151
|
Histone Modifications and Non-Coding RNAs: Mutual Epigenetic Regulation and Role in Pathogenesis. Int J Mol Sci 2022; 23:ijms23105801. [PMID: 35628612 PMCID: PMC9146199 DOI: 10.3390/ijms23105801] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 12/07/2022] Open
Abstract
In the last few years, more and more scientists have suggested and confirmed that epigenetic regulators are tightly connected and form a comprehensive network of regulatory pathways and feedback loops. This is particularly interesting for a better understanding of processes that occur in the development and progression of various diseases. Appearing on the preclinical stages of diseases, epigenetic aberrations may be prominent biomarkers. Being dynamic and reversible, epigenetic modifications could become targets for a novel option for therapy. Therefore, in this review, we are focusing on histone modifications and ncRNAs, their mutual regulation, role in cellular processes and potential clinical application.
Collapse
|
152
|
Ren L, Zhang H, Luo M, Gao X, Cui J, Zhang X, Liu S. Heterosis of growth trait regulated by DNA methylation and miRNA in allotriploid fish. Epigenetics Chromatin 2022; 15:19. [PMID: 35597966 PMCID: PMC9123727 DOI: 10.1186/s13072-022-00455-6] [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: 03/15/2022] [Accepted: 05/04/2022] [Indexed: 11/26/2022] Open
Abstract
Background Heterosis of growth traits in allotriploid fish has benefited the production of aquaculture for many years, yet its genetic and molecular basis has remained obscure. Now, an allotriploid complex, including two triploids and their diploid inbred parents, has provided an excellent model for investigating the potential regulatory mechanisms of heterosis. Results Here, we performed a series of analyses on DNA methylation modification and miRNA expression in combination with gene expression in the allotriploid complex. We first established a model of cis- and trans-regulation related to DNA methylation and miRNA in allotriploids. Then, comparative analyses showed that DNA methylation contributed to the emergence of a dosage compensation effect, which reduced gene expression levels in the triploid to the diploid state. We detected 31 genes regulated by DNA methylation in the subgenomes of the allotriploids. Finally, the patterns of coevolution between small RNAs and their homoeologous targets were classified and used to predict the regulation of miRNA expression in the allotriploids. Conclusions Our results uncovered the regulatory network between DNA methylation and miRNAs in allotriploids, which not only helps us understand the regulatory mechanisms of heterosis of growth traits but also benefits the study and application of epigenetics in aquaculture. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-022-00455-6.
Collapse
Affiliation(s)
- Li Ren
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Hong Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Mengxue Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Xin Gao
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Jialin Cui
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Xueyin Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China.,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Sciences, Hunan Normal University, Changsha, Hunan, 410081, People's Republic of China. .,Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, 510642, Guangdong, People's Republic of China.
| |
Collapse
|
153
|
Cho YD, Kim KH, Lee YM, Ku Y, Seol YJ. Dental-derived cells for regenerative medicine: stem cells, cell reprogramming, and transdifferentiation. J Periodontal Implant Sci 2022; 52:437-454. [PMID: 36468465 PMCID: PMC9807848 DOI: 10.5051/jpis.2103760188] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/08/2021] [Accepted: 01/24/2022] [Indexed: 01/07/2023] Open
Abstract
Embryonic stem cells have been a popular research topic in regenerative medicine owing to their pluripotency and applicability. However, due to the difficulty in harvesting them and their low yield efficiency, advanced cell reprogramming technology has been introduced as an alternative. Dental stem cells have entered the spotlight due to their regenerative potential and their ability to be obtained from biological waste generated after dental treatment. Cell reprogramming, a process of reverting mature somatic cells into stem cells, and transdifferentiation, a direct conversion between different cell types without induction of a pluripotent state, have helped overcome the shortcomings of stem cells and raised interest in their regenerative potential. Furthermore, the potential of these cells to return to their original cell types due to their epigenetic memory has reinforced the need to control the epigenetic background for successful management of cellular differentiation. Herein, we discuss all available sources of dental stem cells, the procedures used to obtain these cells, and their ability to differentiate into the desired cells. We also introduce the concepts of cell reprogramming and transdifferentiation in terms of genetics and epigenetics, including DNA methylation, histone modification, and non-coding RNA. Finally, we discuss a novel therapeutic avenue for using dental-derived cells as stem cells, and explain cell reprogramming and transdifferentiation, which are used in regenerative medicine and tissue engineering.
Collapse
Affiliation(s)
- Young-Dan Cho
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea
| | - Kyoung-Hwa Kim
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea
| | - Yong-Moo Lee
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea
| | - Young Ku
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea
| | - Yang-Jo Seol
- Department of Periodontology, School of Dentistry and Dental Research Institute, Seoul National University and Seoul National University Dental Hospital, Seoul, Korea
| |
Collapse
|
154
|
Fu BF, Xu CY. Transfer RNA-Derived Small RNAs: Novel Regulators and Biomarkers of Cancers. Front Oncol 2022; 12:843598. [PMID: 35574338 PMCID: PMC9096126 DOI: 10.3389/fonc.2022.843598] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 04/06/2022] [Indexed: 11/24/2022] Open
Abstract
Transfer RNA-derived small RNAs (tsRNAs) are conventional non-coding RNAs (ncRNAs) with a length between18 and 40 nucleotides (nt) playing a crucial role in treating various human diseases including tumours. Nowadays, with the use of high-throughput sequencing technologies, it has been proven that certain tsRNAs are dysregulated in multiple tumour tissues as well as in the blood serum of cancer patients. Meanwhile, data retrieved from the literature show that tsRNAs are correlated with the regulation of the hallmarks of cancer, modification of tumour microenvironment, and modulation of drug resistance. On the other side, the emerging role of tsRNAs as biomarkers for cancer diagnosis and prognosis is promising. In this review, we focus on the specific characteristics and biological functions of tsRNAs with a focus on their impact on various tumours and discuss the possibility of tsRNAs as novel potential biomarkers for cancer diagnosis and prognosis.
Collapse
Affiliation(s)
- Bi-Fei Fu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| | - Chao-Yang Xu
- Department of Breast and Thyroid Surgery, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua, China
| |
Collapse
|
155
|
New challenges for microRNAs in acute pancreatitis: progress and treatment. J Transl Med 2022; 20:192. [PMID: 35509084 PMCID: PMC9066850 DOI: 10.1186/s12967-022-03338-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/06/2022] [Indexed: 12/17/2022] Open
Abstract
Acute pancreatitis (AP) is a common clinical abdominal emergency, with a high and increasing incidence each year. Severe AP can easily cause systemic inflammatory response syndrome, multiple organ dysfunction and other complications, leading to higher hospitalization rates and mortality. Currently, there is no specific treatment for AP. Thus, we still need to understand the exact AP pathogenesis to effectively cure AP. With the rise of transcriptomics, RNA molecules, such as microRNAs (miRNAs) transcribed from nonprotein-coding regions of biological genomes, have been found to be of great significance in the regulation of gene expression and to be involved in the occurrence and development of many diseases. Increasing evidence has shown that miRNAs, as regulatory RNAs, can regulate pancreatic acinar necrosis and apoptosis and local and systemic inflammation and play an important role in the development and thus potentially the diagnosis and treatment of AP. Therefore, here, the current research on the relationship between miRNAs and AP is reviewed.
Collapse
|
156
|
Li S, Lu C, Li X, Li F, Zhao Y, Xu M, Jia H, Yuan S. LncRNA HOXA10-AS functions as an oncogene by binding miR-6509-5p to upregulate Y-box binding protein 1 in gastric cancer. Bioengineered 2022; 13:11373-11387. [PMID: 35521747 PMCID: PMC9276040 DOI: 10.1080/21655979.2022.2059615] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 12/30/2022] Open
Abstract
Gastric cancer (GC) is one of the serious malignant diseases, accounting for several cases globally. The prevention, discovery and cure of GC depend on its molecular mechanism. In recent decades, it has been increasingly recognized that the long noncoding RNAs (lncRNAs) have been involved in GC progression. Therefore, the present study is aimed at identifying relevant lncRNAs that could act as biomarkers for GC prognosis. LncRNA HOXA10-AS is identified to be highly expressed in GC using the ENCORI database. Kaplan-Meier plot analysis indicated that the survival rate of the patient is associated with the expression of lncRNA HOXA10-AS. Interference of HOXA10-AS inhibited GC cell proliferation, migration, and invasion as well as facilitated GC apoptosis. The targets of HOXA10-AS included miR-6509-5p and Y-box binding protein 1 (YBX1). Specifically, HOXA10-AS downregulated miR-6509-5p in GC. An increase of miR-6509-5p inhibited GC cell growth. Meanwhile, miR-6509-5p interacted with YBX1 in GC. Together, lncRNA HOXA10-AS potentially acted as an oncogene through the lncRNA HOXA10-AS/miR-6509-5p/YBX1 signaling pathway in GC.
Collapse
Affiliation(s)
- Shanshan Li
- Department of Gastroenterology, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, PR China
| | - Chuanhui Lu
- Department of Colorectal Cancer Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, China
- Department of Colorectal Cancer Surgery, The Third Clinical Medical College, Fujian Medical University, Fuzhou 350108, Fujian Province, China
| | - Xinyu Li
- Department of Gastrointestinal Surgery, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou City 362002, Fujian Province, China
| | - Fan Li
- Department of Colorectal Cancer Surgery, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361003, Fujian Province, China
- Department of Colorectal Cancer Surgery, The Third Clinical Medical College, Fujian Medical University, Fuzhou 350108, Fujian Province, China
| | - Yunfeng Zhao
- Department of Cardiovascular Internal Medicine CCU Ward, First Hospital of Qinhuangdao, Qinhuangdao 066000, Hebei Province, China
| | - Meimei Xu
- Department of Gastroenterology, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, PR China
| | - Hongyu Jia
- Department of Gastroenterology, First Hospital of Qinhuangdao, Qinhuangdao, Hebei, PR China
| | - Sibo Yuan
- Department of Gastrointestinal Surgery and Xiamen City Key Laboratory of Gastrointestinal Cancer, Zhongshan Hospital, Xiamen University, Xiamen 361000, Fujian Province, China
| |
Collapse
|
157
|
Shen Q, Xie B, Galaj E, Yu H, Li X, Lu Y, Zhang M, Wen D, Ma C. CircTmeff-1 in the nucleus accumbens regulates the reconsolidation of cocaine-associated memory. Brain Res Bull 2022; 185:64-73. [PMID: 35489671 DOI: 10.1016/j.brainresbull.2022.04.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/22/2022] [Accepted: 04/23/2022] [Indexed: 12/27/2022]
Abstract
Reconsolidation of drug memories is the process of restoring unstable memories after unconditioned (UCS; e.g., drugs) or conditioned stimulus (CS; e.g., drug-paired contexts), and provides promise for prevention of drug relapse. Circular RNAs (circRNAs) have important effects on the transcription and post-transcriptional regulation of gene expression. However, the role of circRNAs in the reconsolidation of drug memories is unclear. Here, we observed that cocaine-induced memory retrieval significantly increased circTmeff-1 level in the nucleus accumbens (NAc) core but not shell. Importantly, the disrupted expression of circTmeff-1 using virus in the NAc core damaged the reconsolidation of cocaine-associated memories. The knockdown of circTmeff-1 in the NAc shell or without UCS retrieval or 9 h after UCS retrieval had no such effects. Mechanistically, using bioinformatic analysis and loss- or gain- of function assays, we revealed that antagomiR-206 reversed the inhibitory effect of circTmeff-1 knockdown on the expression of brain-derived neurotrophic factor (BDNF) during the reconsolidation of cocaine-associated memories. Taken together, these results demonstrate the role of circTmeff-1 in the reconsolidation of cocaine-associated memory and that circTmeff-1 may function as a decoy for miR-206 to regulate the expression of BDNF.
Collapse
Affiliation(s)
- Qianchao Shen
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Bing Xie
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Ewa Galaj
- Department of Psychological and Brain Sciences, Colgate University, 13 Oak Drive, Hamilton, NY 13346, USA
| | - Hailei Yu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Xiaojie Li
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Yun Lu
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Minglong Zhang
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China
| | - Di Wen
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
| | - Chunling Ma
- College of Forensic Medicine, Hebei Medical University, Hebei Key Laboratory of Forensic Medicine, Collaborative Innovation Center of Forensic Medical Molecular Identification, Shijiazhuang 050017, Hebei, PR China; Research Unit of Digestive Tract Microecosystem Pharmacology and Toxicology, Chinese Academy of Medical Sciences, Shijiazhuang 050017, Hebei, PR China.
| |
Collapse
|
158
|
Yan H, Yan Y, Gao Y, Zhang N, Kumar G, Fang Q, Li Z, Li J, Zhang Y, Song L, Wang J, Sun J, Zhang HT, Ma CG. Transcriptome analysis of fasudil treatment in the APPswe/PSEN1dE9 transgenic (APP/PS1) mice model of Alzheimer's disease. Sci Rep 2022; 12:6625. [PMID: 35459923 PMCID: PMC9033779 DOI: 10.1038/s41598-022-10554-9] [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: 11/24/2021] [Accepted: 03/30/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common cause of progressive dementia. In the present study, we showed hippocampal tissue transcriptome analysis in APPswe/PSEN1dE9 (APP/PS1, AD model) mice treated with fasudil (ADF) and compared with AD mice treated with saline (ADNS) and wild type mice (WT). The competing endogenous RNA (ceRNA) network was constructed and validated the differential expression of mRNA, lncRNA, miRNA, and circRNA. Our study showed differentially expressed mRNAs (DEMs) between WT and ADNS, while enriched in cell growth and death and nervous system pathways. DEMs between ADNS-ADF were enriched in the nervous system, glycosaminoglycan biosynthesis-keratan sulfate (KS) and Quorum sensing pathways. We validated four genes with RT-PCR, whereas enrichment of Acyl-CoA Synthetase Long Chain Family Member 4 (Acsl4, ENSMUST00000112903) in Quorum sensing pathways, and BTG anti-proliferation factor 1 (Btg1, ENSMUST00000038377) in RNA degradation pathways were conducted. Expression of these two genes were higher in ADNS, but were significantly reduced in ADF. Histone H4 transcription factor (Hinfp, ENSMUST00000216508) orchestrate G1/S transition of mitotic cell cycle and co-expressed with mmu-miR-26a-2-3p-mediated ceRNA and mmu-miR-3065-5p-mediated ceRNA; Wnt family member 4 (Wnt4, ENSMUST00000045747) was enriched in mTOR, Hippo and Wnt signaling pathway. Expression of these two genes were significantly lower in ADNS, and fasudil treatment reverse it. The present studies demonstrated four genes: Acsl4, Btg1, Hinfp, Wnt4 could be potential biomarkers of AD and the targets of fasudil treatment. These results will pave a novel direction for future clinic studies for AD and fasudil treatment.
Collapse
Affiliation(s)
- Hailong Yan
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Yuqing Yan
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China. .,The Key Research Laboratory of Benefiting Qi for Acting Blood Circulation, Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong, 030619, China.
| | - Ye Gao
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Nianping Zhang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Gajendra Kumar
- Department of Neuroscience, City University of Hong Kong, Tat Chee Avenue, Kowloon Tong, Hong Kong
| | - Qingli Fang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Ziqing Li
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Jiehui Li
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Yuna Zhang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Lijuan Song
- The Key Research Laboratory of Benefiting Qi for Acting Blood Circulation, Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong, 030619, China
| | - Jiawei Wang
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Jingxian Sun
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China
| | - Han-Ting Zhang
- Department of Pharmacology, Qingdao University School of Pharmacy, Qingdao, 266073, China.
| | - Cun-Gen Ma
- Institute of Brain Science, Shanxi Key Laboratory of Inflammatory Neurodegenerative Diseases, Medical School of Shanxi Datong University, Datong, 037009, China. .,The Key Research Laboratory of Benefiting Qi for Acting Blood Circulation, Research Center of Neurobiology, Shanxi University of Chinese Medicine, Jinzhong, 030619, China.
| |
Collapse
|
159
|
Zhuang SH, Meng CC, Fu JJ, Huang J. Long non-coding RNA ELFN1-AS1-mediated ZBTB16 inhibition augments the progression of gastric cancer by activating the PI3K/AKT axis. Kaohsiung J Med Sci 2022; 38:621-632. [PMID: 35451560 DOI: 10.1002/kjm2.12548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 02/07/2022] [Accepted: 03/07/2022] [Indexed: 12/24/2022] Open
Abstract
Long non-coding RNA ELFN1 antisense RNA 1 (ELFN1-AS1) has been reported as a cancer driver in many human malignancies. This study was conducted to investigate the function of ELFN1-AS1 in gastric cancer (GC) and its mechanism of action. Bioinformatics analysis revealed increased expression of ELFN1-AS1 in GC, and abundant expression of ELFN1-AS1 was observed in the acquired GC cell lines. Knockdown of ELFN1-AS1 in GC cells weakened cell proliferation, invasion, migration, and resistance to apoptosis. ELFN1-AS1 was mainly localized in the nuclei of GC cells. ELFN1-AS1 recruited DNA methyltransferases to the promoter region of ZBTB16 and induced transcriptional repression of ZBTB16 through methylation modification. Furthermore, downregulation of ZBTB16 activated the phosphatidylinositol 3-kinase/protein kinase B (PI3K/AKT) signaling pathway and restored the proliferation and invasiveness of GC cells. In vivo, downregulation of ELFN1-AS1 reduced the growth rate of xenograft tumors in mice. In summary, this study demonstrates that ELFN1-AS1 recruits DNA methyltransferases to the promoter region of ZBTB16 to induce its transcriptional repression, which further augments the development of GC by activating the PI3K/AKT signaling pathway.
Collapse
Affiliation(s)
- Shao-Hua Zhuang
- Department of Gastroenterology, Changzhou No.2 People's Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Chu-Chen Meng
- Department of Endocrinology, Changzhou No.2 People's Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Jin-Jin Fu
- Department of Gastroenterology, Changzhou No.2 People's Hospital Affiliated to Nanjing Medical University, Changzhou, China
| | - Jian Huang
- Department of Gastroenterology, Changzhou No.2 People's Hospital Affiliated to Nanjing Medical University, Changzhou, China
| |
Collapse
|
160
|
Mahabady MK, Mirzaei S, Saebfar H, Gholami MH, Zabolian A, Hushmandi K, Hashemi F, Tajik F, Hashemi M, Kumar AP, Aref AR, Zarrabi A, Khan H, Hamblin MR, Nuri Ertas Y, Samarghandian S. Noncoding RNAs and their therapeutics in paclitaxel chemotherapy: Mechanisms of initiation, progression, and drug sensitivity. J Cell Physiol 2022; 237:2309-2344. [PMID: 35437787 DOI: 10.1002/jcp.30751] [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: 07/10/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 12/16/2022]
Abstract
The identification of agents that can reverse drug resistance in cancer chemotherapy, and enhance the overall efficacy is of great interest. Paclitaxel (PTX) belongs to taxane family that exerts an antitumor effect by stabilizing microtubules and inhibiting cell cycle progression. However, PTX resistance often develops in tumors due to the overexpression of drug transporters and tumor-promoting pathways. Noncoding RNAs (ncRNAs) are modulators of many processes in cancer cells, such as apoptosis, migration, differentiation, and angiogenesis. In the present study, we summarize the effects of ncRNAs on PTX chemotherapy. MicroRNAs (miRNAs) can have opposite effects on PTX resistance (stimulation or inhibition) via influencing YES1, SK2, MRP1, and STAT3. Moreover, miRNAs modulate the growth and migration rates of tumor cells in regulating PTX efficacy. PIWI-interacting RNAs, small interfering RNAs, and short-hairpin RNAs are other members of ncRNAs regulating PTX sensitivity of cancer cells. Long noncoding RNAs (LncRNAs) are similar to miRNAs and can modulate PTX resistance/sensitivity by their influence on miRNAs and drug efflux transport. The cytotoxicity of PTX against tumor cells can also be affected by circular RNAs (circRNAs) and limitation is that oncogenic circRNAs have been emphasized and experiments should also focus on onco-suppressor circRNAs.
Collapse
Affiliation(s)
- Mahmood K Mahabady
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
| | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran
| | - Hamidreza Saebfar
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad H Gholami
- Faculty of Veterinary Medicine, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Amirhossein Zabolian
- Resident of Orthopedics, Department of Orthopedics, School of Medicine, 5th Azar Hospital, Golestan University of Medical Sciences, Golestan, Iran
| | - Kiavash Hushmandi
- Division of Epidemiology, Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Farid Hashemi
- Department of Comparative Biosciences, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Fatemeh Tajik
- Oncopathology Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Alan P Kumar
- NUS Centre for Cancer Research (N2CR), Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Pharmacology, Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Amir R Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.,Xsphera Biosciences Inc, Boston, Massachusetts, USA
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Sariyer, Istanbul, Turkey
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan, Pakistan
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein, South Africa
| | - Yavuz Nuri Ertas
- Department of Biomedical Engineering, Erciyes University, Kayseri, Turkey.,ERNAM-Nanotechnology Research and Application Center, Erciyes University, Kayseri, Turkey
| | - Saeed Samarghandian
- Noncommunicable Diseases Research Center, Neyshabur University of Medical Sciences, Neyshabur, Iran
| |
Collapse
|
161
|
Jia L, Wang J, Luoreng Z, Wang X, Wei D, Yang J, Hu Q, Ma Y. Progress in Expression Pattern and Molecular Regulation Mechanism of LncRNA in Bovine Mastitis. Animals (Basel) 2022; 12:ani12091059. [PMID: 35565486 PMCID: PMC9105470 DOI: 10.3390/ani12091059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/15/2022] [Accepted: 04/16/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary Bovine mastitis is an inflammatory disease of the mammary glands that causes serious harm to cow health and huge economic losses. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate a variety of diseases of humans and animals, especially the immune response and inflammatory disease process. This paper reviews the role of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of lncRNA expression and the molecular regulatory mechanism in bovine mastitis, and looks forward to the research and application prospect of lncRNA in bovine mastitis, intending to provide a reference for scientific researchers to systematically understand this research field. Abstract Bovine mastitis is an inflammatory disease caused by pathogenic microbial infection, trauma, or other factors. Its morbidity is high, and it is difficult to cure, causing great harm to the health of cows and the safety of dairy products. Susceptibility or resistance to mastitis in individual cows is mainly determined by genetic factors, including coding genes and non-coding genes. Long non-coding RNAs (lncRNAs) are a class of endogenous non-coding RNA molecules with a length of more than 200 nucleotides (nt) that have recently been discovered. They can regulate the immune response of humans and animals on three levels (transcription, epigenetic modification, and post-transcription), and are widely involved in the pathological process of inflammatory diseases. Over the past few years, extensive findings revealed basic roles of lncRNAs in inflammation, especially bovine mastitis. This paper reviews the expression pattern and mechanism of long non-coding RNA (lncRNA) in inflammatory diseases, emphasizes on the latest research progress of the lncRNA expression pattern and molecular regulatory mechanism in bovine mastitis, analyzes the molecular regulatory network of differentially expressed lncRNAs, and looks forward to the research and application prospect of lncRNA in bovine mastitis, laying a foundation for molecular breeding and the biological therapy of bovine mastitis.
Collapse
Affiliation(s)
- Li Jia
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jinpeng Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Zhuoma Luoreng
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Xingping Wang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
- Correspondence: (Z.L.); (X.W.)
| | - Dawei Wei
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Jian Yang
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Qichao Hu
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| | - Yun Ma
- School of Agriculture, Ningxia University, Yinchuan 750021, China; (L.J.); (J.W.); (D.W.); (J.Y.); (Q.H.); (Y.M.)
- Key Laboratory of Ruminant Molecular Cell Breeding, Ningxia Hui Autonomous Region, Yinchuan 750021, China
| |
Collapse
|
162
|
Tu K, Lee S, Roy S, Sawant A, Shukla H. Dysregulated Epigenetics of Chordoma: Prognostic Markers and Therapeutic Targets. Curr Cancer Drug Targets 2022; 22:678-690. [PMID: 35440334 DOI: 10.2174/1568009622666220419122716] [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: 01/04/2022] [Revised: 02/08/2022] [Accepted: 02/10/2022] [Indexed: 11/22/2022]
Abstract
Chordoma is a rare, slow-growing sarcoma that is locally aggressive, and typically resistant to conventional chemo- and radiotherapies. Despite its low incidence, chordoma remains a clinical challenge because therapeutic options for chordoma are limited, and little is known about the molecular mechanisms involved in resistance to therapies. Furthermore, there are currently no established predictive or prognostic biomarkers to follow disease progression or treatment. Whole-genome sequencing of chordoma tissues has demonstrated a low-frequency mutation rate compared to other cancers. This has generated interest in the role of epigenetic events in chordoma pathogenesis. In this review, we discuss the current understanding of the epigenetic drivers of chordoma and their potential applications in prognosis and the development of new therapies.
Collapse
Affiliation(s)
- Kevin Tu
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, College Park, MD, USA
| | - Sang Lee
- Department of Orthopedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21287, United States
| | - Sanjit Roy
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA
| | - Amit Sawant
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA
| | - Hem Shukla
- Division of Translational Radiation Sciences, Department of Radiation Oncology, University of Maryland school of Medicine, Baltimore, MD, USA
| |
Collapse
|
163
|
Evolutionary History and Functional Diversification of the JmjC Domain-Containing Histone Demethylase Gene Family in Plants. PLANTS 2022; 11:plants11081041. [PMID: 35448769 PMCID: PMC9029850 DOI: 10.3390/plants11081041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/01/2022] [Accepted: 04/08/2022] [Indexed: 11/23/2022]
Abstract
Histone demethylases containing JumonjiC (JmjC) domains regulate gene transcription and chromatin structure by changing the methylation status of lysine residues and play an important role in plant growth and development. In this study, a total of 332 JmjC family genes were identified from 21 different plant species. The evolutionary analysis results showed that the JmjC gene was detected in each species, that is, the gene has already appeared in algae. The phylogenetic analysis showed that the KDM3/JHDM2 subfamily genes may have appeared when plants transitioned from water to land, but were lost in lycophytes (Selaginella moellendorffii). During the evolutionary process, some subfamily genes may have been lost in individual species. According to the analysis of the conserved domains, all of the plant JmjC genes contained a typical JmjC domain, which was highly conserved during plant evolution. The analysis of cis-acting elements showed that the promoter region of the JmjC gene was rich in phytohormones and biotic and abiotic stress-related elements. The transcriptome data analysis and protein interaction analyses showed that JmjC genes play an important role in plant growth and development. The results clarified the evolutionary history of JmjC family genes in plants and lay the foundation for the analysis of the biological functions of JmjC family genes.
Collapse
|
164
|
Joshi S, Garlapati C, Aneja R. Epigenetic Determinants of Racial Disparity in Breast Cancer: Looking beyond Genetic Alterations. Cancers (Basel) 2022; 14:cancers14081903. [PMID: 35454810 PMCID: PMC9025441 DOI: 10.3390/cancers14081903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary A substantial disparity in breast cancer incidence and mortality exists between African American (AA) and European American (EA) women. However, the basis for these disparities is poorly understood. In this article, we describe that gene–environment interactions mediated through epigenetic modifications may play a significant role in racial disparities in BC incidence and outcomes. Our in silico analyses and an in-depth literature survey suggest that there exists a significant difference in epigenetic patterns between AA and EA women with breast cancer. Herein, we describe the environmental factors that contribute to these epigenetic changes, which may underlie the disparate racial burden in patients with breast cancer. We suggest that AA women with higher basal epigenetic changes, may have higher pre-disposition to cancer onset, and an aggressive disease course. Pre-existing racial differences in epigenetic profiles of breast tissues raises the possibility of examining these profiles for early diagnosis. Abstract Breast cancer (BC) is the most commonly diagnosed cancer in women. Despite advancements in BC screening, prevention, and treatment, BC incidence and mortality remain high among African American (AA) women. Compared with European American (EA) women, AA women tend to be diagnosed with more advanced and aggressive tumors and exhibit worse survival outcomes. Most studies investigating the determinants of racial disparities in BC have focused on genetic factors associated with African ancestry. However, various environmental and social stressors over an individual’s life course can also shape racial stratification in BC. These social and environmental exposures result in long-term changes in gene expression mediated by epigenetic mechanisms. Epigenetics is often portrayed as an intersection of socially patterned stress and genetic expression. The enduring nature of epigenetic changes makes them suitable for studying the effects of different environmental exposures over an individual’s life course on gene expression. The role of differential social and environmental exposures in racial disparities in BC suggests varied epigenetic profiles or signatures associated with specific BC subtypes in AA and EA women. These epigenetic profiles in EA and AA women could be used as biomarkers for early BC diagnosis and disease prognosis and may prove valuable for the development of targeted therapies for BC. This review article discusses the current state of knowledge regarding epigenetic differences between AA and EA women with BC. We also discuss the role of socio-environmental factors, including psychosocial stress, environmental toxicants, and dietary factors, in delineating the different epigenetic profiles in AA and EA patients with BC.
Collapse
Affiliation(s)
- Shriya Joshi
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (C.G.)
| | | | - Ritu Aneja
- Department of Biology, Georgia State University, Atlanta, GA 30303, USA; (S.J.); (C.G.)
- Department of Clinical and Diagnostics Sciences, School of Health Professions, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: or
| |
Collapse
|
165
|
The 90 plus: longevity and COVID-19 survival. Mol Psychiatry 2022; 27:1936-1944. [PMID: 35136227 DOI: 10.1038/s41380-022-01461-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/11/2022] [Accepted: 01/20/2022] [Indexed: 11/08/2022]
Abstract
The world population is getting older and studies aiming to enhance our comprehension of the underlying mechanisms responsible for health span are of utmost interest for longevity and as a measure for health care. In this review, we summarized previous genetic association studies (GWAS) and next-generation sequencing (NGS) of elderly cohorts. We also present the updated hypothesis for the aging process, together with the factors associated with healthy aging. We discuss the relevance of studying older individuals and build databanks to characterize the presence and resistance against late-onset disorders. The identification of about 2 million novel variants in our cohort of more than 1000 elderly Brazilians illustrates the importance of studying highly admixed populations of non-European ancestry. Finally, the ascertainment of nonagenarians and particularly of centenarians who were recovered from COVID-19 or remained asymptomatic opens new avenues of research aiming to enhance our comprehension of biological mechanisms associated with resistance against pathogens.
Collapse
|
166
|
Sun P, Hamblin MH, Yin KJ. Non-coding RNAs in the regulation of blood–brain barrier functions in central nervous system disorders. Fluids Barriers CNS 2022; 19:27. [PMID: 35346266 PMCID: PMC8959280 DOI: 10.1186/s12987-022-00317-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/17/2022] [Indexed: 12/26/2022] Open
Abstract
The blood–brain barrier (BBB) is an essential component of the neurovascular unit that controls the exchanges of various biological substances between the blood and the brain. BBB damage is a common feature of different central nervous systems (CNS) disorders and plays a vital role in the pathogenesis of the diseases. Non-coding RNAs (ncRNAs), such as microRNAs (miRNAs), long non-coding RNA (lncRNAs), and circular RNAs (circRNAs), are important regulatory RNA molecules that are involved in almost all cellular processes in normal development and various diseases, including CNS diseases. Cumulative evidences have demonstrated ncRNA regulation of BBB functions in different CNS diseases. In this review, we have summarized the miRNAs, lncRNAs, and circRNAs that can be served as diagnostic and prognostic biomarkers for BBB injuries, and demonstrated the involvement and underlying mechanisms of ncRNAs in modulating BBB structure and function in various CNS diseases, including ischemic stroke, hemorrhagic stroke, traumatic brain injury (TBI), spinal cord injury (SCI), multiple sclerosis (MS), Alzheimer's disease (AD), vascular cognitive impairment and dementia (VCID), brain tumors, brain infections, diabetes, sepsis-associated encephalopathy (SAE), and others. We have also discussed the pharmaceutical drugs that can regulate BBB functions via ncRNAs-related signaling cascades in CNS disorders, along with the challenges, perspective, and therapeutic potential of ncRNA regulation of BBB functions in CNS diseases.
Collapse
|
167
|
Hanselmann RG, Welter C. Origin of Cancer: Cell work is the Key to Understanding Cancer Initiation and Progression. Front Cell Dev Biol 2022; 10:787995. [PMID: 35300431 PMCID: PMC8921603 DOI: 10.3389/fcell.2022.787995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/31/2022] [Indexed: 11/16/2022] Open
Abstract
The cell is the smallest unit of life. It is a structure that maintains order through self-organization, characterized by a high level of dynamism, which in turn is characterized by work. For this work to take place, a continuous high flow of energy is necessary. However, a focused view of the physical relationship between energy and work is inadequate for describing complex biological/medical mechanisms or systems. In this review, we try to make a connection between the fundamental laws of physics and the mechanisms and functions of biology, which are characterized by self-organization. Many different physical work processes (work) in human cells are called cell work and can be grouped into five forms: synthetic, mechanical, electrical, concentration, and heat generation cell work. In addition to the flow of energy, these cell functions are based on fundamental processes of self-organization that we summarize with the term Entirety of molecular interaction (EoMI). This illustrates that cell work is caused by numerous molecular reactions, flow equilibrium, and mechanisms. Their number and interactions are so complex that they elude our perception in their entirety. To be able to describe cell functions in a biological/medical context, the parameters influencing cell work should be summarized in overarching influencing variables. These are “biological” energy, information, matter, and cell mechanics (EMIM). This makes it possible to describe and characterize the cell work involved in cell systems (e.g., respiratory chain, signal transmission, cell structure, or inheritance processes) and to demonstrate changes. If cell work and the different influencing parameters (EMIM influencing variables) are taken as the central property of the cell, specific gene mutations cannot be regarded as the sole cause for the initiation and progression of cancer. This reductionistic monocausal view does not do justice to the dynamic and highly complex system of a cell. Therefore, we postulate that each of the EMIM influencing variables described above is capable of changing the cell work and thus the order of a cell in such a way that it can develop into a cancer cell.
Collapse
|
168
|
Zou X, Sun P, Xie H, Fan L, Ding K, Wang J, Li Y. Knockdown of long noncoding RNA HUMT inhibits the proliferation and metastasis by regulating miR-455-5p/LRP4 axis in hepatocellular carcinoma. Bioengineered 2022; 13:8051-8063. [PMID: 35293286 PMCID: PMC9162019 DOI: 10.1080/21655979.2022.2051841] [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] [Indexed: 12/02/2022] Open
Abstract
The present study aimed at investigating the effects and mechanism of long noncoding RNA highly upregulated in metastatic triple-negative breast cancer lymph node (lncRNA HUMT) in hepatocellular carcinoma (HCC). Quantitative real-time polymerase chain reaction was used to assess the expression of HUMT, microRNA (miR)-455-5p, and low-density lipoprotein receptor-related protein 4 (LRP4) in HCC tissues. Colony forming and 5-ethynyl-2′-deoxyuridine assays were performed to assess cell proliferation. Transwell assay was performed to measure cell migration and invasion. Cell cycle distribution was assessed using flow cytometry. The protein expression of LRP4, proliferating cell nuclear antigen (PCNA), matrix metallopeptidase 2 (MMP-2), and MMP-9 was detected using western blot. Luciferase reporter assay and RNA immunoprecipitation assay was used to confirm the target association between miR-455-5p and HUMT or LRP4. In our study, the level of HUMT was enhanced in HCC tissues and cells. Cell proliferation, invasion, and migration in HCC cells were repressed by knockdown of HUMT, and knockdown of HUMT arrested cells in G1 phase and decreased the levels of PCNA, MMP-2, and MMP-9. MiR-455-5p was a target of HUMT. Lowexpression of miR-455-5p reversed the inhibitive influence on HCC cells induced by of HUMT silencing. LRP4 was a target of miR-455-5p and was negatively regulated by miR-455-5p. In addition, LRP4 expression was positively modified by HUMT, and LRP4 inhibited the inhibitory effects on HCC cells induced by HUMT silencing. In conclusion, HCC cell proliferation, invasion, and migration were restrained by knockdown of HUMT, which was related to the miR-455-5p/LRP4 axis.
Collapse
Affiliation(s)
- Xianzhi Zou
- Department of Medical Interventional Oncology, Yantai Qishan Hospital, Yantai, Shandong, China
| | - Peng Sun
- Department of Medical Gastroenterology, Yantai Qishan Hospital, Yantai, Shandong, China
| | - Hui Xie
- Department of Internal Medicine, Yantai Qishan Hospital, Yantai, Shandong, China
| | - Lu Fan
- Department of Liver Diseases, Yantai Qishan Hospital, Yantai, Shandong, China
| | - Kun Ding
- Department of Internal Medicine, Yantai Qishan Hospital, Yantai, Shandong, China
| | - Jiyang Wang
- Department of Physical Examination Center, The Second Affiliated Hospital of Shandong University of Chinese Medicine, Jinan, Shandong, China
| | - Yang Li
- General Medical Department, Shanxi Bethune Hospital, Shanxi Academy of Medical Sciences, Tongji Shanxi Hospital, Third Hospital of Shanxi Medical University, Taiyuan, Shanxi, China.,Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| |
Collapse
|
169
|
Zuccarello D, Sorrentino U, Brasson V, Marin L, Piccolo C, Capalbo A, Andrisani A, Cassina M. Epigenetics of pregnancy: looking beyond the DNA code. J Assist Reprod Genet 2022; 39:801-816. [PMID: 35301622 PMCID: PMC9050975 DOI: 10.1007/s10815-022-02451-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/01/2022] [Indexed: 12/19/2022] Open
Abstract
Epigenetics is the branch of genetics that studies the different mechanisms that influence gene expression without direct modification of the DNA sequence. An ever-increasing amount of evidence suggests that such regulatory processes may play a pivotal role both in the initiation of pregnancy and in the later processes of embryonic and fetal development, thus determining long-term effects even in adult life. In this narrative review, we summarize the current knowledge on the role of epigenetics in pregnancy, from its most studied and well-known mechanisms to the new frontiers of epigenetic regulation, such as the role of ncRNAs and the effects of the gestational environment on fetal brain development. Epigenetic mechanisms in pregnancy are a dynamic phenomenon that responds both to maternal-fetal and environmental factors, which can influence and modify the embryo-fetal development during the various gestational phases. Therefore, we also recapitulate the effects of the most notable environmental factors that can affect pregnancy and prenatal development, such as maternal nutrition, stress hormones, microbiome, and teratogens, focusing on their ability to cause epigenetic modifications in the gestational environment and ultimately in the fetus. Despite the promising advancements in the knowledge of epigenetics in pregnancy, more experience and data on this topic are still needed. A better understanding of epigenetic regulation in pregnancy could in fact prove valuable towards a better management of both physiological pregnancies and assisted reproduction treatments, other than allowing to better comprehend the origin of multifactorial pathological conditions such as neurodevelopmental disorders.
Collapse
Affiliation(s)
- Daniela Zuccarello
- Clinical Genetics Unit, Department of Women's and Children's Health, University Hospital of Padova, Padua, Italy.
| | - Ugo Sorrentino
- Clinical Genetics Unit, Department of Women's and Children's Health, University Hospital of Padova, Padua, Italy
| | - Valeria Brasson
- Clinical Genetics Unit, Department of Women's and Children's Health, University Hospital of Padova, Padua, Italy
| | - Loris Marin
- Gynaecological Clinic, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Chiara Piccolo
- Clinical Genetics Unit, Department of Women's and Children's Health, University Hospital of Padova, Padua, Italy
| | | | - Alessandra Andrisani
- Gynaecological Clinic, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Matteo Cassina
- Clinical Genetics Unit, Department of Women's and Children's Health, University Hospital of Padova, Padua, Italy
| |
Collapse
|
170
|
Salehi S, Afzali S, Shahi A, Amirzargar AA, Mansoori Y. Potential Roles of Long Noncoding RNAs as Therapeutic Targets in Organ Transplantation. Front Immunol 2022; 13:835746. [PMID: 35359941 PMCID: PMC8962195 DOI: 10.3389/fimmu.2022.835746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/18/2022] [Indexed: 11/13/2022] Open
Abstract
Organ transplantation is the most preferred treatment option for end-stage organ diseases; however, allograft rejection is the major hurdle in successful long-term transplant survival. In spite of developing better HLA matching and more effective immunosuppressive regimen, one-year graft survival has been increased by nearly 90% and the incidence of acute rejection by one-year post-transplantation has been decreased by 12.2% in the last decades, chronic allograft rejection has remained as one of the major obstacles to the long-lasting survival of the transplanted allograft. Therefore, seemingly preventing the allograft rejection and inducing immunological tolerance against transplanted allografts is one of the primary goals in transplantation research to enable long-lasting graft survival. Various mechanisms such as long noncoding RNAs (lncRNAs) have been proposed that induce immune tolerance by modulating the gene expression and regulating innate and adaptive immune responses during transplantation. Besides, because of involvement in regulating epigenetic, transcriptional, and post-translational mechanisms, lncRNAs could affect allograft status. Therefore, these molecules could be considered as the potential targets for prediction, prognosis, diagnosis, and treatment of graft rejection. It is suggested that the noninvasive predictive biomarkers hold promise to overcome the current limitations of conventional tissue biopsy in the diagnosis of rejection. Hence, this review aims to provide a comprehensive overview of lncRNAs and their function to facilitate diagnosis, prognosis, and prediction of the risk of graft rejection, and the suggestive therapeutic choices after transplantation.
Collapse
Affiliation(s)
- Saeedeh Salehi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shima Afzali
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Shahi
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Ali Akbar Amirzargar
- Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| |
Collapse
|
171
|
Biochemical Characterization and Molecular Determination of Estrogen Receptor-α (ESR1 PvuII-rs2234693 T>C) and MiRNA-146a (rs2910164 C>G) Polymorphic Gene Variations and Their Association with the Risk of Polycystic Ovary Syndrome. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19053114. [PMID: 35270805 PMCID: PMC8910123 DOI: 10.3390/ijerph19053114] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/21/2022] [Accepted: 03/02/2022] [Indexed: 12/15/2022]
Abstract
Polycystic ovary syndrome (PCOS) is regarded as one of the most frequently encountered endocrine disorders and affects millions of young women worldwide, resulting in an array of complex metabolic alterations and reproductive failure. PCOS is a risk factor for diabetes mellitus, obstructive sleep apnea, obesity and depression in patients. Estrogen receptors (ESRs) are significant candidates in endocrine function and ovarian response in women. Moreover, microRNAs and long non-coding RNAs are emerging as principal mediators of gene expression and epigenetic pathways in various disease states. This study has characterized the clinical parameters in PCOS patients with comprehensive biochemical profiling compared to healthy controls and further examined the influence of allelic variations for estrogen receptor-α (ESR1 PvuII-rs2234693 T>C) and miRNA-146a (rs2910164 C>G) gene polymorphism on the risk of and susceptibility to PCOS. In this case-control study, we have used amplification refractory mutation specific (ARMS)-PCR to detect and determine the presence of these polymorphic variants in the study subjects. Our results demonstrated that most of the biochemical markers, which were analyzed in the study, show statistically significant alterations in PCOS patients, including fasting glucose, free insulin, HOMA-IR, LDL, HDL, cholesterol and hormones such as FSH, LH, testosterone and progesterone, which correlate with the established biochemical alterations in the disorder. Further, it is reported that for estrogen receptor-α (ESR1 PvuII-rs2234693 T>C), the frequency of the T allele (fT) was significantly higher among patients (0.64 vs. 0.44) compared to controls, while the frequency of the C allele (fC) was lower in patients (0.36 vs. 0.56) compared to controls. However, it was found that there was no association of an increased risk of PCOS with the ESR1 PvuII-rs2234693 C>T gene polymorphism. On the contrary, the study found strong association of miRNA-146a (rs2910164 C>G) gene polymorphism with an enhanced risk of PCOS. The frequency of the C allele (fC) was significantly higher among patients (0.52 vs. 0.36) compared to controls. The frequency of the G allele (fG) was found to be lower in patients (0.48 vs. 0.64) compared to controls. The codominant, dominant and recessive models display a statistically significant association of polymorphic variations with PCOS. Moreover, the G allele was associated strongly with PCOS susceptibility with an OR = 1.92 (95%) CI = (1.300−2.859), RR = 1.38 (1.130−1.691) p-value < 0.001.
Collapse
|
172
|
Exosomal non-coding RNAs: Emerging roles in bilateral communication between cancer cells and macrophages. Mol Ther 2022; 30:1036-1053. [PMID: 34864204 PMCID: PMC8899606 DOI: 10.1016/j.ymthe.2021.12.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/28/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
The tumor microenvironment (TME) is a dynamic network of cellular organization that comprises diverse cell types and significantly contributes to cancer development. As pivotal immune stromal cells in the TME, macrophages are extensively heterogeneous and exert both antitumor and protumor functions. Exosomes are nanosized extracellular membranous vesicles with diameters between 30 and 150 nm. By transferring multiple bioactive substances such as proteins, lipids, and nucleic acids, exosomes play an important role in the communication between cells. Recently, growing evidence has demonstrated that non-coding RNAs (ncRNAs) are enriched in exosomes and that exosomal ncRNAs are involved in the crosstalk between cancer cells and macrophages. Furthermore, circulating exosomal ncRNAs can be detected in biofluids, serving as promising noninvasive biomarkers for the early diagnosis and prognostic prediction of cancer. Exosome-based therapies are emerging as potent strategies that can be utilized to alleviate tumor progression. Herein, the present knowledge of exosomal ncRNAs and their vital roles in regulating the interplay between cancer cells and macrophages, as well as their clinical applications are summarized.
Collapse
|
173
|
Sirtuins are crucial regulators of T cell metabolism and functions. Exp Mol Med 2022; 54:207-215. [PMID: 35296782 PMCID: PMC8979958 DOI: 10.1038/s12276-022-00739-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 12/23/2021] [Indexed: 01/01/2023] Open
Abstract
It is well known that metabolism underlies T cell differentiation and functions. The pathways regulating T cell metabolism and function are interconnected, and changes in T cell metabolic activity directly impact the effector functions and fate of T cells. Thus, understanding how metabolic pathways influence immune responses and ultimately affect disease progression is paramount. Epigenetic and posttranslational modification mechanisms have been found to control immune responses and metabolic reprogramming. Sirtuins are NAD+-dependent histone deacetylases that play key roles during cellular responses to a variety of stresses and have recently been reported to have potential roles in immune responses. Therefore, sirtuins are of significant interest as therapeutic targets to treat immune-related diseases and enhance antitumor immunity. This review aims to illustrate the potential roles of sirtuins in different subtypes of T cells during the adaptive immune response. Sirtuins, enzymes that regulate how cells respond to stress, regulate T cell metabolism and functions, and therefore blocking or boosting sirtuins influences immune responses. As part of the immune system, some types of T cells attack specific targets; others keep the immune response in check. Imene Hamaidi and Sungjune Kim at H. Lee Moffitt Cancer Center, Tampa, USA, have reviewed how sirtuins affect different subsets of T cells to either promote or suppress immune responses. Boosting sirtuins that increase the function of inflammation-suppressing T cells can improve outcomes for transplant recipients or help treat autoimmune diseases. Conversely, stimulating immune-activating sirtuins can help re-energize exhausted antitumor T cells. Understanding the complex web of sirtuin–T cell interactions may help in developing therapeutic strategies for improving transplant outcomes, and for treating autoimmune diseases and cancer.
Collapse
|
174
|
Dhawan P, Vasishta S, Balakrishnan A, Joshi MB. Mechanistic insights into glucose induced vascular epigenetic reprogramming in type 2 diabetes. Life Sci 2022; 298:120490. [DOI: 10.1016/j.lfs.2022.120490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/22/2022] [Accepted: 03/16/2022] [Indexed: 12/13/2022]
|
175
|
Kitazawa S, Ohno T, Haraguchi R, Kitazawa R. Histochemistry, Cytochemistry and Epigenetics. Acta Histochem Cytochem 2022; 55:1-7. [PMID: 35444348 PMCID: PMC8913277 DOI: 10.1267/ahc.21-00095] [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: 12/05/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022] Open
Abstract
Over the past few decades, many researchers have individually identified tumor-related genes, and have accumulated information on their basic research in a database. With the development of technology that can comprehensively test the expression status within a short time, oncogene panel testing has become attainable. On the other hand, changes in gene expression that do not depend on changes in base sequences, that is, epigenetics, or more comprehensively, epigenomes, are also highly involved in the development and progression of disease. Oncogene panel tests tend to focus on DNA base mutations such as point mutations, deletions, duplications, and chimera formation. Elucidation leads to correct interpretation of diseases and treatment choices, and we are in an era where integrated understanding of the genome and epigenome is indispensable. In this review, we make every effort to cover a wide range of knowledge, including data on histone protein modification, non-coding (nc)RNA and DNA methylation, and recent application trials for demonstrating epigenetic alterations in histologic and cytologic specimens. We hope this review will help marshal the knowledge accumulated by researchers involved in genomic and epigenomic studies.
Collapse
Affiliation(s)
- Sohei Kitazawa
- Department of Molecular Pathology, Ehime University Graduate School of Medicine
| | - Teruyuki Ohno
- Division of Diagnostic Pathology, Ehime University Hospital
| | - Ryuma Haraguchi
- Department of Molecular Pathology, Ehime University Graduate School of Medicine
| | - Riko Kitazawa
- Division of Diagnostic Pathology, Ehime University Hospital
| |
Collapse
|
176
|
Xu F, Hu QF, Li J, Shi CJ, Luo JW, Tian WC, Pan LW. SOX4-activated lncRNA MCM3AP-AS1 aggravates osteoarthritis progression by modulating miR-149-5p/Notch1 signaling. Cytokine 2022; 152:155805. [PMID: 35202986 DOI: 10.1016/j.cyto.2022.155805] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/04/2022] [Accepted: 01/09/2022] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To clarify the expression and underlying network of long non-coding RNA (lncRNA) MCM3AP-AS1 in osteoarthritis (OA). METHODS Human articular cartilage samples, OA model rats and IL-1β-treated C28/I2 cells were used in this study. The expression changes of genes and proteins were assessed by real-time quantitative PCR (qRT-PCR) and western blot. Cell viability, apoptosis, autophagy and extracellular matrix (ECM) degradation were assessed by Cell Counting Kit-8 (CCK-8), immunohistochemistry (IHC), flow cytometry, immunofluorescence and western blot assays, respectively. Molecule interactions were validated by dual luciferase and Chromatin immunoprecipitation (ChIP) assays. H&E staining was used to detect the pathological changes of cartilage. RESULTS MCM3AP-AS1 was upregulated in OA patients and IL-1β-induced chondrocytes. Knockdown of MCM3AP-AS1 enhanced autophagy, while alleviated ECM degradation and cartilage injury. Mechanistically, overexpression of SOX4 boosted the transcription of MCM3AP-AS1. Moreover, MCM3AP-AS1 functioned as a molecular sponge or epigenetic regulator of miR-149-5p to facilitate Notch1 expression. Functional rescue experiments showed that either inhibition of miR-149-5p nor ectopic expression of Notch1 dramatically weakened the biological impacts of MCM3AP-AS1 silencing. CONCLUSION These finding demonstrated that SOX4-activated MCM3AP-AS1 aggravated OA progression by modulating autophagy and ECM degradation via targeting miR-149-5p/Notch1 axis. These data supported that inhibition of MCM3AP-AS1 might be a potential treatment strategy of OA.
Collapse
Affiliation(s)
- Fei Xu
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei Province, People's Republic of China.
| | - Qun-Fang Hu
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei Province, People's Republic of China
| | - Jia Li
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei Province, People's Republic of China
| | - Chang-Jiang Shi
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei Province, People's Republic of China
| | - Jin-Wei Luo
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei Province, People's Republic of China
| | - Wei-Chao Tian
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei Province, People's Republic of China
| | - Li-Wei Pan
- Department of Orthopedics, Affiliated Hospital of Chengde Medical College, Chengde 067000, Hebei Province, People's Republic of China
| |
Collapse
|
177
|
Nilsson EE, Ben Maamar M, Skinner MK. Role of epigenetic transgenerational inheritance in generational toxicology. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac001. [PMID: 35186326 PMCID: PMC8848501 DOI: 10.1093/eep/dvac001] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/04/2021] [Accepted: 02/03/2022] [Indexed: 05/27/2023]
Abstract
Many environmental toxicants have been shown to be associated with the transgenerational inheritance of increased disease susceptibility. This review describes the generational toxicity of some of these chemicals and their role in the induction of epigenetic transgenerational inheritance of disease. Epigenetic factors include DNA methylation, histone modifications, retention of histones in sperm, changes to chromatin structure, and expression of non-coding RNAs. For toxicant-induced epigenetic transgenerational inheritance to occur, exposure to a toxicant must result in epigenetic changes to germ cells (sperm or eggs) since it is the germ cells that carry molecular information to subsequent generations. In addition, the epigenetic changes induced in transgenerational generation animals must cause alterations in gene expression in these animals' somatic cells. In some cases of generational toxicology, negligible changes are seen in the directly exposed generations, but increased disease rates are seen in transgenerational descendants. Governmental policies regulating toxicant exposure should take generational effects into account. A new approach that takes into consideration generational toxicity will be needed to protect our future populations.
Collapse
Affiliation(s)
- Eric E Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA
| | - Michael K Skinner
- **Correspondence address. Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA 99164-4236, USA. Tel: +509-335-1524; E-mail:
| |
Collapse
|
178
|
Han X, Zhang S. Role of Long Non-Coding RNA LINC00641 in Cancer. Front Oncol 2022; 11:829137. [PMID: 35155216 PMCID: PMC8828736 DOI: 10.3389/fonc.2021.829137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding RNAs with more than 200 nucleic acids in length. When lncRNAs are located in the nucleus, they regulate chromosome structure, participate in chromatin remodeling, and act as transcription regulators. When lncRNAs are exported to the cytoplasm, they regulate mRNA stability, regulate translation, and interfere with post-translational modification. In recent years, more and more evidences have shown that lncRNA can regulate the biological processes of tumor proliferation, apoptosis, invasion and metastasis, and can participate in a variety of tumor signaling pathways. Long-gene non-protein coding RNA641 (LINC00641), located on human chromosome 14q11.2, is differentially expressed in a variety of tumors and is related to overall survival and prognosis, etc. Interfering the expression of LINC00641 can lead to changes in tumor cell proliferation, invasion, metastasis, apoptosis and other biological behaviors. Therefore, LINC00641 is a promising new biomarker and potential clinical therapeutic target. In this review, the biological functions, related mechanisms and clinical significance of LINC00641 in many human cancers are described in detail.
Collapse
Affiliation(s)
- Xue Han
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shitai Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| |
Collapse
|
179
|
Cheng M, Zhan X, Xu Y, Wang S, Zhang H, Fang L, Jin H, Chen W. DNA methylation of RNA-binding protein for multiple splicing 2 functions as diagnosis biomarker in gastric cancer pathogenesis and its potential clinical significance. Bioengineered 2022; 13:4347-4360. [PMID: 35137653 PMCID: PMC8973754 DOI: 10.1080/21655979.2022.2032965] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Higher methylation levels of RNA-binding protein for multiple splicing 2 (RBPMS2) was reported to be related with unfavorable outcome in gastric cancer (GC). However, molecular function and diagnostic significance of DNA methylation of RBPMS2 remains indistinct. Here we aimed to whether DNA methylation of RBPMS2 acts as a diagnosis biomarker in GC pathogenesis and its potential clinical significance. Western blot and immunochemistry assays were carried out to explore the level of RBPMS2. GC malignancy behaviors were determined by cell counting kit-8, Transwell, flow cytometry analysis and terminal-deoxynucleoitidyl transferase mediated nick end labeling staining. The inflammatory cell infiltration in xenograft model was observed by hematoxylin and eosin staining. CpG Islands was predicted by MethPrimer and the DNA methylation of RBPMS2 was evaluated by methylation-specific polymerase chain reaction. The results showed that RBPMS2 was downregulated in GC specimens. Poor survival rates were associated with low RBPMS2 expression. Overexpression of RBPMS2 inhibited GC growth while facilitated apoptosis in GC cells. In addition, level of DNA methylation of RBPMS2 in GC tissues was increased and DNA methylation of RBPMS2 was strongly associated with tumor invasion, Borrmann classification and TNM stage. We also observed that DNA methylation inhibitors counteracted the role of RBPMS2 in restraining GC development and tumorigenesis. To sum, our data demonstrated that DNA methylation of RBPMS2 was responsible for its downregulation in GC and promoted tumor progression, indicating DNA methylation of RBPMS2 might serve as a valuable potential parameter in GC pathogenesis.
Collapse
Affiliation(s)
- Ming Cheng
- Department of Gastroenterology, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, Zhejiang, China
| | - Xiaoan Zhan
- Department of Gastrointestinal Surgery, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, Zhejiang, China
| | - Yi Xu
- Department of Gastroenterology, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, Zhejiang, China
| | - Saishan Wang
- Department of Gastroenterology, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, Zhejiang, China
| | - Hongcheng Zhang
- Department of Gastroenterology, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, Zhejiang, China
| | - Limin Fang
- Department of Gastroenterology, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, Zhejiang, China
| | - Hao Jin
- Department of Gastroenterology, Zhejiang Jinhua Guangfu Tumor Hospital, Jinhua, Zhejiang, China
| | - Wei Chen
- Department of Cardiology, Jinhua Fifth Hospital, Jinhua, Zhejiang, China
| |
Collapse
|
180
|
Huang Y, Guo X, Zhang J, Li J, Xu M, Wang Q, Liu Z, Ma Y, Qi Y, Ruan Q. Human cytomegalovirus RNA2.7 inhibits RNA polymerase II (Pol II) Serine-2 phosphorylation by reducing the interaction between Pol II and phosphorylated cyclin-dependent kinase 9 (pCDK9). Virol Sin 2022; 37:358-369. [PMID: 35537980 PMCID: PMC9243627 DOI: 10.1016/j.virs.2022.02.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Human cytomegalovirus (HCMV) is a ubiquitous pathogen belongs to betaherpesvirus subfamily. RNA2.7 is a highly conserved long non-coding RNA accounting for more than 20% of total viral transcripts. In our study, functions of HCMV RNA2.7 were investigated by comparison of host cellular transcriptomes between cells infected with HCMV clinical strain and RNA2.7 deleted mutant. It was demonstrated that RNA polymerase II (Pol II)-dependent host gene transcriptions were significantly activated when RNA2.7 was removed during infection. A 145 nt-in-length motif within RNA2.7 was identified to inhibit the phosphorylation of Pol II Serine-2 (Pol II S2) by reducing the interaction between Pol II and phosphorylated cyclin-dependent kinase 9 (pCDK9). Due to the loss of Pol II S2 phosphorylation, cellular DNA pre-replication complex (pre-RC) factors, including Cdt1 and Cdc6, were significantly decreased, which prevented more cells from entering into S phase and facilitated viral DNA replication. Our results provide new insights of HCMV RNA2.7 functions in regulation of host cellular transcription. HCMV RNA2.7 inhibits the phosphorylation of Pol II Serine-2. RNA2.7 reduces the interactions between Pol II and pCDK9. RNA2.7 regulates cell cycle by preventing cells from entering into S phase.
Collapse
Affiliation(s)
- Yujing Huang
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Xin Guo
- Department of Pediatrics, The Fourth Affiliated Hospital, China Medical University, Shenyang, 110033, China
| | - Jing Zhang
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Jianming Li
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Mingyi Xu
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Qing Wang
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Zhongyang Liu
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yanping Ma
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Ying Qi
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Qiang Ruan
- Virology Laboratory, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, 110004, China; Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
| |
Collapse
|
181
|
He W, Shi X, Guo Z, Wang H, Kang M, Lv Z. Circ_0019693 promotes osteogenic differentiation of bone marrow mesenchymal stem cell and enhances osteogenesis-coupled angiogenesis via regulating microRNA-942-5p-targeted purkinje cell protein 4 in the development of osteoporosis. Bioengineered 2022; 13:2181-2193. [PMID: 35030971 PMCID: PMC8973649 DOI: 10.1080/21655979.2021.2023982] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Circular RNA (circRNA) is a crucial regulator in multiple human diseases, including osteoporosis (OP). However, the function of numerous circRNAs remains unclear. This study aimed to explore the role and mechanism of circ_0019693 in bone marrow mesenchymal stem cell (BMSC) osteogenic differentiation and osteogenesis-coupled angiogenesis. The expression of circ_0019693, miR-942-5p and purkinje cell protein 4 (PCP4) was measured using quantitative real-time PCR (qPCR) or Western blot. Osteogenic differentiation was monitored according to the protein levels of RUNX family transcription factor 2 (RUNX2), osteopontin (OPN) and osteocalcin (OCN) by Western blot analysis, and the activity of alkaline phosphatase (ALP). Angiogenesis was evaluated by tube formation assay. The targeting relationship between miR-942-5p and circ_0019693 or PCP4 was identified using pull-down, dual-luciferase reporter, and RNA immunoprecipitation assays. Circ_0019693 was downregulated in serum samples and bone tissues from OP patients relative to normal subjects. Circ_0019693 expression was enhanced in the stages of BMSC osteogenic differentiation. Circ_0019693 overexpression enhanced the activity of ALP and the expression of RUNX2, OPN and OCN, and its overexpression also promoted angiogenesis. However, circ_0019693 knockdown played the opposite effects. MiR-942-5p was ensured to be a target of circ_0019693, and miR-942-5p enrichment reversed the effects of circ_0019693. In addition, PCP4 was a target of miR-942-5p, and miR-942-5p inhibitor-promoted BMSC osteogenic differentiation and angiogenesis were partly repressed by PCP4 knockdown. In conclusion, circ_0019693 promotes BMSC osteogenic differentiation osteogenesis-coupled angiogenesis via regulating miR-942-5p-targeted PCP4, thus blocking the development of OP.
Collapse
Affiliation(s)
| | | | - Zhenye Guo
- Department of Orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province, China
| | - Huan Wang
- Department of Orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province, China
| | - Mingming Kang
- Department of Orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province, China
| | - Zhi Lv
- Department of Orthopaedics, The Second Hospital of Shanxi Medical University, Taiyuan City, Shanxi Province, China
| |
Collapse
|
182
|
Varela RB, Cararo JH, Tye SJ, Carvalho AF, Valvassori SS, Fries GR, Quevedo J. Contributions of epigenetic inheritance to the predisposition of major psychiatric disorders: theoretical framework, evidence, and implications. Neurosci Biobehav Rev 2022; 135:104579. [DOI: 10.1016/j.neubiorev.2022.104579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 01/10/2022] [Accepted: 02/11/2022] [Indexed: 02/08/2023]
|
183
|
Diamantopoulos MA, Georgoulia KK, Scorilas A. Identification and expression analysis of ten novel small non-coding RNAs (sncRNAs) in cancer cells using a high-throughput sequencing approach. Gene 2022; 809:146025. [PMID: 34710527 DOI: 10.1016/j.gene.2021.146025] [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: 03/17/2021] [Revised: 09/13/2021] [Accepted: 10/14/2021] [Indexed: 01/18/2023]
Abstract
Non-coding RNAs are characterized as RNA molecules, which lack the capacity to encode protein structures and appear to include a level of internal signals. Moreover, they control various stages of gene expression, thus controlling the cell physiology and development. In this study, we implemented a high-throughput sequencing approach based on the primary semi-conductor technology and computational tools, in order to identity novel small non-coding RNAs. Fourteen human cancer cell lines were cultured, and RNA samples were enriched for small RNAs following semi-conductor next generation sequencing (NGS). Bioinformatics analysis of NGS data revealed the existence of several classes of ncRNAs using the miRDeep* and CPSS 2.0 software. To investigate the existence of the predicted non-coding RNA sequences in cDNA pools of cell lines, a developed qPCR-based assay was implemented. The structure of each novel small ncRNA was visualized, using the RNAfold algorithm. Our results support the existence of twenty (20) putative new small ncRNAs, ten (10) of which have had their expression experimentally validated and presented differential profiles in cancerous and normal cells. A deeper comprehension of the ncRNAs interactive network and its role in cancer can therefore be translated into a wide range of clinical applications. Despite this progress, further scientific research from different perspectives and in different fields is needed, so that the riddle of the human transcriptome can be solved.
Collapse
Affiliation(s)
- Marios A Diamantopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Konstantina K Georgoulia
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Greece
| |
Collapse
|
184
|
Coker SJ, Smith-Díaz CC, Dyson RM, Vissers MCM, Berry MJ. The Epigenetic Role of Vitamin C in Neurodevelopment. Int J Mol Sci 2022; 23:ijms23031208. [PMID: 35163133 PMCID: PMC8836017 DOI: 10.3390/ijms23031208] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 02/07/2023] Open
Abstract
The maternal diet during pregnancy is a key determinant of offspring health. Early studies have linked poor maternal nutrition during gestation with a propensity for the development of chronic conditions in offspring. These conditions include cardiovascular disease, type 2 diabetes and even compromised mental health. While multiple factors may contribute to these outcomes, disturbed epigenetic programming during early development is one potential biological mechanism. The epigenome is programmed primarily in utero, and during this time, the developing fetus is highly susceptible to environmental factors such as nutritional insults. During neurodevelopment, epigenetic programming coordinates the formation of primitive central nervous system structures, neurogenesis, and neuroplasticity. Dysregulated epigenetic programming has been implicated in the aetiology of several neurodevelopmental disorders such as Tatton-Brown-Rahman syndrome. Accordingly, there is great interest in determining how maternal nutrient availability in pregnancy might affect the epigenetic status of offspring, and how such influences may present phenotypically. In recent years, a number of epigenetic enzymes that are active during embryonic development have been found to require vitamin C as a cofactor. These enzymes include the ten-eleven translocation methylcytosine dioxygenases (TETs) and the Jumonji C domain-containing histone lysine demethylases that catalyse the oxidative removal of methyl groups on cytosines and histone lysine residues, respectively. These enzymes are integral to epigenetic regulation and have fundamental roles in cellular differentiation, the maintenance of pluripotency and development. The dependence of these enzymes on vitamin C for optimal catalytic activity illustrates a potentially critical contribution of the nutrient during mammalian development. These insights also highlight a potential risk associated with vitamin C insufficiency during pregnancy. The link between vitamin C insufficiency and development is particularly apparent in the context of neurodevelopment and high vitamin C concentrations in the brain are indicative of important functional requirements in this organ. Accordingly, this review considers the evidence for the potential impact of maternal vitamin C status on neurodevelopmental epigenetics.
Collapse
Affiliation(s)
- Sharna J. Coker
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Carlos C. Smith-Díaz
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
| | - Rebecca M. Dyson
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
| | - Margreet C. M. Vissers
- Centre for Free Radical Research, Department of Pathology and Biomedical Science, University of Otago, Christchurch 8140, New Zealand;
- Correspondence: (M.C.M.V.); (M.J.B.)
| | - Mary J. Berry
- Perinatal & Developmental Physiology Group, Department of Paediatrics & Child Health, University of Otago, Wellington 6242, New Zealand; (S.J.C.); (R.M.D.)
- Correspondence: (M.C.M.V.); (M.J.B.)
| |
Collapse
|
185
|
Mohammed SR, Abdelaleem OO, Ahmed FA, Abdelaziz AA, Hussein HA, Eid HM, Kamal M, Ezzat MA, Ali MA. Expression of lncRNAs NEAT1 and lnc-DC in Serum From Patients With Behçet’s Disease Can Be Used as Predictors of Disease. Front Mol Biosci 2022; 8:797689. [PMID: 35127819 PMCID: PMC8809491 DOI: 10.3389/fmolb.2021.797689] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/06/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Behçet’s disease (BD) is a chronic autoimmune disease. The early diagnosis of BD is very important to avoid serious and/or fatal complications such as eye damage, severe neurological involvement, and large vessel occlusion. New, sensitive biomarkers would aid in rapid diagnosis, the monitoring of disease activity, and the response to treatment. Methods: This study’s aim is to identify two immune system-related BD biomarkers. We measured long non-coding RNAs (lncRNAs) NEAT1 (nuclear-enriched abundant transcript 1), and lnc-DC (lncRNA in dendritic cells) in serum by real-time polymerase chain reaction (RT-PCR) in 52 BD patients and 52 controls. We analyzed the association between NEAT1 and lnc-DC and the clinical parameters of BD. Receiver operating characteristic (ROC) curve analysis was performed to explore the diagnostic performance of the studied genes. Results: Compared to controls, the significant upregulation of NEAT1 {median [interquartile range (IQR)] = 1.68 (0.38–7.7), p < 0.0001} and downregulation of lnc-DC [median (IQR) = 0.2 (0.12–1.39), p = 0.03] were detected in the sera collected from BD patients. Higher serum expression levels of NEAT1 and lnc-DC were significantly associated with the following clinical presentations: cutaneous lesions, vascular manifestations, articular manifestations, neurological manifestations, and higher disease activity score. Also, high NEAT1 levels were significantly associated with a negative pathergy test, while higher lnc-DC was significantly associated with a positive family history. ROC curves showed that NEAT1 and lnc-DC levels in serum could be used as predictors of BD with high specificity and fair sensitivity. NEAT1 had an area under the curve (AUC) of 0.692 (95% CI: 0.591–0.794, p = 0.001), and lnc-DC had an AUC of 0.615 (95% CI: 0.508–0.723, p = 0.043). Conclusion: Serum lncRNAs NEAT1 and lnc-DC are biomarkers for BD.
Collapse
Affiliation(s)
- Shereen Rashad Mohammed
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Omayma O. Abdelaleem
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Fatma A. Ahmed
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Ahmed Ali Abdelaziz
- Departments of Rheumatology and Rehabilitation, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | | | - Hanaa M. Eid
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Marwa Kamal
- Department of Clinical Pharmacy, Faculty of Pharmacy, Fayoum University, Fayoum, Egypt
| | - Mostafa Ahmed Ezzat
- Department of Clinical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Marwa A. Ali
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
- *Correspondence: Marwa A. Ali, ,
| |
Collapse
|
186
|
Ho L, Hossen N, Nguyen T, Vo A, Ahsan F. Epigenetic Mechanisms as Emerging Therapeutic Targets and Microfluidic Chips Application in Pulmonary Arterial Hypertension. Biomedicines 2022; 10:biomedicines10010170. [PMID: 35052850 PMCID: PMC8773438 DOI: 10.3390/biomedicines10010170] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/09/2022] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
Pulmonary arterial hypertension (PAH) is a disease that progress over time and is defined as an increase in pulmonary arterial pressure and pulmonary vascular resistance that frequently leads to right-ventricular (RV) failure and death. Epigenetic modifications comprising DNA methylation, histone remodeling, and noncoding RNAs (ncRNAs) have been established to govern chromatin structure and transcriptional responses in various cell types during disease development. However, dysregulation of these epigenetic mechanisms has not yet been explored in detail in the pathology of pulmonary arterial hypertension and its progression with vascular remodeling and right-heart failure (RHF). Targeting epigenetic regulators including histone methylation, acetylation, or miRNAs offers many possible candidates for drug discovery and will no doubt be a tempting area to explore for PAH therapies. This review focuses on studies in epigenetic mechanisms including the writers, the readers, and the erasers of epigenetic marks and targeting epigenetic regulators or modifiers for treatment of PAH and its complications described as RHF. Data analyses from experimental cell models and animal induced PAH models have demonstrated that significant changes in the expression levels of multiple epigenetics modifiers such as HDMs, HDACs, sirtuins (Sirt1 and Sirt3), and BRD4 correlate strongly with proliferation, apoptosis, inflammation, and fibrosis linked to the pathological vascular remodeling during PAH development. The reversible characteristics of protein methylation and acetylation can be applied for exploring small-molecule modulators such as valproic acid (HDAC inhibitor) or resveratrol (Sirt1 activator) in different preclinical models for treatment of diseases including PAH and RHF. This review also presents to the readers the application of microfluidic devices to study sex differences in PAH pathophysiology, as well as for epigenetic analysis.
Collapse
Affiliation(s)
- Linh Ho
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
- Correspondence: (L.H.); (F.A.); Tel.: +1-916-686-7370 (L.H.); +1-916-686-3529 (F.A.)
| | - Nazir Hossen
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
| | - Trieu Nguyen
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
- East Bay Institute for Research & Education (EBIRE), Mather, CA 95655, USA
| | - Au Vo
- Department of Life Sciences, University of California Los Angeles, Los Angeles, CA 90095, USA;
| | - Fakhrul Ahsan
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA; (N.H.); (T.N.)
- Correspondence: (L.H.); (F.A.); Tel.: +1-916-686-7370 (L.H.); +1-916-686-3529 (F.A.)
| |
Collapse
|
187
|
Long D, Xu Y, Mao G, Xin R, Deng Z, Liao H, Li Z, Yang Z, Yu B, Yang Z, He A, Zhang Z, Kang Y. tRNA-derived fragment TRF365 regulates the metabolism of anterior cruciate ligament cells by targeting IKBKB. Cell Death Dis 2022; 8:19. [PMID: 35013149 PMCID: PMC8748987 DOI: 10.1038/s41420-021-00806-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 12/03/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022]
Abstract
tRNA-derived fragments (tRFs) are new noncoding RNAs, and recent studies have shown that tRNAs and tRFs have important functions in cell metabolism via posttranscriptional regulation of gene expression. However, whether tRFs regulate cellular metabolism of the anterior cruciate ligament (ACL) remains elusive. The aim of this study was to investigate the role and action mechanism of tRFs in ACL cell metabolism. A tRF array was used to determine tRF expression profiles in different human ACL cells, and quantitative real-time polymerase chain reaction and fluorescence in situ hybridisation were used to determine TRF365 expression. ACL cells were transfected with a TRF365 mimic or a TRF365 inhibitor to determine whether TRF365 regulates IKBKB expression. A rescue experiment and dual-luciferase reporter assay were conducted to determine whether the 3′-untranslated region (UTR) of IKBKB has a TRF365-binding site. TRF365 was weakly expressed in osteoarthritis (OA) ACL and interleukin-1β-treated ACL cells. IKBKB was highly expressed in OA ACL and interleukin-1β-treated ACL cells; transfection with the TRF365 mimic suppressed IKBKB expression, whereas transfection with the TRF365 inhibitor had the opposite effect. A dual-luciferase reporter assay showed that TRF365 silenced the expression of IKBKB by binding to its 3′-UTR. Thus, TRF365 regulates the metabolism of ACL cells by targeting IKBKB. In summary, TRF365 may provide a new direction for the study of ACL degeneration and on the pathophysiological process of OA.
Collapse
Affiliation(s)
- Dianbo Long
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Yiyang Xu
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Department of Orthopedics, Shengli Clinical Medical College, Fujian Provincial Hospital, Fujian Medical University, Fuzhou, Fujian, 350000, China
| | - Guping Mao
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Ruobing Xin
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zengfa Deng
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Hongyi Liao
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhiwen Li
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhi Yang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Baoxi Yu
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Zhijian Yang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China
| | - Aishan He
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Ziji Zhang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| | - Yan Kang
- Department of Joint Surgery, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China. .,Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, the First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510080, China.
| |
Collapse
|
188
|
Hu H, Liu S, Chu A, Chen J, Xing C, Jing J. Comprehensive analysis of ceRNA network of ERCC4 in colorectal cancer. PeerJ 2022; 9:e12647. [PMID: 34993023 PMCID: PMC8679902 DOI: 10.7717/peerj.12647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/26/2021] [Indexed: 12/12/2022] Open
Abstract
Objective ERCC4 is one of the most significant molecules of Nucleotide Excision Repair (NER), which has been researched due to its high expression in colorectal cancer (CRC). This study aimed to find out the ceRNA (competitive endogenous RNA) network of ERCC4 in CRC. Methods and Materials Pan cancer mRNA expression of ERCC4 was evaluated using TCGA database. The protein expression of ERCC4 was evaluated based on the Human Protein Atlas (HPA). We screened DElncRNAs and DEmiRNAs in two groups of ERCC4high and ERCC4low expression in CRC. Then a lncRNA-miRNA-ERCC4 regulatory network was constructed based on DElncRNAs and DEmiRNAs using Starbase database and visualized by Cytoscape software. Kaplan-Meier analysis was performed to evaluate the prognostic value of the ceRNA network. Further, RT-PCR was performed to validate the expression of the representative molecules in the ceRNA network in CRC and normal tissues. The relationship between drug sensitivity and these molecules were also evaluated using RNAactDrug database. Results ERCC4 was overexpressed in a variety of tumors at mRNA levels, including CRC. High expression of ERCC4 was also observed on protein level in CRC. A total of 1,885 DElncRNAs and 68 DEmiRNAs were identified from CRC samples in ERCC4high and ERCC4low expression groups. Predicted by the Starbase database, we got interacting miRNAs and lncRNAs of ERCC4 from the DEmiRNAs and DElncRNAs, and a lncRNA-miRNA-ERCC4 regulatory network was constructed. Kaplan-Meier survival curves results showed that miR-200c-3p (hazard ratio [HR] = 0.62, P = 0.032), MALAT1 (HR = 1.54, P = 0.016), and AC005520.2 (hazard ratio [HR] = 1.75, P = 0.002) were significantly associated with the prognosis of CRC. After validation by RT-PCR, we found that ERCC4 and MALAT1 were up-regulated in CRC compared with normal tissues, while miR-200c-3p was down-regulated. A strong negative correlation was observed between MALAT1 and miR-200c-3p. Drug sensitivity analysis showed that ERCC4, miR-200c and MALAT1 were all associated with Cisplatin. Conclusion We constructed a ceRNA network of ERCC4 in CRC, of which the MALAT1-miR-200c-3p-ERCC4 axis may be involved in the development, prognosis and chemotherapy sensitivity of CRC. These findings might provide novel clues and insights on the molecular mechanisms of ERCC4 and NER pathway in CRC.
Collapse
Affiliation(s)
- Huixin Hu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Songyi Liu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Aining Chu
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Jing Chen
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| | - Chengzhong Xing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China.,Department of Anorectal Surgery in Liaoning Province, the First Hospital of China Medical of China Medical University, Shenyang, China
| | - Jingjing Jing
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of Cancer Etiology and Prevention in Liaoning Education Department, the First Hospital of China Medical University, Shenyang, China.,Key Laboratory of GI Cancer Etiology and Prevention in Liaoning Province, the First Hospital of China Medical University, Shenyang, China
| |
Collapse
|
189
|
Ogunmwonyi I, Adebajo A, Wilkinson JM. The genetic and epigenetic contributions to the development of nutritional rickets. Front Endocrinol (Lausanne) 2022; 13:1059034. [PMID: 36619587 PMCID: PMC9815715 DOI: 10.3389/fendo.2022.1059034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
Nutritional rickets is an important disease in global health. Although nutritional rickets commonly manifests as bony deformities, there is an increased risk of life-threatening seizures secondary to hypocalcaemia. Dietary vitamin D deficiency is associated with the development of nutritional rickets among children and infants. This is especially true in populations of darker skinned individuals in high-latitude environments due to decreased ultraviolet light exposure, and in populations in tropical and subtropical climates due to cultural practices. A growing body of evidence has demonstrated that genetic factors might influence the likelihood of developing nutritional rickets by influencing an individual's susceptibility to develop deficiencies in vitamin D and/or calcium. This evidence has been drawn from a variety of different techniques ranging from traditional twin studies to next generation sequencing techniques. Additionally, the role of the epigenome in the development of rickets, although poorly understood, may be related to the effects of DNA methylation and non-coding RNAs on genes involved in bone metabolism. This review aims to provide an overview of the current evidence that investigates the genetic and epigenetic determinants of nutritional rickets.
Collapse
|
190
|
Song Z, Wang J. LncRNA ASMTL-AS1/microRNA-1270 differentiate prognostic groups in gastric cancer and influence cell proliferation, migration and invasion. Bioengineered 2022; 13:1507-1517. [PMID: 34986743 PMCID: PMC8805870 DOI: 10.1080/21655979.2021.2021063] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The objective of this study was to determine the expression levels of ASMTL-AS1 and miR-1270 in gastric cancer, and to explore whether ASMTL-AS1 and miR-1270 is associated with cancer prognosis and progression or not. ASMTL-AS1 and miR-1270 expression were quantified in gastric cancer tissues and adjacent normal tissues (n = 167) and cell lines. The potential of ASMTL-AS1 and miR-1270 as prognostic biomarkers was evaluated by the receiver operating characteristic (ROC) curve, Kaplan-Meier, and multivariate Cox regression analyses. The binding between ASMTL-AS1 and miR-1270 was verified by the Luciferase reporter assay and RNA pull-down assay. Functional roles of ASMTL-AS1/miR-1270 on cells were investigated in HGC-27 and NCI-N87 cells by MTS viability, Transwell migration, and Matrigel invasion assay. ASMTL-AS1 was significantly downregulated while miR-1270 was upregulated in gastric cancer tissues as compared with normal tissue and cell lines. According to the studies, ASMTL-AS1 and miR-1270 were related to unfavorable clinical parameters, such as the advanced TNM stage. Downregulated ASMTL-AS1 and upregulated miR-1270 were associated with reduced 5-year overall survival. Functional studies suggested that ASMTL-AS1 inhibits proliferation, migration, and invasion of HGC-27 and NCI-N87 cells by regulation of miR-1270. In summary, ASMTL-AS1 and miR-1270 are associated with poor prognosis of patients with gastric cancer. ASMTL-AS1 inhibited gastric cancer progression by regulating miR-1270. Therefore, ASMTL-AS1/miR-1270 may be a potential prognostic biomarker and novel strategy for gastric cancer targeted therapy.
Collapse
Affiliation(s)
- Zhenhe Song
- Department of Gastroenterology, Weihai Municipal Hospital, Cheeloo College of Medicine, Shandong University, Weihai, Shandong, China
| | - Jian Wang
- Department of Laboratory, Yidu Central Hospital of Weifang, Weifang, Shandong, China
| |
Collapse
|
191
|
Yildiz CB, Zimmer-Bensch G. Role of DNMTs in the Brain. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:363-394. [DOI: 10.1007/978-3-031-11454-0_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
192
|
Ma Q, Yang L, Tolentino K, Wang G, Zhao Y, Litzenburger UM, Shi Q, Zhu L, Yang C, Jiao H, Zhang F, Li R, Tsai MC, Chen JA, Lai I, Zeng H, Li L, Chang HY. Inducible lncRNA transgenic mice reveal continual role of HOTAIR in promoting breast cancer metastasis. eLife 2022; 11:79126. [PMID: 36579891 PMCID: PMC9831604 DOI: 10.7554/elife.79126] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 12/28/2022] [Indexed: 12/30/2022] Open
Abstract
HOTAIR is a 2.2-kb long noncoding RNA (lncRNA) whose dysregulation has been linked to oncogenesis, defects in pattern formation during early development, and irregularities during the process of epithelial-to-mesenchymal transition (EMT). However, the oncogenic transformation determined by HOTAIR in vivo and its impact on chromatin dynamics are incompletely understood. Here, we generate a transgenic mouse model with doxycycline-inducible expression of human HOTAIR in the context of the MMTV-PyMT breast cancer-prone background to systematically interrogate the cellular mechanisms by which human HOTAIR lncRNA acts to promote breast cancer progression. We show that sustained high levels of HOTAIR over time increased breast metastatic capacity and invasiveness in breast cancer cells, promoting migration and subsequent metastasis to the lung. Subsequent withdrawal of HOTAIR overexpression reverted the metastatic phenotype, indicating oncogenic lncRNA addiction. Furthermore, HOTAIR overexpression altered both the cellular transcriptome and chromatin accessibility landscape of multiple metastasis-associated genes and promoted EMT. These alterations are abrogated within several cell cycles after HOTAIR expression is reverted to basal levels, indicating an erasable lncRNA-associated epigenetic memory. These results suggest that a continual role for HOTAIR in programming a metastatic gene regulatory program. Targeting HOTAIR lncRNA may potentially serve as a therapeutic strategy to ameliorate breast cancer progression.
Collapse
Affiliation(s)
- Qing Ma
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Liuyi Yang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Karen Tolentino
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Guiping Wang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Yang Zhao
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Ulrike M Litzenburger
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Quanming Shi
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Lin Zhu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of SciencesShenzhenChina
| | - Chen Yang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Huiyuan Jiao
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Feng Zhang
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Rui Li
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Miao-Chih Tsai
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States
| | - Jun-An Chen
- Institute of Molecular Biology, Academia SinicaTaipeiTaiwan
| | - Ian Lai
- Transgenic, Knockout, and Tumor Model Center, Stanford University School of MedicineStanfordUnited States,Stanford Cancer Institute, Stanford University School of MedicineStanfordUnited States
| | - Hong Zeng
- Transgenic, Knockout, and Tumor Model Center, Stanford University School of MedicineStanfordUnited States,Stanford Cancer Institute, Stanford University School of MedicineStanfordUnited States
| | - Lingjie Li
- Department of Histoembryology, Genetics and Developmental Biology, Shanghai Key Laboratory of Reproductive Medicine, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education,Shanghai Jiao Tong University School of MedicineShanghaiChina
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Program in Epithelial Biology, Stanford University School of MedicineStanfordUnited States,Howard Hughes Medical Institute, Stanford UniversityStanfordUnited States
| |
Collapse
|
193
|
Doan TNA, Akison LK, Bianco-Miotto T. Epigenetic Mechanisms Responsible for the Transgenerational Inheritance of Intrauterine Growth Restriction Phenotypes. Front Endocrinol (Lausanne) 2022; 13:838737. [PMID: 35432208 PMCID: PMC9008301 DOI: 10.3389/fendo.2022.838737] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 03/02/2022] [Indexed: 12/20/2022] Open
Abstract
A poorly functioning placenta results in impaired exchanges of oxygen, nutrition, wastes and hormones between the mother and her fetus. This can lead to restriction of fetal growth. These growth restricted babies are at increased risk of developing chronic diseases, such as type-2 diabetes, hypertension, and kidney disease, later in life. Animal studies have shown that growth restricted phenotypes are sex-dependent and can be transmitted to subsequent generations through both the paternal and maternal lineages. Altered epigenetic mechanisms, specifically changes in DNA methylation, histone modifications, and non-coding RNAs that regulate expression of genes that are important for fetal development have been shown to be associated with the transmission pattern of growth restricted phenotypes. This review will discuss the subsequent health outcomes in the offspring after growth restriction and the transmission patterns of these diseases. Evidence of altered epigenetic mechanisms in association with fetal growth restriction will also be reviewed.
Collapse
Affiliation(s)
- Thu Ngoc Anh Doan
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
| | - Lisa K. Akison
- School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia
| | - Tina Bianco-Miotto
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Adelaide, SA, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, SA, Australia
- *Correspondence: Tina Bianco-Miotto,
| |
Collapse
|
194
|
Ketkar M, Dutt S. Epigenetic Regulation Towards Acquired Drug Resistance in Cancer. Subcell Biochem 2022; 100:473-502. [PMID: 36301503 DOI: 10.1007/978-3-031-07634-3_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Therapy resistance remains the most challenging obstacle in cancer treatment. Substantial efforts and evidences have accumulated over decades suggesting not only genetic but non-genomic mechanisms underlying this adaptation of tumor cells. Alterations in epigenome can have a fundamental effect on cellular functions and response to stresses like anticancer therapy. This chapter discusses the principal mechanisms by which epigenetic modifications in the genome and transcriptome aid tumor cells toward acquisition of resistance to chemotherapy.
Collapse
Affiliation(s)
- Madhura Ketkar
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India
- Homi Bhabha National Institute, Mumbai, India
| | - Shilpee Dutt
- Shilpee Dutt Laboratory, Advanced Centre for Treatment, Research and Education in Cancer (ACTREC), Tata Memorial Centre, Kharghar, Navi Mumbai, India.
- Homi Bhabha National Institute, Mumbai, India.
- ACTREC, Tata Memorial Centre, Kharghar, Navi Mumbai, Maharashtra, India.
| |
Collapse
|
195
|
Trevisan França de Lima L, Müller Bark J, Rasheduzzaman M, Ekanayake Weeramange C, Punyadeera C. Saliva as a matrix for measurement of cancer biomarkers. Cancer Biomark 2022. [DOI: 10.1016/b978-0-12-824302-2.00008-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
196
|
The Role of DNA Methylation and DNA Methyltransferases in Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:317-348. [DOI: 10.1007/978-3-031-11454-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
197
|
Epigenetic Mechanisms in Understanding Nanomaterial-Induced Toxicity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1357:195-223. [DOI: 10.1007/978-3-030-88071-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
198
|
miR-23b-3p Inhibits the Oncogenicity of Colon Adenocarcinoma by Directly Targeting NFE2L3. JOURNAL OF ONCOLOGY 2021; 2021:8493225. [PMID: 34966429 PMCID: PMC8712119 DOI: 10.1155/2021/8493225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 12/02/2021] [Indexed: 01/01/2023]
Abstract
Background and Aims MicroR-23b-3p (miR-23b-3p) has been found to be abnormally expressed in a variety of malignant tumors and to play a role in tumor inhibition or promotion. However, the regulatory mechanism of miR-23b-3p in COAD remains unclear. The purpose of this study was to investigate the clinical significance of miR-23b-3p expression in COAD cells and to explore its role and regulatory mechanism in the growth of COAD. Materials and Methods Quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure miR-23b-3p expression in COAD tissues and cell lines. After transfecting miR-23b-3p mimics into two human COAD cell lines (SW620 and LoVo), the cell counting kit-8 (CCK-8), colony formation, and 5-ethynyl-2′-deoxyuridine (EdU) assays were used to detect cell proliferation, the Transwell assay was used to measure cell migration and invasion capacity, and flow cytometry was used to evaluate cell apoptosis in vitro. In addition, a luciferase reporter assay was used to determine whether miR-23b-3p targets NFE2L3. The downstream regulatory mechanisms of miR-23b-3p action in COAD cells were also investigated. For in vivo tumorigenesis assay, COAD cells stably overexpressing miR-23b-3p were injected subcutaneously into the flank of nude mice to obtain tumors. Results Significantly decreased expression of miR-23b-3p was detected in COAD tissues and cell lines. Exogenous miR-23b-3p expression inhibited cell proliferation, migration, and invasion and promoted cell apoptosis of COAD cells in vitro. Nuclear factor erythroid 2 like 3 (NFE2L3) was identified as a direct target gene of miR-23b-3p. In addition, reintroduction of NFE2L3 partially abolished the anticancer effects of miR-23b-3p on COAD cells. Furthermore, miR-23b-3p overexpression hindered the growth of COAD cells in vivo. Conclusion miR-23b-3p inhibited the oncogenicity of COAD cells in vitro and in vivo by directly targeting NFE2L3, suggesting the importance of the miR-23b-3p/NFE2L3 pathway in the development of COAD.
Collapse
|
199
|
Ameli Mojarad M, Ameli Mojarad M, Shojaee B, Nazemalhosseini-Mojarad E. piRNA: A promising biomarker in early detection of gastrointestinal cancer. Pathol Res Pract 2021; 230:153757. [PMID: 34998210 DOI: 10.1016/j.prp.2021.153757] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 12/27/2021] [Accepted: 12/28/2021] [Indexed: 01/02/2023]
Abstract
Gastrointestinal (GI) cancer has become the primary concern of today's society due to its aggressive nature and poor prognosis. PIWI-interacting RNAs (piRNAs), a subgroup of non-coding RNAs, are mainly expressed in the germline and have emerged as a critical regulator in gene expression and the epigenetic silencing of DNA transposable elements by interacting with PIWI proteins. piRNAs' dysregulations were reported to promote or suppress the initiation and development of different malignancies, especially gastrointestinal cancers. Recently, several studies suggested the use of piRNAs as potential cancer biomarkers associated with the progression and chemoresistance of GI cancer. Hence, this review article aims to focus on the role of piRNAs in GI cancer progression, metastasis, and their molecular mechanisms as therapeutic markers for GI cancer patients.
Collapse
Affiliation(s)
- Melika Ameli Mojarad
- Department of Biology Faculty of Basics Science, Kharazmi University, Tehran, Iran.
| | | | - Bahador Shojaee
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
200
|
Abstract
Diabetic nephropathy (DN), which is a common microvascular complication with a high incidence in diabetic patients, greatly increases the mortality of patients. With further study on DN, it is found that epigenetics plays a crucial role in the pathophysiological process of DN. Epigenetics has an important impact on the development of DN through a variety of mechanisms, and promotes the generation and maintenance of metabolic memory, thus ultimately leading to a poor prognosis. In this review we discuss the methylation of DNA, modification of histone, and regulation of non-coding RNA involved in the progress of cell dysfunction, inflammation and fibrosis in the kidney, which ultimately lead to the deterioration of DN.
Collapse
|