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Song J, Kim D, Jung J, Choi E, Lee Y, Jeong Y, Lee B, Lee S, Shim Y, Won Y, Cho H, Jang DK, Kang HW, Joo JWJ, Jang W. Elucidating immunological characteristics of the adenoma-carcinoma sequence in colorectal cancer patients in South Korea using a bioinformatics approach. Sci Rep 2024; 14:10105. [PMID: 38698020 PMCID: PMC11066069 DOI: 10.1038/s41598-024-56078-2] [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: 08/03/2023] [Accepted: 03/01/2024] [Indexed: 05/05/2024] Open
Abstract
Colorectal cancer (CRC) is one of the top five most common and life-threatening malignancies worldwide. Most CRC develops from advanced colorectal adenoma (ACA), a precancerous stage, through the adenoma-carcinoma sequence. However, its underlying mechanisms, including how the tumor microenvironment changes, remain elusive. Therefore, we conducted an integrative analysis comparing RNA-seq data collected from 40 ACA patients who visited Dongguk University Ilsan Hospital with normal adjacent colons and tumor samples from 18 CRC patients collected from a public database. Differential expression analysis identified 21 and 79 sequentially up- or down-regulated genes across the continuum, respectively. The functional centrality of the continuum genes was assessed through network analysis, identifying 11 up- and 13 down-regulated hub-genes. Subsequently, we validated the prognostic effects of hub-genes using the Kaplan-Meier survival analysis. To estimate the immunological transition of the adenoma-carcinoma sequence, single-cell deconvolution and immune repertoire analyses were conducted. Significant composition changes for innate immunity cells and decreased plasma B-cells with immunoglobulin diversity were observed, along with distinctive immunoglobulin recombination patterns. Taken together, we believe our findings suggest underlying transcriptional and immunological changes during the adenoma-carcinoma sequence, contributing to the further development of pre-diagnostic markers for CRC.
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Affiliation(s)
- Jaeseung Song
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Daeun Kim
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Junghyun Jung
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
- Division of AI Software Convergence, Dongguk University-Seoul, Seoul, 04620, South Korea
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Hollywood, CA, USA
| | - Eunyoung Choi
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Yubin Lee
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Yeonbin Jeong
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Byungjo Lee
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Sora Lee
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Yujeong Shim
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Youngtae Won
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea
| | - Hyeki Cho
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, 10326, South Korea
| | - Dong Kee Jang
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, 07061, South Korea
| | - Hyoun Woo Kang
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, 10326, South Korea.
- Department of Internal Medicine, Seoul Metropolitan Government Seoul National University Boramae Medical Center, Seoul, 07061, South Korea.
| | - Jong Wha J Joo
- Division of AI Software Convergence, Dongguk University-Seoul, Seoul, 04620, South Korea.
| | - Wonhee Jang
- Department of Life Sciences, Dongguk University, Seoul, 04620, South Korea.
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Wu Y, Mou J, Zhou G, Yuan C. CASC19: An Oncogenic Long Non-coding RNA in Different Cancers. Curr Pharm Des 2024; 30:1157-1166. [PMID: 38544395 DOI: 10.2174/0113816128300061240319034243] [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: 12/22/2023] [Accepted: 02/29/2024] [Indexed: 06/28/2024]
Abstract
A 324 bp lncRNA called CASC19 is found on chromosome 8q24.21. Recent research works have revealed that CASC19 is involved in the prognosis of tumors and related to the regulation of the radiation tolerance mechanisms during tumor radiotherapy (RT). This review sheds light on the changes and roles that CASC19 plays in many tumors and diseases, such as nasopharyngeal carcinoma (NPC), cervical cancer, colorectal cancer (CRC), non-small cell lung cancer (NSCLC), clear cell renal cell carcinoma (ccRCC), gastric cancer (GC), pancreatic cancer (PC), hepatocellular carcinoma (HCC), glioma, and osteoarthritis (OA). CASC19 provides a new strategy for targeted therapy, and the regulatory networks of CASC19 expression levels play a key role in the occurrence and development of tumors and diseases. In addition, the expression level of CASC19 has predictive roles in the prognosis of some tumors and diseases, which has major implications for clinical diagnoses and treatments. CASC19 is also unique in that it is a key gene affecting the efficacy of RT in many tumors, and its expression level plays a decisive role in improving the success rate of treatments. Further research is required to determine the precise process by which CASC19 causes changes in diseased cells in some tumors and diseases.
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Affiliation(s)
- Yinxin Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
| | - Jie Mou
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
| | - Gang Zhou
- College of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
- Yichang Hospital of Traditional Chinese Medicine, Yichang 443002, China
| | - Chengfu Yuan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang 443002, China
- College of Basic Medical Science, China Three Gorges University, Yichang 443002, China
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China
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Bakr M, Abd-Elmawla MA, Elimam H, Gamal El-Din H, Fawzy A, Abulsoud AI, Rizk SM. Telomerase RNA component lncRNA as potential diagnostic biomarker promotes CRC cellular migration and apoptosis evasion via modulation of β-catenin protein level. Noncoding RNA Res 2023; 8:302-314. [PMID: 37032720 PMCID: PMC10074408 DOI: 10.1016/j.ncrna.2023.03.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023] Open
Abstract
Aim Long non-coding RNA (LncRNA) telomerase RNA component (TERC) has telomerase-dependent and independent activity in numerous cancer types. The present study purposes to demonstrate the role of lncRNA TERC as a diagnostic serum biomarker in colorectal cancer (CRC) patients and the molecular mechanism of lncRNA TERC in inducing tumor in CRC cell lines. Materials and methods PCR array was performed to examine lncRNAs dysregulated in CRC. LncRNA TERC expression level was evaluated in 70 CRC patients and 35 control subjects using RT-qPCR. Then transfection was performed to build down-expression models of lncRNA TERC. ROC curve analysis was applied to assess the diagnostic value of serum LncRNA CRC. In addition, RT-qPCR was used to detect expression level of lncRNA TERC and β-catenin mRNA. Moreover, ELISA and Western blot were used to detect the level of β-catenin protein in sera of CRC patients and cell lines. The biological functions such as cell growth and migration of CRC cells were assessed using a wound healing assay. Cell cycle analysis and apoptosis analysis were performed using flow cytometry. Results The lncRNA TERC is overexpressed in the sera of CRC patients with high diagnostic and stage discrimination accuracy. Furthermore, lncRNA TERC expression was upregulated in CRC cell lines and lncRNA TERC silencing induced cell arrest and apoptosis and inhibited cell migration. Furthermore, inhibition of lncRNA TERC reduces β-catenin protein levels. Conclusion The lncRNA TERC could be considered as an early stages CRC diagnostic biomarker with a good ability to discriminate between CRC stages. lncRNA TERC induces CRC by promoting cell migration and evading apoptosis by elevating the level of β-catenin protein.
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Mokhtari K, Peymani M, Rashidi M, Hushmandi K, Ghaedi K, Taheriazam A, Hashemi M. Colon cancer transcriptome. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2023; 180-181:49-82. [PMID: 37059270 DOI: 10.1016/j.pbiomolbio.2023.04.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/31/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023]
Abstract
Over the last four decades, methodological innovations have continuously changed transcriptome profiling. It is now feasible to sequence and quantify the transcriptional outputs of individual cells or thousands of samples using RNA sequencing (RNA-seq). These transcriptomes serve as a connection between cellular behaviors and their underlying molecular mechanisms, such as mutations. This relationship, in the context of cancer, provides a chance to unravel tumor complexity and heterogeneity and uncover novel biomarkers or treatment options. Since colon cancer is one of the most frequent malignancies, its prognosis and diagnosis seem to be critical. The transcriptome technology is developing for an earlier and more accurate diagnosis of cancer which can provide better protectivity and prognostic utility to medical teams and patients. A transcriptome is a whole set of expressed coding and non-coding RNAs in an individual or cell population. The cancer transcriptome includes RNA-based changes. The combined genome and transcriptome of a patient may provide a comprehensive picture of their cancer, and this information is beginning to affect treatment decision-making in real-time. A full assessment of the transcriptome of colon (colorectal) cancer has been assessed in this review paper based on risk factors such as age, obesity, gender, alcohol use, race, and also different stages of cancer, as well as non-coding RNAs like circRNAs, miRNAs, lncRNAs, and siRNAs. Similarly, they have been examined independently in the transcriptome study of colon cancer.
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Affiliation(s)
- Khatere Mokhtari
- Department of Modern Biology, ACECR Institute of Higher Education (Isfahan Branch), Isfahan, Iran
| | - Maryam Peymani
- Department of Biology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran.
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, 4815733971, Iran
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Kamran Ghaedi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, Isfahan, Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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Wu Y, Xu X. Long non-coding RNA signature in colorectal cancer: research progression and clinical application. Cancer Cell Int 2023; 23:28. [PMID: 36797749 PMCID: PMC9936661 DOI: 10.1186/s12935-023-02867-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Accepted: 02/05/2023] [Indexed: 02/18/2023] Open
Abstract
Colorectal cancer is one of the top-ranked human malignancies. The development and progression of colorectal cancer are associated with aberrant expression of multiple coding and non-coding genes. Long non-coding RNAs (lncRNAs) have an important role in regulating gene stability as well as gene expression. Numerous current studies have shown that lncRNAs are promising biomarkers and therapeutic targets for colorectal cancer. In this review, we have searched the available literature to list lncRNAs involved in the pathogenesis and regulation of colorectal cancer. We focus on the role of lncRNAs in cancer promotion or suppression, their value in tumor diagnosis, and their role in treatment response and prognosis prediction. In addition, we will discuss the signaling pathways that these lncRNAs are mainly associated with in colorectal cancer. We also summarize the role of lncRNAs in colorectal precancerous lesions and colorectal cancer consensus molecular subgroups. We hope this review article will bring you the latest research progress and outlook on lncRNAs in colorectal cancer.
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Affiliation(s)
- Yudi Wu
- grid.33199.310000 0004 0368 7223GI Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, People’s Republic of China ,grid.33199.310000 0004 0368 7223Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030 People’s Republic of China
| | - Xiangshang Xu
- GI Cancer Research Institute, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, People's Republic of China. .,Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 1095 Jiefang Avenue, Wuhan, 430030, People's Republic of China.
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Zhang X, Jin M, Liu F, Qu H, Chen C. Identification of Key MicroRNAs and Genes between Colorectal Adenoma and Colorectal Cancer via Deep Learning on GEO Databases and Bioinformatics. CONTRAST MEDIA & MOLECULAR IMAGING 2023; 2023:6457152. [PMID: 36793496 PMCID: PMC9922557 DOI: 10.1155/2023/6457152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/10/2022] [Accepted: 11/24/2022] [Indexed: 02/08/2023]
Abstract
Background Deep learning techniques are gaining momentum in medical research. Colorectal adenoma (CRA) is a precancerous lesion that may develop into colorectal cancer (CRC) and its etiology and pathogenesis are unclear. This study aims to identify transcriptome differences between CRA and CRC via deep learning on Gene Expression Omnibus (GEO) databases and bioinformatics in the Chinese population. Methods In this study, three microarray datasets from the GEO database were used to identify the differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) in CRA and CRC. The FunRich software was performed to predict the targeted mRNAs of DEMs. The targeted mRNAs were overlapped with DEGs to determine the key DEGs. Molecular mechanisms of CRA and CRC were evaluated using enrichment analysis. Cytoscape was used to construct protein-protein interaction (PPI) and miRNA-mRNA regulatory networks. We analyzed the expression of key DEMs and DEGs, their prognosis, and correlation with immune infiltration based on the Kaplan-Meier plotter, UALCAN, and TIMER databases. Results A total of 38 DEGs are obtained after the intersection, including 11 upregulated genes and 27 downregulated genes. The DEGs were involved in the pathways, including epithelial-to-mesenchymal transition, sphingolipid metabolism, and intrinsic pathway for apoptosis. The expression of has-miR-34c (P = 0.036), hsa-miR-320a (P = 0.045), and has-miR-338 (P = 0.0063) was correlated with the prognosis of CRC patients. The expression levels of BCL2, PPM1L, ARHGAP44, and PRKACB in CRC tissues were significantly lower than normal tissues (P < 0.001), while the expression levels of TPD52L2 and WNK4 in CRC tissues were significantly higher than normal tissues (P < 0.01). These key genes are significantly associated with the immune infiltration of CRC. Conclusion This preliminary study will help identify patients with CRA and early CRC and establish prevention and monitoring strategies to reduce the incidence of CRC.
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Affiliation(s)
- Xin Zhang
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Mingxin Jin
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Fengjun Liu
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Hui Qu
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
| | - Cheng Chen
- Department of General Surgery, Qilu Hospital of Shandong University, 107 Wenhuaxi Road, Jinan 250012, Shandong, China
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Liau XL, Salvamani S, Gunasekaran B, Chellappan DK, Rhodes A, Ulaganathan V, Tiong YL. CCAT 1- A Pivotal Oncogenic Long Non-Coding RNA in Colorectal Cancer. Br J Biomed Sci 2023; 80:11103. [PMID: 37025163 PMCID: PMC10070472 DOI: 10.3389/bjbs.2023.11103] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/09/2023] [Indexed: 04/08/2023]
Abstract
Colorectal cancer (CRC) is ranked as the third most common cancer and second deadliest cancer in both men and women in the world. Currently, the cure rate and 5-year survival rate of CRC patients remain relatively low. Therefore, discovering a novel molecular biomarker that can be used to improve CRC screening, diagnosis, prognosis, and treatment would be beneficial. Long non-coding RNA colon cancer-associated transcript 1 (CCAT 1) has been found overexpressed in CRC and is associated with CRC tumorigenesis and treatment outcome. CCAT 1 has a high degree of specificity and sensitivity, it is readily detected in CRC tissues and is significantly overexpressed in both premalignant and malignant CRC tissues. Besides, CCAT 1 is associated with clinical manifestation and advanced features of CRC, such as lymph node metastasis, high tumor node metastasis stage, differentiation, invasion, and distant metastasis. In addition, they can upregulate oncogenic c-MYC and negatively modulate microRNAs via different mechanisms of action. Furthermore, dysregulated CCAT 1 also enhances the chemoresistance in CRC cells while downregulation of them reverses the malignant phenotypes of cancer cells. In brief, CCAT 1 serves as a potential screening, diagnostic and prognostic biomarker in CRC, it also serves as a potential therapeutic marker to treat CRC patients.
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Affiliation(s)
- Xiew Leng Liau
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
| | - Shamala Salvamani
- Division of Applied Biomedical Sciences and Biotechnology, School of Health Sciences, International Medical University, Kuala Lumpur, Malaysia
- *Correspondence: Shamala Salvamani, ; Baskaran Gunasekaran,
| | - Baskaran Gunasekaran
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
- *Correspondence: Shamala Salvamani, ; Baskaran Gunasekaran,
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Anthony Rhodes
- Department of Pathology, Faculty of Medicine, University Malaya, Kuala Lumpur, Malaysia
| | - Vaidehi Ulaganathan
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Yee Lian Tiong
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
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Li J, Xu J, Zheng S, Cheng S. LncRNA LINC02535 Induces Colorectal Adenocarcinoma Progression via Modulating miR-30d-5p/CHD1. Mol Biotechnol 2022:10.1007/s12033-022-00628-4. [PMID: 36577835 DOI: 10.1007/s12033-022-00628-4] [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: 05/18/2022] [Accepted: 11/28/2022] [Indexed: 12/29/2022]
Abstract
Growing evidence has suggested that lncRNAs play a significant role in the development of colorectal adenocarcinoma. LncRNA LINC02535 was a potential novel lncRNA marker of neoplastic processes of the colon. Nevertheless, the function and mechanisms of LINC02535 in colorectal adenocarcinoma remain unclear. Proteins levels were measured by western blotting. EdU, CCK-8, Transwell, and wound healing assays were performed to investigate the function of LINC02535 in colorectal adenocarcinoma. The distribution of LINC02535 in cells was evaluated by subcellular fractionation assay. The interaction among RNAs was identified by luciferase reporter and RIP assays. In this study, our findings revealed that LINC02535 was highly expressed in colorectal adenocarcinoma cells. Knockdown of LINC02535 inhibited colorectal adenocarcinoma cell proliferation, migration, and invasion. Mechanistically, LINC02535 bound with miR-30d-5p and worked as a competing endogenous RNA to facilitate the expression of messenger RNA chromodomain helicase DNA-binding protein 1 (CHD1). miR-30d-5p directly targeted the sequence of CHD1 3'-untranslated region. Notably, CHD1 upregulation abolished the suppressive influence of LINC02535 inhibition on the malignant phenotypes of colorectal adenocarcinoma cells. Overall, it was disclosed that LINC02535 played an oncogenic role in colorectal adenocarcinoma progression by sponging miR-30d-5p to upregulate CHD1 expression.
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Affiliation(s)
- Jiguang Li
- Department of Anorectal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xianning, 437100, Hubei, China
| | - Jianhua Xu
- Department of Gastrointestinal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China
| | - Sen Zheng
- Department of Gastrointestinal Surgery, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China.
| | - Si Cheng
- Department of Gastroenterology, Xianning Central Hospital, The First Affiliated Hospital of Hubei University of Science and Technology, Xian'an District, No. 228, Jingui Road, Xianning, 437100, Hubei, China.
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Taghehchian N, Farshchian M, Mahmoudian RA, Asoodeh A, Abbaszadegan MR. The expression of long non-coding RNA LINC01389, LINC00365, RP11-138J23.1, and RP11-354K4.2 in gastric cancer and their impacts on EMT. Mol Cell Probes 2022; 66:101869. [PMID: 36208698 DOI: 10.1016/j.mcp.2022.101869] [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: 04/25/2022] [Revised: 09/13/2022] [Accepted: 09/30/2022] [Indexed: 12/05/2022]
Abstract
BACKGROUND Epithelial cancers acquire the epithelial to mesenchymal transition (EMT), which leads tumor cells to invade and metastasize to adjacent and distant tissues. The mechanisms involved in EMT phenotype are controlled by numerous markers as well as signalling pathways. Recently, long non-coding RNAs (lncRNAs) were introduced that play the regulatory role in EMT via crosstalk with EMT-related transcription factors and signalling pathways. The present study aimed to investigate the expression of four lncRNAs in human GC and elucidate their probable role in EMT procedure and the pathogenesis of gastric cancer (GC). METHODS The expression profile of lncRNAs (LINC01389, LINC00365, RP11-138J23.1, and RP11-354K4.2) and mRNAs (TWIST1, MMP13, MAML1, CD44s, and SALL4) between eighty-three GC and adjacent non-cancerous tissues were assessed by quantitative real-time PCR. RESULTS The significant downregulation of LINC00365 (66.3%) and RP11-354K4.2 (62.7%) were observed in GC samples; while the upregulation of LINC01389, RP11-138J23.1, TWIST1, MMP13, MAML1, CD44s, and SALL4 were found in 67.5%, 45.8%, 56.6%, 44.6%, 59%, 55.4%, and 62.7% tumors samples at the mRNA level, respectively. Dysregulation of these lncRNAs and EMT-related markers was significantly related to each other in a variety of clinicopathological features of patients (P < 0.05), indicating positive correlations between LINC01389, LINC00365, RP11-138J23.1, and RP11-354K4.2 with EMT status in GC. CONCLUSION These EMT-regulating lncRNAs may play a key role in transforming gastric epithelial to mesenchymal phenotype and can be novel therapeutic targets for GC. Our results highlight the importance of discovering new lncRNAs involved in gastric carcinogenesis. Detailed molecular mechanisms of these noncoding-coding markers in GC are urgently required.
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Affiliation(s)
- Negin Taghehchian
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Moein Farshchian
- Stem Cell and Regenerative Medicine Research Group, Academic Center for Education, Culture and Research (ACECR), Khorasan Razavi, Mashhad, Iran.
| | | | - Ahmad Asoodeh
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mohammad Reza Abbaszadegan
- 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.
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Ghafouri-Fard S, Khoshbakht T, Hussen BM, Taheri M, Shojaei S. A review on the role of MEG8 lncRNA in human disorders. Cancer Cell Int 2022; 22:285. [PMID: 36114498 PMCID: PMC9482158 DOI: 10.1186/s12935-022-02705-9] [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: 01/06/2022] [Accepted: 09/06/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractMaternally expressed 8 (MEG8) is a long non-coding RNA which is expressed in the nucleus. It is highly expressed in adrenal, placenta and brain. Recent studies have shown contribution of MEG8 in different disorders ranging from neoplastic ones to diabetic nephropathy, atherosclerosis, ischemic stroke, trophoblast dysfunction and abortion, Henoch-Schonlein purpura and osteoarthritis. It has an oncogenic role in the development of lung, pancreatic and liver cancer. In the current review, we summarize the role of this lncRNA in mentioned disorders, based on the evidence obtained from in vitro, in vivo and human studies.
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Kulkarni A, Gayathrinathan S, Nair S, Basu A, Al-Hilal TA, Roy S. Regulatory Roles of Noncoding RNAs in the Progression of Gastrointestinal Cancers and Health Disparities. Cells 2022; 11:cells11152448. [PMID: 35954293 PMCID: PMC9367924 DOI: 10.3390/cells11152448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 07/31/2022] [Accepted: 08/03/2022] [Indexed: 01/17/2023] Open
Abstract
Annually, more than a million individuals are diagnosed with gastrointestinal (GI) cancers worldwide. With the advancements in radio- and chemotherapy and surgery, the survival rates for GI cancer patients have improved in recent years. However, the prognosis for advanced-stage GI cancers remains poor. Site-specific GI cancers share a few common risk factors; however, they are largely distinct in their etiologies and descriptive epidemiologic profiles. A large number of mutations or copy number changes associated with carcinogenesis are commonly found in noncoding DNA regions, which transcribe several noncoding RNAs (ncRNAs) that are implicated to regulate cancer initiation, metastasis, and drug resistance. In this review, we summarize the regulatory functions of ncRNAs in GI cancer development, progression, chemoresistance, and health disparities. We also highlight the potential roles of ncRNAs as therapeutic targets and biomarkers, mainly focusing on their ethnicity-/race-specific prognostic value, and discuss the prospects of genome-wide association studies (GWAS) to investigate the contribution of ncRNAs in GI tumorigenesis.
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Affiliation(s)
- Aditi Kulkarni
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sharan Gayathrinathan
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Soumya Nair
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Anamika Basu
- Copper Mountain College, Joshua Tree, CA 92252, USA
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Taslim A. Al-Hilal
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Texas at El Paso, El Paso, TX 79968, USA
| | - Sourav Roy
- Department of Biological Sciences, University of Texas at El Paso, El Paso, TX 79968, USA
- Border Biomedical Research Center, University of Texas at El Paso, El Paso, TX 79968, USA
- Correspondence:
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12
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Szigeti KA, Kalmár A, Galamb O, Valcz G, Barták BK, Nagy ZB, Zsigrai S, Felletár I, V. Patai Á, Micsik T, Papp M, Márkus E, Tulassay Z, Igaz P, Takács I, Molnár B. Global DNA hypomethylation of colorectal tumours detected in tissue and liquid biopsies may be related to decreased methyl-donor content. BMC Cancer 2022; 22:605. [PMID: 35655145 PMCID: PMC9164347 DOI: 10.1186/s12885-022-09659-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/03/2022] [Indexed: 02/06/2023] Open
Abstract
Abstract
Background
Hypomethylation of long interspersed nuclear element 1 (LINE-1) is characteristic of various cancer types, including colorectal cancer (CRC). Malfunction of several factors or alteration of methyl-donor molecules’ (folic acid and S-adenosylmethionine) availability can contribute to DNA methylation changes. Detection of epigenetic alterations in liquid biopsies can assist in the early recognition of CRC. Following the investigations of a Hungarian colon tissue sample set, our goal was to examine the LINE-1 methylation of blood samples along the colorectal adenoma-carcinoma sequence and in inflammatory bowel disease. Moreover, we aimed to explore the possible underlying mechanisms of global DNA hypomethylation formation on a multi-level aspect.
Methods
LINE-1 methylation of colon tissue (n = 183) and plasma (n = 48) samples of healthy controls and patients with colorectal tumours were examined with bisulfite pyrosequencing. To investigate mRNA expression, microarray analysis results were reanalysed in silico (n = 60). Immunohistochemistry staining was used to validate DNA methyltransferases (DNMTs) and folate receptor beta (FOLR2) expression along with the determination of methyl-donor molecules’ in situ level (n = 40).
Results
Significantly decreased LINE-1 methylation level was observed in line with cancer progression both in tissue (adenoma: 72.7 ± 4.8%, and CRC: 69.7 ± 7.6% vs. normal: 77.5 ± 1.7%, p ≤ 0.01) and liquid biopsies (adenoma: 80.0 ± 1.7%, and CRC: 79.8 ± 1.3% vs. normal: 82.0 ± 2.0%, p ≤ 0.01). However, no significant changes were recognized in inflammatory bowel disease cases. According to in silico analysis of microarray data, altered mRNA levels of several DNA methylation-related enzymes were detected in tumours vs. healthy biopsies, namely one-carbon metabolism-related genes—which met our analysing criteria—showed upregulation, while FOLR2 was downregulated. Using immunohistochemistry, DNMTs, and FOLR2 expression were confirmed. Moreover, significantly diminished folic acid and S-adenosylmethionine levels were observed in parallel with decreasing 5-methylcytosine staining in tumours compared to normal adjacent to tumour tissues (p ≤ 0.05).
Conclusion
Our results suggest that LINE-1 hypomethylation may have a distinguishing value in precancerous stages compared to healthy samples in liquid biopsies. Furthermore, the reduction of global DNA methylation level could be linked to reduced methyl-donor availability with the contribution of decreased FOLR2 expression.
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Du Z, Tan F, Chen J, Wang B, Liu Y, Zhao F, Wu Y, Yuan C. MEG8:An Indispensable Long Non-coding RNA in Multiple Cancers. Curr Pharm Des 2022; 28:1688-1694. [PMID: 35578848 DOI: 10.2174/1381612828666220516090245] [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: 11/02/2021] [Accepted: 03/29/2022] [Indexed: 11/22/2022]
Abstract
BACKGROUND As a member of long non-coding RNAs (lncRNAs), maternally expressed gene 8 (MEG8) has been found involving in the progression of a variety of cancers and playing a regulatory role. Therefore, MEG8 may turn into a new therapeutic target for cancer in the future. The purpose of this review is to illustrate the molecular mechanism and physiological function of MEG8 in various cancers. METHODS We retrieved and analyzed related articles about MEG8, lncRNAs and cancers, and then summarize the pathophysiological mechanisms of MEG8 in cancer development. RESULTS LncRNA MEG8 participates in various cancers progression, thus influencing the proliferation, migration, and invasion of cancers. However, the expression of MEG8 is abnormally upregulated in non-small cell lung cancer (NSCLC), pancreatic cancer (PC), liver cancer (HCC), pituitary adenoma (PA) and hemangioma (HA), and inhibited in colorectal cancer (CRC), ovarian cancer (OC) and giant cell tumor (GCT), suggesting its clinical value in cancer therapy. CONCLUSIONS LncRNA MEG8 is expected to be a new therapeutic target or biomarker for a wide range of cancers in the future.
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Affiliation(s)
- Zhuoying Du
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Fangshun Tan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Jinlan Chen
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Bei Wang
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Yuling Liu
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Fangnan Zhao
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Yinxin Wu
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
| | - Chengfu Yuan
- Third-grade Pharmacological Laboratory on Traditional Chinese Medicine, State Administration of Traditional Chinese Medicine, China Three Gorges University, Yichang 443002, China.,Medical College, China Three Gorges University, Yichang 443002, China
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Folic Acid Treatment Directly Influences the Genetic and Epigenetic Regulation along with the Associated Cellular Maintenance Processes of HT-29 and SW480 Colorectal Cancer Cell Lines. Cancers (Basel) 2022; 14:cancers14071820. [PMID: 35406592 PMCID: PMC8997840 DOI: 10.3390/cancers14071820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 12/17/2022] Open
Abstract
Simple Summary Folic acid (FA) participates in DNA synthesis and in DNA methylation; hence, it has a dual role in established neoplasms. We aimed to observe this phenomenon on FA-treated colorectal cancer cell lines (HT-29, SW480). Our results demonstrated that the maintenance processes, namely cell proliferation, cell viability, and DNA repair, were altered in HT-29 cells for short-term FA supplementation, while genetic and epigenetic regulations of SW480 cells were also affected. Despite the fact that FA is a precursor molecule in methyl donor formation, DNA methylation alterations were observed in both directions, primarily influencing the pathways of carcinogenesis. Moreover, behind the great number of differentially expressed genes, other FA-related effects than promoter methylation were suspected. All of our results point beyond the attributes related to FA so far. The different response of the two cell lines is worth considering in clinical practice to facilitate the effectiveness of therapy in the case of tumor heterogeneity. Abstract Folic acid (FA) is a synthetic form of vitamin B9, generally used as a nutritional supplement and an adjunctive medication in cancer therapy. FA is involved in genetic and epigenetic regulation; therefore, it has a dual modulatory role in established neoplasms. We aimed to investigate the effect of short-term (72 h) FA supplementation on colorectal cancer; hence, HT-29 and SW480 cells were exposed to different FA concentrations (0, 100, 10,000 ng/mL). HT-29 cell proliferation and viability levels elevated after 100 ng/mL but decreased for 10,000 ng/mL FA. Additionally, a significant (p ≤ 0.05) improvement of genomic stability was detected in HT-29 cells with micronucleus scoring and comet assay. Conversely, the FA treatment did not alter these parameters in SW480 samples. RRBS results highlighted that DNA methylation changes were bidirectional in both cells, mainly affecting carcinogenesis-related pathways. Based on the microarray analysis, promoter methylation status was in accordance with FA-induced expression alterations of 27 genes. Our study demonstrates that the FA effect was highly dependent on the cell type, which can be attributed to the distinct molecular background and the different expression of proliferation- and DNA-repair-associated genes (YWHAZ, HES1, STAT3, CCL2). Moreover, new aspects of FA-regulated DNA methylation and consecutive gene expression were revealed.
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15
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Lacalamita A, Piccinno E, Scalavino V, Bellotti R, Giannelli G, Serino G. A Gene-Based Machine Learning Classifier Associated to the Colorectal Adenoma-Carcinoma Sequence. Biomedicines 2021; 9:biomedicines9121937. [PMID: 34944753 PMCID: PMC8698794 DOI: 10.3390/biomedicines9121937] [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: 11/22/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Colorectal cancer (CRC) carcinogenesis is generally the result of the sequential mutation and deletion of various genes; this is known as the normal mucosa–adenoma–carcinoma sequence. The aim of this study was to develop a predictor-classifier during the “adenoma-carcinoma” sequence using microarray gene expression profiles of primary CRC, adenoma, and normal colon epithelial tissues. Four gene expression profiles from the Gene Expression Omnibus database, containing 465 samples (105 normal, 155 adenoma, and 205 CRC), were preprocessed to identify differentially expressed genes (DEGs) between adenoma tissue and primary CRC. The feature selection procedure, using the sequential Boruta algorithm and Stepwise Regression, determined 56 highly important genes. K-Means methods showed that, using the selected 56 DEGs, the three groups were clearly separate. The classification was performed with machine learning algorithms such as Linear Model (LM), Random Forest (RF), k-Nearest Neighbors (k-NN), and Artificial Neural Network (ANN). The best classification method in terms of accuracy (88.06 ± 0.70) and AUC (92.04 ± 0.47) was k-NN. To confirm the relevance of the predictive models, we applied the four models on a validation cohort: the k-NN model remained the best model in terms of performance, with 91.11% accuracy. Among the 56 DEGs, we identified 17 genes with an ascending or descending trend through the normal mucosa–adenoma–carcinoma sequence. Moreover, using the survival information of the TCGA database, we selected six DEGs related to patient prognosis (SCARA5, PKIB, CWH43, TEX11, METTL7A, and VEGFA). The six-gene-based classifier described in the current study could be used as a potential biomarker for the early diagnosis of CRC.
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Affiliation(s)
- Antonio Lacalamita
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Emanuele Piccinno
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Viviana Scalavino
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Roberto Bellotti
- Dipartimento Interateneo di Fisica, Università degli Studi di Bari Aldo Moro, 70126 Bari, Italy;
- Istituto Nazionale di Fisica Nucleare, Sezione di Bari, 70125 Bari, Italy
| | - Gianluigi Giannelli
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
| | - Grazia Serino
- National Institute of Gastroenterology “S. de Bellis”, Research Hospital, Castellana Grotte, 70013 Bari, Italy; (A.L.); (E.P.); (V.S.); (G.G.)
- Correspondence:
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16
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Jafari-Oliayi A, Dabiri S, Hossein Asadi M. LncRNA SNHG6 Silencing Could Arrest Progression of High Grade Colorectal Cancers. IRANIAN JOURNAL OF PATHOLOGY 2021; 17:29-36. [PMID: 35096086 PMCID: PMC8794560 DOI: 10.30699/ijp.2021.527781.2610] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/30/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND & OBJECTIVE Colorectal cancer (CRC), like other cancers, needs faster and more accurate identifications. A well-timed prognosis of CRC could be an important turning point in the survival of patients. Supplementary signs, such as long non-coding RNAs (lncRNAs), could be helpful for this purpose. A new possible biomarker for CRC identification is introduced by this study. METHODS RNA extraction was performed by the RNX-Plus solution for 64 tumor and non-tumor tissues. Complementary DNAs (cDNAs) were synthesized, and quantitative real-time PCR was performed for relative expression level measurement and the data was analyzed statistically using the Prism 6 software. For Small nucleolar host gene 6 knockdown, siRNA was designed based on Reynolds rules. The cells were cultured in their appropriate media, and the siRNA-lipofectamine complex was formed. The transfection complex was presented for sw48, sw480, and sw1116 as CRC cells with different grades. After transfection, the SNHG6/β actin ratio was determined. Then, the distribution of siRNA-treated cells was determined by the Partec flow cytometer instrument and analyzed by the FloMax software. RESULTS SNHG6 was more expressed in CRC tumors than non-tumor tissues. In tumor tissues, SNHG6 upregulation and tumors' grade progression were concurrent. SNHG6 was upregulated in cases with lymphovascular invasion than in cases with perineural invasion. The knockdown of SNHG6 conduced to G1 arrest in CRC cells, more noticeably in high-grade ones. CONCLUSION SNHG6 could be applied as a consideration to differentiate tumor and non-tumor tissues and grade definition in colorectal malignancies, and it could participate in colorectal tumor formation as a cell cycle progressive factor.
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Affiliation(s)
- Amin Jafari-Oliayi
- Pathology and Stem Cell Research Center, Department of Pathology, Afzalipour Medical School, Kerman University of Medical Sciences, Kerman, Iran
| | - Shahriar Dabiri
- Pathology and Stem Cell Research Center, Department of Pathology, Afzalipour Medical School, Kerman University of Medical Sciences, Kerman, Iran
| | - Malek Hossein Asadi
- Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology Kerman, Iran
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Urinary exosomal long noncoding RNAs serve as biomarkers for early detection of non-small cell lung cancer. Biosci Rep 2021; 41:229852. [PMID: 34580719 PMCID: PMC8521532 DOI: 10.1042/bsr20210908] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/24/2021] [Accepted: 09/27/2021] [Indexed: 12/31/2022] Open
Abstract
Objective: Increasing the efficiency of early diagnosis using noninvasive biomarkers is crucial for enhancing the survival rate of lung cancer patients. We explore the differential expression of non-small cell lung cancer (NSCLC)-related long noncoding RNAs (lncRNAs) in urinary exosomes in NSCLC patients and normal controls to diagnose lung cancer. Methods: A differential expression analysis between NSCLC patients and healthy controls was performed using microarrays. Gene ontology (GO) term and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to predict potential functions of lncRNAs in NSCLC. quantitative real-time PCR (QT-PCR) was used to verify microarray results. Results: A total of 640 lncRNAs (70 up- and 570 down-regulated) were differentially expressed in NSCLC patients in comparison to healthy controls. Six lncRNAs were detected by QT-PCR. GO term and KEGG pathway analyses showed that differential lncRNAs were enriched in cellular component organization or biogenesis, as well as other biological processes and signaling pathways, such as the PI3K-AKT, FOXO, p53, and fatty acid biosynthesis. Conclusions: The differential lncRNAs in urinary exosomes are potential diagnostic biomarkers of NSCLC. The lncRNAs enriched in specific pathways may be associated with tumor cell proliferation, tumor cell apoptosis, and the cell cycle involved in the pathogenesis of NSCLC.
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18
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Elsayed I, Li L, Sheahan K, Moran B, Bakheit S, Wang X. Adenoma to carcinoma: A portrait of molecular and immunological profiles of colorectal sporadic tumors. Int Immunopharmacol 2021; 100:108168. [PMID: 34562842 DOI: 10.1016/j.intimp.2021.108168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/24/2022]
Abstract
An in-depth investigation of the molecular and immunologic properties of colorectal adenoma is important for understanding the mechanisms of colorectal cancer (CRC) initiation and development through the adenoma pathway. We performed a meta-analysis of the gene expression data from seven CRC and colorectal sporadic conventional adenoma datasets. We compared the enrichment levels of immune signatures between adenoma, normal colon, and CRC, then applied immunohistochemistry to compare the CD3 + and CD8 + T cells infiltration using samples of adenoma, contiguous adenoma, and CRC. We identified differentially expressed genes (DEGs) between adenoma, normal colon, and CRC, then performed pathway, network, immune correlation, and survival analyses on the DEGs. Adenoma had lower enrichment levels of antitumor immune signatures (CD8 + T cells, NK cells, and MHC Class I) while higher levels of TGF-β and Th17 signatures. Immunohistochemistry revealed variations in CD3 + and CD8 + T cells infiltration between low-grade and high-grade adenomas and between adenoma, normal colon, and CRC. We identified two groups of genes, which we named (NACupGs and NACdownGs), with consistent expression elevation and reduction respectively across the normal, precancerous, and cancerous stages. 48% of the NACupGs had expression levels highly correlated with Treg and TGF-β immune signatures, of which 39% were inversely correlated with CRC survival. We conclude that anti-tumor immune response is reduced at the precancerous (adenoma) stage which is characterized by prominent TGF-β and Th17 activity. The alterations of molecular and immunological profiles in adenoma can provide new insights into the initiation and development of CRC.
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Affiliation(s)
- Inas Elsayed
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China; Department of Pharmacology, Faculty of Pharmacy, University of Gezira, Wad Madani 20, Sudan
| | - Lin Li
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China
| | - Kieran Sheahan
- Centre for Colorectal Disease, St. Vincent's University Hospital, Elm Park Dublin 4, Ireland; School of Medicine and Medical Sciences, University College Dublin, Belfield Dublin 4, Ireland
| | - Bruce Moran
- Department of Pathology, St. Vincent's University Hospital, Elm Park Dublin 4, Ireland
| | - Salih Bakheit
- Hull Royal Infirmary, Hull University Hospital NHS Trust, Hull, East Yorkshire, UK
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 211198, China; Big Data Research Institute, China Pharmaceutical University, Nanjing 211198, China.
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Debernardi C, Libera L, Berrino E, Sahnane N, Chiaravalli AM, Laudi C, Berselli M, Sapino A, Sessa F, Venesio T, Furlan D. Evaluation of global and intragenic hypomethylation in colorectal adenomas improves patient stratification and colorectal cancer risk prediction. Clin Epigenetics 2021; 13:154. [PMID: 34372923 PMCID: PMC8351348 DOI: 10.1186/s13148-021-01135-0] [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: 05/04/2021] [Accepted: 07/15/2021] [Indexed: 12/16/2022] Open
Abstract
Background Aberrant DNA hypomethylation of the long interspersed nuclear elements (LINE-1 or L1) has been recognized as an early event of colorectal transformation. Simultaneous genetic and epigenetic analysis of colorectal adenomas may be an effective and rapid strategy to identify key biological features leading to accelerated colorectal tumorigenesis. In particular, global and/or intragenic LINE-1 hypomethylation of adenomas may represent a helpful tool for improving colorectal cancer (CRC) risk stratification of patients after surgical removal of polyps. To verify this hypothesis, we analyzed a cohort of 102 adenomas derived from 40 high-risk patients (who developed CRC in a post-polypectomy of at least one year) and 43 low-risk patients (who did not develop CRC in a post-polypectomy of at least 5 years) for their main pathological features, the presence of hotspot variants in driver oncogenes (KRAS, NRAS, BRAF and PIK3CA), global (LINE-1) and intragenic (L1-MET) methylation status. Results In addition to a significantly higher adenoma size and an older patients’ age, adenomas from high-risk patients were more hypomethylated than those from low-risk patients for both global and intragenic LINE-1 assays. DNA hypomethylation, measured by pyrosequencing, was independent from other parameters, including the presence of oncogenic hotspot variants detected by mass spectrometry. Combining LINE-1 and L1-MET analyses and profiling the samples according to the presence of at least one hypomethylated assay improved the discrimination between high and low risk lesions (p = 0.005). Remarkably, adenomas with at least one hypomethylated assay identified the patients with a significantly (p < 0.001) higher risk of developing CRC. Multivariable analysis and logistic regression evaluated by the ROC curves proved that methylation status was an independent variable improving cancer risk prediction (p = 0.02). Conclusions LINE-1 and L1-MET hypomethylation in colorectal adenomas are associated with a higher risk of developing CRC. DNA global and intragenic hypomethylation are independent markers that could be used in combination to successfully improve the stratification of patients who enter a colonoscopy surveillance program. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01135-0.
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Affiliation(s)
- Carla Debernardi
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Laura Libera
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Enrico Berrino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Nora Sahnane
- Pathology Unit, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Anna Maria Chiaravalli
- Pathology Unit, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Cristiana Laudi
- Gastroenterology, Candiolo Cancer Institute, Candiolo, Italy
| | - Mattia Berselli
- Surgical Oncology and Minimally Invasive Unit, Department of Surgery, ASST Sette Laghi, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Anna Sapino
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy.,Department of Medical Sciences, University of Torino, Torino, Italy
| | - Fausto Sessa
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Tiziana Venesio
- Pathology Unit, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy. .,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy.
| | - Daniela Furlan
- Pathology Unit, Department of Medicine and Surgery, University of Insubria, Varese, Italy.,Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery, University of Insubria, Varese, Italy
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20
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Ma Q, Dai X, Lu W, Qu X, Liu N, Zhu C. Silencing long non-coding RNA MEG8 inhibits the proliferation and induces the ferroptosis of hemangioma endothelial cells by regulating miR-497-5p/NOTCH2 axis. Biochem Biophys Res Commun 2021; 556:72-78. [PMID: 33839417 DOI: 10.1016/j.bbrc.2021.03.132] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023]
Abstract
Even though long non-coding RNA (lncRNA) MEG8 plays vital roles in carcinogenesis of malignances, its roles and mechanisms in hemangioma remain unknown. Therefore, we evaluate the oncogenic roles of MEG8 in hemangioma. Small interfering RNA (siRNA)-mediated depletion of MEG8 inhibited the proliferation and increased MDA level in human hemangioma endothelial cells (HemECs). The inhibitors of ferroptosis (ferrostatin-1 and liproxstatin-1) abolished the MEG8 silence induced cell viability loss. Knockdown of MEG8 increased the miR-497-5p expression and reduced the mRNA and protein levels of NOTCH2. Using a dual-luciferase assay, we confirmed the binding between MEG8 and miR-497-5p, and between the miR-497-5p and 3'UTR of NOTCH2. We further found that silencing MEG8 significantly decreased the expressions of SLC7A11 and GPX4 both in mRNA and protein level and had no effect on the level of AIFM2. Importantly, blocking miR-497-5p abrogated the effects of MEG8 loss on cell viability, MDA level and expression levels of NOTCH2, SLC7A11 and GPX4 in HemECs. Taken together, our results suggested that knockdown of long non-coding RNA MEG8 inhibited the proliferation and induced the ferroptosis of hemangioma endothelial cells by regulating miR-497-5p/NOTCH2 axis.
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Affiliation(s)
- Qingjie Ma
- The First People's Hospital of Yunnan Province, Kunming, 650032, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China
| | - Xiaolin Dai
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Weiwei Lu
- Medical School, Kunming University of Science and Technology, Kunming, 650500, China
| | - Xiaowen Qu
- The First People's Hospital of Yunnan Province, Kunming, 650032, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China
| | - Na Liu
- The First People's Hospital of Yunnan Province, Kunming, 650032, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China.
| | - Chongtao Zhu
- The First People's Hospital of Yunnan Province, Kunming, 650032, China; The Affiliated Hospital of Kunming University of Science and Technology, Kunming, 650032, China.
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21
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Zhu HB, Li B, Guo J, Miao YZ, Shen YT, Zhang YZ, Zhao P, Li CZ. LncRNA MEG8 promotes TNF-α expression by sponging miR-454-3p in bone-invasive pituitary adenomas. Aging (Albany NY) 2021; 13:14342-14354. [PMID: 34016788 PMCID: PMC8202870 DOI: 10.18632/aging.203048] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 02/16/2021] [Indexed: 04/12/2023]
Abstract
There are few studies on the mechanism of pituitary adenoma (PA) destroying bone. The current study aimed to investigate the role of MEG8/miR-454-3p/TNF-α in bone-invasive pituitary adenomas (BIPAs). In this study, we report that lncRNA MEG8 and TNF-α are upregulated in BIPA tissues while miR-454-3p is downregulated, which is associated with poor progression-free survival (PFS). Functional assays revealed the role of up-regulated MEG8 and down-regulated miR-454-3p in promoting bone destruction. Mechanistically, MEG8 promotes TNF-α expression by sponging miR-454-3p, which ultimately leads to the occurrence of bone destruction. The mechanism is confirmed in vivo and in vitro. Therefore, our data illustrated a new regulatory mechanism of MEG8/miR-454-3p/TNF-α in BIPAs. It may provide a useful strategy for diagnosis and treatment for BIPA patients.
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Affiliation(s)
- Hai-Bo Zhu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Fengtai 100070, Beijing, China
| | - Bin Li
- Beijing Neurosurgical Institute, Capital Medical University, Fengtai 100070, Beijing, China
| | - Jing Guo
- Beijing Neurosurgical Institute, Capital Medical University, Fengtai 100070, Beijing, China
| | - Ya-Zhou Miao
- Beijing Neurosurgical Institute, Capital Medical University, Fengtai 100070, Beijing, China
| | - Yu-Tao Shen
- Beijing Neurosurgical Institute, Capital Medical University, Fengtai 100070, Beijing, China
| | - Ya-Zhuo Zhang
- Beijing Neurosurgical Institute, Capital Medical University, Fengtai 100070, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Fengtai 100070, Beijing, China
- Beijing Institute for Brain Disorders Brain Tumor Center, Fengtai 100070, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Fengtai 100070, Beijing, China
| | - Peng Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Fengtai 100070, Beijing, China
| | - Chu-Zhong Li
- Beijing Neurosurgical Institute, Capital Medical University, Fengtai 100070, Beijing, China
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Fengtai 100070, Beijing, China
- Beijing Institute for Brain Disorders Brain Tumor Center, Fengtai 100070, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Fengtai 100070, Beijing, China
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22
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Ren MH, Chen S, Wang LG, Rui WX, Li P. LINC00941 Promotes Progression of Non-Small Cell Lung Cancer by Sponging miR-877-3p to Regulate VEGFA Expression. Front Oncol 2021; 11:650037. [PMID: 33869051 PMCID: PMC8044452 DOI: 10.3389/fonc.2021.650037] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/04/2021] [Indexed: 12/21/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play critical roles in carcinoma occurrence and metastasis. LINC00941 has been found to mediate the development of gastric cancer, and LINC00941 was negatively associated with the longer overall survival of lung adenocarcinoma patients. Herein, our aim was to investigate the effects and mechanisms of LINC00941 in NSCLC progression. Microarray was used to identify the change lncRNAs in NSCLC, LINC00941 was found to increase in tumor tissues and patients' plasma. Knockdown of LINC00941 didn't modulate the proliferation of NSCLC cells, but inhibition of LINC00941 in NSCLC cells suppressed the angiogenesis ability of human umbilical vein endothelial cells (HUVECs). Moreover, LINC00941 promoted tumorigenesis in vivo, while si-LINC00941 inhibited tumor development of NSCLC. VEGFA was should to be significantly modulated by LINC00941 in NSCLC cells, then luciferase assay proved that LINC00941 regulated VEGFA expression via interacting with miR-877-3p. Followed functional experiments indicated that overexpression of LINC00941 accelerated angiogenesis and NSCLC tumor progression via miR-877-3p/VEGFA axis both in vitro and in vivo. In conclusion, our results clarified the LINC00941 function for the first time, and LINC00941 promoted the progression of NSCLC, which was mediated by miR-877-3p/VEGFA axis. This study might provide new understanding and targets for NSCLC diagnosis and treatment.
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Affiliation(s)
- Min-Huan Ren
- Department of Respiratory Disease, Taikang Xianlin Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Si Chen
- Department of Respiratory Disease, Taikang Xianlin Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Liang-Ge Wang
- Department of Respiratory Disease, Taikang Xianlin Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Wen-Xiu Rui
- Department of Respiratory Disease, Taikang Xianlin Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Pei Li
- Department of Infectious Diseases, Affiliated Hospital 2 of Nantong University, Nantong, China
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23
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Miao X, Liu Y, Fan Y, Wang G, Zhu H. LncRNA BANCR Attenuates the Killing Capacity of Cisplatin on Gastric Cancer Cell Through the ERK1/2 Pathway. Cancer Manag Res 2021; 13:287-296. [PMID: 33469371 PMCID: PMC7811444 DOI: 10.2147/cmar.s269679] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022] Open
Abstract
Purpose Chemotherapy-based comprehensive treatments are the most important therapeutic methods for patients with advanced gastric cancer, but chemoresistance often cause treatment failure. Long non-coding RNA (LncRNA) BRAF-activated non-coding RNA (BANCR) has been shown to participate in many biological behaviors of multiple cancers. However, the biological roles of LncRNA BANCR in chemoresistance of gastric cancer remain unclear. Here, we aimed to evaluate the functions of LncRNA BANCR on the therapy of gastric cancer. Methods In this study, LncRNA BANCR expression was detected in gastric cancer patient samples and cell lines by quantity polymerase chain reaction (qPCR). Cell proliferation and viability in cisplatin-treated cells were measured using clonogenic survival assay and cell counting kit-8. The levels of ERK1/2 pathway molecules were tested with Western blot. Ly3214996, an inhibitor of ERK signal pathway, was administered to assess the effects of BANCR overexpression on gastric cancer cell with cisplatin-treated resistance. Moreover, the role of BANCR in cisplatin resistance of gastric cancer was validated in xenograft mouse models in vivo. Results Our study revealed that LncRNA BANCR expression was also significantly increased in gastric cancer tissues compared with adjacent normal tissues. Furthermore, we found that BANCR overexpression promoted gastric cancer cell resistance to cisplatin in vitro. Ly3214996 treatment abolished the BANCR overexpression-mediated gastric cancer cell cisplatin resistance via regulating the phosphorylation of ERK protein. Knock-down of BANCR significantly delayed tumor growth in xenograft mouse models. Conclusion BANCR promoted cisplatin resistance of gastric cancer cells by activating ERK1/2 pathway. Inhibition of BANCR markedly suppressed the growth of gastric cancer cells in vitro as well as in vivo. These results provided a new strategy for gastric cancer therapy via targeting BANCR.
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Affiliation(s)
- Xiang Miao
- Department of General Surgery, Lianyungang Municipal Oriental Hospital, Lianyungang, Jiangsu 222042, People's Republic of China
| | - Yixiang Liu
- Department of General Surgery, Lianyungang Municipal Oriental Hospital, Lianyungang, Jiangsu 222042, People's Republic of China
| | - Yuzhu Fan
- Department of General Surgery, Lianyungang Municipal Oriental Hospital, Lianyungang, Jiangsu 222042, People's Republic of China
| | - Guoqiang Wang
- Department of General Surgery, Lianyungang Municipal Oriental Hospital, Lianyungang, Jiangsu 222042, People's Republic of China
| | - Hongbo Zhu
- Department of General Surgery, Lianyungang Municipal Oriental Hospital, Lianyungang, Jiangsu 222042, People's Republic of China
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24
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Nielsen BS, Larsen J, Høffding J, Nhat SL, Madsen NH, Møller T, Holst B, Holmstrøm K. Detection of lncRNA by LNA-Based In Situ Hybridization in Paraffin-Embedded Cancer Cell Spheroids. Methods Mol Biol 2021; 2348:123-137. [PMID: 34160803 DOI: 10.1007/978-1-0716-1581-2_8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Cancer cell spheroids are considered important preclinical tools to evaluate the efficacy of new drugs. In cancer cell spheroids, the cells assemble and grow in 3D structures with cell contact interactions that are partly impermeable, which leads to central hypoxia and necrosis. The cell spheroids thus possess several features identified in clinical tumors. Not only will the effect and behavior of therapeutic drugs in 3D cell spheroids be affected more similarly than in cells grown on culture plates, but molecular interactions and signaling pathways in cells are also more likely to mimic the in vivo situation. The monitoring of various biomarkers including lncRNAs in 3D cell spheroids is important to assess a potentially induced phenotype in the cells and the effects of drugs. Specifically, for lncRNAs, in situ localization can be done using locked nucleic acid (LNA) probe technology. Here we present a protocol for preparation of cell spheroids for use in LNA probe-based in situ hybridization to study lncRNA expression in paraffin embedded 3D cancer cell spheroids.
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Affiliation(s)
| | | | - Jakob Høffding
- Bioneer A/S, Hørsholm, Denmark.,Københavns Professionshøjskole, København, Denmark
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25
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He S, Chen J, Gao H, Yang G, Zhang F, Ding Y, Zhu H. Extended transcriptome analysis reveals genome-wide lncRNA-mediated epigenetic dysregulation in colorectal cancer. Comput Struct Biotechnol J 2020; 18:3507-3517. [PMID: 33304451 PMCID: PMC7695927 DOI: 10.1016/j.csbj.2020.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 10/21/2020] [Accepted: 11/03/2020] [Indexed: 12/30/2022] Open
Abstract
It is estimated that the rate of epigenetic changes may be orders of magnitude higher than that of genetic changes and that purely epigenetic mechanisms may explain why cancers arise with few or no recurrent mutations. However, supporting evidence remains limited, partly due to the cost of experimentally studying genome-wide epigenetic dysregulation. Since genome modification enzymes are recruited by long noncoding RNAs (lncRNAs) to specific genomic sites, analyzing differentially expressed genes and differentially methylated regions (DMRs) at the DNA binding sites of differentially expressed lncRNAs is important for uncovering epigenetic dysregulation. We performed RNA-seq and MeDIP-seq on a set of colorectal cancer (CRC) and normal colon samples and developed an analysis pipeline for combined analyses of gene expression, DNA methylation, and lncRNA/DNA binding. The genes identified in our data and important for CRC agree with widely reported findings. We found that aberrantly transcribed noncoding transcripts may epigenetically dysregulate genes, that correlated gene expression is significantly determined by epigenetic dysregulation, that differentially expressed noncoding transcripts and their epigenetic targets form distinct modules in different cancer cells, and that many hub lncRNAs in these modules are primate-specific. These results suggest that lncRNA-mediated epigenetic dysregulation greatly determines aberrant gene expression and that epigenetic dysregulation is highly species-specific. The analysis pipeline can effectively unveil cancer- and cell-specific modules of epigenetic dysregulation, and such modules may provide novel clues for identifying diagnostic, therapeutic, and prognostic targets for epigenetic dysregulation.
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Affiliation(s)
- Sha He
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Juanzhi Chen
- Department of Pathology, Southern Hospital, Southern Medical University, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huan Gao
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guixian Yang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feixiang Zhang
- Department of Pathology, Southern Hospital, Southern Medical University, China
| | - Yanqing Ding
- Department of Pathology, Southern Hospital, Southern Medical University, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
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26
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Zsigrai S, Kalmár A, Nagy ZB, Barták BK, Valcz G, Szigeti KA, Galamb O, Dankó T, Sebestyén A, Barna G, Szabó V, Pipek O, Medgyes-Horváth A, Csabai I, Tulassay Z, Igaz P, Takács I, Molnár B. S-Adenosylmethionine Treatment of Colorectal Cancer Cell Lines Alters DNA Methylation, DNA Repair and Tumor Progression-Related Gene Expression. Cells 2020; 9:cells9081864. [PMID: 32784836 PMCID: PMC7464653 DOI: 10.3390/cells9081864] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/03/2020] [Accepted: 08/07/2020] [Indexed: 12/24/2022] Open
Abstract
Global DNA hypomethylation is a characteristic feature of colorectal carcinoma (CRC). The tumor inhibitory effect of S-adenosylmethionine (SAM) methyl donor has been described in certain cancers including CRC. However, the molecular impact of SAM treatment on CRC cell lines with distinct genetic features has not been evaluated comprehensively. HT-29 and SW480 cells were treated with 0.5 and 1 mmol/L SAM for 48 h followed by cell proliferation measurements, whole-genome transcriptome and methylome analyses, DNA stability assessments and exome sequencing. SAM reduced cell number and increased senescence by causing S phase arrest, besides, multiple EMT-related genes (e.g., TGFB1) were downregulated in both cell lines. Alteration in the global DNA methylation level was not observed, but certain methylation changes in gene promoters were detected. SAM-induced γ-H2AX elevation could be associated with activated DNA repair pathway showing upregulated gene expression (e.g., HUS1). Remarkable genomic stability elevation, namely, decreased micronucleus number and comet tail length was observed only in SW480 after treatment. SAM has the potential to induce senescence, DNA repair, genome stability and to reduce CRC progression. However, the different therapeutic responses of HT-29 and SW480 to SAM emphasize the importance of the molecular characterization of CRC cases prior to methyl donor supplementation.
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Affiliation(s)
- Sára Zsigrai
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- Correspondence:
| | - Alexandra Kalmár
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - Zsófia B. Nagy
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Barbara K. Barták
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Gábor Valcz
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - Krisztina A. Szigeti
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Orsolya Galamb
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - Titanilla Dankó
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Anna Sebestyén
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Gábor Barna
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Vanessza Szabó
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, 1085 Budapest, Hungary; (T.D.); (A.S.); (G.B.); (V.S.)
| | - Orsolya Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (O.P.); (A.M.-H.); (I.C.)
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (O.P.); (A.M.-H.); (I.C.)
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, 1117 Budapest, Hungary; (O.P.); (A.M.-H.); (I.C.)
| | - Zsolt Tulassay
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
- Department of Internal Medicine and Hematology, Semmelweis University, 1088 Budapest, Hungary
| | - Péter Igaz
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
| | - István Takács
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
| | - Béla Molnár
- Department of Internal Medicine and Oncology, Semmelweis University, 1083 Budapest, Hungary; (A.K.); (Z.B.N.); (B.K.B.); (G.V.); (K.A.S.); (O.G.); (P.I.); (I.T.); (B.M.)
- MTA-SE Molecular Medicine Research Group, Hungarian Academy of Sciences, 1051 Budapest, Hungary;
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27
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Ren Z, Liu J, Li J, Yao L. Decreased lncRNA, TINCR, promotes growth of colorectal carcinoma through upregulating microRNA-31. Aging (Albany NY) 2020; 12:14219-14231. [PMID: 32681722 PMCID: PMC7425505 DOI: 10.18632/aging.103436] [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: 01/20/2020] [Accepted: 04/17/2020] [Indexed: 11/25/2022]
Abstract
Abnormal expression in terminal differentiation-induced noncoding RNA (TINCR), a long non-coding RNA (lncRNA), has been reported in different human cancers, including colorectal carcinoma (CRC). Moreover, the molecular mechanisms that underlie the effects of TINCR on CRC remain unclear. Here, by a set of bioinformatics studies, we found that microRNA-31 (miR-31), the oncogenic miRNA that robustly upregulates in CRC, was a sponge miRNA for TINCR. TINCR and miR-31 levels were inversely correlated in both CRC tissues and CRC cell lines. Luciferase reporter assay revealed a specific binding site on TINCR for miR-31. Suppression of TINCR promoted CRC cell growth and migration in vitro, while overexpression of TINCR inhibited CRC cell growth and migration in vitro. TINCR depletion increased tumor xenograft growth in vivo, while TINCR overexpression inhibited it. Together, our study suggests that re-expressing TINCR may suppress invasive outgrowth of CRC through miR-31.
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Affiliation(s)
- Zhong Ren
- Endoscopy Center, Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jingzheng Liu
- Endoscopy Center, Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jian Li
- Endoscopy Center, Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Liqing Yao
- Endoscopy Center, Endoscopy Research Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
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28
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Zaheed O, Samson J, Dean K. A bioinformatics approach to identify novel long, non-coding RNAs in breast cancer cell lines from an existing RNA-sequencing dataset. Noncoding RNA Res 2020; 5:48-59. [PMID: 32206740 PMCID: PMC7078458 DOI: 10.1016/j.ncrna.2020.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/18/2020] [Accepted: 02/18/2020] [Indexed: 01/17/2023] Open
Abstract
Breast cancer research has traditionally centred on genomic alterations, hormone receptor status and changes in cancer-related proteins to provide new avenues for targeted therapies. Due to advances in next generation sequencing technologies, there has been the emergence of long, non-coding RNAs (lncRNAs) as regulators of normal cellular events, with links to various disease states, including breast cancer. Here we describe our bioinformatic analyses of a previously published RNA sequencing (RNA-seq) dataset to identify lncRNAs with altered expression levels in a subset of breast cancer cell lines. Using a previously published RNA-seq dataset of 675 cancer cell lines, a subset of 18 cell lines was selected for our analyses that included 16 breast cancer lines, one ductal carcinoma in situ line and one normal-like breast epithelial cell line. Principal component analysis demonstrated correlation with well-established categorisation methods of breast cancer (i.e. luminal A/B, HER2 enriched and basal-like A/B). Through detailed comparison of differentially expressed lncRNAs in each breast cancer sub-type with normal-like breast epithelial cells, we identified 15 lncRNAs with consistently altered expression, including three uncharacterised lncRNAs. Utilising data from The Cancer Genome Atlas (TCGA) and The Genotype Tissue Expression (GETx) project via Gene Expression Profiling Interactive Analysis (GEPIA2), we assessed clinical relevance of several identified lncRNAs with invasive breast cancer. Lastly, we determined the relative expression level of six lncRNAs across a spectrum of breast cancer cell lines to experimentally confirm the findings of our bioinformatic analyses. Overall, we show that the use of existing RNA-seq datasets, if re-analysed with modern bioinformatic tools, can provide a valuable resource to identify lncRNAs that could have important biological roles in oncogenesis and tumour progression.
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Affiliation(s)
| | | | - Kellie Dean
- School of Biochemistry and Cell Biology, Western Gateway Building, University College Cork, Cork, T12XF62, Ireland
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29
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Promoter Hypomethylation and Increased Expression of the Long Non-coding RNA LINC00152 Support Colorectal Carcinogenesis. Pathol Oncol Res 2020; 26:2209-2223. [PMID: 32307642 PMCID: PMC7471146 DOI: 10.1007/s12253-020-00800-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 02/27/2020] [Indexed: 12/27/2022]
Abstract
Up-regulation of the long non-coding RNA LINC00152 can contribute to cancer development, proliferation and invasion, including colorectal cancer, however, its mechanism of action in colorectal carcinogenesis and progression is only insufficiently understood. In this work we correlated LINC00152 expression with promoter DNA methylation changes in colorectal tissues along the normal-adenoma-carcinoma sequence and studied the effects of LINC00152 silencing on the cell cycle regulation and on the whole transcriptome in colon carcinoma cells using cell and molecular biology techniques. LINC00152 was significantly up-regulated in adenoma and colorectal cancer (p < 0.001) compared to normal samples, which was confirmed by real-time PCR and in situ hybridization. LINC00152 promoter hypomethylation detected in colorectal cancer (p < 0.01) was strongly correlated with increased LINC00152 expression (r=-0.90). Silencing of LINC00152 significantly suppressed cell growth, induced apoptosis and decreased cyclin D1 expression (p < 0.05). Whole transcriptome analysis of LINC00152-silenced cells revealed significant down-regulation of oncogenic and metastasis promoting genes (e.g. YES proto-oncogene 1, PORCN porcupine O-acyltransferase), and up-regulation of tumour suppressor genes (e.g. DKK1 dickkopf WNT signalling pathway inhibitor 1, PERP p53 apoptosis effector) (adjusted p < 0.05). Pathway analysis confirmed the LINC00152-related activation of oncogenic molecular pathways including those driven by PI3K/Akt, Ras, WNT, TP53, Notch and ErbB. Our results suggest that promoter hypomethylation related overexpression of LINC00152 can contribute to the pathogenesis of colorectal cancer by facilitating cell progression through the up-regulation of several oncogenic and metastasis promoting pathway elements.
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30
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Gu Y, Lin X, Kapoor A, Chow MJ, Jiang Y, Zhao K, Tang D. The Oncogenic Potential of the Centromeric Border Protein FAM84B of the 8q24.21 Gene Desert. Genes (Basel) 2020; 11:genes11030312. [PMID: 32183428 PMCID: PMC7140883 DOI: 10.3390/genes11030312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 12/14/2022] Open
Abstract
FAM84B is a risk gene in breast and prostate cancers. Its upregulation is associated with poor prognosis of prostate cancer, breast cancer, and esophageal squamous cell carcinoma. FAM84B facilitates cancer cell proliferation and invasion in vitro, and xenograft growth in vivo. The FAM84B and Myc genes border a 1.2 Mb gene desert at 8q24.21. Co-amplification of both occurs in 20 cancer types. Mice deficient of a 430 Kb fragment within the 1.2 Mb gene desert have downregulated FAM84B and Myc expressions concurrent with reduced breast cancer growth. Intriguingly, Myc works in partnership with other oncogenes, including Ras. FAM84B shares similarities with the H-Ras-like suppressor (HRASLS) family over their typical LRAT (lecithin:retinal acyltransferase) domain. This domain contains a catalytic triad, H23, H35, and C113, which constitutes the phospholipase A1/2 and O-acyltransferase activities of HRASLS1-5. These enzymatic activities underlie their suppression of Ras. FAM84B conserves H23 and H35 but not C113 with both histidine residues residing within a highly conserved motif that FAM84B shares with HRASLS1-5. Deletion of this motif abolishes FAM84B oncogenic activities. These properties suggest a collaboration of FAM84B with Myc, consistent with the role of the gene desert in strengthening Myc functions. Here, we will discuss recent research on FAM84B-derived oncogenic potential.
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Affiliation(s)
- Yan Gu
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Xiaozeng Lin
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Anil Kapoor
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Mathilda Jing Chow
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Yanzhi Jiang
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Kuncheng Zhao
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
| | - Damu Tang
- Urological Cancer Center for Research and Innovation (UCCRI), St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada; (Y.G.); (X.L.); (M.J.C.); (Y.J.); (K.Z.)
- Department of Surgery, McMaster University, Hamilton, ON L8S 4K1, Canada;
- The Research Institute of St Joe’s Hamilton, St Joseph’s Hospital, Hamilton, ON L8N 4A6, Canada
- Correspondence: ; Tel.: +(905)-522-1155 (ext. 35168)
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Transcriptomic Analyses Revealed Systemic Alterations in Gene Expression in Circulation and Tumor Microenvironment of Colorectal Cancer Patients. Cancers (Basel) 2019; 11:cancers11121994. [PMID: 31835892 PMCID: PMC6966620 DOI: 10.3390/cancers11121994] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/03/2019] [Accepted: 12/05/2019] [Indexed: 12/12/2022] Open
Abstract
Colorectal cancer (CRC) is among the leading causes of cancer-related deaths worldwide, underscoring a need for better understanding of the disease and development of novel diagnostic biomarkers and therapeutic interventions. Herein, we performed transcriptome analyses on peripheral blood mononuclear cells (PBMCs), CRC tumor tissue and adjacent normal tissue from 10 CRC patients and PBMCs from 15 healthy controls. Up regulated transcripts from CRC PBMCs were associated with functions related to immune cell trafficking and cellular movement, while downregulated transcripts were enriched in cellular processes related to cell death. Most affected signaling networks were those involved in tumor necrosis factor (TNF) and interleukin signaling. The expression of selected immune-related genes from the RNA-Seq data were further validated using qRT-PCR. Transcriptome analysis of CRC tumors and ingenuity pathway analysis revealed enrichment in several functional categories related to cellular movement, cell growth and proliferation, DNA replication, recombination and repair, while functional categories related to cell death were suppressed. Upstream regulator analysis revealed activation of ERBB2 and FOXM1 networks. Interestingly, there were 18 common upregulated and 36 common downregulated genes when comparing PBMCs and tumor tissue, suggesting transcriptomic changes in the tumor microenvironment could be reflected, in part, in the periphery with potential utilization as disease biomarkers.
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