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RNA Modifications in Gastrointestinal Cancer: Current Status and Future Perspectives. Biomedicines 2022; 10:biomedicines10081918. [PMID: 36009465 PMCID: PMC9405978 DOI: 10.3390/biomedicines10081918] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/05/2022] [Indexed: 01/05/2023] Open
Abstract
Gastrointestinal (GI) cancer, referring to cancers of the digestive system such as colorectal cancer (CRC), gastric cancer (GC), and liver cancer, is a major cause of cancer-related deaths in the world. A series of genetic, epigenetic, and epitranscriptomic changes occur during the development of GI cancer. The identification of these molecular events provides potential diagnostic, prognostic, and therapeutic targets for cancer patients. RNA modification is required in the posttranscriptional regulation of RNA metabolism, including splicing, intracellular transport, degradation, and translation. RNA modifications such as N6-methyladenosine (m6A) and N1-methyladenosine (m1A) are dynamically regulated by three different types of regulators named methyltransferases (writers), RNA binding proteins (readers), and demethylases (erasers). Recent studies have pointed out that abnormal RNA modification contributes to GI tumorigenesis and progression. In this review, we summarize the latest findings on the functional significance of RNA modification in GI cancer and discuss the therapeutic potential of epitranscriptomic inhibitors for cancer treatment.
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Ma L, He LN, Kang S, Gu B, Gao S, Zuo Z. Advances in detecting N6-methyladenosine modification in circRNAs. Methods 2022; 205:234-246. [PMID: 35878749 DOI: 10.1016/j.ymeth.2022.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/14/2022] Open
Abstract
Circular RNAs (circRNAs) are a class of noncoding RNAs with covalently single-stranded closed loop structures derived from back-splicing event of linear precursor mRNAs (pre-mRNAs). N6-methyladenosine (m6A), the most abundant epigenetic modification in eukaryotic RNAs, has been shown to play a crucial role in regulating the fate and biological function of circRNAs, and thus affecting various physiological and pathological processes. Accurate identification of m6A modification in circRNAs is an essential step to fully elucidate the crosstalk between m6A and circRNAs. In recent years, the rapid development of high-throughput sequencing technology and bioinformatic methodology has propelled the establishment of a multitude of approaches to detect circRNAs and m6A modification, including in vitro-based and in silico methods. Based on this, the research community has started on a new journey to develop methods for identification of m6A modification in circRNAs. In this review, we provide a comprehensive review and evaluation of the existing methods responsible for detecting circRNAs, m6A modification, and especially, m6A modification in circRNAs, which mainly focused on those developed based on high-throughput technologies and methodology of bioinformatics. This handy reference can help researchers figure out towards which direction this field will go.
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Affiliation(s)
- Lixia Ma
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Li-Na He
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shiyang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Bianli Gu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China
| | - Shegan Gao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment, Henan Key Laboratory of Microbiome and Esophageal Cancer Prevention and Treatment, Henan Key Laboratory of Cancer Epigenetics, Cancer Hospital, The First Affiliated Hospital (College of Clinical Medical) of Henan University of Science and Technology, Luoyang, China.
| | - Zhixiang Zuo
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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Xu Z, Chen S, Liu R, Chen H, Xu B, Xu W, Chen M. Circular RNA circPOLR2A promotes clear cell renal cell carcinoma progression by facilitating the UBE3C-induced ubiquitination of PEBP1 and, thereby, activating the ERK signaling pathway. Mol Cancer 2022; 21:146. [PMID: 35840930 PMCID: PMC9284792 DOI: 10.1186/s12943-022-01607-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 06/19/2022] [Indexed: 02/07/2023] Open
Abstract
Background Increasing evidence has demonstrated that circular RNAs (circRNAs) are implicated in cancer progression. However, the aberrant expression and biological functions of circRNAs in clear cell renal cell carcinoma (cRCC) remain largely elusive. Method Differentially expressed circRNAs in cRCC were filtered via bioinformatics analysis. Aberrant circPOLR2A expression was validated in cRCC tissues and cell lines via qRT-PCR. Sanger sequencing was used to identify the backsplicing site of circPOLR2A. In vitro and in vivo functional experiments were performed to evaluate the role of circPOLR2A in cRCC malignancy. RNA pull-down, mass spectrometry, RIP, FISH and immunofluorescence assays were used to identify and validate the circPOLR2A-interacting proteins. Ubiquitination modification and interaction between proteins were detected via Co-IP and western blotting. The m6A modification in circPOLR2A was validated by the meRIP assay. Results Bioinformatics analysis revealed that circPOLR2A was highly expressed in cRCC tissues and metastatic cRCC tissues. CircPOLR2A expression was associated with tumor size and TNM stage in cRCC patients. In vitro and in vivo functional assays revealed that circPOLR2A accelerated cRCC cell proliferation, migration, invasion and angiogenesis, while inhibiting apoptosis. Further mechanistic research suggested that circPOLR2A could interact with UBE3C and PEBP1 proteins, and that UBE3C could act as a specific ubiquitin E3 ligase for the PEBP1 protein. The UBE3C/circPOLR2A/PEBP1 protein-RNA ternary complex enhanced the UBE3C-mediated ubiquitination and degradation of the PEBP1 protein which could inactivate the ERK signaling pathway. Rescue experiments revealed that the PEBP1 protein was the functional downstream target of circPOLR2A. Furthermore, m6A modification in circPOLR2A was confirmed, and the m6A reader YTHDF2 could regulate circPOLR2A expression. Conclusion Our study demonstrated that circPOLR2A modulated the UBE3C-mediated ubiquitination and degradation of the PEBP1 protein, and further activated the ERK pathway during cRCC progression and metastasis. The m6A reader, YTHDF2, regulated circPOLR2A expression in cRCC. Hence, circPOLR2A could be a potential target for the diagnosis and treatment of cRCC. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01607-8.
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Affiliation(s)
- Zhipeng Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China.,Urology Research Center, Southeast University Medical School, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China
| | - Shuqiu Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China.,Urology Research Center, Southeast University Medical School, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China
| | - Ruiji Liu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China.,Urology Research Center, Southeast University Medical School, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China
| | - Hui Chen
- Department of Radiation Oncology, The First Affiliated Hospital of Nanjing Medical University, No.300 Guangzhou Road, Nanjing, 210029, People's Republic of China
| | - Bin Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China.,Urology Research Center, Southeast University Medical School, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China
| | - Weizhang Xu
- Department of Urology, Jiangsu Institute of Cancer Research & Jiangsu Cancer Hospital, No.42 Baiziting Road, Nanjing, 210000, People's Republic of China.
| | - Ming Chen
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China. .,Urology Research Center, Southeast University Medical School, No.87 Dingjiaqiao Road, Nanjing, 210009, People's Republic of China. .,Department of Urology, Nanjing Lishui District People's Hospital, No.86 Chongwen Road, Nanjing, 211200, People's Republic of China.
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Qi L, Zhang W, Ren X, Xu R, Yang Z, Chen R, Tu C, Li Z. Cross-Talk of Multiple Types of RNA Modification Regulators Uncovers the Tumor Microenvironment and Immune Infiltrates in Soft Tissue Sarcoma. Front Immunol 2022; 13:921223. [PMID: 35860263 PMCID: PMC9289169 DOI: 10.3389/fimmu.2022.921223] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/02/2022] [Indexed: 01/10/2023] Open
Abstract
BackgroundSoft-tissue sarcoma (STS) represents a rare and diverse cohort of solid tumors, and encompasses over 100 various histologic and molecular subtypes. In recent years, RNA modifications including m6A, m5C, m1A, and m7G have been demonstrated to regulate immune response and tumorigenesis. Nevertheless, the cross-talk among these RNA modification regulators and related effects upon the tumor microenvironment (TME), immune infiltrates, and immunotherapy in STS remain poorly understood.MethodsIn this study, we comprehensively investigated transcriptional and genetic alterations of 32 RNA modification regulators in STS patients from The Cancer Genome Atlas (TCGA) cohort and validated them in the Gene Expression Omnibus (GEO) cohort. Single-cell transcriptomes were introduced to identify regulators within specific cell types, with own sequencing data and RT-qPCR conducted for biological validation. Distinct regulator clusters and regulator gene subtypes were identified by using unsupervised consensus clustering analysis. We further built the regulator score model based on the prognostic regulator-related differentially expressed genes (DEGs), which could be used to quantitatively assess the risk for individual STS patients. The clinical and biological characteristics of different regulator score groups were further examined.ResultsA total of 455 patients with STS were included in this analysis. The network of 32 RNA modification regulators demonstrated significant correlations within multiple different RNA modification types. Distinct regulator clusters and regulator gene subtypes were characterized by markedly different prognoses and TME landscapes. The low regulator score group in the TCGA-SARC cohort was characterized by poor prognosis. The robustness of the scoring model was further confirmed by the external validation in GSE30929 and GSE17674. The regulator score was negatively correlated with CD4+ T cell, Th2 cell, and Treg cell recruitment and most immunotherapy-predicted pathways, and was also associated with immunotherapy efficacy.ConclusionsOverall, our study is the first to demonstrate the cross-talk of RNA modification regulators and the potential roles in TME and immune infiltrates in STS. The individualized assessment based on the regulator score model could facilitate and optimize personalized treatment.
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Affiliation(s)
- Lin Qi
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Wenchao Zhang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Xiaolei Ren
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Ruiling Xu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Zhimin Yang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
- Department of Microbiology, Immunology & Molecular Genetics, UT Health Science Center, University of Texas Long School of Medicine, San Antonio, TX, United States
| | - Ruiqi Chen
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
| | - Chao Tu
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
- *Correspondence: Zhihong Li, ; Chao Tu,
| | - Zhihong Li
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, China
- Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital, Changsha, China
- *Correspondence: Zhihong Li, ; Chao Tu,
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Liu R, Jia Y, Kong G, He A. Novel insights into roles of N6-methyladenosine reader YTHDF2 in cancer progression. J Cancer Res Clin Oncol 2022; 148:2215-2230. [PMID: 35763107 DOI: 10.1007/s00432-022-04134-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/10/2022] [Indexed: 12/19/2022]
Abstract
N6-methyladenosine (m6A) is the most abundant RNA modification. M6A RNA methylation is reversible: m6A is installed by "writers", removed by "erasers", and recognized by "readers". Readers are executors to regulate RNA metabolism by recognizing specific m6A sites, including RNA splicing, export, translation and decay. YTHDF2 is the first identified m6A reader protein. YTHDF2 interacts with m6A-containing transcripts to accelerate the degradation process and regulate various biological processes, such as viral infection, stem cell development and cancer progression. Although there are some reviews about m6A modification in physiological and pathological processes, few reviews focus on roles of YTHDF2 in cancers to date. Therefore, in this review, we attempted to systematically summarize m6A reader protein YTHDF2: its structure, mechanisms in regulating RNA metabolism, roles in cancer progression and potential application for cancer treatment, which might inspire new ideas for m6A research in cancers and provide novel insights into cancer treatment.
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Affiliation(s)
- Rui Liu
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157, 5th West Road, Xi'an, 710004, Shaanxi, China
| | - Yachun Jia
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157, 5th West Road, Xi'an, 710004, Shaanxi, China
| | - Guangyao Kong
- National-Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China
| | - Aili He
- Department of Hematology, The Second Affiliated Hospital of Xi'an Jiaotong University, 157, 5th West Road, Xi'an, 710004, Shaanxi, China. .,National-Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710004, Shaanxi, China.
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Zhang Y, Wang Y, Ji H, Ding J, Wang K. The interplay between noncoding RNA and YAP/TAZ signaling in cancers: molecular functions and mechanisms. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:202. [PMID: 35701841 PMCID: PMC9199231 DOI: 10.1186/s13046-022-02403-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022]
Abstract
The Hippo signaling pathway was found coordinately modulates cell regeneration and organ size. Its dysregulation contributes to uncontrolled cell proliferation and malignant transformation. YAP/TAZ are two critical effectors of the Hippo pathway and have been demonstrated essential for the initiation or growth of most tumors. Noncoding RNAs (ncRNAs), including miRNAs, lncRNAs, and circRNAs, have been shown to play critical roles in the development of many cancers. In the past few decades, a growing number of studies have revealed that ncRNAs can directly or indirectly regulate YAP/TAZ signaling. YAP/TAZ also regulate ncRNAs expression in return. This review summarizes the interactions between YAP/TAZ signaling and noncoding RNAs together with their biological functions on cancer progression. We also try to describe the complex feedback loop existing between these components.
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Affiliation(s)
- Yirao Zhang
- Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Yang Wang
- Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China
| | - Hao Ji
- Department of Liver Surgery and Liver Transplantation Center, School of Medicine, Renji Hospital, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Jie Ding
- Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China.
| | - Keming Wang
- Department of Oncology, Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, Jiangsu, China.
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