1
|
Choi BM, Cheong JH, Ryu JI, Won YD, Min KW, Han MH. Significant Genes Associated with Mortality and Disease Progression in Grade II and III Glioma. Biomedicines 2024; 12:858. [PMID: 38672212 PMCID: PMC11048596 DOI: 10.3390/biomedicines12040858] [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: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The Wnt/β-catenin pathway plays a critical role in the tumorigenesis and maintenance of glioma stem cells. This study aimed to evaluate significant genes associated with the Wnt/β-catenin pathway involved in mortality and disease progression in patients with grade II and III glioma, using the Cancer Genome Atlas (TCGA) database. METHODS We obtained clinicopathological information and mRNA expression data from 515 patients with grade II and III gliomas from the TCGA database. We performed a multivariate Cox regression analysis to identify genes independently associated with glioma prognosis. RESULTS The analysis of 34 genes involved in Wnt/β-catenin signaling demonstrated that four genes (CER1, FRAT1, FSTL1, and RPSA) related to the Wnt/β-catenin pathway were significantly associated with mortality and disease progression in patients with grade II and III glioma. We also identified additional genes related to the four significant genes of the Wnt/β-catenin pathway mentioned above. The higher expression of BMP2, RPL18A, RPL19, and RPS12 is associated with better outcomes in patients with glioma. CONCLUSIONS Using a large-scale open database, we identified significant genes related to the Wnt/β-catenin signaling pathway associated with mortality and disease progression in patients with grade II and III gliomas.
Collapse
Affiliation(s)
- Bo Mi Choi
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Jin Hwan Cheong
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Je Il Ryu
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Yu Deok Won
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Kyueng-Whan Min
- Department of Pathology, Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu 11759, Gyeonggi-do, Republic of Korea
| | - Myung-Hoon Han
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| |
Collapse
|
2
|
Ma Y, Wang J, He X, Liu Y, Zhen S, An L, Yang Q, Niu F, Wang H, An B, Tai X, Yan Z, Wu C, Yang X, Liu X. Molecular mechanism of human ISG20L2 for the ITS1 cleavage in the processing of 18S precursor ribosomal RNA. Nucleic Acids Res 2024; 52:1878-1895. [PMID: 38153123 PMCID: PMC10899777 DOI: 10.1093/nar/gkad1210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/03/2023] [Accepted: 12/10/2023] [Indexed: 12/29/2023] Open
Abstract
The exonuclease ISG20L2 has been initially characterized for its role in the mammalian 5.8S rRNA 3' end maturation, specifically in the cleavage of ITS2 of 12S precursor ribosomal RNA (pre-rRNA). Here, we show that human ISG20L2 is also involved in 18S pre-rRNA maturation through removing the ITS1 region, and contributes to ribosomal biogenesis and cell proliferation. Furthermore, we determined the crystal structure of the ISG20L2 nuclease domain at 2.9 Å resolution. It exhibits the typical αβα fold of the DEDD 3'-5' exonuclease with a catalytic pocket located in the hollow near the center. The catalytic residues Asp183, Glu185, Asp267, His322 and Asp327 constitute the DEDDh motif in ISG20L2. The active pocket represents conformational flexibility in the absence of an RNA substrate. Using structural superposition and mutagenesis assay, we mapped RNA substrate binding residues in ISG20L2. Finally, cellular assays revealed that ISG20L2 is aberrantly up-regulated in colon adenocarcinoma and promotes colon cancer cell proliferation through regulating ribosome biogenesis. Together, these results reveal that ISG20L2 is a new enzymatic member for 18S pre-rRNA maturation, provide insights into the mechanism of ISG20L2 underlying pre-rRNA processing, and suggest that ISG20L2 is a potential therapeutic target for colon adenocarcinoma.
Collapse
Affiliation(s)
- Yinliang Ma
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Jiaxu Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- College of Life Sciences, State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Normal University, Xinxiang 453002 Henan, China
| | - Xingyi He
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Yuhang Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Shuo Zhen
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Lina An
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Qian Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Fumin Niu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Hong Wang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Boran An
- Affiliated Hospital of Hebei University, Hebei University, Baoding 071002 Hebei, China
| | - Xinyue Tai
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Zhenzhen Yan
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Chen Wu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| | - Xiaoyun Yang
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
- Department of Biology, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xiuhua Liu
- College of Life Sciences, Hebei Innovation Center for Bioengineering and Biotechnology, Institute of Life Sciences and Green Development, Hebei University, Baoding 071002 Hebei, China
| |
Collapse
|
3
|
Yagita K, Sadashima S, Koyama S, Noguchi H, Hamasaki H, Sasagasako N, Honda H. Ribosomal protein SA is a common component of neuronal intranuclear inclusions in polyglutamine diseases and Marinesco bodies. Neuropathology 2024; 44:31-40. [PMID: 37340992 DOI: 10.1111/neup.12927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/17/2023] [Accepted: 05/21/2023] [Indexed: 06/22/2023]
Abstract
Neuronal intranuclear inclusions (NIIs) are common key structures in polyglutamine (polyQ) diseases such as Huntington disease (HD), spinocerebellar ataxia type 1 (SCA1), and SCA3. Marinesco bodies (MBs) of dopaminergic neurons in the substantia nigra are also intranuclear structures and are frequently seen in normal elderly people. Ribosomal dysfunction is closely related to two differential processes; therefore, we aimed to identify the pathological characteristics of ribosomal protein SA (RPSA), a ribosomal protein, in both states. To this end, we evaluated the autopsy findings in four patients with HD, two SCA3, and five normal elderly cases (NCs). Immunohistochemical studies demonstrated that both NIIs and MBs contain RPSA. In polyQ diseases, RPSA was co-localized with polyQ aggregations, and 3D-reconstructed images revealed their mosaic-like distribution. Assessments of the organization of RPSA and p62 in NIIs showed that RPSA was more localized toward the center than p62 and that this unique organization was more evident in the MBs. Immunoblotting of the temporal cortices revealed that the nuclear fraction of HD patients contained more RPSA than that of NCs. In conclusion, our study revealed that RPSA is a common component of both NIIs and MBs, indicating that a similar mechanism contributes to the formation of polyQ NIIs and MBs.
Collapse
Affiliation(s)
- Kaoru Yagita
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shoko Sadashima
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Sachiko Koyama
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideko Noguchi
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideomi Hamasaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naokazu Sasagasako
- Department of Neurology, National Hospital Organization, Omuta National Hospital, Fukuoka, Japan
| | - Hiroyuki Honda
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- Neuropathology Center, National Hospital Organization, Omuta National Hospital, Omuta, Japan
| |
Collapse
|
4
|
Liu Y, Karlsson S. Perspectives of current understanding and therapeutics of Diamond-Blackfan anemia. Leukemia 2024; 38:1-9. [PMID: 37973818 PMCID: PMC10776401 DOI: 10.1038/s41375-023-02082-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/20/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
ABSTACT Diamond-Blackfan anemia (DBA) is a rare congenital bone marrow failure disorder characterized by erythroid hypoplasia. It primarily affects infants and is often caused by heterozygous allelic variations in ribosomal protein (RP) genes. Recent studies also indicated that non-RP genes like GATA1, TSR2, are associated with DBA. P53 activation, translational dysfunction, inflammation, imbalanced globin/heme synthesis, and autophagy dysregulation were shown to contribute to disrupted erythropoiesis and impaired red blood cell production. The main therapeutic option for DBA patients is corticosteroids. However, half of these patients become non-responsive to corticosteroid therapy over prolonged treatment and have to be given blood transfusions. Hematopoietic stem cell transplantation is currently the sole curative option, however, the treatment is limited by the availability of suitable donors and the potential for serious immunological complications. Recent advances in gene therapy using lentiviral vectors have shown promise in treating RPS19-deficient DBA by promoting normal hematopoiesis. With deepening insights into the molecular framework of DBA, emerging therapies like gene therapy hold promise for providing curative solutions and advancing comprehension of the underlying disease mechanisms.
Collapse
Affiliation(s)
- Yang Liu
- Center for Hematology and Regenerative Medicine, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden.
| | - Stefan Karlsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, Sweden.
| |
Collapse
|
5
|
Zhang Y, Liang X, Luo S, Chen Y, Li Y, Ma C, Li N, Gao N. Visualizing the nucleoplasmic maturation of human pre-60S ribosomal particles. Cell Res 2023; 33:867-878. [PMID: 37491604 PMCID: PMC10624882 DOI: 10.1038/s41422-023-00853-9] [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: 05/10/2023] [Accepted: 07/07/2023] [Indexed: 07/27/2023] Open
Abstract
Eukaryotic ribosome assembly is a highly orchestrated process that involves over two hundred protein factors. After early assembly events on nascent rRNA in the nucleolus, pre-60S particles undergo continuous maturation steps in the nucleoplasm, and prepare for nuclear export. Here, we report eleven cryo-EM structures of the nuclear pre-60S particles isolated from human cells through epitope-tagged GNL2, at resolutions of 2.8-4.3 Å. These high-resolution snapshots provide fine details for several major structural remodeling events at a virtual temporal resolution. Two new human nuclear factors, L10K and C11orf98, were also identified. Comparative structural analyses reveal that many assembly factors act as successive place holders to control the timing of factor association/dissociation events. They display multi-phasic binding properties for different domains and generate complex binding inter-dependencies as a means to guide the rRNA maturation process towards its mature conformation. Overall, our data reveal that nuclear assembly of human pre-60S particles is generally hierarchical with short branch pathways, and a few factors display specific roles as rRNA chaperones by confining rRNA helices locally to facilitate their folding, such as the C-terminal domain of SDAD1.
Collapse
Affiliation(s)
- Yunyang Zhang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Xiaomeng Liang
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Sha Luo
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yan Chen
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Yu Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
| | - Chengying Ma
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Ningning Li
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China
- Changping Laboratory, Beijing, China
| | - Ning Gao
- State Key Laboratory of Membrane Biology, Peking-Tsinghua Joint Center for Life Sciences, School of Life Sciences, Peking University, Beijing, China.
- Changping Laboratory, Beijing, China.
- National Biomedical Imaging Center, Peking University, Beijing, China.
| |
Collapse
|
6
|
Bhandari N, Acharya D, Chatterjee A, Mandve L, Kumar P, Pratap S, Malakar P, Shukla SK. Pan-cancer integrated bioinformatic analysis of RNA polymerase subunits reveal RNA Pol I member CD3EAP regulates cell growth by modulating autophagy. Cell Cycle 2023; 22:1986-2002. [PMID: 37795959 PMCID: PMC10761113 DOI: 10.1080/15384101.2023.2265676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
Transcription is a crucial stage in gene expression. An integrated study of 34 RNA polymerase subunits (RNAPS) in the six most frequent cancer types identified several genetic and epigenetic modification. We discovered nine mutant RNAPS with a mutation frequency of more than 1% in at least one tumor type. POLR2K and POLR2H were found to be amplified and overexpressed, whereas POLR3D was deleted and downregulated. Multiple RNAPS were also observed to be regulated by variations in promoter methylation. 5-Aza-2-deoxycytidine mediated re-expression in cell lines verified methylation-driven inhibition of POLR2F and POLR2L expression in BRCA and NSCLC, respectively. Next, we showed that CD3EAP, a Pol I subunit, was overexpressed in all cancer types and was associated with worst survival in breast, liver, lung, and prostate cancers. The knockdown studies showed that CD3EAP is required for cell proliferation and induces autophagy but not apoptosis. Furthermore, autophagy inhibition rescued the cell proliferation in CD3EAP knockdown cells. CD3EAP expression correlated with S and G2 phase cell cycle regulators, and CD3EAP knockdown inhibited the expression of S and G2 CDK/cyclins. We also identified POLR2D, an RNA pol II subunit, as a commonly overexpressed and prognostic gene in multiple cancers. POLR2D knockdown also decreased cell proliferation. POLR2D is related to the transcription of just a subset of RNA POL II transcribe genes, indicating a distinct role. Taken together, we have shown the genetic and epigenetic regulation of RNAPS genes in most common tumors. We have also demonstrated the cancer-specific function of CD3EAP and POLR2D genes.
Collapse
Affiliation(s)
- Nikita Bhandari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Disha Acharya
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Annesha Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Lakshana Mandve
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pranjal Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Shreesh Pratap
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| | - Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu K. Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, India
| |
Collapse
|
7
|
Kawashima N, Bezzerri V, Corey SJ. The Molecular and Genetic Mechanisms of Inherited Bone Marrow Failure Syndromes: The Role of Inflammatory Cytokines in Their Pathogenesis. Biomolecules 2023; 13:1249. [PMID: 37627314 PMCID: PMC10452082 DOI: 10.3390/biom13081249] [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: 07/18/2023] [Revised: 08/09/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Inherited bone marrow failure syndromes (IBMFSs) include Fanconi anemia, Diamond-Blackfan anemia, Shwachman-Diamond syndrome, dyskeratosis congenita, severe congenital neutropenia, and other rare entities such as GATA2 deficiency and SAMD9/9L mutations. The IBMFS monogenic disorders were first recognized by their phenotype. Exome sequencing has validated their classification, with clusters of gene mutations affecting DNA damage response (Fanconi anemia), ribosome structure (Diamond-Blackfan anemia), ribosome assembly (Shwachman-Diamond syndrome), or telomere maintenance/stability (dyskeratosis congenita). The pathogenetic mechanisms of IBMFSs remain to be characterized fully, but an overarching hypothesis states that different stresses elicit TP53-dependent growth arrest and apoptosis of hematopoietic stem, progenitor, and precursor cells. Here, we review the IBMFSs and propose a role for pro-inflammatory cytokines, such as TGF-β, IL-1β, and IFN-α, in mediating the cytopenias. We suggest a pathogenic role for cytokines in the transformation to myeloid neoplasia and hypothesize a role for anti-inflammatory therapies.
Collapse
Affiliation(s)
- Nozomu Kawashima
- Departments of Pediatrics and Cancer Biology, Cleveland Clinic, Cleveland, OH 44195, USA;
| | - Valentino Bezzerri
- Cystic Fibrosis Center, Azienda Ospedaliera Universitaria Integrata, 37126 Verona, Italy;
| | - Seth J. Corey
- Departments of Pediatrics and Cancer Biology, Cleveland Clinic, Cleveland, OH 44195, USA;
| |
Collapse
|
8
|
Hong M, Du Y, Chen D, Shi Y, Hu M, Tang K, Hong Z, Meng X, Xu W, Wu G, Yao Y, Chen L, Chen W, Lau CY, Sheng L, Zhang TH, Huang H, Fang Z, Shen Y, Sun F, Qian J, Qu H, Zheng S, Zhang S, Ding K, Sun R. Martynoside rescues 5-fluorouracil-impaired ribosome biogenesis by stabilizing RPL27A. Sci Bull (Beijing) 2023; 68:1662-1677. [PMID: 37481436 DOI: 10.1016/j.scib.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/11/2023] [Accepted: 06/25/2023] [Indexed: 07/24/2023]
Abstract
Martynoside (MAR), a bioactive component in several well-known tonic traditional Chinese herbs, exhibits pro-hematopoietic activity during 5-fluorouracil (5-FU) treatment. However, the molecular target and the mechanism of MAR are poorly understood. Here, by adopting the mRNA display with a library of even-distribution (md-LED) method, we systematically examined MAR-protein interactions in vitro and identified the ribosomal protein L27a (RPL27A) as a key cellular target of MAR. Structural and mutational analysis confirmed the specific interaction between MAR and the exon 4,5-encoded region of RPL27A. MAR attenuated 5-FU-induced cytotoxicity in bone marrow nucleated cells, increased RPL27A protein stability, and reduced the ubiquitination of RPL27A at lys92 (K92) and lys94 (K94). Disruption of MAR binding at key residues of RPL27A completely abolished the MAR-induced stabilization. Furthermore, by integrating label-free quantitative ubiquitination proteomics, transcriptomics, and ribosome function assays, we revealed that MAR restored RPL27A protein levels and thus rescued ribosome biogenesis impaired by 5-FU. Specifically, MAR increased mature ribosomal RNA (rRNA) abundance, prevented ribosomal protein degradation, facilitated ribosome assembly, and maintained nucleolar integrity. Collectively, our findings characterize the target of a component of Chinese medicine, reveal the importance of ribosome biogenesis in hematopoiesis, and open up a new direction for improving hematopoiesis by targeting RPL27A.
Collapse
Affiliation(s)
- Mengying Hong
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles 90095, USA; Zhejiang Province Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou 310009, China; Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou 310009, China
| | - Yushen Du
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles 90095, USA; Zhejiang Province Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou 310009, China; Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou 310009, China.
| | - Dongdong Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles 90095, USA
| | - Yuan Shi
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles 90095, USA
| | - Menglong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Kejun Tang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Zhuping Hong
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiangzhi Meng
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Department of Microbiology, Immunology, & Molecular Genetics, University of California, Los Angeles 90095, USA; Center for Infectious Disease Research, School of Life Sciences, Institute for Advanced Studies, Westlake University, Hangzhou 310024, China
| | - Wan Xu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Gaoqi Wu
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yuanyuan Yao
- Department of Colorectal Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China
| | - Liubo Chen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Wenteng Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Chit Ying Lau
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Li Sheng
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles 90095, USA
| | - Tian-Hao Zhang
- Molecular Biology Institute, University of California, Los Angeles 90095, USA
| | - Haigen Huang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles 90095, USA
| | - Zheyu Fang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Yong Shen
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Fangfang Sun
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Jing Qian
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Haibin Qu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Zhejiang Province Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou 310009, China; Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou 310009, China
| | - Suzhan Zhang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Zhejiang Province Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou 310009, China; Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou 310009, China
| | - Kefeng Ding
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China; Zhejiang Province Key Laboratory of Molecular Biology in Medical Sciences, Hangzhou 310009, China; Zhejiang Provincial Clinical Research Center for Cancer, Cancer Center of Zhejiang University, Hangzhou 310009, China
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles 90095, USA; School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; Molecular Biology Institute, University of California, Los Angeles 90095, USA; Center for Infectious Disease Research, School of Life Sciences, Institute for Advanced Studies, Westlake University, Hangzhou 310024, China.
| |
Collapse
|
9
|
Gao Y, Wang H. Ribosome Heterogeneity in Development and Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550527. [PMID: 37546733 PMCID: PMC10402066 DOI: 10.1101/2023.07.25.550527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The functional ribosome is composed of ∼80 ribosome proteins. With the intensity-based absolute quantification (iBAQ) value, we calculate the stoichiometry ratio of each ribosome protein. We analyze the ribosome ratio-omics (Ribosome R ), which reflects the holistic signature of ribosome composition, in various biological samples with distinct functions, developmental stages, and pathological outcomes. The Ribosome R reveals significant ribosome heterogeneity among different tissues of fat, spleen, liver, kidney, heart, and skeletal muscles. During tissue development, testes at various stages of spermatogenesis show distinct Ribosome R signatures. During in vitro neuronal maturation, the Ribosome R changes reveal functional association with certain molecular aspects of neurodevelopment. Regarding ribosome heterogeneity associated with pathological conditions, the Ribosome R signature of gastric tumors is functionally linked to pathways associated with tumorigenesis. Moreover, the Ribosome R undergoes dynamic changes in macrophages following immune challenges. Taken together, with the examination of a broad spectrum of biological samples, the Ribosome R barcode reveals ribosome heterogeneity and specialization in cell function, development, and disease. One-Sentence Summary Ratio-omics signature of ribosome deciphers functionally relevant heterogeneity in development and disease.
Collapse
|
10
|
Sola M, Rendon-Angel A, Rojo Martinez V, Sgrignani J, Magrin C, Piovesana E, Cavalli A, Paganetti P, Papin S. Tau protein binds to the P53 E3 ubiquitin ligase MDM2. Sci Rep 2023; 13:10208. [PMID: 37353565 PMCID: PMC10290082 DOI: 10.1038/s41598-023-37046-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 06/14/2023] [Indexed: 06/25/2023] Open
Abstract
Tau gene mutations cause a progressive dementia and neurotoxic Tau forms deposited in neurofibrillary tangles are hallmarks of neurodegenerative tauopathies. Loss of non-canonical Tau functions may contribute to disease. In fact, Tau depletion affects the cellular response to DNA damage and tauopathies exhibit the accumulation of DNA lesions. Moreover, Tau modulates P53 activity and cell fate. Considering that MDM2 is the main antagonist of P53, we investigated, using orthogonal assays, if Tau interacts with MDM2. We report the existence in cells and brain of a Tau-MDM2 complex that, in vitro, exhibits reduced P53 ubiquitination activity in a manner sensitive to a Tau mutation. The Tau-MDM2 interaction involves the microtubule-binding domain of Tau and the acidic domain of MDM2, reminiscent of the binding of Tau to negatively charged microtubules. Notably, MDM2 accumulates aberrantly in neurofibrillary tangles. Aging-associated insults may expose a novel loss-of-function of Tau in neurodegeneration and cancer.
Collapse
Affiliation(s)
- Martina Sola
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Azucena Rendon-Angel
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
| | - Viviana Rojo Martinez
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
| | - Jacopo Sgrignani
- Computational Structural Biology, Institute for Research in Biomedicine, Università Della Svizzera Italiana, Bellinzona, Switzerland
| | - Claudia Magrin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Ester Piovesana
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland
| | - Andrea Cavalli
- Computational Structural Biology, Institute for Research in Biomedicine, Università Della Svizzera Italiana, Bellinzona, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paolo Paganetti
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland.
- PhD Program in Neurosciences, Faculty of Biomedical Sciences, Università Della Svizzera Italiana, Lugano, Switzerland.
- Neurocentro Della Svizzera Italiana, Ente Ospedaliero Cantonale, Lugano, Switzerland.
| | - Stéphanie Papin
- Laboratory for Aging Disorders, Laboratories for Translational Research, Ente Ospedaliero Cantonale, Room 102a, Via Chiesa 5, 6500, Bellinzona, Switzerland
| |
Collapse
|
11
|
Cook J, Greene ES, Ramser A, Mullenix G, Dridi JS, Liyanage R, Wideman R, Dridi S. Comparative- and network-based proteomic analysis of bacterial chondronecrosis with osteomyelitis lesions in broiler's proximal tibiae identifies new molecular signatures of lameness. Sci Rep 2023; 13:5947. [PMID: 37045932 PMCID: PMC10097873 DOI: 10.1038/s41598-023-33060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/06/2023] [Indexed: 04/14/2023] Open
Abstract
Bacterial Chondronecrosis with Osteomyelitis (BCO) is a specific cause of lameness in commercial fast-growing broiler (meat-type) chickens and represents significant economic, health, and wellbeing burdens. However, the molecular mechanisms underlying the pathogenesis remain poorly understood. This study represents the first comprehensive characterization of the proximal tibia proteome from healthy and BCO chickens. Among a total of 547 proteins identified, 222 were differentially expressed (DE) with 158 up- and 64 down-regulated proteins in tibia of BCO vs. normal chickens. Biological function analysis using Ingenuity Pathways showed that the DE proteins were associated with a variety of diseases including cell death, organismal injury, skeletal and muscular disorder, immunological and inflammatory diseases. Canonical pathway and protein-protein interaction network analysis indicated that these DE proteins were involved in stress response, unfolded protein response, ribosomal protein dysfunction, and actin cytoskeleton signaling. Further, we identified proteins involved in bone resorption (osteoclast-stimulating factor 1, OSFT1) and bone structural integrity (collagen alpha-2 (I) chain, COL2A1), as potential key proteins involved in bone attrition. These results provide new insights by identifying key protein candidates involved in BCO and will have significant impact in understanding BCO pathogenesis.
Collapse
Affiliation(s)
- Jennifer Cook
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Elizabeth S Greene
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Alison Ramser
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Garrett Mullenix
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Jalila S Dridi
- École Universitaire de Kinésithérapie, Université d'Orléans, Rue de Chartres, 45100, Orléans, France
| | - Rohana Liyanage
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Robert Wideman
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA
| | - Sami Dridi
- Department of Poultry Science, University of Arkansas, 1260 W. Maple Street, Fayetteville, AR, 72701, USA.
| |
Collapse
|
12
|
Guo Z, Wang X, Li Y, Xing A, Wu C, Li D, Wang C, de Bures A, Zhang Y, Guo S, Sáez-Vasquez J, Shen Z, Hu Z. Arabidopsis SMO2 modulates ribosome biogenesis by maintaining the RID2 abundance during organ growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:96-109. [PMID: 36705084 DOI: 10.1111/tpj.16121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
Ribosome biogenesis is a process of making ribosomes that is tightly linked with plant growth and development. Here, through a suppressor screen for the smo2 mutant, we found that lack of a ribosomal stress response mediator, ANAC082 partially restored growth defects of the smo2 mutant, indicating SMO2 is required for the repression of nucleolar stress. Consistently, the smo2 knock-out mutant exhibited typical phenotypes characteristic of ribosome biogenesis mutants, such as pointed leaves, aberrant leaf venation, disrupted nucleolar structure, abnormal distribution of rRNA precursors, and enhanced tolerance to aminoglycoside antibiotics that target ribosomes. SMO2 interacted with ROOT INITIATION DEFECTIVE 2 (RID2), a methyltransferase-like protein required for pre-rRNA processing. SMO2 enhanced RID2 solubility in Escherichia coli and the loss of function of SMO2 in plant cells reduced RID2 abundance, which may result in abnormal accumulation of FIBRILLARIN 1 (FIB1) and NOP56, two key nucleolar proteins, in high-molecular-weight protein complex. Taken together, our results characterized a novel plant ribosome biogenesis factor, SMO2 that maintains the abundance of RID2, thereby sustaining ribosome biogenesis during plant organ growth.
Collapse
Affiliation(s)
- Zhengfei Guo
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Xiaoyu Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Yan Li
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Aiming Xing
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chengyun Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Daojun Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Chunfei Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
| | - Anne de Bures
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Yonghong Zhang
- Laboratory of Medicinal Plant, Hubei Key Laboratory of Wudang Local Chinese Medicine Research, Academy of Bio-Medicine Research, School of Basic Medicine, Hubei University of Medicine, 442000, Shiyan, China
| | - Siyi Guo
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| | - Julio Sáez-Vasquez
- Laboratoire Génome et Développement des Plantes, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5096, 66860, Perpignan, France
- Laboratoire Génome et Développement des Plantes, Universite Perpignan Via Domitia, 66860, Perpignan, Unité Mixte de Recherche 5096, France
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Zhubing Hu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, 475004, Kaifeng, China
- Sanya Institute of Henan University, 572025, Hainan, Sanya, China
| |
Collapse
|
13
|
Jerome MS, Nanjappa DP, Chakraborty A, Chakrabarty S. Molecular etiology of defective nuclear and mitochondrial ribosome biogenesis: Clinical phenotypes and therapy. Biochimie 2023; 207:122-136. [PMID: 36336106 DOI: 10.1016/j.biochi.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/27/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
Abstract
Ribosomopathies are rare congenital disorders associated with defective ribosome biogenesis due to pathogenic variations in genes that encode proteins related to ribosome function and biogenesis. Defects in ribosome biogenesis result in a nucleolar stress response involving the TP53 tumor suppressor protein and impaired protein synthesis leading to a deregulated translational output. Despite the accepted notion that ribosomes are omnipresent and essential for all cells, most ribosomopathies show tissue-specific phenotypes affecting blood cells, hair, spleen, or skin. On the other hand, defects in mitochondrial ribosome biogenesis are associated with a range of clinical manifestations affecting more than one organ. Intriguingly, the deregulated ribosomal function is also a feature in several human malignancies with a selective upregulation or downregulation of specific ribosome components. Here, we highlight the clinical conditions associated with defective ribosome biogenesis in the nucleus and mitochondria with a description of the affected genes and the implicated pathways, along with a note on the treatment strategies currently available for these disorders.
Collapse
Affiliation(s)
- Maria Sona Jerome
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Dechamma Pandyanda Nanjappa
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India
| | - Anirban Chakraborty
- Division of Molecular Genetics and Cancer, Nitte University Centre for Science Education and Research (NUCSER), NITTE (Deemed to Be University), Deralakate, Mangaluru, 575018, India.
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.
| |
Collapse
|
14
|
Feng Y, Han Y, Hu A, Qu Y, Hu Y, Wu H, Wang X, He L. Heliangin acts as a covalent ligand of RPS2 that disrupts pre-rRNA metabolic processes in NPM1-mutated acute myeloid leukemia. Acta Pharm Sin B 2023; 13:598-617. [PMID: 36873185 PMCID: PMC9979090 DOI: 10.1016/j.apsb.2022.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/05/2022] [Accepted: 09/23/2022] [Indexed: 11/01/2022] Open
Abstract
Although NPM1 mutations are frequently found in acute myeloid leukemia patients, therapeutic strategies are scarce and unsuitable for those who cannot tolerate intensive chemotherapy. Here we demonstrated that heliangin, a natural sesquiterpene lactone, exerts favorable therapeutic responses in NPM1 mutant acute myeloid leukemia cells, with no apparent toxicity to normal hematogenous cells, by inhibiting their proliferation, inducing apoptosis, causing cell cycle arrest, and promoting differentiation. In-depth studies on its mode of action using quantitative thiol reactivity platform screening and subsequent molecular biology validation showed that the ribosomal protein S2 (RPS2) is the main target of heliangin in treating NPM1 mutant AML. Upon covalent binding to the C222 site of RPS2, the electrophilic moieties of heliangin disrupt pre-rRNA metabolic processes, leading to nucleolar stress, which in turn regulates the ribosomal proteins-MDM2-p53 pathway and stabilizes p53. Clinical data shows that the pre-rRNA metabolic pathway is dysregulated in acute myeloid leukemia patients with the NPM1 mutation, leading to a poor prognosis. We found that RPS2 plays a critical role in regulating this pathway and may be a novel treatment target. Our findings suggest a novel treatment strategy and lead compound for acute myeloid leukemia patients, especially those with NPM1 mutations.
Collapse
Affiliation(s)
- Yin Feng
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210046, China.,China Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing 210046, China
| | - Yefan Han
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210046, China.,China Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing 210046, China
| | - Anni Hu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210046, China.,China Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing 210046, China
| | - Yi Qu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210046, China.,China Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing 210046, China
| | - Yili Hu
- Experiment Center for Science and Technology, Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Hao Wu
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210046, China
| | - Xinzhi Wang
- College of Pharmacy, Nanjing University of Chinese Medicine, Nanjing 210046, China.,China Jiangsu Key Laboratory of Research and Development in Marine Bio-resource Pharmaceutics, Nanjing 210046, China
| | - Li He
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan 430071, China
| |
Collapse
|
15
|
Durand S, Bruelle M, Bourdelais F, Bennychen B, Blin-Gonthier J, Isaac C, Huyghe A, Martel S, Seyve A, Vanbelle C, Adrait A, Couté Y, Meyronet D, Catez F, Diaz JJ, Lavial F, Ricci EP, Ducray F, Gabut M. RSL24D1 sustains steady-state ribosome biogenesis and pluripotency translational programs in embryonic stem cells. Nat Commun 2023; 14:356. [PMID: 36690642 PMCID: PMC9870888 DOI: 10.1038/s41467-023-36037-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 01/13/2023] [Indexed: 01/24/2023] Open
Abstract
Embryonic stem cell (ESC) fate decisions are regulated by a complex circuitry that coordinates gene expression at multiple levels from chromatin to mRNA processing. Recently, ribosome biogenesis and translation have emerged as key pathways that efficiently control stem cell homeostasis, yet the underlying molecular mechanisms remain largely unknown. Here, we identified RSL24D1 as highly expressed in both mouse and human pluripotent stem cells. RSL24D1 is associated with nuclear pre-ribosomes and is required for the biogenesis of 60S subunits in mouse ESCs. Interestingly, RSL24D1 depletion significantly impairs global translation, particularly of key pluripotency factors and of components from the Polycomb Repressive Complex 2 (PRC2). While having a moderate impact on differentiation, RSL24D1 depletion significantly alters ESC self-renewal and lineage commitment choices. Altogether, these results demonstrate that RSL24D1-dependant ribosome biogenesis is both required to sustain the expression of pluripotent transcriptional programs and to silence PRC2-regulated developmental programs, which concertedly dictate ESC homeostasis.
Collapse
Affiliation(s)
- Sébastien Durand
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Marion Bruelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
| | - Fleur Bourdelais
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Inovarion, 75005, Paris, France
| | - Bigitha Bennychen
- Dept. of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada
- Human Health Therapeutics Research Centre, National Research Council Canada, Ottawa, ON, K1A 0R6, Canada
| | - Juliana Blin-Gonthier
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - Caroline Isaac
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Aurélia Huyghe
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Sylvie Martel
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Antoine Seyve
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Christophe Vanbelle
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
| | - Annie Adrait
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - Yohann Couté
- University Grenoble Alpes, INSERM, CEA, UA13 BGE, CNRS, CEA, FR2048, 38000, Grenoble, France
| | - David Meyronet
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Institut de Pathologie Est, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Catez
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Jean-Jacques Diaz
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
| | - Fabrice Lavial
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Labex Dev2Can, Lyon, France
- Equipe labellisée la Ligue contre le cancer, Lyon, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et de Modélisation de la Cellule, ENS de Lyon, CNRS UMR 5239, Inserm U1293, Lyon, France
| | - François Ducray
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France
- Institut Convergence Plascan, Lyon, France
- Neuro-oncology department, Hospices Civils de Lyon, Lyon, France
| | - Mathieu Gabut
- Cancer Initiation and Tumoral Cell Identity (CITI) Department. Cancer Research Centre of Lyon (CRCL) INSERM 1052, CNRS 5286, Université Claude Bernard Lyon I, Centre Léon Bérard, Lyon, France.
- Institut Convergence Plascan, Lyon, France.
| |
Collapse
|
16
|
Utilization of Cancer Cell Line Screening to Elucidate the Anticancer Activity and Biological Pathways Related to the Ruthenium-Based Therapeutic BOLD-100. Cancers (Basel) 2022; 15:cancers15010028. [PMID: 36612025 PMCID: PMC9817855 DOI: 10.3390/cancers15010028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/30/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
BOLD-100 (sodium trans-[tetrachlorobis(1H indazole)ruthenate(III)]) is a ruthenium-based anticancer compound currently in clinical development. The identification of cancer types that show increased sensitivity towards BOLD-100 can lead to improved developmental strategies. Sensitivity profiling can also identify mechanisms of action that are pertinent for the bioactivity of complex therapeutics. Sensitivity to BOLD-100 was measured in a 319-cancer-cell line panel spanning 24 tissues. BOLD-100's sensitivity profile showed variation across the tissue lineages, including increased response in esophageal, bladder, and hematologic cancers. Multiple cancers, including esophageal, bile duct and colon cancer, had higher relative response to BOLD-100 than to cisplatin. Response to BOLD-100 showed only moderate correlation to anticancer compounds in the Genomics of Drug Sensitivity in Cancer (GDSC) database, as well as no clear theme in bioactivity of correlated hits, suggesting that BOLD-100 may have a differentiated therapeutic profile. The genomic modalities of cancer cell lines were modeled against the BOLD-100 sensitivity profile, which revealed that genes related to ribosomal processes were associated with sensitivity to BOLD-100. Machine learning modeling of the sensitivity profile to BOLD-100 and gene expression data provided moderative predictive value. These findings provide further mechanistic understanding around BOLD-100 and support its development for additional cancer types.
Collapse
|
17
|
Franklin DA, Liu S, Jin A, Cui P, Guo Z, Arend KC, Moorman NJ, He S, Wang GG, Wan YY, Zhang Y. Ribosomal protein RPL11 haploinsufficiency causes anemia in mice via activation of the RP-MDM2-p53 pathway. J Biol Chem 2022; 299:102739. [PMID: 36435197 PMCID: PMC9793318 DOI: 10.1016/j.jbc.2022.102739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/21/2022] [Accepted: 10/22/2022] [Indexed: 11/25/2022] Open
Abstract
Recent discovery of the ribosomal protein (RP) RPL11 interacting with and inhibiting the E3 ubiquitin ligase function of MDM2 established the RP-MDM2-p53 signaling pathway, which is linked to biological events, including ribosomal biogenesis, nutrient availability, and metabolic homeostasis. Mutations in RPs lead to a diverse array of phenotypes known as ribosomopathies in which the role of p53 is implicated. Here, we generated conditional RPL11-deletion mice to investigate in vivo effects of impaired RP expression and its functional connection with p53. While deletion of one Rpl11 allele in germ cells results in embryonic lethality, deletion of one Rpl11 allele in adult mice does not affect viability but leads to acute anemia. Mechanistically, we found RPL11 haploinsufficiency activates p53 in hematopoietic tissues and impedes erythroid precursor differentiation, resulting in insufficient red blood cell development. We demonstrated that reducing p53 dosage by deleting one p53 allele rescues RPL11 haploinsufficiency-induced inhibition of erythropoietic precursor differentiation and restores normal red blood cell levels in mice. Furthermore, blocking the RP-MDM2-p53 pathway by introducing an RP-binding mutation in MDM2 prevents RPL11 haploinsufficiency-caused p53 activation and rescues the anemia in mice. Together, these findings demonstrate that the RP-MDM2-p53 pathway is a critical checkpoint for RP homeostasis and that p53-dependent cell cycle arrest of erythroid precursors is the molecular basis for the anemia phenotype commonly associated with RP deficiency.
Collapse
Affiliation(s)
- Derek A. Franklin
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shijie Liu
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Aiwen Jin
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pengfei Cui
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Zengli Guo
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Kyle C. Arend
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nathaniel J. Moorman
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Shenghui He
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yisong Y. Wan
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Yanping Zhang
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA,For correspondence: Yanping Zhang
| |
Collapse
|
18
|
Wang B, Gao J, Zhao Z, Zhong X, Cui H, Hou H, Zhang Y, Zheng J, Di J, Liu Y. Identification of a small-molecule RPL11 mimetic that inhibits tumor growth by targeting MDM2-p53 pathway. Mol Med 2022; 28:109. [PMID: 36071402 PMCID: PMC9450376 DOI: 10.1186/s10020-022-00537-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 08/29/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Targeting ribosome biogenesis to activate p53 has recently emerged as a therapeutic strategy in human cancer. Among various ribosomal proteins, RPL11 centralizes the nucleolar stress-sensing pathway by binding MDM2, leading to MDM2 inactivation and p53 activation. Therefore, the identification of MDM2-binding RPL11-mimetics would be valuable for anti-cancer therapeutics. METHODS Based on the crystal structure of the interface between RPL11 and MDM2, we have identified 15 potential allosteric modulators of MDM2 through the virtual screening. RESULTS One of these compounds, named S9, directly binds MDM2 and competitively inhibits the interaction between RPL11 and MDM2, leading to p53 stabilization and activation. Moreover, S9 inhibits cancer cell proliferation in vitro and in vivo. Mechanistic study reveals that MDM2 is required for S9-induced G2 cell cycle arrest and apoptosis, whereas p53 contributes to S9-induced apoptosis. CONCLUSIONS Putting together, S9 may serve as a lead compound for the development of an anticancer drug that specifically targets RPL11-MDM2-p53 pathway.
Collapse
Affiliation(s)
- Bingwu Wang
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Oncology, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, 221000, China
| | - Jian Gao
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China.,Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy, Xuzhou Medical University, Xuzhou, 221000, China
| | - Zhongjun Zhao
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xuefei Zhong
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Hao Cui
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Hui Hou
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China.,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Yanping Zhang
- Department of Radiation and Lineberger Comprehensive Cancer Center, The University of North Carolina at Chapel Hill, 450 West Drive, Chapel Hill, USA
| | - Junnian Zheng
- Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China.
| | - Jiehui Di
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China.
| | - Yong Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China. .,Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China. .,The State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, China.
| |
Collapse
|
19
|
Kowalczyk D, Nakasone MA, Smith BO, Huang DT. Bivalent binding of p14ARF to MDM2 RING and acidic domains inhibits E3 ligase function. Life Sci Alliance 2022; 5:e202201472. [PMID: 35944929 PMCID: PMC9366199 DOI: 10.26508/lsa.202201472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/19/2022] [Accepted: 07/19/2022] [Indexed: 12/29/2022] Open
Abstract
ARF tumor suppressor protein is a key regulator of the MDM2-p53 signaling axis. ARF interferes with MDM2-mediated ubiquitination and degradation of p53 by sequestering MDM2 in the nucleolus and preventing MDM2-p53 interaction and nuclear export of p53. Moreover, ARF also directly inhibits MDM2 ubiquitin ligase (E3) activity, but the mechanism remains elusive. Here, we apply nuclear magnetic resonance and biochemical analyses to uncover the mechanism of ARF-mediated inhibition of MDM2 E3 activity. We show that MDM2 acidic and zinc finger domains (AD-ZnF) form a weak intramolecular interaction with the RING domain, where the binding site overlaps with the E2∼ubiquitin binding surface and thereby partially reduces MDM2 E3 activity. Binding of human N-terminal 32 residues of p14ARF to the acidic domain of MDM2 strengthens the AD-ZnF-RING domain interaction. Furthermore, the N-terminal RxFxV motifs of p14ARF participate directly in the MDM2 RING domain interaction. This bivalent binding mode of p14ARF to MDM2 acidic and RING domains restricts E2∼ubiquitin recruitment and massively hinders MDM2 E3 activity. These findings elucidate the mechanism by which ARF inhibits MDM2 E3 activity.
Collapse
Affiliation(s)
| | | | - Brian O Smith
- Institute of Molecular Cell and System Biology, University of Glasgow, Glasgow, UK
| | - Danny T Huang
- Cancer Research UK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| |
Collapse
|
20
|
Falcon KT, Watt KEN, Dash S, Zhao R, Sakai D, Moore EL, Fitriasari S, Childers M, Sardiu ME, Swanson S, Tsuchiya D, Unruh J, Bugarinovic G, Li L, Shiang R, Achilleos A, Dixon J, Dixon MJ, Trainor PA. Dynamic regulation and requirement for ribosomal RNA transcription during mammalian development. Proc Natl Acad Sci U S A 2022; 119:e2116974119. [PMID: 35881792 PMCID: PMC9351356 DOI: 10.1073/pnas.2116974119] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 05/11/2022] [Indexed: 01/28/2023] Open
Abstract
Ribosomal RNA (rRNA) transcription by RNA polymerase I (Pol I) is a critical rate-limiting step in ribosome biogenesis, which is essential for cell survival. Despite its global function, disruptions in ribosome biogenesis cause tissue-specific birth defects called ribosomopathies, which frequently affect craniofacial development. Here, we describe a cellular and molecular mechanism underlying the susceptibility of craniofacial development to disruptions in Pol I transcription. We show that Pol I subunits are highly expressed in the neuroepithelium and neural crest cells (NCCs), which generate most of the craniofacial skeleton. High expression of Pol I subunits sustains elevated rRNA transcription in NCC progenitors, which supports their high tissue-specific levels of protein translation, but also makes NCCs particularly sensitive to rRNA synthesis defects. Consistent with this model, NCC-specific deletion of Pol I subunits Polr1a, Polr1c, and associated factor Tcof1 in mice cell-autonomously diminishes rRNA synthesis, which leads to p53 protein accumulation, resulting in NCC apoptosis and craniofacial anomalies. Furthermore, compound mutations in Pol I subunits and associated factors specifically exacerbate the craniofacial anomalies characteristic of the ribosomopathies Treacher Collins syndrome and Acrofacial Dysostosis-Cincinnati type. Mechanistically, we demonstrate that diminished rRNA synthesis causes an imbalance between rRNA and ribosomal proteins. This leads to increased binding of ribosomal proteins Rpl5 and Rpl11 to Mdm2 and concomitantly diminished binding between Mdm2 and p53. Altogether, our results demonstrate a dynamic spatiotemporal requirement for rRNA transcription during mammalian cranial NCC development and corresponding tissue-specific threshold sensitivities to disruptions in rRNA transcription in the pathogenesis of congenital craniofacial disorders.
Collapse
Affiliation(s)
- Karla T. Falcon
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | - Soma Dash
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Ruonan Zhao
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
| | - Daisuke Sakai
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biology, Kanazawa Medical University, Uchinada, Ishikawa 920-0293, Japan
| | - Emma L. Moore
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | | | | | - Mihaela E. Sardiu
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Biostatistics and Data Science, University of Kansas Medical Center, Kansas City, KS 66160
| | - Selene Swanson
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Dai Tsuchiya
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - Jay Unruh
- Stowers Institute for Medical Research, Kansas City, MO 64110
| | - George Bugarinovic
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Orthopedic Surgery, Stanford University, Stanford, CA 94305
| | - Lin Li
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23284
| | - Rita Shiang
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, VA 23284
| | - Annita Achilleos
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Basic and Clinical Sciences, University of Nicosia Medical School, Nicosia 2408, Cyprus
| | - Jill Dixon
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Michael J. Dixon
- Faculty of Biology, Medicine, and Health, University of Manchester, Manchester M13 9PL, United Kingdom
| | - Paul A. Trainor
- Stowers Institute for Medical Research, Kansas City, MO 64110
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160
| |
Collapse
|
21
|
Ribosomes and Ribosomal Proteins Promote Plasticity and Stemness Induction in Glioma Cells via Reprogramming. Cells 2022; 11:cells11142142. [PMID: 35883585 PMCID: PMC9323835 DOI: 10.3390/cells11142142] [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: 05/27/2022] [Revised: 07/01/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Glioblastoma multiforme (GBM) is a lethal tumor that develops in the adult brain. Despite advances in therapeutic strategies related to surgical resection and chemo-radiotherapy, the overall survival of patients with GBM remains unsatisfactory. Genetic research on mutation, amplification, and deletion in GBM cells is important for understanding the biological aggressiveness, diagnosis, and prognosis of GBM. However, the efficacy of drugs targeting the genetic abnormalities in GBM cells is limited. Investigating special microenvironments that induce chemo-radioresistance in GBM cells is critical to improving the survival and quality of life of patients with GBM. GBM cells acquire and maintain stem-cell-like characteristics via their intrinsic potential and extrinsic factors from their special microenvironments. The acquisition of stem-cell-like phenotypes and aggressiveness may be referred to as a reprogramming of GBM cells. In addition to protein synthesis, deregulation of ribosome biogenesis is linked to several diseases including cancer. Ribosomal proteins possess both tumor-promotive and -suppressive functions as extra-ribosomal functions. Incorporation of ribosomes and overexpression of ribosomal protein S6 reprogram and induce stem-cell-like phenotypes in GBM cells. Herein, we review recent literature and our published data on the acquisition of aggressiveness by GBM and discuss therapeutic options through reprogramming.
Collapse
|
22
|
Zong C, Yang M, Guo X, Ji W. Chronic restraint stress promotes gastric epithelial malignant transformation by activating the Akt/p53 signaling pathway via ADRB2. Oncol Lett 2022; 24:300. [PMID: 35949623 PMCID: PMC9353258 DOI: 10.3892/ol.2022.13420] [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: 12/11/2021] [Accepted: 06/07/2022] [Indexed: 11/06/2022] Open
Abstract
The etiology of gastric cancer is associated with infectious, environmental and dietary factors, as well as genetic background. Additionally, emerging evidence has supported the vital role of chronic emotional stress on gastric carcinogenesis; however, the underlying mechanism remains unclear. The present study aimed to investigate the effects of chronic stress and a detrimental diet on gastric malignant epithelial transformation in rats. Therefore, 26 Wistar rats were randomly divided into the following four groups: i) Control; ii) detrimental diet (DD); iii) detrimental diet with chronic restraint (DR) and iv) detrimental diet with chronic restraint and propranolol treatment (DRP). ELISA was performed to detect the serum levels of epinephrine and norepinephrine. Epithelial cell apoptosis was analyzed using the TUNEL assay. The mRNA and protein expression levels of Akt and p53 were detected using reverse transcription quantitative PCR and western blotting, respectively. Pathological changes were analyzed using hematoxylin and eosin staining (H&E). The H&E staining results showed that dysplasia in the gastric mucosa occurred in two of eight rats in the DD group and in four of five rats in the DR group, whereas no dysplasia was detected in the DRP group. The apoptotic ratios of gastric epithelial cells were significantly decreased in all treatment groups compared with the control group. Adrenoceptor β2 (ADRB2) protein expression levels were increased significantly only in the DR group and this effect was significantly reduced in the DRP group. The mRNA expression levels of Akt and p53 were significantly upregulated in the DD group, and Akt mRNA expression was further elevated in the DR group. With regard to protein expression, the levels of Akt and p-Akt were significantly increased in the DR group, whereas these effects were reversed in the DRP group. Furthermore, the ratio of p-p53/p53 protein was significantly reduced in the DD or DR groups, but was reversed in the DRP group. Collectively, the findings of the present study suggested that chronic restraint stress potentially aggravates the gastric epithelial malignant transformation induced by a detrimental diet, at least partially via the Akt/p53 signaling pathway mediated via ADRB2.
Collapse
Affiliation(s)
- Chuanju Zong
- Department of Gastroenterology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261031, P.R. China
| | - Maoquan Yang
- Department of Gastroenterology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261031, P.R. China
| | - Xiaojing Guo
- Department of Gastroenterology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261031, P.R. China
| | - Wansheng Ji
- Department of Gastroenterology, Affiliated Hospital of Weifang Medical University, Weifang, Shandong 261031, P.R. China
| |
Collapse
|
23
|
Temaj G, Saha S, Dragusha S, Ejupi V, Buttari B, Profumo E, Beqa L, Saso L. Ribosomopathies and cancer: pharmacological implications. Expert Rev Clin Pharmacol 2022; 15:729-746. [PMID: 35787725 DOI: 10.1080/17512433.2022.2098110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION The ribosome is a ribonucleoprotein organelle responsible for protein synthesis, and its biogenesis is a highly coordinated process that involves many macromolecular components. Any acquired or inherited impairment in ribosome biogenesis or ribosomopathies is associated with the development of different cancers and rare genetic diseases. Interference with multiple steps of protein synthesis has been shown to promote tumor cell death. AREAS COVERED We discuss the current insights about impaired ribosome biogenesis and their secondary consequences on protein synthesis, transcriptional and translational responses, proteotoxic stress, and other metabolic pathways associated with cancer and rare diseases. Studies investigating the modulation of different therapeutic chemical entities targeting cancer in in vitro and in vivo models have also been detailed. EXPERT OPINION Despite the association between inherited mutations affecting ribosome biogenesis and cancer biology, the development of therapeutics targeting the essential cellular machinery has only started to emerge. New chemical entities should be designed to modulate different checkpoints (translating oncoproteins, dysregulation of specific ribosome-assembly machinery, ribosomal stress, and rewiring ribosomal functions). Although safe and effective therapies are lacking, consideration should also be given to using existing drugs alone or in combination for long-term safety, with known risks for feasibility in clinical trials and synergistic effects.
Collapse
Affiliation(s)
| | - Sarmistha Saha
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | | | - Valon Ejupi
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Brigitta Buttari
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Elisabetta Profumo
- Department of Cardiovascular, Endocrine-metabolic Diseases, and Aging, Italian National Institute of Health, Rome, Italy
| | - Lule Beqa
- College UBT, Faculty of Pharmacy, Prishtina, Kosovo
| | - Luciano Saso
- Department of Physiology and Pharmacology "Vittorio Erspamer", Sapienza University of Rome, Italy
| |
Collapse
|
24
|
Cao X, Khitun A, Harold CM, Bryant CJ, Zheng SJ, Baserga SJ, Slavoff SA. Nascent alt-protein chemoproteomics reveals a pre-60S assembly checkpoint inhibitor. Nat Chem Biol 2022; 18:643-651. [PMID: 35393574 PMCID: PMC9423127 DOI: 10.1038/s41589-022-01003-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 02/25/2022] [Indexed: 12/29/2022]
Abstract
Many unannotated microproteins and alternative proteins (alt-proteins) are coencoded with canonical proteins, but few of their functions are known. Motivated by the hypothesis that alt-proteins undergoing regulated synthesis could play important cellular roles, we developed a chemoproteomic pipeline to identify nascent alt-proteins in human cells. We identified 22 actively translated alt-proteins or N-terminal extensions, one of which is post-transcriptionally upregulated by DNA damage stress. We further defined a nucleolar, cell-cycle-regulated alt-protein that negatively regulates assembly of the pre-60S ribosomal subunit (MINAS-60). Depletion of MINAS-60 increases the amount of cytoplasmic 60S ribosomal subunit, upregulating global protein synthesis and cell proliferation. Mechanistically, MINAS-60 represses the rate of late-stage pre-60S assembly and export to the cytoplasm. Together, these results implicate MINAS-60 as a potential checkpoint inhibitor of pre-60S assembly and demonstrate that chemoproteomics enables hypothesis generation for uncharacterized alt-proteins.
Collapse
Affiliation(s)
- Xiongwen Cao
- Department of Chemistry, Yale University, New Haven, CT, USA.,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Alexandra Khitun
- Department of Chemistry, Yale University, New Haven, CT, USA.,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Cecelia M Harold
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Carson J Bryant
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Shu-Jian Zheng
- Department of Chemistry, Yale University, New Haven, CT, USA.,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT, USA
| | - Sarah A Slavoff
- Department of Chemistry, Yale University, New Haven, CT, USA. .,Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA. .,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
| |
Collapse
|
25
|
Kumar AV, Kang T, Thakurta TG, Ng C, Rogers AN, Larsen MR, Lapierre LR. Exportin 1 modulates life span by regulating nucleolar dynamics via the autophagy protein LGG-1/GABARAP. SCIENCE ADVANCES 2022; 8:eabj1604. [PMID: 35363528 PMCID: PMC10938577 DOI: 10.1126/sciadv.abj1604] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 02/08/2022] [Indexed: 06/14/2023]
Abstract
Altered nucleolar and ribosomal dynamics are key hallmarks of aging, but their regulation remains unclear. Building on the knowledge that the conserved nuclear export receptor Exportin 1 (XPO-1/XPO1) modulates proteostasis and life span, we systematically analyzed the impact of nuclear export on protein metabolism. Using transcriptomic and subcellular proteomic analyses in nematodes, we demonstrate that XPO-1 modulates the nucleocytoplasmic distribution of key proteins involved in nucleolar dynamics and ribosome function, including fibrillarin (FIB-1/FBL) and RPL-11 (RPL11). Silencing xpo-1 led to marked reduction in global translation, which was accompanied by decreased nucleolar size and lower fibrillarin levels. A targeted screen of known proteostatic mediators revealed that the autophagy protein LGG-1/GABARAP modulates nucleolar size by regulating RPL-11 levels, linking specific protein degradation to ribosome metabolism. Together, our study reveals that nucleolar size and life span are regulated by LGG-1/GABARAP via ribosome protein surveillance.
Collapse
Affiliation(s)
- Anita V. Kumar
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA
| | - Taewook Kang
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Tara G. Thakurta
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA
| | - Celeste Ng
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA
| | - Aric N. Rogers
- MDI Biological Laboratory, 159 Old Bar Harbor Rd., Salisbury Cove, ME 04672, USA
| | - Martin R. Larsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Louis R. Lapierre
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 185 Meeting St., Providence, RI 02912, USA
| |
Collapse
|
26
|
Lin X, Zhou L, Zhong J, Zhong L, Zhang R, Kang T, Wu Y. RNA binding protein RBM28 can translocate from the nucleolus to the nucleoplasm to inhibit the transcriptional activity of p53. J Biol Chem 2021; 298:101524. [PMID: 34953860 PMCID: PMC8789582 DOI: 10.1016/j.jbc.2021.101524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 12/10/2021] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
RNA binding protein RBM28 (RBM28), as a nucleolar component of spliceosomal small nuclear ribonucleoproteins (snRNPs), is involved in the nucleolar stress response. Whether and how RBM28 regulates tumor progression remain unclear. Here, we report that RBM28 is frequently overexpressed in various types of cancer and that its upregulation is associated with a poor prognosis. Functional and mechanistic assays revealed that RBM28 promotes the survival and growth of cancer cells by interacting with the DNA binding domain of tumor suppressor p53 to inhibit p53 transcriptional activity. Upon treatment with chemotherapeutic drugs (e.g., adriamycin), RBM28 is translocated from the nucleolus to the nucleoplasm, which is likely mediated via phosphorylation of RBM28 at Ser122 by DNA checkpoint kinases 1 and 2 (Chk1/2), indicating that RBM28 may act as a nucleolar stress sensor in response to DNA damage stress. Our findings not only reveal RBM28 as a potential biomarker and therapeutic target for cancers, but also provide mechanistic insights into how cancer cells convert stress signals into a cellular response linking the nucleolus to regulation of the tumor suppressor p53.
Collapse
Affiliation(s)
- Xin Lin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Liwen Zhou
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jianliang Zhong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Li Zhong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China; Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518107, China
| | - Ruhua Zhang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Tiebang Kang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| | - Yuanzhong Wu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China.
| |
Collapse
|
27
|
Ribosomal stress induces 2-cell embryo-like state transition of the mouse ESCs through p53 activation. Biochem Biophys Res Commun 2021; 579:175-180. [PMID: 34607171 DOI: 10.1016/j.bbrc.2021.09.068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 09/26/2021] [Indexed: 12/31/2022]
Abstract
Embryonic stem cells (ESCs) maintain a pluripotent state and genome integrity in long-term culture. A rare population of ESCs showing 2-cell embryo-specific gene expression is believed to play critical roles in sustainable pluripotency and genome stability. However, the molecular mechanism controlling this transition to a 2-cell embryo-like (2CL) state remains unclear. We carried out screening to search for the factors involved in 2CL state induction and found a ribosomal RNA processing factor, Pum3 to be a candidate. Increased 2CL state population accompanied with an accumulation of pre-ribosomal RNA and activated p53 in the Pum3-KO ESC. Furthermore, the increase of 2CL state cells in the Pum3-KO ESCs was completely abrogated by the deletion of p53. The DNA damage induced by the Ultraviolet light (UV) irradiation and Zeocin promoted the transition to a 2CL state in a p53-dependent manner. Thus, our study provides new insights into a 2CL state transition mechanism through stress-dependent p53 activation of ESCs.
Collapse
|
28
|
Kachaev ZM, Ivashchenko SD, Kozlov EN, Lebedeva LA, Shidlovskii YV. Localization and Functional Roles of Components of the Translation Apparatus in the Eukaryotic Cell Nucleus. Cells 2021; 10:3239. [PMID: 34831461 PMCID: PMC8623629 DOI: 10.3390/cells10113239] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/15/2022] Open
Abstract
Components of the translation apparatus, including ribosomal proteins, have been found in cell nuclei in various organisms. Components of the translation apparatus are involved in various nuclear processes, particularly those associated with genome integrity control and the nuclear stages of gene expression, such as transcription, mRNA processing, and mRNA export. Components of the translation apparatus control intranuclear trafficking; the nuclear import and export of RNA and proteins; and regulate the activity, stability, and functional recruitment of nuclear proteins. The nuclear translocation of these components is often involved in the cell response to stimulation and stress, in addition to playing critical roles in oncogenesis and viral infection. Many components of the translation apparatus are moonlighting proteins, involved in integral cell stress response and coupling of gene expression subprocesses. Thus, this phenomenon represents a significant interest for both basic and applied molecular biology. Here, we provide an overview of the current data regarding the molecular functions of translation factors and ribosomal proteins in the cell nucleus.
Collapse
Affiliation(s)
- Zaur M. Kachaev
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
| | - Sergey D. Ivashchenko
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Eugene N. Kozlov
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Lyubov A. Lebedeva
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
| | - Yulii V. Shidlovskii
- Department of Gene Expression Regulation in Development, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia; (Z.M.K.); (S.D.I.); (E.N.K.); (L.A.L.)
- Center for Genetics and Life Science, Sirius University of Science and Technology, 354340 Sochi, Russia
- Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), 119992 Moscow, Russia
| |
Collapse
|
29
|
|
30
|
Lee J, Le LTHL, Kim E, Lee MJ. Formation of Non-Nucleoplasmic Proteasome Foci during the Late Stage of Hyperosmotic Stress. Cells 2021; 10:cells10092493. [PMID: 34572142 PMCID: PMC8467775 DOI: 10.3390/cells10092493] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 09/13/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Cellular stress induces the formation of membraneless protein condensates in both the nucleus and cytoplasm. The nucleocytoplasmic transport of proteins mainly occurs through nuclear pore complexes (NPCs), whose efficiency is affected by various stress conditions. Here, we report that hyperosmotic stress compartmentalizes nuclear 26S proteasomes into dense nuclear foci, independent of signaling cascades. Most of the proteasome foci were detected between the condensed chromatin mass and inner nuclear membrane. The proteasome-positive puncta were not colocalized with other types of nuclear bodies and were reversibly dispersed when cells were returned to the isotonic medium. The structural integrity of 26S proteasomes in the nucleus was slightly affected under the hyperosmotic condition. We also found that these insulator-body-like proteasome foci were possibly formed through disrupted nucleus-to-cytosol transport, which was mediated by the sequestration of NPC components into osmostress-responding stress granules. These data suggest that phase separation in both the nucleus and cytosol may be a major cell survival mechanism during hyperosmotic stress conditions.
Collapse
Affiliation(s)
- Jeeyoung Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Ly Thi Huong Luu Le
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Eunkyoung Kim
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
| | - Min Jae Lee
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea; (J.L.); (L.T.H.L.L.); (E.K.)
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Correspondence:
| |
Collapse
|
31
|
Loh D, Reiter RJ. Melatonin: Regulation of Biomolecular Condensates in Neurodegenerative Disorders. Antioxidants (Basel) 2021; 10:1483. [PMID: 34573116 PMCID: PMC8465482 DOI: 10.3390/antiox10091483] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/13/2021] [Indexed: 12/12/2022] Open
Abstract
Biomolecular condensates are membraneless organelles (MLOs) that form dynamic, chemically distinct subcellular compartments organizing macromolecules such as proteins, RNA, and DNA in unicellular prokaryotic bacteria and complex eukaryotic cells. Separated from surrounding environments, MLOs in the nucleoplasm, cytoplasm, and mitochondria assemble by liquid-liquid phase separation (LLPS) into transient, non-static, liquid-like droplets that regulate essential molecular functions. LLPS is primarily controlled by post-translational modifications (PTMs) that fine-tune the balance between attractive and repulsive charge states and/or binding motifs of proteins. Aberrant phase separation due to dysregulated membrane lipid rafts and/or PTMs, as well as the absence of adequate hydrotropic small molecules such as ATP, or the presence of specific RNA proteins can cause pathological protein aggregation in neurodegenerative disorders. Melatonin may exert a dominant influence over phase separation in biomolecular condensates by optimizing membrane and MLO interdependent reactions through stabilizing lipid raft domains, reducing line tension, and maintaining negative membrane curvature and fluidity. As a potent antioxidant, melatonin protects cardiolipin and other membrane lipids from peroxidation cascades, supporting protein trafficking, signaling, ion channel activities, and ATPase functionality during condensate coacervation or dissolution. Melatonin may even control condensate LLPS through PTM and balance mRNA- and RNA-binding protein composition by regulating N6-methyladenosine (m6A) modifications. There is currently a lack of pharmaceuticals targeting neurodegenerative disorders via the regulation of phase separation. The potential of melatonin in the modulation of biomolecular condensate in the attenuation of aberrant condensate aggregation in neurodegenerative disorders is discussed in this review.
Collapse
Affiliation(s)
- Doris Loh
- Independent Researcher, Marble Falls, TX 78654, USA
| | - Russel J. Reiter
- Department of Cellular and Structural Biology, UT Health Science Center, San Antonio, TX 78229, USA
| |
Collapse
|
32
|
Kang J, Brajanovski N, Chan KT, Xuan J, Pearson RB, Sanij E. Ribosomal proteins and human diseases: molecular mechanisms and targeted therapy. Signal Transduct Target Ther 2021; 6:323. [PMID: 34462428 PMCID: PMC8405630 DOI: 10.1038/s41392-021-00728-8] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 07/12/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Ribosome biogenesis and protein synthesis are fundamental rate-limiting steps for cell growth and proliferation. The ribosomal proteins (RPs), comprising the structural parts of the ribosome, are essential for ribosome assembly and function. In addition to their canonical ribosomal functions, multiple RPs have extra-ribosomal functions including activation of p53-dependent or p53-independent pathways in response to stress, resulting in cell cycle arrest and apoptosis. Defects in ribosome biogenesis, translation, and the functions of individual RPs, including mutations in RPs have been linked to a diverse range of human congenital disorders termed ribosomopathies. Ribosomopathies are characterized by tissue-specific phenotypic abnormalities and higher cancer risk later in life. Recent discoveries of somatic mutations in RPs in multiple tumor types reinforce the connections between ribosomal defects and cancer. In this article, we review the most recent advances in understanding the molecular consequences of RP mutations and ribosomal defects in ribosomopathies and cancer. We particularly discuss the molecular basis of the transition from hypo- to hyper-proliferation in ribosomopathies with elevated cancer risk, a paradox termed "Dameshek's riddle." Furthermore, we review the current treatments for ribosomopathies and prospective therapies targeting ribosomal defects. We also highlight recent advances in ribosome stress-based cancer therapeutics. Importantly, insights into the mechanisms of resistance to therapies targeting ribosome biogenesis bring new perspectives into the molecular basis of cancer susceptibility in ribosomopathies and new clinical implications for cancer therapy.
Collapse
Affiliation(s)
- Jian Kang
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Natalie Brajanovski
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia
| | - Keefe T. Chan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Jiachen Xuan
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia
| | - Richard B. Pearson
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1002.30000 0004 1936 7857Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, VIC Australia
| | - Elaine Sanij
- grid.1055.10000000403978434Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC Australia ,grid.1008.90000 0001 2179 088XDepartment of Clinical Pathology, University of Melbourne, Melbourne, VIC Australia ,grid.1073.50000 0004 0626 201XSt. Vincent’s Institute of Medical Research, Fitzroy, VIC Australia
| |
Collapse
|
33
|
Tsai YY, Su CH, Tarn WY. p53 Activation in Genetic Disorders: Different Routes to the Same Destination. Int J Mol Sci 2021; 22:9307. [PMID: 34502215 PMCID: PMC8430931 DOI: 10.3390/ijms22179307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 08/23/2021] [Accepted: 08/25/2021] [Indexed: 12/18/2022] Open
Abstract
The tumor suppressor p53 is critical for preventing neoplastic transformation and tumor progression. Inappropriate activation of p53, however, has been observed in a number of human inherited disorders that most often affect development of the brain, craniofacial region, limb skeleton, and hematopoietic system. Genes related to these developmental disorders are essentially involved in transcriptional regulation/chromatin remodeling, rRNA metabolism, DNA damage-repair pathways, telomere maintenance, and centrosome biogenesis. Perturbation of these activities or cellular processes may result in p53 accumulation in cell cultures, animal models, and perhaps humans as well. Mouse models of several p53 activation-associated disorders essentially recapitulate human traits, and inactivation of p53 in these models can alleviate disorder-related phenotypes. In the present review, we focus on how dysfunction of the aforementioned biological processes causes developmental defects via excessive p53 activation. Notably, several disease-related genes exert a pleiotropic effect on those cellular processes, which may modulate the magnitude of p53 activation and establish or disrupt regulatory loops. Finally, we discuss potential therapeutic strategies for genetic disorders associated with p53 misactivation.
Collapse
|
34
|
Xuan J, Gitareja K, Brajanovski N, Sanij E. Harnessing the Nucleolar DNA Damage Response in Cancer Therapy. Genes (Basel) 2021; 12:genes12081156. [PMID: 34440328 PMCID: PMC8393943 DOI: 10.3390/genes12081156] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/20/2021] [Accepted: 07/26/2021] [Indexed: 12/19/2022] Open
Abstract
The nucleoli are subdomains of the nucleus that form around actively transcribed ribosomal RNA (rRNA) genes. They serve as the site of rRNA synthesis and processing, and ribosome assembly. There are 400-600 copies of rRNA genes (rDNA) in human cells and their highly repetitive and transcribed nature poses a challenge for DNA repair and replication machineries. It is only in the last 7 years that the DNA damage response and processes of DNA repair at the rDNA repeats have been recognized to be unique and distinct from the classic response to DNA damage in the nucleoplasm. In the last decade, the nucleolus has also emerged as a central hub for coordinating responses to stress via sequestering tumor suppressors, DNA repair and cell cycle factors until they are required for their functional role in the nucleoplasm. In this review, we focus on features of the rDNA repeats that make them highly vulnerable to DNA damage and the mechanisms by which rDNA damage is repaired. We highlight the molecular consequences of rDNA damage including activation of the nucleolar DNA damage response, which is emerging as a unique response that can be exploited in anti-cancer therapy. In this review, we focus on CX-5461, a novel inhibitor of Pol I transcription that induces the nucleolar DNA damage response and is showing increasing promise in clinical investigations.
Collapse
Affiliation(s)
- Jiachen Xuan
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kezia Gitareja
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
| | - Natalie Brajanovski
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
| | - Elaine Sanij
- Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; (J.X.); (K.G.); (N.B.)
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC 3010, Australia
- Department of Clinical Pathology, University of Melbourne, Melbourne, VIC 3010, Australia
- St Vincent’s Institute of Medical Research, Fitzroy, VIC 3065, Australia
- Department of Medicine -St Vincent’s Hospital, University of Melbourne, Melbourne, VIC 3010, Australia
- Correspondence: ; Tel.: +61-3-8559-5279
| |
Collapse
|
35
|
Shi Y, Wang X, Zhu Q, Chen G. The Ribosomal Protein L28 Gene Induces Sorafenib Resistance in Hepatocellular Carcinoma. Front Oncol 2021; 11:685694. [PMID: 34307151 PMCID: PMC8299949 DOI: 10.3389/fonc.2021.685694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/15/2021] [Indexed: 11/17/2022] Open
Abstract
Background Sorafenib is the first molecular-targeted drug for the treatment of advanced hepatocellular carcinoma (HCC). However, its treatment efficiency decreases after a short period of time because of the development of drug resistance. This study investigates the role of key genes in regulating sorafenib-resistance and elucidates the mechanism of drug resistance in hepatocellular carcinoma. Methods The HCC HepG2 cells were used to generate a sorafenib-resistant cell model by culturing the cells in gradually increasing concentration of sorafenib. RNA microarray was applied to profile gene expression and screen key genes associated with sorafenib resistance. Specific targets were knockdown in sorafenib-resistant HepG2 cells for functional studies. The HCC model was established in ACI rats using Morris hepatoma3924A cells to validate selected genes associated with sorafenib resistance in vivo. Results The HepG2 sorafenib-resistant cell model was successfully established. The IC50 of sorafenib was 9.988μM in HepG2 sorafenib-resistant cells. A total of 35 up-regulated genes were detected by expression profile chip. High-content screening technology was used and a potential drug-resistance related gene RPL28 was filtered out. After knocking down RPL28 in HepG2 sorafenib-resistant cells, the results of cell proliferation and apoptosis illustrated that RPL28 is the key gene involving in drug resistance. Furthermore, it was found that both RNA and protein expression of RPL28 increased in HepG2 sorafenib-resistant specimens of Morris Hepatoma rats. In addition, the expression of proliferative protein Ki-67 increased in sorafenib-resistant cells. Conclusion Our study suggested that RPL28 is a key gene inducing sorafenib resistance in HCC and could be a potential target for the treatment of drug-resistant HCC.
Collapse
Affiliation(s)
- Yi Shi
- Departments of Molecular Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China.,The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Xiaojiang Wang
- Departments of Molecular Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China.,The School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Qiong Zhu
- Departments of Molecular Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| | - Gang Chen
- Departments of Molecular Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China.,Departments of Pathology, Fujian Cancer Hospital, Fujian Medical University Cancer Hospital, Fuzhou, China
| |
Collapse
|
36
|
Role of Dietary Antioxidants in p53-Mediated Cancer Chemoprevention and Tumor Suppression. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:9924328. [PMID: 34257824 PMCID: PMC8257365 DOI: 10.1155/2021/9924328] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/31/2021] [Indexed: 02/07/2023]
Abstract
Cancer arises through a complex interplay between genetic, behavioral, metabolic, and environmental factors that combined trigger cellular changes that over time promote malignancy. In terms of cancer prevention, behavioral interventions such as diet can promote genetic programs that may facilitate tumor suppression; and one of the key tumor suppressors responsible for initiating such programs is p53. The p53 protein is activated by various cellular events such as DNA damage, hypoxia, heat shock, and overexpression of oncogenes. Due to its role in cell fate decisions after DNA damage, regulatory pathways controlled by p53 help to maintain genome stability and thus “guard the genome” against mutations that cause cancer. Dietary intake of flavonoids, a C15 group of polyphenols, is known to inhibit cancer progression and assist DNA repair through p53-mediated mechanisms in human cells via their antioxidant activities. For example, quercetin arrests human cervical cancer cell growth by blocking the G2/M phase cell cycle and inducing mitochondrial apoptosis through a p53-dependent mechanism. Other polyphenols such as resveratrol upregulate p53 expression in several cancer cell lines by promoting p53 stability, which in colon cancer cells results in the activation of p53-mediated apoptosis. Finally, among vitamins, folic acid seems to play an important role in the chemoprevention of gastric carcinogenesis by enhancing gastric epithelial apoptosis in patients with premalignant lesions by significantly increased expression of p53. In this review, we discuss the role of these and other dietary antioxidants in p53-mediated cell signaling in relation to cancer chemoprevention and tumor suppression in normal and cancer cells.
Collapse
|
37
|
Wang H, Zhao J, Yang J, Wan S, Fu Y, Wang X, Zhou T, Zhang Z, Shen J. PICT1 is critical for regulating the Rps27a-Mdm2-p53 pathway by microtubule polymerization inhibitor against cervical cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119084. [PMID: 34166715 DOI: 10.1016/j.bbamcr.2021.119084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/28/2021] [Accepted: 06/17/2021] [Indexed: 01/05/2023]
Abstract
In our previous study, it showed that P-3F, a podophyllotoxin derivative, causes the increased level of p53 expression by enhancing p53 stability, resulting from blockage of the Mdm2-p53 feedback loop via nucleolus-to-nucleoplasm translocation of Rps27a in human cervical cancer HeLa cell line. However, the mechanism of regulating Rps27a localization remains to be studied. In the current study, it has been demonstrated that the level of protein interacting with carboxyl terminus 1 (PICT1), originally identified as a tumor suppressor, was decreased in a concentration-dependent manner in response to P-3F, leading to inhibition of human cervical cancer cell lines proliferation. Also remarkably, reduction of serine phosphorylation of STMN1 at position 16 induced by P-3F was required in the downregulation of PICT1, in which p53 activity was likely to be directly involved. Note as well that, PICT1 also played an important role in p53 stability enhancement by inhibiting Mdm2-mediated p53 ubiquitination due to Rps27a translocation from the nucleolus to the nucleoplasm to interact with Mdm2 following treatment with P-3F. Collectively, these findings indicated that P-3F, a microtubule polymerization inhibitor, promotes the decreased level of PICT1 expression, which is critical for regulating the Rps27a-Mdm2-p53 pathway against cervical cancer.
Collapse
Affiliation(s)
- Huai Wang
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Junjie Zhao
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Jian Yang
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Shukun Wan
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Yihong Fu
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Xinlu Wang
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Tong Zhou
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Zhongwei Zhang
- School of Public Health, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China; Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, 461 Ba Yi Avenue, Nanchang, Jiangxi 330006, PR China
| | - Jiaomei Shen
- Department of Gynecology, Wuhan Fifth Hospital, 122 Xian Zheng Street, Wuhan, Hubei 430050, PR China.
| |
Collapse
|
38
|
Suzuki T, Katada E, Mizuoka Y, Takagi S, Kazuki Y, Oshimura M, Shindo M, Hara T. A novel all-in-one conditional knockout system uncovered an essential role of DDX1 in ribosomal RNA processing. Nucleic Acids Res 2021; 49:e40. [PMID: 33503245 PMCID: PMC8053084 DOI: 10.1093/nar/gkaa1296] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/09/2020] [Accepted: 01/04/2021] [Indexed: 11/13/2022] Open
Abstract
Generation of conditional knockout (cKO) and various gene-modified cells is laborious and time-consuming. Here, we established an all-in-one cKO system, which enables highly efficient generation of cKO cells and simultaneous gene modifications, including epitope tagging and reporter gene knock-in. We applied this system to mouse embryonic stem cells (ESCs) and generated RNA helicase Ddx1 cKO ESCs. The targeted cells displayed endogenous promoter-driven EGFP and FLAG-tagged DDX1 expression, and they were converted to Ddx1 KO via FLP recombinase. We further established TetFE ESCs, which carried a reverse tetracycline transactivator (rtTA) expression cassette and a tetracycline response element (TRE)-regulated FLPERT2 cassette in the Gt(ROSA26)Sor locus for instant and tightly regulated induction of gene KO. By utilizing TetFE Ddx1F/F ESCs, we isolated highly pure Ddx1F/F and Ddx1−/− ESCs and found that loss of Ddx1 caused rRNA processing defects, thereby activating the ribosome stress–p53 pathway. We also demonstrated cKO of various genes in ESCs and homologous recombination-non-proficient human HT1080 cells. The frequency of cKO clones was remarkably high for both cell types and reached up to 96% when EGFP-positive clones were analyzed. This all-in-one cKO system will be a powerful tool for rapid and precise analyses of gene functions.
Collapse
Affiliation(s)
- Teruhiko Suzuki
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Eiji Katada
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yuki Mizuoka
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Satoko Takagi
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishicho, Yonago 683-8503, Japan.,Division of Genome and Cellular Functions, Department of Molecular and Cellular Biology, School of Life Science, Faculty of Medicine, Tottori University, Yonago 683-8503, Japan
| | - Mitsuo Oshimura
- Chromosome Engineering Research Center (CERC), Tottori University, 86 Nishicho, Yonago 683-8503, Japan
| | - Mayumi Shindo
- Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan
| | - Takahiko Hara
- Stem Cell Project, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 156-8506, Japan.,Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.,Graduate School of Science, Department of Biological Science, Tokyo Metropolitan University, 1-1 Minami-Osawa, Hachioji-shi, Tokyo 192-0397, Japan
| |
Collapse
|
39
|
Bury M, Le Calvé B, Ferbeyre G, Blank V, Lessard F. New Insights into CDK Regulators: Novel Opportunities for Cancer Therapy. Trends Cell Biol 2021; 31:331-344. [PMID: 33676803 DOI: 10.1016/j.tcb.2021.01.010] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 12/13/2022]
Abstract
Cyclins and their catalytic partners, the cyclin-dependent kinases (CDKs), control the transition between different phases of the cell cycle. CDK/cyclin activity is regulated by CDK inhibitors (CKIs), currently comprising the CDK-interacting protein/kinase inhibitory protein (CIP/KIP) family and the inhibitor of kinase (INK) family. Recent studies have identified a third group of CKIs, called ribosomal protein-inhibiting CDKs (RPICs). RPICs were discovered in the context of cellular senescence, a stable cell cycle arrest with tumor-suppressing abilities. RPICs accumulate in the nonribosomal fraction of senescent cells due to a decrease in rRNA biogenesis. Accordingly, RPICs are often downregulated in human cancers together with other ribosomal proteins, the tumor-suppressor functions of which are still under study. In this review, we discuss unique therapies that have been developed to target CDK activity in the context of cancer treatment or senescence-associated pathologies, providing novel tools for precision medicine.
Collapse
Affiliation(s)
- Marina Bury
- De Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | | | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada.
| | - Volker Blank
- Lady Davis Institute for Medical Research, Departments of Medicine and Physiology, McGill University, Montreal, QC, H3T 1E2, Canada.
| | - Frédéric Lessard
- Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada.
| |
Collapse
|
40
|
Li Q, Mao F, Zhou B, Huang Y, Zou Z, denDekker AD, Xu J, Hou S, Liu J, Dou Y, Rao RC. p53 Integrates Temporal WDR5 Inputs during Neuroectoderm and Mesoderm Differentiation of Mouse Embryonic Stem Cells. Cell Rep 2021; 30:465-480.e6. [PMID: 31940490 PMCID: PMC7024586 DOI: 10.1016/j.celrep.2019.12.039] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 11/11/2019] [Accepted: 12/12/2019] [Indexed: 01/09/2023] Open
Abstract
How ubiquitous transcription factors (TFs) coordinate temporal inputs from broadly expressed epigenetic factors to control cell fate remains poorly understood. Here, we uncover a molecular relationship between p53, an abundant embryonic TF, and WDR5, an essential member of the MLL chromatin modifying complex, that regulates mouse embryonic stem cell fate. Wild-type Wdr5 or transient Wdr5 knockout promotes a distinct pattern of global chromatin accessibility and spurs neuroectodermal differentiation through an RbBP5-dependent process in which WDR5 binds to, and activates transcription of, neural genes. Wdr5 rescue after its prolonged inhibition targets WDR5 to mesoderm lineage-specifying genes, stimulating differentiation toward mesoderm fates in a p53-dependent fashion. Finally, we identify a direct interaction between WDR5 and p53 that enables their co-recruitment to, and regulation of, genes known to control cell proliferation and fate. Our results unmask p53-dependent mechanisms that temporally integrate epigenetic WDR5 inputs to drive neuroectoderm and mesoderm differentiation from pluripotent cells. How ubiquitous chromatin-associated proteins and transcription factors (TFs) regulate cell fate determination is poorly understood. Li et al. show that regulation of the broadly expressed TF p53 by the chromatin-associated protein WDR5 is required for neuroectoderm versus mesoderm lineage determination in mouse embryonic stem cells (ESCs).
Collapse
Affiliation(s)
- Qiang Li
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Fengbiao Mao
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Bo Zhou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yuanhao Huang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Zhenhua Zou
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jing Xu
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Sean Hou
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI, USA
| | - Jie Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Yali Dou
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Rajesh C Rao
- Department of Ophthalmology & Visual Sciences, University of Michigan, Ann Arbor, MI, USA; Department of Pathology, University of Michigan, Ann Arbor, MI, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI, USA; Taubman Institute, University of Michigan, Ann Arbor, MI, USA; Section of Ophthalmology, Surgical Service, Veterans Administration Ann Arbor Healthcare System, Ann Arbor, MI, USA.
| |
Collapse
|
41
|
Reza AMMT, Yuan YG. microRNAs Mediated Regulation of the Ribosomal Proteins and its Consequences on the Global Translation of Proteins. Cells 2021; 10:110. [PMID: 33435549 PMCID: PMC7827472 DOI: 10.3390/cells10010110] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/14/2020] [Indexed: 12/23/2022] Open
Abstract
Ribosomal proteins (RPs) are mostly derived from the energy-consuming enzyme families such as ATP-dependent RNA helicases, AAA-ATPases, GTPases and kinases, and are important structural components of the ribosome, which is a supramolecular ribonucleoprotein complex, composed of Ribosomal RNA (rRNA) and RPs, coordinates the translation and synthesis of proteins with the help of transfer RNA (tRNA) and other factors. Not all RPs are indispensable; in other words, the ribosome could be functional and could continue the translation of proteins instead of lacking in some of the RPs. However, the lack of many RPs could result in severe defects in the biogenesis of ribosomes, which could directly influence the overall translation processes and global expression of the proteins leading to the emergence of different diseases including cancer. While microRNAs (miRNAs) are small non-coding RNAs and one of the potent regulators of the post-transcriptional gene expression, miRNAs regulate gene expression by targeting the 3' untranslated region and/or coding region of the messenger RNAs (mRNAs), and by interacting with the 5' untranslated region, and eventually finetune the expression of approximately one-third of all mammalian genes. Herein, we highlighted the significance of miRNAs mediated regulation of RPs coding mRNAs in the global protein translation.
Collapse
Affiliation(s)
- Abu Musa Md Talimur Reza
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Yu-Guo Yuan
- Jiangsu Co-Innovation Center of Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| |
Collapse
|
42
|
Kyritsis KA, Ouzounis CA, Angelis L, Vizirianakis I. Sequence variation, common tissue expression patterns and learning models: a genome-wide survey of vertebrate ribosomal proteins. NAR Genom Bioinform 2020; 2:lqaa088. [PMID: 33575632 PMCID: PMC7671327 DOI: 10.1093/nargab/lqaa088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/07/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Ribosomal genes produce the constituents of the ribosome, one of the most conserved subcellular structures of all cells, from bacteria to eukaryotes, including animals. There are notions that some protein-coding ribosomal genes vary in their roles across species, particularly vertebrates, through the involvement of some in a number of genetic diseases. Based on extensive sequence comparisons and systematic curation, we establish a reference set for ribosomal proteins (RPs) in eleven vertebrate species and quantify their sequence conservation levels. Moreover, we correlate their coordinated gene expression patterns within up to 33 tissues and assess the exceptional role of paralogs in tissue specificity. Importantly, our analysis supported by the development and use of machine learning models strongly proposes that the variation in the observed tissue-specific gene expression of RPs is rather species-related and not due to tissue-based evolutionary processes. The data obtained suggest that RPs exhibit a complex relationship between their structure and function that broadly maintains a consistent expression landscape across tissues, while most of the variation arises from species idiosyncrasies. The latter may be due to evolutionary change and adaptation, rather than functional constraints at the tissue level throughout the vertebrate lineage.
Collapse
Affiliation(s)
- Konstantinos A Kyritsis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, GR-54124 Thessalonica, Greece
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, GR-57001 Thessalonica, Greece
| | - Christos A Ouzounis
- Biological Computation & Process Laboratory, Chemical Process & Energy Resources Institute, Centre for Research & Technology Hellas, GR-57001 Thessalonica, Greece
- Department of Informatics, Aristotle University of Thessaloniki, GR-54124 Thessalonica, Greece
| | - Lefteris Angelis
- Department of Informatics, Aristotle University of Thessaloniki, GR-54124 Thessalonica, Greece
| | - Ioannis S Vizirianakis
- Laboratory of Pharmacology, School of Pharmacy, Aristotle University of Thessaloniki, GR-54124 Thessalonica, Greece
- FunPATH (Functional Proteomics and Systems Biology Research Group at AUTH) Research Group, KEDEK—Aristotle University of Thessaloniki, Balkan Center, GR-57001 Thessalonica, Greece
- Department of Life and Health Sciences, University of Nicosia, CY-1700 Nicosia, Cyprus
| |
Collapse
|
43
|
Han XR, Sasaki N, Jackson SC, Wang P, Li Z, Smith MD, Xie L, Chen X, Zhang Y, Marzluff WF, Xiong Y. CRL4 DCAF1/VprBP E3 ubiquitin ligase controls ribosome biogenesis, cell proliferation, and development. SCIENCE ADVANCES 2020; 6:6/51/eabd6078. [PMID: 33355139 DOI: 10.1126/sciadv.abd6078] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/27/2020] [Indexed: 06/12/2023]
Abstract
Evolutionarily conserved DCAF1 is a major substrate receptor for the DDB1-CUL4-ROC1 E3 ubiquitin ligase (CRL4) and controls cell proliferation and development. The molecular basis for these functions is unclear. We show here that DCAF1 loss in multiple tissues and organs selectively eliminates proliferating cells and causes perinatal lethality, thymic atrophy, and bone marrow defect. Inducible DCAF1 loss eliminates proliferating, but not quiescent, T cells and MEFs. We identify the ribosome assembly factor PWP1 as a substrate of the CRL4DCAF1 ligase. DCAF1 loss results in PWP1 accumulation, impairing rRNA processing and ribosome biogenesis. Knockdown or overexpression of PWP1 can rescue defects or cause similar defects as DCAF1 loss, respectively, in ribosome biogenesis. DCAF1 loss increases free RPL11, resulting in L11-MDM2 association and p53 activation. Cumulatively, these results reveal a critical function for DCAF1 in ribosome biogenesis and define a molecular basis of DCAF1 function in cell proliferation and development.
Collapse
Affiliation(s)
- Xiao-Ran Han
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Naoya Sasaki
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sarah C Jackson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Pu Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Zhijun Li
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Matthew D Smith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ling Xie
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Xian Chen
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yanping Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William F Marzluff
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| |
Collapse
|
44
|
Babaylova ES, Kolobova AV, Gopanenko AV, Tupikin AE, Kabilov MR, Malygin AA, Karpova GG. The human ribosomal protein eL29 binds in vivo to the cognate mRNA by interacting with its coding sequence, as revealed from in-cell cross-linking data. Biochimie 2020; 177:68-77. [DOI: 10.1016/j.biochi.2020.07.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 01/21/2023]
|
45
|
Johnson AG, Flynn RA, Lapointe CP, Ooi YS, Zhao ML, Richards CM, Qiao W, Yamada SB, Couthouis J, Gitler AD, Carette JE, Puglisi JD. A memory of eS25 loss drives resistance phenotypes. Nucleic Acids Res 2020; 48:7279-7297. [PMID: 32463448 PMCID: PMC7367175 DOI: 10.1093/nar/gkaa444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/11/2020] [Accepted: 05/24/2020] [Indexed: 12/26/2022] Open
Abstract
In order to maintain cellular protein homeostasis, ribosomes are safeguarded against dysregulation by myriad processes. Remarkably, many cell types can withstand genetic lesions of certain ribosomal protein genes, some of which are linked to diverse cellular phenotypes and human disease. Yet the direct and indirect consequences from these lesions are poorly understood. To address this knowledge gap, we studied in vitro and cellular consequences that follow genetic knockout of the ribosomal proteins RPS25 or RACK1 in a human cell line, as both proteins are implicated in direct translational control. Prompted by the unexpected detection of an off-target ribosome alteration in the RPS25 knockout, we closely interrogated cellular phenotypes. We found that multiple RPS25 knockout clones display viral- and toxin-resistance phenotypes that cannot be rescued by functional cDNA expression, suggesting that RPS25 loss elicits a cell state transition. We characterized this state and found that it underlies pleiotropic phenotypes and has a common rewiring of gene expression. Rescuing RPS25 expression by genomic locus repair failed to correct for the phenotypic and expression hysteresis. Our findings illustrate how the elasticity of cells to a ribosome perturbation can drive specific phenotypic outcomes that are indirectly linked to translation and suggests caution in the interpretation of ribosomal protein gene mutation data.
Collapse
Affiliation(s)
- Alex G Johnson
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA.,Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Yaw Shin Ooi
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Michael L Zhao
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | - Wenjie Qiao
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Shizuka B Yamada
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Julien Couthouis
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Aaron D Gitler
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Jan E Carette
- Department of Microbiology & Immunology, Stanford University, Stanford, CA 94305, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
46
|
Li H, Zhang H, Huang G, Dou Z, Xie Y, Si J, Di C. Heavy ion radiation-induced DNA damage mediates apoptosis via the Rpl27a-Rpl5-MDM2-p53/E2F1 signaling pathway in mouse spermatogonia. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 201:110831. [PMID: 32535367 DOI: 10.1016/j.ecoenv.2020.110831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
The risk of exposure to ionizing radiation (IR) environments has increased with the development of nuclear technology. IR exposure induces excessive apoptosis of the spermatogonia, which leads to male infertility. Spermatogonia apoptosis may be involved in ribosomal stress triggered by DNA damage following exposure to IR because ribosomal proteins (RPs) directly interact with mouse double minute 2 homolog (MDM2) to induce apoptosis. This study aimed to use comparative proteomics and transcriptomics approach to screen the differential RPs and ribosomal mRNAs in mouse testes following high linear energy transfer (LET) carbon ion radiation (CIR). The expression of ribosomal large subunit protein 27a (Rpl27a) decreased at both protein and mRNA levels in the spermatogonia in vivo. After 6 h of CIR, the immunofluorescence signal of 8-oxo-dG and phosphorylated ataxia-telangiectasia-mutated protein (ATM)/histone H2Ax increased, but that of Rpl27a decreased in the spermatogonia of p53 wild-type and knockout mouse testes. Moreover, the nucleolin was scattered throughout the nucleoplasm after CIR. These results suggested that CIR-induced DNA damage might trigger ribosomal stress, and the reduction in the expression of Rpl27a was associated with DNA damage in the spermatogonia. Similarly, in vitro, the immunofluorescence signal of 8-oxo-dG increased in the GC-1 cells after CIR. Moreover, the expression of Rpl27a was regulated by DNA damage because the co-transfection of ATM and Rpl27a or inhibition of ATM-treated CIR could restore the expression of Rpl27a. Furthermore, the reduction in the expression of Rpl27a led to weakened binding of E2F transcription factor 1 (E2F1) and p53 to MDM2, causing p53 activation and E2F1 degradation in p53 wild-type and knockdown GC-1 cells. This study proposed that heavy ion radiation-induced DNA damage mediated spermatogonia apoptosis via the Rpl27a-Rpl5-MDM2-p53/E2F1 signaling pathway. The results provided the underlying molecular mechanisms of spermatogonia apoptosis following exposure to high LET radiation.
Collapse
Affiliation(s)
- Hongyan Li
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Lanzhou, 730000, China; School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Hong Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Lanzhou, 730000, China; School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China.
| | - Guomin Huang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Lanzhou, 730000, China; School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Zhihui Dou
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Lanzhou, 730000, China; School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yi Xie
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Lanzhou, 730000, China; School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Jing Si
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Lanzhou, 730000, China; School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Cuixia Di
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China; Key Laboratory of Basic Research on Heavy Ion Radiation Application in Medicine, Lanzhou, 730000, China; School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 100039, China
| |
Collapse
|
47
|
Oyarbide U, Shah AN, Amaya-Mejia W, Snyderman M, Kell MJ, Allende DS, Calo E, Topczewski J, Corey SJ. Loss of Sbds in zebrafish leads to neutropenia and pancreas and liver atrophy. JCI Insight 2020; 5:134309. [PMID: 32759502 PMCID: PMC7526460 DOI: 10.1172/jci.insight.134309] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/29/2020] [Indexed: 01/29/2023] Open
Abstract
Shwachman-Diamond syndrome (SDS) is characterized by exocrine pancreatic insufficiency, neutropenia, and skeletal abnormalities. Biallelic mutations in SBDS, which encodes a ribosome maturation factor, are found in 90% of SDS cases. Sbds–/– mice are embryonic lethal. Using CRISPR/Cas9 editing, we created sbds-deficient zebrafish strains. Sbds protein levels progressively decreased and became undetectable at 10 days postfertilization (dpf). Polysome analysis revealed decreased 80S ribosomes. Homozygous mutant fish developed normally until 15 dpf. Mutant fish subsequently had stunted growth and showed signs of atrophy in pancreas, liver, and intestine. In addition, neutropenia occurred by 5 dpf. Upregulation of tp53 mRNA did not occur until 10 dpf, and inhibition of proliferation correlated with death by 21 dpf. Transcriptome analysis showed tp53 activation through upregulation of genes involved in cell cycle arrest, cdkn1a and ccng1, and apoptosis, puma and mdm2. However, elimination of Tp53 function did not prevent lethality. Because of growth retardation and atrophy of intestinal epithelia, we studied the effects of starvation on WT fish. Starved WT fish showed intestinal atrophy, zymogen granule loss, and tp53 upregulation — similar to the mutant phenotype. In addition, there was reduction in neutral lipid storage and ribosomal protein amount, similar to the mutant phenotype. Thus, loss of Sbds in zebrafish phenocopies much of the human disease and is associated with growth arrest and tissue atrophy, particularly of the gastrointestinal system, at the larval stage. A variety of stress responses, some associated with Tp53, contribute to pathophysiology of SDS. Loss of ribosome maturation factor sbds in the zebrafish phenocopies human Shwachman-Diamond syndrome and is associated with p53 activation, but lethality cannot be rescued by p53 mutation.
Collapse
Affiliation(s)
- Usua Oyarbide
- Departments of Pediatrics, Immunology, and Human and Molecular Genetics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, Virginia, USA.,Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA.,Departments of Pediatrics, Cancer Biology, and Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA
| | - Arish N Shah
- Department of Biology and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Wilmer Amaya-Mejia
- Departments of Pediatrics, Immunology, and Human and Molecular Genetics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, Virginia, USA
| | - Matthew Snyderman
- Departments of Pediatrics, Cancer Biology, and Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA
| | - Margaret J Kell
- Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA
| | | | - Eliezer Calo
- Department of Biology and David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jacek Topczewski
- Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA.,Department of Biochemistry and Molecular Biology, Medical University of Lublin, Lublin, Poland
| | - Seth J Corey
- Departments of Pediatrics, Immunology, and Human and Molecular Genetics, Children's Hospital of Richmond and Massey Cancer Center at Virginia Commonwealth University, Richmond, Virginia, USA.,Department of Pediatrics, Stanley Manne Children's Research Institute, Northwestern University School of Medicine, Chicago, Illinois, USA.,Departments of Pediatrics, Cancer Biology, and Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, Ohio, USA
| |
Collapse
|
48
|
Kaiser RWJ, Erber J, Höpker K, Fabretti F, Müller RU. AATF/Che-1-An RNA Binding Protein at the Nexus of DNA Damage Response and Ribosome Biogenesis. Front Oncol 2020; 10:919. [PMID: 32587828 PMCID: PMC7298124 DOI: 10.3389/fonc.2020.00919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/11/2020] [Indexed: 01/14/2023] Open
Abstract
The DNA damage response (DDR) is a complex signaling network that is activated upon genotoxic stress. It determines cellular fate by either activating cell cycle arrest or initiating apoptosis and thereby ensures genomic stability. The Apoptosis Antagonizing Transcription Factor (AATF/Che-1), an RNA polymerase II-interacting transcription factor and known downstream target of major DDR kinases, affects DDR signaling by inhibiting p53-mediated transcription of pro-apoptotic genes and promoting cell cycle arrest through various pathways instead. Specifically, AATF was shown to inhibit p53 expression at the transcriptional level and repress its pro-apoptotic activity by direct binding to p53 protein and transactivation of anti-apoptotic genes. Solid and hematological tumors of various organs exploit this function by overexpressing AATF. Both copy number gains and high expression levels of AATF were associated with worse prognosis or relapse of malignant tumors. Recently, a number of studies have enabled insights into the molecular mechanisms by which AATF affects both DDR and proliferation. AATF was found to directly localize to sites of DNA damage upon laser ablation and interact with DNA repair proteins. In addition, depletion of AATF resulted in increased DNA damage and decrease of both proliferative activity and genotoxic tolerance. Interestingly, considering the role of ribosomal stress in the regulation of p53, more recent work established AATF as ribosomal RNA binding protein and enabled insights into its role as an important factor for rRNA processing and ribosome biogenesis. This Mini Review summarizes recent findings on AATF and its important role in the DDR, malignancy, and ribosome biogenesis.
Collapse
Affiliation(s)
- Rainer W J Kaiser
- Medizinische Klinik und Poliklinik I, University Hospital Ludwig-Maximilian-University Munich, Munich, Germany.,Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Johanna Erber
- Department I of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.,Department of Medicine II, School of Medicine, Technical University of Munich, University Hospital Rechts der Isar, Munich, Germany
| | - Katja Höpker
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Francesca Fabretti
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Roman-Ulrich Müller
- Department II of Internal Medicine and Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital of Cologne, University of Cologne, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,Systems Biology of Ageing Cologne, University of Cologne, Cologne, Germany
| |
Collapse
|
49
|
Destefanis F, Manara V, Bellosta P. Myc as a Regulator of Ribosome Biogenesis and Cell Competition: A Link to Cancer. Int J Mol Sci 2020; 21:ijms21114037. [PMID: 32516899 PMCID: PMC7312820 DOI: 10.3390/ijms21114037] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/02/2020] [Accepted: 06/03/2020] [Indexed: 12/14/2022] Open
Abstract
The biogenesis of ribosomes is a finely regulated multistep process linked to cell proliferation and growth-processes which require a high rate of protein synthesis. One of the master regulators of ribosome biogenesis is Myc, a well-known proto-oncogene that has an important role in ribosomal function and in the regulation of protein synthesis. The relationship between Myc and the ribosomes was first highlighted in Drosophila, where Myc's role in controlling Pol-I, II and III was evidenced by both microarrays data, and by the ability of Myc to control growth (mass), and cellular and animal size. Moreover, Myc can induce cell competition, a physiological mechanism through which cells with greater fitness grow better and thereby prevail over less competitive cells, which are actively eliminated by apoptosis. Myc-induced cell competition was shown to regulate both vertebrate development and tumor promotion; however, how these functions are linked to Myc's control of ribosome biogenesis, protein synthesis and growth is not clear yet. In this review, we will discuss the major pathways that link Myc to ribosomal biogenesis, also in light of its function in cell competition, and how these mechanisms may reflect its role in favoring tumor promotion.
Collapse
Affiliation(s)
- Francesca Destefanis
- Department of Cellular, Computational and Integrative Biology (CiBio), University of Trento, 38123 Trento, Italy; (F.D.); (V.M.)
| | - Valeria Manara
- Department of Cellular, Computational and Integrative Biology (CiBio), University of Trento, 38123 Trento, Italy; (F.D.); (V.M.)
| | - Paola Bellosta
- Department of Cellular, Computational and Integrative Biology (CiBio), University of Trento, 38123 Trento, Italy; (F.D.); (V.M.)
- Department of Medicine, NYU Langone Medical Center, New York, NY 10016, USA
- Correspondence: ; Tel.: +39-0461-283070
| |
Collapse
|
50
|
Managing Hyperosmotic Stress through Phase Separation. Trends Biochem Sci 2020; 45:721-723. [PMID: 32446814 DOI: 10.1016/j.tibs.2020.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/08/2020] [Accepted: 05/09/2020] [Indexed: 11/22/2022]
Abstract
In a recent study, Yasuda et al. show how liquid-liquid phase separation (LLPS) under hyperosmotic stress conditions allows cells to react to ubiquitinated proteins and to assemble nuclear, liquid compartments that recruit proteasomes and result in aggregate clearance.
Collapse
|