1
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Le Boulch M, Jacquet E, Nhiri N, Shmulevitz M, Jaïs PH. Rational design of an artificial tethered enzyme for non-templated post-transcriptional mRNA polyadenylation by the second generation of the C3P3 system. Sci Rep 2024; 14:5156. [PMID: 38431749 PMCID: PMC10908868 DOI: 10.1038/s41598-024-55947-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 02/29/2024] [Indexed: 03/05/2024] Open
Abstract
We have previously introduced the first generation of C3P3, an artificial system that allows the autonomous in-vivo production of mRNA with m7GpppN-cap. While C3P3-G1 synthesized much larger amounts of capped mRNA in human cells than conventional nuclear expression systems, it produced a proportionately much smaller amount of the corresponding proteins, indicating a clear defect of mRNA translatability. A possible mechanism for this poor translatability could be the rudimentary polyadenylation of the mRNA produced by the C3P3-G1 system. We therefore sought to develop the C3P3-G2 system using an artificial enzyme to post-transcriptionally lengthen the poly(A) tail. This system is based on the mutant mouse poly(A) polymerase alpha fused at its N terminus with an N peptide from the λ virus, which binds to BoxBr sequences placed in the 3'UTR region of the mRNA of interest. The resulting system selectively brings mPAPαm7 to the target mRNA to elongate its poly(A)-tail to a length of few hundred adenosine. Such elongation of the poly(A) tail leads to an increase in protein expression levels of about 2.5-3 times in cultured human cells compared to the C3P3-G1 system. Finally, the coding sequence of the tethered mutant poly(A) polymerase can be efficiently fused to that of the C3P3-G1 enzyme via an F2A sequence, thus constituting the single-ORF C3P3-G2 enzyme. These technical developments constitute an important milestone in improving the performance of the C3P3 system, paving the way for its applications in bioproduction and non-viral human gene therapy.
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Affiliation(s)
- Marine Le Boulch
- Eukarÿs SAS, Pépinière Genopole, 4 rue Pierre Fontaine, Genopole Entreprises Campus 3, 4 Rue Pierre Fontaine, 91000, Evry-Courcouronnes, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-Sur-Yvette, France
| | - Naïma Nhiri
- Institut de Chimie des Substances Naturelles, CNRS UPR2301, Université Paris-Saclay, Avenue de la Terrasse, 91198, Gif-Sur-Yvette, France
| | - Maya Shmulevitz
- Medical Microbiology and Immunology, Li Ka Shing Institute of Virology, University of Alberta, 6-142J Katz Group Centre for Pharmacy and Health Research, 114 Street NW, Edmonton, AB, T6G 2E1, Canada
| | - Philippe H Jaïs
- Eukarÿs SAS, Pépinière Genopole, 4 rue Pierre Fontaine, Genopole Entreprises Campus 3, 4 Rue Pierre Fontaine, 91000, Evry-Courcouronnes, France.
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2
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Vlasova VV, Shmagel KV. T Lymphocyte Metabolic Features and Techniques to Modulate Them. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1857-1873. [PMID: 38105204 DOI: 10.1134/s0006297923110159] [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: 04/28/2023] [Revised: 07/21/2023] [Accepted: 08/27/2023] [Indexed: 12/19/2023]
Abstract
T cells demonstrate high degree of complexity and broad range of functions, which distinguish them from other immune cells. Throughout their lifetime, T lymphocytes experience several functional states: quiescence, activation, proliferation, differentiation, performance of effector and regulatory functions, memory formation, and apoptosis. Metabolism supports all functions of T cells, providing lymphocytes with energy, biosynthetic substrates, and signaling molecules. Therefore, T cells usually restructure their metabolism as they transition from one functional state to another. Strong association between the metabolism and T cell functions implies that the immune response can be controlled by manipulating metabolic processes within T lymphocytes. This review aims to highlight the main metabolic adaptations necessary for the T cell function, as well as the recent progress in techniques to modulate metabolic features of lymphocytes.
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Affiliation(s)
- Violetta V Vlasova
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 614081, Perm, Russia.
| | - Konstantin V Shmagel
- Institute of Ecology and Genetics of Microorganisms, Perm Federal Research Center, Ural Branch of the Russian Academy of Sciences, 614081, Perm, Russia
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3
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Kiparaki M, Baker NE. Ribosomal protein mutations and cell competition: autonomous and nonautonomous effects on a stress response. Genetics 2023; 224:iyad080. [PMID: 37267156 PMCID: PMC10691752 DOI: 10.1093/genetics/iyad080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 04/16/2023] [Indexed: 06/04/2023] Open
Abstract
Ribosomal proteins (Rps) are essential for viability. Genetic mutations affecting Rp genes were first discovered in Drosophila, where they represent a major class of haploinsufficient mutations. One mutant copy gives rise to the dominant "Minute" phenotype, characterized by slow growth and small, thin bristles. Wild-type (WT) and Minute cells compete in mosaics, that is, Rp+/- are preferentially lost when their neighbors are of the wild-type genotype. Many features of Rp gene haploinsufficiency (i.e. Rp+/- phenotypes) are mediated by a transcriptional program. In Drosophila, reduced translation and slow growth are under the control of Xrp1, a bZip-domain transcription factor induced in Rp mutant cells that leads ultimately to the phosphorylation of eIF2α and consequently inhibition of most translation. Rp mutant phenotypes are also mediated transcriptionally in yeast and in mammals. In mammals, the Impaired Ribosome Biogenesis Checkpoint activates p53. Recent findings link Rp mutant phenotypes to other cellular stresses, including the DNA damage response and endoplasmic reticulum stress. We suggest that cell competition results from nonautonomous inputs to stress responses, bringing decisions between adaptive and apoptotic outcomes under the influence of nearby cells. In Drosophila, cell competition eliminates aneuploid cells in which loss of chromosome leads to Rp gene haploinsufficiency. The effects of Rp gene mutations on the whole organism, in Minute flies or in humans with Diamond-Blackfan Anemia, may be inevitable consequences of pathways that are useful in eliminating individual cells from mosaics. Alternatively, apparently deleterious whole organism phenotypes might be adaptive, preventing even more detrimental outcomes. In mammals, for example, p53 activation appears to suppress oncogenic effects of Rp gene haploinsufficiency.
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Affiliation(s)
- Marianthi Kiparaki
- Institute for Fundamental Biomedical Research, Biomedical Sciences Research Center “Alexander Fleming”, Vari 16672, Greece
| | - Nicholas E Baker
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Visual Sciences and Ophthalmology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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4
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Purhonen J, Banerjee R, Wanne V, Sipari N, Mörgelin M, Fellman V, Kallijärvi J. Mitochondrial complex III deficiency drives c-MYC overexpression and illicit cell cycle entry leading to senescence and segmental progeria. Nat Commun 2023; 14:2356. [PMID: 37095097 PMCID: PMC10126100 DOI: 10.1038/s41467-023-38027-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/12/2023] [Indexed: 04/26/2023] Open
Abstract
Accumulating evidence suggests mitochondria as key modulators of normal and premature aging, yet whether primary oxidative phosphorylation (OXPHOS) deficiency can cause progeroid disease remains unclear. Here, we show that mice with severe isolated respiratory complex III (CIII) deficiency display nuclear DNA damage, cell cycle arrest, aberrant mitoses, and cellular senescence in the affected organs such as liver and kidney, and a systemic phenotype resembling juvenile-onset progeroid syndromes. Mechanistically, CIII deficiency triggers presymptomatic cancer-like c-MYC upregulation followed by excessive anabolic metabolism and illicit cell proliferation against lack of energy and biosynthetic precursors. Transgenic alternative oxidase dampens mitochondrial integrated stress response and the c-MYC induction, suppresses the illicit proliferation, and prevents juvenile lethality despite that canonical OXPHOS-linked functions remain uncorrected. Inhibition of c-MYC with the dominant-negative Omomyc protein relieves the DNA damage in CIII-deficient hepatocytes in vivo. Our results connect primary OXPHOS deficiency to genomic instability and progeroid pathogenesis and suggest that targeting c-MYC and aberrant cell proliferation may be therapeutic in mitochondrial diseases.
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Affiliation(s)
- Janne Purhonen
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Rishi Banerjee
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Vilma Wanne
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
| | - Nina Sipari
- Viikki Metabolomics Unit, University of Helsinki, P.O.Box 65, Helsinki, Finland
| | - Matthias Mörgelin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, P.O.Box 117, 221 00, Lund, Sweden
- Colzyx AB, Scheelevägen 2, 22381, Lund, Sweden
| | - Vineta Fellman
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland
- Department of Clinical Sciences, Lund, Pediatrics, Lund University, P.O.Box 117, 221 00, Lund, Sweden
- Children's Hospital, Clinicum, University of Helsinki, P.O. Box 22, 00014, Helsinki, Finland
| | - Jukka Kallijärvi
- Folkhälsan Research Center, Haartmaninkatu 8, 00290, Helsinki, Finland.
- Stem Cells and Metabolism Research Program, Faculty of Medicine, University of Helsinki, P.O.Box 63, 00014, Helsinki, Finland.
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5
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Chen YN, Shih CY, Guo SL, Liu CY, Shen MH, Chang SC, Ku WC, Huang CC, Huang CJ. Potential prognostic and predictive value of UBE2N, IMPDH1, DYNC1LI1 and HRASLS2 in colorectal cancer stool specimens. Biomed Rep 2023; 18:22. [PMID: 36846616 PMCID: PMC9945078 DOI: 10.3892/br.2023.1604] [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: 08/31/2022] [Accepted: 12/20/2022] [Indexed: 02/10/2023] Open
Abstract
Colorectal cancer (CRC) is the most common gastrointestinal malignancy worldwide. The poor specificity and sensitivity of the fecal occult blood test has prompted the development of CRC-related genetic markers for CRC screening and treatment. Gene expression profiles in stool specimens are effective, sensitive and clinically applicable. Herein, a novel advantage of using cells shed from the colon is presented for cost-effective CRC screening. Molecular panels were generated through a series of leave-one-out cross-validation and discriminant analyses. A logistic regression model following reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and immunohistochemistry was used to validate a specific panel for CRC prediction. The panel, consisting of ubiquitin-conjugating enzyme E2 N (UBE2N), inosine monophosphate dehydrogenase 1 (IMPDH1), dynein cytoplasmic 1 light intermediate chain 1 (DYNC1LI1) and phospholipase A and acyltransferase 2 (HRASLS2), accurately recognized patients with CRC and could thus be further investigated as a potential prognostic and predictive biomarker for CRC. UBE2N, IMPDH1 and DYNC1LI1 expression levels were upregulated and HRASLS2 expression was downregulated in CRC tissues. The predictive power of the panel was 96.6% [95% confidence interval (CI), 88.1-99.6%] sensitivity and 89.7% (95% CI, 72.6-97.8%) specificity at a predicted cut-off value at 0.540, suggesting that this four-gene panel testing of stool specimens can faithfully mirror the state of the colon. On the whole, the present study demonstrates that screening for CRC or cancer detection in stool specimens collected non-invasively does not require the inclusion of an excessive number of genes, and colonic defects can be identified via the detection of an aberrant protein in the mucosa or submucosa.
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Affiliation(s)
- Yu-Nung Chen
- Division of Colorectal Surgery, Department of Surgery, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C
| | - Cheng-Yen Shih
- Division of Gastroenterology, Department of Internal Medicine, Sijhih Cathay General Hospital, New Taipei 22174, Taiwan, R.O.C
| | - Shu-Lin Guo
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C.,Department of Anesthesiology, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C,Department of Anesthesiology, Tri-Service General Hospital and National Defense Medical Center, Taipei 11490, Taiwan, R.O.C
| | - Chih-Yi Liu
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C.,Division of Pathology, Sijhih Cathay General Hospital, New Taipei City 22174, Taiwan, R.O.C
| | - Ming-Hung Shen
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C.,Department of Surgery, Fu Jen Catholic University Hospital, New Taipei 24352, Taiwan, R.O.C.,PhD Program in Nutrition and Food Science, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C
| | - Shih-Chang Chang
- Division of Colorectal Surgery, Department of Surgery, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C
| | - Wei-Chi Ku
- School of Medicine, College of Medicine, Fu Jen Catholic University, New Taipei 24205, Taiwan, R.O.C
| | - Chi-Cheng Huang
- Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, Taipei 11217, Taiwan, R.O.C.,Institute of Epidemiology and Preventive Medicine, College of Public Health, National Taiwan University, Taipei 10090, Taiwan, R.O.C.,Correspondence to: Dr Chi-Cheng Huang, Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, No. 201, Section 2, Shipai Road, Taipei 11217, Taiwan, R.O.C.
| | - Chi-Jung Huang
- Department of Medical Research, Cathay General Hospital, Taipei 10630, Taiwan, R.O.C.,Department of Biochemistry, National Defense Medical Center, Taipei 11490, Taiwan, R.O.C.,Correspondence to: Dr Chi-Cheng Huang, Comprehensive Breast Health Center, Department of Surgery, Taipei Veterans General Hospital, No. 201, Section 2, Shipai Road, Taipei 11217, Taiwan, R.O.C.
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6
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Jiao L, Liu Y, Yu XY, Pan X, Zhang Y, Tu J, Song YH, Li Y. Ribosome biogenesis in disease: new players and therapeutic targets. Signal Transduct Target Ther 2023; 8:15. [PMID: 36617563 PMCID: PMC9826790 DOI: 10.1038/s41392-022-01285-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/01/2022] [Accepted: 12/08/2022] [Indexed: 01/10/2023] Open
Abstract
The ribosome is a multi-unit complex that translates mRNA into protein. Ribosome biogenesis is the process that generates ribosomes and plays an essential role in cell proliferation, differentiation, apoptosis, development, and transformation. The mTORC1, Myc, and noncoding RNA signaling pathways are the primary mediators that work jointly with RNA polymerases and ribosome proteins to control ribosome biogenesis and protein synthesis. Activation of mTORC1 is required for normal fetal growth and development and tissue regeneration after birth. Myc is implicated in cancer development by enhancing RNA Pol II activity, leading to uncontrolled cancer cell growth. The deregulation of noncoding RNAs such as microRNAs, long noncoding RNAs, and circular RNAs is involved in developing blood, neurodegenerative diseases, and atherosclerosis. We review the similarities and differences between eukaryotic and bacterial ribosomes and the molecular mechanism of ribosome-targeting antibiotics and bacterial resistance. We also review the most recent findings of ribosome dysfunction in COVID-19 and other conditions and discuss the consequences of ribosome frameshifting, ribosome-stalling, and ribosome-collision. We summarize the role of ribosome biogenesis in the development of various diseases. Furthermore, we review the current clinical trials, prospective vaccines for COVID-19, and therapies targeting ribosome biogenesis in cancer, cardiovascular disease, aging, and neurodegenerative disease.
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Affiliation(s)
- Lijuan Jiao
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yuzhe Liu
- grid.452829.00000000417660726Department of Orthopedics, the Second Hospital of Jilin University, Changchun, Jilin 130000 P. R. China
| | - Xi-Yong Yu
- grid.410737.60000 0000 8653 1072Key Laboratory of Molecular Target & Clinical Pharmacology and the NMPA State Key Laboratory of Respiratory Disease, Guangzhou Medical University, Guangzhou, Guangdong 511436 P. R. China
| | - Xiangbin Pan
- grid.506261.60000 0001 0706 7839Department of Structural Heart Disease, National Center for Cardiovascular Disease, China & Fuwai Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, P. R. China ,Key Laboratory of Cardiovascular Appratus Innovation, Beijing, 100037 P. R. China
| | - Yu Zhang
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Junchu Tu
- grid.263761.70000 0001 0198 0694Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu 215123 P. R. China
| | - Yao-Hua Song
- Cyrus Tang Hematology Center, Collaborative Innovation Center of Hematology, Soochow University, National Clinical Research Center for Hematologic Diseases, the First Affiliated Hospital of Soochow University, Suzhou, P. R. China. .,State Key Laboratory of Radiation Medicine and Protection, Soochow University, Suzhou, 215123, P. R. China.
| | - Yangxin Li
- Institute for Cardiovascular Science and Department of Cardiovascular Surgery, First Affiliated Hospital and Medical College of Soochow University, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, Jiangsu, 215123, P. R. China.
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7
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Ribosome-Directed Therapies in Cancer. Biomedicines 2022; 10:biomedicines10092088. [PMID: 36140189 PMCID: PMC9495564 DOI: 10.3390/biomedicines10092088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/22/2022] [Accepted: 08/22/2022] [Indexed: 12/29/2022] Open
Abstract
The human ribosomes are the cellular machines that participate in protein synthesis, which is deeply affected during cancer transformation by different oncoproteins and is shown to provide cancer cell proliferation and therefore biomass. Cancer diseases are associated with an increase in ribosome biogenesis and mutation of ribosomal proteins. The ribosome represents an attractive anti-cancer therapy target and several strategies are used to identify specific drugs. Here we review the role of different drugs that may decrease ribosome biogenesis and cancer cell proliferation.
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8
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Diehl FF, Miettinen TP, Elbashir R, Nabel CS, Darnell AM, Do BT, Manalis SR, Lewis CA, Vander Heiden MG. Nucleotide imbalance decouples cell growth from cell proliferation. Nat Cell Biol 2022; 24:1252-1264. [PMID: 35927450 PMCID: PMC9359916 DOI: 10.1038/s41556-022-00965-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 06/21/2022] [Indexed: 12/26/2022]
Abstract
Nucleotide metabolism supports RNA synthesis and DNA replication to enable cell growth and division. Nucleotide depletion can inhibit cell growth and proliferation, but how cells sense and respond to changes in the relative levels of individual nucleotides is unclear. Moreover, the nucleotide requirement for biomass production changes over the course of the cell cycle, and how cells coordinate differential nucleotide demands with cell cycle progression is not well understood. Here we find that excess levels of individual nucleotides can inhibit proliferation by disrupting the relative levels of nucleotide bases needed for DNA replication and impeding DNA replication. The resulting purine and pyrimidine imbalances are not sensed by canonical growth regulatory pathways like mTORC1, Akt and AMPK signalling cascades, causing excessive cell growth despite inhibited proliferation. Instead, cells rely on replication stress signalling to survive during, and recover from, nucleotide imbalance during S phase. We find that ATR-dependent replication stress signalling is activated during unperturbed S phases and promotes nucleotide availability to support DNA replication. Together, these data reveal that imbalanced nucleotide levels are not detected until S phase, rendering cells reliant on replication stress signalling to cope with this metabolic problem and disrupting the coordination of cell growth and division.
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Affiliation(s)
- Frances F Diehl
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Teemu P Miettinen
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Medical Research Council Laboratory for Molecular Cell Biology, University College London, London, UK
| | - Ryan Elbashir
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Christopher S Nabel
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Alicia M Darnell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Brian T Do
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard-MIT Health Sciences and Technology, Cambridge, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Departments of Biological Engineering and Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Matthew G Vander Heiden
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Dana-Farber Cancer Institute, Boston, MA, USA.
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9
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Mekawy AS, Alaswad Z, Ibrahim AA, Mohamed AA, AlOkda A, Elserafy M. The consequences of viral infection on host DNA damage response: a focus on SARS-CoVs. J Genet Eng Biotechnol 2022; 20:104. [PMID: 35829826 PMCID: PMC9277982 DOI: 10.1186/s43141-022-00388-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/04/2022] [Indexed: 12/03/2022]
Abstract
DNA damage and genome instability in host cells are introduced by many viruses during their life cycles. Severe acute respiratory syndrome coronaviruses (SARS-CoVs) manipulation of DNA damage response (DDR) is an important area of research that is still understudied. Elucidation of the direct and indirect interactions between SARS-CoVs and DDR not only provides important insights into how the viruses exploit DDR pathways in host cells but also contributes to our understanding of their pathogenicity. Here, we present the known interactions of both SARS-CoV and SARS-CoV-2 with DDR pathways of the host cells, to further understand the consequences of infection on genome integrity. Since this area of research is in its early stages, we try to connect the unlinked dots to speculate and propose different consequences on DDR mechanisms. This review provides new research scopes that can be further investigated in vitro and in vivo, opening new avenues for the development of anti-SARS-CoV-2 drugs.
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Affiliation(s)
- Asmaa S Mekawy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Zina Alaswad
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Aya A Ibrahim
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Ahmed A Mohamed
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt.,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt
| | - Abdelrahman AlOkda
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada.,Metabolic Disorders and Complications Program and Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Menattallah Elserafy
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Giza, Egypt. .,University of Science and Technology, Zewail City of Science and Technology, Giza, 12578, Egypt.
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10
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p53 at the crossroad of DNA replication and ribosome biogenesis stress pathways. Cell Death Differ 2022; 29:972-982. [PMID: 35444234 PMCID: PMC9090812 DOI: 10.1038/s41418-022-00999-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/05/2023] Open
Abstract
Despite several decades of intense research focused on understanding function(s) and disease-associated malfunction of p53, there is no sign of any “mid-life crisis” in this rapidly advancing area of biomedicine. Firmly established as the hub of cellular stress responses and tumor suppressor targeted in most malignancies, p53’s many talents continue to surprise us, providing not only fresh insights into cell and organismal biology, but also new avenues to cancer treatment. Among the most fruitful lines of p53 research in recent years have been the discoveries revealing the multifaceted roles of p53-centered pathways in the fundamental processes of DNA replication and ribosome biogenesis (RiBi), along with cellular responses to replication and RiBi stresses, two intertwined areas of cell (patho)physiology that we discuss in this review. Here, we first provide concise introductory notes on the canonical roles of p53, the key interacting proteins, downstream targets and post-translational modifications involved in p53 regulation. We then highlight the emerging involvement of p53 as a key component of the DNA replication Fork Speed Regulatory Network and the mechanistic links of p53 with cellular checkpoint responses to replication stress (RS), the driving force of cancer-associated genomic instability. Next, the tantalizing, yet still rather foggy functional crosstalk between replication and RiBi (nucleolar) stresses is considered, followed by the more defined involvement of p53-mediated monitoring of the multistep process of RiBi, including the latest updates on the RPL5/RPL11/5 S rRNA-MDM2-p53-mediated Impaired Ribosome Biogenesis Checkpoint (IRBC) pathway and its involvement in tumorigenesis. The diverse defects of RiBi and IRBC that predispose and/or contribute to severe human pathologies including developmental syndromes and cancer are then outlined, along with examples of promising small-molecule-based strategies to therapeutically target the RS- and particularly RiBi- stress-tolerance mechanisms to which cancer cells are addicted due to their aberrant DNA replication, repair, and proteo-synthesis demands. ![]()
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11
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Graphene oxide leads to mitochondrial-dependent apoptosis by activating ROS-p53-mPTP pathway in intestinal cells. Int J Biochem Cell Biol 2022; 146:106206. [PMID: 35398141 DOI: 10.1016/j.biocel.2022.106206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/15/2022] [Accepted: 03/23/2022] [Indexed: 12/17/2022]
Abstract
Owing to its unique physical and chemical properties, graphene oxide (GO) has a wide range of applications in biomedical field. However, with the gradual improvement of biosafety investigations on nanomaterials, growing literatures have pointed out that GO could lead to oxidative stress, aggravation of inflammatory responses, and even irreversible lesions in human multi-tissues, while its damage to small intestinal remained unclear. In this study, we conducted an in-depth study on the toxicological effect of GO on intestinal tissues, and further clarified its toxic effect and molecular mechanism on inducing intestinal cell death. Firstly, we characterized the shape size, potential value, Fourier Transform infrared spectroscopy (FT-IR) characterization and pro-oxidant properties of GO nanosheets. The cytotoxicity of different concentrations of GO to Caco-2 and IEC-6 cell lines was thereafter observed, which was specifically manifested as invoking NADPH Oxidase 1 (NOX1) proteins, accompanied generation of reactive oxygen species (ROS). Since that, more p53 flowed into mitochondria to combine with cyclophilin D (CYPD), thus induced mitochondrial permeability transition pore (mPTP) opening. Through ROS-CyPD-mPTP signaling pathway, GO exerted imbalance of mitochondrial homeostasis, while released cytochrome c (CytC) would ultimate caspase-dependent cell apoptosis. In vivo experiment also confirmed that the microstructure of small intestine was damaged, and the apoptosis rate and oxidative markers were significantly increased in GO-treated Sprague- Dawley (SD) rats (40 mg/kg once every other day from day 1 to day 9 by oral gavage). Based on these findings, we conclude that the adverse effects of oral exposure of GO on the biological system mainly concentrate in the digestive tract, and clarify the key role of ROS-mitochondrial homeostasis-apoptosis axis in GO-derived intestinal toxicity. Considering all these results and the fact that GO exhibited intestinal toxicity, we believe that this research providing a safety reference for its biomedical applications.
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12
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Targeting nucleotide metabolism: a promising approach to enhance cancer immunotherapy. J Hematol Oncol 2022; 15:45. [PMID: 35477416 PMCID: PMC9044757 DOI: 10.1186/s13045-022-01263-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/18/2022] [Indexed: 12/12/2022] Open
Abstract
Targeting nucleotide metabolism can not only inhibit tumor initiation and progression but also exert serious side effects. With in-depth studies of nucleotide metabolism, our understanding of nucleotide metabolism in tumors has revealed their non-proliferative effects on immune escape, indicating the potential effectiveness of nucleotide antimetabolites for enhancing immunotherapy. A growing body of evidence now supports the concept that targeting nucleotide metabolism can increase the antitumor immune response by (1) activating host immune systems via maintaining the concentrations of several important metabolites, such as adenosine and ATP, (2) promoting immunogenicity caused by increased mutability and genomic instability by disrupting the purine and pyrimidine pool, and (3) releasing nucleoside analogs via microbes to regulate immunity. Therapeutic approaches targeting nucleotide metabolism combined with immunotherapy have achieved exciting success in preclinical animal models. Here, we review how dysregulated nucleotide metabolism can promote tumor growth and interact with the host immune system, and we provide future insights into targeting nucleotide metabolism for immunotherapeutic treatment of various malignancies.
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13
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Targeting Ribosome Biogenesis in Cancer: Lessons Learned and Way Forward. Cancers (Basel) 2022; 14:cancers14092126. [PMID: 35565259 PMCID: PMC9100539 DOI: 10.3390/cancers14092126] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/18/2022] [Accepted: 04/22/2022] [Indexed: 01/05/2023] Open
Abstract
Simple Summary Cells need to produce ribosomes to sustain continuous proliferation and expand in numbers, a feature that is even more prominent in uncontrollably proliferating cancer cells. Certain cancer cell types are expected to depend more on ribosome biogenesis based on their genetic background, and this potential vulnerability can be exploited in designing effective, targeted cancer therapies. This review provides information on anti-cancer molecules that target the ribosome biogenesis machinery and indicates avenues for future research. Abstract Rapid growth and unrestrained proliferation is a hallmark of many cancers. To accomplish this, cancer cells re-wire and increase their biosynthetic and metabolic activities, including ribosome biogenesis (RiBi), a complex, highly energy-consuming process. Several chemotherapeutic agents used in the clinic impair this process by interfering with the transcription of ribosomal RNA (rRNA) in the nucleolus through the blockade of RNA polymerase I or by limiting the nucleotide building blocks of RNA, thereby ultimately preventing the synthesis of new ribosomes. Perturbations in RiBi activate nucleolar stress response pathways, including those controlled by p53. While compounds such as actinomycin D and oxaliplatin effectively disrupt RiBi, there is an ongoing effort to improve the specificity further and find new potent RiBi-targeting compounds with improved pharmacological characteristics. A few recently identified inhibitors have also become popular as research tools, facilitating our advances in understanding RiBi. Here we provide a comprehensive overview of the various compounds targeting RiBi, their mechanism of action, and potential use in cancer therapy. We discuss screening strategies, drug repurposing, and common problems with compound specificity and mechanisms of action. Finally, emerging paths to discovery and avenues for the development of potential biomarkers predictive of therapeutic outcomes across cancer subtypes are also presented.
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14
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Groarke EM, Calado RT, Liu JM. Cell senescence and malignant transformation in the inherited bone marrow failure syndromes: Overlapping pathophysiology with therapeutic implications. Semin Hematol 2022; 59:30-37. [PMID: 35491056 PMCID: PMC9062194 DOI: 10.1053/j.seminhematol.2022.01.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/19/2022] [Accepted: 01/26/2022] [Indexed: 02/02/2023]
Abstract
Fanconi anemia, telomeropathies and ribosomopathies are members of the inherited bone marrow failure syndromes, rare genetic disorders that lead to failure of hematopoiesis, developmental abnormalities, and cancer predisposition. While each disorder is caused by different genetic defects in seemingly disparate processes of DNA repair, telomere maintenance, or ribosome biogenesis, they appear to lead to a common pathway characterized by premature senescence of hematopoietic stem cells. Here we review the experimental data on senescence and inflammation underlying marrow failure and malignant transformation. We conclude with a critical assessment of current and future therapies targeting these pathways in inherited bone marrow failure syndromes patients.
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Affiliation(s)
- Emma M Groarke
- Hematology Branch, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD.
| | - Rodrigo T Calado
- Department of Medical Imaging, Hematology, and Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Johnson M Liu
- Division of Hematology, Maine Medical Center, Portland, ME
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15
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Kokina A, Tanilas K, Ozolina Z, Pleiko K, Shvirksts K, Vamza I, Liepins J. Purine Auxotrophic Starvation Evokes Phenotype Similar to Stationary Phase Cells in Budding Yeast. J Fungi (Basel) 2021; 8:29. [PMID: 35049969 PMCID: PMC8780165 DOI: 10.3390/jof8010029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/24/2021] [Indexed: 11/25/2022] Open
Abstract
Purine auxotrophy is an abundant trait among eukaryotic parasites and a typical marker for many budding yeast strains. Supplementation with an additional purine source (such as adenine) is necessary to cultivate these strains. If not supplied in adequate amounts, purine starvation sets in. We explored purine starvation effects in a model organism, a budding yeast Saccharomyces cerevisiae ade8 knockout, at the level of cellular morphology, central carbon metabolism, and global transcriptome. We observed that purine-starved cells stopped their cycle in G1/G0 state and accumulated trehalose, and the intracellular concentration of AXP decreased, but adenylate charge remained stable. Cells became tolerant to severe environmental stresses. Intracellular RNA concentration decreased, and massive downregulation of ribosomal biosynthesis genes occurred. We proved that the expression of new proteins during purine starvation is critical for cells to attain stress tolerance phenotype Msn2/4p targets are upregulated in purine-starved cells when compared to cells cultivated in purine-rich media. The overall transcriptomic response to purine starvation resembles that of stationary phase cells. Our results demonstrate that the induction of a strong stress resistance phenotype in budding yeast can be caused not only by natural starvation, but also starvation for metabolic intermediates, such as purines.
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Affiliation(s)
- Agnese Kokina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Kristel Tanilas
- Center of Food and Fermentation Technologies, Akadeemia Tee 15A, 12618 Tallinn, Estonia;
| | - Zane Ozolina
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Karlis Pleiko
- Faculty of Medicine, University of Latvia, Jelgavas 3, LV-1004 Riga, Latvia;
- Laboratory of Precision and Nanomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, 50411 Tartu, Estonia
| | - Karlis Shvirksts
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Ilze Vamza
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
| | - Janis Liepins
- Institute of Microbiology and Biotechnology, University of Latvia, Jelgavas 1, LV-1004 Riga, Latvia; (Z.O.); (K.S.); (I.V.); (J.L.)
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16
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Tawa GJ, Braisted J, Gerhold D, Grewal G, Mazcko C, Breen M, Sittampalam G, LeBlanc AK. Transcriptomic profiling in canines and humans reveals cancer specific gene modules and biological mechanisms common to both species. PLoS Comput Biol 2021; 17:e1009450. [PMID: 34570764 PMCID: PMC8523068 DOI: 10.1371/journal.pcbi.1009450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 10/18/2021] [Accepted: 09/14/2021] [Indexed: 12/25/2022] Open
Abstract
Understanding relationships between spontaneous cancer in companion (pet) canines and humans can facilitate biomarker and drug development in both species. Towards this end we developed an experimental-bioinformatic protocol that analyzes canine transcriptomics data in the context of existing human data to evaluate comparative relevance of canine to human cancer. We used this protocol to characterize five canine cancers: melanoma, osteosarcoma, pulmonary carcinoma, B- and T-cell lymphoma, in 60 dogs. We applied an unsupervised, iterative clustering method that yielded five co-expression modules and found that each cancer exhibited a unique module expression profile. We constructed cancer models based on the co-expression modules and used the models to successfully classify the canine data. These canine-derived models also successfully classified human tumors representing the same cancers, indicating shared cancer biology between canines and humans. Annotation of the module genes identified cancer specific pathways relevant to cells-of-origin and tumor biology. For example, annotations associated with melanin production (PMEL, GPNMB, and BACE2), synthesis of bone material (COL5A2, COL6A3, and COL12A1), synthesis of pulmonary surfactant (CTSH, LPCAT1, and NAPSA), ribosomal proteins (RPL8, RPS7, and RPLP0), and epigenetic regulation (EDEM1, PTK2B, and JAK1) were unique to melanoma, osteosarcoma, pulmonary carcinoma, B- and T-cell lymphoma, respectively. In total, 152 biomarker candidates were selected from highly expressing modules for each cancer type. Many of these biomarker candidates are under-explored as drug discovery targets and warrant further study. The demonstrated transferability of classification models from canines to humans enforces the idea that tumor biology, biomarker targets, and associated therapeutics, discovered in canines, may translate to human medicine.
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Affiliation(s)
- Gregory J. Tawa
- National Institutes of Health, National Center for Advancing Translational Sciences, Division of Preclinical Innovation, Therapeutic Development Branch, Rockville, Maryland, United States of America
| | - John Braisted
- National Institutes of Health, National Center for Advancing Translational Sciences, Division of Preclinical Innovation, Therapeutic Development Branch, Rockville, Maryland, United States of America
| | - David Gerhold
- National Institutes of Health, National Center for Advancing Translational Sciences, Division of Preclinical Innovation, Therapeutic Development Branch, Rockville, Maryland, United States of America
| | - Gurmit Grewal
- National Institutes of Health, National Center for Advancing Translational Sciences, Division of Preclinical Innovation, Therapeutic Development Branch, Rockville, Maryland, United States of America
| | - Christina Mazcko
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Comparative Oncology Program, Bethesda, Maryland, United States of America
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, North Carolina State University, College of Veterinary Medicine, Raleigh, North Carolina, United States of America
| | - Gurusingham Sittampalam
- National Institutes of Health, National Center for Advancing Translational Sciences, Division of Preclinical Innovation, Therapeutic Development Branch, Rockville, Maryland, United States of America
| | - Amy K. LeBlanc
- National Institutes of Health, National Cancer Institute, Center for Cancer Research, Comparative Oncology Program, Bethesda, Maryland, United States of America
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17
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Ellison V, Annor GK, Freedman C, Xiao G, Lundine D, Freulich E, Prives C, Bargonetti J. Frame-shift mediated reduction of gain-of-function p53 R273H and deletion of the R273H C-terminus in breast cancer cells result in replication-stress sensitivity. Oncotarget 2021; 12:1128-1146. [PMID: 34136083 PMCID: PMC8202772 DOI: 10.18632/oncotarget.27975] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/15/2021] [Indexed: 11/25/2022] Open
Abstract
We recently documented that gain-of-function (GOF) mutant p53 (mtp53) R273H in triple negative breast cancer (TNBC) cells interacts with replicating DNA and PARP1. The missense R273H GOF mtp53 has a mutated central DNA binding domain that renders it unable to bind specifically to DNA, but maintains the capacity to interact tightly with chromatin. Both the C-terminal domain (CTD) and oligomerization domain (OD) of GOF mtp53 proteins are intact and it is unclear whether these regions of mtp53 are responsible for chromatin-based DNA replication activities. We generated MDA-MB-468 cells with CRISPR-Cas9 edited versions of the CTD and OD regions of mtp53 R273H. These included a frame-shift mtp53 R273Hfs387, which depleted mtp53 protein expression; mtp53 R273HΔ381-388, which had a small deletion within the CTD; and mtp53 R273HΔ347-393, which had both the OD and CTD regions truncated. The mtp53 R273HΔ347-393 existed exclusively as monomers and disrupted the chromatin interaction of mtp53 R273H. The CRISPR variants proliferated more slowly than the parental cells and mt53 R273Hfs387 showed the most extreme phenotype. We uncovered that after thymidine-induced G1/S synchronization, but not hydroxyurea or aphidicholin, R273Hfs387 cells displayed impairment of S-phase progression while both R273HΔ347-393 and R273HΔ381-388 displayed only moderate impairment. Moreover, reduced chromatin interaction of MCM2 and PCNA in mtp53 depleted R273Hfs387 cells post thymidine-synchronization revealed delayed kinetics of replisome assembly underscoring the slow S-phase progression. Taken together our findings show that the CTD and OD domains of mtp53 R273H play critical roles in mutant p53 GOF that pertain to processes associated with DNA replication.
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Affiliation(s)
- Viola Ellison
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - George K. Annor
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- The Graduate Center Biology and Biochemistry Programs, City University of New York, New York, NY, USA
| | - Clara Freedman
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Gu Xiao
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
| | - Devon Lundine
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- The Graduate Center Biology and Biochemistry Programs, City University of New York, New York, NY, USA
| | - Elzbieta Freulich
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Carol Prives
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Jill Bargonetti
- The Department of Biological Sciences, Hunter College, City University of New York, New York, NY, USA
- The Graduate Center Biology and Biochemistry Programs, City University of New York, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY, USA
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18
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Kim J, Lee S, Kim H, Lee H, Seong KM, Youn H, Youn B. Autophagic Organelles in DNA Damage Response. Front Cell Dev Biol 2021; 9:668735. [PMID: 33912571 PMCID: PMC8072393 DOI: 10.3389/fcell.2021.668735] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 03/23/2021] [Indexed: 12/19/2022] Open
Abstract
Autophagy is an important subcellular event engaged in the maintenance of cellular homeostasis via the degradation of cargo proteins and malfunctioning organelles. In response to cellular stresses, like nutrient deprivation, infection, and DNA damaging agents, autophagy is activated to reduce the damage and restore cellular homeostasis. One of the responses to cellular stresses is the DNA damage response (DDR), the intracellular pathway that senses and repairs damaged DNA. Proper regulation of these pathways is crucial for preventing diseases. The involvement of autophagy in the repair and elimination of DNA aberrations is essential for cell survival and recovery to normal conditions, highlighting the importance of autophagy in the resolution of cell fate. In this review, we summarized the latest information about autophagic recycling of mitochondria, endoplasmic reticulum (ER), and ribosomes (called mitophagy, ER-phagy, and ribophagy, respectively) in response to DNA damage. In addition, we have described the key events necessary for a comprehensive understanding of autophagy signaling networks. Finally, we have highlighted the importance of the autophagy activated by DDR and appropriate regulation of autophagic organelles, suggesting insights for future studies. Especially, DDR from DNA damaging agents including ionizing radiation (IR) or anti-cancer drugs, induces damage to subcellular organelles and autophagy is the key mechanism for removing impaired organelles.
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Affiliation(s)
- Jeongha Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Sungmin Lee
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Hyunwoo Kim
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Haksoo Lee
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea
| | - Ki Moon Seong
- Laboratory of Low Dose Risk Assessment, National Radiation Emergency Medical Center, Korea Institute of Radiological and Medical Sciences, Seoul, South Korea
| | - HyeSook Youn
- Department of Integrative Bioscience and Biotechnology, Sejong University, Seoul, South Korea
| | - BuHyun Youn
- Department of Integrated Biological Science, Pusan National University, Busan, South Korea.,Department of Biological Sciences, Pusan National University, Busan, South Korea
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19
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Bursać S, Prodan Y, Pullen N, Bartek J, Volarević S. Dysregulated Ribosome Biogenesis Reveals Therapeutic Liabilities in Cancer. Trends Cancer 2020; 7:57-76. [PMID: 32948502 DOI: 10.1016/j.trecan.2020.08.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/30/2020] [Accepted: 08/17/2020] [Indexed: 12/24/2022]
Abstract
Ribosome biogenesis (RiBi) is one of the most complex and energy demanding processes in human cells, critical for cell growth and proliferation. Strong causal links between inherited and acquired impairment in RiBi with cancer pathogenesis are emerging, pointing to RiBi as an attractive therapeutic target for cancer. Here, we will highlight new knowledge about causes of excessive or impaired RiBi and the impact of these changes on protein synthesis. We will also discuss how new knowledge about secondary consequences of dysregulated RiBi and protein synthesis, including proteotoxic stress, metabolic alterations, adaptive transcriptional and translational programs, and the impaired ribosome biogenesis checkpoint (IRBC) provide a foundation for the development of new anticancer therapies.
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Affiliation(s)
- Slađana Bursać
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Ylenia Prodan
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia
| | - Nick Pullen
- Bristol Myers Squibb, 200 Cambridge Park Drive, Cambridge, MA 02140, USA
| | - Jiri Bartek
- Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Solna, 171 76, Stockholm, Sweden; The Danish Cancer Society Research Center, DK-2100 Copenhagen, Denmark.
| | - Siniša Volarević
- Department of Molecular Medicine and Biotechnology, Faculty of Medicine, University of Rijeka, 51000 Rijeka, Croatia.
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20
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Pelletier J, Riaño-Canalias F, Almacellas E, Mauvezin C, Samino S, Feu S, Menoyo S, Domostegui A, Garcia-Cajide M, Salazar R, Cortés C, Marcos R, Tauler A, Yanes O, Agell N, Kozma SC, Gentilella A, Thomas G. Nucleotide depletion reveals the impaired ribosome biogenesis checkpoint as a barrier against DNA damage. EMBO J 2020; 39:e103838. [PMID: 32484960 PMCID: PMC7327477 DOI: 10.15252/embj.2019103838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2019] [Revised: 03/07/2020] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
Many oncogenes enhance nucleotide usage to increase ribosome content, DNA replication, and cell proliferation, but in parallel trigger p53 activation. Both the impaired ribosome biogenesis checkpoint (IRBC) and the DNA damage response (DDR) have been implicated in p53 activation following nucleotide depletion. However, it is difficult to reconcile the two checkpoints operating together, as the IRBC induces p21‐mediated G1 arrest, whereas the DDR requires that cells enter S phase. Gradual inhibition of inosine monophosphate dehydrogenase (IMPDH), an enzyme required for de novo GMP synthesis, reveals a hierarchical organization of these two checkpoints. We find that the IRBC is the primary nucleotide sensor, but increased IMPDH inhibition leads to p21 degradation, compromising IRBC‐mediated G1 arrest and allowing S phase entry and DDR activation. Disruption of the IRBC alone is sufficient to elicit the DDR, which is strongly enhanced by IMPDH inhibition, suggesting that the IRBC acts as a barrier against genomic instability.
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Affiliation(s)
- Joffrey Pelletier
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Ferran Riaño-Canalias
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Eugènia Almacellas
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Caroline Mauvezin
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Sara Samino
- Metabolomics Platform, IISPV & University Rovira i Virgili, Tarragona, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Sonia Feu
- Department of Biomedicine, Faculty of Medicine, IDIBAPS Biomedical Research Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Sandra Menoyo
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Ana Domostegui
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Marta Garcia-Cajide
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Ramon Salazar
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain.,Catalan Institute of Oncology (ICO), Barcelona, Spain
| | - Constanza Cortés
- Department of Genetics and Microbiology, Faculty of Biosciences, Autonomous University of Barcelona, Barcelona, Spain
| | - Ricard Marcos
- Department of Genetics and Microbiology, Faculty of Biosciences, Autonomous University of Barcelona, Barcelona, Spain
| | - Albert Tauler
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain.,Department of Biochemistry and Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - Oscar Yanes
- Metabolomics Platform, IISPV & University Rovira i Virgili, Tarragona, Spain.,Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
| | - Neus Agell
- Department of Biomedicine, Faculty of Medicine, IDIBAPS Biomedical Research Institute, Hospital Clinic, University of Barcelona, Barcelona, Spain
| | - Sara C Kozma
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain
| | - Antonio Gentilella
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain.,Department of Biochemistry and Physiology, Faculty of Pharmacy, University of Barcelona, Barcelona, Spain
| | - George Thomas
- Laboratory of Cancer Metabolism, ONCOBELL Program, Institut d'Investigació Biomèdica de Bellvitge-IDIBELL, L'Hospitalet de Llobregat, Spain.,Department of Physiological Sciences, Faculty of Medicine and Health Science, University of Barcelona, Barcelona, Spain
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