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Aubé F, Fontrodona N, Guiguettaz L, Vallin E, Fabbri L, Lapendry A, Vagner S, Ricci EP, Auboeuf D. Metabolism-dependent secondary effect of anti-MAPK cancer therapy on DNA repair. NAR Cancer 2024; 6:zcae019. [PMID: 38690580 PMCID: PMC11059277 DOI: 10.1093/narcan/zcae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/08/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024] Open
Abstract
Amino acid bioavailability impacts mRNA translation in a codon-dependent manner. Here, we report that the anti-cancer MAPK inhibitors (MAPKi) decrease the intracellular concentration of aspartate and glutamate in melanoma cells. This coincides with the accumulation of ribosomes on codons corresponding to these amino acids and triggers the translation-dependent degradation of mRNAs encoding aspartate- and glutamate-rich proteins, involved in DNA metabolism such as DNA replication and repair. Consequently, cells that survive MAPKi degrade aspartate and glutamate likely to generate energy, which simultaneously decreases their requirement for amino acids due to the downregulation of aspartate- and glutamate-rich proteins involved in cell proliferation. Concomitantly, the downregulation of aspartate- and glutamate-rich proteins involved in DNA repair increases DNA damage loads. Thus, DNA repair defects, and therefore mutations, are at least in part a secondary effect of the metabolic adaptation of cells exposed to MAPKi.
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Affiliation(s)
- Fabien Aubé
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Nicolas Fontrodona
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Laura Guiguettaz
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Elodie Vallin
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Lucilla Fabbri
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France
- Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
- Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Audrey Lapendry
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
| | - Stephan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France
- Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France
- Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Emiliano P Ricci
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
| | - Didier Auboeuf
- Laboratoire de Biologie et Modélisation de la Cellule, Ecole Normale Supérieure de Lyon, CNRS, UMR 5239, Inserm, U1293, Université Claude Bernard Lyon 1, 46 allée d’Italie F-69364 Lyon, France
- Equipe Labellisée Ligue Nationale Contre le Cancer, LBMC, ENS, Lyon, France
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2
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Huang L, Bai D, Su X. Altered expression of transfer RNAs and their possible roles in brain white matter injury. Neuroreport 2024; 35:536-541. [PMID: 38597261 DOI: 10.1097/wnr.0000000000002036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Transfer RNAs (tRNAs) can regulate cell behavior and are associated with neurological disorders. Here, we aimed to investigate the expression levels of tRNAs in oligodendrocyte precursor cells (OPCs) and their possible roles in the regulation of brain white matter injury (WMI). Newborn Sprague-Dawley rats (postnatal day 5) were used to establish a model that mimicked neonatal brain WMI. RNA-array analysis was performed to examine the expression of tRNAs in OPCs. psRNAtarget software was used to predict target mRNAs of significantly altered tRNAs. Gene ontology (GO) and KEGG were used to analyze the pathways for target mRNAs. Eighty-nine tRNAs were changed after WMI (fold change absolute ≥1.5, P < 0.01), with 31 downregulated and 58 upregulated. Among them, three significantly changed tRNAs were identified, with two being significantly increased (chr10.trna1314-ProTGG and chr2.trna2771-ProAGG) and one significantly decreased (chr10.trna11264-GlyTCC). Further, target mRNA prediction and GO/KEGG pathway analysis indicated that the target mRNAs of these tRNAs are mainly involved in G-protein coupled receptor signaling pathways and beta-alanine metabolism, which are both related to myelin formation. In summary, the expression of tRNAs in OPCs was significantly altered after brain WMI, suggesting that tRNAs may play important roles in regulating WMI. This improves the knowledge about WMI pathophysiology and may provide novel treatment targets for WMI.
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Affiliation(s)
- Lingyi Huang
- Department of Orthodontics, West China College of Stomatology/State Key Laboratory of Oral Diseases, Sichuan University
| | - Ding Bai
- Department of Orthodontics, West China College of Stomatology/State Key Laboratory of Oral Diseases, Sichuan University
| | - Xiaojuan Su
- Department of Pediatrics/Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University Hospital, Sichuan University, Chengdu, China
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3
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Kobayashi-Ishihara M, Tsunetsugu-Yokota Y. Post-Transcriptional HIV-1 Latency: A Promising Target for Therapy? Viruses 2024; 16:666. [PMID: 38793548 PMCID: PMC11125802 DOI: 10.3390/v16050666] [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: 04/04/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Human Immunodeficiency Virus type 1 (HIV-1) latency represents a significant hurdle in finding a cure for HIV-1 infections, despite tireless research efforts. This challenge is partly attributed to the intricate nature of HIV-1 latency, wherein various host and viral factors participate in multiple physiological processes. While substantial progress has been made in discovering therapeutic targets for HIV-1 transcription, targets for the post-transcriptional regulation of HIV-1 infections have received less attention. However, cumulative evidence now suggests the pivotal contribution of post-transcriptional regulation to the viral latency in both in vitro models and infected individuals. In this review, we explore recent insights on post-transcriptional latency in HIV-1 and discuss the potential of its therapeutic targets, illustrating some host factors that restrict HIV-1 at the post-transcriptional level.
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Affiliation(s)
- Mie Kobayashi-Ishihara
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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4
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Zhou M, He X, Zhang J, Mei C, Zhong B, Ou C. tRNA-derived small RNAs in human cancers: roles, mechanisms, and clinical application. Mol Cancer 2024; 23:76. [PMID: 38622694 PMCID: PMC11020452 DOI: 10.1186/s12943-024-01992-2] [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: 01/03/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are a new type of non-coding RNAs (ncRNAs) produced by the specific cleavage of precursor or mature tRNAs. tsRNAs are involved in various basic biological processes such as epigenetic, transcriptional, post-transcriptional, and translation regulation, thereby affecting the occurrence and development of various human diseases, including cancers. Recent studies have shown that tsRNAs play an important role in tumorigenesis by regulating biological behaviors such as malignant proliferation, invasion and metastasis, angiogenesis, immune response, tumor resistance, and tumor metabolism reprogramming. These may be new potential targets for tumor treatment. Furthermore, tsRNAs can exist abundantly and stably in various bodily fluids (e.g., blood, serum, and urine) in the form of free or encapsulated extracellular vesicles, thereby affecting intercellular communication in the tumor microenvironment (TME). Meanwhile, their abnormal expression is closely related to the clinicopathological features of tumor patients, such as tumor staging, lymph node metastasis, and poor prognosis of tumor patients; thus, tsRNAs can be served as a novel type of liquid biopsy biomarker. This review summarizes the discovery, production, and expression of tsRNAs and analyzes their molecular mechanisms in tumor development and potential applications in tumor therapy, which may provide new strategies for early diagnosis and targeted therapy of tumors.
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Affiliation(s)
- Manli Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jing Zhang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Cheng Mei
- Department of Blood Transfusion, Xiangya Hospital, Clinical Transfusion Research Center, Central South University, Changsha, Hunan, 410008, China.
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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5
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Zhang M, Tang C, Wang Z, Chen S, Zhang D, Li K, Sun K, Zhao C, Wang Y, Xu M, Dai L, Lu G, Shi H, Ren H, Chen L, Geng J. Real-time detection of 20 amino acids and discrimination of pathologically relevant peptides with functionalized nanopore. Nat Methods 2024; 21:609-618. [PMID: 38443507 PMCID: PMC11009107 DOI: 10.1038/s41592-024-02208-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
Precise identification and quantification of amino acids is crucial for many biological applications. Here we report a copper(II)-functionalized Mycobacterium smegmatis porin A (MspA) nanopore with the N91H substitution, which enables direct identification of all 20 proteinogenic amino acids when combined with a machine-learning algorithm. The validation accuracy reaches 99.1%, with 30.9% signal recovery. The feasibility of ultrasensitive quantification of amino acids was also demonstrated at the nanomolar range. Furthermore, the capability of this system for real-time analyses of two representative post-translational modifications (PTMs), one unnatural amino acid and ten synthetic peptides using exopeptidases, including clinically relevant peptides associated with Alzheimer's disease and cancer neoantigens, was demonstrated. Notably, our strategy successfully distinguishes peptides with only one amino acid difference from the hydrolysate and provides the possibility to infer the peptide sequence.
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Affiliation(s)
- Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Chao Tang
- Biosafety Laboratory of West China Hospital, West China Hospital, Sichuan University, Chengdu, China
| | - Zichun Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Shanchuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China
| | - Mengying Xu
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, China
| | - Hubing Shi
- Laboratory of Tumor Targeted and Immune Therapy, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Haiyan Ren
- Division of Respiratory and Critical Care Medicine, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, Chengdu, China
| | - Lu Chen
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, Chengdu, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, Clinical Laboratory Medicine Research Center, West China Hospital, Sichuan University, Chengdu, China.
- Tianfu Jincheng Laboratory, City of Future Medicine, Chengdu, China.
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6
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Li X, Zhang L, Huang X, Peng Q, Zhang S, Tang J, Wang J, Gui D, Zeng F. High-throughput metabolomics identifies new biomarkers for cervical cancer. Discov Oncol 2024; 15:90. [PMID: 38551775 PMCID: PMC10980666 DOI: 10.1007/s12672-024-00948-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 03/21/2024] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND Cervical cancer (CC) is a danger to women's health, especially in many developing countries. Metabolomics can make the connection between genotypes and phenotypes. It provides a wide spectrum profile of biological processes under pathological or physiological conditions. METHOD In this study, we conducted plasma metabolomics of healthy volunteers and CC patients and integratively analyzed them with public CC tissue transcriptomics from Gene Expression Omnibus (GEO). RESULT Here, we screened out a panel of 5 metabolites to precisely distinguish CC patients from healthy volunteers. Furthermore, we utilized multi-omics approaches to explore patients with stage I-IIA1 and IIA2-IV4 CC and comprehensively analyzed the dysregulation of genes and metabolites in CC progression. We identified that plasma levels of trimethylamine N-oxide (TMAO) were associated with tumor size and regarded as a risk factor for CC. Moreover, we demonstrated that TMAO could promote HeLa cell proliferation in vitro. In this study, we delineated metabolic profiling in healthy volunteers and CC patients and revealed that TMAO was a potential biomarker to discriminate between I-IIA1 and IIA2-IV patients to indicate CC deterioration. CONCLUSION Our study identified a diagnostic model consisting of five metabolites in plasma that can effectively distinguish CC from healthy volunteers. Furthermore, we proposed that TMAO was associated with CC progression and might serve as a potential non-invasive biomarker to predict CC substage. IMPACT These findings provided evidence of the important role of metabolic molecules in the progression of cervical cancer disease, as well as their ability as potential biomarkers.
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Affiliation(s)
- Xue Li
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, 635000, Sichuan, China
| | - Liyi Zhang
- Department of Gynaecology and Obstetrics, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Xuan Huang
- Department of Medical Research Center, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Qi Peng
- Department of Gynaecology and Obstetrics, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Shoutao Zhang
- Department of Gynaecology and Obstetrics, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Jiangming Tang
- Department of Gynaecology and Obstetrics, Dazhou Central Hospital, Dazhou, Sichuan, China
| | - Jing Wang
- Department of Clinical Laboratory, Beijing Anding Hospital, Capital Medical University, Beijing, China.
| | - Dingqing Gui
- Department of Gynaecology and Obstetrics, Dazhou Central Hospital, Dazhou, Sichuan, China.
| | - Fanxin Zeng
- Department of Clinical Research Center, Dazhou Central Hospital, Dazhou, 635000, Sichuan, China.
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7
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Ghashghaei M, Liu Y, Ettles J, Bombaci G, Ramkumar N, Liu Z, Escano L, Miko SS, Kim Y, Waldron JA, Do K, MacPherson K, Yuen KA, Taibi T, Yue M, Arsalan A, Jin Z, Edin G, Karsan A, Morin GB, Kuchenbauer F, Perna F, Bushell M, Vu LP. Translation efficiency driven by CNOT3 subunit of the CCR4-NOT complex promotes leukemogenesis. Nat Commun 2024; 15:2340. [PMID: 38491013 PMCID: PMC10943099 DOI: 10.1038/s41467-024-46665-2] [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: 09/05/2023] [Accepted: 03/04/2024] [Indexed: 03/18/2024] Open
Abstract
Protein synthesis is frequently deregulated during tumorigenesis. However, the precise contexts of selective translational control and the regulators of such mechanisms in cancer is poorly understood. Here, we uncovered CNOT3, a subunit of the CCR4-NOT complex, as an essential modulator of translation in myeloid leukemia. Elevated CNOT3 expression correlates with unfavorable outcomes in patients with acute myeloid leukemia (AML). CNOT3 depletion induces differentiation and apoptosis and delayed leukemogenesis. Transcriptomic and proteomic profiling uncovers c-MYC as a critical downstream target which is translationally regulated by CNOT3. Global analysis of mRNA features demonstrates that CNOT3 selectively influences expression of target genes in a codon usage dependent manner. Furthermore, CNOT3 associates with the protein network largely consisting of ribosomal proteins and translation elongation factors in leukemia cells. Overall, our work elicits the direct requirement for translation efficiency in tumorigenesis and propose targeting the post-transcriptional circuitry via CNOT3 as a therapeutic vulnerability in AML.
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Affiliation(s)
- Maryam Ghashghaei
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Yilin Liu
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Department of Experimental Medicine, University of British Columbia, Vancouver, Canada
| | - James Ettles
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Giuseppe Bombaci
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
| | - Niveditha Ramkumar
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zongmin Liu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Leo Escano
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Sandra Spencer Miko
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Yerin Kim
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
- Bioinformatics program, University of British Columbia, Vancouver, Canada
| | - Joseph A Waldron
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Kim Do
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kyle MacPherson
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Katie A Yuen
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Thilelli Taibi
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Marty Yue
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aaremish Arsalan
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Zhen Jin
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Glenn Edin
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Aly Karsan
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
| | - Gregg B Morin
- Genome Sciences Centre, British Columbia Cancer Research Centre, Vancouver, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Florian Kuchenbauer
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada
| | - Fabiana Perna
- Department of Medicine, Indiana University Simon Comprehensive Cancer Center, Indianapolis, IN, USA
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffit Cancer Center, Tampa, FL, USA
| | - Martin Bushell
- CRUK Beatson Institute, Glasgow, UK
- School of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Ly P Vu
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, Canada.
- Terry Fox Laboratory, British Columbia Cancer Research Centre Vancouver, Vancouver, Canada.
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8
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Thumsi A, Martínez D, Swaminathan SJ, Esrafili A, Suresh AP, Jaggarapu MMC, Lintecum K, Halim M, Mantri SV, Sleiman Y, Appel N, Gu H, Curtis M, Zuniga C, Acharya AP. Inverse-Vaccines for Rheumatoid Arthritis Re-establish Metabolic and Immunological Homeostasis in Joint Tissues. Adv Healthc Mater 2024:e2303995. [PMID: 38469995 DOI: 10.1002/adhm.202303995] [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: 11/14/2023] [Revised: 03/06/2024] [Indexed: 03/13/2024]
Abstract
Rheumatoid arthritis (RA) causes immunological and metabolic imbalances in tissue, exacerbating inflammation in affected joints. Changes in immunological and metabolic tissue homeostasis at different stages of RA are not well understood. Herein, the changes in the immunological and metabolic profiles in different stages in collagen induced arthritis (CIA), namely, early, intermediate, and late stage is examined. Moreover, the efficacy of the inverse-vaccine, paKG(PFK15+bc2) microparticle, to restore tissue homeostasis at different stages is also investigated. Immunological analyses of inverse-vaccine-treated group revealed a significant decrease in the activation of pro-inflammatory immune cells and remarkable increase in regulatory T-cell populations in the intermediate and late stages compared to no treatment. Also, glycolysis in the spleen is normalized in the late stages of CIA in inverse-vaccine-treated mice, which is similar to no-disease tissues. Metabolomics analyses revealed that metabolites UDP-glucuronic acid and L-Glutathione oxidized are significantly altered between treatment groups, and thus might provide new druggable targets for RA treatment. Flux metabolic modeling identified amino acid and carnitine pathways as the central pathways affected in arthritic tissue with CIA progression. Overall, this study shows that the inverse-vaccines initiate early re-establishment of homeostasis, which persists through the disease span.
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Affiliation(s)
- Abhirami Thumsi
- Department of Pathology, Case Western REserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Diego Martínez
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | | | - Arezoo Esrafili
- Department of Chemical Engineering, School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85281, USA
| | - Abhirami P Suresh
- Department of Pathology, Case Western REserve University School of Medicine, Cleveland, OH, 44106, USA
| | | | - Kelly Lintecum
- Department of Chemical Engineering, School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85281, USA
| | - Michelle Halim
- Department of Chemical Engineering, School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85281, USA
| | - Shivani V Mantri
- Department of Biomedical Engineering, School of Biological and Health System Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Yasmine Sleiman
- Department of Biomedical Engineering, School of Biological and Health System Engineering, Arizona State University, Tempe, AZ, 85281, USA
| | - Nicole Appel
- Department of Chemical Engineering, School for the Engineering of Matter, Transport, and Energy, Arizona State University, Tempe, AZ, 85281, USA
| | - Haiwei Gu
- College of Health Solutions, Arizona State University, Phoenix, AZ, 85281, USA
| | - Marion Curtis
- Department of Cancer Biology, Mayo Clinic, Scottsdale, AZ, 85259, USA
- College of Medicine and Science, Mayo Clinic, Scottsdale, AZ, 85259, USA
| | - Cristal Zuniga
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - Abhinav P Acharya
- Department of Pathology, Case Western REserve University School of Medicine, Cleveland, OH, 44106, USA
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, 44106, USA
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9
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Sharma S, Zhang X, Azhar G, Patyal P, Verma A, KC G, Wei JY. Valine improves mitochondrial function and protects against oxidative stress. Biosci Biotechnol Biochem 2024; 88:168-176. [PMID: 38093456 PMCID: PMC10807754 DOI: 10.1093/bbb/zbad169] [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: 09/09/2023] [Accepted: 11/07/2023] [Indexed: 01/26/2024]
Abstract
Among the branched-chain amino acids, leucine and isoleucine have been well studied for their roles in improving mitochondrial function and reducing oxidative stress. However, role of valine in mitochondrial function regulation and oxidative stress management remains elusive. This study investigated valine effect on mitochondrial function and oxidative stress in vitro. Valine increased expression of genes involved in mitochondrial biogenesis and dynamics. It upregulates mitochondrial function at complexes I, II, and IV levels of electron transport chain. Flow cytometry studies revealed, valine reduced oxidative stress by significantly lowering mitochondrial reactive oxygen species and protein expression of 4-hydroxynonenal. Functional role of valine against oxidative stress was analyzed by XFe96 Analyzer. Valine sustained oxidative phosphorylation and improved ATP generation rates during oxidative stress. In conclusion, our findings shed more light on the critical function of valine in protecting mitochondrial function thereby preventing mitochondrial/cellular damage induced by oxidative stress.
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Affiliation(s)
- Shakshi Sharma
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Xiaomin Zhang
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gohar Azhar
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Pankaj Patyal
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ambika Verma
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Grishma KC
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jeanne Y Wei
- Donald W. Reynolds Department of Geriatrics, Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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10
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Sizer RE, Butterfield SP, Hancocks LA, Gato De Sousa L, White RJ. Selective Occupation by E2F and RB of Loci Expressed by RNA Polymerase III. Cancers (Basel) 2024; 16:481. [PMID: 38339234 PMCID: PMC10854548 DOI: 10.3390/cancers16030481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 02/12/2024] Open
Abstract
In all cases tested, TFIIIB is responsible for recruiting pol III to its genetic templates. In mammalian cells, RB binds TFIIIB and prevents its interactions with both promoter DNA and pol III, thereby suppressing transcription. As TFIIIB is not recruited to its target genes when bound by RB, the mechanism predicts that pol III-dependent templates will not be occupied by RB; this contrasts with the situation at most genes controlled by RB, where it can be tethered by promoter-bound sequence-specific DNA-binding factors such as E2F. Contrary to this prediction, however, ChIP-seq data reveal the presence of RB in multiple cell types and the related protein p130 at many loci that rely on pol III for their expression, including RMRP, RN7SL, and a variety of tRNA genes. The sets of genes targeted varies according to cell type and growth state. In such cases, recruitment of RB and p130 can be explained by binding of E2F1, E2F4 and/or E2F5. Genes transcribed by pol III had not previously been identified as common targets of E2F family members. The data provide evidence that E2F may allow for the selective regulation of specific non-coding RNAs by RB, in addition to its influence on overall pol III output through its interaction with TFIIIB.
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Affiliation(s)
| | | | | | | | - Robert J. White
- Department of Biology, University of York, York YO10 5DD, UK; (R.E.S.)
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11
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Cherkaoui S, Yang L, McBride M, Turn CS, Lu W, Eigenmann C, Allen GE, Panasenko OO, Zhang L, Vu A, Liu K, Li Y, Gandhi OH, Surrey L, Wierer M, White E, Rabinowitz JD, Hogarty MD, Morscher RJ. Reprogramming neuroblastoma by diet-enhanced polyamine depletion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.07.573662. [PMID: 38260457 PMCID: PMC10802427 DOI: 10.1101/2024.01.07.573662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Neuroblastoma is a highly lethal childhood tumor derived from differentiation-arrested neural crest cells1,2. Like all cancers, its growth is fueled by metabolites obtained from either circulation or local biosynthesis3,4. Neuroblastomas depend on local polyamine biosynthesis, with the inhibitor difluoromethylornithine showing clinical activity5. Here we show that such inhibition can be augmented by dietary restriction of upstream amino acid substrates, leading to disruption of oncogenic protein translation, tumor differentiation, and profound survival gains in the TH-MYCN mouse model. Specifically, an arginine/proline-free diet decreases the polyamine precursor ornithine and augments tumor polyamine depletion by difluoromethylornithine. This polyamine depletion causes ribosome stalling, unexpectedly specifically at adenosine-ending codons. Such codons are selectively enriched in cell cycle genes and low in neuronal differentiation genes. Thus, impaired translation of these codons, induced by the diet-drug combination, favors a pro-differentiation proteome. These results suggest that the genes of specific cellular programs have evolved hallmark codon usage preferences that enable coherent translational rewiring in response to metabolic stresses, and that this process can be targeted to activate differentiation of pediatric cancers.
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Affiliation(s)
- Sarah Cherkaoui
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
| | - Lifeng Yang
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Matthew McBride
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Christina S. Turn
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wenyun Lu
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Caroline Eigenmann
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
| | - George E. Allen
- Bioinformatics Support Platform, Faculty of Medicine, University of Geneva 1211, Switzerland
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Olesya O. Panasenko
- Department of Microbiology and Molecular Medicine, Institute of Genetics and Genomics Geneva, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
- BioCode: RNA to proteins (R2P) Platform, University of Geneva, 1211 Geneva, Switzerland
| | - Lu Zhang
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Annette Vu
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kangning Liu
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yimei Li
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Om H. Gandhi
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Lea Surrey
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael Wierer
- Proteomics Research Infrastructure, Panum Institute, Blegdamsvej 3B, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Eileen White
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08901, USA
- Department of Molecular Biology and Biochemistry, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08901, USA
| | - Joshua D. Rabinowitz
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Ludwig Institute for Cancer Research, Princeton Branch, Princeton University, Princeton, NJ 08544, USA
| | - Michael D. Hogarty
- Division of Oncology and Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Raphael J. Morscher
- Pediatric Cancer Metabolism Laboratory, Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Oncology, University Children’s Hospital Zurich and Children’s Research Center, University of Zurich, 8032 Zurich, Switzerland
- Division of Human Genetics, Medical University Innsbruck, Peter-Mayr-Str. 1, 6020 Innsbruck, Austria
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12
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Zhang YW, Velasco-Hernandez T, Mess J, Lalioti ME, Romero-Mulero MC, Obier N, Karantzelis N, Rettkowski J, Schönberger K, Karabacz N, Jäcklein K, Morishima T, Trincado JL, Romecin P, Martinez A, Takizawa H, Shoumariyeh K, Renders S, Zeiser R, Pahl HL, Béliveau F, Hébert J, Lehnertz B, Sauvageau G, Menendez P, Cabezas-Wallscheid N. GPRC5C drives branched-chain amino acid metabolism in leukemogenesis. Blood Adv 2023; 7:7525-7538. [PMID: 37639313 PMCID: PMC10761356 DOI: 10.1182/bloodadvances.2023010460] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 08/01/2023] [Accepted: 08/13/2023] [Indexed: 08/29/2023] Open
Abstract
Leukemia stem cells (LSCs) share numerous features with healthy hematopoietic stem cells (HSCs). G-protein coupled receptor family C group 5 member C (GPRC5C) is a regulator of HSC dormancy. However, GPRC5C functionality in acute myeloid leukemia (AML) is yet to be determined. Within patient AML cohorts, high GPRC5C levels correlated with poorer survival. Ectopic Gprc5c expression increased AML aggression through the activation of NF-κB, which resulted in an altered metabolic state with increased levels of intracellular branched-chain amino acids (BCAAs). This onco-metabolic profile was reversed upon loss of Gprc5c, which also abrogated the leukemia-initiating potential. Targeting the BCAA transporter SLC7A5 with JPH203 inhibited oxidative phosphorylation and elicited strong antileukemia effects, specifically in mouse and patient AML samples while sparing healthy bone marrow cells. This antileukemia effect was strengthened in the presence of venetoclax and azacitidine. Our results indicate that the GPRC5C-NF-κB-SLC7A5-BCAAs axis is a therapeutic target that can compromise leukemia stem cell function in AML.
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Affiliation(s)
- Yu Wei Zhang
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Talia Velasco-Hernandez
- Department of Biomedicine, Josep Carreras Leukaemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Julian Mess
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School for Biology and Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | | | - Mari Carmen Romero-Mulero
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Nadine Obier
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Nikolaos Karantzelis
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
| | - Jasmin Rettkowski
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Faculty of Biology, University of Freiburg, Freiburg, Germany
- Spemann Graduate School for Biology and Medicine, University of Freiburg, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
| | | | - Noémie Karabacz
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Karin Jäcklein
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Tatsuya Morishima
- Laboratory of Stem Cell Stress, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory of Hematopoietic Stem Cell Engineering, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Juan Luis Trincado
- Department of Biomedicine, Josep Carreras Leukaemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Paola Romecin
- Department of Biomedicine, Josep Carreras Leukaemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Alba Martinez
- Department of Biomedicine, Josep Carreras Leukaemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain
| | - Hitoshi Takizawa
- Laboratory of Stem Cell Stress, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
- Laboratory of Hematopoietic Stem Cell Engineering, International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Khalid Shoumariyeh
- Department of Medicine I, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium, Partner Site Freiburg, and German Cancer Research Center, Heidelberg, Germany
| | - Simon Renders
- Department of Internal Medicine V, Heidelberg University Hospital, Heidelberg, Germany
| | - Robert Zeiser
- Department of Medicine I, Medical Center – University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Heike L. Pahl
- Department of Hematology, Oncology and Stem Cell Transplantation, University Medical Center Freiburg, Freiburg, Germany
| | - François Béliveau
- Quebec leukemia cell bank, Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
| | - Josée Hébert
- Quebec leukemia cell bank, Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
- Division of Hematology and Oncology, Hôpital Maisonneuve-Rosemont, Montréal, QC, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Bernhard Lehnertz
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer, University of Montreal, Montreal, Canada
| | - Pablo Menendez
- Department of Biomedicine, Josep Carreras Leukaemia Research Institute, School of Medicine, University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer, ISIII, Barcelona, Spain
- RICORS-TERAV Network, ISCIII, Madrid, Spain
- Instituciò Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Nina Cabezas-Wallscheid
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg, Germany
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13
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Shi Y, Feng Y, Wang Q, Dong G, Xia W, Jiang F. The Role of tRNA-Centered Translational Regulatory Mechanisms in Cancer. Cancers (Basel) 2023; 16:77. [PMID: 38201505 PMCID: PMC10778012 DOI: 10.3390/cancers16010077] [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: 12/05/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer is a leading cause of morbidity and mortality worldwide. While numerous factors have been identified as contributing to the development of malignancy, our understanding of the mechanisms involved remains limited. Early cancer detection and the development of effective treatments are therefore critical areas of research. One class of molecules that play a crucial role in the transmission of genetic information are transfer RNAs (tRNAs), which are the most abundant RNA molecules in the human transcriptome. Dysregulated synthesis of tRNAs directly results in translation disorders and diseases, including cancer. Moreover, various types of tRNA modifications and the enzymes responsible for these modifications have been implicated in tumor biology. Furthermore, alterations in tRNA modification can impact tRNA stability, and impaired stability can prompt the cleavage of tRNAs into smaller fragments known as tRNA fragments (tRFs). Initially believed to be random byproducts lacking any physiological function, tRFs have now been redefined as non-coding RNA molecules with distinct roles in regulating RNA stability, translation, target gene expression, and other biological processes. In this review, we present recent findings on translational regulatory models centered around tRNAs in tumors, providing a deeper understanding of tumorigenesis and suggesting new directions for cancer treatment.
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Affiliation(s)
- Yuanjian Shi
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Yipeng Feng
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Qinglin Wang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
| | - Gaochao Dong
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Wenjie Xia
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
| | - Feng Jiang
- Department of Thoracic Surgery, Nanjing Medical University Affiliated Cancer Hospital & Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research, Nanjing 211166, China; (Y.S.); (Y.F.); (Q.W.); (G.D.)
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Cancer Institute of Jiangsu Province, Nanjing 210009, China
- The Fourth Clinical College, Nanjing Medical University, Nanjing 210029, China
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14
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Melnick AF, Mullin C, Lin K, McCarter AC, Liang S, Liu YE, Wang Q, Jerome NA, Choe E, Kunnath N, Bodanapu G, Akter F, Magnuson B, Kumar S, Lombard DB, Muntean AG, Ljungman M, Sekiguchi J, Ryan RJH, Chiang MY. Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress. Blood 2023; 142:2159-2174. [PMID: 37616559 PMCID: PMC10733839 DOI: 10.1182/blood.2023020144] [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: 02/16/2023] [Revised: 07/13/2023] [Accepted: 07/31/2023] [Indexed: 08/26/2023] Open
Abstract
ABSTRACT Activated Notch signaling is highly prevalent in T-cell acute lymphoblastic leukemia (T-ALL), but pan-Notch inhibitors showed excessive toxicity in clinical trials. To find alternative ways to target Notch signals, we investigated cell division cycle 73 (Cdc73), which is a Notch cofactor and key component of the RNA polymerase-associated transcriptional machinery, an emerging target in T-ALL. Although we confirmed previous work that CDC73 interacts with NOTCH1, we also found that the interaction in T-ALL was context-dependent and facilitated by the transcription factor ETS1. Using mouse models, we showed that Cdc73 is important for Notch-induced T-cell development and T-ALL maintenance. Mechanistically, chromatin and nascent gene expression profiling showed that Cdc73 intersects with Ets1 and Notch at chromatin within enhancers to activate expression of known T-ALL oncogenes through its enhancer functions. Cdc73 also intersects with these factors within promoters to activate transcription of genes that are important for DNA repair and oxidative phosphorylation through its gene body functions. Consistently, Cdc73 deletion induced DNA damage and apoptosis and impaired mitochondrial function. The CDC73-induced DNA repair expression program co-opted by NOTCH1 is more highly expressed in T-ALL than in any other cancer. These data suggest that Cdc73 might induce a gene expression program that was eventually intersected and hijacked by oncogenic Notch to augment proliferation and mitigate the genotoxic and metabolic stresses of elevated Notch signaling. Our report supports studying factors such as CDC73 that intersect with Notch to derive a basic scientific understanding on how to combat Notch-dependent cancers without directly targeting the Notch complex.
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Affiliation(s)
- Ashley F. Melnick
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Carea Mullin
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Karena Lin
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Anna C. McCarter
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Shannon Liang
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Yiran E. Liu
- Cancer Biology Program, Stanford University, Stanford, CA
| | - Qing Wang
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
| | - Nicole A. Jerome
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
| | - Elizabeth Choe
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI
| | - Nicholas Kunnath
- Center for Healthcare Outcomes and Policy, University of Michigan School of Medicine, Ann Arbor, MI
| | - Geethika Bodanapu
- School of Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA
| | - Fatema Akter
- Department of Anesthesiology, Perioperative and Pain Medicine, Stanford University, Stanford, CA
| | - Brian Magnuson
- Michigan Center for Translational Pathology, University of Michigan School of Medicine, Ann Arbor, MI
| | - Surinder Kumar
- Department of Pathology and Laboratory Medicine and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL
| | - David B. Lombard
- Department of Pathology and Laboratory Medicine and Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL
| | - Andrew G. Muntean
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Mats Ljungman
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Radiology Oncology, University of Michigan School of Medicine, Ann Arbor, MI
| | - JoAnn Sekiguchi
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Human Genetics, University of Michigan School of Medicine, Ann Arbor, MI
| | - Russell J. H. Ryan
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Department of Pathology, University of Michigan, Ann Arbor, MI
| | - Mark Y. Chiang
- Cellular and Molecular Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
- Division of Hematology-Oncology, Department of Internal Medicine, University of Michigan School of Medicine, Ann Arbor, MI
- Cancer Biology Program, University of Michigan School of Medicine, Ann Arbor, MI
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15
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Assis AJB, Santana BLDO, Gualberto ACM, Pittella-Silva F. Therapeutic applications of CRISPR/Cas9 mediated targeted gene editing in acute lymphoblastic leukemia: current perspectives, future challenges, and clinical implications. Front Pharmacol 2023; 14:1322937. [PMID: 38130408 PMCID: PMC10733529 DOI: 10.3389/fphar.2023.1322937] [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: 10/17/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023] Open
Abstract
Acute Lymphoblastic Leukemia (ALL) is the predominant hematological malignancy in pediatric populations, originating from B- or T-cell precursors within the bone marrow. The disease exhibits a high degree of heterogeneity, both at the molecular level and in terms of clinical presentation. A complex interplay between inherited and acquired genetic alterations contributes to disease pathogenesis, often resulting in the disruption of cellular functions integral to the leukemogenic process. The advent of CRISPR/Cas9 as a gene editing tool has revolutionized biological research, underscoring its potential to modify specific genomic loci implicated in cancer. Enhanced understanding of molecular alterations in ALL has facilitated significant advancements in therapeutic strategies. In this review, we scrutinize the application of CRISPR/Cas9 as a tool for identifying genetic targets to improve therapy, circumvent drug resistance, and facilitate CAR-T cell-based immunotherapy. Additionally, we discuss the challenges and future prospects of CRISPR/Cas9 applications in ALL.
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Affiliation(s)
| | | | | | - Fabio Pittella-Silva
- Laboratory of Molecular Pathology of Cancer, Faculty of Health Sciences and Medicine, University of Brasília, Brasília, Brazil
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16
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van Breugel ME, van Kruijsbergen I, Mittal C, Lieftink C, Brouwer I, van den Brand T, Kluin RJC, Hoekman L, Menezes RX, van Welsem T, Del Cortona A, Malik M, Beijersbergen RL, Lenstra TL, Verstrepen KJ, Pugh BF, van Leeuwen F. Locus-specific proteome decoding reveals Fpt1 as a chromatin-associated negative regulator of RNA polymerase III assembly. Mol Cell 2023; 83:4205-4221.e9. [PMID: 37995691 DOI: 10.1016/j.molcel.2023.10.037] [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: 04/18/2023] [Revised: 09/27/2023] [Accepted: 10/26/2023] [Indexed: 11/25/2023]
Abstract
Transcription of tRNA genes by RNA polymerase III (RNAPIII) is tuned by signaling cascades. The emerging notion of differential tRNA gene regulation implies the existence of additional regulatory mechanisms. However, tRNA gene-specific regulators have not been described. Decoding the local chromatin proteome of a native tRNA gene in yeast revealed reprogramming of the RNAPIII transcription machinery upon nutrient perturbation. Among the dynamic proteins, we identified Fpt1, a protein of unknown function that uniquely occupied RNAPIII-regulated genes. Fpt1 binding at tRNA genes correlated with the efficiency of RNAPIII eviction upon nutrient perturbation and required the transcription factors TFIIIB and TFIIIC but not RNAPIII. In the absence of Fpt1, eviction of RNAPIII was reduced, and the shutdown of ribosome biogenesis genes was impaired upon nutrient perturbation. Our findings provide support for a chromatin-associated mechanism required for RNAPIII eviction from tRNA genes and tuning the physiological response to changing metabolic demands.
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Affiliation(s)
- Maria Elize van Breugel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ila van Kruijsbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Chitvan Mittal
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Cor Lieftink
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Ineke Brouwer
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Teun van den Brand
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Liesbeth Hoekman
- Proteomics Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Renée X Menezes
- Biostatistics Centre and Division of Psychosocial Research and Epidemiology, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Andrea Del Cortona
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis and Robotics and Screening Center, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Genomics Core Facility, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands
| | - Tineke L Lenstra
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Division of Gene Regulation, Netherlands Cancer Institute, Oncode Institute, Amsterdam 1066 CX, the Netherlands
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, KU Leuven, 3001 Heverlee-Leuven, Belgium
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Biotechnology Building, Cornell University, Ithaca, NY 14853, USA
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam 1066 CX, the Netherlands; Department of Medical Biology, Amsterdam UMC, University of Amsterdam, Amsterdam 1105 AZ, the Netherlands.
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17
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Bartman CR, Faubert B, Rabinowitz JD, DeBerardinis RJ. Metabolic pathway analysis using stable isotopes in patients with cancer. Nat Rev Cancer 2023; 23:863-878. [PMID: 37907620 DOI: 10.1038/s41568-023-00632-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/25/2023] [Indexed: 11/02/2023]
Abstract
Metabolic reprogramming is central to malignant transformation and cancer cell growth. How tumours use nutrients and the relative rates of reprogrammed pathways are areas of intense investigation. Tumour metabolism is determined by a complex and incompletely defined combination of factors intrinsic and extrinsic to cancer cells. This complexity increases the value of assessing cancer metabolism in disease-relevant microenvironments, including in patients with cancer. Stable-isotope tracing is an informative, versatile method for probing tumour metabolism in vivo. It has been used extensively in preclinical models of cancer and, with increasing frequency, in patients with cancer. In this Review, we describe approaches for using in vivo isotope tracing to define fuel preferences and pathway engagement in tumours, along with some of the principles that have emerged from this work. Stable-isotope infusions reported so far have revealed that in humans, tumours use a diverse set of nutrients to supply central metabolic pathways, including the tricarboxylic acid cycle and amino acid synthesis. Emerging data suggest that some activities detected by stable-isotope tracing correlate with poor clinical outcomes and may drive cancer progression. We also discuss current challenges in isotope tracing, including comparisons of in vivo and in vitro models, and opportunities for future discovery in tumour metabolism.
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Affiliation(s)
- Caroline R Bartman
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Brandon Faubert
- Department of Medicine, Section of Hematology/Oncology, University of Chicago, Chicago, IL, USA
| | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
| | - Ralph J DeBerardinis
- Howard Hughes Medical Institute and Children's Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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18
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Zhou L, Yang L, Feng Y, Chen S. Pooled screening with next-generation gene editing tools. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023; 28:100479. [PMID: 38222973 PMCID: PMC10786633 DOI: 10.1016/j.cobme.2023.100479] [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] [Indexed: 01/16/2024]
Abstract
Pooled screening creates a pool of cells with genetic variants, allowing for the simultaneous examination for changes in behavior or function. By selectively inducing mutations or perturbing expression, it enables scientists to systematically investigate the function of genes or genetic elements. Emerging gene editing tools, such as CRISPR, coupled with advances in sequencing and computational capabilities, provide growing opportunities to understand biological processes in humans, animals, and plants as well as to identify potential targets for therapeutic interventions and agricultural research. In this review, we highlight the recent advances of pooled screens using next-generation gene editing tools along with relevant challenges and describe potential future directions of this technology.
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Affiliation(s)
- Liqun Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
| | - Luojia Yang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Yanzhi Feng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
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19
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Pinzaru AM, Tavazoie SF. Transfer RNAs as dynamic and critical regulators of cancer progression. Nat Rev Cancer 2023; 23:746-761. [PMID: 37814109 DOI: 10.1038/s41568-023-00611-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 10/11/2023]
Abstract
Transfer RNAs (tRNAs) have been historically viewed as non-dynamic adaptors that decode the genetic code into proteins. Recent work has uncovered dynamic regulatory roles for these fascinating molecules. Advances in tRNA detection methods have revealed that specific tRNAs can become modulated upon DNA copy number and chromatin alterations and can also be perturbed by oncogenic signalling and transcriptional regulators in cancer cells or the tumour microenvironment. Such alterations in the levels of specific tRNAs have been shown to causally impact cancer progression, including metastasis. Moreover, sequencing methods have identified tRNA-derived small RNAs that influence various aspects of cancer progression, such as cell proliferation and invasion, and could serve as diagnostic and prognostic biomarkers or putative therapeutic targets in various cancers. Finally, there is accumulating evidence, including from genetic models, that specific tRNA synthetases - the enzymes responsible for charging tRNAs with amino acids - can either promote or suppress tumour formation. In this Review, we provide an overview of how deregulation of tRNAs influences cancer formation and progression.
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Affiliation(s)
- Alexandra M Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
| | - Sohail F Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA.
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20
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Ma J, Chen K, Ding Y, Li X, Tang Q, Jin B, Luo RY, Thyparambil S, Han Z, Chou CJ, Zhou A, Schilling J, Lin Z, Ma Y, Li Q, Zhang M, Sylvester KG, Nagpal S, McElhinney DB, Ling XB, Chen B. High-throughput quantitation of amino acids and acylcarnitine in cerebrospinal fluid: identification of PCNSL biomarkers and potential metabolic messengers. Front Mol Biosci 2023; 10:1257079. [PMID: 38028545 PMCID: PMC10644155 DOI: 10.3389/fmolb.2023.1257079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Background: Due to the poor prognosis and rising occurrence, there is a crucial need to improve the diagnosis of Primary Central Nervous System Lymphoma (PCNSL), which is a rare type of non-Hodgkin's lymphoma. This study utilized targeted metabolomics of cerebrospinal fluid (CSF) to identify biomarker panels for the improved diagnosis or differential diagnosis of primary central nervous system lymphoma (PCNSL). Methods: In this study, a cohort of 68 individuals, including patients with primary central nervous system lymphoma (PCNSL), non-malignant disease controls, and patients with other brain tumors, was recruited. Their cerebrospinal fluid samples were analyzed using the Ultra-high performance liquid chromatography - tandem mass spectrometer (UHPLC-MS/MS) technique for targeted metabolomics analysis. Multivariate statistical analysis and logistic regression modeling were employed to identify biomarkers for both diagnosis (Dx) and differential diagnosis (Diff) purposes. The Dx and Diff models were further validated using a separate cohort of 34 subjects through logistic regression modeling. Results: A targeted analysis of 45 metabolites was conducted using UHPLC-MS/MS on cerebrospinal fluid (CSF) samples from a cohort of 68 individuals, including PCNSL patients, non-malignant disease controls, and patients with other brain tumors. Five metabolic features were identified as biomarkers for PCNSL diagnosis, while nine metabolic features were found to be biomarkers for differential diagnosis. Logistic regression modeling was employed to validate the Dx and Diff models using an independent cohort of 34 subjects. The logistic model demonstrated excellent performance, with an AUC of 0.83 for PCNSL vs. non-malignant disease controls and 0.86 for PCNSL vs. other brain tumor patients. Conclusion: Our study has successfully developed two logistic regression models utilizing metabolic markers in cerebrospinal fluid (CSF) for the diagnosis and differential diagnosis of PCNSL. These models provide valuable insights and hold promise for the future development of a non-invasive and reliable diagnostic tool for PCNSL.
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Affiliation(s)
- Jingjing Ma
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Kun Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Yun Ding
- mProbe Inc., Palo Alto, CA, United States
| | - Xiao Li
- mProbe Inc., Palo Alto, CA, United States
| | | | - Bo Jin
- mProbe Inc., Palo Alto, CA, United States
| | - Ruben Y. Luo
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, United States
| | - Sheeno Thyparambil
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhi Han
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, United States
| | - C. James Chou
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | | | | | - Zhiguang Lin
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yan Ma
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Qing Li
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Mengxue Zhang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
| | - Karl G. Sylvester
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Seema Nagpal
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, United States
| | - Doff B. McElhinney
- Departments of Cardiothoracic Surgery and Pediatrics (Cardiology), Stanford University School of Medicine, Stanford, CA, United States
| | - Xuefeng B. Ling
- Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
| | - Bobin Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai, China
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21
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Rodríguez-Vázquez GO, Diaz-Quiñones AO, Chorna N, Salgado-Villanueva IK, Tang J, Ortiz WIS, Maldonado HM. Synergistic interactions of cytarabine-adavosertib in leukemic cell lines proliferation and metabolomic endpoints. Biomed Pharmacother 2023; 166:115352. [PMID: 37633054 PMCID: PMC10530627 DOI: 10.1016/j.biopha.2023.115352] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/09/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023] Open
Abstract
Drug synergy allows reduced dosing, side effects and tolerance. Optimization of drug synergy chemotherapy is fundamental in acute lymphocytic leukemia and other cancers. This study aimed to analyze the pharmacodynamic synergy between the anti-metabolite cytarabine and WEE1 inhibitor adavosertib on acute leukemia cell lines CCRF-CEM and Jurkat. In both cell lines analysis of concentration-inhibition curves of adavosertib-cytarabine combinations and synergy matrixes supported mutually synergistic drug interactions. Overall mean ( ± SD) synergy scores were higher in Jurkat than CCRF-CEM: Jurkat, ZIP 22.51 ± 1.1, Bliss 22.49 ± 1.1, HSA 23.44 ± 1.0, Loewe 14.16 ± 1.2; and, CCRF-CEM, ZIP 9.17 ± 1.9, Bliss 8.13 ± 2.1, HSA 11.48 ± 1.9 and Loewe 4.99 ± 1.8. Jurkat also surpassed CCRF-CEM in high-degree synergistic adavosertib-cytarabine interactions with mean across-models synergy values of ∼89.1% ± 2.9 for 63 nM cytarabine-97 nM adavosertib (91.4% inhibition synergy barometer). Combination sensitivity scores scatter plots confirmed combination's synergy efficacy. This combined approach permitted identification and prioritization of 63 nM cytarabine-97 nM adavosertib for multiple endpoints analysis. This combination did not affect PBMC viability, while exhibiting Jurkat selective synergy. Immunoblots also revealed Jurkat selective synergistically increased γH2AX phosphorylation, while CDC2 phosphorylation effects were attributed to adavosertib's WEE1 inhibition. In conclusion, the high synergistic efficacy combination of cytarabine (63 nM) and adavosertib (97 nM) was associated with remarkable alterations in metabolites related to the Krebs cycle in Jurkat. The metabolic pathways and processes are related to gluconeogenesis, amino acids, nucleotides, glutathione, electron transport and Warburg effect. All above relate to cell survival, apoptosis, and cancer progression. Our findings could pave the way for novel biomarkers in treatment, diagnosis, and prognosis of leukemia and other cancers.
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Affiliation(s)
- Gabriel O Rodríguez-Vázquez
- Pharmacology Department, Universidad Central del Caribe, School of Medicine, PO Box 60327, Bayamón, PR 00960-6032, USA
| | - Adriana O Diaz-Quiñones
- Pharmacology Department, Universidad Central del Caribe, School of Medicine, PO Box 60327, Bayamón, PR 00960-6032, USA
| | - Nataliya Chorna
- Biochemistry Department, University of Puerto Rico Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067, USA
| | - Iris K Salgado-Villanueva
- Pharmacology Department, Universidad Central del Caribe, School of Medicine, PO Box 60327, Bayamón, PR 00960-6032, USA
| | - Jing Tang
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00290, Finland; Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 8, Helsinki 00290, Finland
| | - Walter I Silva Ortiz
- Physiology Department, University of Puerto Rico Medical Sciences Campus, PO Box 365067, San Juan, PR 00936-5067, USA.
| | - Héctor M Maldonado
- Pharmacology Department, Universidad Central del Caribe, School of Medicine, PO Box 60327, Bayamón, PR 00960-6032, USA
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22
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Shi R, DU W, He Y, Hu J, Yu H, Zhou W, Guo J, Feng X. High expression of VARS promotes the growth of multiple myeloma cells by causing imbalance in valine metabolism. ZHONG NAN DA XUE XUE BAO. YI XUE BAN = JOURNAL OF CENTRAL SOUTH UNIVERSITY. MEDICAL SCIENCES 2023; 48:795-808. [PMID: 37587064 PMCID: PMC10930441 DOI: 10.11817/j.issn.1672-7347.2023.220602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Indexed: 08/18/2023]
Abstract
OBJECTIVES Multiple myeloma (MM) is a plasma cell malignancy occurring in middle and old age. MM is still an incurable disease due to its frequent recurrence and drug resistance. However, its pathogenesis is still unclear. Abnormal amino acid metabolism is one of the important characteristics of MM, and the important metabolic pathway of amino acids participates in protein synthesis as basic raw materials. Aminoacyl transfer ribonucleic acid synthetase (ARS) gene is a key regulatory gene in protein synthesis. This study aims to explore the molecular mechanism for ARS, a key factor of amino acid metabolism, in regulating amino acid metabolism in MM and affecting MM growth. METHODS The corresponding gene number was combined with the gene expression profile GSE5900 dataset and GSE2658 dataset in Gene Expression Omnibus (GEO) database to standardize the gene expression data of ARS. GSEA_4.2.0 software was used to analyze the difference of gene enrichment between healthy donors (HD) and MM patients in GEO database. GraphPad Prism 7 was used to draw heat maps and perform data analysis. Kaplan-Meier and Cox regression model were used to analyze the expression of ARS gene and the prognosis of MM patients, respectively. Bone marrow samples from 7 newly diagnosed MM patients were collected, CD138+ and CD138- cells were obtained by using CD138 antibody magnetic beads, and the expression of ARS in MM clinical samples was analyzed by real-time RT-PCR. Human B lymphocyte GM12878 cells and human MM cell lines ARP1, NCI-H929, OCI-MY5, U266, RPMI 8266, OPM-2, JJN-3, KMS11, MM1.s cells were selected as the study objects. The expression of ARS in MM cell lines was analyzed by real-time RT-PCR and Western blotting. Short hairpin RNA (shRNA) lentiviruses were used to construct gene knock-out plasmids (VARS-sh group). No-load plasmids (scramble group) and gene knock-out plasmids (VARS-sh group) were transfected into HEK 293T cells with for virus packaging, respectively. Stable expression cell lines were established by infecting ARP1 and OCI-MY5 cells, and the effects of knockout valyl-tRNA synthetase (VARS) gene on proliferation and apoptosis of MM cells were detected by cell counting and flow cytometry, respectively. GEO data were divided into a high expression group and a low expression group according to the expression of VARS. Bioinformatics analysis was performed to explore the downstream pathways affected by VARS. Gas chromatography time-of-flight mass spectrometry (GC-TOF/MS) and high performance liquid chromatography (HPLC) were used to detect the valine content in CD138+ cells and ARP1, OCI-MY5 cells and supernatant of knockdown VARS gene in bone marrow samples from patients, respectively. RESULTS Gene enrichment analysis showed that tRNA processing related genes were significantly enriched in MM compared with HD (P<0.0001). Further screening of tRNA processing-pathway related subsets revealed that cytoplasmic aminoacyl tRNA synthetase family genes were significantly enriched in MM (P<0.0001). The results of gene expression heat map showed that the ARS family genes except alanyl-tRNA synthetase (AARS), arginyl-tRNA synthetase (RARS), seryl-tRNA synthetase (SARS) in GEO data were highly expressed in MM (all P<0.01). With the development of monoclonal gammopathy of undetermined significance (MGUS) to MM, the gene expression level was increased gradually. Kaplan-Meier univariate analysis of survival results showed that there were significant differences in the prognosis of MM patients in methionyl-tRNA synthetase (MARS), asparaginyl-tRNA synthetase (NARS) and VARS between the high expression group and the low expression group (all P<0.05). Cox regression model multivariate analysis showed that the high expression of VARS was associated with abnormal overall survival time of MM (HR=1.83, 95% CI 1.10 to 3.06, P=0.021). The high expression of NARS (HR=0.90, 95% CI 0.34 to 2.38) and MARS (HR=1.59, 95% CI 0.73 to 3.50) had no effect on the overall survival time of MM patients (both P>0.05). Real-time RT-PCR and Western blotting showed that VARS, MARS and NARS were highly expressed in CD138+ MM cells and MM cell lines of clinical patients (all P<0.05). Cell counting and flow cytometry results showed that the proliferation of MM cells by knockout VARS was significantly inhibited (P<0.01), the proportion of apoptosis was significantly increased (P<0.05). Bioinformatics analysis showed that in addition to several pathways including the cell cycle regulated by VARS, the valine, leucine and isoleucine catabolic pathways were upregulated. Non-targeted metabolomics data showed reduced valine content in CD138+ tumor cells in MM patients compared to HD (P<0.05). HPLC results showed that compared with the scramble group, the intracellular and medium supernatant content of ARP1 cells and the medium supernatant of OCI-MY5 in the VARS-shRNA group was increased (all P<0.05). CONCLUSIONS MM patients with abnormal high expression of VARS have a poor prognosis. VARS promotes the malignant growth of MM cells by affecting the regulation of valine metabolism.
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Affiliation(s)
- Rui Shi
- Department of Health Inspection and Quarantine, Xiangya School of Public Health, Central South University, Changsha 410006.
| | - Wanqing DU
- Department of Health Inspection and Quarantine, Xiangya School of Public Health, Central South University, Changsha 410006
| | - Yanjuan He
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008
| | - Jian Hu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008
| | - Han Yu
- Department of Health Inspection and Quarantine, Xiangya School of Public Health, Central South University, Changsha 410006
| | - Wen Zhou
- Cancer Research Institute, School of Basic Medical Sciences, Central South University, Changsha 410078, China
| | - Jiaojiao Guo
- Department of Hematology, Xiangya Hospital, Central South University, Changsha 410008.
| | - Xiangling Feng
- Department of Health Inspection and Quarantine, Xiangya School of Public Health, Central South University, Changsha 410006.
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23
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Ren D, Mo Y, Yang M, Wang D, Wang Y, Yan Q, Guo C, Xiong W, Wang F, Zeng Z. Emerging roles of tRNA in cancer. Cancer Lett 2023; 563:216170. [PMID: 37054943 DOI: 10.1016/j.canlet.2023.216170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 04/15/2023]
Abstract
Transfer RNAs (tRNAs) play pivotal roles in the transmission of genetic information, and abnormality of tRNAs directly leads to translation disorders and causes diseases, including cancer. The complex modifications enable tRNA to execute its delicate biological function. Alteration of appropriate modifications may affect the stability of tRNA, impair its ability to carry amino acids, and disrupt the pairing between anticodons and codons. Studies confirmed that dysregulation of tRNA modifications plays an important role in carcinogenesis. Furthermore, when the stability of tRNA is impaired, tRNAs are cleaved into small tRNA fragments (tRFs) by specific RNases. Though tRFs have been found to play vital regulatory roles in tumorigenesis, its formation process is far from clear. Understanding improper tRNA modifications and abnormal formation of tRFs in cancer is conducive to uncovering the role of metabolic process of tRNA under pathological conditions, which may open up new avenues for cancer prevention and treatment.
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Affiliation(s)
- Daixi Ren
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Yongzhen Mo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Mei Yang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Dan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China; Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Can Guo
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Fuyan Wang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China; Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China.
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24
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Tau S, Miller TW. The role of cancer cell bioenergetics in dormancy and drug resistance. Cancer Metastasis Rev 2023; 42:87-98. [PMID: 36696004 PMCID: PMC10233409 DOI: 10.1007/s10555-023-10081-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/11/2023] [Indexed: 01/26/2023]
Abstract
While anti-cancer drug treatments are often effective for the clinical management of cancer, these treatments frequently leave behind drug-tolerant persister cancer cells that can ultimately give rise to recurrent disease. Such persistent cancer cells can lie dormant for extended periods of time, going undetected by conventional clinical means. Understanding the mechanisms that such dormant cancer cells use to survive, and the mechanisms that drive emergence from dormancy, is critical to the development of improved therapeutic strategies to prevent and manage disease recurrence. Cancer cells often exhibit metabolic alterations compared to their non-transformed counterparts. An emerging body of evidence supports the notion that dormant cancer cells also have unique metabolic adaptations that may offer therapeutically targetable vulnerabilities. Herein, we review mechanisms through which cancer cells metabolically adapt to persist during drug treatments and develop drug resistance. We also highlight emerging therapeutic strategies to target dormant cancer cells via their metabolic features.
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Affiliation(s)
- Steven Tau
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth Cancer Center, Lebanon, NH, USA
| | - Todd W Miller
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Dartmouth Cancer Center, Lebanon, NH, USA.
- Dartmouth-Hitchcock Medical Center, One Medical Center Drive, HB-7936, Lebanon, NH 03756, USA.
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25
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Melnick A, Liang S, Liu Y, Wang Q, Dean N, Choe E, Kunnath N, Bodanapu G, Mullin C, Akter F, Lin K, Magnuson B, Kumar S, Lombard DB, Muntean AG, Ljungman M, Sekiguchi J, Ryan RJH, Chiang MY. Cdc73 protects Notch-induced T-cell leukemia cells from DNA damage and mitochondrial stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525059. [PMID: 36711472 PMCID: PMC9882378 DOI: 10.1101/2023.01.22.525059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Activated Notch signaling is highly prevalent in T-cell acute lymphoblastic leukemia (T-ALL) but pan-Notch inhibitors were toxic in clinical trials. To find alternative ways to target Notch signals, we investigated Cell division cycle 73 (Cdc73), which is a Notch cofactor and component of transcriptional machinery, a potential target in T-ALL. While we confirmed previous work that CDC73 interacts with NOTCH1, we also found that the interaction in T-ALL was context-dependent and facilitated by the lymphoid transcription factor ETS1. Using mouse models, we showed that Cdc73 is important for Notch-induced T-cell development and T-ALL maintenance. Mechanistically, Cdc73, Ets1, and Notch intersect chromatin at promoters and enhancers to activate oncogenes and genes that are important for DNA repair and oxidative phosphorylation. Consistently, Cdc73 deletion in T-ALL cells induced DNA damage and impaired mitochondrial function. Our data suggests that Cdc73 might promote a gene expression program that was eventually intersected by Notch to mitigate the genotoxic and metabolic stresses of elevated Notch signaling. We also provide mechanistic support for testing inhibitors of DNA repair, oxidative phosphorylation, and transcriptional machinery. Inhibiting pathways like Cdc73 that intersect with Notch at chromatin might constitute a strategy to weaken Notch signals without directly targeting the Notch complex.
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Hsu DJ, Gao J, Yamaguchi N, Pinzaru A, Wu Q, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie SF. Arginine limitation drives a directed codon-dependent DNA sequence evolution response in colorectal cancer cells. SCIENCE ADVANCES 2023; 9:eade9120. [PMID: 36608131 PMCID: PMC9821863 DOI: 10.1126/sciadv.ade9120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/01/2022] [Indexed: 05/18/2023]
Abstract
Utilization of specific codons varies between organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine limitation-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced an adaptive proteomic shift toward low-arginine codon-containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.
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Affiliation(s)
- Dennis J. Hsu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Gao
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Norihiro Yamaguchi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Alexandra Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Qiushuang Wu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Nandan Mandayam
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Maria Liberti
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
| | - Sohail F. Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
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27
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Ghazimoradi MH, Karimpour-Fard N, Babashah S. The Promising Role of Non-Coding RNAs as Biomarkers and Therapeutic Targets for Leukemia. Genes (Basel) 2023; 14:131. [PMID: 36672872 PMCID: PMC9859176 DOI: 10.3390/genes14010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Early-stage leukemia identification is crucial for effective disease management and leads to an improvement in the survival of leukemia patients. Approaches based on cutting-edge biomarkers with excellent accuracy in body liquids provide patients with the possibility of early diagnosis with high sensitivity and specificity. Non-coding RNAs have recently received a great deal of interest as possible biomarkers in leukemia due to their participation in crucial oncogenic processes such as proliferation, differentiation, invasion, apoptosis, and their availability in body fluids. Recent studies have revealed a strong correlation between leukemia and the deregulated non-coding RNAs. On this basis, these RNAs are also great therapeutic targets. Based on these advantages, we tried to review the role of non-coding RNAs in leukemia. Here, the significance of several non-coding RNA types in leukemia is highlighted, and their potential roles as diagnostic, prognostic, and therapeutic targets are covered.
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Affiliation(s)
- Mohammad H. Ghazimoradi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Naeim Karimpour-Fard
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
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Hsu DJ, Gao J, Yamaguchi N, Pinzaru A, Mandayam N, Liberti M, Heissel S, Alwaseem H, Tavazoie S, Tavazoie SF. Arginine limitation causes a directed DNA sequence evolution response in colorectal cancer cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.02.521806. [PMID: 36711568 PMCID: PMC9881871 DOI: 10.1101/2023.01.02.521806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Utilization of specific codons varies significantly across organisms. Cancer represents a model for understanding DNA sequence evolution and could reveal causal factors underlying codon evolution. We found that across human cancer, arginine codons are frequently mutated to other codons. Moreover, arginine restriction-a feature of tumor microenvironments-is sufficient to induce arginine codon-switching mutations in human colon cancer cells. Such DNA codon switching events encode mutant proteins with arginine residue substitutions. Mechanistically, arginine limitation caused rapid reduction of arginine transfer RNAs and the stalling of ribosomes over arginine codons. Such selective pressure against arginine codon translation induced a proteomic shift towards low arginine codon containing genes, including specific amino acid transporters, and caused mutational evolution away from arginine codons-reducing translational bottlenecks that occurred during arginine starvation. Thus, environmental availability of a specific amino acid can influence DNA sequence evolution away from its cognate codons and generate altered proteins.
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Affiliation(s)
- Dennis J. Hsu
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jenny Gao
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Norihiro Yamaguchi
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Alexandra Pinzaru
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Nandan Mandayam
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Maria Liberti
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
| | - Søren Heissel
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Hanan Alwaseem
- Proteomics Resource Center, The Rockefeller University, New York, NY, USA
| | - Saeed Tavazoie
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY USA
| | - Sohail F. Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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29
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Dietary regulation in health and disease. Signal Transduct Target Ther 2022; 7:252. [PMID: 35871218 PMCID: PMC9308782 DOI: 10.1038/s41392-022-01104-w] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/21/2022] [Accepted: 07/04/2022] [Indexed: 02/08/2023] Open
Abstract
Nutriments have been deemed to impact all physiopathologic processes. Recent evidences in molecular medicine and clinical trials have demonstrated that adequate nutrition treatments are the golden criterion for extending healthspan and delaying ageing in various species such as yeast, drosophila, rodent, primate and human. It emerges to develop the precision-nutrition therapeutics to slow age-related biological processes and treat diverse diseases. However, the nutritive advantages frequently diversify among individuals as well as organs and tissues, which brings challenges in this field. In this review, we summarize the different forms of dietary interventions extensively prescribed for healthspan improvement and disease treatment in pre-clinical or clinical. We discuss the nutrient-mediated mechanisms including metabolic regulators, nutritive metabolism pathways, epigenetic mechanisms and circadian clocks. Comparably, we describe diet-responsive effectors by which dietary interventions influence the endocrinic, immunological, microbial and neural states responsible for improving health and preventing multiple diseases in humans. Furthermore, we expatiate diverse patterns of dietotheroapies, including different fasting, calorie-restricted diet, ketogenic diet, high-fibre diet, plants-based diet, protein restriction diet or diet with specific reduction in amino acids or microelements, potentially affecting the health and morbid states. Altogether, we emphasize the profound nutritional therapy, and highlight the crosstalk among explored mechanisms and critical factors to develop individualized therapeutic approaches and predictors.
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Abstract
tRNAs are key adaptor molecules that decipher the genetic code during translation of mRNAs in protein synthesis. In contrast to the traditional view of tRNAs as ubiquitously expressed housekeeping molecules, awareness is now growing that tRNA-encoding genes display tissue-specific and cell type-specific patterns of expression, and that tRNA gene expression and function are both dynamically regulated by post-transcriptional RNA modifications. Moreover, dysregulation of tRNAs, mediated by alterations in either their abundance or function, can have deleterious consequences that contribute to several distinct human diseases, including neurological disorders and cancer. Accumulating evidence shows that reprogramming of mRNA translation through altered tRNA activity can drive pathological processes in a codon-dependent manner. This Review considers the emerging evidence in support of the precise control of functional tRNA levels as an important regulatory mechanism that coordinates mRNA translation and protein expression in physiological cell homeostasis, and highlights key examples of human diseases that are linked directly to tRNA dysregulation.
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Affiliation(s)
- Esteban A Orellana
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Elisabeth Siegal
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Richard I Gregory
- Stem Cell Program, Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
- Harvard Initiative for RNA Medicine, Harvard University, Boston, MA, USA.
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Sanchez-Burgos L, Navarro-González B, García-Martín S, Sirozh O, Mota-Pino J, Fueyo-Marcos E, Tejero H, Antón ME, Murga M, Al-Shahrour F, Fernandez-Capetillo O. Activation of the integrated stress response is a vulnerability for multidrug-resistant FBXW7-deficient cells. EMBO Mol Med 2022; 14:e15855. [PMID: 35861150 PMCID: PMC9449593 DOI: 10.15252/emmm.202215855] [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: 02/08/2022] [Revised: 07/06/2022] [Accepted: 07/08/2022] [Indexed: 12/04/2022] Open
Abstract
FBXW7 is one of the most frequently mutated tumor suppressors, deficiency of which has been associated with resistance to some anticancer therapies. Through bioinformatics and genome‐wide CRISPR screens, we here reveal that FBXW7 deficiency leads to multidrug resistance (MDR). Proteomic analyses found an upregulation of mitochondrial factors as a hallmark of FBXW7 deficiency, which has been previously linked to chemotherapy resistance. Despite this increased expression of mitochondrial factors, functional analyses revealed that mitochondria are under stress, and genetic or chemical targeting of mitochondria is preferentially toxic for FBXW7‐deficient cells. Mechanistically, the toxicity of therapies targeting mitochondrial translation such as the antibiotic tigecycline relates to the activation of the integrated stress response (ISR) in a GCN2 kinase‐dependent manner. Furthermore, the discovery of additional drugs that are toxic for FBXW7‐deficient cells showed that all of them unexpectedly activate a GCN2‐dependent ISR regardless of their accepted mechanism of action. Our study reveals that while one of the most frequent mutations in cancer reduces the sensitivity to the vast majority of available therapies, it renders cells vulnerable to ISR‐activating drugs.
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Affiliation(s)
- Laura Sanchez-Burgos
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Belén Navarro-González
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | | | - Oleksandra Sirozh
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Jorge Mota-Pino
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Elena Fueyo-Marcos
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Héctor Tejero
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Marta Elena Antón
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Matilde Murga
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Fátima Al-Shahrour
- Bioinformatics Unit, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Oscar Fernandez-Capetillo
- Genomic Instability Group, Spanish National Cancer Research Centre (CNIO), Madrid, Spain.,Science for Life Laboratory, Division of Genome Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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Trautman ME, Richardson NE, Lamming DW. Protein restriction and branched-chain amino acid restriction promote geroprotective shifts in metabolism. Aging Cell 2022; 21:e13626. [PMID: 35526271 PMCID: PMC9197406 DOI: 10.1111/acel.13626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 04/13/2022] [Accepted: 04/21/2022] [Indexed: 01/20/2023] Open
Abstract
The proportion of humans suffering from age‐related diseases is increasing around the world, and creative solutions are needed to promote healthy longevity. Recent work has clearly shown that a calorie is not just a calorie—and that low protein diets are associated with reduced mortality in humans and promote metabolic health and extended lifespan in rodents. Many of the benefits of protein restriction on metabolism and aging are the result of decreased consumption of the three branched‐chain amino acids (BCAAs), leucine, isoleucine, and valine. Here, we discuss the emerging evidence that BCAAs are critical modulators of healthy metabolism and longevity in rodents and humans, as well as the physiological and molecular mechanisms that may drive the benefits of BCAA restriction. Our results illustrate that protein quality—the specific composition of dietary protein—may be a previously unappreciated driver of metabolic dysfunction and that reducing dietary BCAAs may be a promising new approach to delay and prevent diseases of aging.
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Affiliation(s)
- Michaela E. Trautman
- Department of Medicine University of Wisconsin‐Madison Madison Wisconsin USA
- William S. Middleton Memorial Veterans Hospital Madison Wisconsin USA
- Interdepartmental Graduate Program in Nutritional Sciences University of Wisconsin‐Madison Madison Wisconsin USA
| | - Nicole E. Richardson
- Department of Medicine University of Wisconsin‐Madison Madison Wisconsin USA
- William S. Middleton Memorial Veterans Hospital Madison Wisconsin USA
- Endocrinology and Reproductive Physiology Graduate Training Program University of Wisconsin‐Madison Madison Wisconsin USA
| | - Dudley W. Lamming
- Department of Medicine University of Wisconsin‐Madison Madison Wisconsin USA
- William S. Middleton Memorial Veterans Hospital Madison Wisconsin USA
- Endocrinology and Reproductive Physiology Graduate Training Program University of Wisconsin‐Madison Madison Wisconsin USA
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34
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Lee AK, Aifantis I, Thandapani P. Emerging roles for tRNAs in hematopoiesis and hematological malignancies. Trends Immunol 2022; 43:466-477. [PMID: 35490133 DOI: 10.1016/j.it.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 11/26/2022]
Abstract
tRNAs are central players in decoding the genetic code linking codons in mRNAs with cognate amino acids during protein synthesis. Recent discoveries have placed tRNAs as key regulators of gene expression during hematopoiesis, especially in hematopoietic stem cell (HSC) maintenance and immune development. These functions have been shown to be influenced by dynamic changes in tRNA expression, post-transcriptional base modifications, tRNA-interacting proteins, and tRNA fragmentation; these events underlie the complexity of tRNA-mediated regulatory events in hematopoiesis. In this review, we discuss these recent findings and highlight how deregulation of tRNA biogenesis can contribute to hematological malignancies.
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Affiliation(s)
- Anna K Lee
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Iannis Aifantis
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
| | - Palaniraja Thandapani
- Department of Pathology and Laura and Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
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36
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Sasaki K, Fujiwara T, Ochi T, Ono K, Kato H, Onodera K, Ichikawa S, Fukuhara N, Onishi Y, Yokoyama H, Miyata T, Harigae H. TM5614, an Inhibitor of Plasminogen Activator Inhibitor-1, Exerts an Antitumor Effect on Chronic Myeloid Leukemia. TOHOKU J EXP MED 2022; 257:211-224. [DOI: 10.1620/tjem.2022.j036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
| | - Tohru Fujiwara
- Department of Hematology, Tohoku University Graduate School
| | - Tetsuro Ochi
- Department of Hematology, Tohoku University Graduate School
| | - Koya Ono
- Department of Hematology, Tohoku University Graduate School
| | - Hiroki Kato
- Department of Hematology, Tohoku University Graduate School
| | - Koichi Onodera
- Department of Hematology, Tohoku University Graduate School
| | | | | | - Yasushi Onishi
- Department of Hematology, Tohoku University Graduate School
| | | | - Toshio Miyata
- Department of Molecular Medicine and Therapy, United Centers for Advanced Research and Translational Medicine
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