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Luo Q, Dai T, Dong Y, Liang J, Xu Z, Sun Z. N6-methyladenosine-modified TRIM37 augments sunitinib resistance by promoting the ubiquitin-degradation of SmARCC2 and activating the Wnt signaling pathway in renal cell carcinoma. Cell Death Discov 2024; 10:418. [PMID: 39349442 PMCID: PMC11442835 DOI: 10.1038/s41420-024-02187-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 09/05/2024] [Accepted: 09/19/2024] [Indexed: 10/02/2024] Open
Abstract
Tripartite motif-containing 37 (TRIM37) is reportedly a key member of the superfamily of TRIM proteins. Emerging evidence underscores the close association between dysregulated TRIM37 expression and the progression of various human malignancies. However, the precise biological functions and regulatory mechanisms of TRIM37 remain elusive. This study aimed to elucidate the impact of TRIM37 on the chemotherapy sensitivity of renal cell carcinoma (RCC) and uncover its specific molecular regulatory role. Using RT-qPCR and western blot assays, we assessed TRIM37 expression in both RCC patients and RCC cells. Through in vitro and in vivo experiments, we investigated the effects of TRIM37 silencing and overexpression on RCC cell proliferation, stemness capacity, and chemotherapy sensitivity using colony formation and sphere formation assays. Additionally, a co-immunoprecipitation (Co-IP) experiment was conducted to explore putative interacting proteins. Our results revealed elevated TRIM37 expression in both RCC patient tumor tissues and RCC cells. Functional experiments consistently demonstrated that TRIM37 silencing reduced proliferation and stemness capacity while enhancing chemotherapy sensitivity in RCC cells. Furthermore, we discovered that TRIM37 mediates the degradation of SMARCC2 via ubiquitin-proteasome pathways, thereby further activating the Wnt signaling pathway. In conclusion, this study not only sheds light on the biological role of TRIM37 in RCC progression but also identifies a potential molecular target for therapeutic intervention in RCC patients.
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Affiliation(s)
- Qiang Luo
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, 130000, Jilin, China
| | - Ting Dai
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, 130000, Jilin, China
| | - Yihong Dong
- Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Jianpeng Liang
- The First Peoples Hospital of Foshan, Foshan, 528000, Guangdong, China
| | - Zhipeng Xu
- Third Xiangya Hospital of Central South University, Changsha, 410013, Hunan, China
| | - Zhixia Sun
- Department of Ultrasound, China-Japan Union Hospital of Jilin University, Changchun, 130000, Jilin, China.
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Wu S, Tu Q, Yuan H, Wu Z, Yang Y, Chen C, Huang C. Comprehensive Analysis for Predicting Prognoses and Immune Responses of m6A-Related lncRNAs in Women with Lung Adenocarcinoma. Biochem Genet 2024; 62:2702-2720. [PMID: 37999876 DOI: 10.1007/s10528-023-10572-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
During the past decade, the average 5-year survival rate of patients with Lung adenocarcinoma (LUAD) has remained < 20%, although the targeted therapies and novel immunotherapy approaches have held promise. Epigenetic modifications could provide prognostic value as molecular biomarkers, and we aimed to identify the independent risk of m6A-related lncRNAs to establish a risk model for the clinical prediction of prognoses in women with LUAD. In this study, we first assessed 31 N6-methyladenosine (m6A)-related lncRNAs associated with overall survival. Moreover, we evaluated the expression of the oncogenic driver and the tumor immune microenvironment (TIME) in two female LUAD subtypes (clusters 1 and 2) using consensus clustering. We also found 16 m6A-related lncRNAs as the independent prognostic indicator of women with LUAD and established a risk model developed from these lncRNAs. We comprehensively investigated the correlation between the TIME and m6A-related lncRNA and found that m6A-related lncRNA may significantly affect the immune cell infiltration level in LUAD. In conclusion, our study provides evidence on the prognostic prediction in women with LUAD and may help elucidate the processes and mechanisms of m6A-regulated lncRNAs.
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Affiliation(s)
- Sijie Wu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
| | - Qinxian Tu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
| | - Haoyong Yuan
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China
| | - Zhongshi Wu
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China
| | - Yifeng Yang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
| | - Chunyang Chen
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China
| | - Can Huang
- Department of Cardiovascular Surgery, The Second Xiangya Hospital, Central South University, #139 Renmin Road, Changsha, 410011, Hunan, China.
- Engineering Laboratory of Hunan Province for Cardiovascular Biomaterials, Changsha, 410008, Hunan, China.
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Wu H, Huang Q, Xu T, Zhang J, Zeng J, Wang Q, Zhang Y, Yu Z. LncRNA OIP5-AS1 Upregulates the Cyclin D2 Levels to Promote Metastasis of Breast Cancer by Targeting miR-150-5p. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04992-6. [PMID: 38888699 DOI: 10.1007/s12010-024-04992-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2024] [Indexed: 06/20/2024]
Abstract
OBJECTIVE Breast cancer (BC) is a cancer that seriously affects women's health. BC cell migration increases the mortality of BC patients. Current studies have shown that long noncoding RNAs (LncRNAs) are related to the metastasis mechanism of BC. This study aimed to explore the function and role of LncRNA OIP5-AS1 in BC. And we analyzed its regulatory mechanism and related modification process. METHODS Our study analyzed the expression pattern of OIP5-AS1 in BC tissues and cell lines by qRT-PCR. The effects of OIP5-AS1 on the function of BC cells were detected by CCK-8 and transwell experiments. Bioinformatics analysis and double luciferase reporter gene detection were used to confirm the correlation between OIP5-AS1 and miR-150-5p and between miR-150-5p and Cyclin D2 (CCND2). The rescue test analyzed the effect of miR-150-5p regulating OIP5-AS1. In addition, the N6-methyladenosine (m6A) modification process of OIP5-AS1 was analyzed by RNA m6A dot blot, RIP assay, and double luciferase report experiment. RESULTS OIP5-AS1 was significantly upregulated in BC tissues and cell lines. OIP5-AS1 knockdown inhibited BC cell viability, migration and invasion. OIP5-AS1 upregulated CCND2 by binding with miR-150-5p. This process affected the metastasis of BC. Higher degree of m6A methylation was confirmed in BC cell lines. There were some binding sites between methyltransferase like 3 (METTL3) and OIP5-AS1. Moreover, the silencing of METTL3 inhibited the OIP5-AS1 expression through decreasing the m6A methylation levels. CONCLUSIONS LncRNA OIP5-AS1 promoted cell viability and metastasis of BC cells by targeting miR-150-5p/CCND2 axis. This process was modified by m6A methylation of METTL3.
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Affiliation(s)
- Heming Wu
- Center for Precision Medicine, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China
| | - Qingyan Huang
- Center for Precision Medicine, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China
| | - Tai Xu
- Department of Breast Surgery, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China
| | - Jinfeng Zhang
- Department of Medical Oncology, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China
| | - Juanzi Zeng
- Department of Medical Oncology, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China
| | - Qiuming Wang
- Department of Medical Oncology, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China
| | - Yunuo Zhang
- Department of Medical Oncology, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China
| | - Zhikang Yu
- Center for Precision Medicine, Meizhou People's Hospital, Meizhou Academy of Medical Sciences, No. 63 Huangtang Road, Meijiang District, Meizhou, People's Republic of China.
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Liu Q, Zhang N, Chen J, Zhou M, Zhou D, Chen Z, Huang Z, Xie Y, Qiao G, Tu X. WTAP-induced N 6-methyladenosine of PD-L1 blocked T-cell-mediated antitumor activity under hypoxia in colorectal cancer. Cancer Sci 2024; 115:1749-1762. [PMID: 38508217 PMCID: PMC11145145 DOI: 10.1111/cas.16136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/22/2024] Open
Abstract
N6-Methyladenosine (m6A) is a important process regulating gene expression post-transcriptionally. Programmed death ligand 1 (PD-L1) is a major immune inhibitive checkpoint that facilitates immune evasion and is expressed in tumor cells. In this research we discovered that Wilms' tumor 1-associated protein (WTAP) degradation caused by ubiquitin-mediated cleavage in cancer cells (colorectal cancer, CRC) under hypoxia was inhibited by Pumilio homolog 1 (PUM1) directly bound to WTAP. WTAP enhanced PD-L1 expression in a way that was m6A-dependent. m6A "reader," Insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) identified methylated PD-L1 transcripts and subsequently fixed its mRNA. Additionally, we found that T-cell proliferation and its cancer cell-killing effects were prevented by overexpression of WTAP in vitro and in vivo. Overexpression prevented T cells from proliferating and killing CRC by maintaining the expression of PD-L1. Further evidence supporting the WTAP-PD-L1 regulatory axis was found in human CRC and organoid tissues. Tumors with high WTAP levels appeared more responsive to anti-PD1 immunotherapy, when analyzing samples from patients undergoing treatment. Overall, our findings demonstrated a novel PD-L1 regulatory mechanism by WTAP-induced mRNA epigenetic regulation and the possible application of targeting WTAP as immunotherapy for tumor hypoxia.
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Affiliation(s)
- Qi‐zhi Liu
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Nan Zhang
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Jun‐yi Chen
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Min‐jun Zhou
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - De‐hua Zhou
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Zhuo Chen
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Zhen‐xing Huang
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yu‐xiang Xie
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Guang‐lei Qiao
- Department of Oncology, Tongren HospitalShanghai Jiao Tong University School of MedicineShanghaiChina
| | - Xiao‐huang Tu
- Department of Gastrointestinal Surgery, Shanghai Fourth People's Hospital, School of MedicineTongji UniversityShanghaiChina
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Guan Q, Zhang X, Liu J, Zhou C, Zhu J, Wu H, Zhuo Z, He J. ALKBH5 gene polymorphisms and risk of neuroblastoma in Chinese children from Jiangsu Province. CANCER INNOVATION 2024; 3:e103. [PMID: 38946930 PMCID: PMC11212286 DOI: 10.1002/cai2.103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 09/13/2023] [Accepted: 09/18/2023] [Indexed: 07/02/2024]
Abstract
Background Neuroblastoma is one of the most common extracranial malignant solid tumors in children. AlkB homolog 5 (ALKBH5) is an RNA N6-methyladenosine (m6A) demethylase that plays a critical role in tumorigenesis and development. We assessed the association between single nucleotide polymorphisms (SNPs) in ALKBH5 and the risk of neuroblastoma in a case-control study including 402 patients and 473 non-cancer controls. Methods Genotyping was determined by the TaqMan method. The association between ALKBH5 polymorphisms (rs1378602 and rs8400) and the risk of neuroblastoma was evaluated using the odds ratio (OR) and 95% confidence interval (CI). Results We found no strong association of ALKBH5 rs1378602 and rs8400 with neuroblastoma risk. Further stratification analysis by age, sex, primary site, and clinical stage showed that the rs1378602 AG/AA genotype was associated with a lower risk of neuroblastoma in males (adjusted OR = 0.58, 95% CI = 0.35-0.97, p = 0.036) and children with retroperitoneal neuroblastoma (adjusted OR = 0.58, 95% CI = 0.34-0.98, p = 0.040). Conclusions ALKBH5 SNPs do not seem to be associated with neuroblastoma risk. More studies are required to confirm this negative result and reveal the relationship between gene polymorphisms of the m6A modifier ALKBH5 and neuroblastoma.
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Affiliation(s)
- Qian Guan
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Xinxin Zhang
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Jiabin Liu
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
| | - Chunlei Zhou
- Department of PathologyChildren's Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Jinhong Zhu
- Department of Clinical Laboratory, BiobankHarbin Medical University Cancer HospitalHarbinHeilongjiangChina
| | - Haiyan Wu
- Department of PathologyChildren's Hospital of Nanjing Medical UniversityNanjingJiangsuChina
| | - Zhenjian Zhuo
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
- Laboratory Animal Center, School of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhenGuangdongChina
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangdong Provincial Key Laboratory of Research in Structural Birth Defect Disease, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Women and Children's Medical CenterGuangzhou Medical UniversityGuangzhouGuangdongChina
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Hashemi M, Daneii P, Zandieh MA, Raesi R, Zahmatkesh N, Bayat M, Abuelrub A, Khazaei Koohpar Z, Aref AR, Zarrabi A, Rashidi M, Salimimoghadam S, Entezari M, Taheriazam A, Khorrami R. Non-coding RNA-Mediated N6-Methyladenosine (m 6A) deposition: A pivotal regulator of cancer, impacting key signaling pathways in carcinogenesis and therapy response. Noncoding RNA Res 2024; 9:84-104. [PMID: 38075202 PMCID: PMC10700483 DOI: 10.1016/j.ncrna.2023.11.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/23/2023] [Accepted: 11/08/2023] [Indexed: 06/20/2024] Open
Abstract
The emergence of RNA modifications has recently been considered as critical post-transcriptional regulations which governed gene expression. N6-methyladenosine (m6A) modification is the most abundant type of RNA modification which is mediated by three distinct classes of proteins called m6A writers, readers, and erasers. Accumulating evidence has been made in understanding the role of m6A modification of non-coding RNAs (ncRNAs) in cancer. Importantly, aberrant expression of ncRNAs and m6A regulators has been elucidated in various cancers. As the key role of ncRNAs in regulation of cancer hallmarks is well accepted now, it could be accepted that m6A modification of ncRNAs could affect cancer progression. The present review intended to discuss the latest knowledge and importance of m6A epigenetic regulation of ncRNAs including mircoRNAs, long non-coding RNAs, and circular RNAs, and their interaction in the context of cancer. Moreover, the current insight into the underlying mechanisms of therapy resistance and also immune response and escape mediated by m6A regulators and ncRNAs are discussed.
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Affiliation(s)
- Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Pouria Daneii
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mohammad Arad Zandieh
- Department of Food Hygiene and Quality Control, Division of Epidemiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Rasoul Raesi
- Department of Health Services Management, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical-Surgical Nursing, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Zahmatkesh
- Department of Genetics, Zanjan Branch, Islamic Azad University, Zanjan, Iran
| | - Mehrsa Bayat
- Department of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Anwar Abuelrub
- Neuroscience Laboratory, Health Sciences Institute, Bahcesehir University, Istanbul, Turkey
| | - Zeinab Khazaei Koohpar
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | - Amir Reza Aref
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul, 34396, Turkey
| | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
- The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shokooh Salimimoghadam
- Department of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Maliheh Entezari
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
- Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
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Duan M, Liu H, Xu S, Yang Z, Zhang F, Wang G, Wang Y, Zhao S, Jiang X. IGF2BPs as novel m 6A readers: Diverse roles in regulating cancer cell biological functions, hypoxia adaptation, metabolism, and immunosuppressive tumor microenvironment. Genes Dis 2024; 11:890-920. [PMID: 37692485 PMCID: PMC10491980 DOI: 10.1016/j.gendis.2023.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/24/2023] [Accepted: 06/14/2023] [Indexed: 09/12/2023] Open
Abstract
m6A methylation is the most frequent modification of mRNA in eukaryotes and plays a crucial role in cancer progression by regulating biological functions. Insulin-like growth factor 2 mRNA-binding proteins (IGF2BP) are newly identified m6A 'readers'. They belong to a family of RNA-binding proteins, which bind to the m6A sites on different RNA sequences and stabilize them to promote cancer progression. In this review, we summarize the mechanisms by which different upstream factors regulate IGF2BP in cancer. The current literature analyzed here reveals that the IGF2BP family proteins promote cancer cell proliferation, survival, and chemoresistance, inhibit apoptosis, and are also associated with cancer glycolysis, angiogenesis, and the immune response in the tumor microenvironment. Therefore, with the discovery of their role as 'readers' of m6A and the characteristic re-expression of IGF2BPs in cancers, it is important to elucidate their mechanism of action in the immunosuppressive tumor microenvironment. We also describe in detail the regulatory and interaction network of the IGF2BP family in downstream target RNAs and discuss their potential clinical applications as diagnostic and prognostic markers, as well as recent advances in IGF2BP biology and associated therapeutic value.
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Affiliation(s)
- Meiqi Duan
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Haiyang Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Shasha Xu
- Department of Gastroendoscopy, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Zhi Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Fusheng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Guang Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Yutian Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Shan Zhao
- Department of Rheumatology and Immunology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110002, China
| | - Xiaofeng Jiang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
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Xie K, Wang B, Pang P, Li G, Yang Q, Fang C, Jiang W, Feng Y, Ma H. A novel disulfidptosis-related prognostic gene signature and experimental validation identify ACTN4 as a novel therapeutic target in lung adenocarcinoma. Cancer Biomark 2024:CBM230276. [PMID: 38517776 DOI: 10.3233/cbm-230276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2024]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a prevalent form of malignancy globally. Disulfidptosis is novel programmed cell death pathway based on disulfide proteins, may have a positive impact on the development of LUAD treatment strategies. OBJECTIVE To investigate the impact of disulfidptosis-related genes (DRGs) on the prognosis of LUAD, developed a risk model to facilitate the diagnosis and prognostication of patients. We also explored ACTN4 (DRGs) as a new therapeutic biomarker for LUAD. METHODS We investigated the expression patterns of DRGs in both LUAD and noncancerous tissues. To assess the prognostic value of the DRGs, we developed risk models through univariate Cox analysis and lasso regression. The expression and function of ACTN4 was evaluated by qRT-PCR, immunohistochemistry and in vitro experiments. The TIMER examined the association between ACTN4 expression and immune infiltration in LUAD. RESULTS Ten differentially expressed DRGs were identified. And ACTN4 was identified as potential risk factors through univariate Cox regression analysis (P< 0.05). ACTN4 expression and riskscore were used to construct a risk model to predict overall survival in LUAD, and high-risk demonstrated a significantly higher mortality rate compared to the low-risk cohort. qRT-PCR and immunohistochemistry assays indicated ACTN4 was upregulated in LUAD, and the upregulation was associated with clinicopathologic features. In vitro experiments showed the knockdown of ACTN4 expression inhibited the proliferation in LUAD cells. The TIMER analysis demonstrated a correlation between the expression of ACTN4 and the infiltration of diverse immune cells. Elevated ACTN4 expression was associated with a reduction in memory B cell count. Additionally, the ACTN4 expression was associated with m6A modification genes. CONCLUSIONS Our study introduced a prognostic model based on DRGs, which could forecast the prognosis of patients with LUAD. The biomarker ACTN4 exhibits promise for the diagnosis and management of LUAD, given its correlation with tumor immune infiltration and m6A modification.
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Affiliation(s)
- Kai Xie
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Bin Wang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Pei Pang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Guangbin Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Qianqian Yang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Chen Fang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Wei Jiang
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yu Feng
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Haitao Ma
- Department of Thoracic Surgery, The Fourth Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
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9
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Li Y, Jiang M, Aye L, Luo L, Zhang Y, Xu F, Wei Y, Peng D, He X, Gu J, Yu X, Li G, Ge D, Lu C. UPP1 promotes lung adenocarcinoma progression through the induction of an immunosuppressive microenvironment. Nat Commun 2024; 15:1200. [PMID: 38331898 PMCID: PMC10853547 DOI: 10.1038/s41467-024-45340-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
The complexity of the tumor microenvironment (TME) is a crucial factor in lung adenocarcinoma (LUAD) progression. To gain deeper insights into molecular mechanisms of LUAD, we perform an integrative single-cell RNA sequencing (scRNA-seq) data analysis of 377,574 cells from 117 LUAD patient samples. By linking scRNA-seq data with bulk gene expression data, we identify a cluster of prognostic-related UPP1high tumor cells. These cells, primarily situated at the invasive front of tumors, display a stronger association with the immunosuppressive components in the TME. Our cytokine array analysis reveals that the upregulation of UPP1 in tumor cells leads to the increased release of various immunosuppressive cytokines, with TGF-β1 being particularly prominent. Furthermore, this UPP1 upregulation also elevates the expression of PD-L1 through the PI3K/AKT/mTOR pathway, which contributes to the suppression of CD8 + T cells. Cytometry by time-of-flight (CyTOF) analysis provides additional evidence of the role of UPP1 in shaping the immunosuppressive nature of the TME. Using patient-derived organoids (PDOs), we discover that UPP1high tumors exhibit relatively increased sensitivity to Bosutinib and Dasatinib. Collectively, our study highlights the immunosuppressive role of UPP1 in LUAD, and these findings may provide insights into the molecular features of LUAD and facilitate the development of personalized treatment strategies.
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Affiliation(s)
- Yin Li
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Manling Jiang
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, Chengdu, 610031, Sichuan, China
| | - Ling Aye
- Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Li Luo
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, Chengdu, 610031, Sichuan, China
| | - Yong Zhang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Fengkai Xu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yongqi Wei
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Dan Peng
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, Chengdu, 610031, Sichuan, China
| | - Xiang He
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, Chengdu, 610031, Sichuan, China
| | - Jie Gu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaofang Yu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Guoping Li
- Laboratory of Allergy and Precision Medicine, Chengdu Institute of Respiratory Health, Affiliated Hospital of Southwest Jiaotong University, The Third People's Hospital of Chengdu, Chengdu, 610031, Sichuan, China.
| | - Di Ge
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Chunlai Lu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
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10
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Chen C, Wan M, Peng X, Zhang Q, Liu Y. GPR37-centered ceRNA network contributes to metastatic potential in lung adenocarcinoma: Evidence from high-throughput sequencing. Transl Oncol 2024; 39:101819. [PMID: 37979558 PMCID: PMC10656721 DOI: 10.1016/j.tranon.2023.101819] [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: 06/11/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/20/2023] Open
Abstract
The competing endogenous RNA (ceRNA)-based profiling has been extensively studied in carcinogenesis of lung adenocarcinoma (LUAD), while it has seldomly been applied to investigate the metastatic potential of LUAD. This study aims to examine the function and in-depth mechanism of GPR37-centered ceRNA network in LUAD. Cancer tissues and adjacent normal tissues from three LUAD patients were collected for high-throughput sequencing to screen for differentially expressed genes. A PPI network was constructed to screen the key gene GPR37, followed by analysis for the functions and pathways. Clinical data from LUAD patients were integrated with gene expression data in TCGA-LUAD dataset for survival analysis. Based on the miRNAs targeting_GPR37 and lncRNAs targeting_miRNAs, a lncRNA-miRNA-mRNA ceRNA network was established. GPR37 was up-regulated in LUAD tissue samples, and it may be a key gene involved in LUAD progression. GPR37 in LUAD was mainly enriched in the mitosis-related pathways. High GPR37 expression corresponded to poor prognosis in LUAD patients. Meanwhile, GPR37 could be used as an independent factor to predict the prognosis in LUAD patients. LncRNA DLEU1, up-regulated in LUAD tissue samples, may competitively bind to miR-4458 to up-regulate the expression of the miR-4458 downstream target GPR37. DLEU1 was associated with poor prognosis and tumor metastasis in LUAD patients. Altogether, our findings reveal a novel ceRNA network of DLEU1/miR-4458/GPR37 in LUAD growth and metastasis.
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Affiliation(s)
- Chuanhui Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Mengzhi Wan
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Xiong Peng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Qing Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
| | - Yu Liu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang 330006, PR China.
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11
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Ramsoomair CK, Ceccarelli M, Heiss JD, Shah AH. The epitranscriptome of high-grade gliomas: a promising therapeutic target with implications from the tumor microenvironment to endogenous retroviruses. J Transl Med 2023; 21:893. [PMID: 38071304 PMCID: PMC10709919 DOI: 10.1186/s12967-023-04725-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
Glioblastoma (GBM) comprises 45.6% of all primary malignant brain cancers and is one of the most common and aggressive intracranial tumors in adults. Intratumoral heterogeneity with a wide range of proteomic, genetic, and epigenetic dysregulation contributes to treatment resistance and poor prognosis, thus demanding novel therapeutic approaches. To date, numerous clinical trials have been developed to target the proteome and epigenome of high-grade gliomas with promising results. However, studying RNA modifications, or RNA epitranscriptomics, is a new frontier within neuro-oncology. RNA epitranscriptomics was discovered in the 1970s, but in the last decade, the extent of modification of mRNA and various non-coding RNAs has emerged and been implicated in transposable element activation and many other oncogenic processes within the tumor microenvironment. This review provides background information and discusses the therapeutic potential of agents modulating epitranscriptomics in high-grade gliomas. A particular emphasis will be placed on how combination therapies that include immune agents targeting hERV-mediated viral mimicry could improve the treatment of GBM.
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Affiliation(s)
- Christian K Ramsoomair
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
- Medical Scientist Training Program, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, 1550 N.W. 10Th Avenue, Miami, FL, 33136, USA
| | - John D Heiss
- Surgical Neurology Branch, Disorders and Stroke, National Institute of Neurological, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Ashish H Shah
- Section of Virology and Immunotherapy, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, 1095 NW 14Th Terrace, Miami, FL, 33136, USA.
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12
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Qian S, Liu J, Liao W, Wang F. METTL3 promotes non-small-cell lung cancer growth and metastasis by inhibiting FDX1 through copper death-associated pri-miR-21-5p maturation. Epigenomics 2023; 15:1237-1255. [PMID: 38126112 DOI: 10.2217/epi-2023-0230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023] Open
Abstract
Objective: We probed into the significance of METTL3 in the maturation process of pri-miR-21-5p. We specifically investigated its impact on the regulation of FDX1 and its involvement in the progression of non-small-cell lung cancer (NSCLC). Methods: The Cancer Genome Atlas (TCGA) identified NSCLC factors. Methylation-specific PCR (MSP), clonogenic tests and flow cytometry analyzed cells. Methylated RNA immunoprecipitation (Me-RIP) and dual-luciferase studied miR-21-5p/FDX1. Mice xenografts showed METTL3's tumorigenic effect. Results: METTL3, with high expression but low methylation in NSCLC, influenced cell behaviors. Its suppression reduced oncogenic properties. METTL3 enhanced miR-21-5p maturation, targeting FDX1 and boosting NSCLC tumorigenicity in mice. Conclusion: METTL3 may promote NSCLC development by facilitating pri-miR-21-5p maturation, upregulating miR-21-5p and targeting inhibition of FDX1.
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Affiliation(s)
- Shuai Qian
- Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, People's Republic of China
| | - Jun Liu
- Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, People's Republic of China
| | - Wenliang Liao
- Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, People's Republic of China
| | - Fengping Wang
- Department of Clinical Laboratory, The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, People's Republic of China
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13
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Tang J, Yu Z, Xia J, Jiang R, Chen S, Ye D, Sheng H, Lin J. METTL14-Mediated m6A Modification of TNFAIP3 Involved in Inflammation in Patients With Active Rheumatoid Arthritis. Arthritis Rheumatol 2023; 75:2116-2129. [PMID: 37327357 DOI: 10.1002/art.42629] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 05/03/2023] [Accepted: 06/12/2023] [Indexed: 06/18/2023]
Abstract
OBJECTIVE The aim of the study was to investigate the role of N6 -methyladenosine (m6A) modification in the progression of rheumatoid arthritis (RA). METHODS Peripheral blood mononuclear cells (PBMCs) from patients with RA and healthy controls were collected. The expression of m6A modification-related proteins and m6A levels were detected using polymerase chain reaction (PCR), western blot, and m6A enzyme-linked immunosorbent assay (ELISA). The roles of methyltransferase-like 14 (METTL14) in the regulation of inflammation in RA was explored using methylated RNA immunoprecipitation (MeRIP) sequencing and RNA immunoprecipitation assays. Collagen antibody-induced arthritis (CAIA) mice were used as an in vivo model to study the role of METTL14 in the inflammation progression of RA. RESULTS We found that m6A writer METTL14 and m6A levels were decreased in PBMCs of patients with active RA and correlated negatively with the disease activity score using 28 joint counts (DAS28). Knockdown of METTL14 downregulated m6A and promoted the secretion of inflammatory cytokines interleukin 6 (IL-6) and IL-17 in PBMCs of patients with RA. Consistently, METTL14 knockdown promoted joint inflammation accompanied by upregulation of IL-6 and IL-17 in CAIA mice. MeRIP sequencing and functional studies confirmed that tumor necrosis factor α induced protein 3 (TNFAIP3), a key suppressor of the nuclear factor-κB inflammatory pathway, was involved in m6A-regulated PBMCs. Mechanistic investigations revealed that m6A affected TNFAIP3 expression by regulation of messenger RNA stability and translocation in TNFAIP3 protein coding sequence. CONCLUSIONS Our study highlights the critical roles of m6A on regulation of inflammation in RA progression. Treatment strategies targeting m6A modification may represent a new option for management of RA.
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Affiliation(s)
- Jifeng Tang
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China and Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Ziqing Yu
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China and Department of Pathology, Fujian Cancer Hospital, Fuzhou, China
| | - Jinfang Xia
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Renquan Jiang
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Shuhui Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Detai Ye
- Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Huiming Sheng
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinpiao Lin
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China and Department of Laboratory Medicine, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
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Zhang J, Fang Z, Song C. Molecular characteristics and clinical implications of serine/arginine-rich splicing factors in human cancer. Aging (Albany NY) 2023; 15:13287-13311. [PMID: 38015716 DOI: 10.18632/aging.205241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/17/2023] [Indexed: 11/30/2023]
Abstract
As critical splicing regulators, serine/arginine-rich splicing factors (SRSFs) play pivotal roles in carcinogenesis. As dysregulation of SRSFs may confer potential cancer risks, targeting SRSFs could provide important insights into cancer therapy. However, a global and comprehensive pattern to elaborate the molecular characteristics, mechanisms, and clinical links of SRSFs in a wide variety of human cancer is still lacking. In this study, a systematic analysis was conducted to reveal the molecular characteristics and clinical implications of SRSFs covering more than 10000 tumour samples of 33 human cancer types. We found that SRSFs experienced prevalent genomic alterations and expression perturbations in multiple cancer types. The DNA methylation, m6A modification, and miRNA regulation of SRSFs were all cancer context-dependent. Importantly, we found that SRSFs were strongly associated with cancer immunity, and were capable of predicting response to immunotherapy. And SRSFs had colossal potential for predicting survival in multiple cancer types, including those that have received immunotherapy. Moreover, we also found that SRSFs could indicate the drug sensitivity of targeted therapy and chemotherapy. Our research highlights the significance of SRSFs in cancer occurrence and development, and provides sufficient resources for understanding the biological characteristics of SRSFs, offering a new and unique perspective for developing cancer therapeutic strategies.
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Affiliation(s)
- Jinjin Zhang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Zhicheng Fang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Congkuan Song
- Department of Thoracic Surgery, Renmin Hospital of Wuhan University, Wuhan, China
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15
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Liang Y, Chen S, Xie J, Yan G, Guo T, Li T, Liu S, Zeng W, Zhang S, Ma K, Chen H, Ou Y, Wang B, Gu W, Duan Y. Establishment of a prognostic model based on m 6A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data. J Cancer Res Clin Oncol 2023; 149:12881-12896. [PMID: 37466793 PMCID: PMC10587019 DOI: 10.1007/s00432-023-05045-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/28/2023] [Indexed: 07/20/2023]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) with high incidence and mortality is one of the most common malignant cancers worldwide. Increasing evidence has reported that N6-methyladenosine (m6A) modification has been considered as a major contribution to the occurrence and development of tumors. METHOD In our study, we comprehensively analyzed the connection between m6A regulatory factors and cancer stem cells (CSCs) of HCC to establish a clinical tool for predicting its outcome. First, we concluded that the expression level of m6A regulatory factors was related with the stemness of hepatocellular carcinoma. Subsequently, we gained a ten hub regulatory factors that were associated with prognosis of hepatocellular carcinoma by overall survival (OS) analysis using ICGC and TCGA datasets, and these regulatory factors included YTHDF1, IGF2BP1, METTL3, IGF2BP3, HNRNPA2B1, IGF2BP2, RBM15B, HNRNPC, RBMX, and LRPPR. Next, we found that these ten hub m6A regulatory factors were highly expressed in CSCs, and CSCs related pathways were also enriched by the gene set variation analysis (GSVA). Then, correlation, consensus clustering and PCA analysis were performed to reveal potential therapeutic benefits of HCC. Moreover, univariate Cox regression (UNICOX), LASSON and multivariate Cox regression (MULTICOX) analyses were adopted to establish HCC prognosis prediction signature. RESULTS Four regulatory factors RBM15B, LRPPRC, IGF2BP1, and IGF2BP3 were picked as valuable prognostic indicators. CONCLUSION In summary, these ten hub regulatory factors would be useful therapeutic targets for HCC treatment, and RBM15B/LRPPRC/IGF2BP1/IGF2BP3 prognostic indicators can be used to guide therapy for HCC patients.
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Affiliation(s)
- Yan Liang
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Sen Chen
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China
| | - Jinghe Xie
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Guanrong Yan
- School of Biomedical Sciences and Engineering, Guangzhou International Campus, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Tingting Guo
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China
| | - Tianyang Li
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China
| | - Shoupei Liu
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China
| | - Weiping Zeng
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, 510180, China
| | - Shuai Zhang
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China
| | - Keqiang Ma
- Department of Hepatobiliary Pancreatic Surgery, Huadu District People's Hospital of Guangzhou, Guangzhou, 510800, People's Republic of China
| | - Honglin Chen
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China
| | - Yimeng Ou
- Department of General Surgery, The First Affiliated Hospital of Guangdong Pharmaceutical University, 19 Nonglin Xia Road, Guangzhou, 510699, People's Republic of China.
| | - Bailin Wang
- Department of General Surgery, Guangzhou Red Cross Hospital, Jinan University, 601 Huangpu Dadao West Road, Guangzhou, 510220, People's Republic of China.
| | - Weili Gu
- Department of Gastroenterology and Hepatology, Guangzhou Digestive Disease Center, School of Medicine, Guangzhou First People's Hospital, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China.
| | - Yuyou Duan
- Laboratory of Stem Cells and Translational Medicine, School of Medicine, South China University of Technology, Guangzhou, 510006, People's Republic of China.
- Laboratory of Stem Cells and Translational Medicine, Institute for Medical Research, The Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou, 510180, China.
- National Engineering Research Center for Tissue Restoration and Reconstruction, South China University of Technology, Guangzhou, 510180, China.
- Laboratory of Stem Cells and Translational Medicine, Institute for Clinical Medicine, The Second Affiliated Hospital, School of Medicine, South China University of Technology, No.1 Panfu Road, Guangzhou, 510180, People's Republic of China.
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16
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Chen P, Shen J. A Disulfidptosis-Related Gene Signature Associated with Prognosis and Immune Cell Infiltration in Osteosarcoma. Bioengineering (Basel) 2023; 10:1121. [PMID: 37892851 PMCID: PMC10603950 DOI: 10.3390/bioengineering10101121] [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: 08/22/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Osteosarcoma (OS) stands as a leading aggressive bone malignancy that primarily affects children and adolescents worldwide. A recently identified form of programmed cell death, termed Disulfidptosis, may have implications for cancer progression. Yet, its role in OS remains elusive. To elucidate this, we undertook a thorough examination of Disulfidptosis-related genes (DRGs) within OS. This involved parsing expression data, clinical attributes, and survival metrics from the TARGET and GEO databases. Our analysis unveiled a pronounced association between the expression of specific DRGs, particularly MYH9 and LRPPRC, and OS outcome. Subsequent to this, we crafted a risk model and a nomogram, both honed for precise prognostication of OS prognosis. Intriguingly, risks associated with DRGs strongly resonated with immune cell infiltration levels, myriad immune checkpoints, genes tethered to immunotherapy, and sensitivities to systematic treatments. To conclude, our study posits that DRGs, especially MYH9 and LRPPRC, hold potential as pivotal architects of the tumor immune milieu in OS. Moreover, they may offer predictive insights into treatment responses and serve as reliable prognostic markers for those diagnosed with OS.
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Affiliation(s)
| | - Jingnan Shen
- Department of Musculoskeletal Oncology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
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17
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Yao J, Song Y, Yu X, Lin Z. Interaction between N 6-methyladenosine modification and the tumor microenvironment in colorectal cancer. Mol Med 2023; 29:129. [PMID: 37737134 PMCID: PMC10515252 DOI: 10.1186/s10020-023-00726-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/08/2023] [Indexed: 09/23/2023] Open
Abstract
The incidence and mortality of colorectal cancer (CRC) are rapidly increasing worldwide. Recently, there has been significant attention given to N6-methyladenosine (m6A), the most common mRNA modification, especially for its effects on CRC development. It is important to note that the progression of CRC would be greatly hindered without the tumor microenvironment (TME). The interaction between CRC cells and their surroundings can activate and influence complex signaling mechanisms of epigenetic changes to affect the survival of tumor cells with a malignant phenotype. Additionally, the TME is influenced by m6A regulatory factors, impacting the progression and prognosis of CRC. In this review, we describe the interactions and specific mechanisms between m6A modification and the metabolic, hypoxia, inflammatory, and immune microenvironments of CRC. Furthermore, we summarize the therapeutic role that m6A modification can play in the CRC microenvironment, and discuss the current status, limitations, and potential future directions in this field. This review aims to provide new insights into the molecular targets and theoretical foundations for the treatment of CRC.
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Affiliation(s)
- Jiali Yao
- Department of Immunology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yeke Song
- Department of Immunology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiaoping Yu
- Health Management Center, Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Zhijie Lin
- Department of Immunology, Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Key Laboratory of Experimental and Translational Non-Coding RNA Research, Yangzhou University, Yangzhou, 225001, China.
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18
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Zhang H, Wu D, Wang Y, Guo K, Spencer CB, Ortoga L, Qu M, Shi Y, Shao Y, Wang Z, Cata JP, Miao C. METTL3-mediated N6-methyladenosine exacerbates ferroptosis via m6A-IGF2BP2-dependent mitochondrial metabolic reprogramming in sepsis-induced acute lung injury. Clin Transl Med 2023; 13:e1389. [PMID: 37715457 PMCID: PMC10504453 DOI: 10.1002/ctm2.1389] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/13/2023] [Accepted: 08/18/2023] [Indexed: 09/17/2023] Open
Abstract
Neutrophil extracellular traps (NETs), released by polymorphonuclear neutrophils (PMNs), exert a robust antimicrobial function in infectious diseases such as sepsis. NETs also contribute to the pathogenesis and exacerbation of sepsis. Although the lung is highly vulnerable to infections, few studies have explored the role of NETs in sepsis-induced acute lung injury (SI-ALI). We demonstrate that NETs induce SI-ALI via enhanced ferroptosis in alveolar epithelial cells. Our findings reveal that the excessive release of NETs in patients and mice with SI-ALI is accompanied by upregulation of ferroptosis depending on METTL3-induced m6A modification of hypoxia-inducible factor-1α (HIF-1α) and subsequent mitochondrial metabolic reprogramming. In addition to conducting METTL3 overexpression and knockdown experiments in vitro, we also investigated the impact of ferroptosis on SI-ALI caused by NETs in a caecum ligation and puncture (CLP)-induced SI-ALI model using METTL3 condition knockout (CKO) mice and wild-type mice. Our results indicate the crucial role of NETs in the progression of SI-ALI via NET-activated METTL3 m6A-IGF2BP2-dependent m6A modification of HIF-1α, which further contributes to metabolic reprogramming and ferroptosis in alveolar epithelial cells.
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Affiliation(s)
- Hao Zhang
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Dan Wu
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yanghanzhao Wang
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Kefang Guo
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | | | - Lilibeth Ortoga
- Department of Biomedical EngineeringOhio State UniversityColumbusOhioUSA
| | - Mengdi Qu
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yuxin Shi
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yuwen Shao
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
| | - Zhiping Wang
- Department of AnesthesiologyAffiliated Hospital of Xuzhou Medical UniversityXuzhouChina
| | - Juan P. Cata
- Department of Anesthesiology and Perioperative MedicineUniversity of Texas‐MD Anderson Cancer CenterHoustonTexasUSA
- Anesthesiology and Surgical Oncology Research GroupHoustonTexasUSA
| | - Changhong Miao
- Department of AnesthesiologyZhongshan HospitalFudan UniversityShanghaiChina
- Shanghai Key Laboratory of Perioperative Stress and ProtectionShanghaiChina
- Department of AnesthesiologyShanghai Medical CollegeFudan UniversityShanghaiChina
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Dai L, Han Y, Yang Z, Zeng Y, Liang W, Shi Z, Tao Y, Liang X, Liu W, Zhou S, Xing Z, Hu W, Wang X. Identification and validation of SOCS1/2/3/4 as potential prognostic biomarkers and correlate with immune infiltration in glioblastoma. J Cell Mol Med 2023. [PMID: 37315184 PMCID: PMC10399539 DOI: 10.1111/jcmm.17807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/11/2023] [Accepted: 06/01/2023] [Indexed: 06/16/2023] Open
Abstract
Suppressor of cytokine signalling (SOCS) 1/2/3/4 are involved in the occurrence and progression of multiple malignancies; however, their prognostic and developmental value in patients with glioblastoma (GBM) remains unclear. The present study used TCGA, ONCOMINE, SangerBox3.0, UALCAN, TIMER2.0, GENEMANIA, TISDB, The Human Protein Atlas (HPA) and other databases to analyse the expression profile, clinical value and prognosis of SOCS1/2/3/4 in GBM, and to explore the potential development mechanism of action of SOCS1/2/3/4 in GBM. The majority of analyses showed that SOCS1/2/3/4 transcription and translation levels in GBM tissues were significantly higher than those in normal tissues. qRT-PCR, western blotting (WB) and immunohistochemical staining were used to verify that SOCS3 was expressed at higher mRNA and protein levels in GBM than in normal tissues or cells. High SOCS1/2/3/4 mRNA expression was associated with poor prognosis in patients with GBM, especially SOCS3. SOCS1/2/3/4 were highly contraindicated, which had few mutations, and were not associated with clinical prognosis. Furthermore, SOCS1/2/3/4 were associated with the infiltration of specific immune cell types. In addition, SOCS3 may affect the prognosis of patients with GBM through JAK/STAT signalling pathway. Analysis of the GBM-specific protein interaction (PPI) network showed that SOCS1/2/3/4 were involved in multiple potential carcinogenic mechanisms of GBM. In addition, colony formation, Transwell, wound healing and western blotting assays revealed that inhibition of SOCS3 decreased the proliferation, migration and invasion of GBM cells. In conclusion, the present study elucidated the expression profile and prognostic value of SOCS1/2/3/4 in GBM, which may provide potential prognostic biomarkers and therapeutic targets for GBM, especially SOCS3.
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Affiliation(s)
- Lirui Dai
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yongjie Han
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zhuo Yang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yuling Zeng
- Department of Blood Transfusion, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Wulong Liang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zimin Shi
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Yiran Tao
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Xianyin Liang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Wanqing Liu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Shaolong Zhou
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Zhe Xing
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Weihua Hu
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
| | - Xinjun Wang
- Department of Neurosurgery, The Fifth Affiliated Hospital of Zhengzhou University, Zhengzhou University, Zhengzhou, China
- Institute of Neuroscience, Zhengzhou University, Zhengzhou, China
- Henan International Joint Laboratory of Glioma Metabolism and Microenvironment Research, Zhengzhou, China
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20
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Zhu TY, Hong LL, Ling ZQ. Oncofetal protein IGF2BPs in human cancer: functions, mechanisms and therapeutic potential. Biomark Res 2023; 11:62. [PMID: 37280679 PMCID: PMC10245617 DOI: 10.1186/s40364-023-00499-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/10/2023] [Indexed: 06/08/2023] Open
Abstract
N6-methyladenosine (m6A) is the most prevalent and well-characterized internal chemical modification in eukaryotic RNA, influencing gene expression and phenotypic changes by controlling RNA fate. Insulin-like growth factor-2 mRNA-binding proteins (IGF2BPs) preferentially function as m6A effector proteins, promoting stability and translation of m6A-modified RNAs. IGF2BPs, particularly IGF2BP1 and IGF2BP3, are widely recognized as oncofetal proteins predominantly expressed in cancer rather than normal tissues, playing a critical role in tumor initiation and progression. Consequently, IGF2BPs hold potential for clinical applications and serve as a good choice for targeted treatment strategies. In this review, we discuss the functions and mechanisms of IGF2BPs as m6A readers and explore the therapeutic potential of targeting IGF2BPs in human cancer.
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Affiliation(s)
- Tian-Yu Zhu
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China
- The Second School of Clinical Medicine, Wenzhou Medical University, No.109 Xueyuan West Road, Wenzhou, 325027 Zhejiang, China
- Jinhua People's Hospital, No.267 Danxi East Road, Jinhua, 321000 Zhejiang, China
| | - Lian-Lian Hong
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China
| | - Zhi-Qiang Ling
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang, China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310018, Zhejiang, China.
- The Second School of Clinical Medicine, Wenzhou Medical University, No.109 Xueyuan West Road, Wenzhou, 325027 Zhejiang, China.
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21
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Li D, Chen T, Li QG. Identification of a m 6A-related ferroptosis signature as a potential predictive biomarker for lung adenocarcinoma. BMC Pulm Med 2023; 23:128. [PMID: 37072786 PMCID: PMC10111681 DOI: 10.1186/s12890-023-02410-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 03/31/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND Both N6-methyladenosine (m6A) and ferroptosis-related genes are associated with the prognosis of lung adenocarcinoma. However, the predictive value of m6A-related ferroptosis genes remains unclear. Here, we aimed to identify the prognostic value of m6A-related ferroptosis genes in lung adenocarcinoma. METHODS Lung adenocarcinoma sample data were downloaded from the University of California Santa Cruz Xena and Gene Expression Omnibus databases. Spearman's correlation analysis was used to screen for m6A-related ferroptosis genes. Univariate Cox regression, Kaplan-Meier, and Lasso analyses were conducted to identify prognostic m6A-related ferroptosis genes, and stepwise regression was used to construct a prognostic gene signature. The predictive value of the gene signature was assessed using a multivariate Cox analysis. In the validation cohort, survival analysis was performed to verify gene signature stability. The training cohort was divided into high- and low-risk groups according to the median risk score to assess differences between the two groups in terms of gene set variation analysis, somatic mutations, and tumor immune infiltration cells. RESULTS Six m6A-related ferroptosis genes were used to construct a gene signature in the training cohort and a multivariate Cox analysis was conducted to determine the independent prognostic value of these genes in lung adenocarcinoma. In the validation cohort, Kaplan-Meier and receiver operating characteristic analyses confirmed the strong predictive power of this signature for the prognosis of lung adenocarcinoma. Gene set variation analysis showed that the low-risk group was mainly related to immunity, and the high-risk group was mainly related to DNA replication. Somatic mutation analysis revealed that the TP53 gene had the highest mutation rate in the high-risk group. Tumor immune infiltration cell analysis showed that the low-risk group had higher levels of resting CD4 memory T cells and lower levels of M0 macrophages. CONCLUSION Our study identified a novel m6A-related ferroptosis-associated six-gene signature (comprising SLC2A1, HERPUD1, EIF2S1, ACSL3, NCOA4, and CISD1) for predicting lung adenocarcinoma prognosis, yielding a useful prognostic biomarker and potential therapeutic target.
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Affiliation(s)
- Dongdong Li
- Medical College of Nanchang University, Nanchang, 330006, Jiangxi, P. R. China
- Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi, P. R. China
| | - Ting Chen
- Department of Pulmonary and Critical Care Medicine, Wuhan Wuchang Hospital, Wuhan, 430063, Hubei, P. R. China
| | - Qiu-Gen Li
- Medical College of Nanchang University, Nanchang, 330006, Jiangxi, P. R. China.
- Department of Pulmonary and Critical Care Medicine, Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, 330006, Jiangxi, P. R. China.
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22
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Shen HY, Zhang J, Xu D, Xu Z, Liang MX, Chen WQ, Tang JH, Xia WJ. Construction of an m6A-related lncRNA model for predicting prognosis and immunotherapy in patients with lung adenocarcinoma. Medicine (Baltimore) 2023; 102:e33530. [PMID: 37058053 PMCID: PMC10101303 DOI: 10.1097/md.0000000000033530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 03/24/2023] [Indexed: 04/15/2023] Open
Abstract
N6-methyladenosine (m6A)-related lncRNAs could be involved in the development of multiple tumors with an unknown role in lung adenocarcinoma (LUAD). Hence, gene expression data and clinical data of LUAD patients were acquired from The Cancer Genome Atlas Database. The prognostic m6A-related lncRNAs were identified through differential lncRNA expression analysis and Spearman's correlation analysis. The least absolute shrinkage and selection operator regression was used to establish the prognostic risk model, so as to evaluate and validate the predictive performance with survival analysis and receiver operating characteristic curve analysis. The expression of immune checkpoints, immune cell infiltration and drug sensitivity of patients in different risk groups were analyzed separately. A total of 19 prognostic m6A-related lncRNAs were identified to set up the prognostic risk model. The patients were divided into high- and low-risk groups based on the median value of the risk scores. Compared with the patients in the low-risk group, the prognosis of the patients in the high-risk group was relatively worse. The receiver operating characteristic curves indicated that this model had excellent sensitivity and specificity. Multivariate Cox regression analysis demonstrated that the risk score could be supposed as an independent prognostic risk factor. We highlighted that the risk scores were correlated with immune cell infiltration and drug sensitivity for constructing a prognostic risk model in LUAD patients based on m6A-related lncRNAs.
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Affiliation(s)
- Hong-Yu Shen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Gusu School, Nanjing Medical University, Nanjing, China
| | - Jin Zhang
- Department of General Practice, Geriatric Hospital of Nanjing Medical University, Jiangsu Province Geriatric Hospital, Nanjing, China
| | - Di Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zheng Xu
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ming-Xing Liang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Wen-Quan Chen
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jin-Hai Tang
- Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
- Gusu School, Nanjing Medical University, Nanjing, China
| | - Wen-Jia Xia
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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23
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Liu L, Liang L, Li H, Shao W, Yang C, Lin F, Liu J, Zhang J. The role of m6A-mediated PD-1/PD-L1 in antitumor immunity. Biochem Pharmacol 2023; 210:115460. [PMID: 36822438 DOI: 10.1016/j.bcp.2023.115460] [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: 12/18/2022] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023]
Abstract
N6-methyladenosine (m6A) is the most prevalent, abundant and conserved type of internal posttranscriptional RNA modification in eukaryotic cells. Emerging evidence suggests that m6A modifications perform important functions that affect antitumor immunity. Programmed death 1 (PD-1) and programmed cell death-ligand 1 (PD-L1) are the two most well-studied immune checkpoint pathways. The interaction of PD-L1 with its receptor PD-1 inhibits cytotoxic T-cell-mediated tumor responses, and blockade of this interaction has proven to be an effective immunotherapy strategy in various cancers. Unfortunately, few cancer patients benefit from the two tools due to uncertain resistance. m6A plays an important role in affecting RNA biogenesis and process in various cancers. Understanding the molecular mechanism of drug resistance will promote the development of personalized clinical management. In this review, we systematically discussed the mechanisms by which m6A regulates PD-1 and PD-L1 expression and further their functions in the process of tumor immunotherapy and the potential application prospects of m6A-associated molecules. Moreover, mounting m6Ascore is established to evaluate the prognosis of cancer.
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Affiliation(s)
- Li Liu
- The First Affiliated Hospital, Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan, China
| | - Long Liang
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078 Hunan, China
| | - Hui Li
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078 Hunan, China; Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Wenjun Shao
- The First Affiliated Hospital, Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan, China
| | - Chaoying Yang
- Hunan Province Key Laboratory of Basic and Applied Hematology, Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, 410078 Hunan, China
| | - Feng Lin
- Department of Urology Surgery, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, 518033 Guangdong, China.
| | - Jing Liu
- Department of Dermatology, Hunan Key Laboratory of Skin Cancer and Psoriasis, Hunan Engineering Research Center of Skin Health and Disease, Xiangya Clinical Research Center for Cancer Immunotherapy, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China.
| | - Ji Zhang
- The First Affiliated Hospital, Department of Clinical Laboratory Medicine, Institution of Microbiology and Infectious Diseases, Hengyang Medical School, University of South China, Hengyang, 421001 Hunan, China; The Affiliated Nanhua Hospital, Department of Clinical Laboratory, Hengyang Medical School, University of South China, Hengyang, 421002 Hunan, China.
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24
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Wu X, Wang W, Fan S, You L, Li F, Zhang X, Wu H, Tang J, Qi Y, Feng W, Yan L, Ren M. U-shaped association between serum IGF2BP3 and T2DM: A cross-sectional study in Chinese population. J Diabetes 2023; 15:349-361. [PMID: 36891946 PMCID: PMC10101838 DOI: 10.1111/1753-0407.13378] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/03/2023] [Accepted: 02/20/2023] [Indexed: 03/10/2023] Open
Abstract
OBJECTIVE To clarify the expression of N6-methyladenosine (m6 A) modulators involved in the pathogenesis of type 2 diabetes mellitus (T2DM). We further explored the association of serum insulin-like growth factor 2 mRNA-binding proteins 3 (IGF2BP3) levels and odds of T2DM in a high-risk population. METHODS The gene expression data set GSE25724 was obtained from the Gene Expression Omnibus, and a cluster heatmap was generated by using the R package ComplexHeatmap. Differential expression analysis for 13 m6 A RNA methylation regulators between nondiabetic controls and T2DM subjects was performed using an unpaired t test. A cross-sectional design, including 393 subjects (131 patients with newly diagnosed T2DM, 131 age- and sex-matched subjects with prediabetes, and 131 healthy controls), was carried out. The associations between serum IGF2BP3 concentrations and T2DM were modeled by restricted cubic spline and logistic regression models. RESULTS Two upregulated (IGF2BP2 and IGF2BP3) and 5 downregulated (methyltransferase-like 3 [METTL3], alkylation repair homolog protein 1 [ALKBH1], YTH domain family 2 [YTHDF2], YTHDF3, and heterogeneous nuclear ribonucleoprotein [HNRNPC]) m6 A-related genes were found in islet samples of T2DM patients. A U-shaped association existed between serum IGF2BP3 levels and odds of T2DM according to cubic natural spline analysis models, after adjustment for body mass index, waist circumference, diastolic blood pressure, total cholesterol, and triglyeride. Multivariate logistic regression showed that progressively higher odds of T2DM were observed when serum IGF2BP3 levels were below 0.62 ng/mL (odds ratio 3.03 [95% confidence interval 1.23-7.47]) in model 4. CONCLUSION Seven significantly altered m6 A RNA methylation genes were identified in T2DM. There was a U-shaped association between serum IGF2BP3 levels and odds of T2DM in the general Chinese adult population. This study provides important evidence for further examination of the role of m6 A RNA methylation, especially serum IGF2BP3 in T2DM risk assessment.
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Affiliation(s)
- Xiaoying Wu
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
- Department of EndocrinologyNational Center of Gerontology, Beijing Hospital, Peking University Fifth School of Clinical MedicineBeijingChina
| | - Wei Wang
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Shujin Fan
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Lili You
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Feng Li
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Xiaoyun Zhang
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Hongshi Wu
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Juying Tang
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Yiqin Qi
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Wanting Feng
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Li Yan
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
| | - Meng Ren
- Department of EndocrinologySun Yat‐sen Memorial Hospital, Sun Yat‐sen UniversityGuangzhouPeople's Republic of China
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25
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Rehman MU, Tayara H, Chong KT. DL-m6A: Identification of N6-Methyladenosine Sites in Mammals Using Deep Learning Based on Different Encoding Schemes. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:904-911. [PMID: 35857733 DOI: 10.1109/tcbb.2022.3192572] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
N6-methyladenosine (m6A) is a common post-transcriptional alteration that plays a critical function in a variety of biological processes. Although experimental approaches for identifying m6A sites have been developed and deployed, they are currently expensive for transcriptome-wide m6A identification. Some computational strategies for identifying m6A sites have been presented as an effective complement to the experimental procedure. However, their performance still requires improvement. In this study, we have proposed a novel tool called DL-m6A for the identification of m6A sites in mammals using deep learning based on different encoding schemes. The proposed tool uses three encoding schemes which give the required contextual feature representation to the input RNA sequence. Later these contextual feature vectors individually go through several neural network layers for shallow feature extraction after which they are concatenated to a single feature vector. The concatenated feature map is then used by several other layers to extract the deep features so that the insight features of the sequence can be used for the prediction of m6A sites. The proposed tool is firstly evaluated on the tissue-specific dataset and later on a full transcript dataset. To ensure the generalizability of the tool we assessed the proposed model by training it on a full transcript dataset and test on the tissue-specific dataset. The achieved results by the proposed model have outperformed the existing tools. The results demonstrate that the proposed tool can be of great use for the biology experts and therefore a freely accessible web-server is created which can be accessed at: http://nsclbio.jbnu.ac.kr/tools/DL-m6A/.
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26
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Yu W, Lin J, Yu T, Lou J, Qian C, Xu A, Liu B, Tao H, Jin L. The regulation of N6-methyladenosine modification in PD-L1-induced anti-tumor immunity. Immunol Cell Biol 2023; 101:204-215. [PMID: 36630591 DOI: 10.1111/imcb.12620] [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: 09/08/2022] [Revised: 12/09/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
There is growing evidence that programmed death ligand-1 (PD-L1) has exciting therapeutic efficacy in hematological malignancy and partial solid tumors. However, many patients still face failure with the treatment of immune checkpoint blockade because of PD-L1 expression regulation during transcription and post-transcription processes, including N6-methyladenosine (m6A). Similar to the epigenetic regulation in DNA and histones, recent research has revealed the essential regulation of m6A modification in RNA nuclear export, metabolism and translation. Recent studies have shown that m6A-induced PD-L1 expression emerges as one of the main reasons for the immunological alteration in this process and contributes to the failure of T cell-induced anti-tumor immunity. The results of preclinical studies demonstrate the potential of m6A-targeted therapy in combination with immune checkpoint blockade. The comprehensive expression of m6A-related genes also provided the possibility to indicate the prognosis and to optimize the treatment for patients of various cancer types. In this review, we focus on the m6A modification in PD-L1 mRNA as well as the regulation of PD-L1 expression in cancer cells and summarize its clinical value in anti-PD-L1 cancer immune therapy.
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Affiliation(s)
- Wei Yu
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Jinti Lin
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Tao Yu
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Jianan Lou
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Chao Qian
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Ankai Xu
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Bing Liu
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Huimin Tao
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
| | - Libin Jin
- Department of Orthopedics, 2nd Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.,Orthopedics Research Institute of Zhejiang University, Hangzhou, China
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27
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Cheng H, Li L, Xue J, Ma J, Ge J. TNC Accelerates Hypoxia-Induced Cardiac Injury in a METTL3-Dependent Manner. Genes (Basel) 2023; 14:591. [PMID: 36980863 PMCID: PMC10048594 DOI: 10.3390/genes14030591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Cardiac fibrosis and cardiomyocyte apoptosis are reparative processes after myocardial infarction (MI), which results in cardiac remodeling and heart failure at last. Tenascin-C (TNC) consists of four distinct domains, which is a large multimodular glycoprotein of the extracellular matrix. It is also a key regulator of proliferation and apoptosis in cardiomyocytes. As a significant m6A regulator, METTL3 binds m6A sites in mRNA to control its degradation, maturation, stabilization, and translation. Whether METTL3 regulates the occurrence and development of myocardial infarction through the m6A modification of TNC mRNA deserves our study. Here, we have demonstrated that overexpression of METTL3 aggravated cardiac dysfunction and cardiac fibrosis after 4 weeks after MI. Moreover, we also demonstrated that TNC resulted in cardiac fibrosis and cardiomyocyte apoptosis after MI. Mechanistically, METTL3 led to enhanced m6A levels of TNC mRNA and promoted TNC mRNA stability. Then, we mutated one m6A site "A" to "T", and the binding ability of METTL3 was reduced. In conclusion, METTL3 is involved in cardiac fibrosis and cardiomyocyte apoptosis by increasing m6A levels of TNC mRNA and may be a promising target for the therapy of cardiac fibrosis after MI.
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Affiliation(s)
- Hao Cheng
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Linnan Li
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Junqiang Xue
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Jianying Ma
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
| | - Junbo Ge
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Shanghai Institute of Cardiovascular Diseases, Shanghai 200032, China
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Geng Q, Cao X, Fan D, Wang Q, Wang X, Zhang M, Zhao L, Jiao Y, Deng T, Liu H, Zhou J, Lou Y, Liang J, Xiao C. Potential medicinal value of N6-methyladenosine in autoimmune diseases and tumours. Br J Pharmacol 2023. [PMID: 36624563 DOI: 10.1111/bph.16030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/23/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
Autoimmune diseases (ADs) are closely related to malignant tumours. On the one hand, ADs can increase the incidence of tumours; on the other hand, malignant tumours can cause rheumatic disease-like manifestations. With the increasing depth of analysis into the mechanism of N6 -methyladenosine (m6A) modification, it has been found that changes in m6A-related modification enzymes are closely related to the occurrence and development of ADs and malignant tumours. In this review, we explore the pathogenesis of ADs and tumours based on m6A modification. According to systematic assessment of the similarities between ADs and tumours, m6A may represent a common target of both diseases. At present, most of the drugs targeting m6A are in the research and development stage, not in clinical trials. Therefore, advancing the development of drugs targeting m6A is of great significance for both the combined treatment of ADs and malignant tumours and improving the quality of life and prognosis of patients.
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Affiliation(s)
- Qishun Geng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xiaoxue Cao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Danping Fan
- Beijing Key Laboratory of Research of Chinese Medicine on Prevention and Treatment for Major Diseases, Experimental Research Center, China Academy of Chinese Medical Sciences, Beijing, China
| | - Qiong Wang
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Xing Wang
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Mengxiao Zhang
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Lu Zhao
- China-Japan Friendship Hospital, Capital Medical University, Beijing, China
| | - Yi Jiao
- China-Japan Friendship Clinical Medical College, Beijing University of Chinese Medicine, Beijing, China
| | - Tingting Deng
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Honglin Liu
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Jing Zhou
- Department of Physiology, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yanni Lou
- Oncology Department of Integrated Traditional Chinese and Western Medicine, China-Japan Friendship Hospital, Beijing, China
| | - Jing Liang
- Department of Obstetrics and Gynecology, China-Japan Friendship Hospital, Beijing, China
| | - Cheng Xiao
- Institute of Clinical Medicine, China-Japan Friendship Hospital, Beijing, China
- China-Japan Friendship Hospital (Institute of Clinical Medical Sciences), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Department of Emergency, China-Japan Friendship Hospital, Beijing, China
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Tian C, An Y, Zhao J, Zhu X, Wei W, Ruan G, Li Y, Pan X. Bone Marrow Mesenchymal Stem Cells Reversed Ovarian Aging-related m6A RNA Methylation Modification Profile in Aged Granulosa Cells. Stem Cell Rev Rep 2023; 19:953-967. [PMID: 36609903 DOI: 10.1007/s12015-022-10485-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/01/2022] [Indexed: 01/09/2023]
Abstract
BACKGROUND Ovarian ageing causes endocrine disturbances and the degeneration of systemic tissue and organ functions to seriously affect women's physical and mental health, and effective treatment methods are urgently needed. Based on our previous studies using juvenile rhesus monkey bone marrow mesenchymal stem cells (BMMSCs) to treat ovarian ageing in rhesus monkey, we found that BMMSCs improved ovarian structure and function. This study continues to explore the mechanism by which BMMSCs reversed granulosa cell (GC) ageing. METHODS A GC ageing model and coculture system of BMMSCs were established, changes in the level of the N6-methyladenosine (m6A) methylation modification were detected, m6A-modified RNA immunoprecipitation sequencing (MeRIP-seq) were performed, correlations between m6A peaks and mRNA expression were determined, and the expression of hub genes was identified using Q-PCR, immunofluorescence staining, and western blot. RESULTS Our results showed that H2O2 successfully induced GC ageing and that BMMSCs reversed measures of GC ageing. BMMSCs increased the expression of the FTO protein and reduced the overall level of m6A. We identified 797 m6A peaks (348 hypomethylated and 449 hypermethylated peaks) and 817 differentially expressed genes (DEGs) (412 upregulated and 405 downregulated) after aged GCs were cocultured with BMMSCs, which significantly associated with ovarian function and epigenetic modification. The epigenetic repressive mark and important cell cycle regulator lysine demethylase 8 (KDM8) was downregulated at both the mRNA and protein levels, histone H3 was upregulated in aged GCs after BMMSC coculture, and KDM8 was upregulated after FTO was inhibited through FB23. CONCLUSIONS Our study revealed an essential role for m6A in BMMSCs in reversing GC ageing, and FTO regulated KDM8 mediates histone H3 changes may as a novel regulatory mechanism in BMMSCs to reverse GC ageing.
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Affiliation(s)
- Chuan Tian
- The Basic Medical Laboratory of the 920Th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan Province, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming, 650032, Yunnan Province, China
| | - Yuanyuan An
- The Affiliated Stomatology of Kunming Medical University, Kunming, 650106, Yunnan Province, China
| | - Jing Zhao
- The Basic Medical Laboratory of the 920Th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan Province, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming, 650032, Yunnan Province, China
| | - Xiangqing Zhu
- The Basic Medical Laboratory of the 920Th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan Province, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming, 650032, Yunnan Province, China
| | - Wei Wei
- The Basic Medical Laboratory of the 920Th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan Province, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming, 650032, Yunnan Province, China
| | - Guangping Ruan
- The Basic Medical Laboratory of the 920Th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan Province, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming, 650032, Yunnan Province, China
| | - Ye Li
- The Basic Medical Laboratory of the 920Th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan Province, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming, 650032, Yunnan Province, China
| | - Xinghua Pan
- The Basic Medical Laboratory of the 920Th Hospital of Joint Logistics Support Force of PLA, The Transfer Medicine Key Laboratory of Cell Therapy Technology of Yunan Province, The Integrated Engineering Laboratory of Cell Biological Medicine of State and Regions, Kunming, 650032, Yunnan Province, China.
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Chen P, Xu J, Cui Z, Wu S, Xie T, Zhang X. Multi-omics analysis of N6-methyladenosine reader IGF2BP3 as a promising biomarker in pan-cancer. Front Immunol 2023; 14:1071675. [PMID: 36761737 PMCID: PMC9905439 DOI: 10.3389/fimmu.2023.1071675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023] Open
Abstract
Background Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) has been reported to exhibit an oncogenic effect as an RNA-binding protein (RBP) by promoting tumor cell proliferation, migration and invasion in several tumor types. However, a pan-cancer analysis of IGF2BP3 is not currently available, and the exact roles of IGF2BP3 in prognosis and immunology in cancer patients remain enigmatic. The main aim of this study was to provide visualization of the systemic prognostic landscape of IGF2BP3 in pan-cancer and to uncover the potential relationship between IGF2BP3 expression in the tumor microenvironment and immune infiltration profile. Methods Raw data on IGF2BP3 expression were obtained from GTEx, CCLE, TCGA, and HPA data portals. We have investigated the expression patterns, diagnostic and prognostic significance, mutation landscapes, functional analysis, and functional states of IGF2BP3 utilizing multiple databases, including HPA, TISIDB, cBioPortal, GeneMANIA, GESA, and CancerSEA. Moreover, the relationship of IGF2BP3 expression with immune infiltrates, TMB, MSI and immune-related genes was evaluated in pan-cancer. IGF2BP3 with drug sensitivity analysis was performed from the CellMiner database. Furthermore, the expression of IGF2BP3 in different grades of glioma was detected by immunohistochemical staining and western blot. Results We found that IGF2BP3 was ubiquitously highly expressed in pan-cancer and significantly correlated with diagnosis, prognosis, TMB, MSI, and drug sensitivity in various types of cancer. Besides, IGF2BP3 was involved in many cancer pathways and varied in different immune and molecular subtypes of cancers. Additionally, IGF2BP3 is critically associated with genetic markers of immunomodulators in various cancers. Finally, we validated that IGF2BP3 protein expression was significantly higher in glioma than in normal tissue, especially in GBM. Conclusions IGF2BP3 may be a potential molecular biomarker for diagnosis and prognosis in pan-cancer, especially for glioma. It could become a novel therapeutic target for various cancers.
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Affiliation(s)
- Pin Chen
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jing Xu
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Zihan Cui
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Medical College of Soochow University, Suzhou, China.,Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Silin Wu
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Xie
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Cancer Center, Shanghai Zhongshan Hospital, Fudan University, Shanghai, China
| | - Xiaobiao Zhang
- Department of Neurosurgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Cancer Center, Shanghai Zhongshan Hospital, Fudan University, Shanghai, China.,Digital Medical Research Center, Fudan University, Shanghai, China
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Wang H, Tang A, Cui Y, Gong H, Li H. LRPPRC facilitates tumor progression and immune evasion through upregulation of m 6A modification of PD-L1 mRNA in hepatocellular carcinoma. Front Immunol 2023; 14:1144774. [PMID: 37063837 PMCID: PMC10097877 DOI: 10.3389/fimmu.2023.1144774] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/07/2023] [Indexed: 04/18/2023] Open
Abstract
Objective LRPPRC is a newly discovered N6-methyladenosine (m6A) modification reader, which potentially affects hepatocellular carcinoma (HCC) progression. PD-L1 in tumor cells is essential for tumor immune evasion. This work investigated the LRPPRC-mediated m6A-modification effect on PD-L1 mRNA and immune escape in HCC. Methods Expression and clinical implication of LRPPRC and PD-L1 were measured in human HCC cohorts. The influence of LRPPRC on malignant behaviors of HCC cells was investigated through in vitro assays and xenograft tumor murine models. The posttranscriptional mechanism of LRPPRC on PD-L1 and anti-tumor immunity was elucidated in HCC cells via RIP, MeRIP-qPCR, RNA stability, immunohistochemical staining, and so forth. Results LRPPRC exhibited the notable upregulated in human HCC tissues, which was in relation to advanced stage and worse overall survival and disease-free survival. Impaired proliferative capacity and G2/M phage arrest were found in LRPPRC-knockout cells, with increased apoptotic level, and attenuated migratory and invasive abilities. In HCC patients and murine models, LRPPRC presented a positive interaction with PD-L1, with negative associations with CD8+, and CD4+ T-cell infiltrations and chemokines CXCL9, and CXCL10. LRPPRC loss downregulated the expression of PD-L1 and its m6A level in HCC cells. Moreover, LRPPRC suppression mitigated tumor growth in murine models and improved anti-tumor immunity and immune infiltration in tumors. Conclusion This work unveiled that LRPPRC may posttranscriptionally upregulate PD-L1 partially with an m6A-dependent manner for heightening mRNA stabilization of PD-L1 and provided a new mechanism for m6A regulator-mediated immunosuppression in HCC.
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Affiliation(s)
- Houhong Wang
- Department of General Surgery, The Affiliated Bozhou Hospital of Anhui Medical University, Bozhou, Anhui, China
| | - Amao Tang
- Department of Gastroenterology, The Affiliated Hangzhou First People’s Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yayun Cui
- Department of Cancer Radiotherapy, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China (Anhui Provincial Cancer Hospital), Hefei, Anhui, China
| | - Huihui Gong
- Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Heng Li
- Department of Comprehensive Surgery, Anhui Provincial Cancer Hospital, West District of The First Affiliated Hospital of USTC, Hefei, Anhui, China
- *Correspondence: Heng Li,
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Fang F, Wang P, Huang H, Ye M, Liu X, Li Q. m 6A RNA methylation regulator-based signature for prognostic prediction and its potential immunological role in uterine corpus endometrial carcinoma. BMC Cancer 2022; 22:1364. [PMID: 36581816 PMCID: PMC9801604 DOI: 10.1186/s12885-022-10490-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/26/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Uterine corpus endometrial carcinoma (UCEC) is the most common female pelvic malignancy worldwide. N6-methyladenosine (m6A) plays an important role in various cellular responses, especially in cancer progression. However, the correlation between prognostic UCEC and m6A RNA methylation regulators remains unclear. METHODS We used The Cancer Genome Atlas (TCGA) to provide a gene signature that could improve the prognostic evaluation of UCEC patients according to the distinct genetic trait of m6A RNA methylation regulators from a bioinformatics perspective. After comparing UCEC subgroups with different genetic profiles of m6A regulators, we identified 71 differentially expressed genes associated with overall survival (OS) and generated a nine-gene signature through least absolute shrinkage and selection operator (LASSO) Cox regression analysis. Finally, we used in vitro and in vivo tumor cell experiments as well as the immune correlation analysis to verify the function of each gene in the proposed gene signature. RESULTS Time-dependent receiver operating characteristic (ROC) curves revealed that the proposed gene signature could predict the outcome of UCEC patients accurately. We found that CDKN2A mainly acted from the perspective of tumor cells, while COL4A4, PXDN, TIGIT, CHODL, LMO3, KCNJ12, L1CAM, and EPHB1 might play a role in UCEC from an immunological point of view. CONCLUSIONS From an epigenetics perspective, the m6A RNA methylation regulator-based gene signature can predict the prognosis of UCEC patients and immune therapeutic efficacy.
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Affiliation(s)
- Fang Fang
- grid.452929.10000 0004 8513 0241Department of Laboratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China ,grid.452929.10000 0004 8513 0241Anhui Province Clinical Research Center for Critical Respiratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China
| | - Peipei Wang
- grid.443626.10000 0004 1798 4069School of Medical Information, Wannan Medical College, Wuhu, 241001 China ,grid.443626.10000 0004 1798 4069Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, 241001 China
| | - Haoyu Huang
- grid.452929.10000 0004 8513 0241Department of Laboratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China ,grid.452929.10000 0004 8513 0241Anhui Province Clinical Research Center for Critical Respiratory Medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China
| | - Mingquan Ye
- grid.443626.10000 0004 1798 4069School of Medical Information, Wannan Medical College, Wuhu, 241001 China ,grid.443626.10000 0004 1798 4069Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, 241001 China
| | - Xiaocen Liu
- grid.452929.10000 0004 8513 0241Department of Nuclear medicine, Yijishan Hospital, the First Affiliated Hospital of Wannan Medical College, Wuhu, 241001 China
| | - Qingqing Li
- grid.443626.10000 0004 1798 4069School of Medical Information, Wannan Medical College, Wuhu, 241001 China ,grid.443626.10000 0004 1798 4069Research Center of Health Big Data Mining and Applications, Wannan Medical College, Wuhu, 241001 China
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Pang Q, Chen H, Wu H, Wang Y, An C, Lai S, Xu J, Wang R, Zhou J, Xiao H. N6-methyladenosine regulators-related immune genes enable predict graft loss and discriminate T-cell mediate rejection in kidney transplantation biopsies for cause. Front Immunol 2022; 13:1039013. [PMID: 36483557 PMCID: PMC9722771 DOI: 10.3389/fimmu.2022.1039013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/01/2022] [Indexed: 11/23/2022] Open
Abstract
Objective The role of m6A modification in kidney transplant-associated immunity, especially in alloimmunity, still remains unknown. This study aims to explore the potential value of m6A-related immune genes in predicting graft loss and diagnosing T cell mediated rejection (TCMR), as well as the possible role they play in renal graft dysfunction. Methods Renal transplant-related cohorts and transcript expression data were obtained from the GEO database. First, we conducted correlation analysis in the discovery cohort to identify the m6A-related immune genes. Then, lasso regression and random forest were used respectively to build prediction models in the prognosis and diagnosis cohort, to predict graft loss and discriminate TCMR in dysfunctional renal grafts. Connectivity map (CMap) analysis was applied to identify potential therapeutic compounds for TCMR. Results The prognostic prediction model effectively predicts the prognosis and survival of renal grafts with clinical indications (P< 0.001) and applies to both rejection and non-rejection situations. The diagnostic prediction model discriminates TCMR in dysfunctional renal grafts with high accuracy (area under curve = 0.891). Meanwhile, the classifier score of the diagnostic model, as a continuity index, is positively correlated with the severity of main pathological injuries of TCMR. Furthermore, it is found that METTL3, FTO, WATP, and RBM15 are likely to play a pivotal part in the regulation of immune response in TCMR. By CMap analysis, several small molecular compounds are found to be able to reverse TCMR including fenoldopam, dextromethorphan, and so on. Conclusions Together, our findings explore the value of m6A-related immune genes in predicting the prognosis of renal grafts and diagnosis of TCMR.
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Affiliation(s)
- Qidan Pang
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Chen
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Hang Wu
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Yong Wang
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Changyong An
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Suhe Lai
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Jia Xu
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Ruiqiong Wang
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China
| | - Juan Zhou
- Department of Nephrology, Bishan Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Hanyu Xiao, ; Juan Zhou,
| | - Hanyu Xiao
- Department of General Surgery/Gastrointestinal Surgery, Bishan Hospital of Chongqing Medical University, Chongqing, China,*Correspondence: Hanyu Xiao, ; Juan Zhou,
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Li Z, Zeng T, Zhou C, Chen Y, Yin W. A prognostic signature model for unveiling tumor progression in lung adenocarcinoma. Front Oncol 2022; 12:1019442. [PMID: 36387251 PMCID: PMC9663930 DOI: 10.3389/fonc.2022.1019442] [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: 08/15/2022] [Accepted: 10/17/2022] [Indexed: 01/24/2023] Open
Abstract
A more accurate prognosis is important for clinical treatment of lung adenocarcinoma. However, due to the limitation of sample and technical bias, most prognostic signatures lacked reproducibility, and few were applied to clinical practice. In addition, understanding the molecular driving mechanism is indispensable for developing more promising therapies for lung adenocarcinoma. Here, we built an unbiased prognostic significance model to perform an integrative analysis, including differentially expressed genes and clinical data with lung adenocarcinoma patients from TCGA. Multivariable Cox proportional hazards model with the Lasso penalty and 10-fold cross-validate were used to identify the best gene signature. We generated a 17-gene signature for prognostic risk prediction based on the overall survival time of lung adenocarcinoma patients. To further test the model's predictive ability, we have applied an independent GEO database to verify the predictive ability of prognostic signature. The model can more objectively describe several biological processes related to tumors and reveal important molecular mechanisms in tumor development by GO and KEGG analysis. Furthermore, differential expression analysis by GSEA revealed that tumor microenvironments such as ER stress, exosome, and immune microenvironment were enriched. Using single-cell RNA sequence technology, we found that risk score was positively correlated with lung adenocarcinoma marker genes and copy number variation but negatively correlated with lung epithelial marker genes. High-risk cell populations with the model had stronger cancer stemness and tumor-related pathway activation. As we expected, the risk score was in accordance with the malignancy of each cluster from tumor progression. In conclusion, the risking model established in this study is more reliable than others in evaluating the prognosis of LUAD patients.
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Affiliation(s)
- Zijian Li
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Tao Zeng
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Chong Zhou
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Yan Chen
- Department of Chinese Medicine, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu, China,*Correspondence: Wu Yin, ; Yan Chen,
| | - Wu Yin
- State Key Lab of Pharmaceutical Biotechnology, College of Life Sciences, Nanjing University, Nanjing, Jiangsu, China,*Correspondence: Wu Yin, ; Yan Chen,
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Pan YQ, Xiao Y, Long T, Liu C, Gao WH, Sun YY, Liu C, Shi YJ, Li S, Shao AZ. Prognostic value of lncRNAs related to fatty acid metabolism in lung adenocarcinoma and their correlation with tumor microenvironment based on bioinformatics analysis. Front Oncol 2022; 12:1022097. [DOI: 10.3389/fonc.2022.1022097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/01/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundAs a key regulator of metabolic pathways, long non-coding RNA (lncRNA) has received much attention for its relationship with reprogrammed fatty acid metabolism (FAM). This study aimed to investigate the role of the FAM-related lncRNAs in the prognostic management of patients with lung adenocarcinoma (LUAD) using bioinformatics analysis techniques.MethodsWe obtained LUAD-related transcriptomic data and clinical information from The Cancer Genome Atlas (TCGA) database. The lncRNA risk models associated with FMA were constructed by single-sample gene set enrichment analysis (ssGSEA), weighted gene co-expression network (WGCNA), differential expression analysis, overlap analysis, and Cox regression analysis. Kaplan-Meier (K-M) and receiver operating characteristic (ROC) curves were utilized to assess the predictive validity of the risk model. Gene set variation analysis (GSVA) revealed molecular mechanisms associated with the risk model. ssGSEA and microenvironment cell populations-counter (MCP-counter) demonstrated the immune landscape of LUAD patients. The relationships between lncRNAs, miRNAs, and mRNAs were predicted by using LncBase v.2 and miRTarBase. The lncRNA-miRNA-mRNA regulatory network was visualized with Cytoscape v3.4.0. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was performed using DAVID v6.8. Quantitative real-time fluorescence PCR (qRT-PCR) was performed to verify the expression levels of the prognostic lncRNAs.ResultsWe identified 249 differentially expressed FMA-related lncRNAs in TCGA-LUAD, six of which were used to construct a risk model with appreciable predictive power. GSVA results suggested that the risk model may be involved in regulating fatty acid synthesis/metabolism, gene repair, and immune/inflammatory responses in the LUAD process. Immune landscape analysis demonstrated a lower abundance of immune cells in the high-risk group of patients associated with poor prognosis. Moreover, we predicted 279 competing endogenous RNA (ceRNA) mechanisms for 6 prognostic lncRNAs with 39 miRNAs and 201 mRNAs. Functional enrichment analysis indicated that the ceRNA network may be involved in the process of LUAD by participating in genomic transcription, influencing the cell cycle, and regulating tissue and organogenesis. In vitro experiments showed that prognostic lncRNA CTA-384D8.35, lncRNA RP5-1059L7.1, and lncRNA Z83851.4 were significantly upregulated in LUAD primary tumor tissues, while lncRNA RP11-401P9.4, lncRNA CTA-384D8.35, and lncRNA RP11-259K15.2 were expressed at higher levels in paraneoplastic tissues.ConclusionIn summary, the prognostic factors identified in this study can be used as potential biomarkers for clinical applications. ceRNA network construction provides a new vision for the study of LUAD pathogenesis.
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Wu X, Deng Z, Zhao Q. Immunotherapy improves disease prognosis by affecting the tumor microenvironment: A bibliometric study. Front Immunol 2022; 13:967076. [PMID: 36275770 PMCID: PMC9582136 DOI: 10.3389/fimmu.2022.967076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Accepted: 09/15/2022] [Indexed: 12/24/2022] Open
Abstract
Background Immunotherapy has shown great potential for the treatment of multiple cancer and has been proven to be closely related to the tumor microenvironment. This article reveals collaborations and interactions among authors, nations, organizations, and periodicals assesses the knowledge base, and discovers hot tendencies and new topics associated with immunotherapy-tumor microenvironment (TME) research. Methods This article utilized bibliometrics and visual methods to provide a comprehensive overview of immunotherapy-TME research. Our team retrieved the WoSCC for research and reviews associated with immunotherapy and the tumor microenvironment. VOSviewer and Citespace were primarily used for literature measurement and knowledge graph analysis. Result All English articles and reviews on cancer immunotherapy effectiveness were collected, and 1,419 academic journals with 53,773 authors from 7,008 institutions in 92 countries/regions were found. Publications associated with immunotherapy-TME research were stably increasing. Frontiers of Immunology (n = 722) published the most papers on immunotherapy-TME, and Cancer Research (n = 6761) was the top co-cited journal. The published journals and co-cited journals focused on cancer and immunology fields. The League of European Research Universities (n = 978), Harvard University (n = 528), and the University of Texas system (n = 520) were the most productive institutions. Yang Liu (n = 34) and Topalian (n = 1978) ranked first among the top 10 scholars and co-cited scholars. Simultaneously, immunotherapy-TME researchers were involved in active collaborations. Elements of TME, the foundation of immunotherapy, and the application of immunotherapy in cancers represented the three principal aspects of immunotherapy-TME research. The latest hot spots are drug resistance, prognosis prediction, efficacy prediction, and m6A. Nanomedicine and m6A may be future hot topics. Future research in immunotherapy-TME may be directed at discovering how m6A modification affects tumor development by altering the tumor microenvironment and exploring how to enhance response or reduce drug resistance to immunotherapy by reversing or mediating the physicochemical properties of the TME. Conclusions M6A and nanomedicine are also emerging hotspots in time zone diagrams with high centrality, and prognosis prediction using bioinformatics based on the development of prediction technology may be another future research hotspot.
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Affiliation(s)
- Xin Wu
- Department of Spine Surgery, Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhen Deng
- Department of Hepatopancreatobiliary Surgery, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Qiangqiang Zhao
- Department of Hematology, The Qinghai Provincial People’s Hospital, Xining, China
- *Correspondence: Qiangqiang Zhao,
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Li Y, Zhang W, Dai Y, Chen K. Identification and verification of IGFBP3 and YTHDC1 as biomarkers associated with immune infiltration and mitophagy in hypertrophic cardiomyopathy. Front Genet 2022; 13:986995. [PMID: 36267414 PMCID: PMC9577180 DOI: 10.3389/fgene.2022.986995] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/20/2022] [Indexed: 11/27/2022] Open
Abstract
Background: Hypertrophic cardiomyopathy (HCM) is the main cause of sudden cardiac death among young adults, yet its pathogenesis remains vague. N6-methyladenosine (m6A) methylation modification was involved in various cardiovascular diseases such as coronary heart disease and heart failure, although its influence on HCM remains unclear. This study aimed to explore the potential role of m6A in the diagnosis and pathogenesis of HCM. Methods: GSE36961 including 106 HCM and 39 controls was used in the study. The HCM-related m6A regulators were selected using support vector machine recursive feature elimination and random forest algorithm. A significant gene signature was then established using least absolute shrinkage and selection operator and then verified by GSE130036. Subgroup classification of HCM was performed based on the expression of m6A biomarkers. Gene set variation analysis was employed to explore the functional difference between distinct subgroups. Weighted gene co-expression network analysis was used to determine the m6A-related hub module. Single-sample gene set enrichment analysis was conducted to assess the immune and mitophagy features between subgroups. Besides, transfection of recombinant plasmids with targeted genes into H9c2 cells was performed to further verify the function of the significant biomarkers. Results: Significant difference existed in m6A landscape between HCM and control patients, among which IGFBP3 and YTHDC1 were identified as the independent biomarkers of HCM. Highly infiltrated immune cells (MDSC, macrophages, etc.), more enriched immune-related pathways (TNFα signaling via NFκB and IL6-JAK-STAT3 signaling) and cardiac remodeling-associated pathways (epithelial mesenchymal transition, angiogenesis, etc.) were identified in the subgroup with higher IGFBP3. Consistently, overexpression of IGFBP3 in H9c2 cells led to upregulation of extracellular-matrix-related genes (COL1A2, COL3A1 and MMP9) and inflammation-related genes (TNFα and IL6). Besides, higher YTHDC1 expression seemed to be consistent with less-activated mitophagy (PINK1-PRKN mediated mitophagy) and energy metabolism. Further experiments demonstrated that overexpression of YTHDC1 resulted in up-regulation of PINK and PRKN in cardiomyocytes, which are essential genes mediating mitophagy. Conclusion: Two m6A readers (IGFBP3 and YTHDC1) well distinguished HCM and may facilitate clinical diagnosis. IGFBP3 may play a role in the immune-microenvironments and remodeling of cardiac tissues, while YTHDC1 may influence mitophagy and energy metabolism in HCM.
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Affiliation(s)
- Yao Li
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Zhang
- Department of Urology, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yan Dai
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yan Dai, ; Keping Chen,
| | - Keping Chen
- State Key Laboratory of Cardiovascular Disease, Fuwai Hospital, National Center for Cardiovascular Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Yan Dai, ; Keping Chen,
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Lin CX, Chen ZJ, Peng QL, Xiang KR, Xiao DQ, Chen RX, Cui T, Huang YS, Liu HW. The m 6A-methylated mRNA pattern and the activation of the Wnt signaling pathway under the hyper-m 6A-modifying condition in the keloid. Front Cell Dev Biol 2022; 10:947337. [PMID: 36263010 PMCID: PMC9574062 DOI: 10.3389/fcell.2022.947337] [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: 05/18/2022] [Accepted: 09/08/2022] [Indexed: 11/13/2022] Open
Abstract
Purpose: The present study was carried out to investigate the global m6A-modified RNA pattern and possible mechanisms underlying the pathogenesis of keloid. Method: In total, 14 normal skin and 14 keloid tissue samples were first collected on clinics. Then, three samples from each group were randomly selected to be verified with the Western blotting to determine the level of methyltransferase and demethylase. The total RNA of all samples in each group was isolated and subjected to the analysis of MeRIP sequencing and RNA sequencing. Using software of MeTDiff and htseq-count, the m6A peaks and differentially expressed genes (DEGs) were determined within the fold change >2 and p-value < 0.05. The top 10 pathways of m6A-modified genes in each group and the differentially expressed genes were enriched by the Kyoto Encyclopedia of Genes and Genomes signaling pathways. Finally, the closely associated pathway was determined using the Western blotting and immunofluorescence staining. Results: There was a higher protein level of WTAP and Mettl3 in the keloid than in the normal tissue. In the keloid samples, 21,020 unique m6A peaks with 6,573 unique m6A-associated genetic transcripts appeared. In the normal tissue, 4,028 unique m6A peaks with 779 m6A-associated modified genes appeared. In the RNA sequencing, there were 847 genes significantly changed between these groups, transcriptionally. The genes with m6A-methylated modification and the upregulated differentially expressed genes between two tissues were both mainly related to the Wnt signaling pathway. Moreover, the hyper-m6A-modified Wnt/β-catenin pathway in keloid was verified with Western blotting. From the immunofluorescence staining results, we found that the accumulated fibroblasts were under a hyper-m6A condition in the keloid, and the Wnt/β-Catenin signaling pathway was mainly activated in the fibroblasts. Conclusion: The fibroblasts in the keloid were under a cellular hyper-m6A-methylated condition, and the hyper-m6A-modified highly expressed Wnt/β-catenin pathway in the dermal fibroblasts might promote the pathogenesis of keloid.
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Affiliation(s)
- Can-Xiang Lin
- Department of Plastic Surgery of the First Affiliated Hospital of Jinan University, Institute of New Technology of Plastic Surgery of Jinan University, Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou, China
| | - Zhi-Jing Chen
- Department of Plastic Surgery of the First Affiliated Hospital of Jinan University, Institute of New Technology of Plastic Surgery of Jinan University, Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou, China
| | - Qi-Lin Peng
- The Research Center of Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Ke-Rong Xiang
- Department of Plastic Surgery of the First Affiliated Hospital of Jinan University, Institute of New Technology of Plastic Surgery of Jinan University, Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou, China
| | - Du-Qing Xiao
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ruo-Xi Chen
- Department of Plastic Surgery of the First Affiliated Hospital of Jinan University, Institute of New Technology of Plastic Surgery of Jinan University, Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou, China
| | - Taixing Cui
- Department of Cell Biology and Anatomy, University of South Carolina School of Medicine, Columbia, SC, United States,*Correspondence: Taixing Cui, ; Yue-Sheng Huang, ; Hong-Wei Liu,
| | - Yue-Sheng Huang
- Department of Wound Repair, Institute of Wound Repair and Regeneration Medicine, Southern University of Science and Technology Hospital, Southern University of Science and Technology School of Medicine, Shenzhen, China,*Correspondence: Taixing Cui, ; Yue-Sheng Huang, ; Hong-Wei Liu,
| | - Hong-Wei Liu
- Department of Plastic Surgery of the First Affiliated Hospital of Jinan University, Institute of New Technology of Plastic Surgery of Jinan University, Key Laboratory of Regenerative Medicine of Ministry of Education, Guangzhou, China,*Correspondence: Taixing Cui, ; Yue-Sheng Huang, ; Hong-Wei Liu,
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Wu H, Xu H, Huang S, Tang Y, Tang J, Zhou H, Xie L, Qiao G. m 6A-binding protein IGF2BP1 promotes the malignant phenotypes of lung adenocarcinoma. Front Oncol 2022; 12:989817. [PMID: 36249006 PMCID: PMC9554348 DOI: 10.3389/fonc.2022.989817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/06/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Lung adenocarcinoma (LUAD), the most common type of lung cancer, poses a significant threat to the life of patients. N6-methyladenosine modification is the most abundant epigenetic modification and may play an important role in the lung carcinogenesis. IGF2BP1 is a newly discovered m6A-binding protein, but little is known about its role in LUAD. METHODS Data from TCGA, GEO, Kaplan-Meier Plotter, and GEPIA databases were systematically analyzed to access the expression and prognostic value of IGF2BP1 on LUAD. Real-time polymerase chain reaction, Western blot, and immunohistochemistry were performed to detect the mRNA and protein level of IGF2BP1 in LUAD tissues and para-carcinoma tissues. Functional cell experiments, including Cell Counting Kit-8 assay, Transwell invasion assay, wound healing assay, Annexin V-FITC/PI double-staining assay, and TUNEL assay, were used to investigate the functions of IGF2BP1 on LUAD cell proliferation, invasion, migration, and apoptosis, respectively. The top 50 genes that were positively or negatively related to the expression of IGF2BP1 were identified, and pathway enrichment analysis was performed. m6A modification sites within IGF2BP1-related genes were predicted by SRAMP. RESULT 16 m6A regulators were significantly differentially expressed in LUAD tissues. IGF2BP1 was upregulated in LUAD tissues compared with para-carcinoma tissues. High expression of IGF2PB1 was significantly associated with higher clinical stages and poor prognosis of LUAD patients. Furthermore, our functional experiments indicated that IGF2BP1 facilitated cell proliferation, invasion, and migration and suppressed apoptosis in LUAD. Functional enrichment analysis of IGF2BP1-related genes indicated enrichment in several pathways related to oncogenesis. Additionally, m6A modification sites were detected within IGF2BP1-related genes. CONCLUSIONS Our findings demonstrate that IGF2BP1 plays a contributory role in the development and progression of LUAD. IGF2BP1 has the potential to become a prognostic predictor and therapeutic target for LUAD.
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Affiliation(s)
- Hansheng Wu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Haijie Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou, China
- Shantou University Medical College, Shantou, China
| | - Shujie Huang
- Shantou University Medical College, Shantou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yong Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jiming Tang
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Liang Xie
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Guibin Qiao
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Thoracic Surgery, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
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Li Y, Dong Y, Zhao S, Gao J, Hao X, Wang Z, Li M, Wang M, Liu Y, Yu X, Xu W. Serum-derived piR-hsa-164586 of extracellular vesicles as a novel biomarker for early diagnosis of non-small cell lung cancer. Front Oncol 2022; 12:850363. [PMID: 36249068 PMCID: PMC9559724 DOI: 10.3389/fonc.2022.850363] [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: 01/07/2022] [Accepted: 08/10/2022] [Indexed: 11/13/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is a major cause of death in those with malignant tumors. To achieve the early diagnosis of NSCLC, we investigated serum-derived Piwi-interacting RNA (piRNA) of extracellular vesicles to filter diagnostic biomarkers for NSCLC. High-throughput sequencing from cancerous tissues and adjacent noncancerous tissues in patients with NSCLC was first applied to recognize candidate piRNAs as diagnostic biomarkers. These screened piRNAs were further validated in 115 patients (including 95 cases in stage I) and 47 healthy individuals using quantitative real-time PCR (qRT-PCR). We showed that piR-hsa-164586 was significantly upregulated compared with paracancerous tissues and extracellular vesicles from the serum samples of healthy individuals. Moreover, the area under the curve (AUC) value of piR-hsa-164586 was 0.623 and 0.624 to distinguish patients with all stages or stage I of NSCLC, respectively, from healthy individuals. The diagnostic performance of piR-hsa-164586 was greatly improved compared with the cytokeratin-19-fragment (CYFRA21-1). Additionally, piR-hs-164586 was associated with the clinical characteristics of patients with NSCLC. Its expression was associated with the age and TNM stage of patients with NSCLC, indicating that it can serve as an effective and promising biomarker for the early diagnosis of NSCLC.
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Affiliation(s)
- Yanli Li
- Department of Pathology and Pathophysiology, The Medical Faculty of Qingdao University, Qingdao, China
| | - Yanhan Dong
- Institute of Translational Medicine, Qingdao University, Qingdao, China
| | - Shupeng Zhao
- Asset and Laboratory Management Office, Qingdao University, Qingdao, China
| | - Jinning Gao
- Institute of Translational Medicine, Qingdao University, Qingdao, China
| | - Xiaodan Hao
- Institute of Translational Medicine, Qingdao University, Qingdao, China
| | - Zibo Wang
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Meng Li
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Mengyuan Wang
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Yiming Liu
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
| | - Xiaoling Yu
- Department of Pathology and Pathophysiology, The Medical Faculty of Qingdao University, Qingdao, China
- *Correspondence: Xiaoling Yu, ; Wenhua Xu,
| | - Wenhua Xu
- Department of Inspection, The Medical Faculty of Qingdao University, Qingdao, China
- *Correspondence: Xiaoling Yu, ; Wenhua Xu,
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Huang S, Chen S, Zhang D, Gao J, Liu L. Enhancer-associated regulatory network and gene signature based on transcriptome and methylation data to predict the survival of patients with lung adenocarcinoma. Front Genet 2022; 13:fgene-2022-1008602. [PMID: 36212131 PMCID: PMC9538943 DOI: 10.3389/fgene.2022.1008602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
Accumulating evidence has proved that aberrant methylation of enhancers plays regulatory roles in gene expression for various cancers including lung adenocarcinoma (LUAD). In this study, the transcriptome and methylation data of The Cancer Genome Atlas (TCGA)-LUAD cohort were comprehensively analyzed with a five-step Enhancer Linking by Methylation/Expression Relationships (ELMER) process. Step 1: 131,371 distal (2 kb upstream from the transcription start site) probes were obtained. Step 2: 10,665 distal hypomethylated probes were identified in an unsupervised mode with the get.diff.meth function. Step 3: 699 probe-gene pairs with negative correlations were screened using the get.pair function in an unsupervised mode. Step 4: After mapping with probes, 768 motifs were obtained and 24 of them were enriched. Step 5: 127 transcription factors (TFs) with differential expressions and negative correlations with methylation levels were screened, which were corresponding to 21 motifs. After the ELMER process, a prognostic “TFs-motifs-genes” regulatory network was constructed. The Least absolute shrinkage and selection operator (LASSO) and Stepwise regression analyses were further applied to identify variables in the TCGA-LUAD cohort and an eight-gene signature was constructed for calculating the risk score. The risk score was verified in two independent validation cohorts. The area under curve values of receiver operating characteristic curves predicting 1-, 3-, and 5-years survival ranged from 0.633 to 0.764. With the increase of the risk scores, both the survival statuses and clinical traits showed a worse tendency. There were significant differences in the degrees of immune cell infiltration, TMB values, and TIDE scores between the high-risk and low-risk groups. Finally, a better-performing prognostic nomogram was integrated with the risk score and other clinical traits. In short, this multi-omics analysis demonstrated the application of ELMER in analyzing enhancer-associated regulatory network in LUAD, which provided promising strategies for epigenetic therapy and prognostic biomarkers.
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Affiliation(s)
- Shihao Huang
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, Dalian, Liaoning, China
| | - Shiyu Chen
- Department of Laboratory Medicine, Nanxishan Hospital of Guangxi Zhuang Autonomous Region, Guilin, China
| | - Di Zhang
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, Dalian, Liaoning, China
| | - Jiamei Gao
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, Dalian, Liaoning, China
| | - Linhua Liu
- Department of Biochemistry, Institute of Glycobiology, Dalian Medical University, Dalian, Liaoning, China
- *Correspondence: Linhua Liu,
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Chen Z, Yang J, Li Y, Zeng W, Bai Y, Ding C, Xu C, Li C, Chen J, Ju S, Tang L, Zhao J. Integration of single-cell and bulk RNA-seq to establish a predictive signature based on the differentiation trajectory of M2 macrophages in lung adenocarcinoma. Front Genet 2022; 13:1010440. [PMID: 36171876 PMCID: PMC9510778 DOI: 10.3389/fgene.2022.1010440] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 08/29/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Tumor-associated macrophages as important members of the tumor microenvironment, are highly plastic and heterogeneous. TAMs can be classified into two preliminary subtypes: M1 and M2 macrophages. M2 macrophages are significantly associated with the progression of lung adenocarcinoma. However, no study has investigated the heterogeneity among M2 macrophages and their differentiation-related genes at the single-cell level to guide the clinical treatment of lung adenocarcinoma. Methods: Using the available annotation information from the Tumor Immune Single-cell Hub database, we clustered and annotated 12 lung adenocarcinoma samples using the R package ‘Seurat’. Subsequently, we extracted M2 macrophages for secondary clustering analysis and performed cell trajectory analysis using the R package ‘monocle2’. Based on heterogeneous genes associated with the differentiation trajectory of M2 macrophages, we established a prognostic lung adenocarcinoma model using Lasso-Cox and multivariate stepwise regression. In addition, we also performed immunotherapy and chemotherapy predictions. Results: M2 macrophages exhibit heterogeneity among themselves. M2 macrophages in different differentiation states showed significant differences in pathway activation and immune cell communication. Prognostic signature based on heterogeneous genes can be used to classify the prognostic status and abundance of immune cell infiltration in lung adenocarcinoma patients. In addition, the calculation of the Tumor Immune Dysfunction and Exclusion (TIDE) algorithm and the validation of the GSE126044 database indicated that lung adenocarcinoma patients with high-risk scores had poorer treatment outcomes when receiving immune checkpoint inhibitors treatment. Conclusion: Based on scRNA-seq and Bulk-seq data, we identified M2 macrophage-associated prognostic signature with a potential clinical utility to improve precision therapy.
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Affiliation(s)
- Zhike Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yu Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Weibiao Zeng
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yiling Bai
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Cheng Ding
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chun Xu
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Chang Li
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Chen
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Sheng Ju
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Sheng Ju, ; Lijuan Tang, ; Jun Zhao,
| | - Lijuan Tang
- Dalian Medical University, Dalian, Liaoning, China
- Department of Pathology, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
- *Correspondence: Sheng Ju, ; Lijuan Tang, ; Jun Zhao,
| | - Jun Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- Institute of Thoracic Surgery, The First Affiliated Hospital of Soochow University, Suzhou, China
- *Correspondence: Sheng Ju, ; Lijuan Tang, ; Jun Zhao,
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Shen X, Zhong J, He J, Han J, Chen N. Identification of m6A modification patterns and development of m6A-hypoxia prognostic signature to characterize tumor microenvironment in triple-negative breast cancer. Front Immunol 2022; 13:978092. [PMID: 36105819 PMCID: PMC9465332 DOI: 10.3389/fimmu.2022.978092] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 08/10/2022] [Indexed: 11/20/2022] Open
Abstract
Background N6-methylation (m6A) modification of RNA has been found to have essential effects on aspects of the tumor microenvironment (TME) including hypoxia status and mobilization of immune cells. However, there are no studies to explore the combined effect of m6A modification and hypoxia on molecular heterogeneity and TME of triple-negative breast cancer (TNBC). Methods We collected The Cancer Genome Atlas (TCGA-TNBC, N=139), the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC-TNBC, N=297), the GSE103091, GSE21653, and GSE135565 series from the Gene Expression Omnibus (GEO-TNBC, N=247), and FUSCCTNBC (N=245) for our study. The non-negative matrix factorization algorithm was used to cluster TNBC samples. Immune cell infiltration was analyzed by the CIBERSORT algorithm. The enrichment scores were calculated by single-sample gene set enrichment analysis(ssGSEA) to characterize TME in TNBC samples. Immunohistochemistry (IHC) and qRT-PCR were performed to detect the gene expression. Results Based on the expression of m6A-related genes, we identified three distinct m6A clusters (denoted A, B, and C) in TNBC samples. Comparing the TME characteristics among the three clusters, we observed that cluster C was strongly related to hypoxia status and immune suppression, whereas clusters A and B displayed more immune cell infiltration. Therefore, we combine m6A and hypoxia related genes to classify two m6A-hypoxia clusters of TNBC and screened six prognostic genes by LASSO-Cox regression to construct a m6A-hypoxia signature(MHPS), which divided TNBC samples into high- and low-risk groups. We identified different TME features, immune cell infiltration between the two groups, and a better immunotherapy response was observed in the low-risk group. A nomogram was constructed with tumor size, lymph node, and risk score to improve clinical application of MHPS. Conclusion We identified distinct TME characteristics of TNBC based on three different m6A modification patterns. Then, we constructed a specific m6A-hypoxia signature for TNBC to evaluate risk and predict immunotherapy response of patients, to enable more accurate treatment in the future.
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Affiliation(s)
- Xi Shen
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jianxin Zhong
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China
| | - Jinlan He
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Jiaqi Han
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Nianyong Chen
- Department of Head and Neck Oncology and Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, China
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Comprehensive Analysis of Gene Signatures of m6ARNA Methylation Regulators in Lung Adenocarcinoma and Development of a Risk Scoring System. J Immunol Res 2022; 2022:7519838. [PMID: 36061307 PMCID: PMC9428682 DOI: 10.1155/2022/7519838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/15/2022] [Indexed: 12/02/2022] Open
Abstract
The recent application of targeted immunotherapy has greatly improved the clinical outcomes of patients with lung adenocarcinoma (LUAD), but drug resistance continues to emerge, and to evaluate and to improve patient prognosis are arduous. The diagnostic and prognostic value of N6-methyladenosine (M6A) in LUAD has attracted increasing attention. We systematically studied correlations among important M6A methylation regulators, tumor mutational burden (TMB), and immune infiltration in clinical and sequencing data from the LUAD cohort of the cancer genome map (TCGA). The molecular subtype clusters 1 and 2 were identified by the consensus clustering of 16 M6A regulatory factors. Clinical prognosis, M6A regulatory factor expression, TMB, pathway enrichment, and immune cell infiltration significantly differed between clusters 1 and 2. Compared with other clinical traits, a prognostic risk score system constructed using the M6A regulatory factors HNRNPA2B1 and HNRNPC can serve as an independent prognostic method for LUAD, with higher predictive sensitivity and specificity. Risk scores were significantly higher for cluster 2 than 1, which was consistent with the trend towards a better prognosis in cluster 1. Overall, our findings revealed an important role of M6A methylation regulators in LUAD, and our risk scoring system involving these regulators might help to screen groups at high risk for LUAD and provide important theoretical bioinformatic support for evaluating the prognosis of such patients.
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Song C, Lin W, Meng H, Li N, Geng Q. Integrated Analysis Reveals the Potential Significance of HDAC Family Genes in Lung Adenocarcinoma. Front Genet 2022; 13:862977. [PMID: 36072664 PMCID: PMC9441483 DOI: 10.3389/fgene.2022.862977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 06/22/2022] [Indexed: 11/22/2022] Open
Abstract
Histone deacetylases comprise a family of 18 genes, and classical HDACs are a promising class of novel anticancer drug targets. However, to date, no systematic study has been comprehensive to reveal the potential significance of these 18 genes in lung adenocarcinoma (LUAD). Here, we used a systematic bioinformatics approach to comprehensively describe the biological characteristics of the HDACs in LUAD. Unsupervised consensus clustering was performed to identify LUAD molecular subtypes. The ssGSEA, CIBERSORT, MCP counter, and ESTIMATE algorithms were used to depict the tumor microenvironment (TME) landscape. The Cox proportional hazards model and LASSO regression analyses were used to construct the HDAC scoring system for evaluating the prognosis of individual tumors. In this study, three distinct HDAC-mediated molecular subtypes were determined, which were also related to different clinical outcomes and biological pathways. HDACsCluster-C subtype had lowest PD-L1/PD-1/CTLA4 expression and immune score. The constructed HDAC scoring system (HDACsScore) could be used as an independent predictor to assess patient prognosis and effectively identify patients with different prognosis. High- and low-HDACsScore groups presented distinct genetic features, immune infiltration, and biological processes. The high-HDACsScore group was more likely to benefit from immunotherapy, as well as from the application of common chemotherapeutic agents (cyclopamine, docetaxel, doxorubicin, gemcitabine, paclitaxel, and pyrimethamine). Overall, HDAC family genes play important roles in LUAD, and the three LUAD subtypes and the HDAC scoring system identified in this study would help enhance our perception of LUAD prognostic differences and provide important insights into the efficacy of immunotherapy and chemotherapy.
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Ning J, Wang F, Bu J, Zhu K, Liu W. Down-regulated m6A reader FTO destabilizes PHF1 that triggers enhanced stemness capacity and tumor progression in lung adenocarcinoma. Cell Death Dis 2022; 8:354. [PMID: 35945194 PMCID: PMC9363432 DOI: 10.1038/s41420-022-01125-y] [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: 03/17/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/28/2022]
Abstract
Aberrant epigenetic drivers or suppressors contribute to LUAD progression and drug resistance, including KRAS, PTEN, Keap1. Human Plant Homeodomain (PHD) finger protein 1 (PHF1) coordinates with H3K36me3 to increase nucleosomal DNA accessibility. Previous studies revealed that PHF1 is markedly upregulated in various tumors and enhances cell proliferation, migration and tumorigenesis. However, its roles in LUAD are still unknown. We aimed to depict the biological roles of PHF1 and identify useful targets for clinical treatment of LUAD. Based on the bioinformatic analysis, we found that PHF1 was down-regulated in LUAD samples and low PHF1 expressions correlated with unfavorable clinical characteristics. Patients with low PHF1 had poorer survival outcomes relative to those with high PHF1. Targeting PHF1 potentiated cell growth, migration and in vivo proliferation. Mechanistically, FTO mediated the stabilization of PHF1 mRNA by demethylating m6A, which particularly prevented YTHDF2 from degrading PHF1 transcripts. Of note, FTO also expressed lowly in LUAD that predicts poor prognosis of patients. FTO inhibition promoted LUAD progression, and PHF1 overexpression could reverse the effect. Lastly, down-regulated FTO/PHF1 axis could mainly elevate FOXM1 expression to potentiate the self-renewal capacity. Targeting FOXM1 was effective to suppress PHF1low/− LUAD growth. Collectively, our findings revealed that FTO positively regulates PHF1 expression and determined the tumor-suppressive role of FTO/PHF1 axis, thereby highlighting insights into its epigenetic remodeling mechanisms in LUAD progression and treatment.
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Affiliation(s)
- Jinfeng Ning
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Harbin, 150081, Heilongjiang, China
| | - Fengjiao Wang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Harbin, 150081, Heilongjiang, China
| | - Jianlong Bu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Harbin, 150081, Heilongjiang, China
| | - Kaibin Zhu
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Harbin, 150081, Heilongjiang, China
| | - Wei Liu
- The forth department of medical oncology, Harbin Medical University Cancer Hospital, No. 150, Haping Road, Harbin, 150081, Heilongjiang, China.
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Gao C, Kong N, Zhang F, Zhou L, Xu M, Wu L. Development and validation of the potential biomarkers based on m6A-related lncRNAs for the predictions of overall survival in the lung adenocarcinoma and differential analysis with cuproptosis. BMC Bioinformatics 2022; 23:327. [PMID: 35941550 PMCID: PMC9358839 DOI: 10.1186/s12859-022-04869-7] [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: 05/28/2021] [Accepted: 07/30/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The treatment and prognosis of lung adenocarcinoma (LUAD) remains a challenge. The study aimed to conduct a systematic analysis of the predictive capacity of N6-methyladenosine (m6A)-related long non-coding RNAs (lncRNAs) in the prognosis of LUAD. METHODS 594 samples were totally selected from a dataset from The Cancer Genome Atlas. The identification of prognostic m6A-related lncRNAs were performed by Pearson correlation analysis and Cox regression analysis. Systematic analyses, including cluster analysis, survival analysis, and immuno-correlated analysis, were conducted. A prognosis model was built from the optimized subset of m6A-related lncRNAs. The assessment of model was performed by survival analysis, and receiver operating characteristic (ROC) curve. Finally, the risk score of patients with LUAD calculated by the prognosis model was implemented by the analysis of Cox regression. Differential analysis was for further evaluation of the cuproptosis-related genes in two risk sets. RESULTS These patients were grouped into two clusters according to the expression levels of 22 prognostic m6A-related lncRNAs. The patients with LUAD in cluster 2 was significantly worse in the overall survival (OS) (P = 0.006). Three scores calculated by the ESTIMATE methods in cluster 2 were significantly lower. After the least absolute shrinkage and selection operator algorithm, 10 prognostic m6A-related lncRNAs were totally selected to construct the final model to obtain the risk score. Then the area under the ROC curve of the prognosis model for 1, 3, and 5-year OS was 0.767, 0.709, and 0.736 in the training set, and 0.707, 0.691, and 0.675 in the test set. The OS of the low-risk cohort was significantly higher than that of the high-risk cohort in both the training set (P < 0.001) and test set (P < 0.001). After the analysis of Cox regression, the risk score [Hazard ratio (HR) = 5.792; P < 0.001] and stage (HR = 1.576; P < 0.001) were both considered as independent indicators of prognosis for LUAD. The expression levels of five cuproptosis-related genes were significantly different in two risk sets. CONCLUSIONS The study constructed a predictive model for the OS of patients with LUAD and these OS-related m6A-lncRNAs might have potential roles in LUAD progression.
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Affiliation(s)
- Chen Gao
- grid.417400.60000 0004 1799 0055Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 54 Youdian Road, Hangzhou, China ,grid.268505.c0000 0000 8744 8924The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Ning Kong
- grid.417400.60000 0004 1799 0055Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 54 Youdian Road, Hangzhou, China ,grid.268505.c0000 0000 8744 8924The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Fan Zhang
- grid.417400.60000 0004 1799 0055Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 54 Youdian Road, Hangzhou, China ,grid.268505.c0000 0000 8744 8924The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Liuzhi Zhou
- grid.13402.340000 0004 1759 700XDepartment of Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Maosheng Xu
- Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 54 Youdian Road, Hangzhou, China. .,The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China.
| | - Linyu Wu
- Department of Radiology, The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Traditional Chinese Medicine), 54 Youdian Road, Hangzhou, China. .,The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China.
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Hallmark guided identification and characterization of a novel immune-relevant signature for prognostication of recurrence in stage I–III lung adenocarcinoma. Genes Dis 2022. [DOI: 10.1016/j.gendis.2022.07.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Mo X, Hu D, Yang P, Li Y, Bashir S, Nai A, Ma F, Jia G, Xu M. A novel cuproptosis-related prognostic lncRNA signature and lncRNA MIR31HG/miR-193a-3p/TNFRSF21 regulatory axis in lung adenocarcinoma. Front Oncol 2022; 12:927706. [PMID: 35936736 PMCID: PMC9353736 DOI: 10.3389/fonc.2022.927706] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 06/27/2022] [Indexed: 01/10/2023] Open
Abstract
Lung adenocarcinoma (LUAD) remains the most common subtype of lung malignancy. Cuproptosis is a newly identified cell death which could regulate tumor cell proliferation and progression. Long non-coding RNAs (lncRNAs) are key molecules and potential biomarkers for diagnosing and treating various diseases. However, the effects of cuproptosis-related lncRNAs on LUAD are still unclear. In our study, 7 cuproptosis-related lncRNAs were selected to establish a prognostic model using univariate Cox regression analysis, LASSO algorithm, and multivariate analysis. Furthermore, we evaluated AC008764.2, AL022323.1, ELN-AS1, and LINC00578, which were identified as protective lncRNAs, while AL031667.3, AL606489.1, and MIR31HG were identified as risk lncRNAs. The risk score calculated by the prognostic model proved to be an effective independent factor compared with other clinical features by Cox regression analyses [univariate analysis: hazard ratio (HR) = 1.065, 95% confidence interval (CI) = 1.043–1.087, P < 0.001; multivariate analysis: HR = 1.067, 95% CI = 1.044–1.091, P < 0.001]. In addition, both analyses (ROC and nomogram) were used to corroborate the accuracy and reliability of this signature. The correlation between cuproptosis-related lncRNAs and immune microenvironment was elucidated, where 7 immune cells and 8 immune-correlated pathways were found to be differentially expressed between two risk groups. Furthermore, our results also identified and verified the ceRNA of cuproptosis-related lncRNA MIR31HG/miR-193a-3p/TNFRSF21 regulatory axis using bioinformatics tools. MIR31HG was highly expressed in LUAD specimens and some LUAD cell lines. Inhibition of MIR31HG clearly reduced the proliferation, migration, and invasion of the LUAD cells. MIR31HG showed oncogenic features via sponging miR-193a-3p and tended to positively regulate TNFRSF21 expression. In a word, lncRNA MIR31HG acts as an oncogene in LUAD by targeting miR-193a-3p to modulate TNFRSF21, which may be beneficial to the gene therapy of LUAD.
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Affiliation(s)
- Xiaocong Mo
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Di Hu
- Department of Neurology and Stroke Centre, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Pingshan Yang
- Department of Thoracic Surgery, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yin Li
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Shoaib Bashir
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Aitao Nai
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Feng Ma
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Guoxia Jia
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Meng Xu
- Department of Oncology, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
- *Correspondence: Meng Xu,
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Zhang S, Sun X, Mou M, Amahong K, Sun H, Zhang W, Shi S, Li Z, Gao J, Zhu F. REGLIV: Molecular regulation data of diverse living systems facilitating current multiomics research. Comput Biol Med 2022; 148:105825. [PMID: 35872412 DOI: 10.1016/j.compbiomed.2022.105825] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/29/2022] [Accepted: 07/03/2022] [Indexed: 12/24/2022]
Abstract
Multiomics is a powerful technique in molecular biology that facilitates the identification of new associations among different molecules (genes, proteins & metabolites). It has attracted tremendous research interest from the scientists worldwide and has led to an explosive number of published studies. Most of these studies are based on the regulation data provided in available databases. Therefore, it is essential to have molecular regulation data that are strictly validated in the living systems of various cell lines and in vivo models. However, no database has been developed yet to provide comprehensive molecular regulation information validated by living systems. Herein, a new database, Molecular Regulation Data of Living System Facilitating Multiomics Study (REGLIV) is introduced to describe various types of molecular regulation tested by the living systems. (1) A total of 2996 regulations describe the changes in 1109 metabolites triggered by alterations in 284 genes or proteins, and (2) 1179 regulations describe the variations in 926 proteins induced by 125 endogenous metabolites. Overall, REGLIV is unique in (a) providing the molecular regulation of a clearly defined regulatory direction other than simple correlation, (b) focusing on molecular regulations that are validated in a living system not simply in an in vitro test, and (c) describing the disease/tissue/species specific property underlying each regulation. Therefore, REGLIV has important implications for the future practice of not only multiomics, but also other fields relevant to molecular regulation. REGLIV is freely accessible at: https://idrblab.org/regliv/.
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Affiliation(s)
- Song Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Xiuna Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Minjie Mou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Kuerbannisha Amahong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Huaicheng Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Wei Zhang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shuiyang Shi
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Zhaorong Li
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China
| | - Jianqing Gao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 330110, China.
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