1
|
Vejdandoust F, Moosavi R, Fattahi Dolatabadi N, Zamani A, Tabatabaeian H. MIMT1 and LINC01550 are uncharted lncRNAs down-regulated in colorectal cancer. Int J Exp Pathol 2023; 104:107-116. [PMID: 36727289 PMCID: PMC10182369 DOI: 10.1111/iep.12467] [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: 07/27/2022] [Revised: 12/11/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023] Open
Abstract
Incomplete knowledge of the molecular basis of colorectal cancer, with subsequent limitations in early diagnosis and effective treatment, has contributed to this form of malignancy becoming the second most common cause of cancer-related death worldwide. With the advances in high-throughput profiling techniques and the availability of public data sets such as The Cancer Genome Atlas Program (TCGA), a broad range of coding transcripts have been profiled and their underlying modes of action have been mapped. However, there is still a huge gap in our understanding of noncoding RNA dysregulation. To this end, we used a bioinformatics approach to shortlist and evaluate yet-to be-profiled long noncoding RNAs (lncRNAs) in colorectal cancer. We analysed the TCGA RNA-seq data and followed this by validating the expression patterns using a qPCR technique. Analysing in-house clinical samples, the real-time PCR method revealed that the shortlisted lncRNAs, that is MER1 Repeat Containing Imprinted Transcript 1 (MIMT1) and Non-Protein Coding RNA 1550 (LINC01550), were down-regulated in colorectal cancer tumours compared with the paired adjacent normal tissues. Mechanistically, the in silico results suggest that LINC01550 could form a complex competitive endogenous RNA (ceRNA) network leading to the subsequent regulation of colorectal cancer-related genes, such as CUGBP Elav-Like Family Member (CELF2), Polypyrimidine Tract Binding Protein 1 (PTBP1) and ELAV Like RNA Binding Protein 1 (ELAV1). The findings of this work indicate that MIMT1 and LINC01550 could be novel tumour suppressor genes that can be studied further to assess their roles in regulating the cancer signalling pathway(s).
Collapse
Affiliation(s)
| | - Rahmaneh Moosavi
- Institute of Biomedical and Clinical ScienceUniversity of Exeter Medical SchoolExeterDevonUK
| | | | - Atefeh Zamani
- Gene Raz Bu AliGenetics and Biotechnology AcademyIsfahanIran
| | - Hossein Tabatabaeian
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and TechnologyUniversity of IsfahanIsfahanIran
- Anahid Cancer ClinicIsfahan Healthcare CityIsfahanIran
| |
Collapse
|
2
|
Su C, Wang W, Mo J, Liu F, Zhang H, Liu Y, Chen X, Liao Z, Zhang B, Zhu P. Long noncoding RNA HOXC-AS3 interacts with CDK2 to promote proliferation in hepatocellular carcinoma. Biomark Res 2022; 10:65. [PMID: 36031658 PMCID: PMC9420287 DOI: 10.1186/s40364-022-00411-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/09/2022] [Indexed: 11/24/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is a type of cancer that affects the liver and has a high mortality rate. Long non-coding RNAs (lncRNAs) dysregulation can contribute to cancer occurrence and progression, although the underlying molecular pathways are mostly unclear. HOXC-AS3 was found to be considerably overexpressed in HCC in this investigation. The goal of this work was to look into the involvement of HOXC-AS3 in HCC and the various molecular pathways that underpin it. Methods Normal liver and paired HCC tissues from HCC patients were used to evaluate HOXC-AS3 expression by qRT-PCR. The role of HOXC-AS3 in HCC was assessed both in vitro and in vivo. RNA pulldown, RIP and co-IP were used to demonstrate the potential mechanism by which HOXC-AS3 regulates the progression of HCC. Results Using qRT-PCR, it was discovered that HOXC-AS3 was substantially expressed in HCC. In vitro and in vivo, overexpression of HOXC-AS3 aided proliferation and cell cycle progression. HOXC-AS3 interacted with CDK2 to facilitate CDK2’s decreased binding to p21, resulting in enhanced CDK2 activity, which promoted the phosphorylation of Rb and the progression of HCC. Conclusions HOXC-AS3 is highly expressed in HCC and can promote the progression of HCC by interacting with CDK2. Therefore, targeting HOXC-AS3 is very likely to provide a new strategy for the treatment of HCC and for improving patient prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s40364-022-00411-2.
Collapse
|
3
|
Yang X, Qin C, Zhao B, Li T, Wang Y, Li Z, Li T, Wang W. Long Noncoding RNA and Circular RNA: Two Rising Stars in Regulating Epithelial-Mesenchymal Transition of Pancreatic Cancer. Front Oncol 2022; 12:910678. [PMID: 35719940 PMCID: PMC9204003 DOI: 10.3389/fonc.2022.910678] [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: 04/01/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant tumor with especially poor prognosis. However, the molecular mechanisms of pancreatic oncogenesis and malignant progression are not fully elucidated. Epithelial-mesenchymal transition (EMT) process is important to drive pancreatic carcinogenesis. Recently, long noncoding RNAs (lncRNAs) and circular RNAs(circRNAs) have been characterized to participate in EMT in PDAC, which can affect the migration and invasion of tumor cells by playing important roles in epigenetic processes, transcription, and post-transcriptional regulation. LncRNAs can act as competing endogenous RNAs (ceRNA) to sequester target microRNAs(miRNAs), bind to the genes which localize physically nearby, and directly interact with EMT-related proteins. Currently known circRNAs mostly regulate the EMT process in PDAC also by acting as a miRNA sponge, directly affecting the protein degradation process. Therefore, exploring the functions of lncRNAs and circRNAs in EMT during pancreatic cancer might help pancreatic cancer treatments.
Collapse
Affiliation(s)
- Xiaoying Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cheng Qin
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bangbo Zhao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianhao Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuanyang Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zeru Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tianyu Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Weibin Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| |
Collapse
|
4
|
Xu H, Hu X, Yan X, Zhong W, Yin D, Gai Y. Exploring noncoding RNAs in thyroid cancer using a graph convolutional network approach. Comput Biol Med 2022; 145:105447. [DOI: 10.1016/j.compbiomed.2022.105447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/20/2022] [Accepted: 03/21/2022] [Indexed: 12/01/2022]
|
5
|
Peng S, Chen L, Yuan Z, Duan S. Suppression of MIR31HG affects the functional properties of thyroid cancer cells depending on the miR-761/MAPK1 axis. BMC Endocr Disord 2022; 22:107. [PMID: 35443670 PMCID: PMC9022350 DOI: 10.1186/s12902-022-00962-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/16/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Thyroid cancer is the most prevalent endocrine malignancy. Long non-coding RNA (lncRNA) MIR31HG is abnormally expressed in thyroid cancer tissues. However, the precise, critical role of MIR31HG in thyroid cancer development remains unclear. METHODS MIR31HG, microRNA (miR)-761 and mitogen-activated protein kinase 1 (MAPK1) were quantified by quantitative real-time PCR (qRT-PCR) and immunoblotting. Cell viability, proliferation, apoptosis, invasion and migration abilities were evaluated by MTS, 5-Ethynyl-2'-Deoxyuridine (EdU), flow cytometry, transwell and wound-healing assays, respectively. Dual-luciferase reporter assays were used to validate the direct relationship between miR-761 and MIR31HG or MAPK1. RESULTS MIR31HG was overexpressed in human thyroid cancer, and its overexpression predicted poor prognosis. Suppression of MIR31HG impeded cell proliferation, invasion and migration, as well as promoted cell apoptosis in vitro, and diminished the growth of xenograft tumors in vivo. Mechanistically, MIR31HG targeted and regulated miR-761. Moreover, miR-761 was identified as a molecular mediator of MIR30HG function in regulating thyroid cancer cell behaviors. MAPK1 was established as a direct and functional target of miR-761 and MAPK1 knockdown phenocopied miR-761 overexpression in impacting thyroid cancer cell behaviors. Furthermore, MIR31HG modulated MAPK1 expression by competitively binding to miR-761 via the shared binding sequence. CONCLUSION Our findings demonstrate that MIR31HG targets miR-761 to regulate the functional behaviors of thyroid cancer cells by upregulating MAPK1, highlighting a strong rationale for developing MIR31HG as a novel therapeutic target against thyroid cancer.
Collapse
Affiliation(s)
- Shuwang Peng
- Department of Gastrointestinal and Thyroid and Vascular Surgery, The First Hospital of Hunan University of Chinese Medicine, Ward 22, 13th floor, Zhihe Building, No.95 Shaoshan Middle Road, Yuhua District, Changsha, 410000, Hunan, Province, China.
| | - Luyang Chen
- Department of Ultrasound Imaging, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan, China
| | - Zhengtai Yuan
- Department of Gastrointestinal and Thyroid and Vascular Surgery, The First Hospital of Hunan University of Chinese Medicine, Ward 22, 13th floor, Zhihe Building, No.95 Shaoshan Middle Road, Yuhua District, Changsha, 410000, Hunan, Province, China
| | - Shanshan Duan
- Department of Gastrointestinal and Thyroid and Vascular Surgery, The First Hospital of Hunan University of Chinese Medicine, Ward 22, 13th floor, Zhihe Building, No.95 Shaoshan Middle Road, Yuhua District, Changsha, 410000, Hunan, Province, China
| |
Collapse
|
6
|
Liu Y, Khan S, Li L, ten Hagen TL, Falahati M. Molecular mechanisms of thyroid cancer: A competing endogenous RNA (ceRNA) point of view. Biomed Pharmacother 2022; 146:112251. [DOI: 10.1016/j.biopha.2021.112251] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 12/25/2022] Open
|
7
|
Liang Y, Zhang Q, Xin T, Zhang DL. A four-enhancer RNA-based prognostic signature for thyroid cancer. Exp Cell Res 2022; 412:113023. [PMID: 35033555 DOI: 10.1016/j.yexcr.2022.113023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 12/13/2021] [Accepted: 01/07/2022] [Indexed: 11/04/2022]
Abstract
Enhancer RNAs (eRNAs) can serve as an independent prognostic factor for poor outcomes of cancer patients. The purpose of this study was to identify a vital eRNA signature that has prognostic value for thyroid cancer based on GTEx and TCGA screening. We downloaded gene expression data and clinical data of thyroid cancer included in the GTEx and TCGA databases and conducted data consolidation. eRNA expression data were extracted, and subjected to differential analysis and cluster analysis. Univariate Cox regression was used to screen the prognostic factors of thyroid cancer. Multivariate Cox regression was applied for prognostic risk assessment model construction, with the efficacy evaluated by receiver operating characteristic (ROC) curve. Downstream regulatory genes of candidate eRNAs were determined using correlation analysis. There were 79 differentially expressed eRNAs associated with thyroid cancer. These differentially expressed eRNAs could assign all thyroid cancer samples into three molecular subtypes, which showed a strong link to lymph node metastasis (N stage) of thyroid cancer patients. Additionally, four key eRNAs AC141930.1, NBDY, MEG3 and AP002358.1 closely related to the prognosis of thyroid cancer patients. The risk model based on the four eRNAs predicted the prognosis of thyroid cancer patients effectively. TPO, MGST2, THBS2 and SLC25A47P1 were potential downstream regulators of the four eRNAs involved in the development of thyroid cancer. Collectively, our data suggest that a four-eRNA signature consisting of AC141930.1, NBDY, MEG3 and AP002358.1 can accurately predict the prognosis of thyroid cancer patients.
Collapse
Affiliation(s)
- Yuan Liang
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, PR China
| | - Qi Zhang
- Criminal Investigation Police University of China, Shenyang, 110854, China
| | - Tian Xin
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, PR China
| | - Da-Lin Zhang
- Department of Thyroid Surgery, The 1st Affiliated Hospital, China Medical University, Shenyang, 110001, China.
| |
Collapse
|
8
|
Jafari N, Nasiran Najafabadi A, Hamzei B, Ataee N, Ghasemi Z, Sadeghian-Rizi T, Honardoost MA, Zamani A, Dolatabadi NF, Tabatabaeian H. ESRG, LINC00518 and PWRN1 are newly-identified deregulated lncRNAs in colorectal cancer. Exp Mol Pathol 2021; 124:104732. [PMID: 34896077 DOI: 10.1016/j.yexmp.2021.104732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/22/2021] [Accepted: 12/04/2021] [Indexed: 01/05/2023]
Abstract
Colorectal cancer is the 2nd leading cause of death in humans because of cancer. This rank of death could be due to the high rate of incidence from one hand, and the lack of sufficient diagnostic and therapeutic approaches from the other hand. Thus, molecular tools have been emerging as the potential biomarker to improve the early diagnosis and therapeutic management that subsequently could lead to the heightened survival rate of colorectal cancer patients. Long non-coding RNA (lncRNAs) have shown promising capabilities to be used in clinics. The profiling methods could identify novel aberrantly expressed lncRNAs in colorectal cancer. We, thus, performed a comprehensive and unbiased approach to shortlist the dysregulated lncRNAs based on the colon adenocarcinoma TCGA data. An unbiased in silico method was used to rank the yet to profiled lncRNAs in colorectal cancer. qPCR was used to measure the expression level of selected lncRNAs. Our results nominated ESRG, LINC00518, PWRN1, and TTTY14 lncRNAs as the top-hit novel lncRNAs with aberrant expression in colon cancer. The qPCR method was used to profile these lncRNAs that showed the up-regulation of ESRG and LINC00518, and down-regulation of TTTY14 in thirty paired colorectal cancer specimens. The statistical analyses demonstrated that ESRG, LINC00518 and PWRN1 could distinguish the tumor from normal samples. Moreover, ESRG showed a negative correlation with the overall survival of patients. These diagnostic and prognostic results suggest that profiling ESRG, LINC00518 and PWRN1 s may have implications in clinics.
Collapse
Affiliation(s)
- Nasrin Jafari
- Department of Genetics, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Arezo Nasiran Najafabadi
- Gene Raz Bu Ali, Genetics and Biotechnology Academy, Isfahan, Iran; Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Behnaz Hamzei
- Gene Raz Bu Ali, Genetics and Biotechnology Academy, Isfahan, Iran
| | - Nioosha Ataee
- Gene Raz Bu Ali, Genetics and Biotechnology Academy, Isfahan, Iran; Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Zahra Ghasemi
- Gene Raz Bu Ali, Genetics and Biotechnology Academy, Isfahan, Iran; Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Tahereh Sadeghian-Rizi
- Department of Biotechnology, Faculty of Biological Sciences and Technology, Shahid Ashrafi Esfahani University, Isfahan, Iran
| | - Mohammad Amin Honardoost
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | - Atefeh Zamani
- Gene Raz Bu Ali, Genetics and Biotechnology Academy, Isfahan, Iran
| | | | - Hossein Tabatabaeian
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran; Anahid Cancer Clinic, Isfahan Healthcare City, Isfahan, Iran.
| |
Collapse
|
9
|
Paulsson JO, Zedenius J, Juhlin CC. TERT Promoter Mutated Follicular Thyroid Carcinomas Exhibit a Distinct microRNA Expressional Profile with Potential Implications for Tumor Progression. Endocr Pathol 2021; 32:513-516. [PMID: 34676499 PMCID: PMC8608760 DOI: 10.1007/s12022-021-09695-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 12/23/2022]
Affiliation(s)
- Johan O Paulsson
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Jan Zedenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Breast, Endocrine Tumors and Sarcoma, Karolinska University Hospital, Stockholm, Sweden
| | - C Christofer Juhlin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.
- Department of Pathology and Cytology, Karolinska University Hospital, Stockholm, Sweden.
| |
Collapse
|
10
|
Dissecting the critical pathway crosstalk mechanisms of thyroid cancer based on drug-target genes and disease genes. Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00869-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
11
|
Ramos A, Sadeghi S, Tabatabaeian H. Battling Chemoresistance in Cancer: Root Causes and Strategies to Uproot Them. Int J Mol Sci 2021; 22:9451. [PMID: 34502361 PMCID: PMC8430957 DOI: 10.3390/ijms22179451] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 02/07/2023] Open
Abstract
With nearly 10 million deaths, cancer is the leading cause of mortality worldwide. Along with major key parameters that control cancer treatment management, such as diagnosis, resistance to the classical and new chemotherapeutic reagents continues to be a significant problem. Intrinsic or acquired chemoresistance leads to cancer recurrence in many cases that eventually causes failure in the successful treatment and death of cancer patients. Various determinants, including tumor heterogeneity and tumor microenvironment, could cause chemoresistance through a diverse range of mechanisms. In this review, we summarize the key determinants and the underlying mechanisms by which chemoresistance appears. We then describe which strategies have been implemented and studied to combat such a lethal phenomenon in the management of cancer treatment, with emphasis on the need to improve the early diagnosis of cancer complemented by combination therapy.
Collapse
Affiliation(s)
- Alisha Ramos
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore;
| | - Samira Sadeghi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228, Singapore;
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), Singapore 138672, Singapore
| | - Hossein Tabatabaeian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| |
Collapse
|
12
|
Dastjerdi S, Valizadeh M, Nemati R, Honardoost MA, Dolatabadi NF, Zamani A, Tabatabaeian H. Highly expressed TLX1NB and NPSR1-AS1 lncRNAs could serve as diagnostic tools in colorectal cancer. Hum Cell 2021; 34:1765-1774. [PMID: 34406628 DOI: 10.1007/s13577-021-00597-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 08/14/2021] [Indexed: 01/05/2023]
Abstract
Colorectal cancer is the main cause of human death due to cancer. This fact could be due to the insufficiency of early diagnosis or poor therapeutic strategies. Various molecular tools have been utilized in studies to assess their potentials as diagnostic biomarkers or determining factors in precision medicine. Among these molecules, long non-coding RNAs (lncRNA) have been emerging as accurate and potent transcripts to improve the detection of cancer. The overexpressed lncRNAs could also be deeply studied as the molecules for the targeted therapy in different malignancies, in particular colorectal cancer. Thus, we utilized an unbiased approach to select the up-regulated lncRNAs in colon adenocarcinoma via analyzing the TCGA dataset. Then, we validated the overexpression of two first-ranked lncRNAs, i.e., NPSR1-AS1 and TLX1NB, in our in-house colorectal cancer samples as compared to the paired adjacent normal tissues. The analyses revealed that these lncRNAs could significantly distinguish the tumor against the normal samples. The results may have implications in the early diagnosis and targeted therapy of colorectal cancer.
Collapse
Affiliation(s)
- Shaghayegh Dastjerdi
- Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran.,Department of Cellular and Molecular Sciences, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehdi Valizadeh
- Unit of Genomics Research, Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Rasoul Nemati
- Department of Internal Medicine, School of Medicine and Allied Medical Sciences, Digestive Diseases Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Mohammad Amin Honardoost
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran
| | | | - Atefeh Zamani
- Gene Raz Bu Ali, Genetic and Biotechnology Academy, Isfahan, Iran
| | - Hossein Tabatabaeian
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran. .,Anahid Cancer Clinic, Isfahan Healthcare City, Isfahan, Iran.
| |
Collapse
|
13
|
He H, Liyanarachchi S, Li W, Comiskey DF, Yan P, Bundschuh R, Turkoglu AM, Brock P, Ringel MD, de la Chapelle A. Transcriptome analysis discloses dysregulated genes in normal appearing tumor-adjacent thyroid tissues from patients with papillary thyroid carcinoma. Sci Rep 2021; 11:14126. [PMID: 34238982 PMCID: PMC8266864 DOI: 10.1038/s41598-021-93526-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/22/2021] [Indexed: 01/10/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. The molecular characteristics of histologically normal appearing tissue adjacent to the tumor (NAT) from PTC patients are not well characterized. The aim of this study was to characterize the global gene expression profile of NAT and compare it with those of normal and tumor thyroid tissues. We performed total RNA sequencing with fresh frozen thyroid tissues from a cohort of three categories of samples including NAT, normal thyroid (N), and PTC tumor (T). Transcriptome analysis shows that NAT presents a unique gene expression profile, which was not associated with sex or the presence of lymphocytic thyroiditis. Among the differentially expressed genes (DEGs) of NAT vs N, 256 coding genes and 5 noncoding genes have been reported as cancer genes involved in cell proliferation, apoptosis, and/or tumorigenesis. Bioinformatics analysis with Ingenuity Pathway Analysis software revealed that “Cancer, Organismal Injury and Abnormalities, Cellular Response to Therapeutics, and Cellular Movement” were major dysregulated pathways in the NAT tissues. This study provides improved insight into the complexity of gene expression changes in the thyroid glands of patients with PTC.
Collapse
Affiliation(s)
- Huiling He
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA
| | - Sandya Liyanarachchi
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA
| | - Wei Li
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA
| | - Daniel F Comiskey
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA
| | - Pearlly Yan
- Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA
| | - Ralf Bundschuh
- Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA.,Department of Physics, The Ohio State University, Columbus, OH, 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH, 43210, USA
| | - Altan M Turkoglu
- Department of Physics, The Ohio State University, Columbus, OH, 43210, USA
| | - Pamela Brock
- Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA
| | - Matthew D Ringel
- Division of Endocrinology, Diabetes, and Metabolism, Department of Internal Medicine, The Ohio State University, Columbus, OH, 43210, USA. .,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA.
| | - Albert de la Chapelle
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, 43210, USA.,The Ohio State University Comprehensive Cancer Center, The Ohio State University, McCampbell Hall South Room 565, 1581 Dodd Drive, Columbus, OH, 43210, USA
| |
Collapse
|
14
|
Miralaei N, Hoghoughi N, Azadeh M, Alborzian K, Ghaedi K. rs12287003 modifies the susceptibility to breast cancer by altering the interactions between KDM2A and miRNAs. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
15
|
Deciphering miRNA-Target Relationships to Understand miRNA-Mediated Carcinogenesis. Cancers (Basel) 2021; 13:cancers13102415. [PMID: 34067691 PMCID: PMC8156494 DOI: 10.3390/cancers13102415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/16/2022] Open
|
16
|
Yin YL, Liu TL, Yao Q, Wang YX, Wu XM, Wang XT, Yang X, Song JK, Zhao GH. Circular RNA ciRS-7 affects the propagation of Cryptosporidium parvum in HCT-8 cells by sponging miR-1270 to activate the NF-κB signaling pathway. Parasit Vectors 2021; 14:238. [PMID: 33957927 PMCID: PMC8101149 DOI: 10.1186/s13071-021-04739-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 04/21/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cryptosporidium is an important zoonotic pathogen responsible for severe enteric diseases in humans and animals. However, the molecular mechanisms underlying host and Cryptosporidium interactions are still not clear. METHODS To study the roles of circRNAs in host cells during Cryptosporidium infection, the expression profiles of circRNAs in HCT-8 cells infected with C. parvum were investigated using a microarray assay, and the regulatory role of a significantly upregulated circRNA, ciRS-7, was investigated during C. parvum infection. RESULTS C. parvum infection caused notable alterations in the expression profiles of circRNAs in HCT-8 cells, and a total of 178 (including 128 up- and 50 downregulated) circRNAs were significantly differentially expressed following C. parvum infection. Among them, ciRS-7 was significantly upregulated and regulated the NF-κB signaling pathway by sponging miR-1270 during C. parvum infection. Furthermore, the ciRS-7/miR-1270/relA axis markedly affected the propagation of C. parvum in HCT-8 cells. CONCLUSIONS Our results revealed that ciRS-7 would promote C. parvum propagation by regulating the miR-1270/relA axis and affecting the NF-κB pathway. To the best of our knowledge, this is the first study to investigate the role of circRNA during Cryptosporidium infection, and the findings provide a novel view for implementing control strategies against Cryptosporidium infection.
Collapse
Affiliation(s)
- Yan-Ling Yin
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Ting-Li Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Qian Yao
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yu-Xin Wang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xue-Mei Wu
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xue-Ting Wang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xin Yang
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Jun-Ke Song
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Guang-Hui Zhao
- Department of Parasitology, College of Veterinary Medicine, Northwest A&F University, Yangling, China.
| |
Collapse
|
17
|
Di Fiore R, Suleiman S, Pentimalli F, O’Toole SA, O’Leary JJ, Ward MP, Conlon NT, Sabol M, Ozretić P, Erson-Bensan AE, Reed N, Giordano A, Herrington CS, Calleja-Agius J. Could MicroRNAs Be Useful Tools to Improve the Diagnosis and Treatment of Rare Gynecological Cancers? A Brief Overview. Int J Mol Sci 2021; 22:ijms22083822. [PMID: 33917022 PMCID: PMC8067678 DOI: 10.3390/ijms22083822] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/01/2021] [Accepted: 04/05/2021] [Indexed: 02/07/2023] Open
Abstract
Gynecological cancers pose an important public health issue, with a high incidence among women of all ages. Gynecological cancers such as malignant germ-cell tumors, sex-cord-stromal tumors, uterine sarcomas and carcinosarcomas, gestational trophoblastic neoplasia, vulvar carcinoma and melanoma of the female genital tract, are defined as rare with an annual incidence of <6 per 100,000 women. Rare gynecological cancers (RGCs) are associated with poor prognosis, and given the low incidence of each entity, there is the risk of delayed diagnosis due to clinical inexperience and limited therapeutic options. There has been a growing interest in the field of microRNAs (miRNAs), a class of small non-coding RNAs of ∼22 nucleotides in length, because of their potential to regulate diverse biological processes. miRNAs usually induce mRNA degradation and translational repression by interacting with the 3' untranslated region (3'-UTR) of target mRNAs, as well as other regions and gene promoters, as well as activating translation or regulating transcription under certain conditions. Recent research has revealed the enormous promise of miRNAs for improving the diagnosis, therapy and prognosis of all major gynecological cancers. However, to date, only a few studies have been performed on RGCs. In this review, we summarize the data currently available regarding RGCs.
Collapse
Affiliation(s)
- Riccardo Di Fiore
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Correspondence: (R.D.F.); (J.C.-A.); Tel.: +356-2340-3871 (R.D.F.); +356-2340-1892 (J.C.-A.)
| | - Sherif Suleiman
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
| | - Francesca Pentimalli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Napoli, Italy;
| | - Sharon A. O’Toole
- Departments of Obstetrics and Gynaecology and Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, 8 Dublin, Ireland;
| | - John J. O’Leary
- Department of Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, 8 Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - Mark P. Ward
- Department of Histopathology, Trinity St James’s Cancer Institute, Trinity College Dublin, 8 Dublin, Ireland; (J.J.O.); (M.P.W.)
| | - Neil T. Conlon
- National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, 9 Dublin, Ireland;
| | - Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.S.); (P.O.)
| | - Petar Ozretić
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (M.S.); (P.O.)
| | - Ayse Elif Erson-Bensan
- Department of Biological Sciences, Middle East Technical University, Ankara 06810, Turkey;
| | - Nicholas Reed
- Beatson Oncology Centre, Gartnavel General Hospital, 1053 Great Western Road, Glasgow G12 0YN, UK;
| | - Antonio Giordano
- Center for Biotechnology, Sbarro Institute for Cancer Research and Molecular Medicine, College of Science and Technology, Temple University, Philadelphia, PA 19122, USA;
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - C. Simon Herrington
- Cancer Research UK Edinburgh Centre, Western General Hospital, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XR, UK;
| | - Jean Calleja-Agius
- Department of Anatomy, Faculty of Medicine and Surgery, University of Malta, MSD 2080 Msida, Malta;
- Correspondence: (R.D.F.); (J.C.-A.); Tel.: +356-2340-3871 (R.D.F.); +356-2340-1892 (J.C.-A.)
| |
Collapse
|
18
|
Wang G, Le Y, Wei L, Cheng L. CREB3 Transactivates lncRNA ZFAS1 to Promote Papillary Thyroid Carcinoma Metastasis by Modulating miR-373-3 p/MMP3 Regulatory Axis. Int J Endocrinol 2021; 2021:9981683. [PMID: 34249125 PMCID: PMC8238556 DOI: 10.1155/2021/9981683] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/22/2021] [Accepted: 06/07/2021] [Indexed: 01/16/2023] Open
Abstract
The incidence rate of thyroid carcinoma ranks ninth among human malignancies, and it accounts for the most frequent malignancy in endocrine-related tumors. This study aimed to investigate the role of long noncoding RNA (lncRNA) ZFAS1 in the metastasis of papillary thyroid carcinoma (PTC) and the potential molecular mechanisms. Both ZFAS1 and MMP3 were highly expressed in thyroid carcinoma and PTC cell, as measured by the q-PCR and TCGA database. In addition, ZFAS1 induced TPC-1 metastasis through inducing the epithelial-mesenchymal transition (EMT) process. Besides, ZFAS1 knockdown by siRNA induced miR-373-3p expression and reduced MMP3 expression, as quantified by q-PCR and Western blotting. According to the luciferase assay, both ZFAS1 and MMP3 were classified as the direct targets of miR-373-3p. However, MMP3 itself did not affect ZFAS1. Using the online prediction tool, CREB3 was predicted as the transcription factor (TF) of ZFAS1 that contained two binding sites on its promoter region, and CREB3 was positively correlated with ZFAS1 in thyroid carcinoma cohorts. Results from the dual-luciferase assay and ChIP-qPCR indicated that both the two binding sites were essential for the transcription of ZFAS1. In conclusion, CREB3 activated lncRNA ZFAS1 at the transcriptional level to promote PTC metastasis by modulating miR-373-3p/MMP3.
Collapse
Affiliation(s)
- Gang Wang
- Department of General Surgery (Thyroid Surgery), Affiliated Hospital of Southwest Medical University, Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| | - Yuan Le
- Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, China
| | - Liping Wei
- Pediatric Surgery, The Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, China
| | - Lian Cheng
- Department of General Surgery (Thyroid Surgery), Affiliated Hospital of Southwest Medical University, Cardiovascular and Metabolic Diseases Key Laboratory of Luzhou, Luzhou, China
| |
Collapse
|