1
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Shen D, Xia Y, Fu Y, Cao Q, Chen W, Zhu Y, Guo K, Sun L. Hedgehog pathway and cancer: A new area (Review). Oncol Rep 2024; 52:116. [PMID: 38994763 PMCID: PMC11267502 DOI: 10.3892/or.2024.8775] [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: 11/17/2023] [Accepted: 06/21/2024] [Indexed: 07/13/2024] Open
Abstract
In years of research on classical pathways, the composition, information transmission mechanism, crosstalk with other pathways, and physiological and pathological effects of hedgehog (HH) pathway have been gradually clarified. HH also plays a critical role in tumor formation and development. According to the update of interpretation of tumor phenotypes, the latest relevant studies have been sorted out, to explore the specific mechanism of HH pathway in regulating different tumor phenotypes through gene mutation and signal regulation. The drugs and natural ingredients involved in regulating HH pathway were also reviewed; five approved drugs and drugs under research exert efficacy by blocking HH pathway, and at least 22 natural components have potential to treat tumors by HH pathway. Nevertheless, there is a deficiency of existing studies. The present review confirmed the great potential of HH pathway in future cancer treatment with factual basis.
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Affiliation(s)
- Deyi Shen
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Yuwei Xia
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Yuhan Fu
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Qiaochang Cao
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Wenqian Chen
- The First School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Ying Zhu
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
| | - Kaibo Guo
- Department of Cancer Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310006, P.R. China
| | - Leitao Sun
- The First Affiliated Hospital of Zhejiang Chinese Medical University (Zhejiang Provincial Hospital of Chinese Medicine), Hangzhou, Zhejiang 310006, P.R. China
- Academy of Chinese Medical Science, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
- Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
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2
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Zhou H, Ye P, Xiong W, Duan X, Jing S, He Y, Zeng Z, Wei Y, Ye Q. Genome-scale CRISPR-Cas9 screening in stem cells: theories, applications and challenges. Stem Cell Res Ther 2024; 15:218. [PMID: 39026343 PMCID: PMC11264826 DOI: 10.1186/s13287-024-03831-z] [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: 03/06/2024] [Accepted: 07/02/2024] [Indexed: 07/20/2024] Open
Abstract
Due to the rapid development of stem cell technology, there have been tremendous advances in molecular biological and pathological research, cell therapy as well as organoid technologies over the past decades. Advances in genome editing technology, particularly the discovery of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-related protein 9 (Cas9), have further facilitated the rapid development of stem cell researches. The CRISPR-Cas9 technology now goes beyond creating single gene editing to enable the inhibition or activation of endogenous gene loci by fusing inhibitory (CRISPRi) or activating (CRISPRa) domains with deactivated Cas9 proteins (dCas9). These tools have been utilized in genome-scale CRISPRi/a screen to recognize hereditary modifiers that are synergistic or opposing to malady mutations in an orderly and fair manner, thereby identifying illness mechanisms and discovering novel restorative targets to accelerate medicinal discovery investigation. However, the application of this technique is still relatively rare in stem cell research. There are numerous specialized challenges in applying large-scale useful genomics approaches to differentiated stem cell populations. Here, we present the first comprehensive review on CRISPR-based functional genomics screening in the field of stem cells, as well as practical considerations implemented in a range of scenarios, and exploration of the insights of CRISPR-based screen into cell fates, disease mechanisms and cell treatments in stem cell models. This review will broadly benefit scientists, engineers and medical practitioners in the areas of stem cell research.
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Affiliation(s)
- Heng Zhou
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Peng Ye
- Department of Pharmacy, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Wei Xiong
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Xingxiang Duan
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Shuili Jing
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China
| | - Yan He
- Institute of Regenerative and Translational Medicine, Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, 430064, Hubei, People's Republic of China
- Department of Oral and Maxillofacial Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, 02114, USA
| | - Zhi Zeng
- Department of Pathology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.
| | - Yen Wei
- The Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 100084, People's Republic of China.
| | - Qingsong Ye
- Center of Regenerative Medicine and Department of Stomatology, Renmin Hospital of Wuhan University, Wuhan, 430060, People's Republic of China.
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3
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Chui JS, Izuel‐Idoype T, Qualizza A, de Almeida RP, Piessens L, van der Veer BK, Vanmarcke G, Malesa A, Athanasouli P, Boon R, Vriens J, van Grunsven L, Koh KP, Verfaillie CM, Lluis F. Osmolar Modulation Drives Reversible Cell Cycle Exit and Human Pluripotent Cell Differentiation via NF-κВ and WNT Signaling. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2307554. [PMID: 38037844 PMCID: PMC10870039 DOI: 10.1002/advs.202307554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Indexed: 12/02/2023]
Abstract
Terminally differentiated cells are commonly regarded as the most stable cell state in adult organisms, characterized by growth arrest while fulfilling their specialized functions. A better understanding of the mechanisms involved in promoting cell cycle exit will improve the ability to differentiate pluripotent cells into mature tissues for both pharmacological and therapeutic use. Here, it demonstrates that a hyperosmolar environment enforces a protective p53-independent quiescent state in immature hepatoma cells and in pluripotent stem cell-derived models of human hepatocytes and endothelial cells. Prolonged culture in hyperosmolar conditions stimulates changes in gene expression promoting functional cell maturation. Interestingly, hyperosmolar conditions do not only trigger growth arrest and cellular maturation but are also necessary to maintain this maturated state, as switching back to plasma osmolarity reverses the changes in expression of maturation and proliferative markers. Transcriptome analysis revealed sequential stages of osmolarity-regulated growth arrest followed by cell maturation, mediated by activation of NF-κВ, and repression of WNT signaling, respectively. This study reveals that a modulated increase in osmolarity serves as a biochemical signal to promote long-term growth arrest and cellular maturation into different lineages, providing a practical method to generate differentiated hiPSCs that resemble their mature counterpart more closely.
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Affiliation(s)
- Jonathan Sai‐Hong Chui
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Teresa Izuel‐Idoype
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Alessandra Qualizza
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Rita Pires de Almeida
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Lindsey Piessens
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Bernard K. van der Veer
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Gert Vanmarcke
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Aneta Malesa
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Paraskevi Athanasouli
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Ruben Boon
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Joris Vriens
- Laboratory of Endometrium, Endometriosis and Reproductive MedicineDepartment of Development and RegenerationKU LeuvenHerestraat 49Leuven3000Belgium
| | - Leo van Grunsven
- Liver Cell Biology Research GroupVrije Universiteit BrusselLaarbeeklaan 103Brussels1090Belgium
| | - Kian Peng Koh
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Catherine M. Verfaillie
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
| | - Frederic Lluis
- KU LeuvenDepartment of Development and RegenerationStem Cell InstituteHerestraat 49Leuven3000Belgium
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4
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Radak M, Ghamari N, Fallahi H. Identification of common factors among fibrosarcoma, rhabdomyosarcoma, and osteosarcoma by network analysis. Biosystems 2024; 235:105093. [PMID: 38052344 DOI: 10.1016/j.biosystems.2023.105093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 11/13/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023]
Abstract
Sarcoma cancers are uncommon malignant tumors, and there are many subgroups, including fibrosarcoma (FS), which mainly affects middle-aged and older adults in deep soft tissues. Rhabdomyosarcoma (RMS), on the other hand, is the most common soft-tissue sarcoma in children and is located in the head and neck area. Osteosarcomas (OS) is the predominant form of primary bone cancer among young adults, primarily resulting from sporadically random mutations. This frequently results in the dissemination of cancer cells to the lungs, commonly known as metastasis. Mesodermal cells are the origin of sarcoma cancers. In this study, a rather radical approach has been applied. Instead of comparing homogenous cancer types, we focus on three main subtypes of sarcoma: fibrosarcoma, rhabdomyosarcoma, and osteosarcoma, and compare their gene expression with normal cell groups to identify the differentially expressed genes (DEGs). Next, by applying protein-protein interaction (PPI) network analysis, we determine the hub genes and crucial factors, such as transcription factors (TFs), affected by these types of cancer. Our findings indicate a modification in a range of pathways associated with cell cycle, extracellular matrix, and DNA repair in these three malignancies. Results showed that fibrosarcoma (FS), rhabdomyosarcoma (RMS), and osteosarcoma (OS) had 653, 1270, and 2823 differentially expressed genes (DEGs), respectively. Interestingly, there were 24 DEGs common to all three types. Network analysis showed that the fibrosarcoma network had two sub-networks identified in FS that contributed to the catabolic process of collagen via the G-protein coupled receptor signaling pathway. The rhabdomyosarcoma network included nine sub-networks associated with cell division, extracellular matrix organization, mRNA splicing via spliceosome, and others. The osteosarcoma network has 13 sub-networks, including mRNA splicing, sister chromatid cohesion, DNA repair, etc. In conclusion, the common DEGs identified in this study have been shown to play significant and multiple roles in various other cancers based on the literature review, indicating their significance.
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Affiliation(s)
- Mehran Radak
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, Kermanshah, 6714967346, Iran.
| | - Nakisa Ghamari
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, Kermanshah, 6714967346, Iran.
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Baq-e-Abrisham, Kermanshah, 6714967346, Iran.
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5
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Rouka E, Jagirdar RM, Sarrigeorgiou I, Pitaraki E, Sinis SI, Varsamas C, Papazoglou ED, Kotsiou OS, Lymberi P, Giannou A, Hatzoglou C, Gourgoulianis KI, Zarogiannis SG. Changes in expression of mesothelial BBS genes in 2D and 3D after lithium chloride and ammonium sulphate induction of primary cilium disturbance: a pilot study. Pharmacol Rep 2023; 75:1230-1239. [PMID: 37542187 PMCID: PMC10539424 DOI: 10.1007/s43440-023-00513-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Malignant pleural mesothelioma (MPM), a rare and aggressive pleural tumor, has significant histological and molecular heterogeneity. Primary Cilium (PC), an organelle of emerging importance in malignancies, has been scarcely investigated in MPM. A critical molecular complex for the PC function is the BBSome and here we aimed at assessing its expression patterns in ordinary 2D and spheroid 3D cell cultures. METHODS A human benign mesothelial cell line (MeT-5A), MPM cell lines (M14K, epithelioid MPM; MSTO, biphasic MPM), and primary MPM cells (pMPM) were used. Primers specific for the human BBS1, 2, 4, 5, 7, 9, 18 transcripts were designed, and quantitative real-time PCR (qRT-PCR) was done with β-actin as the gene of reference. The relative gene expression across 2D and 3D cultures was analyzed by the expression factor (mean of 1/ΔCt values). With the 2-∆∆Ct method the gene expression fold changes were assessed from qRT-PCR data. Molecular changes using the PC-modulating drugs ammonium sulfate (AS) and lithium chloride (LC) were also determined. RESULTS PC was present in all cells used in the study at approximately 15% of the observed area. BBSome transcripts were differentially expressed in different dimensions of cell culture (2D vs. 3D) in all cell lines and pMPM. Treatment with AS and LC affected the expression of the ciliary BBS2 and BBS18 genes in the benign as well as in the MPM cells. CONCLUSIONS These data indicate distinct BBSome molecular profiles in human benign and MPM cells cultured in 2D and 3D dimensions and support the notion that PC genes should be investigated as potential MPM therapeutic targets.
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Affiliation(s)
- Erasmia Rouka
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
- Department of Nursing, School of Health Sciences, University of Thessaly, GAIOPOLIS, 41500, Larissa, Greece
| | - Rajesh M Jagirdar
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
| | - Ioannis Sarrigeorgiou
- Laboratory of Immunology, Department of Immunology, Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Eleanna Pitaraki
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
| | - Sotirios I Sinis
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
| | - Charalambos Varsamas
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
| | - Eleftherios D Papazoglou
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
| | - Ourania S Kotsiou
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
- Laboratory of Human Pathophysiology, Department of Nursing, School of Health Sciences, University of Thessaly, GAIOPOLIS, 41500, Larissa, Greece
| | - Peggy Lymberi
- Laboratory of Immunology, Department of Immunology, Hellenic Pasteur Institute, 11521, Athens, Greece
| | - Anastasios Giannou
- Section of Molecular Immunology and Gastroenterology, I. Department of Medicine, UKE, 20246, Hamburg, Germany
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
- Hamburg Center for Translational Immunology (HCTI), University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - Chrissi Hatzoglou
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
| | - Konstantinos I Gourgoulianis
- Department of Respiratory Medicine, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece
| | - Sotirios G Zarogiannis
- Department of Physiology, Faculty of Medicine, School of Health Sciences, University of Thessaly, BIOPOLIS, 41500, Larissa, Greece.
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6
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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7
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Tao D, Zhang L, Ding Y, Tang N, Xu X, Li G, Niu P, Yue R, Wang X, Shen Y, Sun Y. Primary cilia support cartilage regeneration after injury. Int J Oral Sci 2023; 15:22. [PMID: 37268650 DOI: 10.1038/s41368-023-00223-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 03/24/2023] [Indexed: 06/04/2023] Open
Abstract
In growing children, growth plate cartilage has limited self-repair ability upon fracture injury always leading to limb growth arrest. Interestingly, one type of fracture injuries within the growth plate achieve amazing self-healing, however, the mechanism is unclear. Using this type of fracture mouse model, we discovered the activation of Hedgehog (Hh) signaling in the injured growth plate, which could activate chondrocytes in growth plate and promote cartilage repair. Primary cilia are the central transduction mediator of Hh signaling. Notably, ciliary Hh-Smo-Gli signaling pathways were enriched in the growth plate during development. Moreover, chondrocytes in resting and proliferating zone were dynamically ciliated during growth plate repair. Furthermore, conditional deletion of the ciliary core gene Ift140 in cartilage disrupted cilia-mediated Hh signaling in growth plate. More importantly, activating ciliary Hh signaling by Smoothened agonist (SAG) significantly accelerated growth plate repair after injury. In sum, primary cilia mediate Hh signaling induced the activation of stem/progenitor chondrocytes and growth plate repair after fracture injury.
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Affiliation(s)
- Dike Tao
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Lei Zhang
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Yunpeng Ding
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Na Tang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoqiao Xu
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Gongchen Li
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University, Shanghai, China
| | - Pingping Niu
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai, China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Rui Yue
- Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, China
| | - Xiaogang Wang
- Key Laboratory of Big Data-Based Precision Medicine, School of Engineering Medicine, Beihang University, Beijing, China
| | - Yidong Shen
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yao Sun
- Department of Implantology, School & Hospital of Stomatology, Tongji University, Shanghai, China.
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China.
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8
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Ahmed M, Muffat J, Li Y. Understanding neural development and diseases using CRISPR screens in human pluripotent stem cell-derived cultures. Front Cell Dev Biol 2023; 11:1158373. [PMID: 37101616 PMCID: PMC10123288 DOI: 10.3389/fcell.2023.1158373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/30/2023] [Indexed: 04/28/2023] Open
Abstract
The brain is arguably the most complex part of the human body in form and function. Much remains unclear about the molecular mechanisms that regulate its normal and pathological physiology. This lack of knowledge largely stems from the inaccessible nature of the human brain, and the limitation of animal models. As a result, brain disorders are difficult to understand and even more difficult to treat. Recent advances in generating human pluripotent stem cells (hPSCs)-derived 2-dimensional (2D) and 3-dimensional (3D) neural cultures have provided an accessible system to model the human brain. Breakthroughs in gene editing technologies such as CRISPR/Cas9 further elevate the hPSCs into a genetically tractable experimental system. Powerful genetic screens, previously reserved for model organisms and transformed cell lines, can now be performed in human neural cells. Combined with the rapidly expanding single-cell genomics toolkit, these technological advances culminate to create an unprecedented opportunity to study the human brain using functional genomics. This review will summarize the current progress of applying CRISPR-based genetic screens in hPSCs-derived 2D neural cultures and 3D brain organoids. We will also evaluate the key technologies involved and discuss their related experimental considerations and future applications.
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Affiliation(s)
- Mai Ahmed
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Julien Muffat
- Program in Neurosciences and Mental Health, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Yun Li
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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9
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Chen Z, Zhou K, Xue J, Small A, Xiao G, Nguyen LXT, Zhang Z, Prince E, Weng H, Huang H, Zhao Z, Qing Y, Shen C, Li W, Han L, Tan B, Su R, Qin H, Li Y, Wu D, Gu Z, Ngo VN, He X, Chao J, Leung K, Wang K, Dong L, Qin X, Cai Z, Sheng Y, Chen Y, Wu X, Zhang B, Shi Y, Marcucci G, Qian Z, Xu M, Müschen M, Chen J, Deng X. Phosphorylation stabilized TET1 acts as an oncoprotein and therapeutic target in B cell acute lymphoblastic leukemia. Sci Transl Med 2023; 15:eabq8513. [PMID: 36989375 PMCID: PMC11163962 DOI: 10.1126/scitranslmed.abq8513] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 03/06/2023] [Indexed: 03/31/2023]
Abstract
Although the overall survival rate of B cell acute lymphoblastic leukemia (B-ALL) in childhood is more than 80%, it is merely 30% in refractory/relapsed and adult patients with B-ALL. This demonstrates a need for improved therapy targeting this subgroup of B-ALL. Here, we show that the ten-eleven translocation 1 (TET1) protein, a dioxygenase involved in DNA demethylation, is overexpressed and plays a crucial oncogenic role independent of its catalytic activity in B-ALL. Consistent with its oncogenic role in B-ALL, overexpression of TET1 alone in normal precursor B cells is sufficient to transform the cells and cause B-ALL in mice within 3 to 4 months. We found that TET1 protein is stabilized and overexpressed because of its phosphorylation mediated by protein kinase C epsilon (PRKCE) and ATM serine/threonine kinase (ATM), which are also overexpressed in B-ALL. Mechanistically, TET1 recruits STAT5B to the promoters of CD72 and JCHAIN and promotes their transcription, which in turn promotes B-ALL development. Destabilization of TET1 protein by treatment with PKC or ATM inhibitors (staurosporine or AZD0156; both tested in clinical trials), or by pharmacological targeting of STAT5B, greatly decreases B-ALL cell viability and inhibits B-ALL progression in vitro and in vivo. The combination of AZD0156 with staurosporine or vincristine exhibits a synergistic effect on inhibition of refractory/relapsed B-ALL cell survival and leukemia progression in PDX models. Collectively, our study reveals an oncogenic role of the phosphorylated TET1 protein in B-ALL independent of its catalytic activity and highlights the therapeutic potential of targeting TET1 signaling for the treatment of refractory/relapsed B-ALL.
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Affiliation(s)
- Zhenhua Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Keren Zhou
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Jianhuang Xue
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Andrew Small
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Gang Xiao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Institute of Immunology, Zhejiang University School of Medicine, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou 311121, China
| | - Le Xuan Truong Nguyen
- Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Gehr Family Center for Leukemia Research, City of Hope Medical Center and Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Zheng Zhang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Emily Prince
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Hengyou Weng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Guangzhou Laboratory, Guangzhou, Guangdong 510005, China
| | - Huilin Huang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong 510060, China
| | - Zhicong Zhao
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Department of Liver Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Chao Shen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Wei Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Li Han
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Brandon Tan
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Rui Su
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Hanjun Qin
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Yangchan Li
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Department of Radiation Oncology, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong 510080, China
| | - Dong Wu
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Zhaohui Gu
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Vu N. Ngo
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Xin He
- Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Jianfei Chao
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Keith Leung
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Kitty Wang
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Lei Dong
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Xi Qin
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
| | - Zhenming Cai
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Department of Immunology, Key Laboratory of Immune Microenvironment and Diseases, Nanjing Medical University, Nanjing 211166, China
| | - Yue Sheng
- Department of Medicine and Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, FL 32611, USA
- Department of Hematology, Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China
| | - Yu Chen
- Molecular Instrumentation Center, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiwei Wu
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Bin Zhang
- Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Gehr Family Center for Leukemia Research, City of Hope Medical Center and Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Yanhong Shi
- Division of Stem Cell Biology Research, Department of Developmental and Stem Cell Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Guido Marcucci
- Department of Hematological Malignancies Translational Science, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Gehr Family Center for Leukemia Research, City of Hope Medical Center and Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Zhijian Qian
- Department of Medicine and Department of Biochemistry and Molecular Biology, UF Health Cancer Center, University of Florida, Gainesville, FL 32611, USA
| | - Mingjiang Xu
- Department of Molecular Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Markus Müschen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Center of Molecular and Cellular Oncology, Yale Cancer Center, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
- Gehr Family Center for Leukemia Research, City of Hope Medical Center and Comprehensive Cancer Center, Duarte, CA 91010, USA
| | - Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA 91016, USA
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10
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Payal N, Sharma L, Sharma A, Hobanii YH, Hakami MA, Ali N, Rashid S, Sachdeva M, Gulati M, Yadav S, Chigurupati S, Singh A, Khan H, Behl T. Understanding the Therapeutic Approaches for Neuroprotection. Curr Pharm Des 2023; 29:3368-3384. [PMID: 38151849 DOI: 10.2174/0113816128275761231103102125] [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: 08/10/2023] [Accepted: 10/07/2023] [Indexed: 12/29/2023]
Abstract
The term "neurodegenerative disorders" refers to a group of illnesses in which deterioration of nerve structure and function is a prominent feature. Cognitive capacities such as memory and decision-making deteriorate as a result of neuronal damage. The primary difficulty that remains is safeguarding neurons since they do not proliferate or regenerate spontaneously and are therefore not substituted by the body after they have been damaged. Millions of individuals throughout the world suffer from neurodegenerative diseases. Various pathways lead to neurodegeneration, including endoplasmic reticulum stress, calcium ion overload, mitochondrial dysfunction, reactive oxygen species generation, and apoptosis. Although different treatments and therapies are available for neuroprotection after a brain injury or damage, the obstacles are inextricably connected. Several studies have revealed the pathogenic effects of hypothermia, different breathed gases, stem cell treatments, mitochondrial transplantation, multi-pharmacological therapy, and other therapies that have improved neurological recovery and survival outcomes after brain damage. The present review highlights the use of therapeutic approaches that can be targeted to develop and understand significant therapies for treating neurodegenerative diseases.
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Affiliation(s)
- Nazrana Payal
- Department of Pharmacy, School of Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India
| | - Lalit Sharma
- Department of Pharmacology, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Aditi Sharma
- Department of Pharmacology, School of Pharmaceutical Sciences, Shoolini University, Solan, Himachal Pradesh, India
| | - Yahya Hosan Hobanii
- Department of Pharmacy, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia
| | | | - Nemat Ali
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj, Saudi Arabia
| | - Monika Sachdeva
- Department of Pharmacy, Fatima College of Health Sciences, Al Ain, United Arab Emirates
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 1444411, India
- ARCCIM, Faculty of Health, University of Technology, Sydney, Ultimo, NSW 2007, Australia
| | - Shivam Yadav
- School of Pharmacy, Babu Banarasi Das University, Lucknow, Uttar Pradesh, India
| | - Sridevi Chigurupati
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, Qassim University, Buraydah 52571, Kingdom of Saudi Arabia
- Department of Biotechnology, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Saveetha Nagar, Thandalam, Chennai 602105, India
| | - Abhiav Singh
- Department of Pharmacy, Indian Council of Medical Research, New Delhi, India
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Tapan Behl
- Department of Pharmacy, School of Health Sciences and Technology, University of Petroleum and Energy Studies, Bidholi, Dehradun, Uttarakhand, India
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11
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The role of Hedgehog and Notch signaling pathway in cancer. MOLECULAR BIOMEDICINE 2022; 3:44. [PMID: 36517618 PMCID: PMC9751255 DOI: 10.1186/s43556-022-00099-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/25/2022] [Indexed: 12/23/2022] Open
Abstract
Notch and Hedgehog signaling are involved in cancer biology and pathology, including the maintenance of tumor cell proliferation, cancer stem-like cells, and the tumor microenvironment. Given the complexity of Notch signaling in tumors, its role as both a tumor promoter and suppressor, and the crosstalk between pathways, the goal of developing clinically safe, effective, tumor-specific Notch-targeted drugs has remained intractable. Drugs developed against the Hedgehog signaling pathway have affirmed definitive therapeutic effects in basal cell carcinoma; however, in some contexts, the challenges of tumor resistance and recurrence leap to the forefront. The efficacy is very limited for other tumor types. In recent years, we have witnessed an exponential increase in the investigation and recognition of the critical roles of the Notch and Hedgehog signaling pathways in cancers, and the crosstalk between these pathways has vast space and value to explore. A series of clinical trials targeting signaling have been launched continually. In this review, we introduce current advances in the understanding of Notch and Hedgehog signaling and the crosstalk between pathways in specific tumor cell populations and microenvironments. Moreover, we also discuss the potential of targeting Notch and Hedgehog for cancer therapy, intending to promote the leap from bench to bedside.
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12
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pTINCR microprotein promotes epithelial differentiation and suppresses tumor growth through CDC42 SUMOylation and activation. Nat Commun 2022; 13:6840. [PMID: 36369429 PMCID: PMC9652315 DOI: 10.1038/s41467-022-34529-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 10/27/2022] [Indexed: 11/13/2022] Open
Abstract
The human transcriptome contains thousands of small open reading frames (sORFs) that encode microproteins whose functions remain largely unexplored. Here, we show that TINCR lncRNA encodes pTINCR, an evolutionary conserved ubiquitin-like protein (UBL) expressed in many epithelia and upregulated upon differentiation and under cellular stress. By gain- and loss-of-function studies, we demonstrate that pTINCR is a key inducer of epithelial differentiation in vitro and in vivo. Interestingly, low expression of TINCR associates with worse prognosis in several epithelial cancers, and pTINCR overexpression reduces malignancy in patient-derived xenografts. At the molecular level, pTINCR binds to SUMO through its SUMO interacting motif (SIM) and to CDC42, a Rho-GTPase critical for actin cytoskeleton remodeling and epithelial differentiation. Moreover, pTINCR increases CDC42 SUMOylation and promotes its activation, triggering a pro-differentiation cascade. Our findings suggest that the microproteome is a source of new regulators of cell identity relevant for cancer.
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13
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Xu J, Yang W, Pan Y, Xu H, He L, Zheng B, Xie Y, Wu X. Lucidenic acid A inhibits the binding of hACE2 receptor with spike protein to prevent SARS-CoV-2 invasion. Food Chem Toxicol 2022; 169:113438. [PMID: 36179993 PMCID: PMC9526994 DOI: 10.1016/j.fct.2022.113438] [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: 05/12/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 11/20/2022]
Abstract
High infection caused by mutations of SARS-CoV-2 calls for new prevention strategy. Ganoderma lucidum known as a superior immunoenhancer exhibits various antiviral effects, whether it can resist SARS-CoV-2 remains unclear. Herein, virtual screening combined with in vitro hACE2 inhibition assays were used to investigate its anti SARS-CoV-2 effect. Potential 54 active components, 80 core targets and 20 crucial pathways were identified by the component-target-pathway network. The binding characters of these components to hACE2 and its complexes with spike protein including omicron variant was analyzed by molecular docking. Lucidenic acid A was selected as the top molecule with high affinity to all receptors by forming hydrogen bonds. Molecular dynamics simulation showed it had good binding stability with the receptor proteins. Finally, in vitro FRET test demonstrated it inhibited the hACE2 activity with IC50 2 μmol/mL. Therefore, lucidenic acid A can prevent the virus invasion by blocking hACE2 binding with SARS-CoV-2.
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Affiliation(s)
- Juan Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - WenTao Yang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YiFeng Pan
- Hangzhou Xihu District Center for Disease Control and Prevention, Hangzhou, 310030, PR China
| | - HaiShun Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - Liang He
- Zhejiang Provincial Academy of Forestry, Hangzhou, 310000, Zhejiang, China
| | - BingSong Zheng
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China
| | - YingQiu Xie
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - XueQian Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, PR China; Zhejiang Provincial Key Laboratory of Characteristic Traditional Chinese Medicine Resources Protection and Innovative Utilization, Zhejiang A&F University, Lin'an, 311300, PR China; National Innovation Alliance of Lingzhi and Sanyeqing Industry, Lin'an, 311300, China.
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14
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Qi S, Sivakumar S, Yu H. CRISPR-Cas9 screen in human embryonic stem cells to identify genes required for neural differentiation. STAR Protoc 2022; 3:101682. [PMID: 36115024 PMCID: PMC9490198 DOI: 10.1016/j.xpro.2022.101682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 07/22/2022] [Accepted: 08/10/2022] [Indexed: 01/25/2023] Open
Abstract
Human embryonic stem cells (hESCs) continuously self-renew in culture and can be induced to differentiate into multiple cell types, including neural progenitor cells (NPCs). Here, we present a protocol to perform a CRISPR-Cas9 screen in hESCs to identify regulators that promote SOX1 expression during NPC formation. This screening protocol can be adapted with other endpoint reporters for the identification of genes involved in the commitment of hESCs to other cell lineages. For complete details on the use and execution of this protocol, please refer to Sivakumar et al. (2022).
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Affiliation(s)
- Shutao Qi
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China,School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
| | - Sushama Sivakumar
- Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA
| | - Hongtao Yu
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China,School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China,Department of Pharmacology, University of Texas Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX 75390, USA,Corresponding author
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15
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Michel N, Young HMR, Atkin ND, Arshad U, Al-Humadi R, Singh S, Manukyan A, Gore L, Burbulis IE, Wang YH, McConnell MJ. Transcription-associated DNA DSBs activate p53 during hiPSC-based neurogenesis. Sci Rep 2022; 12:12156. [PMID: 35840793 PMCID: PMC9287420 DOI: 10.1038/s41598-022-16516-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/11/2022] [Indexed: 11/09/2022] Open
Abstract
Neurons are overproduced during cerebral cortical development. Neural progenitor cells (NPCs) divide rapidly and incur frequent DNA double-strand breaks (DSBs) throughout cortical neurogenesis. Although half of the neurons born during neurodevelopment die, many neurons with inaccurate DNA repair survive leading to brain somatic mosaicism. Recurrent DNA DSBs during neurodevelopment are associated with both gene expression level and gene length. We used imaging flow cytometry and a genome-wide DNA DSB capture approach to quantify and map DNA DSBs during human induced pluripotent stem cell (hiPSC)-based neurogenesis. Reduced p53 signaling was brought about by knockdown (p53KD); p53KD led to elevated DNA DSB burden in neurons that was associated with gene expression level but not gene length in neural progenitor cells (NPCs). Furthermore, DNA DSBs incurred from transcriptional, but not replicative, stress lead to p53 activation in neurotypical NPCs. In p53KD NPCs, DNA DSBs accumulate at transcription start sites of genes that are associated with neurological and psychiatric disorders. These findings add to a growing understanding of how neuronal genome dynamics are engaged by high transcriptional or replicative burden during neurodevelopment.
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Affiliation(s)
- Nadine Michel
- Neuroscience Graduate Program, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Heather M Raimer Young
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Naomi D Atkin
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Umar Arshad
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Reem Al-Humadi
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Sandeep Singh
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Arkadi Manukyan
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Lana Gore
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA
| | - Ian E Burbulis
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
- Sede de la Patagonia, Facultad de Medicina y Ciencias, Universidad San Sebastián, Puerto Montt, Chile
| | - Yuh-Hwa Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, 1340 Jefferson Park Avenue, Charlottesville, VA, 22908, USA
| | - Michael J McConnell
- Lieber Institute for Brain Development, 855 N. Wolfe St., Ste. 300, Baltimore, MD, 21205, USA.
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16
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p53 at the crossroad of DNA replication and ribosome biogenesis stress pathways. Cell Death Differ 2022; 29:972-982. [PMID: 35444234 PMCID: PMC9090812 DOI: 10.1038/s41418-022-00999-w] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 01/05/2023] Open
Abstract
Despite several decades of intense research focused on understanding function(s) and disease-associated malfunction of p53, there is no sign of any “mid-life crisis” in this rapidly advancing area of biomedicine. Firmly established as the hub of cellular stress responses and tumor suppressor targeted in most malignancies, p53’s many talents continue to surprise us, providing not only fresh insights into cell and organismal biology, but also new avenues to cancer treatment. Among the most fruitful lines of p53 research in recent years have been the discoveries revealing the multifaceted roles of p53-centered pathways in the fundamental processes of DNA replication and ribosome biogenesis (RiBi), along with cellular responses to replication and RiBi stresses, two intertwined areas of cell (patho)physiology that we discuss in this review. Here, we first provide concise introductory notes on the canonical roles of p53, the key interacting proteins, downstream targets and post-translational modifications involved in p53 regulation. We then highlight the emerging involvement of p53 as a key component of the DNA replication Fork Speed Regulatory Network and the mechanistic links of p53 with cellular checkpoint responses to replication stress (RS), the driving force of cancer-associated genomic instability. Next, the tantalizing, yet still rather foggy functional crosstalk between replication and RiBi (nucleolar) stresses is considered, followed by the more defined involvement of p53-mediated monitoring of the multistep process of RiBi, including the latest updates on the RPL5/RPL11/5 S rRNA-MDM2-p53-mediated Impaired Ribosome Biogenesis Checkpoint (IRBC) pathway and its involvement in tumorigenesis. The diverse defects of RiBi and IRBC that predispose and/or contribute to severe human pathologies including developmental syndromes and cancer are then outlined, along with examples of promising small-molecule-based strategies to therapeutically target the RS- and particularly RiBi- stress-tolerance mechanisms to which cancer cells are addicted due to their aberrant DNA replication, repair, and proteo-synthesis demands. ![]()
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