. Of particular interest are long non-coding RNA (lncRNA) genes, which generate transcripts longer than 200 nucleotides that are not translated into proteins. While most of the estimated ~20,000 lncRNAs currently remain of unknown function, a growing number of genetic studies link lncRNA gene aberrations with the development of human diseases, including diabetes, AIDS, inflammatory bowel disease, or cancer. This suggests that the protein-centric view of human diseases does not capture the full complexity of molecular patho-mechanisms, with important consequences for molecular diagnostics and therapy. This review illustrates well-documented lncRNA gene aberrations causatively linked to human diseases and discusses potential lessons for molecular disease models, diagnostics, and therapy.
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Affiliation(s)
- Marina Aznaourova
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Nils Schmerer
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany
| | - Bernd Schmeck
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Marburg, Germany
| | - Leon N Schulte
- Institute for Lung Research, Philipps University Marburg, Marburg, Germany.,Systems Biology Platform, German Center for Lung Research (DZL), Philipps University Marburg, Marburg, Germany
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25
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Gao S, Tang K, Chen J, Wang J. The single nucleotide polymorphisms of interleukin-10 are associated with the risk of leukaemia: Evidence from 18 case-control studies. Medicine (Baltimore) 2020; 99:e23006. [PMID: 33126384 PMCID: PMC7598852 DOI: 10.1097/md.0000000000023006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Interleukin-10(IL-10) is an immunosuppressive cytokine and plays an important role in inflammation and cancers. Numerous studies have explored the association between single nucleotide polymorphisms of IL-10 and leukemia, but their results were conflicting, so we performed this meta-analysis to elucidate the association between 3 common single nucleotide polymorphisms of IL-10 (rs1800896, rs1800871 and rs1800872) and risk of leukemia.We conducted a comprehensive research in Pubmed, Chinese Biomedical Literature Database disc and Embase using related terms. After strict selection, 18 studies with 2264 cases and 3846 controls were included into this meta-analysis. Odds ratio and 95% confidence interval were used to evaluate the strength of the association.We found that polymorphism of IL-10 -1082A/G was associated with decreased risk of leukemia both in overall analysis and in stratified analysis according to ethnicity and cancer type. A strong relationship was also uncovered between polymorphism of IL-10 -592C/A and increased risk of leukemia in non-Chinese.GG genotype of IL-10 -1082A/G is associated with decreased risk of leukemia, especially chronic lymphocytic leukemia. CC genotype of -592C/A is associated with decreased risk of leukemia in non-Chinese.
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26
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Pichler M, Rodriguez-Aguayo C, Nam SY, Dragomir MP, Bayraktar R, Anfossi S, Knutsen E, Ivan C, Fuentes-Mattei E, Lee SK, Ling H, Ivkovic TC, Huang G, Huang L, Okugawa Y, Katayama H, Taguchi A, Bayraktar E, Bhattacharya R, Amero P, He WR, Tran AM, Vychytilova-Faltejskova P, Klec C, Bonilla DL, Zhang X, Kapitanovic S, Loncar B, Gafà R, Wang Z, Cristini V, Hanash S, Bar-Eli M, Lanza G, Slaby O, Goel A, Rigoutsos I, Lopez-Berestein G, Calin GA. Therapeutic potential of FLANC, a novel primate-specific long non-coding RNA in colorectal cancer. Gut 2020; 69:1818-1831. [PMID: 31988194 PMCID: PMC7382985 DOI: 10.1136/gutjnl-2019-318903] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/21/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022]
Abstract
OBJECTIVE To investigate the function of a novel primate-specific long non-coding RNA (lncRNA), named FLANC, based on its genomic location (co-localised with a pyknon motif), and to characterise its potential as a biomarker and therapeutic target. DESIGN FLANC expression was analysed in 349 tumours from four cohorts and correlated to clinical data. In a series of multiple in vitro and in vivo models and molecular analyses, we characterised the fundamental biological roles of this lncRNA. We further explored the therapeutic potential of targeting FLANC in a mouse model of colorectal cancer (CRC) metastases. RESULTS FLANC, a primate-specific lncRNA feebly expressed in normal colon cells, was significantly upregulated in cancer cells compared with normal colon samples in two independent cohorts. High levels of FLANC were associated with poor survival in two additional independent CRC patient cohorts. Both in vitro and in vivo experiments demonstrated that the modulation of FLANC expression influenced cellular growth, apoptosis, migration, angiogenesis and metastases formation ability of CRC cells. In vivo pharmacological targeting of FLANC by administration of 1,2-dioleoyl-sn-glycero-3-phosphatidylcholine nanoparticles loaded with a specific small interfering RNA, induced significant decrease in metastases, without evident tissue toxicity or pro-inflammatory effects. Mechanistically, FLANC upregulated and prolonged the half-life of phosphorylated STAT3, inducing the overexpression of VEGFA, a key regulator of angiogenesis. CONCLUSIONS Based on our findings, we discovered, FLANC as a novel primate-specific lncRNA that is highly upregulated in CRC cells and regulates metastases formation. Targeting primate-specific transcripts such as FLANC may represent a novel and low toxic therapeutic strategy for the treatment of patients.
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Affiliation(s)
- Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Research Unit of Non-Coding RNA and Genome Editing, Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Su Youn Nam
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Gastroenterology Department, Kyungpook National University Chilgok Hospital, Daegu, Korea
| | - Mihnea P. Dragomir
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Recep Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Simone Anfossi
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Erik Knutsen
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Department of Medical Biology, Faculty of Health Sciences, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Enrique Fuentes-Mattei
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sang Kil Lee
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Institute of Gastroenterology, Department of Internal Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Tina Catela Ivkovic
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Guoliang Huang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: China-America Cancer Research Institute, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan 523808, Guangdong, P.R. China
| | - Li Huang
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yoshinaga Okugawa
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX
| | - Hiroyuki Katayama
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Ayumu Taguchi
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Emine Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rajat Bhattacharya
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William Ruixian He
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anh M. Tran
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Petra Vychytilova-Faltejskova
- Molecular Oncology II - Solid Cancers, Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Czech Republic
| | - Christiane Klec
- Research Unit of Non-Coding RNA and Genome Editing, Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Diana L. Bonilla
- Department of Stem Cell Transplantation, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xinna Zhang
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Present address: Medical and Molecular Genetics Department, Indiana University, Indianapolis, IN, USA
| | - Sanja Kapitanovic
- Laboratory for Personalized Medicine, Division of Molecular Medicine, Ruder Boskovic Institute, Zagreb, Croatia
| | - Bozo Loncar
- Department of Surgery, Clinical Hospital Dubrava, Zagreb, Croatia
| | - Roberta Gafà
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Zhihui Wang
- Mathematics in Medicine Program, The Houston Methodist Research Institute HMRI R8-122, 6670 Bertner Ave, Houston, TX 77030
| | - Vittorio Cristini
- Mathematics in Medicine Program, The Houston Methodist Research Institute HMRI R8-122, 6670 Bertner Ave, Houston, TX 77030
| | - Samir Hanash
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Giovanni Lanza
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Ondrej Slaby
- Molecular Oncology II - Solid Cancers, Molecular Medicine, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, Czech Republic
| | - Ajay Goel
- Center for Gastrointestinal Research and Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX,Present address: Department of Molecular Diagnostics, Therapeutics and Translational Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Isidore Rigoutsos
- Computational Medicine Center and Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA .,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Center for RNA interference and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX, USA,Corresponding authors George A. Calin, M.D., Ph.D. Professor, Department of Experimental Therapeutics, Center for RNA Interference and Non-Coding RNAs, Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, P.O. Box 301429, Houston, Texas 77030-1429, and Gabriel Lopez-Berestein, M.D., Professor, Department of Experimental Therapeutics, Center for RNA Interference and Non-Coding RNAs, Department of Experimental Therapeutics - Unit 1950, The University of Texas MD Anderson Cancer Center, P.O. Box 301429, Houston, Texas 77030-1429,
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27
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Teodorescu P, Pasca S, Jurj A, Gafencu G, Joelsson JP, Selicean S, Moldovan C, Munteanu R, Onaciu A, Tigu AB, Buse M, Zimta AA, Stiufiuc R, Petrushev B, Desmirean M, Dima D, Vlad C, Bergthorsson JT, Berce C, Ciurea S, Ghiaur G, Tomuleasa C. Transforming growth factor β-mediated micromechanics modulates disease progression in primary myelofibrosis. J Cell Mol Med 2020; 24:11100-11110. [PMID: 32889753 PMCID: PMC7576271 DOI: 10.1111/jcmm.15526] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 05/29/2020] [Indexed: 12/15/2022] Open
Abstract
Primary myelofibrosis (PMF) is a Ph‐negative myeloproliferative neoplasm (MPN), characterized by advanced bone marrow fibrosis and extramedullary haematopoiesis. The bone marrow fibrosis results from excessive proliferation of fibroblasts that are influenced by several cytokines in the microenvironment, of which transforming growth factor‐β (TGF‐β) is the most important. Micromechanics related to the niche has not yet been elucidated. In this study, we hypothesized that mechanical stress modulates TGF‐β signalling leading to further activation and subsequent proliferation and invasion of bone marrow fibroblasts, thus showing the important role of micromechanics in the development and progression of PMF, both in the bone marrow and in extramedullary sites. Using three PMF‐derived fibroblast cell lines and transforming growth factor‐β receptor (TGFBR) 1 and 2 knock‐down PMF‐derived fibroblasts, we showed that mechanical stress does stimulate the collagen synthesis by the fibroblasts in patients with myelofibrosis, through the TGFBR1, which however seems to be activated through alternative pathways, other than TGFBR2.
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Affiliation(s)
- Patric Teodorescu
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania
| | - Sergiu Pasca
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Ancuta Jurj
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Grigore Gafencu
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Molecular Haematology Unit - Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Jon-Petur Joelsson
- Stem Cell Research Unit, Biomedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland.,Department of Laboratory Hematology, Landspitali University Hospital, Reykjavík, Iceland
| | - Sonia Selicean
- Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Graduate School for Cellular and Biomedical Sciences, Universität Bern, Bern, Switzerland
| | - Cristian Moldovan
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Raluca Munteanu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Anca Onaciu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Adrian-Bogdan Tigu
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Mihail Buse
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Alina-Andreea Zimta
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Rares Stiufiuc
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Bobe Petrushev
- Medfuture Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Minodora Desmirean
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Pathology, Constantin Papilian Military Hospital, Cluj Napoca, Romania
| | - Delia Dima
- Department of Hematology, Ion Chiricuta Clinical Research Center, Cluj Napoca, Romania
| | - Cristina Vlad
- Department of Cardiology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Cardiology, Rehabilitation Hospital, Cluj Napoca, Romania
| | - Jon Thor Bergthorsson
- Stem Cell Research Unit, Biomedical Center, School of Health Sciences, University of Iceland, Reykjavík, Iceland.,Department of Laboratory Hematology, Landspitali, University Hospital, Reykjavík, Iceland
| | - Cristian Berce
- Animal Facility, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
| | - Stefan Ciurea
- Department of Cellular Therapies and Stem Cell Transplantation, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gabriel Ghiaur
- Department of Leukemia, Sidney Kimmel Cancer Center at Johns Hopkins, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ciprian Tomuleasa
- Department of Hematology, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania.,Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj Napoca, Romania.,Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj Napoca, Romania
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28
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Abstract
RNA abasic sites and the mechanisms involved in their regulation are mostly unknown; in contrast, DNA abasic sites are well-studied. We found surprisingly that, in yeast and human cells, RNA abasic sites are prevalent. When a base is lost from RNA, the remaining ribose is found as a closed-ring or an open-ring sugar with a reactive C1' aldehyde group. Using primary amine-based reagents that react with the aldehyde group, we uncovered evidence for abasic sites in nascent RNA, messenger RNA, and ribosomal RNA from yeast and human cells. Mass spectroscopic analysis confirmed the presence of RNA abasic sites. The RNA abasic sites were found to be coupled to R-loops. We show that human methylpurine DNA glycosylase cleaves N-glycosidic bonds on RNA and that human apurinic/apyrimidinic endonuclease 1 incises RNA abasic sites in RNA-DNA hybrids. Our results reveal that, in yeast and human cells, there are RNA abasic sites, and we identify a glycosylase that generates these sites and an AP endonuclease that processes them.
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29
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Barth DA, Juracek J, Slaby O, Pichler M, Calin GA. lncRNA and Mechanisms of Drug Resistance in Cancers of the Genitourinary System. Cancers (Basel) 2020; 12:cancers12082148. [PMID: 32756406 PMCID: PMC7463785 DOI: 10.3390/cancers12082148] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 02/08/2023] Open
Abstract
Available systemic treatment options for cancers of the genitourinary system have experienced great progress in the last decade. However, a large proportion of patients eventually develop resistance to treatment, resulting in disease progression and shorter overall survival. Biomarkers indicating the increasing resistance to cancer therapies are yet to enter clinical routine. Long non-coding RNAs (lncRNA) are non-protein coding RNA transcripts longer than 200 nucleotides that exert multiple types of regulatory functions of all known cellular processes. Increasing evidence supports the role of lncRNAs in cancer development and progression. Additionally, their involvement in the development of drug resistance across various cancer entities, including genitourinary malignancies, are starting to be discovered. Consequently, lncRNAs have been suggested as factors in novel therapeutic strategies to overcome drug resistance in cancer. In this review, the existing evidences on lncRNAs and their involvement in mechanisms of drug resistance in cancers of the genitourinary system, including renal cell carcinoma, bladder cancer, prostate cancer, and testicular cancer, will be highlighted and discussed to facilitate and encourage further research in this field. We summarize a significant number of lncRNAs with proposed pathways in drug resistance and available reported studies.
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Affiliation(s)
- Dominik A. Barth
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (D.A.B.); (M.P.)
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
| | - Jaroslav Juracek
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 62500 Brno, Czech Republic;
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Ondrej Slaby
- Department of Comprehensive Cancer Care, Masaryk Memorial Cancer Institute, 62500 Brno, Czech Republic;
- Central European Institute of Technology, Masaryk University, 62500 Brno, Czech Republic
| | - Martin Pichler
- Research Unit of Non-Coding RNAs and Genome Editing in Cancer, Division of Clinical Oncology, Department of Medicine, Comprehensive Cancer Center Graz, Medical University of Graz, 8036 Graz, Austria; (D.A.B.); (M.P.)
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - George A. Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA;
- Correspondence:
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30
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Zou H, Wu LX, Tan L, Shang FF, Zhou HH. Significance of Single-Nucleotide Variants in Long Intergenic Non-protein Coding RNAs. Front Cell Dev Biol 2020; 8:347. [PMID: 32523949 PMCID: PMC7261909 DOI: 10.3389/fcell.2020.00347] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/20/2020] [Indexed: 12/15/2022] Open
Abstract
Single-nucleotide variants (SNVs) are the most common genetic variants and universally present in the human genome. Genome-wide association studies (GWASs) have identified a great number of disease or trait-associated variants, many of which are located in non-coding regions. Long intergenic non-protein coding RNAs (lincRNAs) are the major subtype of long non-coding RNAs; lincRNAs play crucial roles in various disorders and cellular models via multiple mechanisms. With rapid growth in the number of the identified lincRNAs and genetic variants, there is great demand for an investigation of SNVs in lincRNAs. Hence, in this article, we mainly summarize the significant role of SNVs within human lincRNA regions. Some pivotal variants may serve as risk factors for the development of various disorders, especially cancer. They may also act as important regulatory signatures involved in the modulation of lincRNAs in a tissue- or disorder-specific manner. An increasing number of researches indicate that lincRNA variants would potentially provide additional options for genetic testing and disease risk assessment in the personalized medicine era.
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Affiliation(s)
- Hecun Zou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Lan-Xiang Wu
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Lihong Tan
- Chongqing Medical and Pharmaceutical College, Chongqing, China.,Xiangya Hospital, Central South University, Changsha, China
| | - Fei-Fei Shang
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China
| | - Hong-Hao Zhou
- Institute of Life Sciences, Chongqing Medical University, Chongqing, China.,Xiangya Hospital, Central South University, Changsha, China
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31
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Li J, Xue Y, Amin MT, Yang Y, Yang J, Zhang W, Yang W, Niu X, Zhang HY, Gong J. ncRNA-eQTL: a database to systematically evaluate the effects of SNPs on non-coding RNA expression across cancer types. Nucleic Acids Res 2020; 48:D956-D963. [PMID: 31410488 PMCID: PMC6943077 DOI: 10.1093/nar/gkz711] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 07/26/2019] [Accepted: 08/02/2019] [Indexed: 12/20/2022] Open
Abstract
Numerous studies indicate that non-coding RNAs (ncRNAs) have critical functions across biological processes, and single-nucleotide polymorphisms (SNPs) could contribute to diseases or traits through influencing ncRNA expression. However, the associations between SNPs and ncRNA expression are largely unknown. Therefore, genome-wide expression quantitative trait loci (eQTL) analysis to assess the effects of SNPs on ncRNA expression, especially in multiple cancer types, will help to understand how risk alleles contribute toward tumorigenesis and cancer development. Using genotype data and expression profiles of ncRNAs of >8700 samples from The Cancer Genome Atlas (TCGA), we developed a computational pipeline to systematically identify ncRNA-related eQTLs (ncRNA-eQTLs) across 33 cancer types. We identified a total of 6 133 278 and 721 122 eQTL-ncRNA pairs in cis-eQTL and trans-eQTL analyses, respectively. Further survival analyses identified 8312 eQTLs associated with patient survival times. Furthermore, we linked ncRNA-eQTLs to genome-wide association study (GWAS) data and found 262 332 ncRNA-eQTLs overlapping with known disease- and trait-associated loci. Finally, a user-friendly database, ncRNA-eQTL (http://ibi.hzau.edu.cn/ncRNA-eQTL), was developed for free searching, browsing and downloading of all ncRNA-eQTLs. We anticipate that such an integrative and comprehensive resource will improve our understanding of the mechanistic basis of human complex phenotypic variation, especially for ncRNA- and cancer-related studies.
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Affiliation(s)
- Jiang Li
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Yawen Xue
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Muhammad Talal Amin
- National Institute of Genomics and Advanced Biotechnology, National Agriculture Research Center, Islamabad 44051, Pakistan
| | - Yanbo Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jiajun Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Wen Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Wenqian Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Xiaohui Niu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China
| | - Jing Gong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P.R. China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, P.R. China
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32
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Allelic-Specific Regulation of xCT Expression Increases Susceptibility to Tuberculosis by Modulating microRNA-mRNA Interactions. mSphere 2020; 5:5/2/e00263-20. [PMID: 32321821 PMCID: PMC7178550 DOI: 10.1128/msphere.00263-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of death from a single infectious agent globally, and the development of multidrug resistance represents a serious health concern, particularly in the developing world. Novel effective treatments are urgently required. xCT expression is known to increase susceptibility to TB, and certain polymorphisms in the gene encoding this protein interrupt the binding of microRNA and prevent its suppression. Taking advantage of the FDA approval for the use of sulfasalazine (SASP), which inhibits xCT-mediated cystine transport in humans, we demonstrate how host genotype-specific therapies tailored to the xCT genotype can improve TB outcomes. xCT forms part of the xc− cysteine-glutamate antiporter which inhibits antimicrobial inflammatory immune functions and thus increases susceptibility to tuberculosis (TB). However, the associations between xCT gene polymorphisms and susceptibility to TB, as well as whether these modulate xCT expression or affect treatment with the xCT inhibitor sulfasalazine (SASP), are unclear. In the present study, we genotyped xCT polymorphisms in a large Chinese cohort and found that the single-nucleotide polymorphism (SNP) rs13120371 was associated with susceptibility to TB. The rs13120371 AA genotype was strongly associated with an increased risk of TB and increased xCT mRNA expression levels compared to those with the GG or AG genotype. rs13120371 is located on the 3′ untranslated (UTR) region of the xCT gene, in the putative binding site for miR-142-3p, and the results of luciferase reporter assays indicated that the rs13120371 AA genotype inhibited the binding of miR-42-3p to xCT. Bacterial burden was also significantly higher in cells with the AA genotype than in those with the GG genotype. Furthermore, pretreatment with SASP alleviated this burden in cells with the AA genotype but conferred no benefit in cells with the GG phenotype. In summary, we identified a functional SNP (rs13120371) in the xCT 3′ UTR region that increases susceptibility to TB through interacting with miR-142-3p. IMPORTANCE Tuberculosis (TB) is the leading cause of death from a single infectious agent globally, and the development of multidrug resistance represents a serious health concern, particularly in the developing world. Novel effective treatments are urgently required. xCT expression is known to increase susceptibility to TB, and certain polymorphisms in the gene encoding this protein interrupt the binding of microRNA and prevent its suppression. Taking advantage of the FDA approval for the use of sulfasalazine (SASP), which inhibits xCT-mediated cystine transport in humans, we demonstrate how host genotype-specific therapies tailored to the xCT genotype can improve TB outcomes.
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33
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Silverman EK, Schmidt HHHW, Anastasiadou E, Altucci L, Angelini M, Badimon L, Balligand JL, Benincasa G, Capasso G, Conte F, Di Costanzo A, Farina L, Fiscon G, Gatto L, Gentili M, Loscalzo J, Marchese C, Napoli C, Paci P, Petti M, Quackenbush J, Tieri P, Viggiano D, Vilahur G, Glass K, Baumbach J. Molecular networks in Network Medicine: Development and applications. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1489. [PMID: 32307915 DOI: 10.1002/wsbm.1489] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Revised: 02/29/2020] [Accepted: 03/20/2020] [Indexed: 12/14/2022]
Abstract
Network Medicine applies network science approaches to investigate disease pathogenesis. Many different analytical methods have been used to infer relevant molecular networks, including protein-protein interaction networks, correlation-based networks, gene regulatory networks, and Bayesian networks. Network Medicine applies these integrated approaches to Omics Big Data (including genetics, epigenetics, transcriptomics, metabolomics, and proteomics) using computational biology tools and, thereby, has the potential to provide improvements in the diagnosis, prognosis, and treatment of complex diseases. We discuss briefly the types of molecular data that are used in molecular network analyses, survey the analytical methods for inferring molecular networks, and review efforts to validate and visualize molecular networks. Successful applications of molecular network analysis have been reported in pulmonary arterial hypertension, coronary heart disease, diabetes mellitus, chronic lung diseases, and drug development. Important knowledge gaps in Network Medicine include incompleteness of the molecular interactome, challenges in identifying key genes within genetic association regions, and limited applications to human diseases. This article is categorized under: Models of Systems Properties and Processes > Mechanistic Models Translational, Genomic, and Systems Medicine > Translational Medicine Analytical and Computational Methods > Analytical Methods Analytical and Computational Methods > Computational Methods.
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Affiliation(s)
- Edwin K Silverman
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Harald H H W Schmidt
- Department of Pharmacology and Personalized Medicine, School of Mental Health and Neuroscience, Faculty of Health, Medicine and Life Science, Maastricht University, Maastricht, The Netherlands
| | - Eleni Anastasiadou
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Marco Angelini
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Lina Badimon
- Cardiovascular Program-ICCC, IR-Hospital de la Santa Creu i Sant Pau, CiberCV, IIB-Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Jean-Luc Balligand
- Pole of Pharmacology and Therapeutics (FATH), Institute for Clinical and Experimental Research (IREC), UCLouvain, Brussels, Belgium
| | - Giuditta Benincasa
- Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Giovambattista Capasso
- Department of Translational Medical Sciences, University of Campania "L. Vanvitelli", Naples, Italy.,BIOGEM, Ariano Irpino, Italy
| | - Federica Conte
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Antonella Di Costanzo
- Department of Precision Medicine, University of Campania 'Luigi Vanvitelli', Naples, Italy
| | - Lorenzo Farina
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Giulia Fiscon
- Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Laurent Gatto
- de Duve Institute, Brussels, Belgium.,Institute for Experimental and Clinical Research (IREC), UCLouvain, Brussels, Belgium
| | - Michele Gentili
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Joseph Loscalzo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Division of Cardiovascular Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Cinzia Marchese
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Claudio Napoli
- Department of Advanced Clinical and Surgical Sciences, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Paola Paci
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - Manuela Petti
- Department of Computer, Control and Management Engineering, Sapienza University of Rome, Rome, Italy
| | - John Quackenbush
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Paolo Tieri
- CNR National Research Council of Italy, IAC Institute for Applied Computing, Rome, Italy
| | - Davide Viggiano
- BIOGEM, Ariano Irpino, Italy.,Department of Medicine and Health Sciences, University of Molise, Campobasso, Italy
| | - Gemma Vilahur
- Cardiovascular Program-ICCC, IR-Hospital de la Santa Creu i Sant Pau, CiberCV, IIB-Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Kimberly Glass
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Jan Baumbach
- Department of Experimental Bioinformatics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Maximus-von-Imhof-Forum 3, Freising, Germany.,Institute of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
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34
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Dragomir MP, Kopetz S, Ajani JA, Calin GA. Non-coding RNAs in GI cancers: from cancer hallmarks to clinical utility. Gut 2020; 69:748-763. [PMID: 32034004 DOI: 10.1136/gutjnl-2019-318279] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 12/11/2022]
Abstract
One of the most unexpected discoveries in molecular oncology, in the last decades, was the identification of a new layer of protein coding gene regulation by transcripts that do not codify for proteins, the non-coding RNAs. These represent a heterogeneous category of transcripts that interact with many types of genetic elements, including regulatory DNAs, coding and other non-coding transcripts and directly to proteins. The final outcome, in the malignant context, is the regulation of any of the cancer hallmarks. Non-coding RNAs represent the most abundant type of hormones that contribute significantly to cell-to cell communication, revealing a complex interplay between tumour cells, tumour microenvironment cells and immune cells. Consequently, profiling their abundance in bodily fluids became a mainstream of biomarker identification. Therapeutic targeting of non-coding RNAs represents a new option for clinicians that is currently under development. This review will present the biology and translational value of three of the most studied categories on non-coding RNAs, the microRNAs, the long non-coding RNAs and the circular RNAs. We will also focus on some aspirational concepts that can help in the development of clinical applications related to non-coding RNAs, including using pyknons to discover new non-coding RNAs, targeting human-specific transcripts which are expressed specifically in the tumour cell and using non-coding RNAs to increase the efficiency of immunotherapy.
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Affiliation(s)
- Mihnea Paul Dragomir
- Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - George Adrian Calin
- Experimental Therapeutics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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35
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Du X, Liu L, Li Q, Zhang L, Pan Z, Li Q. NORFA, long intergenic noncoding RNA, maintains sow fertility by inhibiting granulosa cell death. Commun Biol 2020; 3:131. [PMID: 32188888 PMCID: PMC7080823 DOI: 10.1038/s42003-020-0864-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/27/2020] [Indexed: 02/07/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) have been proved to be involved in regulating female reproduction. However, to what extent lincRNAs are involved in ovarian functions and fertility is incompletely understood. Here we show that a lincRNA, NORFA is involved in granulosa cell apoptosis, follicular atresia and sow fertility. We found that NORFA was down-regulated during follicular atresia, and inhibited granulosa cell apoptosis. NORFA directly interacted with miR-126 and thereby preventing it from binding to TGFBR2 3'-UTR. miR-126 enhanced granulosa cell apoptosis by attenuating NORFA-induced TGF-β signaling pathway. Importantly, a breed-specific 19-bp duplication was detected in NORFA promoter, which proved association with sow fertility through enhancing transcription activity of NORFA by recruiting transcription factor NFIX. In summary, our findings identified a candidate lincRNA for sow prolificacy, and provided insights into the mechanism of follicular atresia and female fertility.
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Affiliation(s)
- Xing Du
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lu Liu
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qiqi Li
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Lifan Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zengxiang Pan
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China
| | - Qifa Li
- College of Animal Science and Technology, Nanjing Agricultural University, 210095, Nanjing, China.
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36
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Wu Q, Zhong H, Bai H, Liu T, Song J, Wen Y, Song X, Ying B. Clinical relevance of the lnc-HNF1B-3:1 genetic polymorphisms in Western Chinese tuberculosis patients. J Clin Lab Anal 2020; 34:e23076. [PMID: 31692082 PMCID: PMC7083404 DOI: 10.1002/jcla.23076] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 09/26/2019] [Accepted: 09/27/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Tuberculosis remains a global public health problem. Genetic polymorphisms may affect the susceptibility, clinical characteristics, and adverse drug reactions of patients with TB. The present study aimed to examine the association of single nucleotide polymorphisms of lncRNA-HNF1B-3:1 with the clinical manifestation of TB in a Western Chinese population. METHOD A total of 526 tuberculosis patients and 561 healthy subjects were recruited in Western China. The correlation between lnc-HNF1B-3:1 polymorphism and tuberculosis susceptibility was investigated. Moreover, the influence on adverse drug reactions following treatment was explored. A total of 7 SNPs within the lnc-HNF1B-3:1 locus was genotyped by the improved multiplex ligation detection reaction method. RESULTS No significant associations were noted between TB susceptibility and the presence of all 7 SNPs of the lnc-HNF1B-3:1 as determined by single-locus analysis (All P > .05). The AA genotype of rs12939622 (in the dominant model) and the AA genotype of rs4262994 (in the recessive model) caused increased susceptibility of the subjects to fever (P < .001 and P = .008, respectively). The Rs2542670 G allele was associated with increased risk of thrombocytopenia, leukopenia, and chronic kidney damage following drug administration (P = .007, .029, .003, respectively). CONCLUSION The present study reported for the first time that the rs12939622, rs4262994 and rs2542670 genotypes in lnc-HNF1B-3:1 locus may influence the clinical manifestations of tuberculosis.
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Affiliation(s)
- Qian Wu
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
| | - Huiyu Zhong
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
| | - Hao Bai
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
| | - Tangyuheng Liu
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
| | - Jiajia Song
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
| | - Yang Wen
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
| | - Xingbo Song
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
| | - Binwu Ying
- Department of Laboratory MedicineWest China HospitalSichuan UniversityChengduP. R China
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37
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Mussazhanova Z, Rogounovitch TI, Saenko VA, Krykpayeva A, Espenbetova M, Azizov B, Kondo H, Matsuda K, Kalmatayeva Z, Issayeva R, Yeleubayeva Z, Madiyeva M, Mukanova A, Sandybayev M, Bolsynbekova S, Kozykenova Z, Yamashita S, Nakashima M. The Contribution of Genetic Variants to the Risk of Papillary Thyroid Carcinoma in the Kazakh Population: Study of Common Single Nucleotide Polymorphisms and Their Clinicopathological Correlations. Front Endocrinol (Lausanne) 2020; 11:543500. [PMID: 33551988 PMCID: PMC7862756 DOI: 10.3389/fendo.2020.543500] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 12/01/2020] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVE Risk for developing papillary thyroid carcinoma (PTC), the most common endocrine malignancy, is thought to be mediated by lifestyle, environmental exposures and genetic factors. Recent progress in the genome-wide association studies of thyroid cancer leads to the identification of several genetic variants conferring risk to this malignancy across different ethnicities. We set out to elucidate the impact of selected single nucleotide polymorphisms (SNPs) on PTC risk and to evaluate clinicopathological correlations of these genetic variants in the Kazakh population for the first time. METHODS Eight SNPs were genotyped in 485 patients with PTC and 1,008 healthy control Kazakh subjects. The association analysis and multivariable modeling of PTC risk by the genetic factors, supplemented with rigorous statistical validation, were performed. RESULT Five of the eight SNPs: rs965513 (FOXE1/PTCSC2, P = 1.3E-16), rs1867277 (FOXE1 5'UTR, P = 7.5E-06), rs2439302 (NRG1 intron 1, P = 4.0E-05), rs944289 (PTCSC3/NKX2-1, P = 4.5E-06) and rs10136427 (BATF upstream, P = 9.8E-03) were significantly associated with PTC. rs966423 (DIRC3, P = 0.07) showed a suggestive association. rs7267944 (DHX35) was associated with PTC risk in males (P = 0.02), rs1867277 (FOXE1) conferred the higher risk in subjects older than 55 years (P = 7.0E-05), and rs6983267 (POU5F1B/CCAT2) was associated with pT3-T4 tumors (P = 0.01). The contribution of genetic component (unidirectional independent effects of rs965513, rs944289, rs2439302 and rs10136427 adjusted for age and sex) to PTC risk in the analyzed series was estimated to be 30-40%. CONCLUSION Genetic factors analyzed in the present work display significant association signals with PTC either on the whole group analysis or in particular clinicopathological groups and account for about one-third of the risk for PTC in the Kazakh population.
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Affiliation(s)
- Zhanna Mussazhanova
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Tatiana I. Rogounovitch
- Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Vladimir A. Saenko
- Department of Radiation Molecular Epidemiology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
- *Correspondence: Vladimir A. Saenko,
| | - Ainur Krykpayeva
- Department of Endocrinology, Semey Medical University, Semey, Kazakhstan
| | - Maira Espenbetova
- Department of Endocrinology, Semey Medical University, Semey, Kazakhstan
| | - Bauyrzhan Azizov
- Endovascular Laboratory of Training Hospital, Semey Medical University, Semey, Kazakhstan
| | - Hisayoshi Kondo
- Biostatics Section, Division of Scientific Data Registry, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Katsuya Matsuda
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Zhanna Kalmatayeva
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Raushan Issayeva
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Zhanar Yeleubayeva
- Faculty of Medicine and Health Care, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Center of Morphological Examination, Kazakh Institute of Oncology and Radiology, Almaty, Kazakhstan
| | - Madina Madiyeva
- Radiology and Nuclear Medicine, Semey Medical University, Semey, Kazakhstan
| | - Aray Mukanova
- Radiology and Nuclear Medicine, Semey Medical University, Semey, Kazakhstan
| | - Marat Sandybayev
- Center of Nuclear Medicine and Oncology of Semey, Semey, Kazakhstan
| | | | - Zhanna Kozykenova
- Department of Pathological Physiology, Semey Medical University, Semey, Kazakhstan
| | - Shunichi Yamashita
- Department of Radiation Medical Sciences, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Masahiro Nakashima
- Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
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Rezaeian AH, Khanbabaei H, Calin GA. Therapeutic Potential of the miRNA-ATM Axis in the Management of Tumor Radioresistance. Cancer Res 2019; 80:139-150. [PMID: 31767626 DOI: 10.1158/0008-5472.can-19-1807] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Revised: 10/09/2019] [Accepted: 11/14/2019] [Indexed: 11/16/2022]
Abstract
The ataxia-telangiectasia mutated (ATM) protein kinase is widely known for its function as a chief mobilizer of the DNA damage response (DDR) upon DNA double-strand breaks. ATM orchestrates the DDR by modulating the expression of various miRNAs through several mechanisms. On the other hand, a set of miRNAs contribute to tight regulation of ATM by directly targeting the 3'-untranslated region of ATM mRNA. This review addresses the therapeutic application and molecular mechanisms that underlie the intricate interactions between miRNAs and ATM. It also describes therapeutic delivery of miRNAs in different environments such as hypoxic tumor microenvironments.
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Affiliation(s)
- Abdol-Hossein Rezaeian
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Hashem Khanbabaei
- Department of Medical Physics, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - George A Calin
- Departments of Experimental Therapeutics and Leukemia and the Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Zimta AA, Tomuleasa C, Sahnoune I, Calin GA, Berindan-Neagoe I. Long Non-coding RNAs in Myeloid Malignancies. Front Oncol 2019; 9:1048. [PMID: 31681586 PMCID: PMC6813191 DOI: 10.3389/fonc.2019.01048] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022] Open
Abstract
Acute myeloid leukemia (AML) represents 80% of adult leukemias and 15-20% of childhood leukemias. AML are characterized by the presence of 20% blasts or more in the bone marrow, or defining cytogenetic abnormalities. Laboratory diagnoses of myelodysplastic syndromes (MDS) depend on morphological changes based on dysplasia in peripheral blood and bone marrow, including peripheral blood smears, bone marrow aspirate smears, and bone marrow biopsies. As leukemic cells are not functional, the patient develops anemia, neutropenia, and thrombocytopenia, leading to fatigue, recurrent infections, and hemorrhage. The genetic background and associated mutations in AML blasts determine the clinical course of the disease. Over the last decade, non-coding RNAs transcripts that do not codify for proteins but play a role in regulation of functions have been shown to have multiple applications in the diagnosis, prognosis and therapeutic approach of various types of cancers, including myeloid malignancies. After a comprehensive review of current literature, we found reports of multiple long non-coding RNAs (lncRNAs) that can differentiate between AML types and how their exogenous modulation can dramatically change the behavior of AML cells. These lncRNAs include: H19, LINC00877, RP11-84C10, CRINDE, RP11848P1.3, ZNF667-AS1, AC111000.4-202, SFMBT2, LINC02082-201, MEG3, AC009495.2, PVT1, HOTTIP, SNHG5, and CCAT1. In addition, by performing an analysis on available AML data in The Cancer Genome Atlas (TCGA), we found 10 lncRNAs with significantly differential expression between patients in favorable, intermediate/normal, or poor cytogenetic risk categories. These are: DANCR, PRDM16-DT, SNHG6, OIP5-AS1, SNHG16, JPX, FTX, KCNQ1OT1, TP73-AS1, and GAS5. The identification of a molecular signature based on lncRNAs has the potential for have deep clinical significance, as it could potentially help better define the evolution from low-grade MDS to high-grade MDS to AML, changing the course of therapy. This would allow clinicians to provide a more personalized, patient-tailored therapeutic approach, moving from transfusion-based therapy, as is the case for low-grade MDS, to the introduction of azacytidine-based chemotherapy or allogeneic stem cell transplantation, which is the current treatment for high-grade MDS.
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Affiliation(s)
- Alina-Andreea Zimta
- MedFuture - Research Center for Advanced Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Ciprian Tomuleasa
- Department of Hematology, Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Hematology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
| | - Iman Sahnoune
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - George A. Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Ioana Berindan-Neagoe
- MedFuture - Research Center for Advanced Medicine, Research Center for Functional Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
- Department of Functional Genomics and Experimental Pathology, Ion Chiricuta Clinical Cancer Center, Cluj-Napoca, Romania
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Ghafouri-Fard S, Taheri M. Colon Cancer-Associated Transcripts 1 and 2: Roles and functions in human cancers. J Cell Physiol 2019; 234:14581-14600. [PMID: 30693526 DOI: 10.1002/jcp.28176] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023]
Abstract
The long noncoding RNAs (lncRNAs) Colon Cancer-Associated Transcripts 1 and 2 (CCAT1 and CCAT2) are located in a recurrently amplified region in cancers. Their proximity with the Myc oncogene and their interactions with its promoter provided further evidence for their contribution in the tumorigenesis processes. Several cell line and clinical studies have shown upregulation of these lncRNAs in diverse malignancies. Moreover, some single nucleotide variants within these genes have been associated with cancer risk or therapeutic response in different populations. Besides, these two lncRNAs act as sponges for some tumor suppressor microRNAs (miRNAs), thus promoting cancer evolution. In the current study, we review recent literature about their expression level, interaction with cancer-related pathways, their role in determination of cell fate and their contribution in malignant phenotype characteristics. Taken together, the current literature shows that these lncRNAs are putative targets for design of novel treatment strategies. Moreover, their expression levels in biopsied samples, exosomes, and sera of patients might be applied as diagnostic biomarkers or markers for patient follow-up.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Student Research Committee, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Fabbri M, Girnita L, Varani G, Calin GA. Decrypting noncoding RNA interactions, structures, and functional networks. Genome Res 2019; 29:1377-1388. [PMID: 31434680 PMCID: PMC6724670 DOI: 10.1101/gr.247239.118] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The world of noncoding RNAs (ncRNAs) is composed of an enormous and growing number of transcripts, ranging in length from tens of bases to tens of kilobases, involved in all biological processes and altered in expression and/or function in many types of human disorders. The premise of this review is the concept that ncRNAs, like many large proteins, have a multidomain architecture that organizes them spatially and functionally. As ncRNAs are beginning to be imprecisely classified into functional families, we review here how their structural properties might inform their functions with focus on structural architecture–function relationships. We will describe the properties of “interactor elements” (IEs) involved in direct physical interaction with nucleic acids, proteins, or lipids and of “structural elements” (SEs) directing their wiring within the “ncRNA interactor networks” through the emergence of secondary and/or tertiary structures. We suggest that spectrums of “letters” (ncRNA elements) are assembled into “words” (ncRNA domains) that are further organized into “phrases” (complete ncRNA structures) with functional meaning (signaling output) through complex “sentences” (the ncRNA interactor networks). This semiotic analogy can guide the exploitation of ncRNAs as new therapeutic targets through the development of IE-blockers and/or SE-lockers that will change the interactor partners’ spectrum of proteins, RNAs, DNAs, or lipids and consequently influence disease phenotypes.
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Affiliation(s)
- Muller Fabbri
- University of Hawaii Cancer Center, Cancer Biology Program, Honolulu, Hawaii 96813, USA
| | - Leonard Girnita
- Department of Oncology-Pathology, Cellular and Molecular Tumor Pathology, Karolinska Institute, and Karolinska University Hospital, Stockholm, 17164 Sweden
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington 98195-1700, USA
| | - George A Calin
- Department of Experimental Therapeutics, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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Pardini B, Sabo AA, Birolo G, Calin GA. Noncoding RNAs in Extracellular Fluids as Cancer Biomarkers: The New Frontier of Liquid Biopsies. Cancers (Basel) 2019; 11:E1170. [PMID: 31416190 PMCID: PMC6721601 DOI: 10.3390/cancers11081170] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/04/2019] [Accepted: 08/10/2019] [Indexed: 02/06/2023] Open
Abstract
The last two decades of cancer research have been devoted in two directions: (1) understanding the mechanism of carcinogenesis for an effective treatment, and (2) improving cancer prevention and screening for early detection of the disease. This last aspect has been developed, especially for certain types of cancers, thanks also to the introduction of new concepts such as liquid biopsies and precision medicine. In this context, there is a growing interest in the application of alternative and noninvasive methodologies to search for cancer biomarkers. The new frontiers of the research lead to a search for RNA molecules circulating in body fluids. Searching for biomarkers in extracellular body fluids represents a better option for patients because they are easier to access, less painful, and potentially more economical. Moreover, the possibility for these types of samples to be taken repeatedly, allows a better monitoring of the disease progression or treatment efficacy for a better intervention and dynamic treatment of the patient, which is the fundamental basis of personalized medicine. RNA molecules, freely circulating in body fluids or packed in microvesicles, have all the characteristics of the ideal biomarkers owing to their high stability under storage and handling conditions and being able to be sampled several times for monitoring. Moreover, as demonstrated for many cancers, their plasma/serum levels mirror those in the primary tumor. There are a large variety of RNA species noncoding for proteins that could be used as cancer biomarkers in liquid biopsies. Among them, the most studied are microRNAs, but recently the attention of the researcher has been also directed towards Piwi-interacting RNAs, circular RNAs, and other small noncoding RNAs. Another class of RNA species, the long noncoding RNAs, is larger than microRNAs and represents a very versatile and promising group of molecules which, apart from their use as biomarkers, have also a possible therapeutic role. In this review, we will give an overview of the most common noncoding RNA species detectable in extracellular fluids and will provide an update concerning the situation of the research on these molecules as cancer biomarkers.
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Affiliation(s)
- Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy.
- Unit of Molecular Epidemiology and Exposome, Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy.
| | - Alexandru Anton Sabo
- Department of Pediatrics, Marie Curie Emergency Clinical Hospital for Children, 077120 Bucharest, Romania
| | - Giovanni Birolo
- Department of Medical Sciences, University of Turin, 10124 Turin, Italy
- Unit of Molecular Epidemiology and Exposome, Italian Institute for Genomic Medicine (IIGM), 10126 Turin, Italy
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Association of lncRNA CCAT2 and CASC8 Gene Polymorphisms with Hepatocellular Carcinoma. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16162833. [PMID: 31398859 PMCID: PMC6720737 DOI: 10.3390/ijerph16162833] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 07/26/2019] [Accepted: 08/06/2019] [Indexed: 12/20/2022]
Abstract
The worldwide incidence of hepatocellular carcinoma (HCC), the major histological type of primary liver cancer, is heterogeneous due to the variable prevalence of etiological factors, indicating a correlation of HCC risk with genetic variations among individuals. Among long non-coding RNAs (lncRNAs) located in the chromosome 8q24 loci and involved in the carcinogenesis are colon cancer associated transcript 2 (CCAT2) and cancer susceptibility candidate 8 (CASC8). In this study, the association of CCAT2 and CASC8 gene polymorphisms with the occurrence of HCC was explored between 397 HCC patients and 1195 controls. We found that carriers of rs6983267 GG in CCAT2 were more susceptible to HCC, with the odds ratio (OR) and adjusted odds ratio (AOR) being 1.532 (95% CI, 1.103–2.129; p = 0.011) and 1.627 (95% CI, 1.120–2.265; p = 0.033), respectively. Moreover, for patients stratified by age (under 65), gender (male only), or status of drinking (habitual drinkers), a protective effect of CASC8 rs3843549 on presenting high Child–Pugh scores, metastatic vascular invasion, or large-size tumors was observed in a dominant model. Collectively, our data reveal association of CCAT2 and CASC8 gene polymorphisms with the occurrence and progression of HCC.
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Approach to the Adult Acute Lymphoblastic Leukemia Patient. J Clin Med 2019; 8:jcm8081175. [PMID: 31390838 PMCID: PMC6722778 DOI: 10.3390/jcm8081175] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/29/2019] [Accepted: 08/01/2019] [Indexed: 02/06/2023] Open
Abstract
During recent decades, understanding of the molecular mechanisms of acute lymphoblastic leukemia (ALL) has improved considerably, resulting in better risk stratification of patients and increased survival rates. Age, white blood cell count (WBC), and specific genetic abnormalities are the most important factors that define risk groups for ALL. State-of-the-art diagnosis of ALL requires cytological and cytogenetical analyses, as well as flow cytometry and high-throughput sequencing assays. An important aspect in the diagnostic characterization of patients with ALL is the identification of the Philadelphia (Ph) chromosome, which warrants the addition of tyrosine kinase inhibitors (TKI) to the chemotherapy backbone. Data that support the benefit of hematopoietic stem cell transplantation (HSCT) in high risk patient subsets or in late relapse patients are still questioned and have yet to be determined conclusive. This article presents the newly published data in ALL workup and treatment, putting it into perspective for the attending physician in hematology and oncology.
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Ravegnini G, Serrano C, Simeon V, Sammarini G, Nannini M, Roversi E, Urbini M, Ferrè F, Ricci R, Tarantino G, Pantaleo MA, Hrelia P, Angelini S. The rs17084733 variant in the KIT 3' UTR disrupts a miR-221/222 binding site in gastrointestinal stromal tumour: a sponge-like mechanism conferring disease susceptibility. Epigenetics 2019; 14:545-557. [PMID: 30983504 PMCID: PMC6557610 DOI: 10.1080/15592294.2019.1595997] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Several miRNAs are dysregulated in gastrointestinal stromal tumours (GIST), and miR-221/222 appear to have a prominent role in GIST biology. Therefore, we investigated the role of DNA variants located in miR-221/222 precursor sequences and their target KIT 3'UTR. Ninety-five polymorphisms were analysed in 115 GIST cases and 88 healthy controls. KIT 3'UTR rs17084733 and pri-miR-222 rs75246947 were found significantly associated with GIST susceptibility. Specifically, KIT rs17084733 A allele was more common in GIST, particularly in KIT wild-type (WT) patients (Padj = 0.017). rs17084733 variant is located within one of the three miR-221/222 binding sites in the KIT 3'UTR, resulting in a mismatch in this seed region. Conversely, KIT mRNA levels were lower in patients carrying the variant allele, except for KIT mutant GIST. Luciferase assay data in GIST cells, generated using a construct containing all the three miR-221/222 binding sites, are consistent with KIT mRNA levels in GIST patients. Reporter assay data, generated using a construct containing only the site encompassing rs17084733, confirmed that this is a functional variant disrupting the miR-221/222 binding site. In conclusion, this is the first study investigating the role of SNPs on miR-221/222 precursor sequences and their binding region on KIT 3'UTR in GIST. We identified the KIT variant rs17084733 as a possible novel genetic biomarker for risk of developing KIT-WT GIST. Moreover, our findings suggest the role of one of the three miR-221/222 binding sites on KIT 3'UTR as endogenous sponge, soaking up and subtracting miR-221/222 to the other two sites characterized by a higher affinity.
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Affiliation(s)
- Gloria Ravegnini
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - César Serrano
- b Medical Oncology Department , Vall d'Hebron Institute of Oncology, Vall d'Hebron University Hospital , Barcelona , Spain
| | - Vittorio Simeon
- c Medical Statistics Unit , University of Campania "Luigi Vanvitelli" , Naples , Italy
| | - Giulia Sammarini
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Margherita Nannini
- d Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy
| | - Erica Roversi
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Milena Urbini
- e "Giorgio Prodi" Cancer Research Center , University of Bologna , Bologna , Italy
| | - Fabrizio Ferrè
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Riccardo Ricci
- f UOC di Anatomia Patologica, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy.,g Department of Pathology , Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giuseppe Tarantino
- e "Giorgio Prodi" Cancer Research Center , University of Bologna , Bologna , Italy
| | - Maria A Pantaleo
- d Department of Specialized, Experimental and Diagnostic Medicine, Sant'Orsola-Malpighi Hospital , University of Bologna , Bologna , Italy.,e "Giorgio Prodi" Cancer Research Center , University of Bologna , Bologna , Italy
| | - Patrizia Hrelia
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
| | - Sabrina Angelini
- a Department of Pharmacy and Biotechnology , University of Bologna , Bologna , Italy
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Liu Y, Wang D, Li Y, Yan S, Dang H, Yue H, Ling J, Chen F, Zhao Y, Gou L, Tang P, Huang A, Tang H. Long noncoding RNA CCAT2 promotes hepatocellular carcinoma proliferation and metastasis through up-regulation of NDRG1. Exp Cell Res 2019; 379:19-29. [PMID: 30922920 DOI: 10.1016/j.yexcr.2019.03.029] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 03/11/2019] [Accepted: 03/22/2019] [Indexed: 12/11/2022]
Abstract
BACKGROUND Emerging studies demonstrate that long noncoding RNAs (lncRNAs) play crucial roles in hepatocarcinogenesis through various mechanisms. LncRNA CCAT2 was a newly discovered lncRNA and amplified in several cancers. However, the mechanisms involved in function of CCAT2 in hepatocellular carcinoma (HCC) remain to be explored. METHODS CCAT2 expressions in HCC tissues and cell lines were measured by RT-qPCR. MTS assay, colony formation assay, wound-healing assay and transwell assay were used to explore the biological functions of CCAT2 on HCC cells proliferation and metastasis. Experiments in vivo were carried out to confirm these effects. The underlying mechanisms were analyzed by western blot and dual-luciferase reporter assay. RESULTS In this study, we found that CCAT2 were significantly elevated in HCC tissues and cell lines, and it promoted HCC cells proliferation and metastasis both in vitro and in vivo. Additionally, we identified that NDRG1 was a downstream target of CCAT2. Meanwhile, depletion of CCAT2 inhibited cellular proliferation and metastasis behaviors induced by NDRG1- overexpression. Analysis of mechanism underlying these effects revealed that CCAT2 increased the expression of NDRG1 by enhancing its promoter activity. Furthermore, the active region between CCAT2 and NDRG1 promoter was confirmed by dual-luciferase reporter assay. CONCLUSIONS All these observations demonstrate that CCAT2 acts as an oncogene by up-regulating NDRG1, which may have the potential to be used as a promising prognostic biomarker and therapeutic target for HCC.
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Affiliation(s)
- Yuyang Liu
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China; Department of Clinical Laboratory, The Sixth People's Hospital of Chengdu, Chengdu, Sichuan, China.
| | - Dan Wang
- Department of Clinical Laboratory, The People's Hospital of Rongchang, Chongqing, China.
| | - Yongguo Li
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China.
| | - Shaoying Yan
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Hao Dang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Huan Yue
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Jiaji Ling
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Fengjiao Chen
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Yannan Zhao
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Luxia Gou
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Ping Tang
- Department of Otorhinolaryngology Head and Neck Surgery, The Third Hospital of Mianyang, SiChuan Mental Health Center, China.
| | - Ailong Huang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
| | - Hua Tang
- Key Laboratory of Molecular Biology for Infectious Diseases (Ministry of Education), Institute for Viral Hepatitis, Department of Infectious Diseases, The Second Affiliated Hospital, Chongqing Medical University, Chongqing, China.
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Pardini B, Calin GA. MicroRNAs and Long Non-Coding RNAs and Their Hormone-Like Activities in Cancer. Cancers (Basel) 2019; 11:cancers11030378. [PMID: 30884898 PMCID: PMC6468345 DOI: 10.3390/cancers11030378] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/02/2019] [Accepted: 03/11/2019] [Indexed: 12/12/2022] Open
Abstract
Hormones are messengers circulating in the body that interact with specific receptors on the cell membrane or inside the cells and regulate, at a distal site, the activities of specific target organs. The definition of hormone has evolved in the last years. Hormones are considered in the context of cell–cell communication and mechanisms of cellular signaling. The best-known mechanisms of this kind are chemical receptor-mediated events, the cell–cell direct interactions through synapses, and, more recently, the extracellular vesicle (EV) transfer between cells. Recently, it has been extensively demonstrated that EVs are used as a way of communication between cells and that they are transporters of specific messenger signals including non-coding RNAs (ncRNAs) such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Circulating ncRNAs in body fluids and extracellular fluid compartments may have endocrine hormone-like effects because they can act at a distance from secreting cells with widespread consequences within the recipient cells. Here, we discuss and report examples of the potential role of miRNAs and lncRNAs as mediator for intercellular communication with a hormone-like mechanism in cancer.
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Affiliation(s)
- Barbara Pardini
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, 1515 Holcombe Boulevard, Unit 422, Houston, TX 77030, USA.
- Department of Medical Sciences, University of Turin, Turin 10126, Italy.
- Italian Institute for Genomic Medicine (IIGM), Turin 10126, Italy.
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, 1515 Holcombe Boulevard, Unit 422, Houston, TX 77030, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Farooqi AA, Fuentes-Mattei E, Fayyaz S, Raj P, Goblirsch M, Poltronieri P, Calin GA. Interplay between epigenetic abnormalities and deregulated expression of microRNAs in cancer. Semin Cancer Biol 2019; 58:47-55. [PMID: 30742906 DOI: 10.1016/j.semcancer.2019.02.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/23/2019] [Accepted: 02/07/2019] [Indexed: 02/07/2023]
Abstract
Epigenetic abnormalities and aberrant expression of non-coding RNAs are two emerging features of cancer cells, both of which are responsible for deregulated gene expression. In this review, we describe the interplay between the two. Specific themes include epigenetic silencing of tumor suppressor miRNAs, epigenetic activation of oncogenic miRNAs, epigenetic aberrations caused by miRNAs, and naturally occurring compounds which modulate miRNA expression through epigenetic mechanisms.
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Affiliation(s)
| | - Enrique Fuentes-Mattei
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Priyank Raj
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Matthew Goblirsch
- College of Science, Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Palmiro Poltronieri
- National Research Council Italy Institute of Sciences of Food Productions (CNR-ISPA), Via Lecce-Monteroni km 7, 73100 Lecce, Italy
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Gulei D, Raduly L, Berindan-Neagoe I, Calin GA. CRISPR-based RNA editing: diagnostic applications and therapeutic options. Expert Rev Mol Diagn 2019; 19:83-88. [DOI: 10.1080/14737159.2019.1568242] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Diana Gulei
- MedFuture Research Center for Advanced Medicine, University of Medicine and Pharmacy “Iuliu-Hatieganu”, Cluj-Napoca, Romania
| | - Lajos Raduly
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy “Iuliu-Hatieganu”, Cluj-Napoca, Romania
- Department of Pathophysiology, University of Agricultural Sciences and Veterinary Medicine, Cluj-Napoca, Romania
| | - Ioana Berindan-Neagoe
- MedFuture Research Center for Advanced Medicine, University of Medicine and Pharmacy “Iuliu-Hatieganu”, Cluj-Napoca, Romania
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, University of Medicine and Pharmacy “Iuliu-Hatieganu”, Cluj-Napoca, Romania
- Department of Functional Genomics and Experimental Pathology, The Oncology Institute “Prof. Dr. Ion Chiricuţă”, Cluj-Napoca, Romania
| | - George Adrian Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Center for RNA Inference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TXUSA
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Xie J, Chen J, Wang B, He X, Huang H. Bone mesenchymal stromal cells exhibit functional inhibition but no chromosomal aberrations in chronic myelogenous leukemia. Oncol Lett 2019; 17:999-1007. [PMID: 30655859 PMCID: PMC6312938 DOI: 10.3892/ol.2018.9681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 09/06/2018] [Indexed: 11/21/2022] Open
Abstract
Chronic myelogenous leukemia (CML) is a myeloproliferative neoplasia characterized by the presence of the Philadelphia (Ph) chromosome in hematopoietic cells (HCs). As one of the most important components of the bone marrow microenvironment (BMM), bone mesenchymal stromal cells (BMSCs) are critical in the development of leukemia and essential in the regulation of hematopoiesis. However, little is known regarding the alterations of BMSCs in CML. The current study performed Cell Counting Kit-8 and colony-forming unit fibroblast assays to evaluate the proliferative ability of BMSCs. The percentage of senescent BMSCs was evaluated by a senescence-associated β-galactosidase staining assay. Subsequently, a long-term culture-initiating cell assay was designed to explore the HC-supporting capacity of the BMSCs. Furthermore, cytogenetics were detected by conventional cytogenetic analysis and fluorescence in situ hybridization analysis. The current results revealed that CML-BMSCs exhibited decreased cell proliferation and impaired HC-support capacity, as well as increased susceptibility to senescence. No chromosomal aberrations, including the absence of the Ph chromosome, were noted in all CML-BMSCs. In conclusion, the current study demonstrated functional inhibition of CML-BMSCs; however, no signs of chromosomal aberrations were observed, thereby providing insight into the changes occurring in the CML-BMM.
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Affiliation(s)
- Jieqiong Xie
- Central Laboratory, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Jiadi Chen
- Fujian Institute of Hematology, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Bin Wang
- Central Laboratory, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Xuchun He
- Department of Medical Technology, Fujian Health Career Technical College, Fuzhou, Fujian 350101, P.R. China
| | - Huifang Huang
- Central Laboratory, Fujian Provincial Key Laboratory of Hematology, Fujian Medical University Union Hospital, Fuzhou, Fujian 350001, P.R. China
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