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Jiang Q, Yang X, Deng T, Yan J, Guo F, Mo L, An S, Huang Q. Comprehensive machine learning-based integration develops a novel prognostic model for glioblastoma. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200838. [PMID: 39072291 PMCID: PMC11278295 DOI: 10.1016/j.omton.2024.200838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 04/09/2024] [Accepted: 06/14/2024] [Indexed: 07/30/2024]
Abstract
In this study, we developed a new prognostic model for glioblastoma (GBM) based on an integrated machine learning algorithm. We used univariate Cox regression analysis to identify prognostic genes by combining six GBM cohorts. Based on the prognostic genes, 10 machine learning algorithms were integrated into 117 algorithm combinations, and the artificial intelligence prognostic signature (AIPS) with the greatest average C-index was chosen. The AIPS was compared with 10 previously published models by univariate Cox analysis and the C-index. We compared the differences in prognosis, tumor immune microenvironment (TIME), and immunotherapy sensitivity between the high and low AIPS score groups. The AIPS based on the random survival forest algorithm with the highest average C-index (0.868) was selected. Compared with the previous 10 prognostic models, our AIPS has the highest C-index. The AIPS was closely linked to the clinical features of GBM. We discovered that patients in the low score group had improved prognoses, a more active TIME, and were more sensitive to immunotherapy. Finally, we verified the expression of several key genes by western blotting and immunohistochemistry. We identified an ideal prognostic signature for GBM, which might provide new insights into stratified treatment approaches for GBM patients.
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Affiliation(s)
- Qian Jiang
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Xiawei Yang
- Transplant Medical Center, The Second Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Teng Deng
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Jun Yan
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Fangzhou Guo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Ligen Mo
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Sanqi An
- Biosafety Level-3 Laboratory, Life Sciences Institute & Guangxi Collaborative Innovation Center for Biomedicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Qianrong Huang
- Department of Neurosurgery, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
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2
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Shelton WJ, Zandpazandi S, Nix JS, Gokden M, Bauer M, Ryan KR, Wardell CP, Vaske OM, Rodriguez A. Long-read sequencing for brain tumors. Front Oncol 2024; 14:1395985. [PMID: 38915364 PMCID: PMC11194609 DOI: 10.3389/fonc.2024.1395985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/27/2024] [Indexed: 06/26/2024] Open
Abstract
Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.
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Affiliation(s)
- William J. Shelton
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sara Zandpazandi
- Department of Neurosurgery, Medical University of South Carolina, Charleston, SC, United States
| | - J Stephen Nix
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Murat Gokden
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Katie Rose Ryan
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Christopher P. Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Olena Morozova Vaske
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, CA, United States
| | - Analiz Rodriguez
- Department of Neurosurgery, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, United States
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3
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Wu L, Zhao Z, Shin YJ, Yin Y, Raju A, Vaiyapuri TS, Idzham K, Son M, Lee Y, Sa JK, Chua JYH, Unal B, Zhai Y, Fan W, Huang L, Hu H, Gunaratne J, Nam DH, Jiang T, Tergaonkar V. Tumour microenvironment programming by an RNA-RNA-binding protein complex creates a druggable vulnerability in IDH-wild-type glioblastoma. Nat Cell Biol 2024; 26:1003-1018. [PMID: 38858501 PMCID: PMC11178504 DOI: 10.1038/s41556-024-01428-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 04/25/2024] [Indexed: 06/12/2024]
Abstract
Patients with IDH-wild-type glioblastomas have a poor five-year survival rate along with limited treatment efficacy due to immune cell (glioma-associated microglia and macrophages) infiltration promoting tumour growth and resistance. To enhance therapeutic options, our study investigated the unique RNA-RNA-binding protein complex LOC-DHX15. This complex plays a crucial role in driving immune cell infiltration and tumour growth by establishing a feedback loop between cancer and immune cells, intensifying cancer aggressiveness. Targeting this complex with blood-brain barrier-permeable small molecules improved treatment efficacy, disrupting cell communication and impeding cancer cell survival and stem-like properties. Focusing on RNA-RNA-binding protein interactions emerges as a promising approach not only for glioblastomas without the IDH mutation but also for potential applications beyond cancer, offering new avenues for developing therapies that address intricate cellular relationships in the body.
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Affiliation(s)
- Lele Wu
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Zheng Zhao
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Yong Jae Shin
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Yiyun Yin
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Anandhkumar Raju
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Thamil Selvan Vaiyapuri
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Khaireen Idzham
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Miseol Son
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Yeri Lee
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Jason K Sa
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joelle Yi Heng Chua
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Bilal Unal
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - You Zhai
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Wenhua Fan
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lijie Huang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Huimin Hu
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Jayantha Gunaratne
- Laboratory of Translational Biomedical Proteomics, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore
| | - Do-Hyun Nam
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Republic of Korea
- Department of Neurosurgery, Samsung Medical Center, Seoul, Republic of Korea
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China.
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signalling, Institute of Molecular and Cell Biology (IMCB), Agency for Science Technology and Research (A*STAR), Singapore, Republic of Singapore.
- Department of Pathology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Republic of Singapore.
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, Republic of Singapore.
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4
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Huang F, Jin L, Zhang X, Wang M, Zhou C. Integrated pan-cancer analysis reveals the immunological and prognostic potential of RBFOX2 in human tumors. Front Pharmacol 2024; 15:1302134. [PMID: 38881877 PMCID: PMC11176534 DOI: 10.3389/fphar.2024.1302134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 05/08/2024] [Indexed: 06/18/2024] Open
Abstract
Background The role of RNA-binding fox one homolog 2 (RBFOX2) in the progression of multiple tumors is increasingly supported by evidence. However, the unclearness pertaining to the expression of RBFOX2, its prognostic potential, and its correlation with the tumor microenvironment (TME) in pan-cancer persists. This study aims to comprehensively investigate the immunological prognostic value of RBFOX2. Methods The Cancer Genome Atlas Gene Expression Omnibus Genotype-Tissue Expression (GTEx), TIMER2.0, Kaplan-Meier (K-M) Plotter, University of Alabama at Birmingham Cancer data analysis Portal (UALCAN), cbioportal, and Gene Expression Profiling Interactive Analysis 2 (GEPIA2) were utilized for a systematic analysis of RBFOX2. This analysis included studying its expression, prognostic value, DNA methylation, enrichment analysis, immune infiltration cells, and immune-related genes. Additionally, qRT-PCR, CCK-8, colony formation, transwell assays, and immunohistochemistry were employed to analyze the expression and biological function of RBFOX2 in liver cancer. Results Variations in RBFOX2 expression have been observed across diverse tumors and have been identified as indicators of unfavorable prognosis. It is closely linked to immune infiltration cells, immune checkpoints, chemokines, and chemokine receptors in the TME. Higher levels of RBFOX2 have been significantly associated with low response and poor prognosis in patients with non-small cell lung cancer (NSCLC) and melanoma who receive immunotherapy. Furthermore, the DNA methylation of RBFOX2 varies across different types of cancer and has shown better prognosis in patients with BLCA, BRCA, CESC, COAD, DLBC, HNSC, LAML, LGG, LUAD, PAAD, SKCM and THYM. Interestingly, RBFOX2 expression was found to be lower in hepatocellular carcinoma (HCC) patients' tumor tissues compared to their paired adjacent tissues. In vitro studies have shown that knockdown of RBFOX2 significantly promotes the growth and metastasis of liver cancer cells. Conclusion This study investigates the correlation between DNA methylation, prognostic value, and immune cell infiltration with the expression of RBFOX2 in pan-cancer and indicates its potential role to inhibit metastasis of liver cancer.
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Affiliation(s)
- Fengxian Huang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Long Jin
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Xinyue Zhang
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
| | - Min Wang
- Department of Science and Education, Xi'an Children's Hospital Affiliated of Xi'an Jiaotong University, Xi'an, China
| | - Congya Zhou
- Department of Radiation Oncology, Shaanxi Provincial People's Hospital, Xi'an, China
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5
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Bak M, van Nimwegen E, Kouzel IU, Gur T, Schmidt R, Zavolan M, Gruber AJ. MAPP unravels frequent co-regulation of splicing and polyadenylation by RNA-binding proteins and their dysregulation in cancer. Nat Commun 2024; 15:4110. [PMID: 38750024 PMCID: PMC11096328 DOI: 10.1038/s41467-024-48046-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 04/15/2024] [Indexed: 05/18/2024] Open
Abstract
Maturation of eukaryotic pre-mRNAs via splicing and polyadenylation is modulated across cell types and conditions by a variety of RNA-binding proteins (RBPs). Although there exist over 1,500 RBPs in human cells, their binding motifs and functions still remain to be elucidated, especially in the complex environment of tissues and in the context of diseases. To overcome the lack of methods for the systematic and automated detection of sequence motif-guided pre-mRNA processing regulation from RNA sequencing (RNA-Seq) data we have developed MAPP (Motif Activity on Pre-mRNA Processing). Applying MAPP to RBP knock-down experiments reveals that many RBPs regulate both splicing and polyadenylation of nascent transcripts by acting on similar sequence motifs. MAPP not only infers these sequence motifs, but also unravels the position-dependent impact of the RBPs on pre-mRNA processing. Interestingly, all investigated RBPs that act on both splicing and 3' end processing exhibit a consistently repressive or activating effect on both processes, providing a first glimpse on the underlying mechanism. Applying MAPP to normal and malignant brain tissue samples unveils that the motifs bound by the PTBP1 and RBFOX RBPs coordinately drive the oncogenic splicing program active in glioblastomas demonstrating that MAPP paves the way for characterizing pre-mRNA processing regulators under physiological and pathological conditions.
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Affiliation(s)
- Maciej Bak
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Erik van Nimwegen
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Ian U Kouzel
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany
| | - Tamer Gur
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany
| | - Ralf Schmidt
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Mihaela Zavolan
- Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
- Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Andreas J Gruber
- Department of Biology, University of Konstanz, D-78464, Konstanz, Germany.
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6
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Song X, Tiek D, Miki S, Huang T, Lu M, Goenka A, Iglesia R, Yu X, Wu R, Walker M, Zeng C, Shah H, Weng SHS, Huff A, Zhang W, Koga T, Hubert C, Horbinski CM, Furnari FB, Hu B, Cheng SY. RNA splicing analysis deciphers developmental hierarchies and reveals therapeutic targets in adult glioma. J Clin Invest 2024; 134:e173789. [PMID: 38662454 PMCID: PMC11142752 DOI: 10.1172/jci173789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 04/16/2024] [Indexed: 06/02/2024] Open
Abstract
Widespread alterations in RNA alternative splicing (AS) have been identified in adult gliomas. However, their regulatory mechanism, biological significance, and therapeutic potential remain largely elusive. Here, using a computational approach with both bulk and single-cell RNA-Seq, we uncover a prognostic AS signature linked with neural developmental hierarchies. Using advanced iPSC glioma models driven by glioma driver mutations, we show that this AS signature could be enhanced by EGFRvIII and inhibited by in situ IDH1 mutation. Functional validations of 2 isoform switching events in CERS5 and MPZL1 show regulations of sphingolipid metabolism and SHP2 signaling, respectively. Analysis of upstream RNA binding proteins reveals PTBP1 as a key regulator of the AS signature where targeting of PTBP1 suppresses tumor growth and promotes the expression of a neuron marker TUJ1 in glioma stem-like cells. Overall, our data highlights the role of AS in affecting glioma malignancy and heterogeneity and its potential as a therapeutic vulnerability for treating adult gliomas.
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Affiliation(s)
- Xiao Song
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Deanna Tiek
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shunichiro Miki
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, UCSD, La Jolla, California, USA
| | - Tianzhi Huang
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Minghui Lu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Anshika Goenka
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rebeca Iglesia
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Xiaozhou Yu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Runxin Wu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Maya Walker
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chang Zeng
- Department of Preventive Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hardik Shah
- Metabolomics Platform, Comprehensive Cancer Center, and
| | - Shao Huan Samuel Weng
- Proteomics Platform, Office of Shared Research Facilities, Biological Sciences Division, The University of Chicago, Chicago, Illinois, USA
| | - Allen Huff
- Proteomics Platform, Office of Shared Research Facilities, Biological Sciences Division, The University of Chicago, Chicago, Illinois, USA
| | - Wei Zhang
- Department of Preventive Medicine, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Tomoyuki Koga
- Department of Neurosurgery, The University of Minnesota, Minneapolis, Minnesota, USA
| | - Christopher Hubert
- Department of Biochemistry, School of Medicine, Case Western Reserved University, Cleveland, Ohio, USA
| | - Craig M. Horbinski
- Departments of Pathology and Neurological Surgery, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Frank B. Furnari
- Department of Medicine, Division of Regenerative Medicine, Sanford Stem Cell Institute, UCSD, La Jolla, California, USA
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, The Lou and Jean Malnati Brain Tumor Institute, The Robert H. Lurie Comprehensive Cancer Center, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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7
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Dion W, Tao Y, Chambers M, Zhao S, Arbuckle RK, Sun M, Kubra S, Nie Y, Ye M, Larsen MB, Camarco D, Ickes E, DuPont C, Wang H, Wang B, Liu S, Pi S, Chen BB, Chen Y, Chen X, Zhu B. Nuclear speckle rejuvenation alleviates proteinopathies at the expense of YAP1. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590103. [PMID: 38659924 PMCID: PMC11042303 DOI: 10.1101/2024.04.18.590103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Current treatments targeting individual protein quality control have limited efficacy in alleviating proteinopathies, highlighting the prerequisite for a common upstream druggable target capable of global proteostasis modulation. Building on our prior research establishing nuclear speckles as pivotal organelles responsible for global proteostasis transcriptional control, we aim to alleviate proteinopathies through nuclear speckle rejuvenation. We identified pyrvinium pamoate as a small-molecule nuclear speckle rejuvenator that enhances protein quality control while suppressing YAP1 signaling via decreasing the surface tension of nuclear speckle condensates through interaction with the intrinsically disordered region of nuclear speckle scaffold protein SON. In pre-clinical models, pyrvinium pamoate reduced tauopathy and alleviated retina degeneration by promoting autophagy and ubiquitin-proteasome system. Aberrant nuclear speckle morphology, reduced protein quality control and increased YAP1 activity were also observed in human tauopathies. Our study uncovers novel therapeutic targets for tackling protein misfolding disorders within an expanded proteostasis framework encompassing nuclear speckles and YAP1.
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Affiliation(s)
- William Dion
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuren Tao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Maci Chambers
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shanshan Zhao
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Riley K. Arbuckle
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Human Genetics, University of Pittsburgh Graduate School of Public Health, Pittsburgh, PA, USA
| | - Michelle Sun
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Syeda Kubra
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuhang Nie
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Megan Ye
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Mads B. Larsen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Daniel Camarco
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Eleanor Ickes
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Claire DuPont
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Haokun Wang
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Bingjie Wang
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Silvia Liu
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Shaohua Pi
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Bill B Chen
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
| | - Yuanyuan Chen
- Department of Ophthalmology, University of Pittsburgh School of Medicine, PA, U.S.A
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, PA, U.S.A
| | - Xu Chen
- Department of Neuroscience, School of Medicine, University of California, San Diego, CA, U.S.A
| | - Bokai Zhu
- Aging Institute of UPMC, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA, U.S.A
- Division of Endocrinology and Metabolism, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, U.S.A
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8
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Zhou AX, Jeansson M, He L, Wigge L, Tonelius P, Tati R, Cederblad L, Muhl L, Uhrbom M, Liu J, Björnson Granqvist A, Lerman LO, Betsholtz C, Hansen PBL. Renal Endothelial Single-Cell Transcriptomics Reveals Spatiotemporal Regulation and Divergent Roles of Differential Gene Transcription and Alternative Splicing in Murine Diabetic Nephropathy. Int J Mol Sci 2024; 25:4320. [PMID: 38673910 PMCID: PMC11050020 DOI: 10.3390/ijms25084320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Endothelial cell (EC) injury is a crucial contributor to the progression of diabetic kidney disease (DKD), but the specific EC populations and mechanisms involved remain elusive. Kidney ECs (n = 5464) were collected at three timepoints from diabetic BTBRob/ob mice and non-diabetic littermates. Their heterogeneity, transcriptional changes, and alternative splicing during DKD progression were mapped using SmartSeq2 single-cell RNA sequencing (scRNAseq) and elucidated through pathway, network, and gene ontology enrichment analyses. We identified 13 distinct transcriptional EC phenotypes corresponding to different kidney vessel subtypes, confirmed through in situ hybridization and immunofluorescence. EC subtypes along nephrons displayed extensive zonation related to their functions. Differential gene expression analyses in peritubular and glomerular ECs in DKD underlined the regulation of DKD-relevant pathways including EIF2 signaling, oxidative phosphorylation, and IGF1 signaling. Importantly, this revealed the differential alteration of these pathways between the two EC subtypes and changes during disease progression. Furthermore, glomerular and peritubular ECs also displayed aberrant and dynamic alterations in alternative splicing (AS), which is strongly associated with DNA repair. Strikingly, genes displaying differential transcription or alternative splicing participate in divergent biological processes. Our study reveals the spatiotemporal regulation of gene transcription and AS linked to DKD progression, providing insight into pathomechanisms and clues to novel therapeutic targets for DKD treatment.
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Affiliation(s)
- Alex-Xianghua Zhou
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Marie Jeansson
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
- Department of Immunology, Genetics and Pathology, Uppsala University, 753 10 Uppsala, Sweden
| | - Liqun He
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
- Department of Immunology, Genetics and Pathology, Uppsala University, 753 10 Uppsala, Sweden
| | - Leif Wigge
- Data Sciences and Quantitative Biology, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden
| | - Pernilla Tonelius
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Ramesh Tati
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Linda Cederblad
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Lars Muhl
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
| | - Martin Uhrbom
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
| | - Jianping Liu
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
| | - Anna Björnson Granqvist
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
| | - Lilach O. Lerman
- Division of Nephrology and Hypertension, Mayo Clinic, Rochester, MN 55902, USA;
| | - Christer Betsholtz
- Department of Medicine Huddinge, Karolinska Institutet, 141 52 Huddinge, Sweden; (M.J.); (J.L.)
- Department of Immunology, Genetics and Pathology, Uppsala University, 753 10 Uppsala, Sweden
| | - Pernille B. L. Hansen
- Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, 43162 Mölndal, Sweden; (A.-X.Z.); (P.T.); (M.U.)
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9
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Wu R, Sun C, Chen X, Yang R, Luan Y, Zhao X, Yu P, Luo R, Hou Y, Tian R, Bian S, Li Y, Dong Y, Liu Q, Dai W, Fan Z, Yan R, Pan B, Feng S, Wu J, Chen F, Yang C, Wang H, Dai H, Shu M. NSUN5/TET2-directed chromatin-associated RNA modification of 5-methylcytosine to 5-hydroxymethylcytosine governs glioma immune evasion. Proc Natl Acad Sci U S A 2024; 121:e2321611121. [PMID: 38547058 PMCID: PMC10998593 DOI: 10.1073/pnas.2321611121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Malignant glioma exhibits immune evasion characterized by highly expressing the immune checkpoint CD47. RNA 5-methylcytosine(m5C) modification plays a pivotal role in tumor pathogenesis. However, the mechanism underlying m5C-modified RNA metabolism remains unclear, as does the contribution of m5C-modified RNA to the glioma immune microenvironment. In this study, we demonstrate that the canonical 28SrRNA methyltransferase NSUN5 down-regulates β-catenin by promoting the degradation of its mRNA, leading to enhanced phagocytosis of tumor-associated macrophages (TAMs). Specifically, the NSUN5-induced suppression of β-catenin relies on its methyltransferase activity mediated by cysteine 359 (C359) and is not influenced by its localization in the nucleolus. Intriguingly, NSUN5 directly interacts with and deposits m5C on CTNNB1 caRNA (chromatin-associated RNA). NSUN5-induced recruitment of TET2 to chromatin is independent of its methyltransferase activity. The m5C modification on caRNA is subsequently oxidized into 5-hydroxymethylcytosine (5hmC) by TET2, which is dependent on its binding affinity for Fe2+ and α-KG. Furthermore, NSUN5 enhances the chromatin recruitment of RBFOX2 which acts as a 5hmC-specific reader to recognize and facilitate the degradation of 5hmC caRNA. Notably, hmeRIP-seq analysis reveals numerous mRNA substrates of NSUN5 that potentially undergo this mode of metabolism. In addition, NSUN5 is epigenetically suppressed by DNA methylation and is negatively correlated with IDH1-R132H mutation in glioma patients. Importantly, pharmacological blockage of DNA methylation or IDH1-R132H mutant and CD47/SIRPα signaling synergistically enhances TAM-based phagocytosis and glioma elimination in vivo. Our findings unveil a general mechanism by which NSUN5/TET2/RBFOX2 signaling regulates RNA metabolism and highlight NSUN5 targeting as a potential strategy for glioma immune therapy.
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Affiliation(s)
- Ruixin Wu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Chunming Sun
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurology, Huashan hospital, Fudan University, Shanghai200040, China
| | - Xi Chen
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Runyue Yang
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Endocrinology and Metabolism, Zhongshan Hospital, Fudan University, Shanghai200032, China
| | - Yuxuan Luan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Xiang Zhao
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Panpan Yu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Rongkui Luo
- Department of Pathology, Zhongshan hospital, Fudan University, Shanghai200032, China
| | - Yingyong Hou
- Department of Pathology, Zhongshan hospital, Fudan University, Shanghai200032, China
| | - Ruotong Tian
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Shasha Bian
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Yuli Li
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Yinghua Dong
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Logistics, Dalian No.3 People’s hospital Affiliated to Dalian Medical University, Dalian116033, China
| | - Qian Liu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Weiwei Dai
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Zhuoyang Fan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Rucheng Yan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Binyang Pan
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Siheng Feng
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Jing Wu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Fangzhen Chen
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Changle Yang
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai200040, China
| | - Hanlin Wang
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Haochen Dai
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
| | - Minfeng Shu
- Department of Pharmacology, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
- Department of Microbiology, Key Laboratory of Medical Molecular Virology (Ministry of Education/ National Health Commission/ Chinese Academy of Medical Sciences), Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai200032, China
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10
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Altina NH, Maranon DG, Anderson JR, Donaldson MK, Elmegerhi S, St Clair LA, Perera R, Geiss BJ, Wilusz J. The leader RNA of SARS-CoV-2 sequesters polypyrimidine tract binding protein (PTBP1) and influences pre-mRNA splicing in infected cells. Virology 2024; 592:109986. [PMID: 38290414 PMCID: PMC10923090 DOI: 10.1016/j.virol.2024.109986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/02/2023] [Accepted: 01/04/2024] [Indexed: 02/01/2024]
Abstract
The large amount of viral RNA produced during infections has the potential to interact with and effectively sequester cellular RNA binding proteins, thereby influencing aspects of post-transcriptional gene regulation in the infected cell. Here we demonstrate that the abundant 5' leader RNA region of SARS-CoV-2 viral RNAs can interact with the cellular polypyrimidine tract binding protein (PTBP1). Interestingly, the effect of a knockdown of PTBP1 protein on cellular gene expression is also mimicked during SARS-CoV-2 infection, suggesting that this protein may be functionally sequestered by viral RNAs. Consistent with this model, the alternative splicing of mRNAs that is normally controlled by PTBP1 is dysregulated during SARS-CoV-2 infection. Collectively, these data suggest that the SARS-CoV-2 leader RNA sequesters the cellular PTBP1 protein during infection, resulting in significant impacts on the RNA biology of the host cell. These alterations in post-transcriptional gene regulation may play a role in SARS-CoV-2 mediated molecular pathogenesis.
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Affiliation(s)
- Noelia H Altina
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - David G Maranon
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Meghan K Donaldson
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Suad Elmegerhi
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Laura A St Clair
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Rushika Perera
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Brian J Geiss
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, CO, 80523, USA.
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11
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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12
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Huang W, Li J, Zhu H, Qin X, Chen C, Wang B, Wei J, Song Y, Lu X, Li Z, Xia W, He A, Cheng L, Yu X, Shu K, Wang W. A novel EGFR variant EGFRx maintains glioblastoma stem cells through STAT5. Neuro Oncol 2024; 26:85-99. [PMID: 37616578 PMCID: PMC10768976 DOI: 10.1093/neuonc/noad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Glioblastomas are universally lethal brain tumors containing tumor-propagating glioblastoma stem cells (GSCs). EGFR gene amplification or mutation is frequently detected in GBMs and is associated with poor prognosis. However, EGFR variants in GSCs and their role in the maintenance of GSCs and progression of GBM are unclear. METHODS EGFR variants were detected through bioinformatic HISAT-StringTie-Ballgown pipeline and verified through 5' RACE, RT-PCR, ribonuclease protection, and northern blotting assays. EGFRx function was investigated through neurosphere, cell viability, intracranial xenograft and RNA-seq assays. EGFRx-STAT5 signaling was investigated through western blotting, coimmunoprecipitation, immunofluorescence, luciferase reporter, RT-PCR and CUT&Tag assays. RESULTS We identified a novel EGFR variant (EGFRx), that is specifically expressed in GSCs. Unlike the EGFRvIII variant, which lacks exons 2-7, EGFRx is characterized by the absence of exons 2-14, and encodes an EGFR protein that does not possess the entire extracellular ligand-binding domain. We observed that EGFRx exhibits significant glycosylation, is required for GSC self-renewal, proliferation, and tumorigenesis, and highly active in glioblastomas compared to normal brain tissue. Mechanistically, EGFRx constitutively and specifically activates STAT5 in GSCs through spontaneous asymmetric dimerization of the kinase domain. CONCLUSIONS EGFRx plays essential roles in the maintenance of the GSC phenotype through constitutive activation of STAT5 and promotes GBM progression, suggesting that EGFRx-STAT5 signaling represents a promising therapeutic target for GBM.
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Affiliation(s)
- Wei Huang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongtao Zhu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xuhui Qin
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Chen
- Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bing Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jinxia Wei
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanyang Song
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xia Lu
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhongyu Li
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenqing Xia
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aodi He
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Lidong Cheng
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xingjiang Yu
- Department of Histology and Embryology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Kai Shu
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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13
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Yu Q, Wu T, Xu W, Wei J, Zhao A, Wang M, Li M, Chi G. PTBP1 as a potential regulator of disease. Mol Cell Biochem 2023:10.1007/s11010-023-04905-x. [PMID: 38129625 DOI: 10.1007/s11010-023-04905-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family, which plays a key role in alternative splicing of precursor mRNA and RNA metabolism. PTBP1 is universally expressed in various tissues and binds to multiple downstream transcripts to interfere with physiological and pathological processes such as the tumor growth, body metabolism, cardiovascular homeostasis, and central nervous system damage, showing great prospects in many fields. The function of PTBP1 involves the regulation and interaction of various upstream molecules, including circular RNAs (circRNAs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). These regulatory systems are inseparable from the development and treatment of diseases. Here, we review the latest knowledge regarding the structure and molecular functions of PTBP1 and summarize its functions and mechanisms of PTBP1 in various diseases, including controversial studies. Furthermore, we recommend future studies on PTBP1 and discuss the prospects of targeting PTBP1 in new clinical therapeutic approaches.
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Affiliation(s)
- Qi Yu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Tongtong Wu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Wenhong Xu
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Junyuan Wei
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Anqi Zhao
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Miaomiao Wang
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China
| | - Meiying Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
| | - Guangfan Chi
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, 130021, Jilin, People's Republic of China.
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14
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Nale V, Chiodi A, Di Nanni N, Cifola I, Moscatelli M, Cocola C, Gnocchi M, Piscitelli E, Sula A, Zucchi I, Reinbold R, Milanesi L, Mezzelani A, Pelucchi P, Mosca E. scMuffin: an R package to disentangle solid tumor heterogeneity by single-cell gene expression analysis. BMC Bioinformatics 2023; 24:445. [PMID: 38012590 PMCID: PMC10680269 DOI: 10.1186/s12859-023-05563-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 11/08/2023] [Indexed: 11/29/2023] Open
Abstract
INTRODUCTION Single-cell (SC) gene expression analysis is crucial to dissect the complex cellular heterogeneity of solid tumors, which is one of the main obstacles for the development of effective cancer treatments. Such tumors typically contain a mixture of cells with aberrant genomic and transcriptomic profiles affecting specific sub-populations that might have a pivotal role in cancer progression, whose identification eludes bulk RNA-sequencing approaches. We present scMuffin, an R package that enables the characterization of cell identity in solid tumors on the basis of a various and complementary analyses on SC gene expression data. RESULTS scMuffin provides a series of functions to calculate qualitative and quantitative scores, such as: expression of marker sets for normal and tumor conditions, pathway activity, cell state trajectories, Copy Number Variations, transcriptional complexity and proliferation state. Thus, scMuffin facilitates the combination of various evidences that can be used to distinguish normal and tumoral cells, define cell identities, cluster cells in different ways, link genomic aberrations to phenotypes and identify subtle differences between cell subtypes or cell states. We analysed public SC expression datasets of human high-grade gliomas as a proof-of-concept to show the value of scMuffin and illustrate its user interface. Nevertheless, these analyses lead to interesting findings, which suggest that some chromosomal amplifications might underlie the invasive tumor phenotype and the presence of cells that possess tumor initiating cells characteristics. CONCLUSIONS The analyses offered by scMuffin and the results achieved in the case study show that our tool helps addressing the main challenges in the bioinformatics analysis of SC expression data from solid tumors.
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Affiliation(s)
- Valentina Nale
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alice Chiodi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Noemi Di Nanni
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ingrid Cifola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Marco Moscatelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Cinzia Cocola
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Matteo Gnocchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Eleonora Piscitelli
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ada Sula
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Ileana Zucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Rolland Reinbold
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Luciano Milanesi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Alessandra Mezzelani
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy
| | - Paride Pelucchi
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
| | - Ettore Mosca
- Institute of Biomedical Technologies, National Research Council, Via Fratelli Cervi 93, 20054, Segrate, Milan, Italy.
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15
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Li S, Qi Y, Yu J, Hao Y, Xu L, Ding X, Zhang M, Geng J. Aurora kinase A regulates cancer-associated RNA aberrant splicing in breast cancer. Heliyon 2023; 9:e17386. [PMID: 37415951 PMCID: PMC10320321 DOI: 10.1016/j.heliyon.2023.e17386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
The contribution of oncogenes to tumor-associated RNA splicing and the relevant molecular mechanisms therein require further elaboration. Here, we show that oncogenic Aurora kinase A (AURKA) promotes breast cancer-related RNA aberrant splicing in a context-dependent manner. AURKA regulated pan-breast cancer-associated RNA splicing events including GOLGA4, RBM4 and UBQLN1. Aberrant splicing of GOLGA4 and RBM4 was closely related to breast cancer development. Mechanistically, AURKA interacted with the splicing factor YBX1 and promoted AURKA-YBX1 complex-mediated GOLGA4 exon inclusion. AURKA binding to the splicing factor hnRNPK promoted AURKA-hnRNPK complex-mediated RBM4 exon skipping. Analysis of clinical data identified an association between the AURKA-YBX1/hnRNPK complex and poor prognosis in breast cancer. Blocking AURKA nuclear translocation with small molecule drugs partially reversed the oncogenic splicing of RBM4 and GOLGA4 in breast cancer cells. In summary, oncogenic AURKA executes its function on modulating breast cancer-related RNA splicing, and nuclear AURKA is distinguished as a hopeful target in the case of treating breast cancer.
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Affiliation(s)
- Sisi Li
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Jiachuan Yu
- Department of Anesthesiology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yuchao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Lingzhi Xu
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xudong Ding
- Department of Pathology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
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16
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Jeong JH, Park SH, Kim H, Nam HY, Kim SH, Jeong M, Kong MJ, Son J, Jeong JE, Song JH, Kim SW, Choi KC. ZBTB7A suppresses glioblastoma tumorigenesis through the transcriptional repression of EPB41L5. Exp Mol Med 2023; 55:43-54. [PMID: 36596853 PMCID: PMC9898510 DOI: 10.1038/s12276-022-00908-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/26/2022] [Accepted: 11/02/2022] [Indexed: 01/05/2023] Open
Abstract
Glioblastoma multiforme (GBM), the most aggressive and malignant glioma, has a poor prognosis. Although patients with GBM are treated with surgery, chemotherapy, and radiation therapy, GBM is highly resistant to treatment, making it difficult and expensive to treat. In this study, we analyzed the Gene Expression Profiling Interactive Analysis dataset, the Cancer Genome Atlas dataset, and Gene Expression Omnibus array data. ZBTB7A (also called FBI1/POKEMON/LRF) was found to be highly expressed in low-grade glioma but significantly downregulated in patients with GBM. ZBTB7A is a transcription factor that plays an important role in many developmental stages, including cell proliferation. The activation of epithelial-mesenchymal transition (EMT) is a key process in cancer progression and metastasis. Erythrocyte membrane protein band 4.1 like 5 (EPB41L5) is an essential protein for EMT progression and metastasis in various types of cancer. We found that ZBTB7A depletion in U87 cells induced GBM progression and metastasis. Based on RNA sequencing data, ZBTB7A directly binds to the promoter of the EPB41L5 gene, reducing its expression and inhibiting GBM progression. We demonstrated that ZBTB7A dramatically inhibits GBM tumor growth through transcriptional repression of EPB41L5. Thus, both ZBTB7A and EPB41L5 may be potential biomarkers and novel therapeutic targets for GBM treatment. Overall, we discovered the role of a novel tumor suppressor that directly inhibits GBM progression (ZBTB7A) and identified EPB41L5 as a therapeutic target protein for patients with GBM.
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Affiliation(s)
- Ji-Hoon Jeong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Seung-Ho Park
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hyunhee Kim
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Hae Yun Nam
- grid.413967.e0000 0001 0842 2126Department of Biochemistry and Molecular Biology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Sung-Hak Kim
- grid.14005.300000 0001 0356 9399Department of Animal Science, Chonnam National University, Gwangju, Korea
| | - Minseok Jeong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Min-Jeong Kong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Jihyun Son
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ji-Eun Jeong
- grid.413967.e0000 0001 0842 2126Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea
| | - Ji-Hye Song
- grid.418974.70000 0001 0573 0246Korea Food Research Institute, Wanju-gun, 55365 Korea
| | - Seong Who Kim
- Department of Biochemistry and Molecular Biology, AMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
| | - Kyung-Chul Choi
- Department of Biomedical Sciences, AAMIST, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Korea.
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17
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Drongitis D, Verrillo L, De Marinis P, Orabona P, Caiola A, Turitto G, Alfieri A, Bruscella S, Gentile M, Moriello V, Sannino E, Di Muccio I, Costa V, Miano MG, de Bellis A. The Chromatin-Oxygen Sensor Gene KDM5C Associates with Novel Hypoxia-Related Signatures in Glioblastoma Multiforme. Int J Mol Sci 2022; 23:ijms231810250. [PMID: 36142158 PMCID: PMC9498997 DOI: 10.3390/ijms231810250] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/26/2022] [Accepted: 08/31/2022] [Indexed: 11/22/2022] Open
Abstract
Glioblastoma multiforme (GBM) is a fatal brain tumor without effective drug treatment. In this study, we highlight, for the first time, the contribution of chromatin remodeling gene Lysine (K)-specific demethylase 5C (KDM5C) in GBM via an extensive analysis of clinical, expression, and functional data, integrated with publicly available omic datasets. The expression analysis on GBM samples (N = 37) revealed two informative subtypes, namely KDM5CHigh and KDM5CLow, displaying higher/lower KDM5C levels compared to the controls. The former subtype displays a strong downregulation of brain-derived neurotrophic factor (BDNF)—a negative KDM5C target—and a robust overexpression of hypoxia-inducible transcription factor-1A (HIF1A) gene, a KDM5C modulator. Additionally, a significant co-expression among the prognostic markers HIF1A, Survivin, and p75 was observed. These results, corroborated by KDM5C overexpression and hypoxia-related functional assays in T98G cells, suggest a role for the HIF1A-KDM5C axis in the hypoxic response in this tumor. Interestingly, fluorescence-guided surgery on GBM sections further revealed higher KDM5C and HIF1A levels in the tumor rim niche compared to the adjacent tumor margin, indicating a regionally restricted hyperactivity of this regulatory axis. Analyzing the TCGA expression and methylation data, we found methylation changes between the subtypes in the genes, accounting for the hypoxia response, stem cell differentiation, and inflammation. High NANOG and IL6 levels highlight a distinctive stem cell-like and proinflammatory signature in the KDM5CHigh subgroup and GBM niches. Taken together, our results indicate HIF1A-KDM5C as a new, relevant cancer axis in GBM, opening a new, interesting field of investigation based on KDM5C as a potential therapeutic target of the hypoxic microenvironment in GBM.
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Affiliation(s)
- Denise Drongitis
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
- Maria Rosaria Maglione Foundation Onlus, 80122 Naples, Italy
| | - Lucia Verrillo
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
| | - Pasqualino De Marinis
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Pasquale Orabona
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Pathology, 81100 Caserta, Italy
| | - Agnese Caiola
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Pathology, 81100 Caserta, Italy
| | - Giacinto Turitto
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Oncology, 81100 Caserta, Italy
| | - Alessandra Alfieri
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Sara Bruscella
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Marisa Gentile
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Vania Moriello
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Ettore Sannino
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Ines Di Muccio
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
| | - Valerio Costa
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
| | - Maria Giuseppina Miano
- Institute of Genetics and Biophysics Adriano Buzzati-Traverso, CNR, 80131 Naples, Italy
- Correspondence: (M.G.M.); (A.d.B.)
| | - Alberto de Bellis
- Maria Rosaria Maglione Foundation Onlus, 80122 Naples, Italy
- A.O.R.N. S. Anna and S. Sebastiano Hospital, Division of Neurosurgery, 81100 Caserta, Italy
- Correspondence: (M.G.M.); (A.d.B.)
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18
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Chen C, Shang A, Gao Y, Huang J, Liu G, Cho WC, Li D. PTBPs: An immunomodulatory-related prognostic biomarker in pan-cancer. Front Mol Biosci 2022; 9:968458. [PMID: 36203873 PMCID: PMC9531344 DOI: 10.3389/fmolb.2022.968458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/02/2022] [Indexed: 11/20/2022] Open
Abstract
Background: The polypyrimidine tract-binding protein (PTBP) nuclear ribonucleoprotein family of proteins, including PTBP1, PTBP2 and PTBP3, regulate the process of cell proliferation, differentiation, apoptosis and carcinogenesis. PTBPs exhibit oncogenic effects in certain tumors. However, the role of PTBPs in pan-cancer remains unclear. Our study examined the clinical significance and mechanism of PTBPs in pan-cancer. Methods: We compared the expression of PTBPs in paired and unpaired tissue samples from the Cancer Genome Atlas (TCGA) database. Univariate and multivariate Cox regression, Kaplan–Meier curves, and time-dependent receiver operating characteristic (ROC) curves were used to assess the prognostic significance of PTBPs in pan-cancer. The cBioPortal database also identified genomic abnormalities in PTBPs. TISIDB, TCGA, and Cellminer were used to investigate the relationship between PTBP expression and immune subtypes, immune checkpoint (ICP) genes, tumor mutational burden (TMB), microsatellite instability (MSI), tumor-infiltrating immune cells, and chemosensitivity. cBioPortal was used to search for PTBP co-expressing genes in pan-cancer, and GO and KEGG enrichment analyses were performed to search for PTBP-related signaling pathways. Results:PTBPs were shown to be widely upregulated in human tumor tissues. PTBP1 showed good prognostic value in ACC, KIRP, and LGG; PTBP2 in ACC and KICH; and PTBP3 in ACC, LGG, and PAAD, with AUC >0.7. PTBPs were differentially expressed in tumor immune subtypes and had a strong correlation with tumor-infiltrating lymphocytes (TILs) in the tumor microenvironment (TME). In addition, PTBP expressions were related to ICP, TMB, and MSI, suggesting that these three PTBPs may be potential tumor immunotherapeutic targets and predict the efficacy of immunotherapy. Enrichment analysis of co-expressed genes of PTBPs showed that they may be involved in alternative splicing, cell cycle, cellular senescence, and protein modification. Conclusion: PTBPs are involved in the malignant progression of tumors. PTBP1, PTBP2 and PTBP3 may be potential biomarkers for prognosis and immunotherapy in pan-cancer and may be novel immunotherapeutic targets.
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Affiliation(s)
- Chen Chen
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Anquan Shang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yuting Gao
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Jingjuan Huang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Gege Liu
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong, Hong Kong SAR, China
- *Correspondence: William C. Cho, ; Dong Li,
| | - Dong Li
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: William C. Cho, ; Dong Li,
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19
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Kuo YH, Hung HS, Tsai CW, Chiu SC, Liu SP, Chiang YT, Shyu WC, Lin SZ, Fu RH. A Novel Splice Variant of BCAS1 Inhibits β-Arrestin 2 to Promote the Proliferation and Migration of Glioblastoma Cells, and This Effect Was Blocked by Maackiain. Cancers (Basel) 2022; 14:cancers14163890. [PMID: 36010884 PMCID: PMC9405932 DOI: 10.3390/cancers14163890] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 11/16/2022] Open
Abstract
Brain-enriched myelin-associated protein 1 (BCAS1) is frequently highly expressed in human cancer, but its detailed function is unclear. Here, we identified a novel splice variant of the BCAS1 gene in glioblastoma multiforme (GBM) named BCAS1-SV1. The expression of BCAS1-SV1 was weak in heathy brain cells but high in GBM cell lines. The overexpression of BCAS1-SV1 significantly increased the proliferation and migration of GBM cells, whereas the RNA-interference-mediated knockdown of BCAS1-SV1 reduced proliferation and migration. Moreover, using a yeast-two hybrid assay, immunoprecipitation, and immunofluorescence staining, we confirmed that β-arrestin 2 is an interaction partner of BCAS1-SV1 but not BCAS1. The downregulation of β-arrestin 2 directly enhanced the malignancy of GBM and abrogated the effects of BCAS1-SV1 on GBM cells. Finally, we used a yeast two-hybrid-based growth assay to identify that maackiain (MK) is a potential inhibitor of the interaction between BCAS1-SV1 and β-arrestin 2. MK treatment lessened the proliferation and migration of GBM cells and prolonged the lifespan of tumor-bearing mice in subcutaneous xenograft and intracranial U87-luc xenograft models. This study provides the first evidence that the gain-of-function BCAS1-SV1 splice variant promotes the development of GBM by suppressing the β-arrestin 2 pathway and opens up a new therapeutic perspective in GBM.
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Affiliation(s)
- Yun-Hua Kuo
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
| | - Huey-Shan Hung
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Translational Medicine Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Chia-Wen Tsai
- Department of Nutrition, China Medical University, Taichung 40402, Taiwan
| | - Shao-Chih Chiu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
| | - Shih-Ping Liu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Translational Medicine Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Yu-Ting Chiang
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
| | - Woei-Cherng Shyu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Translational Medicine Research Center, China Medical University Hospital, Taichung 40447, Taiwan
| | - Shinn-Zong Lin
- Buddhist Tzu Chi Bioinnovation Center, Tzu Chi Foundation, Hualien 970, Taiwan
- Department of Neurosurgery, Buddhist Tzu Chi General Hospital, Hualien 970, Taiwan
| | - Ru-Huei Fu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Translational Medicine Research Center, China Medical University Hospital, Taichung 40447, Taiwan
- Correspondence: ; Tel.: +886-422052121-7826
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20
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van den Bosch QCC, Nguyen JQN, Brands T, van den Bosch TPP, Verdijk RM, Paridaens D, Naus NC, de Klein A, Kiliç E, Brosens E. FOXD1 Is a Transcription Factor Important for Uveal Melanocyte Development and Associated with High-Risk Uveal Melanoma. Cancers (Basel) 2022; 14:cancers14153668. [PMID: 35954332 PMCID: PMC9367502 DOI: 10.3390/cancers14153668] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/12/2022] [Accepted: 07/22/2022] [Indexed: 11/27/2022] Open
Abstract
Simple Summary Despite successful treatment of primary uveal melanoma (UM), metastases still occur in approximately 50% of the patients. Unfortunately, little is known about the mechanism behind metastasized UM. By reanalyzing publicly available single-cell RNA sequencing data of embryonic zebrafish larvae and validating the results with UM data, we have identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. The most significant finding is FOXD1, which is nearly exclusively expressed in high-risk UM and is associated with poor survival. FOXD1 is a novel gene which could be involved in the metastatic capability of UM. Elucidating its function and role in metastatic UM could help to understand and develop treatment for UM. Abstract Uveal melanoma (UM) is a deadly ocular malignancy, originating from uveal melanocytes. Although much is known regarding prognostication in UM, the exact mechanism of metastasis is mostly unknown. Metastatic tumor cells are known to express a more stem-like RNA profile which is seen often in cell-specific embryonic development to induce tumor progression. Here, we identified novel transcription regulators by reanalyzing publicly available single cell RNA sequencing experiments. We identified five transcription regulators of interest: ELL2, KDM5B, REXO4, RBFOX2 and FOXD1. Our most significant finding is FOXD1, as this gene is nearly exclusively expressed in high-risk UM and its expression is associated with a poor prognosis. Even within the BAP1-mutated UM, the expression of FOXD1 is correlated with poor survival. FOXD1 is a novel factor which could potentially be involved in the metastatic capacity of high-risk UM. Elucidating the function of FOXD1 in UM could provide insight into the malignant transformation of uveal melanocytes, especially in high-risk UM.
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Affiliation(s)
- Quincy C. C. van den Bosch
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Josephine Q. N. Nguyen
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Tom Brands
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Thierry P. P. van den Bosch
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
| | - Robert M. Verdijk
- Department of Pathology, Section Ophthalmic Pathology, Erasmus MC Cancer Institute, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (T.P.P.v.d.B.); (R.M.V.)
- Department of Pathology, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Dion Paridaens
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands;
| | - Nicole C. Naus
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
| | - Annelies de Klein
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
| | - Emine Kiliç
- Department of Ophthalmology, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands; (Q.C.C.v.d.B.); (J.Q.N.N.); (T.B.); (N.C.N.)
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC Cancer Center, Erasmus MC University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands;
- Correspondence: (E.K.); (E.B.); Tel.: +31-107030683 (E.B.)
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21
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LPS Administration Impacts Glial Immune Programs by Alternative Splicing. Biomolecules 2022; 12:biom12020277. [PMID: 35204777 PMCID: PMC8961644 DOI: 10.3390/biom12020277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 02/04/2023] Open
Abstract
We performed transcriptome analysis in the hippocampus 24 h after lipopolysaccharide (LPS) administration. We observed glial-specific genes, comprised of two-thirds of all differentially expressed genes (DEGs). We found microglial DEGs that were the most numerous in LPS group. On the contrary, differential alternative splicing (DAS) analysis revealed the most numerous DAS events in astrocytes. Besides, we observed distinct major isoform switching in the Ptbp1 gene, with skipping of exon 8 in LPS group. Ptbp1 usually considered a pluripotency sustaining agent in brain embryonic development, according to the previous studies. Analyzing the splicing tune-up upon LPS exposure, we came to a supposition that the short Ptbp1 isoform de-represses immune-specific response by Ptbp1 adjusted splicing architecture. Additionally, the Ptbp3 (NOD1) immune-specific splicing factor has apparently been de-repressed by the Ptbp1 short isoform in glial cells. Notably, both the Ptbp1 and Ptbp3 genes express primarily in microglial/endothelial brain cells. We also report immune-related genes, altering their major isoforms upon LPS exposure. The results revealed immune modulating role of alternative splicing in brain.
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