1
|
Ganguly C, Rostami S, Long K, Aribam SD, Rajan R. Unity among the diverse RNA-guided CRISPR-Cas interference mechanisms. J Biol Chem 2024:107295. [PMID: 38641067 DOI: 10.1016/j.jbc.2024.107295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 04/08/2024] [Accepted: 04/10/2024] [Indexed: 04/21/2024] Open
Abstract
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are adaptive immune systems that protect bacteria and archaea from invading mobile genetic elements (MGEs). The Cas protein-CRISPR RNA (crRNA) complex uses complementarity of the crRNA "guide" region to specifically recognize the invader genome. CRISPR effectors that perform targeted destruction of the foreign genome have emerged independently as multi-subunit protein complexes (Class 1 systems) and as single multi-domain proteins (Class 2). These different CRISPR-Cas systems can cleave RNA, DNA, and protein in an RNA-guided manner to eliminate the invader, and in some cases, they initiate programmed cell death/dormancy. The versatile mechanisms of the different CRISPR-Cas systems to target and destroy nucleic acids have been adapted to develop various programmable-RNA-guided tools and have revolutionized the development of fast, accurate, and accessible genomic applications. In this review, we present the structure and interference mechanisms of different CRISPR-Cas systems and an analysis of their unified features. The three types of Class 1 systems (I, III, and IV) have a conserved right-handed helical filamentous structure that provides a backbone for sequence-specific targeting while using unique proteins with distinct mechanisms to destroy the invader. Similarly, all three Class 2 types (II, V, and VI) have a bilobed architecture that binds the RNA-DNA/RNA hybrid and uses different nuclease domains to cleave invading MGEs. Additionally, we highlight the mechanistic similarities of CRISPR-Cas enzymes with other RNA cleaving enzymes and briefly present the evolutionary routes of the different CRISPR-Cas systems.
Collapse
Affiliation(s)
- Chhandosee Ganguly
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Saadi Rostami
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Kole Long
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Swarmistha Devi Aribam
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Rakhi Rajan
- Department of Chemistry and Biochemistry, Price Family Foundation Institute of Structural Biology, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| |
Collapse
|
2
|
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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [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.
Collapse
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.
| |
Collapse
|
3
|
Choi Y, Um B, Na Y, Kim J, Kim JS, Kim VN. Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle. Mol Cell 2024:S1097-2765(24)00222-3. [PMID: 38593806 DOI: 10.1016/j.molcel.2024.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/16/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside in human cells, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA binding proteins (RBPs) across ten time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed RBPs with unexpected dynamics: the transcription-export (TREX) complex recruited posttranscriptionally after nuclear export factor 1 (NXF1) binding, challenging the current view of transcription-coupled mRNA export, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of the mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with Gene Ontology (GO) annotations. Our data can be explored at chronology.rna.snu.ac.kr.
Collapse
Affiliation(s)
- Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Buyeon Um
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| |
Collapse
|
4
|
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. Adv Sci (Weinh) 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
5
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
6
|
Yang M, Liu J, Kim P, Zhou X. Study of prognostic splicing factors in cancer using machine learning approaches. Hum Mol Genet 2024:ddae047. [PMID: 38538560 DOI: 10.1093/hmg/ddae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 02/11/2024] [Accepted: 03/07/2024] [Indexed: 04/12/2024] Open
Abstract
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing the generation of oncogenic proteins involved in cancer hallmarks. In this study, we investigated the genes that encode RNA-binding proteins and identified potential splicing factors that contribute to the aberrant splicing applying a random forest classification model. The result suggested 56 splicing factors were related to the prognosis of 13 cancers, two SF complexes in liver hepatocellular carcinoma, and one SF complex in esophageal carcinoma. Further systematic bioinformatics studies on these cancer prognostic splicing factors and their related alternative splicing events revealed the potential regulations in a cancer-specific manner. Our analysis found high ILF2-ILF3 expression correlates with poor prognosis in LIHC through alternative splicing. These findings emphasize the importance of SFs as potential indicators for prognosis or targets for therapeutic interventions. Their roles in cancer exhibit complexity and are contingent upon the specific context in which they operate. This recognition further underscores the need for a comprehensive understanding and exploration of the role of SFs in different types of cancer, paving the way for their potential utilization in prognostic assessments and the development of targeted therapies.
Collapse
Affiliation(s)
- Mengyuan Yang
- School of Life Sciences, Zhengzhou University, No. 100, Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Jiajia Liu
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
| | - Pora Kim
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
| | - Xiaobo Zhou
- Center for Computational Systems Medicine, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St Suite 600, Houston, Texas 77030, United States
- McGovern Medical School, The University of Texas Health Science Center at Houston, 6431 Fannin St, Houston, Texas 77030, United States
- School of Dentistry, The University of Texas Health Science Center at Houston, 7500 Cambridge St, Houston, Texas 77054, United States
| |
Collapse
|
7
|
Kellermann G, Leulliot N, Cherfils-Vicini J, Blaud M, Brest P. Activated B-Cells enhance epitope spreading to support successful cancer immunotherapy. Front Immunol 2024; 15:1382236. [PMID: 38571942 PMCID: PMC10989059 DOI: 10.3389/fimmu.2024.1382236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 02/26/2024] [Indexed: 04/05/2024] Open
Abstract
Immune checkpoint therapies (ICT) have transformed the treatment of cancer over the past decade. However, many patients do not respond or suffer relapses. Successful immunotherapy requires epitope spreading, but the slow or inefficient induction of functional antitumoral immunity delays the benefit to patients or causes resistances. Therefore, understanding the key mechanisms that support epitope spreading is essential to improve immunotherapy. In this review, we highlight the major role played by B-cells in breaking immune tolerance by epitope spreading. Activated B-cells are key Antigen-Presenting Cells (APC) that diversify the T-cell response against self-antigens, such as ribonucleoproteins, in autoimmunity but also during successful cancer immunotherapy. This has important implications for the design of future cancer vaccines.
Collapse
Affiliation(s)
| | - Nicolas Leulliot
- Université Paris Cité, Centre national de la recherche scientifique (CNRS), Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), Paris, France
| | - Julien Cherfils-Vicini
- Université Côte d’Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre national de la recherche scientifique (CNRS), Institut national de la santé et de la recherche médicale (INSERM), Centre Antoine Lacassagne, Institut Hospitalo-Universitaire (IHU), RESPIRera, Fédérations Hospitalo-Universitaires (FHU)OncoAge, Nice, France
| | - Magali Blaud
- Université Paris Cité, Centre national de la recherche scientifique (CNRS), Cibles Thérapeutiques et Conception de Médicaments (CiTCoM), Paris, France
| | - Patrick Brest
- Université Côte d’Azur, Institute for Research on Cancer and Aging, Nice (IRCAN), Centre national de la recherche scientifique (CNRS), Institut national de la santé et de la recherche médicale (INSERM), Centre Antoine Lacassagne, Institut Hospitalo-Universitaire (IHU), RESPIRera, Fédérations Hospitalo-Universitaires (FHU)OncoAge, Nice, France
| |
Collapse
|
8
|
Zhang Z, Dong L, Tao H, Dong Y, Xiang W, Tao F, Zhao Y. RNA-binding proteins potentially regulate the alternative splicing of apoptotic genes during knee osteoarthritis progression. BMC Genomics 2024; 25:293. [PMID: 38504181 PMCID: PMC10949708 DOI: 10.1186/s12864-024-10181-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Alternative splicing (AS) is a principal mode of genetic regulation and one of the most widely used mechanisms to generate structurally and functionally distinct mRNA and protein variants. Dysregulation of AS may result in aberrant transcription and protein products, leading to the emergence of human diseases. Although considered important for regulating gene expression, genome-wide AS dysregulation, underlying mechanisms, and clinical relevance in knee osteoarthritis (OA) remain unelucidated. Therefore, in this study, we elucidated and validated AS events and their regulatory mechanisms during OA progression. RESULTS In this study, we identified differentially expressed genes between human OA and healthy meniscus samples. Among them, the OA-associated genes were primarily enriched in biological pathways such as extracellular matrix organization and ossification. The predominant OA-associated regulated AS (RAS) events were found to be involved in apoptosis during OA development. The expression of the apoptosis-related gene BCL2L13, XAF1, and NF2 were significantly different between OA and healthy meniscus samples. The construction of a covariation network of RNA-binding proteins (RBPs) and RAS genes revealed that differentially expressed RBP genes LAMA2 and CUL4B may regulate the apoptotic genes XAF1 and BCL2L13 to undergo AS events during OA progression. Finally, RT-qPCR revealed that CUL4B expression was significantly higher in OA meniscus samples than in normal controls and that the AS ratio of XAF1 was significantly different between control and OA samples; these findings were consistent with their expected expression and regulatory relationships. CONCLUSIONS Differentially expressed RBPs may regulate the AS of apoptotic genes during knee OA progression. XAF1 and its regulator, CUL4B, may serve as novel biomarkers and potential therapeutic targets for this disease.
Collapse
Affiliation(s)
- Zheng Zhang
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China.
| | - Limei Dong
- School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, Hubei, China
| | - Hai Tao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Yusong Dong
- School of Basic Medical Sciences, Wuhan University, 430071, Wuhan, Hubei, China
| | - Wei Xiang
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Fenghua Tao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| | - Yingchun Zhao
- Department of Orthopedics, Renmin Hospital of Wuhan University, 238, Jiefang Road, Wuchang District, 430060, Wuhan, Hubei, China
| |
Collapse
|
9
|
Hom Choudhury S, Bhattacharjee S, Mukherjee K, Bhattacharyya SN. Human antigen R transfers miRNA to Syntaxin 5 to synergize miRNA export from activated macrophages. J Biol Chem 2024; 300:107170. [PMID: 38492777 PMCID: PMC11040126 DOI: 10.1016/j.jbc.2024.107170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 03/07/2024] [Accepted: 03/09/2024] [Indexed: 03/18/2024] Open
Abstract
Intercellular miRNA exchange acts as a key mechanism to control gene expression post-transcriptionally in mammalian cells. Regulated export of repressive miRNAs allows the expression of inflammatory cytokines in activated macrophages. Intracellular trafficking of miRNAs from the endoplasmic reticulum to endosomes is a rate-determining step in the miRNA export process and plays an important role in controlling cellular miRNA levels and inflammatory processes in macrophages. We have identified the SNARE protein Syntaxin 5 (STX5) to show a synchronized expression pattern with miRNA activity loss in activated mammalian macrophage cells. STX5 is both necessary and sufficient for macrophage activation and clearance of the intracellular pathogen Leishmania donovani from infected macrophages. Exploring the mechanism of how STX5 acts as an immunostimulant, we have identified the de novo RNA-binding property of this SNARE protein that binds specific miRNAs and facilitates their accumulation in endosomes in a cooperative manner with human ELAVL1 protein, Human antigen R. This activity ensures the export of miRNAs and allows the expression of miRNA-repressed cytokines. Conversely, in its dual role in miRNA export, this SNARE protein prevents lysosomal targeting of endosomes by enhancing the fusion of miRNA-loaded endosomes with the plasma membrane to ensure accelerated release of extracellular vesicles and associated miRNAs.
Collapse
Affiliation(s)
- Sourav Hom Choudhury
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shreya Bhattacharjee
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Kamalika Mukherjee
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center (UNMC), Omaha, Nebraska, USA.
| | - Suvendra N Bhattacharyya
- RNA Biology Research Laboratory, Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India; Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center (UNMC), Omaha, Nebraska, USA.
| |
Collapse
|
10
|
Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
Collapse
Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
| |
Collapse
|
11
|
Huang GW, Yang TQ, Chen QQ, Liu XM, Xie LH, Huang W, Chen XL, Geng YQ, Gu J. circular RNA circ-231 promotes protein biogenesis of TPI1 and PRDX6 through mediating the interaction of eIF4A3 with STAU1 to facilitate unwinding of secondary structure in 5' UTR, enhancing progression of human esophageal squamous cell carcinoma (ESCC). J Cancer 2024; 15:2518-2537. [PMID: 38577609 PMCID: PMC10988296 DOI: 10.7150/jca.92578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/06/2024] [Indexed: 04/06/2024] Open
Abstract
Background: The nuclear cap-binding complex (CBC)-dependent translation (CT) is an important initial translation pathway for 5'-cap-dependent translation in normal mammal cells. Eukaryotic translation initiation factor 4A-III (eIF4A3), as an RNA helicase, is recruited to CT complex and enhances CT efficiency through participating in unwinding of secondary structure in the 5' UTR. However, the detailed mechanism for eIF4A3 implicated in unwinding of secondary structure in the 5' UTR in normal mammal cells is still unclear. Specially, we need to investigate whether the kind of mechanism in normal mammal cells extrapolates to cancer cells, e.g. ESCC, and further interrogate whether and how the mechanism triggers malignant phenotype of ESCC, which are important for identifying a potential therapeutic target for patients with ESCC. Methods: Bioinformatics analysis, RNA immunoprecipitation and RNA pulldown assays were performed to detect the interaction of circular RNA circ-231 with eIF4A3. In vitro and in vivo assays were performed to detect biological roles of circ-231 in ESCC. RNA immunoprecipitation, RNA pulldown, mass spectrometry analysis and co-immunoprecipitation assays were used to measure the interaction of circ-231, eIF4A3 and STAU1 in HEK293T and ESCC. In vitro EGFP reporter and 5' UTR of mRNA pulldown assays were performed to probe for the binding of circ-231, eIF4A3 and STAU1 to secondary structure of 5' UTR. Results: RNA immunoprecipitation assays showed that circ-231 interacted with eIF4A3 in HEK293T and ESCC. Further study confirmed that circ-231 orchestrated with eIF4A3 to control protein expression of TPI1 and PRDX6, but not for mRNA transcripts. The in-depth mechanism study uncovered that both circ-231 and eIF4A3 were involved in unwinding of secondary structure in 5' UTR of TPI1 and PRDX6. More importantly, circ-231 promoted the interaction between eIF4A3 and STAU1. Intriguingly, both circ-231 and eIF4A3 were dependent on STAU1 binding to secondary structure in 5' UTR. Biological function assays revealed that circ-231 promoted the migration and proliferation of ESCC via TPI1 and PRDX6. In ESCC, the up-regulated expression of circ-231 was observed and patients with ESCC characterized by higher expression of circ-231 have concurrent lymph node metastasis, compared with control. Conclusions: Our data unravels the detailed mechanism by which STAU1 binds to secondary structure in 5' UTR of mRNAs and recruits eIF4A3 through interacting with circ-231 and thereby eIF4A3 is implicated in unwinding of secondary structure, which is common to HEK293T and ESCC. However, importantly, our data reveals that circ-231 promotes migration and proliferation of ESCC and the up-regulated circ-231 greatly correlates with tumor lymph node metastasis, insinuating that circ-231 could be a therapeutic target and an indicator of risk of lymph node metastasis for patients with ESCC.
Collapse
Affiliation(s)
- Guo-Wei Huang
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Ti-Qun Yang
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Qian-Qian Chen
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Xing-Mu Liu
- Department of Surgery, Second Affiliated Hospital, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Ling-Hui Xie
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Wei Huang
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Xue-Ling Chen
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Yi-Qun Geng
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| | - Jiang Gu
- Department of Pathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
- Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Shantou University Medical College, Shantou, 515041, Guangdong, P.R. China
| |
Collapse
|
12
|
Song L, Pan Q, Zhou G, Liu S, Zhu B, Lin P, Hu X, Zha J, Long Y, Luo B, Chen J, Tang Y, Tang J, Xiang X, Xie X, Deng X, Chen G. SHMT2 Mediates Small-Molecule-Induced Alleviation of Alzheimer Pathology Via the 5'UTR-dependent ADAM10 Translation Initiation. Adv Sci (Weinh) 2024; 11:e2305260. [PMID: 38183387 PMCID: PMC10953581 DOI: 10.1002/advs.202305260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 11/27/2023] [Indexed: 01/08/2024]
Abstract
It is long been suggested that one-carbon metabolism (OCM) is associated with Alzheimer's disease (AD), whereas the potential mechanisms remain poorly understood. Taking advantage of chemical biology, that mitochondrial serine hydroxymethyltransferase (SHMT2) directly regulated the translation of ADAM metallopeptidase domain 10 (ADAM10), a therapeutic target for AD is reported. That the small-molecule kenpaullone (KEN) promoted ADAM10 translation via the 5' untranslated region (5'UTR) and improved cognitive functions in APP/PS1 mice is found. SHMT2, which is identified as a target gene of KEN and the 5'UTR-interacting RNA binding protein (RBP), mediated KEN-induced ADAM10 translation in vitro and in vivo. SHMT2 controls AD signaling pathways through binding to a large number of RNAs and enhances the 5'UTR activity of ADAM10 by direct interaction with GAGGG motif, whereas this motif affected ribosomal scanning of eukaryotic initiation factor 2 (eIF2) in the 5'UTR. Together, KEN exhibits therapeutic potential for AD by linking OCM with RNA processing, in which the metabolic enzyme SHMT2 "moonlighted" as RBP by binding to GAGGG motif and promoting the 5'UTR-dependent ADAM10 translation initiation.
Collapse
Affiliation(s)
- Li Song
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Qiu‐Ling Pan
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Gui‐Feng Zhou
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Sheng‐Wei Liu
- Department of PharmacyYongchuan Hospital of Chongqing Medical UniversityChongqing402160China
| | - Bing‐Lin Zhu
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Pei‐Jia Lin
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Xiao‐Tong Hu
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
- Department of Health ManagementDaping HospitalArmy Medical universityChongqing400042China
| | - Jing‐Si Zha
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
- Department of Internal MedicineThe Southwest University HospitalChongqing400715China
| | - Yan Long
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
- Department of Geriatric MedicineDaping HospitalArmy Medical universityChongqing400042China
| | - Biao Luo
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Jian Chen
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Ying Tang
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
- Department of NeurologyWest China HospitalSichuan UniversityChengdu610041China
| | - Jing Tang
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Xiao‐Jiao Xiang
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
- Department of Nuclear MedicineThe Second Affiliated Hospital of Chongqing Medical UniversityChongqing400010China
| | - Xiao‐Yong Xie
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Xiao‐Juan Deng
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| | - Guo‐Jun Chen
- Department of NeurologyChongqing Key Laboratory of Major Neurological and Mental DisordersThe First Affiliated Hospital of Chongqing Medical UniversityChongqing400016China
| |
Collapse
|
13
|
Kristofich J, Nicchitta C. High-throughput quantitation of protein-RNA UV-crosslinking efficiencies as a predictive tool for high confidence identification of RNA binding proteins. RNA 2024:rna.079848.123. [PMID: 38423626 DOI: 10.1261/rna.079848.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/12/2024] [Indexed: 03/02/2024]
Abstract
UV-crosslinking has proven to be an invaluable tool for the identification of RNA-protein interactomes. The paucity of methods for distinguishing background from bona fide RNA-protein interactions however makes attribution of RNA binding function on UV-crosslinking alone challenging. To address this need, we previously reported an RNA binding protein (RBP) confidence scoring metric, (RCS), incorporating both signal-to-noise (S:N) and protein abundance determinations to distinguish high and low confidence candidate RBPs. Although RCS has utility, we sought a direct metric for quantification and comparative evaluation of protein-RNA interactions. Here we propose the use of protein-specific UV-crosslinking efficiency (%CL), representing the molar fraction of a protein that is crosslinked to RNA, for functional evaluation of candidate RBPs. Application to the HeLa RNA interactome yielded %CL values for 1,097 proteins. Remarkably, %CL values span over five orders of magnitude. For the HeLa RNA interactome, %CL values comprise a range from high efficiency, high specificity interactions, e.g., the Elav protein HuR and the Pumilio homolog Pum2, with %CL values of 45.9 and 24.2, respectively, to very low efficiency and specificity interactions e.g., the metabolic enzymes glyceraldehyde-3-phosphate dehydrogenase, fructose-bisphosphate aldolase, and alpha-enolase, with %CL values of 0.0016, 0.006, and 0.008, respectively. We further extend the utility of %CL through prediction of protein domains and classes with known RNA-binding functions, thus establishing it as a useful metric for RNA interactome analysis. We anticipate that this approach will benefit efforts to establish functional RNA interactomes and support development of more predictive computational approaches for RNA binding protein identification.
Collapse
|
14
|
Gan P, Wang Z, Bezprozvannaya S, McAnally JR, Tan W, Li H, Bassel-Duby R, Liu N, Olson EN. RBPMS regulates cardiomyocyte contraction and cardiac function through RNA alternative splicing. Cardiovasc Res 2024; 120:56-68. [PMID: 37890031 PMCID: PMC10898938 DOI: 10.1093/cvr/cvad166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/20/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
AIMS RNA binding proteins play essential roles in mediating RNA splicing and are key post-transcriptional regulators in the heart. Our recent study demonstrated that RBPMS (RNA binding protein with multiple splicing) is crucial for cardiac development through modulating mRNA splicing, but little is known about its functions in the adult heart. In this study, we aim to characterize the post-natal cardiac function of Rbpms and its mechanism of action. METHODS AND RESULTS We generated a cardiac-specific knockout mouse line and found that cardiac-specific loss of Rbpms caused severe cardiomyocyte contractile defects, leading to dilated cardiomyopathy and early lethality in adult mice. We showed by proximity-dependent biotin identification assay and mass spectrometry that RBPMS associates with spliceosome factors and other RNA binding proteins, such as RBM20, that are important in cardiac function. We performed paired-end RNA sequencing and RT-PCR and found that RBPMS regulates mRNA alternative splicing of genes associated with sarcomere structure and function, such as Ttn, Pdlim5, and Nexn, generating new protein isoforms. Using a minigene splicing reporter assay, we determined that RBPMS regulates target gene splicing through recognizing tandem intronic CAC motifs. We also showed that RBPMS knockdown in human induced pluripotent stem cell-derived cardiomyocytes impaired cardiomyocyte contraction. CONCLUSION This study identifies RBPMS as an important regulator of cardiomyocyte contraction and cardiac function by modulating sarcomeric gene alternative splicing.
Collapse
Affiliation(s)
- Peiheng Gan
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Zhaoning Wang
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA 92093, USA
| | - Svetlana Bezprozvannaya
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - John R McAnally
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Wei Tan
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Hui Li
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Rhonda Bassel-Duby
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Ning Liu
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Eric N Olson
- Department of Molecular Biology, Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX 75390, USA
| |
Collapse
|
15
|
Ma Q, Yang F, Xiao B, Guo X. Emerging roles of circular RNAs in tumorigenesis, progression, and treatment of gastric cancer. J Transl Med 2024; 22:207. [PMID: 38414006 PMCID: PMC10897999 DOI: 10.1186/s12967-024-05001-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024] Open
Abstract
With an estimated one million new cases reported annually, gastric cancer (GC) ranks as the fifth most diagnosed malignancy worldwide. The early detection of GC remains a major challenge, and the prognosis worsens either when patients develop resistance to chemotherapy or radiotherapy or when the cancer metastasizes. The precise pathogenesis underlying GC is not well understood, which further complicates its treatment. Circular RNAs (circRNAs), a recently discovered class of noncoding RNAs that originate from parental genes through "back-splicing", have been shown to play a key role in various biological processes in both eukaryotes and prokaryotes. CircRNAs have been linked to cardiovascular diseases, diabetes, hypertension, Alzheimer's disease, and the occurrence and progression of tumors. Prior studies have established that circRNAs play a crucial role in GC, impacting tumorigenesis, diagnosis, progression, and therapy resistance. This review aims to summarize how circRNAs contribute to GC tumorigenesis and progression, examine their roles in the development of drug resistance, discuss their potential as biotechnological drugs, and summarize their response to therapeutic drugs and microorganism in GC.
Collapse
Affiliation(s)
- Qiang Ma
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
- Translational Medicine Research Center & School of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Feifei Yang
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China
| | - Bin Xiao
- College of Pharmacy, Chongqing Medical University, Chongqing, 400016, People's Republic of China.
| | - Xiaolan Guo
- Department of Clinical Laboratory, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
- Translational Medicine Research Center & School of Laboratory Medicine, North Sichuan Medical College, Nanchong, 637000, People's Republic of China.
| |
Collapse
|
16
|
Conti M, Kunitomi C. A genome-wide perspective of the maternal mRNA translation program during oocyte development. Semin Cell Dev Biol 2024; 154:88-98. [PMID: 36894378 DOI: 10.1016/j.semcdb.2023.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 02/01/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023]
Abstract
Transcriptional and post-transcriptional regulations control gene expression in most cells. However, critical transitions during the development of the female gamete relies exclusively on regulation of mRNA translation in the absence of de novo mRNA synthesis. Specific temporal patterns of maternal mRNA translation are essential for the oocyte progression through meiosis, for generation of a haploid gamete ready for fertilization and for embryo development. In this review, we will discuss how mRNAs are translated during oocyte growth and maturation using mostly a genome-wide perspective. This broad view on how translation is regulated reveals multiple divergent translational control mechanisms required to coordinate protein synthesis with progression through the meiotic cell cycle and with development of a totipotent zygote.
Collapse
Affiliation(s)
- Marco Conti
- Center for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA.
| | - Chisato Kunitomi
- Center for Reproductive Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Department of Obstetrics and Gynecology and Reproductive Sciences, University of California, San Francisco, CA 94143, USA
| |
Collapse
|
17
|
Yang B, Wang YW, Zhang K. Interactions between circRNA and protein in breast cancer. Gene 2024; 895:148019. [PMID: 37984538 DOI: 10.1016/j.gene.2023.148019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/10/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
Circular RNA (circRNA) is a newly discovered endogenous non-coding RNA that plays important roles in the occurrence and development of various cancers. Current research indicates that circRNA can inhibit the function of miRNA by acting as an miRNA sponge, interacting with proteins, and being translated into proteins. Most current research focuses on the circRNA-miRNA interaction; however, few studies have investigated the interaction between circRNAs and RNA binding proteins (RBPs) in breast cancer. In this review, we systematically summarize the potential molecular mechanism of the circRNA-protein interaction in breast cancer. Specifically, we elaborate on the direct interaction between circRNAs and proteins in breast cancer, including the functions of circRNA as protein sponges, decoys, and scaffolds, thereby affecting the progression of breast cancer. We also discuss the indirect interaction between circRNAs and proteins in breast cancer in which RBPs, transcription factors and m6A modifying enzymes could in turn regulate the expression and formation of circRNA. Finally, we discuss the potential application of circRNA-protein interaction for treating breast cancer, providing a reference for further research in this field.
Collapse
Affiliation(s)
- Bin Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan 250012, Shandong, People's Republic of China
| | - Ya-Wen Wang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan 250012, Shandong, People's Republic of China
| | - Kai Zhang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Jinan 250012, Shandong, People's Republic of China.
| |
Collapse
|
18
|
Hou H, Wu C, Huo J, Liu N, Jiang Y, Sui S, Li Z. Integrated transcriptome and proteome analysis provides insights into CpFPA1 for floral induction in Chimonanthus praecox (Magnoliidae) without FLC in genome. Plant Cell Rep 2024; 43:66. [PMID: 38341387 DOI: 10.1007/s00299-024-03145-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 12/31/2023] [Indexed: 02/12/2024]
Abstract
KEY MESSAGE We used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud differentiation stages and overexpression of CpFPA1 in Arabidopsis resulted in earlier flowering. Wintersweet (Chimonanthus praecox), a rare winter-flowering woody plant, is well known for its unique blooming time, fragrance and long flowering period. However, the molecular mechanism of flowering in C. praecox remains poorly unclear. In this study, we used transcriptomic and proteomic association analysis to reveal the critical genes/proteins at three key flower bud (FB) differentiation stages (FB.Apr, FB.May and FB.Nov) in C. praecox. The results showed that a total of 952 differential expressed genes (DEGs) and 40 differential expressed proteins (DEPs) were identified. Gene ontology (GO) enrichment revealed that DEGs in FB.Apr/FB.May comparison group were mainly involved in metabolic of biological process, cell and cell part of cellular component and catalytic activity of molecular function. In the EuKaryotic Orthologous Groups (KOG) functional classification, DEPs were predicted mainly in the function of general function prediction only (KOG0118), post-translational modification, protein turnover and chaperones. The autonomous pathway genes play an essential role in the floral induction. Based on transcriptome and proteome correlation analysis, six candidate genes associated with the autonomous pathway were identified, including FPA1, FPA2a, FPA2b, FCA, FLK, FY. Furthermore, CpFPA1 was isolated and functionally characterized, and ectopic expression of CpFPA1 in Arabidopsis Columbia (Col-0) resulted in earlier flowering. These data could contribute to understand the function of CpFPA1 for floral induction and provide information for further research on the molecular mechanisms of flowering in wintersweet.
Collapse
Affiliation(s)
- Huifang Hou
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Chunyu Wu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Juntao Huo
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Ning Liu
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Yingjie Jiang
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Shunzhao Sui
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China
| | - Zhineng Li
- Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing, 400715, China.
| |
Collapse
|
19
|
Dou DR, Zhao Y, Belk JA, Zhao Y, Casey KM, Chen DC, Li R, Yu B, Srinivasan S, Abe BT, Kraft K, Hellström C, Sjöberg R, Chang S, Feng A, Goldman DW, Shah AA, Petri M, Chung LS, Fiorentino DF, Lundberg EK, Wutz A, Utz PJ, Chang HY. Xist ribonucleoproteins promote female sex-biased autoimmunity. Cell 2024; 187:733-749.e16. [PMID: 38306984 PMCID: PMC10949934 DOI: 10.1016/j.cell.2023.12.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/03/2023] [Accepted: 12/31/2023] [Indexed: 02/04/2024]
Abstract
Autoimmune diseases disproportionately affect females more than males. The XX sex chromosome complement is strongly associated with susceptibility to autoimmunity. Xist long non-coding RNA (lncRNA) is expressed only in females to randomly inactivate one of the two X chromosomes to achieve gene dosage compensation. Here, we show that the Xist ribonucleoprotein (RNP) complex comprising numerous autoantigenic components is an important driver of sex-biased autoimmunity. Inducible transgenic expression of a non-silencing form of Xist in male mice introduced Xist RNP complexes and sufficed to produce autoantibodies. Male SJL/J mice expressing transgenic Xist developed more severe multi-organ pathology in a pristane-induced lupus model than wild-type males. Xist expression in males reprogrammed T and B cell populations and chromatin states to more resemble wild-type females. Human patients with autoimmune diseases displayed significant autoantibodies to multiple components of XIST RNP. Thus, a sex-specific lncRNA scaffolds ubiquitous RNP components to drive sex-biased immunity.
Collapse
Affiliation(s)
- Diana R Dou
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yanding Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia A Belk
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Yang Zhao
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | - Derek C Chen
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bingfei Yu
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Suhas Srinivasan
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Brian T Abe
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ceke Hellström
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Ronald Sjöberg
- Autoimmunity and Serology Profiling, Division of Affinity Proteomics, Department of Protein Science, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden
| | - Sarah Chang
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Allan Feng
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - Daniel W Goldman
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ami A Shah
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michelle Petri
- Department of Medicine, Division of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lorinda S Chung
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA
| | - David F Fiorentino
- Department of Dermatology, Stanford University School of Medicine, Redwood City, CA, USA
| | - Emma K Lundberg
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SciLifeLab, Stockholm, Sweden; Departments of Bioengineering and Pathology, Stanford University, Stanford, CA, USA
| | - Anton Wutz
- Department of Biology, Institute of Molecular Health Sciences, Swiss Federal Institute of Technology, ETH Hönggerberg, Zurich, Switzerland
| | - Paul J Utz
- Department of Medicine, Division of Immunology and Rheumatology, Stanford University School of Medicine, Stanford, CA, USA; Institute for Immunity, Transplantation and Infection, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Program in Epithelial Biology, Department of Dermatology, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
20
|
Wilson ML, Romano SN, Khatri N, Aharon D, Liu Y, Kaufman OH, Draper BW, Marlow FL. Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component, Mios. bioRxiv 2024:2024.01.25.577235. [PMID: 38328218 PMCID: PMC10849709 DOI: 10.1101/2024.01.25.577235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary in character. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes (Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator of rboRNAs, which include testis factors and ribosome biogenesis factors. Further, genetic analyses indicate that Rbpms2 promotes nucleolar amplification via the mTorc1 signaling pathway, specifically through the mTorc1-activating Gap activity towards Rags 2 (Gator2) component, Missing oocyte (Mios). Cumulatively, our findings indicate that early gonocytes are in a dual poised, bipotential state in which Rbpms2 acts as a binary fate-switch. Specifically, Rbpms2 represses testis factors and promotes oocyte factors to promote oocyte progression through an essential Gator2-mediated checkpoint, thereby integrating regulation of sexual differentiation factors and nutritional availability pathways in zebrafish oogenesis.
Collapse
Affiliation(s)
- Miranda L. Wilson
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Shannon N. Romano
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Nitya Khatri
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Devora Aharon
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
| | - Yulong Liu
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA 95616
| | - Odelya H. Kaufman
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine. 1300 Morris Park Avenue, Bronx, NY 10461
| | - Bruce W. Draper
- Department of Molecular and Cellular Biology. University of California. 1 Shields Ave, Davis, CA 95616
| | - Florence L. Marlow
- Department of Cell, Developmental, and Regenerative Biology. Icahn School of Medicine at Mount Sinai. One Gustave L. Levy Place Box 1020 New York, NY 10029-6574
- Department of Developmental and Molecular Biology. Albert Einstein College of Medicine. 1300 Morris Park Avenue, Bronx, NY 10461
| |
Collapse
|
21
|
Chanda S, Lepikhov K, Dahlem C, Schymik HS, Hoppstädter J, Geber AK, Wagner K, Kessler SM, Empting M, Kiemer AK. Gene Editing and Small Molecule Inhibitors of the RNA Binding Protein IGF2BP2/IMP2 Show its Potential as an Anti-Cancer Drug Target. FRONT BIOSCI-LANDMRK 2024; 29:41. [PMID: 38287808 DOI: 10.31083/j.fbl2901041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/13/2023] [Accepted: 10/26/2023] [Indexed: 01/31/2024]
Abstract
BACKGROUND The RNA-binding protein IGF2BP2/IMP2/VICKZ2/p62 is an oncofetal protein that is overexpressed in several cancer entities. Employing IMP2 knockout colorectal cancer cells, we could show the important role of IMP2 in several hallmarks of cancer. This study aimed to functionally characterize IMP2 in lung (A549, LLC1) and hepatocellular carcinoma (HepG2, Huh7) cell lines to assess its role as a potential target for these cancer entities. METHODS IMP2 knockouts were generated by CRISPR/Cas9 and its variant approach prime editing; the editing efficiency of two single guide RNAs (sgRNAs) was verified via next-generation sequencing. We studied the effect of IMP2 knockout on cell proliferation, colony formation, and migration and employed small-molecule inhibitors of IMP2. RESULTS Despite multiple attempts, it was not possible to generate IMP2 biallelic knockouts in A549 and Huh7 cells. Both sgRNAs showed good editing efficiency. However, edited cells lost their ability to proliferate. The attempt to generate an IMP2 biallelic knockout in LLC1 cells using CRISPR/Cas9 was successful. Monoallelic knockout cell lines of IMP2 showed a reduction in 2D cell proliferation and reduced migration. In 3D cultures, a change in morphology from compact spheroids to loose aggregates and a distinct reduction in the colony formation ability of the IMP2 knockouts was observed, an effect that was mimicked by previously identified IMP2 inhibitor compounds that also showed an inhibitory effect on colony formation. CONCLUSIONS Our in vitro target validation supports that IMP2 is essential for tumor cell proliferation, migration, and colony formation in several cancer entities.
Collapse
Affiliation(s)
- Shilpee Chanda
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany
| | | | - Charlotte Dahlem
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Hanna S Schymik
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany
| | - Jessica Hoppstädter
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany
| | - An-Kristin Geber
- Department of Genetics, Saarland University, 66123 Saarbrücken, Germany
| | - Konrad Wagner
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, 66123 Saarbrücken, Germany
| | - Sonja M Kessler
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany
- Halle Research Centre for Drug Therapy (HRCDT), 06120 Halle, Germany
- Institute of Pharmacy, Experimental Pharmacology for Natural Sciences, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Martin Empting
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany
- Department of Drug Design and Optimization, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarland University, 66123 Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123 Saarbrücken, Germany
- Center for Gender-Specific Biology and Medicine (CGBM), 66421 Homburg, Germany
| |
Collapse
|
22
|
Corrales-Guerrero L, Díaz-Moreno I. Deciphering the role of Zn 2+ -binding histidines from TIA-1 on the assembly and dynamics of stress granules. Biofactors 2024. [PMID: 38193795 DOI: 10.1002/biof.2037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/19/2023] [Indexed: 01/10/2024]
Abstract
T-cell intracellular antigen-1 (TIA-1) is a key RNA-binding protein that participates in translation regulation and RNA splicing. TIA-1 undergoes liquid-liquid phase separation as a fundamental mechanism that enables the condensation of RNA and proteins into membraneless organelles called stress granules (SGs). However, this dynamic behavior can lead to aberrant fibril formation, implicated in neurodegenerative disorders, and must be tightly regulated. In this study, we investigated the role in the cell of histidine residues His94 and His96, responsible for Zn2+ binding. Using fluorescence microscopy, we found that the specific binding site formed by these residues is critical for SG assembly. Furthermore, it also plays a role maintaining the dynamic behavior of SG-assembled TIA-1. Collectively, our findings confirm the physiological relevance of TIA-1 His94 and His96 in the Zn2+ -mediated regulatory mechanism for protection against fibril formation in SGs.
Collapse
Affiliation(s)
| | - Irene Díaz-Moreno
- Institute for Chemical Research, University of Seville-CSIC, Seville, Spain
| |
Collapse
|
23
|
Wen X, Fang G, Li H, Jiang Z, Du X, Liao Z, Liu R, Huang G, Meng F, Liao W, Zhang Z. CircIRAK3 exerts negative feedback regulation on inflammation by binding to HNRNP U and destabilizing proinflammatory cytokine mRNA in osteoarthritis and chondrogenesis. Int J Biol Macromol 2024; 256:128453. [PMID: 38016613 DOI: 10.1016/j.ijbiomac.2023.128453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 11/30/2023]
Abstract
Osteoarthritis (OA) is the most prevalent age-related and degenerative joint disease with limited treatment options. Previous studies have identified the therapeutic effects of mesenchymal stem cells (MSCs) therapy. Nevertheless, chronic inflammation impedes MSCs therapeutic effect. There have been reports suggesting that circular RNAs (circRNAs) are involved in OA and chondrogenesis. The combination of MSCs and circRNAs in therapies appears to be a promising option. In this study, we identified circIRAK3 as a significant regulator in cartilage degeneration and chondrogenesis through high-throughput sequencing analyses. We observed increased circIRAK3 in OA cartilage and during MSCs chondrogenesis. Knockdown of circIRAK3 resulted in excessive apoptosis, inhibited proliferation, and degradation of chondrocytes, along with the inhibition of MSCs chondrogenesis. Mechanistically, circIRAK3 bound to HNRNP U and competitively prevented its binding to IL-1β, TNFα, and IL6 mRNA, thereby promoting mRNA degradation. Notably, circIRAK3 expression in plasma increased with higher OARSI scores. Intra-articular injection of adeno-associated virus-circIRAK3 delayed cartilage degeneration and reduced inflammation in DMM mouse model. Our study highlights a compensatory regulation network of circIRAK3 in chondrocytes in response to inflammation. CircIRAK3 has the potential to serve as a new therapeutic target for OA. Furthermore, therapies targeting circIRAK3 combined with MSCs hold promise.
Collapse
Affiliation(s)
- Xingzhao Wen
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China; Department of Medicine, Solna, Karolinska Institutet, Centre for Molecular Medicine, Karolinska University Hospital, Stockholm 171 64, Sweden
| | - Guibin Fang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China
| | - Hongyi Li
- Department of Orthopaedics, Qingyuan People's Hospital/the Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan, China
| | - Zongrui Jiang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China
| | - Xue Du
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China
| | - Zhuangyao Liao
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510120, China
| | - Ruonan Liu
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China
| | - Guiwu Huang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China
| | - Fangang Meng
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China
| | - Weiming Liao
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China
| | - Zhiqi Zhang
- Department of Joint Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China; Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Guangzhou, Guangdong 510080, China.
| |
Collapse
|
24
|
Ferrara S, Bertoni G. Genome-Scale Analysis of the Structure and Function of RNA Pathways and Networks in Pseudomonas aeruginosa. Methods Mol Biol 2024; 2721:183-195. [PMID: 37819523 DOI: 10.1007/978-1-0716-3473-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
In recent years, several genome-wide approaches based on RNA sequencing (RNA-seq) have been developed. These methods allow a comprehensive and dynamic view of the structure and function of the multi-layered RNA pathways and networks. Many of these approaches, including the promising one of single-cell transcriptome analysis, have been successfully applied to Pseudomonas aeruginosa. However, we are only at the beginning because only a few surrounding conditions have been considered. Here, we aim to illustrate the different types of approaches based on RNA-seq that will lead us in the future to a better understanding of the dynamics of RNA biology in P. aeruginosa.
Collapse
Affiliation(s)
- Silvia Ferrara
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy
| | - Giovanni Bertoni
- Department of Biosciences, Università degli Studi di Milano, Milan, Milano, Italy.
| |
Collapse
|
25
|
Huang H, Liang X, Wu W, Yuan T, Chen Z, Wang L, Wu Z, Zhang T, Yang K, Wen K. FOXP3-regulated lncRNA NONHSAT136151 promotes colorectal cancer progression by disrupting QKI interaction with target mRNAs. J Cell Mol Med 2024; 28:e18068. [PMID: 38041531 PMCID: PMC10826441 DOI: 10.1111/jcmm.18068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/03/2023] Open
Abstract
The role of lncRNAs in the pathogenesis of cancer, including colorectal cancer (CRC), has repeatedly been demonstrated. However, very few lncRNAs have been well annotated functionally. Our study identified a novel lncRNA upregulated in CRC, NONHSAT136151, which was correlated with clinical progression. In functional assays, NONHSAT136151 significantly enhanced CRC cell proliferation, migration and invasion. Mechanistically, NONHSAT136151 interacted with RNA-binding protein (RBP) QKI (Quaking) to interfere with QKI binding to target mRNAs and regulate their expression. As well, FOXP3 may be causally related to the dysregulation of NONHSAT136151 in CRC cells through its transcriptional activity. In conclusion, our findings identified a novel lncRNA regulated by FOXP3 participates in CRC progression through interacting with QKI, indicating a novel lncRNA-RBP interaction mechanism is involved in CRC pathogenesis.
Collapse
Affiliation(s)
- Handong Huang
- Soochow University Medical CollegeSuzhouJiangsuChina
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Xiaoxiang Liang
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Weizheng Wu
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Tao Yuan
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Zhengquan Chen
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Lin Wang
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Zhenyu Wu
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Tao Zhang
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Kai Yang
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| | - Kunming Wen
- Soochow University Medical CollegeSuzhouJiangsuChina
- Department of General SurgeryAffiliated Hospital of Zunyi Medical UniversityZunyiGuizhouChina
| |
Collapse
|
26
|
Zhan Y, Wang W, Wang H, Xu Y, Zhang Y, Ning Y, Zheng H, Luo J, Yang Y, Zang H, Zhou M, Fan S. G3BP1 Interact with JAK2 mRNA to Promote the Malignant Progression of Nasopharyngeal Carcinoma via Activating JAK2/STAT3 Signaling Pathway. Int J Biol Sci 2024; 20:94-112. [PMID: 38164170 PMCID: PMC10750281 DOI: 10.7150/ijbs.85341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 10/19/2023] [Indexed: 01/03/2024] Open
Abstract
Ras-GTPase-activating protein (GAP)-binding protein 1 (G3BP1) is an RNA-binding protein implicated in various malignancies. However, its role in nasopharyngeal carcinoma (NPC) remains elusive. This study elucidates the potential regulation mechanisms of G3BP1 and its significance in NPC advancement. Through knockdown and overexpression approaches, we validate G3BP1's oncogenic role by promoting proliferation, migration, and invasion in vitro and in vivo. Moreover, G3BP1 emerges as a key regulator of the JAK2/STAT3 signaling pathway, augmenting JAK2 expression via mRNA binding. Notably, epigallocatechin gallate (EGCG), a green tea-derived antioxidant, counteracts G3BP1-mediated pathway activation. Clinical analysis reveals heightened G3BP1, JAK2, and p-STAT3 as powerful prognostic markers, with G3BP1's expression standing as an independent indicator of poorer outcomes for NPC patients. In conclusion, the study unveils the oncogenic prowess of G3BP1, its orchestration of the JAK2/STAT3 signaling pathway, and its pivotal role in NPC progression.
Collapse
Affiliation(s)
- Yuting Zhan
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Weiyuan Wang
- Department of Pathology, Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haihua Wang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Xu
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yuting Zhang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yue Ning
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongmei Zheng
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiadi Luo
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yang Yang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hongjing Zang
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- Cancer Research Institute and School of Basic Medicine Sciences, Central South University, Changsha, Hunan, China
| | - Songqing Fan
- Department of Pathology, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| |
Collapse
|
27
|
Li Z, Liao Y, Tang C, Xu L, Peng B, Xu X. RBM14 promotes DNA end resection during homologous recombination repair. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1864-1873. [PMID: 37559455 PMCID: PMC10753362 DOI: 10.3724/abbs.2023104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 05/25/2023] [Indexed: 08/11/2023] Open
Abstract
DNA double-strand break (DSB) repair by homologous recombination (HR) is crucial for the maintenance of genome stability and integrity. In this study, we aim to identify novel RNA binding proteins (RBPs) involved in HR repair because little is known about RBP function in HR. For this purpose, we carry out pulldown assays using a synthetic ssDNA/dsDNA structure coated with replication protein A (RPA) to mimic resected DNA, a crucial intermediate in HR-mediated DSB repair. Using this approach, we identify RNA-binding motif protein 14 (RBM14) as a potential binding partner. We further show that RBM14 interacts with an essential HR repair factor, CtIP. RBM14 is crucial for CtIP recruitment to DSB sites and for subsequent RPA coating and RAD51 replacement, facilitating efficient HR repair. Moreover, inhibition of RBM14 expression sensitizes cancer cells to X-ray irradiation. Together, our results demonstrate that RBM14 promotes DNA end resection to ensure HR repair and may serve as a potential target for cancer therapy.
Collapse
Affiliation(s)
- Zheng Li
- College of Life SciencesCapital Normal UniversityBeijing100048China
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Yanting Liao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Chen Tang
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil MicrobiologyCollege of Biological SciencesChina Agricultural UniversityBeijing100091China
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine (sgh-dhhCPM)Dehua HospitalDehua362500China
| | - Linli Xu
- College of Life SciencesCapital Normal UniversityBeijing100048China
| | - Bin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer CenterMarshall Laboratory of Biomedical EngineeringShenzhen University Medical SchoolShenzhen UniversityShenzhen518060China
| |
Collapse
|
28
|
Higuera-Rodriguez RA, De Pascali MC, Aziz M, Sattler M, Rant U, Kaiser W. Kinetic FRET Assay to Measure Binding-Induced Conformational Changes of Nucleic Acids. ACS Sens 2023; 8:4597-4606. [PMID: 38060303 PMCID: PMC10749467 DOI: 10.1021/acssensors.3c01527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/27/2023] [Accepted: 11/28/2023] [Indexed: 12/08/2023]
Abstract
The interaction of small molecules or proteins with RNA or DNA often involves changes in the nucleic acid (NA) folding and structure. A biophysical characterization of these processes helps us to understand the underlying molecular mechanisms. Here, we propose kinFRET (kinetics Förster resonance energy transfer), a real-time ensemble FRET methodology to measure binding and folding kinetics. With kinFRET, the kinetics of conformational changes of NAs (DNA or RNA) upon analyte binding can be directly followed via a FRET signal using a chip-based biosensor. We demonstrate the utility of this approach with two representative examples. First, we monitored the conformational changes of different formats of an aptamer (MN19) upon interaction with small-molecule analytes. Second, we characterized the binding kinetics of RNA recognition by tandem K homology (KH) domains of the human insulin-like growth factor II mRNA-binding protein 3 (IMP3), which reveals distinct kinetic contributions of the two KH domains. Our data demonstrate that kinFRET is well suited to study the kinetics and conformational changes of NA-analyte interactions.
Collapse
Affiliation(s)
- R. Anahi Higuera-Rodriguez
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Mareike C. De Pascali
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Masood Aziz
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Helmholtz
Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg 85764, Germany
| | - Michael Sattler
- TUM
School of Natural Sciences, Department of Bioscience, Technical University of Munich, Garching 85748, Germany
- Helmholtz
Munich, Molecular Targets and Therapeutics Center, Institute of Structural Biology, Neuherberg 85764, Germany
| | - Ulrich Rant
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| | - Wolfgang Kaiser
- Dynamic
Biosensors GmbH, Perchtinger Str. 8/10, Munich 81379, Germany
| |
Collapse
|
29
|
Jung M, Ji E, Kang H, Kim C, Ryu S, Han S, Cha S, Lee EK. The microRNA-195-5p/hnRNP A1 axis contributes to the progression of hepatocellular carcinoma by regulating the migration of cancer cells. Biochem Biophys Res Commun 2023; 686:149183. [PMID: 37926044 DOI: 10.1016/j.bbrc.2023.149183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/19/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Dysregulation of gene expression is critical for the progression of cancer. The augmented expression of hnRNP A1 in patients with hepatocellular carcinoma (HCC) has been related to its oncogenic functions. However, the underlying mechanisms responsible for upregulation of hnRNP A1 have not been fully elucidated. In the present study, we identified microRNA-195-5p (miR-195-5p), a miRNA downregulated in HCC, as a novel regulator governing hnRNP A1 expression. Notably, our investigations showed an inverse correlation between hnRNP A1 level, which was increased in HCC, and miR-195-5p level, which was decreased. Our findings demonstrated that hnRNP A1 significantly enhanced the migration and invasion of PLC/PRF/5 cells through its association with mRNAs regulating metastasis. MiR-195-5p also interfered with the hnRNP A1-mediated cell migration by targeting hnRNP A1. Our results underscore the significance of the miR-195-5p/hnRNP A1 axis in regulating the migratory potential of cancer cells and its role in promoting HCC by orchestrating cell migration processes.
Collapse
Affiliation(s)
- Myeongwoo Jung
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Eunbyul Ji
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Hoin Kang
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Chongtae Kim
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Seungyeon Ryu
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Sukyoung Han
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea; Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Seongho Cha
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea; Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea
| | - Eun Kyung Lee
- Department of Biochemistry, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea; Department of Biomedicine & Health Sciences, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea; Institute for Aging and Metabolic Diseases, College of Medicine, The Catholic University of Korea, Seoul, 06591, South Korea.
| |
Collapse
|
30
|
Hoque P, Romero B, Akins RE, Batish M. Exploring the Multifaceted Biologically Relevant Roles of circRNAs: From Regulation, Translation to Biomarkers. Cells 2023; 12:2813. [PMID: 38132133 PMCID: PMC10741722 DOI: 10.3390/cells12242813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
CircRNAs are a category of regulatory RNAs that have garnered significant attention in the field of regulatory RNA research due to their structural stability and tissue-specific expression. Their circular configuration, formed via back-splicing, results in a covalently closed structure that exhibits greater resistance to exonucleases compared to linear RNAs. The distinctive regulation of circRNAs is closely associated with several physiological processes, as well as the advancement of pathophysiological processes in several human diseases. Despite a good understanding of the biogenesis of circular RNA, details of their biological roles are still being explored. With the steady rise in the number of investigations being carried out regarding the involvement of circRNAs in various regulatory pathways, understanding the biological and clinical relevance of circRNA-mediated regulation has become challenging. Given the vast landscape of circRNA research in the development of the heart and vasculature, we evaluated cardiovascular system research as a model to critically review the state-of-the-art understanding of the biologically relevant functions of circRNAs. We conclude the review with a discussion of the limitations of current functional studies and provide potential solutions by which these limitations can be addressed to identify and validate the meaningful and impactful functions of circRNAs in different physiological processes and diseases.
Collapse
Affiliation(s)
- Parsa Hoque
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Robert E Akins
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA;
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
| |
Collapse
|
31
|
Ruffenach G, Medzikovic L, Sun W, Hong J, Eghbali M. Functions of RNA-Binding Proteins in Cardiovascular Disease. Cells 2023; 12:2794. [PMID: 38132114 PMCID: PMC10742114 DOI: 10.3390/cells12242794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Gene expression is under tight regulation from the chromatin structure that regulates gene accessibility by the transcription machinery to protein degradation. At the transcript level, this regulation falls on RNA-binding proteins (RBPs). RBPs are a large and diverse class of proteins involved in all aspects of a transcript's lifecycle: splicing and maturation, localization, stability, and translation. In the past few years, our understanding of the role of RBPs in cardiovascular diseases has expanded. Here, we discuss the general structure and function of RBPs and the latest discoveries of their role in pulmonary and systemic cardiovascular diseases.
Collapse
Affiliation(s)
- Grégoire Ruffenach
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
| | - Lejla Medzikovic
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
| | - Wasila Sun
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
| | - Jason Hong
- Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Mansoureh Eghbali
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
| |
Collapse
|
32
|
Savulescu AF, Doxakis E. Editorial: RNA binding proteins in neuroscience. Front Mol Neurosci 2023; 16:1340721. [PMID: 38115823 PMCID: PMC10728815 DOI: 10.3389/fnmol.2023.1340721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023] Open
Affiliation(s)
- Anca F. Savulescu
- Division of Chemical, Systems and Synthetic Biology, Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| |
Collapse
|
33
|
Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. Assembly of SARS-CoV-2 ribonucleosomes by truncated N ∗ variant of the nucleocapsid protein. J Biol Chem 2023; 299:105362. [PMID: 37863261 PMCID: PMC10665939 DOI: 10.1016/j.jbc.2023.105362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein serine/arginine (SR) region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N∗ or Δ(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we use mass photometry and negative stain electron microscopy to show that purified Δ(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1-209) vRNPs requires the leucine-rich helix of the central disordered region and that this helix promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by phosphorylation.
Collapse
Affiliation(s)
- Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | | | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Alison Ciling
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA; Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
| |
Collapse
|
34
|
Zhai H, Zhong S, Wu R, Mo Z, Zheng S, Xue J, Meng H, Liu M, Chen X, Zhang G, Zheng X, Du F, Li R, Zhou B. Suppressing circIDE/miR-19b-3p/RBMS1 axis exhibits promoting-tumour activity through upregulating GPX4 to diminish ferroptosis in hepatocellular carcinoma. Epigenetics 2023; 18:2192438. [PMID: 36989117 PMCID: PMC10064926 DOI: 10.1080/15592294.2023.2192438] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Ferroptosis is a newly characterized form of iron-dependent non-apoptotic cell death, which is closely associated with cancer progression. However, the functions and mechanisms in regulation of escaping from ferroptosis during hepatocellular carcinoma (HCC) progression remain unknown. In this study, we reported that the RNA binding motif single stranded interacting protein 1 (RBMS1) participated in HCC development,and functioned as a regulator of ferroptosis. Clinically, the downregulation of RBMS1 occurred in HCC tissues, and low RBMS1 expression was associated with worse HCC patients survival. Mechanistically, RBMS1 overexpression inhibited HCC cell growth by attenuating the expression of glutathione peroxidase 4 (GPX4)and further facilitated ferroptosis in vitro and in vivo. More importantly, a novel circIDE (hsa_circ_0000251) was identified to elevate RBMS1 expression via sponging miR-19b-3p in HCC cells. Collectively, our findings established circIDE/miR-19b-3p/RBMS1 axis as a regulator of ferroptosis, which could be a promising therapeutic target and prognostic factor.
Collapse
Affiliation(s)
- Hang Zhai
- Department of Quality and Safety Management, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Sisi Zhong
- Department of Quality and Safety Management, The First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Runxin Wu
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Zhaohong Mo
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shiyang Zheng
- Department of Head and Neck surgery, Cancer Center of Guangzhou Medical University, Guangzhou, China
| | - Jinhua Xue
- Department of Physiology, the School of Basic Medical Sciences of Gannan Medical University, Ganzhou, China
| | - Hongyu Meng
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Maosheng Liu
- Department of Gastroentrology, the First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xianyu Chen
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Guangquan Zhang
- Department of Hepatobiliary and Pancreatic Surgery, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Xiyan Zheng
- Department of Hepatobiliary and Pancreatic Surgery, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Fei Du
- Department of Hepatobiliary and Pancreatic Surgery, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Ruixi Li
- Department of Hepatobiliary and Pancreatic Surgery, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Boxuan Zhou
- Department of Hepatobiliary Surgery, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
35
|
Wang T, Zhang H. Exploring the roles and molecular mechanisms of RNA binding proteins in the sorting of noncoding RNAs into exosomes during tumor progression. J Adv Res 2023:S2090-1232(23)00368-5. [PMID: 38030125 DOI: 10.1016/j.jare.2023.11.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 10/26/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND RNA binding proteins (RBPs) play a role in sorting non-coding RNAs (ncRNAs) into exosomes. These ncRNAs, carried by exosomes, are involved in regulating various aspects of tumor progression, including metastasis, angiogenesis, control of the tumor microenvironment, and drug resistance. Recent studies have emphasized the importance of the RBP-ncRNA-exosome mechanism in tumor regulation. AIM OF REVIEW This comprehensive review aims to explore the RBP-ncRNA-exosome mechanism and its influence on tumor development. By understanding this intricate mechanism provides novel insights into tumor regulation and may lead to innovative treatment strategies in the future. KEY SCIENTIFIC CONCEPTS OF REVIEW The review discusses the formation of exosomes and the complex relationships among RBPs, ncRNAs, and exosomes. The RBP-ncRNA-exosome mechanism is shown to affect various aspects of tumor biology, including metastasis, multidrug resistance, angiogenesis, the immunosuppressive microenvironment, and tumor progression. Tumor development relies on the transmission of information between cells, with RBPs selectively mediating sorting of ncRNAs into exosomes through various mechanisms, which in turn carry ncRNAs to regulate RBPs. The review also provides an overview of potential therapeutic strategies, such as targeted drug discovery and genetic engineering for modifying therapeutic exosomes, which hold great promise for improving cancer treatment.
Collapse
Affiliation(s)
- Ting Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hui Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| |
Collapse
|
36
|
Geng K, Rice-Boucher PJ, Kashentseva EA, Dmitriev IP, Lu ZH, Goedegebuure SP, Gillanders WE, Curiel DT. Engineering a Novel Modular Adenoviral mRNA Delivery Platform Based on Tag/Catcher Bioconjugation. Viruses 2023; 15:2277. [PMID: 38005953 PMCID: PMC10674448 DOI: 10.3390/v15112277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
mRNA vaccines have attracted widespread research attention with clear advantages in terms of molecular flexibility, rapid development, and potential for personalization. However, current mRNA vaccine platforms have not been optimized for induction of CD4/CD8 T cell responses. In addition, the mucosal administration of mRNA based on lipid nanoparticle technology faces challenges in clinical translation. In contrast, adenovirus-based vaccines induce strong T cell responses and have been approved for intranasal delivery. To leverage the inherent strengths of both the mRNA and adenovirus platforms, we developed a novel modular adenoviral mRNA delivery platform based on Tag/Catcher bioconjugation. Specifically, we engineered adenoviral vectors integrating Tag/Catcher proteins at specific locales on the Ad capsid proteins, allowing us to anchor mRNA to the surface of engineered Ad viruses. In proof-of-concept studies, the Ad-mRNA platform successfully mediated mRNA delivery and could be optimized via the highly flexible modular design of both the Ad-mRNA and protein bioconjugation systems.
Collapse
Affiliation(s)
- Kexin Geng
- Department of Radiation Oncology, Biologic Therapeutics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; (K.G.); (P.J.R.-B.); (E.A.K.); (I.P.D.); (Z.H.L.)
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in Saint Louis, St. Louis, MO 63130-4899, USA
| | - Paul J. Rice-Boucher
- Department of Radiation Oncology, Biologic Therapeutics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; (K.G.); (P.J.R.-B.); (E.A.K.); (I.P.D.); (Z.H.L.)
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in Saint Louis, St. Louis, MO 63130-4899, USA
| | - Elena A. Kashentseva
- Department of Radiation Oncology, Biologic Therapeutics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; (K.G.); (P.J.R.-B.); (E.A.K.); (I.P.D.); (Z.H.L.)
| | - Igor P. Dmitriev
- Department of Radiation Oncology, Biologic Therapeutics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; (K.G.); (P.J.R.-B.); (E.A.K.); (I.P.D.); (Z.H.L.)
| | - Zhi Hong Lu
- Department of Radiation Oncology, Biologic Therapeutics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; (K.G.); (P.J.R.-B.); (E.A.K.); (I.P.D.); (Z.H.L.)
| | - S. Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.P.G.); (W.E.G.)
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110, USA
| | - William E. Gillanders
- Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA; (S.P.G.); (W.E.G.)
- Alvin J. Siteman Cancer Center at Barnes-Jewish Hospital and Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David T. Curiel
- Department of Radiation Oncology, Biologic Therapeutics Center, Washington University School of Medicine, St. Louis, MO 63110, USA; (K.G.); (P.J.R.-B.); (E.A.K.); (I.P.D.); (Z.H.L.)
- Department of Biomedical Engineering, McKelvey School of Engineering, Washington University in Saint Louis, St. Louis, MO 63130-4899, USA
| |
Collapse
|
37
|
Brown A, Selkirk ME, Sarkies P. Identification of proteins that bind extracellular microRNAs secreted by the parasitic nematode Trichinella spiralis. Biol Open 2023; 12:bio060096. [PMID: 37906081 PMCID: PMC10660789 DOI: 10.1242/bio.060096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/13/2023] [Indexed: 11/02/2023] Open
Abstract
Small non-coding RNAs such as microRNAs (miRNAs) are conserved across eukaryotes and play key roles in regulating gene expression. In many organisms, miRNAs are also secreted from cells, often encased within vesicles such as exosomes, and sometimes extravesicular. The mechanisms of miRNA secretion, how they are stabilised outside of cells and their functional importance are poorly understood. Recently, we characterised the parasitic nematode Trichinella spiralis as a model to study miRNA secretion. T. spiralis muscle-stage larvae (MSL) secrete abundant miRNAs which are largely extravesicular. Here, we investigated how T. spiralis miRNAs might remain stable outside of cells. Using proteomics, we identified two RNA binding proteins secreted by T. spiralis larvae and characterised their RNA binding properties. One, a homologue of the known RNA binding protein KSRP, binds miRNA in a selective and sequence-specific fashion. Another protein, which is likely a novel RNA binding protein, binds to miRNA without exhibiting sequence specificity. Our results suggest a possible mechanism for miRNA secretion by T. spiralis and may have relevance for understanding the biology of extracellular miRNA more widely.
Collapse
Affiliation(s)
- Alice Brown
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | | | - Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| |
Collapse
|
38
|
Bao T, Liu X, Hu J, Ma M, Li J, Cao L, Yu B, Cheng H, Zhao S, Tian Z. Recruitment of PVT1 Enhances YTHDC1-Mediated m6A Modification of IL-33 in Hyperoxia-Induced Lung Injury During Bronchopulmonary Dysplasia. Inflammation 2023:10.1007/s10753-023-01923-1. [PMID: 37917328 DOI: 10.1007/s10753-023-01923-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/26/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Bronchopulmonary dysplasia (BPD) is a chronic lung disease that specifically affects preterm infants. Oxygen therapy administered to treat BPD can lead to hyperoxia-induced lung injury, characterized by apoptosis of lung alveolar epithelial cells. Our epitranscriptomic microarray analysis of normal mice lungs and hyperoxia-stimulated mice lungs revealed elevated RNA expression levels of IL-33, as well as increased m6A RNA methylation levels of IL-33 and PVT1 in the hyperoxia-stimulated lungs. This study aimed to investigate the role of the PVT1/IL-33 axis in BPD. A mouse model of BPD was established through hyperoxia induction, and lung histological changes were assessed by hematoxylin-eosin staining. Parameters such as radial alveolar count and mean chord length were measured to assess lung function. Mouse and human lung alveolar epithelial cells (MLE12 and A549, respectively) were stimulated with hyperoxia to create an in vitro BPD model. Cell apoptosis was detected using Western blotting and flow cytometry analysis. Our results demonstrated that silencing PVT1 suppressed apoptosis in MLE12 and A549 cells and improved lung function in hyperoxia-stimulated lungs. Additionally, IL-33 reversed the effects of PVT1 both in vivo and in vitro. Through online bioinformatics analysis and RNA-binding protein immunoprecipitation assays, YTHDC1 was identified as a RNA-binding protein (RBP) for both PVT1 and IL-33. We found that PVT1 positively regulated IL-33 expression by recruiting YTHDC1 to mediate m6A modification of IL-33. In conclusion, silencing PVT1 demonstrated beneficial effects in alleviating BPD by facilitating YTHDC1-mediated m6A modification of IL-33. Inhibition of the PVT1/IL-33 axis to suppress apoptosis in lung alveolar epithelial cells may hold promise as a therapeutic approach for managing hyperoxia-induced lung injury in BPD.
Collapse
Affiliation(s)
- Tianping Bao
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Xiangye Liu
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Jian Hu
- Department of Pediatrics, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu, China
| | - Mengmeng Ma
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Jingyan Li
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Linxia Cao
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Bingrui Yu
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Huaiping Cheng
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China
| | - Sai Zhao
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China.
| | - Zhaofang Tian
- Department of Neonatology, The Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, No. 1 Western Huanghe Road, Huai'an, 223300, Jiangsu, China.
| |
Collapse
|
39
|
Singh M, Kumar S. Effect of single nucleotide polymorphisms on the structure of long noncoding RNAs and their interaction with RNA binding proteins. Biosystems 2023; 233:105021. [PMID: 37703988 DOI: 10.1016/j.biosystems.2023.105021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 07/25/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]
Abstract
Long non-coding RNAs (lncRNA) are emerging as a new class of regulatory RNAs with remarkable potential to be utilized as therapeutic targets against many human diseases. Several genome-wide association studies (GWAS) have catalogued Single Nucleotide Polymorphisms (SNPs) present in the noncoding regions of the genome from where lncRNAs originate. In this study, we have selected 67 lncRNAs with GWAS-tagged SNPs and have also investigated their role in affecting the local secondary structures. Majority of the SNPs lead to changes in the secondary structure of lncRNAs to a different extent by altering the base pairing patterns. These structural changes in lncRNA are also manifested in form of alteration in the binding site for RNA binding proteins (RBPs) along with affecting their binding efficacies. Ultimately, these structural modifications may influence the transcriptional and post-transcriptional pathways of these RNAs, leading to the causation of diseases. Hence, it is important to understand the possible underlying mechanism of RBPs in association with GWAS-tagged SNPs in human diseases.
Collapse
Affiliation(s)
- Mandakini Singh
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India
| | - Santosh Kumar
- Department of Life Science, National Institute of Technology, Rourkela, Odisha, 769008, India.
| |
Collapse
|
40
|
Taylor K, Piasecka A, Kajdasz A, Brzęk A, Polay Espinoza M, Bourgeois CF, Jankowski A, Borowiak M, Raczyńska KD, Sznajder ŁJ, Sobczak K. Modulatory role of RNA helicases in MBNL-dependent alternative splicing regulation. Cell Mol Life Sci 2023; 80:335. [PMID: 37882878 PMCID: PMC10602967 DOI: 10.1007/s00018-023-04927-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/14/2023] [Accepted: 08/17/2023] [Indexed: 10/27/2023]
Abstract
Muscleblind-like splicing regulators (MBNLs) activate or repress the inclusion of alternative splicing (AS) events, enabling the developmental transition of fetal mRNA splicing isoforms to their adult forms. Herein, we sought to elaborate the mechanism by which MBNLs mediate AS related to biological processes. We evaluated the functional role of DEAD-box (DDX) RNA helicases, DDX5 and DDX17 in MBNL-dependent AS regulation. Whole-transcriptome analysis and validation approaches revealed a handful of MBNLs-dependent AS events to be affected by DDX5 and DDX17 in mostly an opposite manner. The opposite expression patterns of these two groups of factors during muscle development and coordination of fetal-to-adult splicing transition indicate the importance of these proteins at early stages of development. The identified pathways of how the helicases modulate MBNL splicing activity include DDX5 and DDX17-dependent changes in the ratio of MBNL splicing isoforms and most likely changes in accessibility of MBNL-binding sites. Another pathway involves the mode of action of the helicases independent of MBNL activity. These findings lead to a deeper understanding of the network of interdependencies between RNA-binding proteins and constitute a valuable element in the discussion on developmental homeostasis and pathological states in which the studied protein factors play a significant role.
Collapse
Affiliation(s)
- Katarzyna Taylor
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Agnieszka Piasecka
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Arkadiusz Kajdasz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Aleksandra Brzęk
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Micaela Polay Espinoza
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Cyril F Bourgeois
- Laboratoire de Biologie et Modelisation de la Cellule, Ecole Normale Superieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Universite Claude Bernard Lyon 1, 46 Allee d'Italie, 69364, Lyon, France
| | - Artur Jankowski
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Małgorzata Borowiak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Katarzyna D Raczyńska
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Łukasz J Sznajder
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics and the Genetics Institute, University of Florida, College of Medicine, Gainesville, FL, 32610, USA
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Krzysztof Sobczak
- Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| |
Collapse
|
41
|
Li M, Li D, Lin L, Wang P, Zhao W. Precise Interference of RNA-Protein Interaction by CRISPR-Cas13-Mediated Peptide Competition. ACS Synth Biol 2023; 12:2827-2833. [PMID: 37708031 DOI: 10.1021/acssynbio.3c00287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
RNA-protein interactions are essential nodes of cellular regulatory circuits and play critical roles in normal physiology and disease. However, the precise roles of individual RNA-protein interactions remain elusive. Here we report a method for precise interference of endogenous RNA interacting with the RNA binding protein (RBP). TTP is an RBP that recognizes the AU-rich element (ARE) of mRNA via the binding domain TZF and represses gene expression. We engineer Cas13b, a class 2 type VI CRISPR-Cas endonuclease that exclusively targets RNA, to direct the peptide of TZF to the binding site and compete with endogenous TTP. We show that this tool specifically interferes with TTP interacting with the PIM1 and IL-2 3' UTR under the guidance of the gRNA specific for the AREs. Further, precise interference with the TTP-PIM1 interaction exerts a distinct effect on cell proliferation compared to transcriptome-wide interference. Thus, our work establishes a tool for deep understanding of RNA-RBP interactions.
Collapse
Affiliation(s)
- Meng Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Dan Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Leiruo Lin
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Panpan Wang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Wenxue Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| |
Collapse
|
42
|
Ma N, Xu H, Zhang W, Sun X, Guo R, Liu D, Zhang L, Liu Y, Zhang J, Qiao C, Chen D, Luo A, Bai J. Genome-wide analysis revealed the dysregulation of RNA binding protein-correlated alternative splicing events in myocardial ischemia reperfusion injury. BMC Med Genomics 2023; 16:251. [PMID: 37858115 PMCID: PMC10585833 DOI: 10.1186/s12920-023-01706-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 10/16/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Myocardial ischemia reperfusion injury (MIRI), the tissue damage which is caused by the returning of blood supply to tissue after a period of ischemia, greatly reduces the therapeutic effect of treatment of myocardial infarction. But the underlying functional mechanisms of MIRI are still unclear. METHODS We constructed mouse models of MIRI, extracted injured and healthy myocardial tissues, and performed transcriptome sequencing experiments (RNA-seq) to systematically investigate the dysregulated transcriptome of MIRI, especially the alternative splicing (AS) regulation and RNA binding proteins (RBPs). Selected RBPs and MIRI-associated AS events were then validated by RT-qPCR experiments. RESULTS The differentially expressed gene (DEG) analyses indicated that transcriptome profiles were changed by MIRI and that DEGs' enriched functions were consistent with MIRI's dysregulated pathways. Furthermore, the AS profile was synergistically regulated and showed clear differences between the mouse model and the healthy samples. The exon skipping events significantly increased in MIRI model samples, while the opposite cassette exon events significantly decreased. According to the functional analysis, regulated alternative splicing genes (RASGs) were enriched in protein transport, cell division /cell cycle, RNA splicing, and endocytosis pathways, which were associated with the development of MIRI. Meanwhile, 493 differentially expressed RBPs (DE RBPs) were detected, most of which were correlated with the changed ratios of AS events. In addition, nine DE RBP genes were validated, including Eif5, Pdia6, Tagln2, Vasp, Zfp36l2, Grsf1, Idh2, Ndrg2, and Uqcrc1. These nine DE RBPs were correlated with RASGs enriched in translation process, cell growth and division, and endocytosis pathways, highly consistent with the functions of all RASGs. Finally, we validated the AS ratio changes of five regulated alternative splicing events (RASEs) derived from important regulatory genes, including Mtmr3, Cdc42, Cd47, Fbln2, Vegfa, and Fhl2. CONCLUSION Our study emphasized the critical roles of the dysregulated AS profiles in MIRI development, investigated the potential functions of MIRI-associated RASGs, and identified regulatory RBPs involved in AS regulation. We propose that the identified RASEs and RBPs could serve as important regulators and potential therapeutic targets in MIRI treatment in the future.
Collapse
Affiliation(s)
- Ning Ma
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Hao Xu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Weihua Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Xiaoke Sun
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Ruiming Guo
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Donghai Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Liang Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Yang Liu
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Jian Zhang
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Chenhui Qiao
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China
| | - Dong Chen
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, 430206, Hubei, P.R. China
| | - Ailing Luo
- Wuhan Ruixing Biotechnology Co., Ltd, Wuhan, 430206, Hubei, P.R. China
| | - Jingyun Bai
- Department of Nephrology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, P.R. China.
| |
Collapse
|
43
|
Rynne J, Ortiz-Zapater E, Bagley DC, Zanin O, Doherty G, Kanabar V, Ward J, Jackson DJ, Parsons M, Rosenblatt J, Adcock IM, Martinez-Nunez RT. The RNA binding proteins ZFP36L1 and ZFP36L2 are dysregulated in airway epithelium in human and a murine model of asthma. Front Cell Dev Biol 2023; 11:1241008. [PMID: 37928904 PMCID: PMC10624177 DOI: 10.3389/fcell.2023.1241008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 09/25/2023] [Indexed: 11/07/2023] Open
Abstract
Introduction: Asthma is the most common chronic inflammatory disease of the airways. The airway epithelium is a key driver of the disease, and numerous studies have established genome-wide differences in mRNA expression between health and asthma. However, the underlying molecular mechanisms for such differences remain poorly understood. The human TTP family is comprised of ZFP36, ZFP36L1 and ZFP36L2, and has essential roles in immune regulation by determining the stability and translation of myriad mRNAs encoding for inflammatory mediators. We investigated the expression and possible role of the tristetraprolin (TTP) family of RNA binding proteins (RBPs), poorly understood in asthma. Methods: We analysed the levels of ZFP36, ZFP36L1 and ZFP36L2 mRNA in several publicly available asthma datasets, including single cell RNA-sequencing. We also interrogated the expression of known targets of these RBPs in asthma. We assessed the lung mRNA expression and cellular localization of Zfp36l1 and Zfp36l2 in precision cut lung slices in murine asthma models. Finally, we determined the expression in airway epithelium of ZFP36L1 and ZFP36L2 in human bronchial biopsies and performed rescue experiments in primary bronchial epithelium from patients with severe asthma. Results: We found ZFP36L1 and ZFP36L2 mRNA levels significantly downregulated in the airway epithelium of patients with very severe asthma in different cohorts (5 healthy vs. 8 severe asthma; 36 moderate asthma vs. 37 severe asthma on inhaled steroids vs. 26 severe asthma on oral corticoids). Integrating several datasets allowed us to infer that mRNAs potentially targeted by these RBPs are increased in severe asthma. Zfp36l1 was downregulated in the lung of a mouse model of asthma, and immunostaining of ex vivo lung slices with a dual antibody demonstrated that Zfp36l1/l2 nuclear localization was increased in the airway epithelium of an acute asthma mouse model, which was further enhanced in a chronic model. Immunostaining of human bronchial biopsies showed that airway epithelial cell staining of ZFP36L1 was decreased in severe asthma as compared with mild, while ZFP36L2 was upregulated. Restoring the levels of ZFP36L1 and ZFP36L2 in primary bronchial epithelial cells from patients with severe asthma decreased the mRNA expression of IL6, IL8 and CSF2. Discussion: We propose that the dysregulation of ZFP36L1/L2 levels as well as their subcellular mislocalization contributes to changes in mRNA expression and cytoplasmic fate in asthma.
Collapse
Affiliation(s)
- Jennifer Rynne
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Elena Ortiz-Zapater
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Dustin C. Bagley
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Onofrio Zanin
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - George Doherty
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Varsha Kanabar
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Jon Ward
- Histochemistry Research Unit, University of Southampton, Southampton, United Kingdom
| | - David J. Jackson
- Peter Gorer Department of Immunobiology, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| | - Maddy Parsons
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Jody Rosenblatt
- The Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King’s College London, London, United Kingdom
| | - Ian M. Adcock
- National Heart and Lung Institute and Data Science Institute, Imperial College London, London, United Kingdom
| | - Rocio T. Martinez-Nunez
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King’s College London, London, United Kingdom
| |
Collapse
|
44
|
Turchi L, Sakakini N, Saviane G, Polo B, Saurty-Seerunghen MS, Gabut M, Gouillou CA, Guerlais V, Pasquier C, Vignais ML, Almairac F, Chneiweiss H, Junier MP, Burel-Vandenbos F, Virolle T. CELF2 Sustains a Proliferating/OLIG2+ Glioblastoma Cell Phenotype via the Epigenetic Repression of SOX3. Cancers (Basel) 2023; 15:5038. [PMID: 37894405 PMCID: PMC10605641 DOI: 10.3390/cancers15205038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/23/2023] [Accepted: 08/10/2023] [Indexed: 10/29/2023] Open
Abstract
Glioblastomas (GBs) are incurable brain tumors. The persistence of aggressive stem-like tumor cells after cytotoxic treatments compromises therapeutic efficacy, leading to GBM recurrence. Forcing the GBM cells to irreversibly abandon their aggressive stem-like phenotype may offer an alternative to conventional cytotoxic treatments. Here, we show that the RNA binding protein CELF2 is strongly expressed in mitotic and OLIG2-positive GBM cells, while it is downregulated in differentiated and non-mitotic cells by miR-199a-3p, exemplifying GBM intra-tumor heterogeneity. Using patient-derived cells and human GBM samples, we demonstrate that CELF2 plays a key role in maintaining the proliferative/OLIG2 cell phenotype with clonal and tumorigenic properties. Indeed, we show that CELF2 deficiency in patient-derived GSCs drastically reduced tumor growth in the brains of nude mice. We further show that CELF2 promotes TRIM28 and G9a expression, which drive a H3K9me3 epigenetic profile responsible for the silencing of the SOX3 gene. Thus, CELF2, which is positively correlated with OLIG2 and Ki67 expression in human GBM samples, is inversely correlated with SOX3 and miR-199a-3p. Accordingly, the invalidation of SOX3 in CELF2-deficient patient-derived cells rescued proliferation and OLIG2 expression. Finally, patients expressing SOX3 above the median level of expression tend to have a longer life expectancy. CELF2 is therefore a crucial target for the malignant potential of GBM and warrants attention when developing novel anticancer strategies.
Collapse
Affiliation(s)
- Laurent Turchi
- CNRS, INSERM, Institut de Biologie Valrose, Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity”, Université Côte D’Azur, 06107 Nice, France; (L.T.); (N.S.); (G.S.); (B.P.); (F.A.); (F.B.-V.)
- DRCI, CHU de Nice, 06107 Nice, France
| | - Nathalie Sakakini
- CNRS, INSERM, Institut de Biologie Valrose, Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity”, Université Côte D’Azur, 06107 Nice, France; (L.T.); (N.S.); (G.S.); (B.P.); (F.A.); (F.B.-V.)
| | - Gaelle Saviane
- CNRS, INSERM, Institut de Biologie Valrose, Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity”, Université Côte D’Azur, 06107 Nice, France; (L.T.); (N.S.); (G.S.); (B.P.); (F.A.); (F.B.-V.)
| | - Béatrice Polo
- CNRS, INSERM, Institut de Biologie Valrose, Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity”, Université Côte D’Azur, 06107 Nice, France; (L.T.); (N.S.); (G.S.); (B.P.); (F.A.); (F.B.-V.)
| | - Mirca Saras Saurty-Seerunghen
- CNRS UMR8246, INSERM U1130, Neuroscience Paris Seine-IBPS Laboratory, Team Glial Plasticity and NeuroOncology, Sorbonne Université, 75252 Paris, France; (M.S.S.-S.); (H.C.); (M.-P.J.)
| | - Mathieu Gabut
- Stemness in Gliomas Laboratory, Cancer Initiation and Tumoral Cell Identity (CITI) Department, INSERM 1052, CNRS 5286, Centre Léon Bérard, 69008 Lyon, France;
- Cancer Research Center of Lyon 1, Université Claude Bernard Lyon 1, 69100 Villeurbanne, France
| | | | - Vincent Guerlais
- CNRS, I3S, Université Côte d’Azur, 06560 Valbonne, France; (V.G.); (C.P.)
| | - Claude Pasquier
- CNRS, I3S, Université Côte d’Azur, 06560 Valbonne, France; (V.G.); (C.P.)
| | - Marie Luce Vignais
- CNRS, INSERM, Institut de Génomique Fonctionnelle, IGF, Université de Montpellier, 34090 Montpellier, France;
| | - Fabien Almairac
- CNRS, INSERM, Institut de Biologie Valrose, Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity”, Université Côte D’Azur, 06107 Nice, France; (L.T.); (N.S.); (G.S.); (B.P.); (F.A.); (F.B.-V.)
- Service de Neurochirurgie, Hôpital Pasteur, CHU de Nice, 06107 Nice, France
| | - Hervé Chneiweiss
- CNRS UMR8246, INSERM U1130, Neuroscience Paris Seine-IBPS Laboratory, Team Glial Plasticity and NeuroOncology, Sorbonne Université, 75252 Paris, France; (M.S.S.-S.); (H.C.); (M.-P.J.)
| | - Marie-Pierre Junier
- CNRS UMR8246, INSERM U1130, Neuroscience Paris Seine-IBPS Laboratory, Team Glial Plasticity and NeuroOncology, Sorbonne Université, 75252 Paris, France; (M.S.S.-S.); (H.C.); (M.-P.J.)
| | - Fanny Burel-Vandenbos
- CNRS, INSERM, Institut de Biologie Valrose, Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity”, Université Côte D’Azur, 06107 Nice, France; (L.T.); (N.S.); (G.S.); (B.P.); (F.A.); (F.B.-V.)
- Service d’Anatomopathologie, Hôpital Pasteur, CHU de Nice, 06107 Nice, France
| | - Thierry Virolle
- CNRS, INSERM, Institut de Biologie Valrose, Team INSERM “Cancer Stem Cell Plasticity and Functional Intra-tumor Heterogeneity”, Université Côte D’Azur, 06107 Nice, France; (L.T.); (N.S.); (G.S.); (B.P.); (F.A.); (F.B.-V.)
| |
Collapse
|
45
|
Yang Z, Wang J, Qi Y, Tian X, Mei X, Zhang Z, Wang S. [Bioinformatics analysis of the RNA binding protein DDX39 of Toxoplasma gondii]. Zhongguo Xue Xi Chong Bing Fang Zhi Za Zhi 2023; 35:358-365. [PMID: 37926470 DOI: 10.16250/j.32.1374.2023002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
OBJECTIVE To analyze the RNA binding protein of Toxoplasma gondii (TgDDX39) using bioinformatics technology, and to evaluate the immunogenicity of TgDDX39, so as to provide insights into development of toxoplasmosis vaccines. METHODS The amino acid sequences of TgDDX39 were retrieved from the ToxoDB database, and the physicochemical properties, transmembrane structure domain, signal peptide sites, post-translational modification sites, coils, secondary and tertiary structures, hydrophobicity, and antigenic epitopes of the TgDDX39 protein were predicted using online bioinformatics tools, incluiding ProtParam, TMHMM 2.0, SignalP 5.0, NetPhos 3.1, COILS, SOPMA, Phyre2, ProtScale, ABCpred, SYFPEITHI and DNA-STAR. RESULTS TgDDX39 protein was predicted to be an unstable hydrophilic protein with the molecular formula of C2173H3458N598O661S18, which contained 434 amino acids and had an estimated molecular weight of 49.1 kDa and a theoretical isoelectric point of 5.55. The protein was predicted to have an extremely low possibility of signal peptides, without transmembrane regions, and contain 27 phosphorylation sites. The β turn and random coils accounted for 39.63% of the secondary structure of the TgDDX39 protein, and a coiled helix tended to produce in one site. In addition, the TgDDX39 protein contained multiple B and T cell antigenic epitopes. CONCLUSIONS Bioinformatics analyses predict that TgDDX39 protein has high immunogenicity and contains multiple antigenic epitopes. TgDDX39 protein is a potential candidate antigen for vaccine development.
Collapse
Affiliation(s)
- Z Yang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
- Xinxiang Key Laboratory of Pathogenic Biology, Xinxiang, Henan 453003, China
| | - J Wang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
- Xinxiang Key Laboratory of Pathogenic Biology, Xinxiang, Henan 453003, China
| | - Y Qi
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
| | - X Tian
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
- Xinxiang Key Laboratory of Pathogenic Biology, Xinxiang, Henan 453003, China
| | - X Mei
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
- Xinxiang Key Laboratory of Pathogenic Biology, Xinxiang, Henan 453003, China
| | - Z Zhang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
- Xinxiang Key Laboratory of Pathogenic Biology, Xinxiang, Henan 453003, China
| | - S Wang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, Henan 453003, China
- Xinxiang Key Laboratory of Pathogenic Biology, Xinxiang, Henan 453003, China
| |
Collapse
|
46
|
Sun W, Cui H, Xu T, Yue J, Liang J, You W, Sun W, Yi Q. RNA binding proteins in extracellular vesicles and their potential value for cancer diagnosis and treatment (Review). Int J Oncol 2023; 63:114. [PMID: 37594130 DOI: 10.3892/ijo.2023.5562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
Extracellular vesicles (EVs) are spherical bilayer membrane vesicles released by cells into extracellular spaces and body fluids, including plasma and synovial fluid. EV cargo comprises various biomolecules, such as proteins, DNA, mRNAs, non‑coding RNAs, lipids and metabolites. By delivering these bioactive molecules to recipient cells, EVs mediate intercellular communications and play a critical role in maintaining cellular homeostasis and promoting pathological progression. Of note, cells can selectively sort these bioactive molecules (particularly RNAs) into EVs for secretion, as well as regulate cell‑cell communications. RNA‑binding proteins (RBPs) are a large class of proteins capable of binding to RNA molecules and function in regulating RNA metabolism. There is increasing evidence to indicate that RBPs can be delivered to receipt cells to influence their cell biology and play a significant role in the sorting of coding and non‑coding RNAs in EVs. The present review summarized the current knowledge on EV‑associated RBPs, their functions in tumorigenesis and RBP‑related exosome engineering. It is hoped that the present review may provide novel insight into RBPs and targeted cancer treatment.
Collapse
Affiliation(s)
- Weichao Sun
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518035, P.R. China
| | - Hanwei Cui
- Central Laboratory, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518035, P.R. China
| | - Tianhao Xu
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| | - Jiaji Yue
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518035, P.R. China
| | - Jianhui Liang
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518035, P.R. China
| | - Wei You
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518035, P.R. China
| | - Wei Sun
- Department of Bone Joint and Bone Oncology, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518035, P.R. China
| | - Qian Yi
- Department of Physiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan 646000, P.R. China
| |
Collapse
|
47
|
Kairouani A, Pontier D, Picart C, Mounet F, Martinez Y, Le-Bot L, Fanuel M, Hammann P, Belmudes L, Merret R, Azevedo J, Carpentier MC, Gagliardi D, Couté Y, Sibout R, Bies-Etheve N, Lagrange T. Cell-type-specific control of secondary cell wall formation by Musashi-type translational regulators in Arabidopsis. eLife 2023; 12:RP88207. [PMID: 37773033 PMCID: PMC10541177 DOI: 10.7554/elife.88207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2023] Open
Abstract
Deciphering the mechanism of secondary cell wall/SCW formation in plants is key to understanding their development and the molecular basis of biomass recalcitrance. Although transcriptional regulation is essential for SCW formation, little is known about the implication of post-transcriptional mechanisms in this process. Here we report that two bonafide RNA-binding proteins homologous to the animal translational regulator Musashi, MSIL2 and MSIL4, function redundantly to control SCW formation in Arabidopsis. MSIL2/4 interactomes are similar and enriched in proteins involved in mRNA binding and translational regulation. MSIL2/4 mutations alter SCW formation in the fibers, leading to a reduction in lignin deposition, and an increase of 4-O-glucuronoxylan methylation. In accordance, quantitative proteomics of stems reveal an overaccumulation of glucuronoxylan biosynthetic machinery, including GXM3, in the msil2/4 mutant stem. We showed that MSIL4 immunoprecipitates GXM mRNAs, suggesting a novel aspect of SCW regulation, linking post-transcriptional control to the regulation of SCW biosynthesis genes.
Collapse
Affiliation(s)
- Alicia Kairouani
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Dominique Pontier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Claire Picart
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Fabien Mounet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse III, CNRS, INP, UMR5546Castanet-TolosanFrance
| | - Yves Martinez
- FRAIB-CNRS Plateforme ImagerieCastanet-TolosanFrance
| | - Lucie Le-Bot
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
| | - Mathieu Fanuel
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
- PROBE research infrastructure, BIBS Facility, INRAENantesFrance
| | - Philippe Hammann
- Plateforme Protéomique Strasbourg Esplanade de CNRS, Université de StrasbourgStrasbourgFrance
| | - Lucid Belmudes
- Université Grenoble Alpes, INSERM, UA13 BGE, CNRS, CEA, FR2048GrenobleFrance
| | - Remy Merret
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Jacinthe Azevedo
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Marie-Christine Carpentier
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Dominique Gagliardi
- Institut de Biologie Moléculaire des Plantes, IBMP, CNRS, Université de StrasbourgStrasbourgFrance
| | - Yohann Couté
- Université Grenoble Alpes, INSERM, UA13 BGE, CNRS, CEA, FR2048GrenobleFrance
| | - Richard Sibout
- Biopolymères Interactions Assemblages, UR1268 BIA, INRAENantesFrance
| | - Natacha Bies-Etheve
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| | - Thierry Lagrange
- Laboratoire Génome et Développement des Plantes, Université de Perpignan via Domitia, CNRS, UMR5096PerpignanFrance
| |
Collapse
|
48
|
Yang Y, Hu Z, Kang Y, Gao J, Chen H, Liu H, Wang Y, Liu B. Phage SPO1 Protein Gp49 Is a Novel RNA Binding Protein That Is Involved in Host Iron Metabolism. Int J Mol Sci 2023; 24:14318. [PMID: 37762620 PMCID: PMC10531801 DOI: 10.3390/ijms241814318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/11/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Bacillus subtilis is a model organism for studying Gram-positive bacteria and serves as a cell factory in the industry for enzyme and chemical production. Additionally, it functions as a probiotic in the gastrointestinal tract, modulating the gut microbiota. Its lytic phage SPO1 is also the most studied phage among the genus Okubovrius, including Bacillus phage SPO1 and Camphawk. One of the notable features of SPO1 is the existence of a "host-takeover module", a cluster of 24 genes which occupies most of the terminal redundancy. Some of the gene products from the module have been characterized, revealing their ability to disrupt host metabolism by inhibiting DNA replication, RNA transcription, cell division, and glycolysis. However, many of the gene products which share limited similarity to known proteins remain under researched. In this study, we highlight the involvement of Gp49, a gene product from the module, in host RNA binding and heme metabolism-no observation has been reported in other phages. Gp49 folds into a structure that does not resemble any protein in the database and has a new putative RNA binding motif. The transcriptome study reveals that Gp49 primarily upregulates host heme synthesis which captures cytosolic iron to facilitate phage development.
Collapse
Affiliation(s)
- Yanan Yang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yue Kang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Juanjuan Gao
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Huan Chen
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Hui Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Yanta District, Xi’an 710061, China; (Y.Y.); (Z.H.); (Y.K.); (J.G.); (H.C.); (H.L.)
- Centre for Biobank and Advanced Medical Research of Shaanxi Province, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, China
| |
Collapse
|
49
|
Sharma G, Tran TM, Bansal I, Beg MS, Bhardwaj R, Bassi J, Tan Y, Jaiswal AK, Tso C, Jain A, Singh J, Chattopadhyay P, Singh A, Chopra A, Bakhshi S, Casero D, Rao DS, Palanichamy JK. RNA binding protein IGF2BP1 synergizes with ETV6-RUNX1 to drive oncogenic signaling in B-cell Acute Lymphoblastic Leukemia. J Exp Clin Cancer Res 2023; 42:231. [PMID: 37670323 PMCID: PMC10478443 DOI: 10.1186/s13046-023-02810-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 08/27/2023] [Indexed: 09/07/2023] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common pediatric hematological malignancy, with ETV6::RUNX1 being the most prevalent translocation whose exact pathogenesis remains unclear. IGF2BP1 (Insulin-like Growth Factor 2 Binding Protein 1) is an oncofetal RNA binding protein seen to be specifically overexpressed in ETV6::RUNX1 positive B-ALL. In this study, we have studied the mechanistic role of IGF2BP1 in leukemogenesis and its synergism with the ETV6::RUNX1 fusion protein. METHODS Gene expression was analyzed from patient bone marrow RNA using Real Time RT-qPCR. Knockout cell lines were created using CRISPR-Cas9 based lentiviral vectors. RNA-Seq and RNA Immunoprecipitation sequencing (RIP-Seq) after IGF2BP1 pulldown were performed using the Illumina platform. Mouse experiments were done by retroviral overexpression of donor HSCs followed by lethal irradiation of recipients using a bone marrow transplant model. RESULTS We observed specific overexpression of IGF2BP1 in ETV6::RUNX1 positive patients in an Indian cohort of pediatric ALL (n=167) with a positive correlation with prednisolone resistance. IGF2BP1 expression was essential for tumor cell survival in multiple ETV6::RUNX1 positive B-ALL cell lines. Integrated analysis of transcriptome sequencing after IGF2BP1 knockout and RIP-Seq after IGF2BP1 pulldown in Reh cell line revealed that IGF2BP1 targets encompass multiple pro-oncogenic signalling pathways including TNFα/NFκB and PI3K-Akt pathways. These pathways were also dysregulated in primary ETV6::RUNX1 positive B-ALL patient samples from our center as well as in public B-ALL patient datasets. IGF2BP1 showed binding and stabilization of the ETV6::RUNX1 fusion transcript itself. This positive feedback loop led to constitutive dysregulation of several oncogenic pathways. Enforced co-expression of ETV6::RUNX1 and IGF2BP1 in mouse bone marrow resulted in marrow hypercellularity which was characterized by multi-lineage progenitor expansion and strong Ki67 positivity. This pre-leukemic phenotype confirmed their synergism in-vivo. Clonal expansion of cells overexpressing both ETV6::RUNX1 and IGF2BP1 was clearly observed. These mice also developed splenomegaly indicating extramedullary hematopoiesis. CONCLUSION Our data suggest a combined impact of the ETV6::RUNX1 fusion protein and RNA binding protein, IGF2BP1 in activating multiple oncogenic pathways in B-ALL which makes IGF2BP1 and these pathways as attractive therapeutic targets and biomarkers.
Collapse
Affiliation(s)
- Gunjan Sharma
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Tiffany M Tran
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ishu Bansal
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Mohammad Sabique Beg
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Ruchi Bhardwaj
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jaspal Bassi
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Yuande Tan
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Amit Kumar Jaiswal
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Christine Tso
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Ayushi Jain
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Jay Singh
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Parthaprasad Chattopadhyay
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Archna Singh
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India
| | - Anita Chopra
- Department of Laboratory Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - Sameer Bakhshi
- Department of Medical Oncology, Dr B.R Ambedkar Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, New Delhi, India
| | - David Casero
- F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Dinesh S Rao
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, California, USA
| | - Jayanth Kumar Palanichamy
- Department of Biochemistry, All India Institute of Medical Sciences, Room 4008, Convergence Block, New Delhi, 110029, India.
| |
Collapse
|
50
|
Golubeva VA, Dorn LE, Gilbert CJ, Rabolli CP, Das AS, Wanasinghe VS, Veress R, Terentyev D, Accornero F. Loss of YTHDF2 Alters the Expression of m 6A-Modified Myzap and Causes Adverse Cardiac Remodeling. JACC Basic Transl Sci 2023; 8:1180-1194. [PMID: 37791304 PMCID: PMC10543918 DOI: 10.1016/j.jacbts.2023.03.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 10/05/2023]
Abstract
How post-transcriptional regulation of gene expression, such as through N6-methyladenosine (m6A) messenger RNA methylation, impacts heart function is not well understood. We found that loss of the m6A binding protein YTHDF2 in cardiomyocytes of adult mice drove cardiac dysfunction. By proteomics, we found myocardial zonula adherens protein (MYZAP) within the top up-regulated proteins in knockout cardiomyocytes. We further demonstrated that YTHDF2 binds m6A-modified Myzap messenger RNA and controls its stability. Cardiac overexpression of MYZAP has been associated with cardiomyopathy. Thus, our findings provide an important new mechanism for the YTHDF2-dependent regulation of this target and therein its novel role in the maintenance of cardiac homeostasis.
Collapse
Affiliation(s)
- Volha A. Golubeva
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Lisa E. Dorn
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Christopher J. Gilbert
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Charles P. Rabolli
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Anindhya Sundar Das
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Vishmi S. Wanasinghe
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Roland Veress
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Dmitry Terentyev
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Federica Accornero
- Department of Physiology and Cell Biology, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|