1
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Kodali S, Proietti L, Valcarcel G, López-Rubio AV, Pessina P, Eder T, Shi J, Jen A, Lupión-Garcia N, Starner AC, Bartels MD, Cui Y, Sands CM, Planas-Riverola A, Martínez A, Velasco-Hernandez T, Tomás-Daza L, Alber B, Manhart G, Mayer IM, Kollmann K, Fatica A, Menendez P, Shishkova E, Rau RE, Javierre BM, Coon J, Chen Q, Van Nostrand EL, Sardina JL, Grebien F, Di Stefano B. RNA sequestration in P-bodies sustains myeloid leukaemia. Nat Cell Biol 2024:10.1038/s41556-024-01489-6. [PMID: 39169219 DOI: 10.1038/s41556-024-01489-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 07/18/2024] [Indexed: 08/23/2024]
Abstract
Post-transcriptional mechanisms are fundamental safeguards of progenitor cell identity and are often dysregulated in cancer. Here, we identified regulators of P-bodies as crucial vulnerabilities in acute myeloid leukaemia (AML) through genome-wide CRISPR screens in normal and malignant haematopoietic progenitors. We found that leukaemia cells harbour aberrantly elevated numbers of P-bodies and show that P-body assembly is crucial for initiation and maintenance of AML. Notably, P-body loss had little effect upon homoeostatic haematopoiesis but impacted regenerative haematopoiesis. Molecular characterization of P-bodies purified from human AML cells unveiled their critical role in sequestering messenger RNAs encoding potent tumour suppressors from the translational machinery. P-body dissolution promoted translation of these mRNAs, which in turn rewired gene expression and chromatin architecture in leukaemia cells. Collectively, our findings highlight the contrasting and unique roles of RNA sequestration in P-bodies during tissue homoeostasis and oncogenesis. These insights open potential avenues for understanding myeloid leukaemia and future therapeutic interventions.
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Affiliation(s)
- Srikanth Kodali
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ludovica Proietti
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gemma Valcarcel
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | | | - Patrizia Pessina
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Thomas Eder
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Junchao Shi
- Division of Biomedical Sciences, School of Medicine, University of California, Riverside, Riverside, CA, USA
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA
| | - Núria Lupión-Garcia
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Anne C Starner
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Mason D Bartels
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Yingzhi Cui
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Caroline M Sands
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Alba Martínez
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | | | | | - Bernhard Alber
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gabriele Manhart
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Isabella Maria Mayer
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Karoline Kollmann
- Institute of Pharmacology and Toxicology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Alessandro Fatica
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, Rome, Italy
| | - Pablo Menendez
- Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
| | - Rachel E Rau
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | | | - Joshua Coon
- Department of Biomolecular Chemistry, University of Wisconsin, Madison, WI, USA
- National Center for Quantitative Biology of Complex Systems, Madison, WI, USA
- Department of Chemistry, University of Wisconsin, Madison, WI, USA
- Morgridge Institute for Research, Madison, WI, USA
| | - Qi Chen
- Molecular Medicine Program, Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Eric L Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Biology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Jose L Sardina
- Josep Carreras Leukaemia Research Institute, Badalona, Spain.
| | - Florian Grebien
- Institute for Medical Biochemistry, University of Veterinary Medicine Vienna, Vienna, Austria.
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Bruno Di Stefano
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX, USA.
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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2
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Mei S, Ma X, Zhou L, Wuyun Q, Wang J, Xiao Q, Wang M, Zhang K, Chen C, Yan J, Ding H. CircSMAD3 represses SMAD3 phosphorylation and ameliorates cardiac remodeling by recruiting YBX1. iScience 2024; 27:110200. [PMID: 38993677 PMCID: PMC11237917 DOI: 10.1016/j.isci.2024.110200] [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: 02/14/2024] [Revised: 04/18/2024] [Accepted: 06/03/2024] [Indexed: 07/13/2024] Open
Abstract
Circular RNA (circRNA) has emerged as potential therapeutic targets for cardiovascular diseases. Given the central role of the TGFβ signaling pathway in cardiac remodeling and its potential as a therapeutic target, we hypothesized that a circRNA from this pathway could modulate cardiac remodeling and serve as a heart failure treatment. Therefore, we identified a circRNA, named circSMAD3, that was significantly reduced in murine heart failure models. Functionally, circSMAD3 mitigated cardiomyocyte hypertrophy and inhibited cardiac fibroblast activation in vitro. Mechanistically, circSMAD3 interacts with YBX1, stabilizing it and facilitating its binding to SMAD3 in the nucleus, disrupting the TGFβ/SMAD3 signaling pathway, and ultimately restoring cardiac remodeling. This study highlights circSMAD3 as a promising therapeutic target for heart failure treatment.
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Affiliation(s)
- Shuai Mei
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Xiaozhu Ma
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Li Zhou
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Qidamugai Wuyun
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jing Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Qianqian Xiao
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Man Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Kaiyue Zhang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Chen Chen
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Jiangtao Yan
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
| | - Hu Ding
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, People's Republic of China
- Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan 430030, China
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3
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Dheeraj A, Garcia Marques FJ, Tailor D, Bermudez A, Resendez A, Pandrala M, Grau B, Kumar P, Haley CB, Honkala A, Kujur P, Jeffrey SS, Pitteri S, Malhotra SV. Inhibition of protein translational machinery in triple-negative breast cancer as a promising therapeutic strategy. Cell Rep Med 2024; 5:101552. [PMID: 38729158 PMCID: PMC11148772 DOI: 10.1016/j.xcrm.2024.101552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 07/11/2023] [Accepted: 04/11/2024] [Indexed: 05/12/2024]
Abstract
Y-box binding protein-1 (YB-1) is a proto-oncogenic protein associated with protein translation regulation. It plays a crucial role in the development and progression of triple-negative breast cancer (TNBC). In this study, we describe a promising approach to inhibit YB-1 using SU056, a small-molecule inhibitor. SU056 physically interacts with YB-1 and reduces its expression, which helps to restrain the progression of TNBC. Proteome profiling analysis indicates that the inhibition of YB-1 by SU056 can alter the proteins that regulate protein translation, an essential process for cancer cell growth. Preclinical studies on human cells, mice, and patient-derived xenograft tumor models show the effectiveness of SU056. Moreover, toxicological studies have shown that SU056 treatment and dosing are well tolerated without any adverse effects. Overall, our study provides a strong foundation for the further development of SU056 as a potential treatment option for patients with TNBC by targeting YB-1.
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Affiliation(s)
- Arpit Dheeraj
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Fernando Jose Garcia Marques
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Dhanir Tailor
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Abel Bermudez
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Angel Resendez
- Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mallesh Pandrala
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Benedikt Grau
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Praveen Kumar
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Carrsyn B Haley
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Alexander Honkala
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Praveen Kujur
- Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Stefanie S Jeffrey
- Department of Surgery, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sharon Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Sanjay V Malhotra
- Department of Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA; Department of Radiation Oncology, Stanford University School of Medicine, Palo Alto, CA, USA.
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4
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Gu Y, Zhang X, Li H, Wang R, Jin C, Wang J, Jin Z, Lu J, Ling C, Shao F, Zhang J, Shi L. Novel subsets of peripheral immune cells associated with promoting stroke recovery in mice. CNS Neurosci Ther 2024; 30:e14518. [PMID: 37905680 PMCID: PMC11017448 DOI: 10.1111/cns.14518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
AIMS Peripheral immune cells infiltrating into the brain trigger neuroinflammation after an ischemic stroke. Partial immune cells reprogram their function for neural repair. Which immune cells promote ischemic brain recovery needs further identification. METHODS We performed single-cell transcriptomic profiling of CD45high immune cells isolated from the ischemic hemisphere at subacute (5 days) and chronic (14 days) stages after ischemic stroke. RESULTS A subset of phagocytic macrophages was associated with neuron projection regeneration and tissue remodeling. We also identified a unique type of T cells with highly expressed macrophage markers, including C1q, Apoe, Hexb, and Fcer1g, which showed high abilities in tissue remodeling, myelination regulation, wound healing, and anti-neuroinflammation. Moreover, natural killer cells decreased cytotoxicity and increased energy and metabolic function in the chronic stage after ischemic stroke. Two subgroups of neutrophils upregulated CCL signals to recruit peripheral immune cells and released CXCL2 to keep self-recruiting at the chronic stage. CONCLUSIONS We identified subsets of peripheral immune cells that may provide potential therapeutic targets for promoting poststroke recovery.
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Affiliation(s)
- Yichen Gu
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Xiaotao Zhang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Huaming Li
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Rui Wang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Chenghao Jin
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Junjie Wang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Ziyang Jin
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Jianan Lu
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Chenhan Ling
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Fangjie Shao
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
| | - Jianmin Zhang
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
- Brain Research InstituteZhejiang UniversityHangzhouZhejiangChina
- Collaborative Innovation Center for Brain ScienceZhejiang UniversityHangzhouZhejiangChina
| | - Ligen Shi
- Department of NeurosurgerySecond Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Clinical Research Center for Neurological Diseases of Zhejiang ProvinceHangzhouChina
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5
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Chetty VK, Ghanam J, Lichá K, Brenzel A, Reinhardt D, Thakur BK. Y-box binding protein 1 in small extracellular vesicles reduces mesenchymal stem cell differentiation to osteoblasts-implications for acute myeloid leukaemia. J Extracell Vesicles 2024; 13:e12417. [PMID: 38499475 PMCID: PMC10948369 DOI: 10.1002/jev2.12417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/29/2024] [Accepted: 02/08/2024] [Indexed: 03/20/2024] Open
Abstract
Small extracellular vesicles (sEVs) released by acute myeloid leukaemia (AML) cells have been reported to influence the trilineage differentiation of bone marrow-derived mesenchymal stem cells (BM-MSCs). However, it remains elusive which biological cargo from AML-sEVs is responsible for this effect. In this study, sEVs were isolated from cell-conditioned media and blood plasma using size-exclusion chromatography and ultrafiltration and characterized according to MISEV2018 guidelines. Our results demonstrated that AML-sEVs increased the proliferation of BM-MSCs. Conversely, key proteins that are important for normal haematopoiesis were downregulated in BM-MSCs. Additionally, we revealed that AML-sEVs significantly reduced the differentiation of BM-MSCs to osteoblasts without affecting adipogenic or chondrogenic differentiation. Next, LC-MS/MS proteomics elucidated that various proteins, including Y-box-binding protein 1 (YBX1), were upregulated in both AML-sEVs and BM-MSCs treated with AML-sEVs. Clinically relevant, we found that YBX1 is considerably upregulated in most paediatric AML patient-derived sEVs compared to healthy controls. Interestingly, sEVs isolated after the downregulation of YBX1 in AML cells remarkably rescued the osteoblastic differentiation of BM-MSCs. Altogether, our data demonstrate for the first time that YBX1 containing AML-sEVs is one of the key players that disrupt the normal function of bone marrow microenvironment by reducing the osteogenic differentiation of BM-MSCs.
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Affiliation(s)
| | - Jamal Ghanam
- Department of Pediatrics IIIUniversity Hospital EssenEssenGermany
| | - Kristína Lichá
- Department of Pediatrics IIIUniversity Hospital EssenEssenGermany
- Institute of Molecular Biomedicine, Faculty of MedicineComenius University in BratislavaBratislavaSlovakia
| | | | - Dirk Reinhardt
- Department of Pediatrics IIIUniversity Hospital EssenEssenGermany
| | - Basant Kumar Thakur
- Department of Pediatrics IIIUniversity Hospital EssenEssenGermany
- European Liquid Biopsy SocietyHamburgGermany
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6
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Lattmann E, Räss L, Tognetti M, Gómez JMM, Lapaire V, Bruderer R, Reiter L, Feng Y, Steinmetz LM, Levesque MP. Size-exclusion chromatography combined with DIA-MS enables deep proteome profiling of extracellular vesicles from melanoma plasma and serum. Cell Mol Life Sci 2024; 81:90. [PMID: 38353833 PMCID: PMC10867102 DOI: 10.1007/s00018-024-05137-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 01/18/2024] [Accepted: 01/19/2024] [Indexed: 02/16/2024]
Abstract
Extracellular vesicles (EVs) are important players in melanoma progression, but their use as clinical biomarkers has been limited by the difficulty of profiling blood-derived EV proteins with high depth of coverage, the requirement for large input amounts, and complex protocols. Here, we provide a streamlined and reproducible experimental workflow to identify plasma- and serum- derived EV proteins of healthy donors and melanoma patients using minimal amounts of sample input. SEC-DIA-MS couples size-exclusion chromatography to EV concentration and deep-proteomic profiling using data-independent acquisition. From as little as 200 µL of plasma per patient in a cohort of three healthy donors and six melanoma patients, we identified and quantified 2896 EV-associated proteins, achieving a 3.5-fold increase in depth compared to previously published melanoma studies. To compare the EV-proteome to unenriched blood, we employed an automated workflow to deplete the 14 most abundant proteins from plasma and serum and thereby approximately doubled protein group identifications versus native blood. The EV proteome diverged from corresponding unenriched plasma and serum, and unlike the latter, separated healthy donor and melanoma patient samples. Furthermore, known melanoma markers, such as MCAM, TNC, and TGFBI, were upregulated in melanoma EVs but not in depleted melanoma plasma, highlighting the specific information contained in EVs. Overall, EVs were significantly enriched in intact membrane proteins and proteins related to SNARE protein interactions and T-cell biology. Taken together, we demonstrated the increased sensitivity of an EV-based proteomic workflow that can be easily applied to larger melanoma cohorts and other indications.
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Affiliation(s)
- Evelyn Lattmann
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland
| | - Luca Räss
- Biognosys AG, Schlieren, Switzerland
| | | | - Julia M Martínez Gómez
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland
| | - Valérie Lapaire
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland
| | | | | | | | - Lars M Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Schlieren, Switzerland.
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7
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Lei H, Xu H, Yang L, Wang Y, Zhang Y, Wu Y. USP47 stabilizes YBX1 to promote the progression of acute myeloid leukemia. Oncogene 2024; 43:539-542. [PMID: 38104157 DOI: 10.1038/s41388-023-02921-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 12/06/2023] [Accepted: 12/06/2023] [Indexed: 12/19/2023]
Affiliation(s)
- Hu Lei
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hanzhang Xu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Li Yang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingying Wang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Youping Zhang
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Yingli Wu
- Hongqiao International Institute of Medicine, Shanghai Tongren Hospital/Faculty of Basic Medicine, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- Department of Pathophysiology, Research Unit of Stress and Cancer, Chinese Academy of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China.
- Shanghai Jiao Tong University, Research Units of Stress and Tumor (2019RU043), Chinese Academy of Medical Sciences, Sch Med, Shanghai, 200025, China.
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8
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Kelesoglu N, Kori M, Yilmaz BK, Duru OA, Arga KY. Differential co-expression network analysis elucidated genes associated with sensitivity to farnesyltransferase inhibitor and prognosis of acute myeloid leukemia. Cancer Med 2023; 12:22420-22436. [PMID: 38069522 PMCID: PMC10757125 DOI: 10.1002/cam4.6804] [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: 05/05/2023] [Revised: 11/13/2023] [Accepted: 11/27/2023] [Indexed: 12/31/2023] Open
Abstract
Acute myeloid leukemia (AML) is a heterogeneous disease and the most common form of acute leukemia with a poor prognosis. Due to its complexity, the disease requires the identification of biomarkers for reliable prognosis. To identify potential disease genes that regulate patient prognosis, we used differential co-expression network analysis and transcriptomics data from relapsed, refractory, and previously untreated AML patients based on their response to treatment in the present study. In addition, we combined functional genomics and transcriptomics data to identify novel and therapeutically potential systems biomarkers for patients who do or do not respond to treatment. As a result, we constructed co-expression networks for response and non-response cases and identified a highly interconnected group of genes consisting of SECISBP2L, MAN1A2, PRPF31, VASP, and SNAPC1 in the response network and a group consisting of PHTF2, SLC11A2, PDLIM5, OTUB1, and KLRD1 in the non-response network, both of which showed high prognostic performance with hazard ratios of 4.12 and 3.66, respectively. Remarkably, ETS1, GATA2, AR, YBX1, and FOXP3 were found to be important transcription factors in both networks. The prognostic indicators reported here could be considered as a resource for identifying tumorigenesis and chemoresistance to farnesyltransferase inhibitor. They could help identify important research directions for the development of new prognostic and therapeutic techniques for AML.
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Affiliation(s)
| | - Medi Kori
- Department of BioengineeringMarmara UniversityIstanbulTürkiye
| | - Betul Karademir Yilmaz
- Genetic and Metabolic Diseases Research and Investigation CenterMarmara UniversityIstanbulTürkiye
- Department of Biochemistry, Faculty of MedicineMarmara UniversityIstanbulTürkiye
| | - Ozlem Ates Duru
- Department of Nutrition and Dietetics, School of Health SciencesNişantaşı UniversityIstanbulTürkiye
- Department of Chemical Engineering, Faculty of EngineeringBolu Abant İzzet Baysal UniversityBoluTürkiye
| | - Kazim Yalcin Arga
- Department of BioengineeringMarmara UniversityIstanbulTürkiye
- Genetic and Metabolic Diseases Research and Investigation CenterMarmara UniversityIstanbulTürkiye
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9
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Khozooei S, Veerappan S, Toulany M. YB-1 activating cascades as potential targets in KRAS-mutated tumors. Strahlenther Onkol 2023; 199:1110-1127. [PMID: 37268766 DOI: 10.1007/s00066-023-02092-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/23/2023] [Indexed: 06/04/2023]
Abstract
Y‑box binding protein‑1 (YB-1) is a multifunctional protein that is highly expressed in human solid tumors of various entities. Several cellular processes, e.g. cell cycle progression, cancer stemness and DNA damage signaling that are involved in the response to chemoradiotherapy (CRT) are tightly governed by YB‑1. KRAS gene with about 30% mutations in all cancers, is considered the most commonly mutated oncogene in human cancers. Accumulating evidence indicates that oncogenic KRAS mediates CRT resistance. AKT and p90 ribosomal S6 kinase are downstream of KRAS and are the major kinases that stimulate YB‑1 phosphorylation. Thus, there is a close link between the KRAS mutation status and YB‑1 activity. In this review paper, we highlight the importance of the KRAS/YB‑1 cascade in the response of KRAS-mutated solid tumors to CRT. Likewise, the opportunities to interfere with this pathway to improve CRT outcome are discussed in light of the current literature.
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Affiliation(s)
- Shayan Khozooei
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Soundaram Veerappan
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany
| | - Mahmoud Toulany
- Division of Radiobiology and Molecular Environmental Research, Department of Radiation Oncology, University of Tuebingen, Tuebingen, Germany.
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10
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Eifert T, Hsu CJ, Becker AL, Graessle S, Horne A, Bemmann F, Zhang Q, Heuser M, Vasioukhin V, Scholl S, Hochhaus A, Siegerist F, Endlich N, Bullinger L, Lane SW, Haas S, Schnoeder TM, Heidel FH. Cell fate determinant Llgl1 is required for propagation of acute myeloid leukemia. Leukemia 2023; 37:2027-2035. [PMID: 37587260 PMCID: PMC10539176 DOI: 10.1038/s41375-023-02005-9] [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: 01/30/2023] [Revised: 07/18/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023]
Abstract
Scribble complex proteins can influence cell fate decisions and self-renewal capacity of hematopoietic cells. While specific cellular functions of Scribble complex members are conserved in mammalian hematopoiesis, they appear to be highly context dependent. Using CRISPR/Cas9-based genetic screening, we have identified Scribble complex-related liabilities in AML including LLGL1. Despite its reported suppressive function in HSC self-renewal, inactivation of LLGL1 in AML confirms its relevant role for proliferative capacity and development of AML. Its function was conserved in human and murine models of AML and across various genetic backgrounds. Inactivation of LLGL1 results in loss of stemness-associated gene-expression including HoxA-genes and induces a GMP-like phenotype in the leukemia stem cell compartment. Re-expression of HoxA9 facilitates functional and phenotypic rescue. Collectively, these data establish LLGL1 as a specific dependency and putative target in AML and emphasizes its cell-type specific functions.
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Affiliation(s)
- Theresa Eifert
- Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Chen-Jen Hsu
- Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Alicia L Becker
- Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Sarah Graessle
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115, Berlin, Germany
- Humboldt-Universität zu Berlin, Faculty of Life Sciences, Unter den Linden 6, 10099, Berlin, Germany
| | - Arik Horne
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Department of Translational Oncology, National Center for Tumor Diseases (NCT) Heidelberg, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Franziska Bemmann
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115, Berlin, Germany
| | - Qirui Zhang
- Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Michael Heuser
- Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Hannover Medical School (MHH), Hannover, Germany
| | - Valeri Vasioukhin
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | | | - Florian Siegerist
- Institute of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | - Nicole Endlich
- Institute of Anatomy and Cell Biology, University Medicine Greifswald, Greifswald, Germany
| | | | - Steven W Lane
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- The University of Queensland, Brisbane, QLD, Australia
- Royal Brisbane and Women's Hospital, Herston, QLD, Australia
| | - Simon Haas
- Charité-Universitätsmedizin, 10117, Berlin, Germany
- Berlin Institute of Health (BIH) at Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 10115, Berlin, Germany
- Division of Stem Cells and Cancer, Deutsches Krebsforschungszentrum (DKFZ) and DKFZ - ZMBH Alliance, Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), Heidelberg, Germany
- German Cancer Consortium (DKTK), 69120, Heidelberg, Germany
| | - Tina M Schnoeder
- Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Florian H Heidel
- Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany.
- Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Hannover Medical School (MHH), Hannover, Germany.
- Leibniz Institute on Aging, Fritz-Lipmann-Institute, Jena, Germany.
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11
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Li H, Zhang D, Fu Q, Wang S, Wang Z, Zhang X, Chen X, Zhu X, An N, Chen Y, Zhou L, Lu D, Zhao N. YBX1 as an oncogenic factor in T-cell acute lymphoblastic leukemia. Blood Adv 2023; 7:4874-4885. [PMID: 37339496 PMCID: PMC10469076 DOI: 10.1182/bloodadvances.2022009648] [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: 01/03/2023] [Revised: 04/28/2023] [Accepted: 05/23/2023] [Indexed: 06/22/2023] Open
Abstract
Y-box-binding protein 1 (YBX1), a member of the RNA-binding protein family, is a critical regulator of cell survival in various solid tumors and acute myeloid leukemia. However, the function of YBX1 in T-cell acute lymphoblastic leukemia (T-ALL) remains elusive. Here, we found that YBX1 was upregulated in patients with T-ALL, T-ALL cell lines, and NOTCH1-induced T-ALL mice. Furthermore, depletion of YBX1 dramatically reduced cell proliferation, induced cell apoptosis, and induced G0/G1 phase arrest in vitro. Moreover, YBX1 depletion significantly decreased the leukemia burden in the human T-ALL xenograft and NOTCH1-induced T-ALL mice model in vivo. Mechanistically, downregulation of YBX1 markedly inhibited the expression of total AKT serine/threonine kinase (AKT), p-AKT, total extracellular signal-regulated kinase (ERK), and p-ERK in T-ALL cells. Taken together, our results uncovered a critical role of YBX1 in the leukemogenesis of T-ALL, which may have great potential as a biomarker and therapeutic target in T-ALL.
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Affiliation(s)
- Huan Li
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, China
| | - Danlan Zhang
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Qiuxia Fu
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Shang Wang
- Chongqing Key Laboratory of Traditional Chinese Medicine for Prevention and Cure of Metabolic Diseases, College of Traditional Chinese Medicine, Chongqing Medical University, Chongqing, China
| | - Zhongyuan Wang
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xin Zhang
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xin Chen
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Xiaoyu Zhu
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Na An
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Yun Chen
- Department of Immunology, Key Laboratory of Human Functional Genomics of Jiangsu Province, Gusu School, Nanjing Medical University, Nanjing, China
| | - Liang Zhou
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Desheng Lu
- Department of Pharmacology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, International Cancer Center, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen, China
| | - Na Zhao
- Department of Hematology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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12
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Varma E, Burghaus J, Schwarzl T, Sekaran T, Gupta P, Górska AA, Hofmann C, Stroh C, Jürgensen L, Kamuf-Schenk V, Li X, Medert R, Leuschner F, Kmietczyk V, Freichel M, Katus HA, Hentze MW, Frey N, Völkers M. Translational control of Ybx1 expression regulates cardiac function in response to pressure overload in vivo. Basic Res Cardiol 2023; 118:25. [PMID: 37378715 PMCID: PMC10307726 DOI: 10.1007/s00395-023-00996-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
RNA-protein interactions are central to cardiac function, but how activity of individual RNA-binding protein is regulated through signaling cascades in cardiomyocytes during heart failure development is largely unknown. The mechanistic target of rapamycin kinase is a central signaling hub that controls mRNA translation in cardiomyocytes; however, a direct link between mTOR signaling and RNA-binding proteins in the heart has not been established. Integrative transcriptome and translatome analysis revealed mTOR dependent translational upregulation of the RNA binding protein Ybx1 during early pathological remodeling independent of mRNA levels. Ybx1 is necessary for pathological cardiomyocyte growth by regulating protein synthesis. To identify the molecular mechanisms how Ybx1 regulates cellular growth and protein synthesis, we identified mRNAs bound to Ybx1. We discovered that eucaryotic elongation factor 2 (Eef2) mRNA is bound to Ybx1, and its translation is upregulated during cardiac hypertrophy dependent on Ybx1 expression. Eef2 itself is sufficient to drive pathological growth by increasing global protein translation. Finally, Ybx1 depletion in vivo preserved heart function during pathological cardiac hypertrophy. Thus, activation of mTORC1 links pathological signaling cascades to altered gene expression regulation by activation of Ybx1 which in turn promotes translation through increased expression of Eef2.
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Affiliation(s)
- Eshita Varma
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Jana Burghaus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Thileepan Sekaran
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Parul Gupta
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Agnieszka A Górska
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Christoph Hofmann
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Claudia Stroh
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Verena Kamuf-Schenk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Xue Li
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Rebekka Medert
- Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Florian Leuschner
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Vivien Kmietczyk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Marc Freichel
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
- Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Hugo A Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Norbert Frey
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Mirko Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany.
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13
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Wang Y, Wei J, Feng L, Li O, Huang L, Zhou S, Xu Y, An K, Zhang Y, Chen R, He L, Wang Q, Wang H, Du Y, Liu R, Huang C, Zhang X, Yang YG, Kan Q, Tian X. Aberrant m5C hypermethylation mediates intrinsic resistance to gefitinib through NSUN2/YBX1/QSOX1 axis in EGFR-mutant non-small-cell lung cancer. Mol Cancer 2023; 22:81. [PMID: 37161388 PMCID: PMC10169458 DOI: 10.1186/s12943-023-01780-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 04/21/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND RNA 5-methylcytosine (m5C) modification plays critical roles in the pathogenesis of various tumors. However, the function and molecular mechanism of RNA m5C modification in tumor drug resistance remain unclear. METHODS The correlation between RNA m5C methylation, m5C writer NOP2/Sun RNA methyltransferase family member 2 (NSUN2) and EGFR-TKIs resistance was determined in non-small-cell lung cancer (NSCLC) cell lines and patient samples. The effects of NSUN2 on EGFR-TKIs resistance were investigated by gain- and loss-of-function assays in vitro and in vivo. RNA-sequencing (RNA-seq), RNA bisulfite sequencing (RNA-BisSeq) and m5C methylated RNA immunoprecipitation-qPCR (MeRIP-qPCR) were performed to identify the target gene of NSUN2 involved in EGFR-TKIs resistance. Furthermore, the regulatory mechanism of NSUN2 modulating the target gene expression was investigated by functional rescue and puromycin incorporation assays. RESULTS RNA m5C hypermethylation and NSUN2 were significantly correlated with intrinsic resistance to EGFR-TKIs. Overexpression of NSUN2 resulted in gefitinib resistance and tumor recurrence, while genetic inhibition of NSUN2 led to tumor regression and overcame intrinsic resistance to gefitinib in vitro and in vivo. Integrated RNA-seq and m5C-BisSeq analyses identified quiescin sulfhydryl oxidase 1 (QSOX1) as a potential target of aberrant m5C modification. NSUN2 methylated QSOX1 coding sequence region, leading to enhanced QSOX1 translation through m5C reader Y-box binding protein 1 (YBX1). CONCLUSIONS Our study reveals a critical function of aberrant RNA m5C modification via the NSUN2-YBX1-QSOX1 axis in mediating intrinsic resistance to gefitinib in EGFR-mutant NSCLC.
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Affiliation(s)
- Yueqin Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Jingyao Wei
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Luyao Feng
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ouwen Li
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Lan Huang
- Biotherapy Center, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shaoxuan Zhou
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yingjie Xu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ke An
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yu Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ruiying Chen
- Department of Respiratory Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Lulu He
- Biobank of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Han Wang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yue Du
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Ruijuan Liu
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Chunmin Huang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China
| | - Xiaojian Zhang
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China
| | - Yun-Gui Yang
- Key Laboratory of Genomic and Precision Medicine, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, Chinese Academy of Sciences, China National Center for Bioinformation, Beijing, 100101, China.
| | - Quancheng Kan
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China.
| | - Xin Tian
- Department of Pharmacy, the First Affiliated Hospital of Zhengzhou University, No.1 Jianshedong Rd, Zhengzhou, Henan, 450052, China.
- Henan Key Laboratory of Precision Clinical Pharmacy, Zhengzhou University, Zhengzhou, 450052, China.
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14
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Chen S, Li K, Guo J, Chen HN, Ming Y, Jin Y, Xu F, Zhang T, Yang Y, Ye Z, Liu W, Ma H, Cheng J, Zhou JK, Li Z, Shen S, Dai L, Zhou ZG, Xu H, Peng Y. circNEIL3 inhibits tumor metastasis through recruiting the E3 ubiquitin ligase Nedd4L to degrade YBX1. Proc Natl Acad Sci U S A 2023; 120:e2215132120. [PMID: 36961927 PMCID: PMC10068820 DOI: 10.1073/pnas.2215132120] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/03/2023] [Indexed: 03/26/2023] Open
Abstract
Distant metastasis is a major contributor to cancer-related mortality. However, the role of circRNAs in this process remains unclear. Herein, we profiled the circRNA expression in a cohort of 68 colorectal carcinoma (CRC) primary tumors and their paired liver metastatic lesions. By overlapping with the TGFβ-responsive circRNAs, circNEIL3 (hsa_circ_0001460) was identified as a TGFβ-repressive and metastasis-related circRNA. Functionally, circNEIL3 effectively inhibited tumor metastasis in both and in vivo and in vivo models of various cancer types. Mechanistically, circNEIL3 exerts its metastasis-repressive function through its direct interaction with oncogenic protein, Y-box-binding protein 1 (YBX1), which consequently promotes the Nedd4L-mediated proteasomal degradation of YBX1. Importantly, circNEIL3 expression was negatively correlated to YBX1 protein level and metastatic tendency in CRC patient samples. Collectively, our findings indicate the YBX1-dependent antimetastatic function of circNEIL3 and highlight the potential of circNEIL3 as a biomarker and therapeutic option in cancer treatment.
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Affiliation(s)
- Shuang Chen
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Ke Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Jiawei Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Hai-Ning Chen
- Colorectal Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu610041, China
| | - Yue Ming
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Yang Jin
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Fuyan Xu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Tingting Zhang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Yang Yang
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Zixia Ye
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Wenrong Liu
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Hulin Ma
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Jian Cheng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Jian-Kang Zhou
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Zhang Li
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Shu Shen
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Lunzhi Dai
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Zong-Guang Zhou
- Colorectal Cancer Center, Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu610041, China
| | - Heng Xu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu610041, China
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15
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Chai J, Wang Q, Qiu Q, Han G, Chen Y, Li W, Zhang H. YBX1 regulates the survival of chronic myeloid leukemia stem cells by modulating m6A-mediated YWHAZ stability. Cell Oncol (Dordr) 2022; 46:451-464. [PMID: 36512307 DOI: 10.1007/s13402-022-00762-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
PURPOSE Chronic myeloid leukemia (CML) is a myeloproliferative disease derived from hematopoietic stem cells (HSCs) that harbor Philadelphia chromosome (Ph chromosome). In clinic, leukemia stem cells (LSCs) in CML are insensitive to the treatment with tyrosine kinase inhibitors, and are responsible for disease relapse. However, the molecular mechanisms for maintaining LSCs survival remain elusive. METHODS CML patient-derived cell lines and BCR-ABL-induced CML mouse model were used to explore the role of YBX1 in regulating the survival of CML LSCs. Bone marrow transduction and transplantation, and colony-forming unit assay were used to investigate LSC function. The underlying mechanism of how YBX1 regulates LSCs survival were assessed using flow cytometry, RNA sequencing, western blot, RNA decay assay, co-immunoprecipitation and RNA immunoprecipitation. RESULTS Here we show that RNA-binding protein YBX1 plays an important role in regulating survival of CML LSCs. We find that YBX1 expression is significantly increased in CML cells, and confirm that YBX1 is required for maintaining survival of LSCs. Deletion of YBX1 impairs the propagation of CML through blocking cell proliferation and inducing apoptosis of LSCs. Mechanistically, we find that YBX1 regulates expression of apoptotic associated genes. YBX1 cooperates with RNA m6A reader IGF2BPs to stabilize YWHAZ transcript in an m6A-dependent manner, and loss of YBX1 decreases YWHAZ expression by accelerating mRNA decay. Restoration of YWHAZ efficiently rescues the defects of YBX1-deficient CML cells. CONCLUSION Our findings reveal a critical role of YBX1 in maintaining survival of CML LSCs, which provides a rationale for targeting YBX1 in CML treatment.
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Affiliation(s)
- Jihua Chai
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, No.185, East Lake Road, Wuchang District, Wuhan, Hubei, 430071, People's Republic of China
| | - Qifan Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, No.185, East Lake Road, Wuchang District, Wuhan, Hubei, 430071, People's Republic of China
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Qiang Qiu
- State Key Laboratory of Biotherapy, West China Hospital & Collaborative Innovation Center for Biotherapy, Sichuan University, Chengdu, China
| | - Guoqiang Han
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Yilin Chen
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Weiming Li
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Haojian Zhang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Medical Research Institute, Wuhan University, No.185, East Lake Road, Wuchang District, Wuhan, Hubei, 430071, People's Republic of China.
- Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China.
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16
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George S, Rafi M, Aldarmaki M, ElSiddig M, Al Nuaimi M, Amiri KMA. tRNA derived small RNAs—Small players with big roles. Front Genet 2022; 13:997780. [PMID: 36199575 PMCID: PMC9527309 DOI: 10.3389/fgene.2022.997780] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/29/2022] [Indexed: 11/22/2022] Open
Abstract
In the past 2 decades, small non-coding RNAs derived from tRNA (tsRNAs or tRNA derived fragments; tRFs) have emerged as new powerful players in the field of small RNA mediated regulation of gene expression, translation, and epigenetic control. tRFs have been identified from evolutionarily divergent organisms from Archaea, the higher plants, to humans. Recent studies have confirmed their roles in cancers and other metabolic disorders in humans and experimental models. They have been implicated in biotic and abiotic stress responses in plants as well. In this review, we summarize the current knowledge on tRFs including types of tRFs, their biogenesis, and mechanisms of action. The review also highlights recent studies involving differential expression profiling of tRFs and elucidation of specific functions of individual tRFs from various species. We also discuss potential considerations while designing experiments involving tRFs identification and characterization and list the available bioinformatics tools for this purpose.
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Affiliation(s)
- Suja George
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Maitha Aldarmaki
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mohamed ElSiddig
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Mariam Al Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- *Correspondence: Khaled M. A. Amiri,
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17
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Gouda MB, Hassan NM, Kandil EI, Haroun RAH. Pathogenetic Significance of YBX1 Expression in Acute Myeloid Leukemia Relapse. Curr Res Transl Med 2022; 70:103336. [DOI: 10.1016/j.retram.2022.103336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 12/26/2021] [Accepted: 01/30/2022] [Indexed: 11/03/2022]
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18
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Histone demethylase KDM4C is a functional dependency in JAK2-mutated neoplasms. Leukemia 2022; 36:1843-1849. [PMID: 35654819 PMCID: PMC9252905 DOI: 10.1038/s41375-022-01611-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/09/2022] [Accepted: 05/20/2022] [Indexed: 11/08/2022]
Abstract
Mutations of the JAK2 gene are frequent aberrations in the aging hematopoietic system and in myeloid neoplasms. While JAK-inhibitors efficiently reduce hyperinflammation induced by the constitutively active mutated JAK2 kinase, the malignant clone and abundance of mutated cells remains rather unaffected. Here, we sought to assess for genetic vulnerabilities of JAK2-mutated clones. We identified lysine-specific demethylase KDM4C as a selective genetic dependency that persists upon JAK-inhibitor treatment. Genetic inactivation of KDM4C in human and murine JAK2-mutated cells resulted in loss of cell competition and reduced proliferation. These findings led to reduced disease penetrance and improved survival in xenograft models of human JAK2-mutated cells. KDM4C deleted cells showed alterations in target histone residue methylation and target gene expression, resulting in induction of cellular senescence. In summary, these data establish KDM4C as a specific dependency and therapeutic target in JAK2-mutated cells that is essential for oncogenic signaling and prevents induction of senescence.
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19
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Igelmann S, Lessard F, Ferbeyre G. Liquid-Liquid Phase Separation in Cancer Signaling, Metabolism and Anticancer Therapy. Cancers (Basel) 2022; 14:cancers14071830. [PMID: 35406602 PMCID: PMC8997759 DOI: 10.3390/cancers14071830] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/30/2022] [Accepted: 03/31/2022] [Indexed: 01/07/2023] Open
Abstract
The cancer state is thought to be maintained by genetic and epigenetic changes that drive a cancer-promoting gene expression program. However, recent results show that cellular states can be also stably maintained by the reorganization of cell structure leading to the formation of biological condensates via the process of liquid-liquid phase separation. Here, we review the data showing cancer-specific biological condensates initiated by mutant oncoproteins, RNA-binding proteins, or lincRNAs that regulate oncogenic gene expression programs and cancer metabolism. Effective anticancer drugs may specifically partition into oncogenic biological condensates (OBC).
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Affiliation(s)
- Sebastian Igelmann
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H2X 0A9, Canada
| | - Frédéric Lessard
- Laboratory of Growth and Development, St-Patrick Research Group in Basic Oncology, Cancer Division of the Quebec University Hospital Research Centre, Québec, QC G1R 2J6, Canada;
| | - Gerardo Ferbeyre
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, QC H3C 3J7, Canada;
- Montreal Cancer Institute, CR-CHUM, Université de Montréal, Montréal, QC H2X 0A9, Canada
- Correspondence: ; Tel.: +1-514-343-7571
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20
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Demircan MB, Schnoeder TM, Mgbecheta PC, Schröder K, Böhmer FD, Heidel FH. Context-specific effects of NOX4 inactivation in acute myeloid leukemia (AML). J Cancer Res Clin Oncol 2022; 148:1983-1990. [PMID: 35348887 PMCID: PMC9293823 DOI: 10.1007/s00432-022-03986-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 03/09/2022] [Indexed: 11/24/2022]
Abstract
PURPOSE Oxidative stress has been linked to initiation and progression of cancer and recent studies have indicated a potential translational role regarding modulation of ROS in various cancers, including acute myeloid leukemia (AML). Detailed understanding of the complex machinery regulating ROS including its producer elements in cancer is required to define potential translational therapeutic use. Based on previous studies in acute myeloid leukemia (AML) models, we considered NADPH oxidase (NOX) family members, specifically NOX4 as a potential target in AML. METHODS Pharmacologic inhibition and genetic inactivation of NOX4 in murine and human models of AML were used to understand its functional role. For genetic inactivation, CRISPR-Cas9 technology was used in human AML cell lines in vitro and genetically engineered knockout mice for Nox4 were used for deletion of Nox4 in hematopoietic cells via Mx1-Cre recombinase activation. RESULTS Pharmacologic NOX inhibitors and CRISPR-Cas9-mediated inactivation of NOX4 and p22-phox (an essential NOX component) decreased proliferative capacity and cell competition in FLT3-ITD-positive human AML cells. In contrast, conditional deletion of Nox4 enhanced the myeloproliferative phenotype of an FLT3-ITD induced knock-in mouse model. Finally, Nox4 inactivation in normal hematopoietic stem and progenitor cells (HSPCs) caused a minor reduction in HSC numbers and reconstitution capacity. CONCLUSION The role of NOX4 in myeloid malignancies appears highly context-dependent and its inactivation results in either enhancing or inhibitory effects. Therefore, targeting NOX4 in FLT3-ITD positive myeloid malignancies requires additional pre-clinical assessment.
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Affiliation(s)
- Muhammed Burak Demircan
- Innere Medizin II, Hämatologie und Onkologie, Jena University Hospital, Jena, Germany.,Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany.,Institute of Molecular Cell Biology, CMB, Jena University Hospital, Jena, Germany.,Molecular Biotechnology and Gene Therapy, Paul-Ehrlich-Institut, Langen, Hessen, Germany
| | - Tina M Schnoeder
- Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany
| | - Peter C Mgbecheta
- Institute of Molecular Cell Biology, CMB, Jena University Hospital, Jena, Germany
| | - Katrin Schröder
- Institute for Cardiovascular Physiology, Goethe University, Frankfurt am Main, Germany
| | - Frank-D Böhmer
- Institute of Molecular Cell Biology, CMB, Jena University Hospital, Jena, Germany
| | - Florian H Heidel
- Innere Medizin II, Hämatologie und Onkologie, Jena University Hospital, Jena, Germany. .,Leibniz Institute on Aging, Fritz Lipmann Institute, Jena, Germany. .,Innere Medizin C, Universitätsmedizin Greifswald, Greifswald, Germany.
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21
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Pandey G, Kuykendall AT, Reuther GW. JAK2 inhibitor persistence in MPN: uncovering a central role of ERK activation. Blood Cancer J 2022; 12:13. [PMID: 35082276 PMCID: PMC8792018 DOI: 10.1038/s41408-022-00609-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/22/2022] Open
Abstract
The Philadelphia chromosome negative myeloproliferative neoplasms, including polycythemia vera, essential thrombocytosis, and myelofibrosis, are driven by hyper activation of the JAK2 tyrosine kinase, the result of mutations in three MPN driving genes: JAK2, MPL, and CALR. While the anti-inflammatory effects of JAK2 inhibitors can provide improved quality of life for many MPN patients, the upfront and persistent survival of disease-driving cells in MPN patients undergoing JAK2 inhibitor therapy thwarts potential for remission. Early studies indicated JAK2 inhibitor therapy induces heterodimeric complex formation of JAK2 with other JAK family members leading to sustained JAK2-dependent signaling. Recent work has described novel cell intrinsic details as well as cell extrinsic mechanisms that may contribute to why JAK2 inhibition may be ineffective at targeting MPN driving cells. Diverse experimental strategies aimed at uncovering mechanistic details that contribute to JAK2 inhibitor persistence have each highlighted the role of MEK/ERK activation. These approaches include, among others, phosphoproteomic analyses of JAK2 signaling as well as detailed assessment of JAK2 inhibition in mouse models of MPN. In this focused review, we highlight these and other studies that collectively suggest targeting MEK/ERK in combination with JAK2 inhibition has the potential to improve the efficacy of JAK2 inhibitors in MPN patients. As MPN patients patiently wait for improved therapies, such studies should further strengthen optimism that pre-clinical research is continuing to uncover mechanistic insights regarding the ineffectiveness of JAK2 inhibitors, which may lead to development of improved therapeutic strategies.
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Affiliation(s)
- Garima Pandey
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA
| | | | - Gary W Reuther
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, USA.
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