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Fan L, Wang Y, Huang H, Wang Z, Liang C, Yang X, Ye P, Lin J, Shi W, Zhou Y, Yan H, Long Z, Wang Z, Liu L, Qian J. RNA binding motif 4 inhibits the replication of ebolavirus by directly targeting 3'-leader region of genomic RNA. Emerg Microbes Infect 2024; 13:2300762. [PMID: 38164794 PMCID: PMC10773643 DOI: 10.1080/22221751.2023.2300762] [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: 09/29/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
Ebola virus (EBOV) belongs to Filoviridae family possessing single-stranded negative-sense RNA genome, which is a serious threat to human health. Nowadays, no therapeutics have been proven to be successful in efficiently decreasing the mortality rate. RNA binding proteins (RBPs) are reported to participate in maintaining cell integrity and regulation of viral replication. However, little is known about whether and how RBPs participate in regulating the life cycle of EBOV. In our study, we found that RNA binding motif protein 4 (RBM4) inhibited the replication of EBOV in HEK293T and Huh-7 cells by suppressing viral mRNA production. Such inhibition resulted from the direct interaction between the RRM1 domain of RBM4 and the "CU" enrichment elements located in the PE1 and TSS of the 3'-leader region within the viral genome. Simultaneously, RBM4 could upregulate the expression of some cytokines involved in the host innate immune responses to synergistically exert its antiviral function. The findings therefore suggest that RBM4 might serve as a novel target of anti-EBOV strategy.
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Affiliation(s)
- Linjin Fan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yulong Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Hongxin Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zequn Wang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Chudan Liang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Xiaofeng Yang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Pengfei Ye
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Jingyan Lin
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Wendi Shi
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Yuandong Zhou
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Huijun Yan
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
| | - Zhenyu Long
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Zhongyi Wang
- Beijing Institute of Biotechnology, Beijing, People’s Republic of China
| | - Linna Liu
- Institute of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, People’s Republic of China
| | - Jun Qian
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, People’s Republic of China
- Key Laboratory of Tropical Disease Control (Sun Yat-sen University), Ministry of Education, Guangzhou, People’s Republic of China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, People’s Republic of China
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Li T, Gao R, Xu K, Pan P, Chen C, Wang D, Zhang K, Qiao J, Gu Y. BCL7A inhibits the progression and drug-resistance in acute myeloid leukemia. Drug Resist Updat 2024; 76:101120. [PMID: 39053383 DOI: 10.1016/j.drup.2024.101120] [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: 04/23/2024] [Revised: 06/14/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024]
Abstract
AIMS This study aimed to elucidate the biological roles and regulatory mechanisms of B-cell lymphoma 7 protein family member A (BCL7A) in acute myeloid leukemia (AML), particularly its interaction with polypyrimidine tract binding protein 1 (PTBP1) and the effects on cancer progression and drug resistance. METHODS BCL7A expression levels were analyzed in AML tissues and cell lines, focusing on associations with promoter hypermethylation. Interaction with PTBP1 and effects of differential expression of BCL7A were examined in vitro and in vivo. The impacts on cell proliferation, cycle progression, apoptosis, and differentiation were studied. Additionally, the regulatory roles of BCL7A on interferon regulatory factor 7 (IRF7) and 3-hydroxy-3-methylglutaryl-CoA synthase 1 (HMGCS1) were assessed. RESULTS BCL7A was downregulated in AML due to promoter hypermethylation and negatively regulated by PTBP1. Upregulation of BCL7A impeded AML cell growth, induced apoptosis, promoted cell differentiation, and decreased cell infiltration into lymph nodes, enhancing survival in mouse models. Overexpression of BCL7A upregulated IRF7 and downregulated HMGCS1, linking to reduced AML cell malignancy and decreased resistance to cytarabine. CONCLUSIONS BCL7A acts as a tumor suppressor in AML, inhibiting malignant progression and enhancing drug sensitivity through the IRF7/HMGCS1 pathway. These findings suggest potential therapeutic targets for improving AML treatment outcomes.
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MESH Headings
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/metabolism
- Drug Resistance, Neoplasm/drug effects
- Animals
- Mice
- Polypyrimidine Tract-Binding Protein/metabolism
- Polypyrimidine Tract-Binding Protein/genetics
- Cell Proliferation/drug effects
- Apoptosis/drug effects
- Cell Line, Tumor
- Heterogeneous-Nuclear Ribonucleoproteins/metabolism
- Heterogeneous-Nuclear Ribonucleoproteins/genetics
- DNA Methylation
- Promoter Regions, Genetic
- Disease Progression
- Xenograft Model Antitumor Assays
- Male
- Female
- Tumor Suppressor Proteins/genetics
- Tumor Suppressor Proteins/metabolism
- Cell Differentiation/drug effects
- Gene Expression Regulation, Leukemic/drug effects
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Affiliation(s)
- Tushuai Li
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China; School of Biology and Food Engineering, Changshu Institute of Technology, Suzhou 215500, PR China
| | - Renjie Gao
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China; Graduate Department, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250117, PR China
| | - Kaiwen Xu
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China
| | - Pengpeng Pan
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China
| | - Congcong Chen
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China
| | - Daokuan Wang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China; The First Clinical School of Anhui Medical University, Hefei 230032, PR China
| | - Keyi Zhang
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China
| | - Jilei Qiao
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China; The First Clinical School of Anhui Medical University, Hefei 230032, PR China
| | - Yue Gu
- Key Laboratory of Anti-inflammatory and Immune Medicine, Ministry of Education, Institute of Clinical Pharmacology, Anhui Medical University, Hefei 230032, PR China.
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Liu Y, Shi Q, Liu Y, Li X, Wang Z, Huang S, Chen Z, He X. Fibrillarin Reprograms Glucose Metabolism by Driving the Enhancer-Mediated Transcription of PFKFB4 in Liver Cancer. Cancer Lett 2024:217190. [PMID: 39182558 DOI: 10.1016/j.canlet.2024.217190] [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: 02/22/2024] [Revised: 06/28/2024] [Accepted: 08/12/2024] [Indexed: 08/27/2024]
Abstract
DNA- and RNA-binding proteins (DRBPs) are versatile proteins capable of binding to both DNA and RNA molecules. In this study, we identified fibrillarin (FBL) as a key DRBP that is upregulated in liver cancer tissues vs. normal tissues and is correlated with patient prognosis. FBL promotes the proliferation of liver cancer cells both in vitro and in vivo. Mechanistically, FBL interacts with the transcription factor KHSRP, thereby regulating the expression of genes involved in glucose metabolism and leading to the reprogramming of glucose metabolism. Specifically, FBL and KHSRP work together to transcriptionally activate the glycolytic enzyme PFKFB4 by co-occupying enhancer and promoter elements, thereby further promoting liver cancer growth. Collectively, these findings provide compelling evidence highlighting the role of FBL as a transcriptional regulator in liver cancer cells, working in conjunction with KHSRP. The FBL/KHSRP-PFKFB4 regulatory axis holds potential as both a prognostic indicator and a therapeutic target for liver cancer. SIGNIFICANCE: A novel role of FBL in the transcriptional activation of PFKFB4, leading to glucose metabolism reprogramming in liver cancer.
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Affiliation(s)
- Yizhe Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qili Shi
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yanfang Liu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xinrong Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhen Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China; Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai 200032, China; Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032, China.
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4
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Han H, Yuan Y, Li C, Liu L, Yu H, Han G, Wang Q, Lin M, Huang J. RNA-binding motif protein 28 enhances angiogenesis by improving STAT3 translation in hepatocellular carcinoma. Cancer Lett 2024:217191. [PMID: 39181434 DOI: 10.1016/j.canlet.2024.217191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 08/12/2024] [Accepted: 08/15/2024] [Indexed: 08/27/2024]
Abstract
Hepatocellular carcinoma (HCC) is a prevalent malignant tumor characterized by extensive angiogenesis. However, the underlying mechanisms of HCC pathogenesis remain unclear. Previous studies have shown that RNA-binding proteins (RBPs) are implicated in HCC pathogenesis. In this study, we observed that increased RBM28 expression in HCC tissues was positively correlated with tumor microvascular density and negatively correlated with patient prognosis. Overexpression of RBM28 in HCC cells promoted tubule formation in human umbilical vein endothelial cells, whereas inhibition of RBM28 had the opposite effect, furthermore, the role of RBM28 in the progression of HCC was assessed using transgenic mouse models and chemically induced HCC models. We used various molecular assays and high-throughput detection methods to evaluate the role of RBM28 in promoting angiogenesis in HCC. Increased RBM28 expression in HCC directly binds to STAT3 mRNA, recruiting EIF4E to increase STAT3 expression and enhancing the secretion and expression of vascular endothelial growth factor A; consequently, promoting neovascularization in HCC. The potential of RBM28 as a viable diagnostic and therapeutic target for HCC was assessed using multi-cohort clinical samples and animal models. In summary, our results provide insights into the pathogenesis, clinical diagnosis, and treatment of HCC.
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Affiliation(s)
- Hexu Han
- Department of Gastroenterology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu 225300, People's Republic of China.
| | - Yin Yuan
- Department of Hepatobiliary Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu 225300, People's Republic of China.
| | - Caiying Li
- Department of Vascular Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu 225300, People's Republic of China.
| | - Lei Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; Innovative Institute of Tumor Immunity and Medicine (ITIM), Hefei, Anhui, China; Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China.
| | - Hong Yu
- Department of Pathology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu 225300, People's Republic of China.
| | - Gaohua Han
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu 225300, People's Republic of China.
| | - Qiang Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China; Innovative Institute of Tumor Immunity and Medicine (ITIM), Hefei, Anhui, China; Anhui Province Key Laboratory of Tumor Immune Microenvironment and Immunotherapy, Hefei, Anhui, China.
| | - Mei Lin
- Department of Clinical Laboratory, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu 225300, People's Republic of China.
| | - Junxing Huang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, Jiangsu 225300, People's Republic of China.
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5
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Zhang J, He J, Chen W, Chen G, Wang L, Liu Y, Wang Z, Yang M, Huang G, Yang Y, Ma W, Li Y. Single-cell RNA-binding protein pattern-mediated molecular subtypes depict the hallmarks of the tumor microenvironment in bladder urothelial carcinoma. ONCOLOGIE 2024; 26:657-669. [DOI: 10.1515/oncologie-2024-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Abstract
Objectives
Bladder carcinoma (BC) is a common malignancy of the urinary tract. As a new hallmark of cancer for drug therapy, RNA-binding proteins (RBPs) are key regulatory factors in alternative splicing events. This work is to uncover the relationship between BC and RBP in order to find drug targets in BC.
Methods
In this work, data from single-cell RNA-seq GSE1355337, PRJNA662018, and the TCGA-Bladder urothelial carcinoma (BLCA) cohorts are integrated to identify their relationships. A scoring system is constructed according to RBPs gene expression and patients’ survival. A network is constructed to analyze the alternative splicing events and RBP genes.
Results
A scoring system identified 321 RBPs significantly associated with the prognosis of patients. Subsequent typing of these RBP genes in two single-cell datasets demonstrated that most of the RBP genes had variable copy numbers. Three RBP clusters were identified. Using RBP genes as a signature in BC epithelial cells allows for differentiation between different grades of BC samples. The novel RBP genes-based subtype system reflects BC clinical staging. Notably, CellChat analysis revealed that the RBP genes-associated cell subtypes of T cells had extensive interactions with epithelial cells. Further analysis showed that the ligand-receptor pair MIF-CXCR4 mediated the communication between RBP-associated subtypes of BC epithelial cells and T cells.
Conclusions
Taken together, RBP genes are associated with BC progress and offer new indicators for precision medicine in BC.
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Affiliation(s)
- Jun Zhang
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Jiejie He
- Department of Surgical Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wen Chen
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Guojun Chen
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Liang Wang
- Department of Gastrointestinal Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yuchan Liu
- Department of Gynecology and Obstetrics , Jingmen Central Hospital , Jingmen , Hubei Province , China
| | - Zhanjin Wang
- Medical College of Qinghai University , Xining , Qinghai Province , China
| | - Ming Yang
- Department of Medical Records and Statistic, Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Guoyi Huang
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Yongli Yang
- Department of Gynecology , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wei Ma
- Department of Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yan Li
- Department of Gynecologic Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
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6
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Li Z, Tian Y, Zong H, Wang X, Li D, Keranmu A, Xin S, Ye B, Bai R, Chen W, Yang G, Ye L, Wang S. Deubiquitinating enzyme OTUD4 stabilizes RBM47 to induce ATF3 transcription: a novel mechanism underlying the restrained malignant properties of ccRCC cells. Apoptosis 2024; 29:1051-1069. [PMID: 38553613 DOI: 10.1007/s10495-024-01953-6] [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] [Accepted: 03/03/2024] [Indexed: 07/23/2024]
Abstract
Dysregulation of deubiquitination contributes to various diseases, including cancer, and aberrant expression of deubiquitinating enzymes is involved in carcinoma progression. As a member of the ovarian tumor (OTU) deubiquitinases, OTUD4 is considered a tumor suppressor in many kinds of malignancies. The biological characteristics and mechanisms of OTUD4 in clear cell renal cell carcinoma (ccRCC) remain unclear. The downregulation of OTUD4 in ccRCC was confirmed based on the TCGA database and a validation cohort of 30-paired ccRCC and para-carcinoma samples. Moreover, OTUD4 expression was detected by immunohistochemistry in 50 cases of ccRCC tissues, and patients with lower levels of OTUD4 showed larger tumor size (p = 0.015). TCGA data revealed that patients with high expression of OTUD4 had a longer overall survival rate. In vitro and in vivo studies revealed that downregulation of OTUD4 was essential for tumor cell growth and metastasis in ccRCC, and OTUD4 overexpression inhibited these malignant phenotypes. We further found that OTUD4 sensitized ccRCC cells to Erastin-induced ferroptosis, and ferrostain-1 inhibited OTUD4-induced ferroptotic cell death. Mechanistic studies indicated that OTUD4 functioned as an anti-proliferative and anti-metastasic factor through the regulation of RNA-binding protein 47 (RBM47)-mediated activating transcription factor 3 (ATF3). OTUD4 directly interacted with RBM47 and promoted its stability via deubiquitination events. RBM47 was critical in ccRCC progression by regulating ATF3 mRNA stability, thereby promoting ATF3-mediated ferroptosis. RBM47 interference abolished the suppressive role of OTUD4 overexpression in ccRCC. Our findings provide mechanistic insight into OTUD4 of ccRCC progression and indicate a novel critical pathway OTUD4/RBM47/ATF3 may serve as a potential therapeutic pathway for ccRCC.
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Affiliation(s)
- Ziyao Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
- School of Electrical Engineering of Zhengzhou University, Zhengzhou, China
- Center for Frontier Medical Engineering of Chiba University, Chiba, Japan
| | - Ye Tian
- Department of Urology, Guizhou Provincial People's Hospital, Guiyang, China
| | - Huafeng Zong
- Department of Pathology, Dalian Friendship Hospital, Dalian, China
| | - Xuelei Wang
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Dongyang Li
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Adili Keranmu
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Shiyong Xin
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Bowen Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Rong Bai
- Department of Pharmacy, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Weihua Chen
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Guosheng Yang
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Lin Ye
- Department of Urology, Shanghai East Hospital, School of Medicine, Tongji University, Shanghai, China.
| | - Siyan Wang
- Health Management Center, Huizhou Third People's Hospital, Guangzhou Medical University, Huizhou, China.
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Dai C, Cao J, Tang Y, Jiang Y, Luo C, Zheng J. YTHDF3 phase separation regulates HSPA13-dependent clear cell renal cell carcinoma development and immune evasion. Cancer Sci 2024; 115:2588-2601. [PMID: 38811341 PMCID: PMC11309927 DOI: 10.1111/cas.16228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 05/06/2024] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
Insufficient understanding about the immune evasion mechanism leads to the inability in predicting current immunotherapy effects in clear cell renal cell carcinoma (ccRCC) and sensitizing ccRCC to immunotherapy. RNA binding proteins (RBPs) can promote tumor progression and immune evasion. However, research on RBPs, particularly m6A reader YTHDF3, in ccRCC development and immune evasion is limited. In this study, we found that YTHDF3 level was downregulated in ccRCC and was an independent prognostic biomarker for ccRCC. Decreased YTHDF3 expression was correlated with the malignancy, immune evasion, and poor response to anti-programmed death ligand 1 (PD-L1)/CTLA-4 in ccRCC. YTHDF3 overexpression restrained ccRCC cell malignancy, PD-L1 expression, CD8+ T cell infiltration and activities in vivo, indicating its inhibitory role in ccRCC development and immune evasion. Mechanistically, YTHDF3 WT was found to have phase separation characteristics and suppress ccRCC malignancy and immune evasion. Whereas YTHDF3 mutant, which disrupted phase separation, abolished its function. YTHDF3 enhanced the degradation of its target mRNA HSPA13 by phase separation and recruiting DDX6, resulting in the downregulation of the downstream immune checkpoint PD-L1. HSPA13 overexpression restored ccRCC malignancy and immune evasion suppressed by YTHDF3 overexpression. In all, our results identify a new model of YTHDF3 in regulating ccRCC progression and immune evasion through phase separation.
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Affiliation(s)
- Chenyun Dai
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesCapital Medical UniversityBeijingChina
- Laboratory for Clinical MedicineCapital Medical UniversityBeijingChina
| | - Jianfu Cao
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesCapital Medical UniversityBeijingChina
- Laboratory for Clinical MedicineCapital Medical UniversityBeijingChina
| | - Yuangui Tang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesCapital Medical UniversityBeijingChina
| | - Yuxiao Jiang
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesCapital Medical UniversityBeijingChina
| | - Chenghua Luo
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic DiseasesShihezi University School of MedicineShiheziChina
- Department of Pathology, The First Affiliated HospitalShihezi UniversityShiheziChina
| | - Junfang Zheng
- Beijing Key Laboratory of Cancer Invasion and Metastasis Research, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesCapital Medical UniversityBeijingChina
- Laboratory for Clinical MedicineCapital Medical UniversityBeijingChina
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8
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Joshi P, Keyvani Chahi A, Liu L, Moreira S, Vujovic A, Hope KJ. RNA binding protein-directed control of leukemic stem cell evolution and function. Hemasphere 2024; 8:e116. [PMID: 39175825 PMCID: PMC11339706 DOI: 10.1002/hem3.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 05/06/2024] [Accepted: 05/26/2024] [Indexed: 08/24/2024] Open
Abstract
Strict control over hematopoietic stem cell decision making is essential for healthy life-long blood production and underpins the origins of hematopoietic diseases. Acute myeloid leukemia (AML) in particular is a devastating hematopoietic malignancy that arises from the clonal evolution of disease-initiating primitive cells which acquire compounding genetic changes over time and culminate in the generation of leukemic stem cells (LSCs). Understanding the molecular underpinnings of these driver cells throughout their development will be instrumental in the interception of leukemia, the enabling of effective treatment of pre-leukemic conditions, as well as the development of strategies to target frank AML disease. To this point, a number of precancerous myeloid disorders and age-related alterations are proving as instructive models to gain insights into the initiation of LSCs. Here, we explore this myeloid dysregulation at the level of post-transcriptional control, where RNA-binding proteins (RBPs) function as core effectors. Through regulating the interplay of a myriad of RNA metabolic processes, RBPs orchestrate transcript fates to govern gene expression in health and disease. We describe the expanding appreciation of the role of RBPs and their post-transcriptional networks in sustaining healthy hematopoiesis and their dysregulation in the pathogenesis of clonal myeloid disorders and AML, with a particular emphasis on findings described in human stem cells. Lastly, we discuss key breakthroughs that highlight RBPs and post-transcriptional control as actionable targets for precision therapy of AML.
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Affiliation(s)
- Pratik Joshi
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Ava Keyvani Chahi
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Lina Liu
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Steven Moreira
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Ana Vujovic
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
| | - Kristin J. Hope
- Department of Medical BiophysicsUniversity of TorontoTorontoCanada
- Princess Margaret Cancer CenterUniversity Health NetworkTorontoCanada
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9
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Wipplinger M, Mink S, Bublitz M, Gassner C. Regulation of the Lewis Blood Group Antigen Expression: A Literature Review Supplemented with Computational Analysis. Transfus Med Hemother 2024; 51:225-236. [PMID: 39135855 PMCID: PMC11318966 DOI: 10.1159/000538863] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 08/15/2024] Open
Abstract
Background The Lewis (Le) blood group system, unlike most other blood groups, is not defined by antigens produced internally to the erythrocytes and their precursors but rather by glycan antigens adsorbed on to the erythrocyte membrane from the plasma. These oligosaccharides are synthesized by the two fucosyltransferases FUT2 and FUT3 mainly in epithelial cells of the digestive tract and transferred to the plasma. At their place of synthesis, some Lewis blood group carbohydrate antigen variants also seem to be involved in various gastrointestinal malignancies. However, relatively little is known about the transcriptional regulation of FUT2 and FUT3. Summary To address this question, we screened existing literature and additionally used in silico prediction tools to identify novel candidate regulators for FUT2 and FUT3 and combine these findings with already known data on their regulation. With this approach, we were able to describe a variety of transcription factors, RNA binding proteins and microRNAs, which increase FUT2 and FUT3 transcription and translation upon interaction. Key Messages Understanding the regulation of FUT2 and FUT3 is crucial to fully understand the blood group system Lewis (ISBT 007 LE) phenotypes, to shed light on the role of the different Lewis antigens in various pathologies, and to identify potential new diagnostic targets for these diseases.
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Affiliation(s)
- Martin Wipplinger
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Sylvia Mink
- Central Medical Laboratories, Feldkirch, Austria
- Medical-Scientific Faculty, Private University of the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Maike Bublitz
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Christoph Gassner
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
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10
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Lu Y, Yang Z, Zhang J, Ma X, Bi X, Xu L, Feng K, Wu Z, Ma X, Zhuang L. RNA-binding protein QKI promotes the progression of HCC by interacting with long non-coding RNA EGOT. Int Immunopharmacol 2024; 136:112297. [PMID: 38810307 DOI: 10.1016/j.intimp.2024.112297] [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: 02/11/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND RNA-binding proteins are revealed to play important roles during the progression of hepatocellular carcinoma (HCC). However, the regulatory mechanisms of RNA-binding protein Quaking (QKI) in the expression and role of long non-coding RNAs (lncRNAs) in HCC cells remain not well understood. METHODS Cell Counting Kit-8, wound-healing, Transwell and colony-forming assays were performed to evaluate the effects of QKI and lncRNA EGOT on proliferation and migration of HCC cells. Tumor growth of HCC was analyzed using a mouse xenograft model. Immunoprecipitation (RIP) assay was used to investigate the interaction between QKI and EGOT. RESULTS The expression of QKI was significantly upregulated in HCC tissues and the higher QKI level was significantly associated with a poorer prognosis. Overexpression of QKI promoted the proliferation, migration, and colony-forming ability of HCC cells in vitro and tumor growth of HCC in vivo. Mechanistically, QKI protein could bind to EGOT RNA and increase its expression. Inhibition of EGOT attenuated the effects of QKI on the malignant phenotypes of HCC cells. In addition, both QKI and EGOT could activate the SAPK/JNK signaling pathway in HCC cells. CONCLUSIONS Our findings indicated that QKI exerted promotive effects on the malignant phenotypes of HCC through its interaction with EGOT.
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Affiliation(s)
- Yi Lu
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Zhenpeng Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China
| | - Jie Zhang
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Xuefeng Ma
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Xiaoye Bi
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Longhai Xu
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Keqing Feng
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Zehua Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China
| | - Xiang Ma
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China.
| | - Likun Zhuang
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China.
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11
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Li W, Yang Y, Huang L, Yu X, Wang T, Zhang N, Yang M. The TDP-43/TP63 Positive Feedback Circuit Promotes Esophageal Squamous Cell Carcinoma Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2402913. [PMID: 39023169 DOI: 10.1002/advs.202402913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 06/30/2024] [Indexed: 07/20/2024]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most prevalent malignancies with a 5-year survival rate of only 15% in patients with advanced diseases. Tumor protein 63 (TP63), a master transcription factor (TF) in ESCC, cooperates with other TFs to regulate enhancers and/or promoters of target oncogenes, which in turn promotes tumorigenesis. TAR-DNA-binding protein-43 (TDP-43) is an RNA/DNA binding protein with elevated expression in several neoplasms. However, it remains unclear how TDP-43 contributes to ESCC progression. In this study, TDP-43 is identified as a novel oncogene with markedly upregulated expression in ESCC tissues through profiling expression levels of one hundred and fifty canonical RNA binding protein (RBP) genes in multiple ESCC patient cohorts. Importantly, TDP-43 boosted TP63 expression via post-transcriptionally stabilizing TP63 mRNAs as a RBP and promoting TP63 transcription as a TF binding to the TP63 promoter in ESCC cells. In contrast, the master TF TP63 also bound to the TDP-43 promoter, accelerated TDP-43 transcription, and caused a noticeable increase in TDP-43 expression in ESCC cells. The findings highlight TDP-43 as a viable therapeutic target for ESCC and uncover a hitherto unrecognized TDP-43/TP63 circuit in cancer.
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Affiliation(s)
- Wenwen Li
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- School of Life Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, Shandong, 271021, China
| | - Yanting Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Linying Huang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Xinyuan Yu
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
| | - Teng Wang
- Shandong University Cancer Center, Jinan, Shandong, 250117, China
| | - Nasha Zhang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Jinan, Shandong, 250117, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, Shandong, 250117, China
- School of Life Sciences, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian, Shandong, 271021, China
- Shandong University Cancer Center, Jinan, Shandong, 250117, China
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Jinan, Shandong, 250117, China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, Jiangsu, 211166, China
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12
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Yang D, Li C, Kong Y, Pei Y, Miao B, Dai G, Ding P, Shi P, Wang Z, Pei R. Deciphering the Temporal-Spatial Interactive Heterogeneity of Long Non-Coding RNAs and RNA-Binding Proteins in Living Cells at Single-Cell Resolution. J Am Chem Soc 2024. [PMID: 39016781 DOI: 10.1021/jacs.4c05205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2024]
Abstract
The investigation of long noncoding RNAs (lncRNAs) and RNA binding proteins (RBPs) interactions in living cell holds great significance for elucidating their critical roles in a variety of biological activities, but limited techniques are available to profile the temporal-spatial dynamic heterogeneity. Here, we introduced a molecular beacon-functionalized nanoneedle array designed for spatially resolved profiling of lncRNA-RBP interactions (Nano-SpatiaLR). A nanoneedle array modified with a molecular beacon is employed to selectively isolate specific intracellular lncRNAs and their associated RBPs without affecting cell viability. The RBPs are then in situ analyzed with a fluorescent labeled antibody and colocalized with lncRNA signals to get a quantitative measurement of their dynamic interactions. Additionally, leveraging the spatial distribution and nanoscale modality of the nanoneedle array, this technique provides the spatial heterogeneity information on cellular lncRNA-RBPs interaction at single cell resolution. In this study, we tracked the temporal-spatial interactive heterogeneity dynamics of lncRNA-RBPs interaction within living cells across different biological progresses. Our findings demonstrated that the interactions between lncRNA HOTAIR and RBPs EZH2 and LSD1 undergo significant changes in response to drug treatments, particularly in tumor cells. Moreover, these interactions become more intensified as tumor cells aggregate during the proliferation process.
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Affiliation(s)
- Deyuan Yang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Cheng Li
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Yutong Kong
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Yian Pei
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
- Duke Kunshan University Kunshan 215316, China
| | - Bing Miao
- Key Laboratory of Multifunctional Nanomaterials and Smart Systems, Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Gaole Dai
- Suzhou Institute of Systems Medicine, Suzhou 215123, China
| | - Pi Ding
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Peng Shi
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering, Hong Kong Science Park, Shatin, Hong Kong 999077, China
- Department of Biomedical Engineering, City University of Hong Kong Kowloon, Shatin, Hong Kong 999077, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518000, China
| | - Zixun Wang
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
| | - Renjun Pei
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei 230026, China
- CAS Key Laboratory for Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, China
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13
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Her H, Rothamel KL, Nguyen GG, Boyle EA, Yeo GW. Mudskipper detects combinatorial RNA binding protein interactions in multiplexed CLIP data. CELL GENOMICS 2024; 4:100603. [PMID: 38955188 DOI: 10.1016/j.xgen.2024.100603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/08/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The uncovering of protein-RNA interactions enables a deeper understanding of RNA processing. Recent multiplexed crosslinking and immunoprecipitation (CLIP) technologies such as antibody-barcoded eCLIP (ABC) dramatically increase the throughput of mapping RNA binding protein (RBP) binding sites. However, multiplex CLIP datasets are multivariate, and each RBP suffers non-uniform signal-to-noise ratio. To address this, we developed Mudskipper, a versatile computational suite comprising two components: a Dirichlet multinomial mixture model to account for the multivariate nature of ABC datasets and a softmasking approach that identifies and removes non-specific protein-RNA interactions in RBPs with low signal-to-noise ratio. Mudskipper demonstrates superior precision and recall over existing tools on multiplex datasets and supports analysis of repetitive elements and small non-coding RNAs. Our findings unravel splicing outcomes and variant-associated disruptions, enabling higher-throughput investigations into diseases and regulation mediated by RBPs.
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Affiliation(s)
- Hsuanlin Her
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katherine L Rothamel
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grady G Nguyen
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Evan A Boyle
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA; Sanford Stem Cell Institute Innovation Center and Stem Cell Program, University of California, San Diego, La Jolla, CA 92093, USA; Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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14
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Vijayakumar A, Majumder M, Yin S, Brobbey C, Karam J, Howley B, Howe P, Berto S, Madan L, Gan W, Palanisamy V. PRMT5-mediated arginine methylation of FXR1 is essential for RNA binding in cancer cells. Nucleic Acids Res 2024; 52:7225-7244. [PMID: 38709899 PMCID: PMC11229354 DOI: 10.1093/nar/gkae319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/29/2024] [Accepted: 04/11/2024] [Indexed: 05/08/2024] Open
Abstract
Emerging evidence indicates that arginine methylation promotes the stability of arginine-glycine-rich (RGG) motif-containing RNA-binding proteins (RBPs) and regulates gene expression. Here, we report that post-translational modification of FXR1 enhances the binding with mRNAs and is involved in cancer cell growth and proliferation. Independent point mutations in arginine residues of FXR1's nuclear export signal (R386 and R388) and RGG (R453, R455 and R459) domains prevent it from binding to RNAs that form G-quadruplex (G4) RNA structures. Disruption of G4-RNA structures by lithium chloride failed to bind with FXR1, indicating its preference for G4-RNA structure containing mRNAs. Furthermore, loss-of-function of PRMT5 inhibited FXR1 methylation both in vivo and in vitro, affecting FXR1 protein stability, inhibiting RNA-binding activity and cancer cell growth and proliferation. Finally, the enhanced crosslinking and immunoprecipitation (eCLIP) analyses reveal that FXR1 binds with the G4-enriched mRNA targets such as AHNAK, MAP1B, AHNAK2, HUWE1, DYNC1H1 and UBR4 and controls its mRNA expression in cancer cells. Our findings suggest that PRMT5-mediated FXR1 methylation is required for RNA/G4-RNA binding, which promotes gene expression in cancer cells. Thus, FXR1's structural characteristics and affinity for RNAs preferentially G4 regions provide new insights into the molecular mechanism of FXR1 in oral cancer cells.
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Affiliation(s)
- Anitha Vijayakumar
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
| | - Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Shasha Yin
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Charles Brobbey
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Joseph Karam
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Breege Howley
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Philip H Howe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Stefano Berto
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Lalima K Madan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Wenjian Gan
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Viswanathan Palanisamy
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
- Division of Molecular Medicine, Department of Internal Medicine, University of New Mexico, Albuquerque, NM 87131, USA
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15
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Zhang N, Gao S, Peng H, Wu J, Li H, Gibson C, Wu S, Zhu J, Zheng Q. Chemical Proteomic Profiling of Protein Dopaminylation in Colorectal Cancer Cells. J Proteome Res 2024; 23:2651-2660. [PMID: 38838187 DOI: 10.1021/acs.jproteome.4c00379] [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: 06/07/2024]
Abstract
Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid of H3 (i.e., glutamine) and dopamine. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of its regulator, transglutaminase 2 (TGM2), in colon cancer cells. Due to the enzyme promiscuity of TGM2, nonhistone proteins have also been identified as dopaminylation targets; however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of dopaminylation sites were identified and attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that targeting these pathways may become a promising anticancer strategy.
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Affiliation(s)
- Nan Zhang
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Shuaixin Gao
- Human Nutrition Program, Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Haidong Peng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jinghua Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Huapeng Li
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
| | - Connor Gibson
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sophia Wu
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Columbus Academy, Gahanna, Ohio 43230, United States
| | - Jiangjiang Zhu
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Human Nutrition Program, Department of Human Sciences, College of Education and Human Ecology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Qingfei Zheng
- Department of Radiation Oncology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
- Center for Cancer Metabolism, James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
- Molecular, Cellular, and Developmental Biology Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Biological Chemistry and Pharmacology, College of Medicine, The Ohio State University, Columbus, Ohio 43210, United States
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16
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Zhang X, Yuan L, Zhang W, Zhang Y, Wu Q, Li C, Wu M, Huang Y. Liquid-liquid phase separation in diseases. MedComm (Beijing) 2024; 5:e640. [PMID: 39006762 PMCID: PMC11245632 DOI: 10.1002/mco2.640] [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: 12/25/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 07/16/2024] Open
Abstract
Liquid-liquid phase separation (LLPS), an emerging biophysical phenomenon, can sequester molecules to implement physiological and pathological functions. LLPS implements the assembly of numerous membraneless chambers, including stress granules and P-bodies, containing RNA and protein. RNA-RNA and RNA-protein interactions play a critical role in LLPS. Scaffolding proteins, through multivalent interactions and external factors, support protein-RNA interaction networks to form condensates involved in a variety of diseases, particularly neurodegenerative diseases and cancer. Modulating LLPS phenomenon in multiple pathogenic proteins for the treatment of neurodegenerative diseases and cancer could present a promising direction, though recent advances in this area are limited. Here, we summarize in detail the complexity of LLPS in constructing signaling pathways and highlight the role of LLPS in neurodegenerative diseases and cancers. We also explore RNA modifications on LLPS to alter diseases progression because these modifications can influence LLPS of certain proteins or the formation of stress granules, and discuss the possibility of proper manipulation of LLPS process to restore cellular homeostasis or develop therapeutic drugs for the eradication of diseases. This review attempts to discuss potential therapeutic opportunities by elaborating on the connection between LLPS, RNA modification, and their roles in diseases.
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Affiliation(s)
- Xinyue Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Lin Yuan
- Laboratory of Research in Parkinson's Disease and Related Disorders Health Sciences Institute China Medical University Shenyang China
| | - Wanlu Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Yi Zhang
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Qun Wu
- Department of Pediatrics Ruijin Hospital Affiliated to Shanghai Jiaotong University School of Medicine Shanghai China
| | - Chunting Li
- College of Life and Health Sciences Northeastern University Shenyang China
| | - Min Wu
- Wenzhou Institute University of Chinese Academy of Sciences Wenzhou Zhejiang China
- The Joint Research Center Affiliated Xiangshan Hospital of Wenzhou Medical University Ningbo China
| | - Yongye Huang
- College of Life and Health Sciences Northeastern University Shenyang China
- Key Laboratory of Bioresource Research and Development of Liaoning Province College of Life and Health Sciences Northeastern University Shenyang China
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17
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Garg K, Kumar A, Kizhakkethil V, Kumar P, Singh S. Overlap in oncogenic and pro-inflammatory pathways associated with areca nut and nicotine exposure. CANCER PATHOGENESIS AND THERAPY 2024; 2:187-194. [PMID: 39027148 PMCID: PMC11252521 DOI: 10.1016/j.cpt.2023.09.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 09/08/2023] [Accepted: 09/14/2023] [Indexed: 07/20/2024]
Abstract
Background Betel nut/areca nut/Areca catechu is one of the most commonly used psychoactive substance, and is also a major preventable cause of cancer. Unlike other psychoactive substances, such as nicotine, the mechanisms underlying addiction to areca nuts and related oncogenesis remain elusive. Recent reports suggest a possible overlap in the mechanisms of action of nicotine and areca nuts in the human body. Thus, this study aimed to investigate the interactome of human proteins associated with areca nut exposure and the intricate similarities and differences in the effects of the two psychoactive substances on humans. Methods A list of proteins associated with areca nut use was obtained from the available literature using terms from Medical Subject Headings (MeSH). Protein-protein interaction (PPI) networks and functional enrichment were analyzed. The results obtained for both psychoactive substances were compared. Results Given the limited number of common proteins (36/226, 16%) in the two sets, a substantial overlap (612/1176 nodes, 52%) was observed in the PPI networks, as well as in Gene Ontology. Areca nuts mainly affect signaling pathways through three hub proteins (alpha serine/threonine-protein kinase, tumor protein 53, and interleukin-6), which are common to both psychoactive substances, as well as two unique hub proteins (epidermal growth factor receptor and master regulator of cell cycle entry and proliferative metabolism). Areca nut-related proteins are associated with unique pathways, such as extracellular matrix organization, lipid storage, and metabolism, which are not found in nicotine-associated proteins. Conclusions Areca nuts affect regulatory mechanisms, leading to systemic toxicity and oncogenesis. Areca nuts also affect unique pathways that can be studied as potential markers of exposure, as well as targets for anticancer therapeutic agents.
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Affiliation(s)
- Krati Garg
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology (IIT) Delhi, Delhi 110016, India
| | - Anuj Kumar
- Division of Molecular Biology, ICMR-National Institute of Cancer Prevention and Research (ICMR-NICPR), Indian Council of Medical Research, Noida, Uttar Pradesh 201301, India
| | - Vidisha Kizhakkethil
- Department of Biotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632024, India
| | - Pramod Kumar
- Division of Molecular Biology, ICMR-National Institute of Cancer Prevention and Research (ICMR-NICPR), Indian Council of Medical Research, Noida, Uttar Pradesh 201301, India
| | - Shalini Singh
- ICMR-National Institute of Cancer Prevention & Research (ICMR-NICPR), Indian Council of Medical Research, Noida, Uttar Pradesh 201301, India
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18
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Maroni P, Pesce NA, Lombardi G. RNA-binding proteins in bone pathophysiology. Front Cell Dev Biol 2024; 12:1412268. [PMID: 38966428 PMCID: PMC11222650 DOI: 10.3389/fcell.2024.1412268] [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: 04/04/2024] [Accepted: 06/04/2024] [Indexed: 07/06/2024] Open
Abstract
Bone remodelling is a highly regulated process that maintains mineral homeostasis and preserves bone integrity. During this process, intricate communication among all bone cells is required. Indeed, adapt to changing functional situations in the bone, the resorption activity of osteoclasts is tightly balanced with the bone formation activity of osteoblasts. Recent studies have reported that RNA Binding Proteins (RBPs) are involved in bone cell activity regulation. RBPs are critical effectors of gene expression and essential regulators of cell fate decision, due to their ability to bind and regulate the activity of cellular RNAs. Thus, a better understanding of these regulation mechanisms at molecular and cellular levels could generate new knowledge on the pathophysiologic conditions of bone. In this Review, we provide an overview of the basic properties and functions of selected RBPs, focusing on their physiological and pathological roles in the bone.
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Affiliation(s)
- Paola Maroni
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Noemi Anna Pesce
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
| | - Giovanni Lombardi
- Laboratory of Experimental Biochemistry and Molecular Biology, IRCCS Istituto Ortopedico Galeazzi, Milano, Italy
- Department of Athletics, Strength and Conditioning, Poznań University of Physical Education, Poznań, Poland
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19
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Wang B, Fan X, Wang L, Wei X. The RNA-binding protein sorbin and SH3 domain-containing 2 are transcriptionally regulated by specificity protein 1 and function as tumor suppressors in bladder cancer by stabilizing tissue factor pathway inhibitor. Mol Carcinog 2024; 63:1174-1187. [PMID: 38501385 DOI: 10.1002/mc.23717] [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: 11/08/2023] [Revised: 02/27/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Sorbin and SH3 domain-containing 2 (SORBS2) is an RNA-binding protein and has been implicated in the development of some cancers. However, its role in bladder cancer (BC) is yet to be established. The expression of SORBS2 in BC tissues was determined from the Gene Expression Omnibus and Gene Expression Profiling Interactive Analysis databases and collected paired tumor/normal samples. The effects of SORBS2 on BC cells were detected by CCK-8, colony formation, Transwell, dual-luciferase, RNA immunoprecipitation, chromatin immunoprecipitation, and DNA pull-down assays. In vivo, BC cell growth and metastasis were studied by a xenograft subcutaneous model and a tail-vein metastasis model. The results showed that SORBS2 expression was significantly decreased in BC tissues and cells. SORBS2 overexpression inhibited cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro and tumor growth and metastasis in vivo, while silencing SORBS2 produced the opposite effect. Mechanistically, we found that SORBS2 enhanced the stability of tissue factor pathway inhibitor (TFPI) mRNA via direct binding to its 3' UTR. Restoration of TFPI expression reversed SORBS2 knockdown-induced malignant phenotypes of BC cells. In addition, SORBS2 expression was negatively regulated by the transcription factor specificity protein 1 (SP1). Conversely, SORBS2 can be transcriptionally regulated by SP1 and inhibit BC cell growth and metastasis via stabilization of TFPI mRNA, indicating SORBS2 may be a promising therapeutic target for BC.
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Affiliation(s)
- Beibei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xin Fan
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lingang Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaosong Wei
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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20
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Hu Z, Li M, Chen Y, Chen L, Han Y, Chen C, Lu X, You N, Lou Y, Huang Y, Huo Z, Liu C, Liang C, Liu S, Deng K, Chen L, Chen S, Wan G, Wu X, Fu Y, Xu A. Disruption of PABPN1 phase separation by SNRPD2 drives colorectal cancer cell proliferation and migration through promoting alternative polyadenylation of CTNNBIP1. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1212-1225. [PMID: 38811444 DOI: 10.1007/s11427-023-2495-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/26/2023] [Indexed: 05/31/2024]
Abstract
Generally shortened 3' UTR due to alternative polyadenylation (APA) is widely observed in cancer, but its regulation mechanisms for cancer are not well characterized. Here, with profiling of APA in colorectal cancer tissues and poly(A) signal editing, we firstly identified that the shortened 3' UTR of CTNNIBP1 in colorectal cancer promotes cell proliferation and migration. We found that liquid-liquid phase separation (LLPS) of PABPN1 is reduced albeit with higher expression in cancer, and the reduction of LLPS leads to the shortened 3' UTR of CTNNBIP1 and promotes cell proliferation and migration. Notably, the splicing factor SNRPD2 upregulated in colorectal cancer, can interact with glutamic-proline (EP) domain of PABPN1, and then disrupt LLPS of PABPN1, which attenuates the repression effect of PABPN1 on the proximal poly(A) sites. Our results firstly reveal a new regulation mechanism of APA by disruption of LLPS of PABPN1, suggesting that regulation of APA by interfering LLPS of 3' end processing factor may have the potential as a new way for the treatment of cancer.
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Affiliation(s)
- Zhijie Hu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Mengxia Li
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yufeng Chen
- Department of General Surgery (Colorectal Surgery) & Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases & Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Liutao Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yuting Han
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chengyong Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Xin Lu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Nan You
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yawen Lou
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Yingye Huang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Zhanfeng Huo
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chao Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Cheng Liang
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Susu Liu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Ke Deng
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liangfu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shangwu Chen
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Guohui Wan
- National-Local Joint Engineering Laboratory of Druggability and New Drug Evaluation, National Engineering Research Center for New Drug and Druggability (cultivation), Guangdong Province Key Laboratory of New Drug Design and Evaluation, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China
| | - Xiaojian Wu
- Department of General Surgery (Colorectal Surgery) & Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases & Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China.
| | - Yonggui Fu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
| | - Anlong Xu
- State Key Laboratory of Biocontrol, Guangdong Province Key Laboratory of Pharmaceutical Functional Genes, Department of Biochemistry, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing, 100029, China.
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21
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Chong PSY, Chooi JY, Lim SLJ, Chung TH, Brunmeir R, Leow ACY, Toh SHM, Balan K, Azaman MIB, Wu Z, Subramaniam N, Vardy LA, Chng WJ. Epigenetic dysregulation of eukaryotic initiation factor 3 subunit E (eIF3E) by lysine methyltransferase REIIBP confers a pro-inflammatory phenotype in t(4;14) myeloma. Haematologica 2024; 109:1893-1908. [PMID: 38124661 PMCID: PMC11141660 DOI: 10.3324/haematol.2023.283467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
REIIBP is a lysine methyltransferase aberrantly expressed through alternative promoter usage of NSD2 locus in t(4;14)-translocated multiple myeloma (MM). Clinically, t(4;14) translocation is an adverse prognostic factor found in approximately 15% of MM patients. The contribution of REIIBP relative to other NSD2 isoforms as a dependency gene in t(4;14)-translocated MM remains to be evaluated. Here, we demonstrated that despite homology with NSD2, REIIBP displayed distinct substrate specificity by preferentially catalyzing H3K4me3 and H3K27me3, with little activity on H3K36me2. Furthermore, REIIBP was regulated through microRNA by EZH2 in a Dicer-dependent manner, exemplifying a role of REIIBP in SET-mediated H3K27me3. Chromatin immunoprecipitation sequencing revealed chromatin remodeling characterized by changes in genome-wide and loci-specific occupancy of these opposing histone marks, allowing a bidirectional regulation of its target genes. Transcriptomics indicated that REIIBP induced a pro-inflammatory gene signature through upregulation of TLR7, which in turn led to B-cell receptor-independent activation of BTK and driving NFkB-mediated production of cytokines such as IL-6. Activation of this pathway is targetable using Ibrutinib and partially mitigated bortezomib resistance in a REIIBP xenograft model. Mechanistically, REIIBP upregulated TLR7 through eIF3E, and this relied on eIF3E RNA-binding function instead of its canonical protein synthesis activity, as demonstrated by direct binding to the 3'UTR of TLR7 mRNA. Altogether, we provided a rationale that co-existence of different NSD2 isoforms induced diversified oncogenic programs that should be considered in the strategies for t(4;14)-targeted therapy.
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Affiliation(s)
- Phyllis S Y Chong
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore
| | - Jing Yuan Chooi
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore
| | | | - Tae-Hoon Chung
- Cancer Science Institute of Singapore, National University of Singapore
| | - Reinhard Brunmeir
- Cancer Science Institute of Singapore, National University of Singapore
| | | | | | - Kalpnaa Balan
- Cancer Science Institute of Singapore, National University of Singapore
| | | | - Zhengwei Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Nagavidya Subramaniam
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore
| | - Leah A Vardy
- A*STAR Skin Research Labs and Skin Research Institute of Singapore, A*STAR, Immunos, Singapore
| | - Wee-Joo Chng
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Science Institute of Singapore, National University of Singapore, Singapore; Department of Hematology-Oncology, National University Cancer Institute of Singapore, National University Health System.
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22
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Lei P, Guo Q, Hao J, Liu H, Chen Y, Wu F, He Z, Zhang X, Zhang N, Wen S, Gao W, Wu Y. Exploring the evolving roles and clinical significance of circRNAs in head and neck squamous cell carcinoma. J Cancer 2024; 15:3984-3994. [PMID: 38911371 PMCID: PMC11190751 DOI: 10.7150/jca.96614] [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: 03/25/2024] [Accepted: 05/13/2024] [Indexed: 06/25/2024] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) represents the predominant malignancies in the head and neck region, and has limited therapeutic alternatives. Circular RNAs (circRNAs), a substantial category of non-coding RNA molecules, exert influential roles in human disease development and progression, employing various mechanisms such as microRNA sponging, interaction with RNA-binding proteins, and translational capabilities. Accumulating evidence highlights the differential expression of numerous circRNAs in HNSCC, and numerous dysregulated circRNAs underscore their crucial involvement in malignant advancement and resistance to treatment. This review aims to comprehensively outline the characteristics, biogenesis, and mechanisms of circRNAs, elucidating their functional significance in HNSCC. In addition, we delve into the clinical implications of circRNAs, considering their potential as biomarkers or targets for diagnosis, prognosis, and therapeutic applications in HNSCC. The discussion extends to exploring future challenges in the clinical translation of circRNAs, emphasizing the need for further research.
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Affiliation(s)
- Pengxiang Lei
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Qingbo Guo
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, China
| | - Jiewen Hao
- Department of Otolaryngology Head & Neck Surgery, The Third Hospital of Shanxi Medical University (Shanxi Bethune Hospital), Taiyuan 030032, Shanxi, China
| | - Hui Liu
- Department of Hepatobiliary Surgery, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen 518055, Guangdong, China
| | - Yaofeng Chen
- Department of Otolaryngology Head & Neck Surgery, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen 518055, Guangdong, China
| | - Feng Wu
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, Guangdong, China
| | - Zhao He
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, Guangdong, China
| | - Xiaolong Zhang
- Shenzhen Research Institute, Northwest A&F University, Shenzhen 518000, Guangdong, China
| | - Nannan Zhang
- Department of Otolaryngology Head & Neck Surgery, Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen 518055, Guangdong, China
| | - Shuxin Wen
- Department of Otolaryngology Head & Neck Surgery, The Third Hospital of Shanxi Medical University (Shanxi Bethune Hospital), Taiyuan 030032, Shanxi, China
| | - Wei Gao
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen 518172, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen 518172, Guangdong, China
| | - Yongyan Wu
- Shanxi Key Laboratory of Otorhinolaryngology Head and Neck Cancer, Department of Otolaryngology Head & Neck Surgery, First Hospital of Shanxi Medical University, Taiyuan 030001, Shanxi, China
- Department of Otolaryngology Head & Neck Surgery, Longgang Otolaryngology Hospital, Shenzhen 518172, Guangdong, China
- Shenzhen Institute of Otolaryngology & Key Laboratory of Otolaryngology, Longgang Otolaryngology Hospital, Shenzhen 518172, Guangdong, China
- Shenzhen University General Hospital & Shenzhen University Clinical Medical Academy, Shenzhen University, Shenzhen 518055, Guangdong, China
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23
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Kweon TH, Jung H, Ko JY, Kang J, Kim W, Kim Y, Kim HB, Yi EC, Ku NO, Cho JW, Yang WH. O-GlcNAcylation of RBM14 contributes to elevated cellular O-GlcNAc through regulation of OGA protein stability. Cell Rep 2024; 43:114163. [PMID: 38678556 DOI: 10.1016/j.celrep.2024.114163] [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: 11/01/2023] [Revised: 03/18/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024] Open
Abstract
Dysregulation of O-GlcNAcylation has emerged as a potential biomarker for several diseases, particularly cancer. The role of OGT (O-GlcNAc transferase) in maintaining O-GlcNAc homeostasis has been extensively studied; nevertheless, the regulation of OGA (O-GlcNAcase) in cancer remains elusive. Here, we demonstrated that the multifunctional protein RBM14 is a regulator of cellular O-GlcNAcylation. By investigating the correlation between elevated O-GlcNAcylation and increased RBM14 expression in lung cancer cells, we discovered that RBM14 promotes ubiquitin-dependent proteasomal degradation of OGA, ultimately mediating cellular O-GlcNAcylation levels. In addition, RBM14 itself is O-GlcNAcylated at serine 521, regulating its interaction with the E3 ligase TRIM33, consequently affecting OGA protein stability. Moreover, we demonstrated that mutation of serine 521 to alanine abrogated the oncogenic properties of RBM14. Collectively, our findings reveal a previously unknown mechanism for the regulation of OGA and suggest a potential therapeutic target for the treatment of cancers with dysregulated O-GlcNAcylation.
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Affiliation(s)
- Tae Hyun Kweon
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea; Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Hyeryeon Jung
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul 03080, Republic of Korea
| | - Jeong Yeon Ko
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Jingu Kang
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea; Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Wonyoung Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yeolhoe Kim
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Han Byeol Kim
- Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju 26426, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, School of Convergence Science and Technology and College of Medicine or College of Pharmacy, Seoul National University, Seoul 03080, Republic of Korea
| | - Nam-On Ku
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Jin Won Cho
- Interdisciplinary Program of Integrated OMICS for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea; Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
| | - Won Ho Yang
- Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea.
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24
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Liu X, Xie B, Wang S, Wu Y, Zhang Y, Ruan L. Alteration of RNA m6A methylation mediates aberrant RNA binding protein expression and alternative splicing in condyloma acuminatum. PeerJ 2024; 12:e17376. [PMID: 38784389 PMCID: PMC11114121 DOI: 10.7717/peerj.17376] [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: 12/26/2023] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Background Condyloma acuminatum (CA) is caused by low-risk human papillomavirus, and is characterized by high recurrence after treatment. The RNA modification N6-methyladenosine (m6A) plays an important role during diverse viral infections, including high-risk HPV infection in cervical cancer. However, it is unclear whether low-risk HPV infection changes the RNA m6A methylation in CA. Methods High-throughputm6A-sequencing was performed to profile the transcriptome-wide mRNA modifications of CA tissues infected by LR-HPVs and the paired normal tissues from CA patients. We further investigated the regulation of alternative splicing by RNA binding proteins (RBPs) with altered m6A modification and constructed a regulatory network among these RBPs, regulated alternative splicing events (RASEs) and regulated alternative splicing genes (RASGs) in CA. Results The results show that the m6A level in CA tissues differed from that in the paired controls. Furthermore, cell cycle- and cell adhesion- associated genes with m6A modification were differentially expressed in CA tissues compared to the paired controls. In particular, seven RNA binding protein genes with specific m6A methylated sites, showed a higher or lower expression at the mRNA level in CA tissues than in the paired normal tissues. In addition, these differentially expressed RNA binding protein genes would regulate the alternative splicing pattern of apoptotic process genes in CA tissue. Conclusions Our study reveals a sophisticated m6A modification profile in CA tissue that affects the response of host cells to HPV infection, and provides cues for the further exploration of the roles of m6A and the development of a novel treatment strategy for CA.
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Affiliation(s)
- Xiaoyan Liu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Bo Xie
- Department of Urology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Su Wang
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinhua Wu
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yu Zhang
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Liming Ruan
- Department of Dermatology, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
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25
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Shin CH, Rossi M, Anerillas C, Martindale JL, Yang X, Ji E, Pal A, Munk R, Yang JH, Tsitsipatis D, Mazan-Mamczarz K, Abdelmohsen K, Gorospe M. Increased ANKRD1 Levels in Early Senescence Mediated by RBMS1-Elicited ANKRD1 mRNA Stabilization. Mol Cell Biol 2024; 44:194-208. [PMID: 38769646 PMCID: PMC11123458 DOI: 10.1080/10985549.2024.2350540] [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: 03/19/2024] [Accepted: 04/25/2024] [Indexed: 05/22/2024] Open
Abstract
Cellular senescence is a dynamic biological process triggered by sublethal cell damage and driven by specific changes in gene expression programs. We recently identified ANKRD1 (ankyrin repeat domain 1) as a protein strongly elevated after triggering senescence in fibroblasts. Here, we set out to investigate the mechanisms driving the elevated production of ANKRD1 in the early stages of senescence. Our results indicated that the rise in ANKRD1 levels after triggering senescence using etoposide (Eto) was the result of moderate increases in transcription and translation, and robust mRNA stabilization. Antisense oligomer (ASO) pulldown followed by mass spectrometry revealed a specific interaction of the RNA-binding protein RBMS1 with ANKRD1 mRNA that was confirmed by ribonucleoprotein immunoprecipitation analysis. RBMS1 abundance decreased in the nucleus and increased in the cytoplasm during Eto-induced senescence; in agreement with the hypothesis that RBMS1 may participate in post-transcriptional stabilization of ANKRD1 mRNA, silencing RBMS1 reduced, while overexpressing RBMS1 enhanced ANKRD1 mRNA half-life after Eto treatment. A segment proximal to the ANKRD1 coding region was identified as binding RBMS1 and conferring RBMS1-dependent increased expression of a heterologous reporter. We propose that RBMS1 increases expression of ANKRD1 during the early stages of senescence by stabilizing ANKRD1 mRNA.
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Affiliation(s)
- Chang Hoon Shin
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Martina Rossi
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Carlos Anerillas
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Jennifer L. Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Xiaoling Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Eunbyul Ji
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Apala Pal
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Jen-Hao Yang
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Krystyna Mazan-Mamczarz
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, Maryland, USA
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Wang Z, Zhang C, Guo J, Yang Y, Li P, Wang Z, Liu S, Zhang L, Zeng X, Zhai J, Wang X, Zhao Q, Chen Z, Zhu P, He Q. CRISPR-Cas9 screening identifies INTS3 as an anti-apoptotic RNA-binding protein and therapeutic target for colorectal cancer. iScience 2024; 27:109676. [PMID: 38665208 PMCID: PMC11043890 DOI: 10.1016/j.isci.2024.109676] [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: 12/03/2023] [Revised: 02/17/2024] [Accepted: 04/03/2024] [Indexed: 04/28/2024] Open
Abstract
Growing evidences indicate that RNA-binding proteins (RBPs) play critical roles in regulating the RNA splicing, polyadenylation, stability, localization, translation, and turnover. Abnormal expression of RBPs can promote tumorigenesis. Here, we performed a CRISPR screen using an RBP pooled CRISPR knockout library and identified 27 potential RBPs with role in supporting colorectal cancer (CRC) survival. We found that the deletion/depletion of INTS3 triggered apoptosis in CRC. The in vitro experiments and RNA sequencing revealed that INTS3 destabilized pro-apoptotic gene transcripts and contributed to the survival of CRC cells. INTS3 loss delayed CRC cells growth in vivo. Furthermore, delivery of DOTAP/cholesterol-mshINTS3 nanoparticles inhibited CRC tumor growth. Collectively, our work highlights the role of INTS3 in supporting CRC survival and provides several novel therapeutic targets for treatment.
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Affiliation(s)
- Zhiwei Wang
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Cheng Zhang
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Jing Guo
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Yanmei Yang
- Research Center of Basic Medicine, Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Peixian Li
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Ziyan Wang
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Sijia Liu
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Lulu Zhang
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Xiaoyu Zeng
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Jincheng Zhai
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Xinyong Wang
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Qi Zhao
- Department of oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, China
| | - Zhenzhen Chen
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Pingping Zhu
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
| | - Qiankun He
- School of Life Sciences, Zhengzhou University, 100 Kexue Road, Zhengzhou 450001, China
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Beauchamp E, Gamma JM, Cromwell CR, Moussa EW, Pain R, Kostiuk MA, Acevedo-Morantes C, Iyer A, Yap M, Vincent KM, Postovit LM, Julien O, Hubbard BP, Mackey JR, Berthiaume LG. Multiomics analysis identifies oxidative phosphorylation as a cancer vulnerability arising from myristoylation inhibition. J Transl Med 2024; 22:431. [PMID: 38715059 PMCID: PMC11075276 DOI: 10.1186/s12967-024-05150-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/31/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND In humans, two ubiquitously expressed N-myristoyltransferases, NMT1 and NMT2, catalyze myristate transfer to proteins to facilitate membrane targeting and signaling. We investigated the expression of NMTs in numerous cancers and found that NMT2 levels are dysregulated by epigenetic suppression, particularly so in hematologic malignancies. This suggests that pharmacological inhibition of the remaining NMT1 could allow for the selective killing of these cells, sparing normal cells with both NMTs. METHODS AND RESULTS Transcriptomic analysis of 1200 NMT inhibitor (NMTI)-treated cancer cell lines revealed that NMTI sensitivity relates not only to NMT2 loss or NMT1 dependency, but also correlates with a myristoylation inhibition sensitivity signature comprising 54 genes (MISS-54) enriched in hematologic cancers as well as testis, brain, lung, ovary, and colon cancers. Because non-myristoylated proteins are degraded by a glycine-specific N-degron, differential proteomics revealed the major impact of abrogating NMT1 genetically using CRISPR/Cas9 in cancer cells was surprisingly to reduce mitochondrial respiratory complex I proteins rather than cell signaling proteins, some of which were also reduced, albeit to a lesser extent. Cancer cell treatments with the first-in-class NMTI PCLX-001 (zelenirstat), which is undergoing human phase 1/2a trials in advanced lymphoma and solid tumors, recapitulated these effects. The most downregulated myristoylated mitochondrial protein was NDUFAF4, a complex I assembly factor. Knockout of NDUFAF4 or in vitro cell treatment with zelenirstat resulted in loss of complex I, oxidative phosphorylation and respiration, which impacted metabolomes. CONCLUSIONS Targeting of both, oxidative phosphorylation and cell signaling partly explains the lethal effects of zelenirstat in select cancer types. While the prognostic value of the sensitivity score MISS-54 remains to be validated in patients, our findings continue to warrant the clinical development of zelenirstat as cancer treatment.
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Affiliation(s)
| | - Jay M Gamma
- Department of Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Christopher R Cromwell
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Eman W Moussa
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Rony Pain
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Morris A Kostiuk
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Claudia Acevedo-Morantes
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Aishwarya Iyer
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Megan Yap
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Krista M Vincent
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Lynne M Postovit
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Olivier Julien
- Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Basil P Hubbard
- Department of Pharmacology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | | | - Luc G Berthiaume
- Pacylex Pharmaceuticals Inc., Edmonton, AB, Canada.
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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Chen R, Xie Q, Xie L, Huang J, Hu L, Lu H, Shi P, He Q, Zhang Q, Gong C, Zhang S, Wang B, Yang G, Yang Q. Thioredoxin1 Binding Metastasis-Associated Lung Adenocarcinoma Transcript 1 Attenuates Inflammation and Apoptosis after Intracerebral Hemorrhage. Aging Dis 2024; 15:1384-1397. [PMID: 37196136 PMCID: PMC11081159 DOI: 10.14336/ad.2023.0507] [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: 12/05/2022] [Accepted: 05/07/2023] [Indexed: 05/19/2023] Open
Abstract
Post-transcriptional regulation and RNA-binding proteins (RBPs) play vital roles in the occurrence of secondary injury after intracerebral hemorrhage (ICH). Therefore, we identified RBPs distinctively expressed after ICH by screening and determined thioredoxin1 (Txn1) as one of the most distinctive RBPs. We employed an ICH model and in vitro experiments to investigate the role of Txn1 in ICH. Firstly, we found that Txn1 was mainly expressed in microglia and neurons in the central nervous system, and its expression was significantly reduced in perihematomal tissue. Additionally, adeno-associated virus (AAV) carrying Txn1 was injected into the ICH rat model. Our results showed that overexpression of Txn1 reduced secondary injury and improved outcome in the ICH rat model. Moreover, to understand the therapeutic mechanism of Txn1 after ICH, we performed RNA immunoprecipitation combined with high-throughput sequencing. The results showed that Txn1 binds to inflammation- and apoptosis-related mRNAs and affects gene expression through RNA splicing and translation. Finally, RNA pull-down assays and in vitro experiments confirmed that Txn1 binds to metastasis-associated lung adenocarcinoma transcript 1 (MALAT1), leading to reduced inflammation and apoptosis. Our study suggests that Txn1 is a potential therapeutic target for alleviating ICH-induced brain injury.
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Affiliation(s)
- Ru Chen
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qi Xie
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Lexing Xie
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Jiacheng Huang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Linlin Hu
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Hui Lu
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Peixia Shi
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qian He
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qin Zhang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Changxiong Gong
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Shuang Zhang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Bingqiao Wang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Guoqiang Yang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
| | - Qingwu Yang
- Department of Neurology, Second Affiliated Hospital, Army Medical University (Third Military Medical University), Chongqing 400037, China
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Yang L, Zhang Z, Yao X, Wu X, Zhang Z. HNRNPL facilitates ferroptosis in hepatocellular carcinoma cells by promoting S100A9 expression. Transl Oncol 2024; 43:101908. [PMID: 38368714 PMCID: PMC10884479 DOI: 10.1016/j.tranon.2024.101908] [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: 11/17/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024] Open
Abstract
OBJECTIVE This study probed into the effect of HNRNPL on ferroptosis in hepatocellular carcinoma (HCC) cells and related molecular mechanisms. METHODS Expression patterns of HNRNPL, Recombinant S100 Calcium Binding Protein A9 (S100A9) were analyzed in HCC tissues or cells. Following transfection, HCC cell activity was analyzed, followed by detection of levels of ROS, iron content, LPO, MDA, and GSH as well as the expression of ferroptosis-related proteins. For molecular mechanism, RIP, RNA pull-down assay and actinomycin D assay were implemented to verify the binding relationship between HNRNPL and S100A9. Finally, in vivo nude mouse xenograft tumor experiments were performed for further validate the crucial role of HNENPL expression in HCC. RESULTS HNRNPL and S100A9 were significantly overexpressed in HCC. sh-HNRNPL treatment led to a significant decrease in cellular activity, GSH content, and expression of GPX4 and SLC7A11, and a significant increase in iron content, LPO level, MDA, ROS content, and expression of ACSL4 and TFR1. In addition, after sh-HNRNPL was combined with oe-S100A9 or Fer-1, a ferroptosis inhibitor, both oe-S100A9 and Fer-1 reversed the promotional effect of sh-HNRNPL on ferroptosis of HCC cells when sh-HNRNPL acted alone. Mechanically, HNRNPL promoted S100A9 mRNA stability and expression through RBP. Furthermore, low expression of HNRNPL in vivo delayed the growth of xenograft tumors and the expression of ferroptosis-related proteins. CONCLUSION HNRNPL promotes S100A9 mRNA stability and expression through RBP action, thereby promoting ferroptosis in HCC cells.
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Affiliation(s)
- Lanfang Yang
- Department of Hepatopancreas Biliary, Hernia Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; Department of Hepatopancreas Biliary, Hernia Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; First Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350005, China.
| | - Zhibo Zhang
- Department of Hepatopancreas Biliary, Hernia Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; Department of Hepatopancreas Biliary, Hernia Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; First Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Xiangqing Yao
- Department of Hepatopancreas Biliary, Hernia Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; Department of Hepatopancreas Biliary, Hernia Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; First Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Xukun Wu
- Department of Hepatopancreas Biliary, Hernia Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; Department of Hepatopancreas Biliary, Hernia Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; First Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350005, China
| | - Zhao Zhang
- Department of Hepatopancreas Biliary, Hernia Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; Department of Hepatopancreas Biliary, Hernia Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian 350005, China; First Clinical Medical College, Fujian Medical University, Fuzhou, Fujian 350005, China
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30
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Liu X, Wu L, Wang L, Li Y. Identification and classification of glioma subtypes based on RNA-binding proteins. Comput Biol Med 2024; 174:108404. [PMID: 38582000 DOI: 10.1016/j.compbiomed.2024.108404] [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: 12/04/2023] [Revised: 03/23/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024]
Abstract
BACKGROUND Glioma is a common and aggressive primary malignant cancer known for its high morbidity, mortality, and recurrence rates. Despite this, treatment options for glioma are currently restricted. The dysregulation of RBPs has been linked to the advancement of several types of cancer, but their precise role in glioma evolution is still not fully understood. This study sought to investigate how RBPs may impact the development and prognosis of glioma, with potential implications for prognosis and therapy. METHODS RNA-seq profiles of glioma and corresponding clinical data from the CGGA database were initially collected for analysis. Unsupervised clustering was utilized to identify crucial tumor subtypes in glioma development. Subsequent time-series analysis and MS model were employed to track the progression of these identified subtypes. RBPs playing a significant role in glioma progression were then pinpointed using WGCNA and Lasso Cox regression models. Functional analysis of these key RBP-related genes was conducted through GSEA. Additionally, the CIBERSORT algorithm was utilized to estimate immune infiltrating cells, while the STRING database was consulted to uncover potential mechanisms of the identified biomarkers. RESULTS Six tumor subgroups were identified and found to be highly homogeneous within each subgroup. The progression stages of these tumor subgroups were determined using time-series analysis and a MS model. Through WGCNA, Lasso Cox, and multivariate Cox regression analysis, it was confirmed that BCLAF1 is correlated with survival in glioma patients and is closely linked to glioma progression. Functional annotation suggests that BCLAF1 may impact glioma progression by influencing RNA splicing, which in turn affects the cell cycle, Wnt signaling pathway, and other cancer development pathways. CONCLUSIONS The study initially identified six subtypes of glioma progression and assessed their malignancy ranking. Furthermore, it was determined that BCLAF1 could serve as an RBP-related prognostic marker, offering significant implications for the clinical diagnosis and personalized treatment of glioma.
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Affiliation(s)
- Xudong Liu
- School of Medicine, Chongqing University, Chongqing, 400044, China; Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lei Wu
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China
| | - Lei Wang
- College of Life Sciences, Xinyang Normal University, Xinyang, 464000, China.
| | - Yongsheng Li
- Department of Medical Oncology, Chongqing University Cancer Hospital, Chongqing, 400030, China.
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Abdelsam SS, Ghanem SK, Zahid MA, Abunada HH, Bader L, Raïq H, Khan A, Parray A, Djouhri L, Agouni A. Human antigen R: Exploring its inflammatory response impact and significance in cardiometabolic disorders. J Cell Physiol 2024; 239:e31229. [PMID: 38426269 DOI: 10.1002/jcp.31229] [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: 11/13/2023] [Revised: 01/30/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
RNA-binding proteins (RBPs) play a crucial role in the regulation of posttranscriptional RNA networks, which can undergo dysregulation in many pathological conditions. Human antigen R (HuR) is a highly researched RBP that plays a crucial role as a posttranscriptional regulator. HuR plays a crucial role in the amplification of inflammatory signals by stabilizing the messenger RNA of diverse inflammatory mediators and key molecular players. The noteworthy correlations between HuR and its target molecules, coupled with the remarkable impacts reported on the pathogenesis and advancement of multiple diseases, position HuR as a promising candidate for therapeutic intervention in diverse inflammatory conditions. This review article examines the significance of HuR as a member of the RBP family, its regulatory mechanisms, and its implications in the pathophysiology of inflammation and cardiometabolic illnesses. Our objective is to illuminate potential directions for future research and drug development by conducting a comprehensive analysis of the existing body of research on HuR.
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Affiliation(s)
- Shahenda Salah Abdelsam
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Sarah Khalaf Ghanem
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Muhammad Ammar Zahid
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Hanan H Abunada
- Office of Vice President for Research and Graduate Studies, Qatar University, Doha, Qatar
| | - Loulia Bader
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Hicham Raïq
- Department of Social Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Abbas Khan
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Aijaz Parray
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Laiche Djouhri
- Department of Basic Medical Science, College of Medicine, QU health, Qatar University, Doha, Qatar
| | - Abdelali Agouni
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
- Office of Vice President for Medical & Health Sciences, QU Health, Qatar University, Doha, Qatar
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Huang Y, Zhang R, Lyu H, Xiao S, Guo D, Chen XZ, Zhou C, Tang J. LncRNAs as nodes for the cross-talk between autophagy and Wnt signaling in pancreatic cancer drug resistance. Int J Biol Sci 2024; 20:2698-2726. [PMID: 38725864 PMCID: PMC11077374 DOI: 10.7150/ijbs.91832] [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: 11/02/2023] [Accepted: 02/06/2024] [Indexed: 05/12/2024] Open
Abstract
Pancreatic cancer is a malignancy with high mortality. In addition to the few symptoms until the disease reaches an advanced stage, the high fatality rate is attributed to its rapid development, drug resistance and lack of appropriate treatment. In the selection and research of therapeutic drugs, gemcitabine is the first-line drug for pancreatic cancer. Solving the problem of gemcitabine resistance in pancreatic cancer will contribute to the progress of pancreatic cancer treatment. Long non coding RNAs (lncRNAs), which are RNA transcripts longer than 200 nucleotides, play vital roles in cellular physiological metabolic activities. Currently, our group and others have found that some lncRNAs are aberrantly expressed in pancreatic cancer cells, which can regulate the process of cancer through autophagy and Wnt/β-catenin pathways simultaneously and affect the sensitivity of cancer cells to therapeutic drugs. This review presents an overview of the recent evidence concerning the node of lncRNA for the cross-talk between autophagy and Wnt/β-catenin signaling in pancreatic cancer, together with the practicability of lncRNAs and the core regulatory factors as targets in therapeutic resistance.
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Affiliation(s)
- Yuhan Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Dong Guo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada, T6G2R3
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China, 430068
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Liu W, Wang W, Wang Z, Fan X, Li W, Huang Y, Yang X, Tang Z. CRISPR Screen Identifies the RNA-Binding Protein Eef1a1 as a Key Regulator of Myogenesis. Int J Mol Sci 2024; 25:4816. [PMID: 38732031 PMCID: PMC11084334 DOI: 10.3390/ijms25094816] [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: 03/19/2024] [Revised: 04/22/2024] [Accepted: 04/26/2024] [Indexed: 05/13/2024] Open
Abstract
Skeletal muscle myogenesis hinges on gene regulation, meticulously orchestrated by molecular mechanisms. While the roles of transcription factors and non-coding RNAs in myogenesis are widely known, the contribution of RNA-binding proteins (RBPs) has remained unclear until now. Therefore, to investigate the functions of post-transcriptional regulators in myogenesis and uncover new functional RBPs regulating myogenesis, we employed CRISPR high-throughput RBP-KO (RBP-wide knockout) library screening. Through this approach, we successfully identified Eef1a1 as a novel regulatory factor in myogenesis. Using CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) technologies, we successfully established cellular models for both CRISPRko and CRISPRi. Our findings demonstrated that Eef1a1 plays a crucial role in promoting proliferation in C2C12 myoblasts. Through siRNA inhibition and overexpression methods, we further elucidated the involvement of Eef1a1 in promoting proliferation and suppressing differentiation processes. RIP (RNA immunoprecipitation), miRNA pull-down, and Dual-luciferase reporter assays confirmed that miR-133a-3p targets Eef1a1. Co-transfection experiments indicated that miR-133a-3p can rescue the effect of Eef1a1 on C2C12 myoblasts. In summary, our study utilized CRISPR library high-throughput screening to unveil a novel RBP, Eef1a1, involved in regulating myogenesis. Eef1a1 promotes the proliferation of myoblasts while inhibiting the differentiation process. Additionally, it acts as an antagonist to miR-133a-3p, thus modulating the process of myogenesis.
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Affiliation(s)
- Weiwei Liu
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
| | - Wei Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Zishuai Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Wangchang Li
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Yuxin Huang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
| | - Xiaogan Yang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
| | - Zhonglin Tang
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, College of Animal Science & Technology, Guangxi University, Nanning 530004, China; (W.L.); (W.L.); (Y.H.)
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Foshan 528226, China; (W.W.); (Z.W.); (X.F.)
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China
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Zhang N, Gao S, Peng H, Wu J, Li H, Gibson C, Wu S, Zhu J, Zheng Q. Chemical proteomic profiling of protein dopaminylation in colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.27.591460. [PMID: 38712070 PMCID: PMC11071480 DOI: 10.1101/2024.04.27.591460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Histone dopaminylation is a newly identified epigenetic mark that plays a role in the regulation of gene transcription, where an isopeptide bond is formed between the fifth amino acid residue of H3 ( i.e. , glutamine) and dopamine. In our previous studies, we discovered that the dynamics of this post-translational modification (including installation, removal, and replacement) were regulated by a single enzyme, transglutaminase 2 (TGM2), through reversible transamination. Recently, we developed a chemical probe to specifically label and enrich histone dopaminylation via bioorthogonal chemistry. Given this powerful tool, we found that histone H3 glutamine 5 dopaminylation (H3Q5dop) was highly enriched in colorectal tumors, which could be attributed to the high expression level of TGM2 in colon cancer cells. Due to the enzyme promiscuity of TGM2, non-histone proteins have also been identified as targets of dopaminylation on glutamine residues, however, the dopaminylated proteome in cancer cells still remains elusive. Here, we utilized our chemical probe to enrich dopaminylated proteins from colorectal cancer cells in a bioorthogonal manner and performed the chemical proteomics analysis. Therefore, 425 dopaminylated proteins were identified, many of which are involved in nucleic acid metabolism and transcription pathways. More importantly, a number of modification sites of these dopaminylated proteins were identified, attributed to the successful application of our chemical probe. Overall, these findings shed light on the significant association between cellular protein dopaminylation and cancer development, further suggesting that to block the installation of protein dopaminylation may become a promising anti-cancer strategy. TOC
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Weidle UH, Birzele F. Deregulated circRNAs in Epithelial Ovarian Cancer With Activity in Preclinical In Vivo Models: Identification of Targets and New Modalities for Therapeutic Intervention. Cancer Genomics Proteomics 2024; 21:213-237. [PMID: 38670587 PMCID: PMC11059596 DOI: 10.21873/cgp.20442] [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: 01/25/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/28/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is associated with a dismal prognosis due to development of resistance to chemotherapy and metastasis in the peritoneal cavity and distant organs. In order to identify new targets and treatment modalities we searched the literature for up- and and down-regulated circRNAs with efficacy in preclinical EOC-related in vivo systems. Our search yielded circRNAs falling into the following categories: cisplatin and paclitaxel resistance, transmembrane receptors, secreted factors, transcription factors, RNA splicing and processing factors, RAS pathway-related components, proteolysis and cell-cycle regulation, signaling-related proteins, and circRNAs regulating proteins in additional categories. These findings can be potentially translated by validation and manipulation of the corresponding targets, inhibition of circRNAs with antisense oligonucleotides (ASO), small interfering RNAs (siRNA) or small hairpin RNA (shRNA) or by reconstituting their activity.
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Affiliation(s)
- Ulrich H Weidle
- Roche Pharma Research and Early Development, Roche Innovation Center Munich, Penzberg, Germany;
| | - Fabian Birzele
- Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, Basel, Switzerland
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Sun Y, Chen D, Sun S, Ren M, Zhou L, Chen C, Zhao J, Wei H, Zhao Q, Qi Y, Zhang J, Zhang G, Liu H, Yang Q, Liu Q, Wang Y, Zhang W. RBMS1 Coordinates with the m 6A Reader YTHDF1 to Promote NSCLC Metastasis through Stimulating S100P Translation. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307122. [PMID: 38342601 PMCID: PMC11022699 DOI: 10.1002/advs.202307122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/05/2024] [Indexed: 02/13/2024]
Abstract
Metastasis is the leading cause for the high mortality of lung cancer, however, effective anti-metastatic drugs are still limited. Here it is reported that the RNA-binding protein RBMS1 is positively associated with increased lymph node metastasis in non-small cell lung cancer (NSCLC). Depletion of RBMS1 suppresses cancer cell migration and invasion in vitro and inhibits cancer cell metastasis in vivo. Mechanistically, RBMS1 interacts with YTHDF1 to promote the translation of S100P, thereby accelerating NSCLC cell metastasis. The RRM2 motif of RBMS1 and the YTH domain of YTHDF1 are required for the binding of RBMS1 and YTHDF1. RBMS1 ablation inhibits the translation of S100P and suppresses tumor metastasis. Targeting RBMS1 with NTP, a small molecular chemical inhibitor of RBMS1, attenuates tumor metastasis in a mouse lung metastasis model. Correlation studies in lung cancer patients further validate the clinical relevance of the findings. Collectively, the study provides insight into the molecular mechanism by which RBMS1 promotes NSCLC metastasis and offers a therapeutic strategy for metastatic NSCLC.
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Affiliation(s)
- Yu Sun
- Sino‐US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem CellDalian Medical UniversityDalian116023China
| | - Dan Chen
- Department of Pathologythe First Affiliated Hospital of Dalian Medical UniversityDalian Medical UniversityDalian116011China
| | - Siwen Sun
- Department of Oncology & Sino‐US Research Center for Cancer Translational Medicinethe Second Affiliated HospitalDalian Medical UniversityDalian116023China
| | - Menglin Ren
- Sino‐US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem CellDalian Medical UniversityDalian116023China
| | - Liang Zhou
- Sino‐US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem CellDalian Medical UniversityDalian116023China
| | - Chaoqun Chen
- Sino‐US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem CellDalian Medical UniversityDalian116023China
| | - Jinyao Zhao
- Institute of Cancer Stem CellDalian Medical UniversityDalian116044China
| | - Huanhuan Wei
- CAS Key Laboratory of Computational BiologyBio‐Med Big Data CenterShanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai200031China
| | - Qingzhi Zhao
- Sino‐US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem CellDalian Medical UniversityDalian116023China
| | - Yangfan Qi
- Institute of Cancer Stem CellDalian Medical UniversityDalian116044China
| | - Jinrui Zhang
- Institute of Cancer Stem CellDalian Medical UniversityDalian116044China
| | - Ge Zhang
- Department of ImmunologyCollege of Basic Medical SciencesDalian Medical UniversityDalian116044China
| | - Han Liu
- Institute of Cancer Stem CellDalian Medical UniversityDalian116044China
| | - Qingkai Yang
- Institute of Cancer Stem CellDalian Medical UniversityDalian116044China
| | - Quentin Liu
- Institute of Cancer Stem CellDalian Medical UniversityDalian116044China
| | - Yang Wang
- Sino‐US Research Center for Cancer Translational Medicine of the Second Affiliated Hospital of Dalian Medical University & Institute of Cancer Stem CellDalian Medical UniversityDalian116023China
| | - Wenjing Zhang
- Institute of Cancer Stem CellDalian Medical UniversityDalian116044China
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Ren J, Huang B, Li W, Wang Y, Pan X, Ma Q, Liu Y, Wang X, Liang C, Zhang Y, Wang S, Yang F, Li H, Ning H, Jiang Y, Qin C, Ran A, Xiao B. RNA-binding protein IGF2BP2 suppresses metastasis of clear cell renal cell carcinoma by enhancing CKB mRNA stability and expression. Transl Oncol 2024; 42:101904. [PMID: 38341962 PMCID: PMC10867445 DOI: 10.1016/j.tranon.2024.101904] [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: 11/17/2023] [Revised: 01/15/2024] [Accepted: 02/03/2024] [Indexed: 02/13/2024] Open
Abstract
Clear cell renal cell carcinoma (ccRCC) is the most prevalent kidney cancer, with a highly aggressive phenotype and poor prognosis. RNA binding proteins (RBPs) play crucial roles in post-transcriptional gene regulation and have been implicated in tumorigenesis. RBPs have the potential to become a new therapeutic target for ccRCC. In this study, we screened and validated that insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2) as an RBP, was down-regulated in ccRCC tissues and cell lines. Functionally, we verified that IGF2BP2 significantly suppressed the migration and invasion ability of ccRCC in vitro and in vivo. Mechanistically, RIP-seq and actinomycin D experiments results showed that IGF2BP2 enhanced the expression of Creatine Kinase B (CKB) by binding to CKB mRNA and enhancing its mRNA stability. Thus, IGF2BP2 inhibited ccRCC metastasis through enhancing the expression of CKB. Taken together, these finding suggests that IGF2BP2 is a novel metastasis suppressor of ccRCC and may serve as a potential therapeutic target.
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Affiliation(s)
- Junwu Ren
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Bo Huang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China; Key Laboratory of Basic Pharmacology of Ministry of Education and Joint International Research Laboratory of Ethnomedicine of Ministry of Education, Zunyi Medical University, Zunyi 563006, PR China
| | - Wei Li
- Department of Pharmacy, Chongqing University Cancer Hospital, Chongqing 400030, PR China
| | - Yongquan Wang
- Department of Urology, Southwest Hospital, Army Medical University, Chongqing 400038, PR China
| | - Xiaojuan Pan
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Qiang Ma
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Yuying Liu
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Xiaolin Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Ce Liang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Yuying Zhang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Shimin Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Feifei Yang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Haiping Li
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Hao Ning
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Yan Jiang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Changhong Qin
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Ai Ran
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China
| | - Bin Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, PR China.
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Liang C, Zhai B, Wei D, Niu B, Ma J, Yao Y, Lin Y, Liu Y, Liu X, Wang P. FXR1 stabilizes SNORD63 to regulate blood-tumor barrier permeability through SNORD63 mediated 2'-O-methylation of POU6F1. Int J Biol Macromol 2024; 265:130642. [PMID: 38460644 DOI: 10.1016/j.ijbiomac.2024.130642] [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: 08/04/2023] [Revised: 01/04/2024] [Accepted: 03/03/2024] [Indexed: 03/11/2024]
Abstract
How selectively increase blood-tumor barrier (BTB) permeability is crucial to enhance the delivery of chemotherapeutic agents to brain tumor tissues. In this study, we established in vitro models of the blood-brain barrier (BBB) and BTB using endothelial cells (ECs) co-cultured with human astrocytes (AECs) and glioma cells (GECs), respectively. The findings revealed high expressions of the RNA-binding protein FXR1 and SNORD63 in GECs, where FXR1 was found to bind and stabilize SNORD63. Knockdown of FXR1 resulted in decreased expression of tight-junction-related proteins and increased BTB permeability by down-regulating SNORD63. SNORD63 played a role in mediating the 2'-O-methylation modification of POU6F1 mRNA, leading to the downregulation of POU6F1 protein expression. POU6F1 showed low expression in GECs and acted as a transcription factor to regulate BTB permeability by binding to the promoter regions of ZO-1, occludin, and claudin-5 mRNAs and negatively regulating their expressions. Finally, the targeted regulation of FXR1, SNORD63, and POU6F1 expressions, individually or in combination, effectively enhanced doxorubicin passage through the BTB and induced apoptosis in glioma cells. This study aims to elucidate the underlying mechanism of the FXR1/SNORD63/POU6F1 axis in regulating BTB permeability, offering a novel strategy to improve the efficacy of glioma chemotherapy.
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Affiliation(s)
- Chanchan Liang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Bei Zhai
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Deng Wei
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Ben Niu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Jun Ma
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yilong Yao
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yang Lin
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang 110004, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang 110122, China; Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang 110004, China.
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Chitluri KK, Emerson IA. The importance of protein domain mutations in cancer therapy. Heliyon 2024; 10:e27655. [PMID: 38509890 PMCID: PMC10950675 DOI: 10.1016/j.heliyon.2024.e27655] [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: 10/11/2023] [Revised: 02/28/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Cancer is a complex disease that is caused by multiple genetic factors. Researchers have been studying protein domain mutations to understand how they affect the progression and treatment of cancer. These mutations can significantly impact the development and spread of cancer by changing the protein structure, function, and signalling pathways. As a result, there is a growing interest in how these mutations can be used as prognostic indicators for cancer prognosis. Recent studies have shown that protein domain mutations can provide valuable information about the severity of the disease and the patient's response to treatment. They may also be used to predict the response and resistance to targeted therapy in cancer treatment. The clinical implications of protein domain mutations in cancer are significant, and they are regarded as essential biomarkers in oncology. However, additional techniques and approaches are required to characterize changes in protein domains and predict their functional effects. Machine learning and other computational tools offer promising solutions to this challenge, enabling the prediction of the impact of mutations on protein structure and function. Such predictions can aid in the clinical interpretation of genetic information. Furthermore, the development of genome editing tools like CRISPR/Cas9 has made it possible to validate the functional significance of mutants more efficiently and accurately. In conclusion, protein domain mutations hold great promise as prognostic and predictive biomarkers in cancer. Overall, considerable research is still needed to better define genetic and molecular heterogeneity and to resolve the challenges that remain, so that their full potential can be realized.
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Affiliation(s)
- Kiran Kumar Chitluri
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
| | - Isaac Arnold Emerson
- Bioinformatics Programming Lab, Department of Bio-Sciences, School of Bio Sciences and Technology, Vellore Institute of Technology, Vellore, TN, 632014, India
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Shao C, Yan X, Pang S, Nian D, Ren L, Li H, Sun J. Bifunctional molecular probe targeting tumor PD-L1 enhances anti-tumor efficacy by promoting ferroptosis in lung cancer mouse model. Int Immunopharmacol 2024; 130:111781. [PMID: 38442580 DOI: 10.1016/j.intimp.2024.111781] [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: 12/27/2023] [Revised: 02/19/2024] [Accepted: 02/27/2024] [Indexed: 03/07/2024]
Abstract
PURPOSE Immune checkpoint inhibitors (ICIs) targeting tumor-specific PD-1/PD-L1 significantly improve the overall survival rate of patients with advanced cancer by reactivating the immune system to attack cancer cells. To explore their tumor killing effect, we used the radionuclide iodine-131 (131I) to label the anti-PD-L1 antibody Atezolizumab (131I-PD-L1 mAb). METHOD We prepared the radioimmunoassay molecular probe 131I-PD-L1 mAb by the chloramine-T method and evaluated its affinity using Lewis lung cancer (LLC) cells. The uptake of 131I-PD-L1 mAb by transplanted tumors was examined through SPECT and its in vivo distribution. We then compared the in vitro and in vivo anti-tumor efficacy of groups treated with control, PD-L1 mAb, 131I-PD-L1 mAb, and 131I-PD-L1 mAb + PD-L1 mAb combined treatment. We performed H&E staining to examine the changes in tumor, as well as the damage in major tissues and organs caused by potential side effects. The anti-tumor mechanism of 131I-PD-L1 mAb was analyzed by Western blot, RT-qPCR and immunohistochemistry (IHC). RESULT 131I-PD-L1 mAb was highly stable and specific, and easily penetrated into tumor. 131I-PD-L1 mAb suppressed cancer cell proliferation in vitro, and inhibited tumor growth in vivo by inducing ferroptosis, thus prolonging the survival of experimental animals while demonstrating biological safety. CONCLUSION Therefore, our study suggested that 131I-PD-L1 mAb affected the expression of tumor-related factors through β-rays and thus promoted ferroptosis in tumor. Combined treatment showed better anti-tumor effect compared to single ICI treatment.
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Affiliation(s)
- Chenxu Shao
- Department of Nuclear Medicine, School of Laboratory Medicine, Bengbu Medical University, Anhui Province, Bengbu 233000, PR China
| | - Xiaoping Yan
- Department of Radiology, The People's Hospital of Jiangyou, Jiangyou 621700, PR China
| | - Shangjie Pang
- Department of Nuclear Medicine, School of Laboratory Medicine, Bengbu Medical University, Anhui Province, Bengbu 233000, PR China
| | - Di Nian
- Department of Nuclear Medicine, School of Laboratory Medicine, Bengbu Medical University, Anhui Province, Bengbu 233000, PR China
| | - Li Ren
- Department of Nuclear Medicine, School of Laboratory Medicine, Bengbu Medical University, Anhui Province, Bengbu 233000, PR China
| | - Hui Li
- Department of Nuclear Medicine, First Affiliated Hospital of Bengbu Medical University, Bengbu 233000, PR China
| | - Junjie Sun
- Department of Nuclear Medicine, School of Laboratory Medicine, Bengbu Medical University, Anhui Province, Bengbu 233000, PR China.
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Kim Y, You JH, Ryu Y, Park G, Lee U, Moon HE, Park HR, Song CW, Ku JL, Park SH, Paek SH. ELAVL2 loss promotes aggressive mesenchymal transition in glioblastoma. NPJ Precis Oncol 2024; 8:79. [PMID: 38548861 PMCID: PMC10978835 DOI: 10.1038/s41698-024-00566-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 03/08/2024] [Indexed: 04/01/2024] Open
Abstract
Glioblastoma (GBM), the most lethal primary brain cancer, exhibits intratumoral heterogeneity and molecular plasticity, posing challenges for effective treatment. Despite this, the regulatory mechanisms underlying such plasticity, particularly mesenchymal (MES) transition, remain poorly understood. In this study, we elucidate the role of the RNA-binding protein ELAVL2 in regulating aggressive MES transformation in GBM. We found that ELAVL2 is most frequently deleted in GBM compared to other cancers and associated with distinct clinical and molecular features. Transcriptomic analysis revealed that ELAVL2-mediated alterations correspond to specific GBM subtype signatures. Notably, ELAVL2 expression negatively correlated with epithelial-to-mesenchymal transition (EMT)-related genes, and its loss promoted MES process and chemo-resistance in GBM cells, whereas ELAVL2 overexpression exerted the opposite effect. Further investigation via tissue microarray analysis demonstrated that high ELAVL2 protein expression confers a favorable survival outcome in GBM patients. Mechanistically, ELAVL2 was shown to directly bind to the transcripts of EMT-inhibitory molecules, SH3GL3 and DNM3, modulating their mRNA stability, potentially through an m6A-dependent mechanism. In summary, our findings identify ELAVL2 as a critical tumor suppressor and mRNA stabilizer that regulates MES transition in GBM, underscoring its role in transcriptomic plasticity and glioma progression.
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Affiliation(s)
- Yona Kim
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Ji Hyeon You
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Yeonjoo Ryu
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University College of Biological Sciences, Seoul, Korea
| | - Gyuri Park
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Urim Lee
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
- Interdisciplinary Program in Caner Biology, Seoul National University College of Medicine, Seoul, Korea
| | - Hyo Eun Moon
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Hye Ran Park
- Department of Neurosurgery, Soonchunhyang University Seoul Hospital, Seoul, Korea
| | - Chang W Song
- Department of Radiation Oncology, University of Minnesota Medical School, Minneapolis, MN, 55455, USA
| | - Ja-Lok Ku
- Korean Cell Line Bank, Laboratory of Cell Biology, Cancer Research Institute, Seoul National University College of Medicine, Seoul, Korea
| | - Sung-Hye Park
- Department of Pathology, Seoul National University Hospital, Seoul, Korea
| | - Sun Ha Paek
- Department of Neurosurgery, Cancer Research Institute and Ischemic/Hypoxic Disease Institute, Seoul National University College of Medicine, Seoul, Korea.
- Advanced Institute of Convergence Technology, Seoul National University, Suwon, Korea.
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42
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Yang N, Zhang N, Lu G, Zeng S, Xing Y, Du L. RNA-binding proteins potentially regulate the alternative splicing of cell cycle-associated genes in proliferative diabetic retinopathy. Sci Rep 2024; 14:6731. [PMID: 38509306 PMCID: PMC10954754 DOI: 10.1038/s41598-024-57516-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 03/19/2024] [Indexed: 03/22/2024] Open
Abstract
RNA-binding proteins (RBPs) contribute to the pathogenesis of proliferative diabetic retinopathy (PDR) by regulating gene expression through alternative splicing events (ASEs). However, the RBPs differentially expressed in PDR and the underlying mechanisms remain unclear. Thus, this study aimed to identify the differentially expressed genes in the neovascular membranes (NVM) and retinas of patients with PDR. The public transcriptome dataset GSE102485 was downloaded from the Gene Expression Omnibus database, and samples of PDR and normal retinas were analyzed. A mouse model of oxygen-induced retinopathy was used to confirm the results. The top 20 RBPs were screened for co-expression with alternative splicing genes (ASGs). A total of 403 RBPs were abnormally expressed in the NVM and retina samples. Functional analysis demonstrated that the ASGs were enriched in cell cycle pathways. Cell cycle-associated ASEs and an RBP-AS regulatory network, including 15 RBPs and their regulated ASGs, were extracted. Splicing factor proline/glutamine rich (SFPQ), microtubule-associated protein 1 B (MAP1B), heat-shock protein 90-alpha (HSP90AA1), microtubule-actin crosslinking factor 1 (MACF1), and CyclinH (CCNH) expression remarkably differed in the mouse model. This study provides novel insights into the RBP-AS interaction network in PDR and for developing screening and treatment options to prevent diabetic retinopathy-related blindness.
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Affiliation(s)
- Ning Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ningzhi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Guojing Lu
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Siyu Zeng
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Lei Du
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Wuhan, China.
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Wang Q, Chen F, He Y, Gao Y, Wang J, Chu S, Xie P, Zhong J, Shan H, Bai J, Hou P. Polypyrimidine tract-binding protein 3/insulin-like growth factor 2 mRNA-binding proteins 3/high-mobility group A1 axis promotes renal cancer growth and metastasis. iScience 2024; 27:109158. [PMID: 38405614 PMCID: PMC10884747 DOI: 10.1016/j.isci.2024.109158] [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: 09/11/2023] [Revised: 01/05/2024] [Accepted: 02/05/2024] [Indexed: 02/27/2024] Open
Abstract
Polypyrimidine tract-binding protein 3 (PTBP3) plays an important role in the post-transcriptional regulation of gene expression, including mRNA splicing, translation, and stability. Increasing evidence has shown that PTBP3 promotes cancer progression in several tumor types. However, the molecular mechanisms of PTBP3 in renal cell carcinoma (RCC) remain unknown. Here, tissue microarrays (TMAs) suggested that PTBP3 expression was increased in human RCC and that high PTBP3 expression was correlated with poor five-year overall survival and disease-free survival. We also showed that PTBP3 binds with HMGA1 mRNA in the 3'UTR region and let-7 miRNAs. PTBP3 interacted with IGF2BP3, and the PTBP3/IGF2BP3 axis prevented let-7 mediated HMGA1 mRNA silencing. PTBP3 promotes renal cancer cell growth and metastasis in vitro and in vivo. Taken together, our findings indicate PTBP3 serves as a regulator of HMGA1 and suggest its potential as a therapeutic agent for RCC.
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Affiliation(s)
- Qianqing Wang
- Department of Gynecology Oncology, Xinxiang Central Hospital, The Fourth Clinical College of Xinxiang Medical University, Xinxiang, Henan 453000, China
| | - Fang Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Yu He
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Yue Gao
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Jiawen Wang
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Sufang Chu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
| | - Pei Xie
- Department of Gynecology Oncology, Xinxiang Central Hospital, The Fourth Clinical College of Xinxiang Medical University, Xinxiang, Henan 453000, China
| | - Jiateng Zhong
- Department of Gynecology Oncology, Xinxiang Central Hospital, The Fourth Clinical College of Xinxiang Medical University, Xinxiang, Henan 453000, China
| | - Haixia Shan
- Department of Oncology, The Affiliated Hospital of Xuzhou Medical University, 99 Huaihai Road, Xuzhou, Jiangsu 221002, China
| | - Jin Bai
- Department of Gynecology Oncology, Xinxiang Central Hospital, The Fourth Clinical College of Xinxiang Medical University, Xinxiang, Henan 453000, China
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu 221004, China
| | - Pingfu Hou
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu 221004, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu 221004, China
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Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 PMCID: PMC11253550 DOI: 10.1016/j.devcel.2024.01.005] [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: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Wang S, Sun H, Chen G, Wu C, Sun B, Lin J, Lin D, Zeng D, Lin B, Huang G, Lu X, Lin H, Liang Y. RNA-binding proteins in breast cancer: Biological implications and therapeutic opportunities. Crit Rev Oncol Hematol 2024; 195:104271. [PMID: 38272151 DOI: 10.1016/j.critrevonc.2024.104271] [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: 06/27/2023] [Revised: 01/05/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
RNA-binding proteins (RBPs) refer to a class of proteins that participate in alternative splicing, RNA stability, polyadenylation, localization and translation of RNAs, thus regulating gene expression in post-transcriptional manner. Dysregulation of RNA-RBP interaction contributes to various diseases, including cancer. In breast cancer, disorders in RBP expression and function influence the biological characteristics of tumor cells. Targeting RBPs has fostered the development of innovative therapies for breast cancer. However, the RBP-related mechanisms in breast cancer are not completely clear. In this review, we summarize the regulatory mechanisms of RBPs and their signaling crosstalk in breast cancer. Specifically, we emphasize the potential of certain RBPs as prognostic factors due to their effects on proliferation, invasion, apoptosis, and therapy resistance of breast cancer cells. Most importantly, we present a comprehensive overview of the latest RBP-related therapeutic strategies and novel therapeutic targets that have proven to be useful in the treatment of breast cancer.
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Affiliation(s)
- Shimeng Wang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Hexing Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Guanyuan Chen
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Chengyu Wu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Bingmei Sun
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Jiajia Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Danping Lin
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - De Zeng
- Department of Medical Oncology, Cancer Hospital of SUMC, Shantou 515000, China
| | - Baohang Lin
- Department of Thyroid, Breast and Vascular Surgery, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Guan Huang
- Department of Pathology, Longgang District Central Hospital of Shenzhen, Shenzhen 518116, China
| | - Xiaofeng Lu
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China
| | - Haoyu Lin
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
| | - Yuanke Liang
- Department of Thyroid and Breast Surgery, Clinical Research Center, The First Affiliated Hospital of Shantou University Medical College (SUMC), 57 Changping Road, Shantou 515041, China.
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Li T, Huang M, Sun N, Hua X, Chen R, Xie Q, Huang S, Du M, Zhao Y, Lin Q, Xu J, Han X, Zhao Y, Tian Z, Zhang Y, Chen W, Shen X, Huang C. Tumorigenesis of basal muscle invasive bladder cancer was mediated by PTEN protein degradation resulting from SNHG1 upregulation. J Exp Clin Cancer Res 2024; 43:50. [PMID: 38365726 PMCID: PMC10874020 DOI: 10.1186/s13046-024-02966-4] [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: 07/10/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Phosphatase and tensin homolog deleted on chromosome ten (PTEN) serves as a powerful tumor suppressor, and has been found to be downregulated in human bladder cancer (BC) tissues. Despite this observation, the mechanisms contributing to PTEN's downregulation have remained elusive. METHODS We established targeted genes' knockdown or overexpressed cell lines to explore the mechanism how it drove the malignant transformation of urothelial cells or promoted anchorageindependent growth of human basal muscle invasive BC (BMIBC) cells. The mice model was used to validate the conclusion in vivo. The important findings were also extended to human studies. RESULTS In this study, we discovered that mice exposed to N-butyl-N-(4-hydroxybu-tyl)nitrosamine (BBN), a specific bladder chemical carcinogen, exhibited primary BMIBC accompanied by a pronounced reduction in PTEN protein expression in vivo. Utilizing a lncRNA deep sequencing high-throughput platform, along with gain- and loss-of-function analyses, we identified small nucleolar RNA host gene 1 (SNHG1) as a critical lncRNA that might drive the formation of primary BMIBCs in BBN-treated mice. Cell culture results further demonstrated that BBN exposure significantly induced SNHG1 in normal human bladder urothelial cell UROtsa. Notably, the ectopic expression of SNHG1 alone was sufficient to induce malignant transformation in human urothelial cells, while SNHG1 knockdown effectively inhibited anchorage-independent growth of human BMIBCs. Our detailed investigation revealed that SNHG1 overexpression led to PTEN protein degradation through its direct interaction with HUR. This interaction reduced HUR binding to ubiquitin-specific peptidase 8 (USP8) mRNA, causing degradation of USP8 mRNA and a subsequent decrease in USP8 protein expression. The downregulation of USP8, in turn, increased PTEN polyubiquitination and degradation, culminating in cell malignant transformation and BMIBC anchorageindependent growth. In vivo studies confirmed the downregulation of PTEN and USP8, as well as their positive correlations in both BBN-treated mouse bladder urothelium and tumor tissues of bladder cancer in nude mice. CONCLUSIONS Our findings, for the first time, demonstrate that overexpressed SNHG1 competes with USP8 for binding to HUR. This competition attenuates USP8 mRNA stability and protein expression, leading to PTEN protein degradation, consequently, this process drives urothelial cell malignant transformation and fosters BMIBC growth and primary BMIBC formation.
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Affiliation(s)
- Tengda Li
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Maowen Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Ning Sun
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaohui Hua
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Ruifan Chen
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Qipeng Xie
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Shirui Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Mengxiang Du
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yazhen Zhao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Qianqian Lin
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Jiheng Xu
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Xiaoyun Han
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yunping Zhao
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Zhongxian Tian
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Yu Zhang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Wei Chen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China.
| | - Xian Shen
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, 325027, China.
| | - Chuanshu Huang
- Oujiang Laboratory (Zhejiang Lab for Regenerative Medicine, Vision and Brain Health), Key Laboratory of Laboratory Medicine, Ministry of Education, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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Han C, Hu C, Liu T, Sun Y, Hu F, He Y, Zhang J, Chen J, Ding J, Fan J, Zhang X, Wang J, Qiao X, Jiang D, Yang K, Yang S. IGF2BP3 enhances lipid metabolism in cervical cancer by upregulating the expression of SCD. Cell Death Dis 2024; 15:138. [PMID: 38355626 PMCID: PMC10867090 DOI: 10.1038/s41419-024-06520-0] [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: 10/07/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/16/2024]
Abstract
Cervical cancer (CC) is the most common gynecologic malignancy, which seriously threatens the health of women. Lipid metabolism is necessary for tumor proliferation and metastasis. However, the molecular mechanism of the relationship between CC and lipid metabolism remains poorly defined. We revealed the expression of IGF2BP3 in CC exceeded adjacent tissues, and was positively associated with tumor stage using human CC tissue microarrays. The Cell Counting Kit-8, colony formation assay, 5-ethynyl-2'-deoxyuridine assay, transwell assays, wound-healing assays, and flow cytometry assessed the role of IGF2BP3 in proliferation and metastasis of CC cells. Besides, exploring the molecular mechanism participating in IGF2BP3-driven lipid metabolism used RNA-seq, which determined SCD as the target of IGF2BP3. Further, lipid droplets, cellular triglyceride (TG) contents, and fatty acids were accessed to discover that IGF2BP3 can enhance lipid metabolism in CC. Moreover, RIP assay and methylated RNA immunoprecipitation experiments seeked the aimed-gene-binding specificity. Lastly, the IGF2BP3 knockdown restrained CC growth and lipid metabolism, after which SCD overexpression rescued the influence in vitro and in vivo using nude mouse tumor-bearing model. Mechanistically, IGF2BP3 regulated SCD mRNA m6A modifications via IGF2BP3-METTL14 complex, thereby enhanced CC proliferation, metastasis, and lipid metabolism. Our study highlights IGF2BP3 plays a crucial role in CC progression and represents a therapeutic latent strategy. It is a potential tactic that blocks the metabolic pathway relevant to IGF2BP3 with the purpose of treating CC.
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Affiliation(s)
- Chenying Han
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Chenchen Hu
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Tianyue Liu
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Yuanjie Sun
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Feiming Hu
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Yuanli He
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Jiaxing Zhang
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Jiaxi Chen
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Jiaqi Ding
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
- Department of Neurology, Tangdu Hospital, Fourth Military Medical University, 710038, Xi'an, Shaanxi, China
| | - Jiangjiang Fan
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, 710038, Xi'an, China
| | - Xiyang Zhang
- Military Medical Innovation Center, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Jing Wang
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Xupeng Qiao
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Dongbo Jiang
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China
| | - Kun Yang
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China.
- Department of Rheumatology and Immunology, Tangdu Hospital of the Air Force Medical University, 710038, Xi'an, Shaanxi, China.
| | - Shuya Yang
- Department of Immunology, the Fourth Military Medical University, 710032, Xi'an, Shaanxi, China.
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Alsenan S, Al-Turaiki I, Aldayel M, Tounsi M. Role of Optimization in RNA-Protein-Binding Prediction. Curr Issues Mol Biol 2024; 46:1360-1373. [PMID: 38392205 PMCID: PMC11154364 DOI: 10.3390/cimb46020087] [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: 12/07/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024] Open
Abstract
RNA-binding proteins (RBPs) play an important role in regulating biological processes, such as gene regulation. Understanding their behaviors, for example, their binding site, can be helpful in understanding RBP-related diseases. Studies have focused on predicting RNA binding by means of machine learning algorithms including deep convolutional neural network models. One of the integral parts of modeling deep learning is achieving optimal hyperparameter tuning and minimizing a loss function using optimization algorithms. In this paper, we investigate the role of optimization in the RBP classification problem using the CLIP-Seq 21 dataset. Three optimization methods are employed on the RNA-protein binding CNN prediction model; namely, grid search, random search, and Bayesian optimizer. The empirical results show an AUC of 94.42%, 93.78%, 93.23% and 92.68% on the ELAVL1C, ELAVL1B, ELAVL1A, and HNRNPC datasets, respectively, and a mean AUC of 85.30 on 24 datasets. This paper's findings provide evidence on the role of optimizers in improving the performance of RNA-protein binding prediction.
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Affiliation(s)
- Shrooq Alsenan
- Information Systems Department, College of Computer and Information Sciences, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | - Isra Al-Turaiki
- Department of Computer Science, College of Computer and Information Sciences, King Saud University, Riyadh 11653, Saudi Arabia;
| | - Mashael Aldayel
- Information Technology Department, College of Computer and Information Sciences, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohamed Tounsi
- Department of Computer Science, College of Computer and information Sciences, Prince Sultan University, P.O. Box 66833, Riyadh 12435, Saudi Arabia;
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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Sannigrahi MK, Cao AC, Rajagopalan P, Sun L, Brody RM, Raghav L, Gimotty PA, Basu D. A novel pipeline for prioritizing cancer type-specific therapeutic vulnerabilities using DepMap identifies PAK2 as a target in head and neck squamous cell carcinomas. Mol Oncol 2024; 18:336-349. [PMID: 37997254 PMCID: PMC10850805 DOI: 10.1002/1878-0261.13558] [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: 06/10/2023] [Revised: 10/23/2023] [Accepted: 11/22/2023] [Indexed: 11/25/2023] Open
Abstract
There is limited guidance on exploiting the genome-wide loss-of-function CRISPR screens in cancer Dependency Map (DepMap) to identify new targets for individual cancer types. This study integrated multiple tools to filter these data in order to seek new therapeutic targets specific to head and neck squamous cell carcinoma (HNSCC). The resulting pipeline prioritized 143 targetable dependencies that represented both well-studied targets and emerging target classes like mitochondrial carriers and RNA-binding proteins. In total, 14 targets had clinical inhibitors used for other cancers or nonmalignant diseases that hold near-term potential to repurpose for HNSCC therapy. Comparing inhibitor response data that were publicly available for 13 prioritized targets between the cell lines with high vs. low dependency on each target uncovered novel therapeutic potential for the PAK2 serine/threonine kinase. PAK2 gene dependency was found to be associated with wild-type p53, low PAK2 mRNA, and diploid status of the 3q amplicon containing PAK2. These findings establish a generalizable pipeline to prioritize clinically relevant targets for individual cancer types using DepMap. Its application to HNSCC highlights novel relevance for PAK2 inhibition and identifies biomarkers of PAK2 inhibitor response.
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Affiliation(s)
- Malay K. Sannigrahi
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Austin C. Cao
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Pavithra Rajagopalan
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lova Sun
- Department of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Robert M. Brody
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Lovely Raghav
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Phyllis A. Gimotty
- Department of Biostatistics, Epidemiology and InformaticsUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Devraj Basu
- Department of Otorhinolaryngology‐Head and Neck SurgeryUniversity of PennsylvaniaPhiladelphiaPAUSA
- Ellen and Ronald Caplan Cancer CenterThe Wistar InstitutePhiladelphiaPAUSA
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