1
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Ni Q, Sun SX. Pump up the volume. eLife 2024; 13:e100032. [PMID: 38953882 PMCID: PMC11219035 DOI: 10.7554/elife.100032] [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] [Indexed: 07/04/2024] Open
Abstract
An influx of water molecules can help immune cells called neutrophils to move to where they are needed in the body.
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Affiliation(s)
- Qin Ni
- Institute for NanoBioTechnology and Department of Mechanical Engineering, Johns Hopkins UniversityBaltimoreUnited States
| | - Sean X Sun
- Institute for NanoBioTechnology and Department of Mechanical Engineering, Johns Hopkins UniversityBaltimoreUnited States
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2
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Shorthouse D, Zhuang L, Rahrmann EP, Kosmidou C, Wickham Rahrmann K, Hall M, Greenwood B, Devonshire G, Gilbertson RJ, Fitzgerald RC, Hall BA. KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas. Life Sci Alliance 2023; 6:e202302124. [PMID: 37748809 PMCID: PMC10520261 DOI: 10.26508/lsa.202302124] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/27/2023] Open
Abstract
Voltage-sensitive potassium channels play an important role in controlling membrane potential and ionic homeostasis in the gut and have been implicated in gastrointestinal (GI) cancers. Through large-scale analysis of 897 patients with gastro-oesophageal adenocarcinomas (GOAs) coupled with in vitro models, we find KCNQ family genes are mutated in ∼30% of patients, and play therapeutically targetable roles in GOA cancer growth. KCNQ1 and KCNQ3 mediate the WNT pathway and MYC to increase proliferation through resultant effects on cadherin junctions. This also highlights novel roles of KCNQ3 in non-excitable tissues. We also discover that activity of KCNQ3 sensitises cancer cells to existing potassium channel inhibitors and that inhibition of KCNQ activity reduces proliferation of GOA cancer cells. These findings reveal a novel and exploitable role of potassium channels in the advancement of human cancer, and highlight that supplemental treatments for GOAs may exist through KCNQ inhibitors.
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Affiliation(s)
- David Shorthouse
- https://ror.org/02jx3x895 Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, London, UK
| | - Lizhe Zhuang
- Institute for Early Detection, CRUK Cambridge Centre, Cambridge, UK
| | - Eric P Rahrmann
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | | | - Michael Hall
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Benedict Greenwood
- https://ror.org/02jx3x895 Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, London, UK
| | - Ginny Devonshire
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Richard J Gilbertson
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | | | - Benjamin A Hall
- https://ror.org/02jx3x895 Department of Medical Physics and Biomedical Engineering, Malet Place Engineering Building, University College London, London, UK
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3
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Zhong J, Dong J, Ruan W, Duan X. Potential Theranostic Roles of SLC4 Molecules in Human Diseases. Int J Mol Sci 2023; 24:15166. [PMID: 37894847 PMCID: PMC10606849 DOI: 10.3390/ijms242015166] [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: 08/29/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
The solute carrier family 4 (SLC4) is an important protein responsible for the transport of various ions across the cell membrane and mediating diverse physiological functions, such as the ion transporting function, protein-to-protein interactions, and molecular transduction. The deficiencies in SLC4 molecules may cause multisystem disease involving, particularly, the respiratory system, digestive, urinary, endocrine, hematopoietic, and central nervous systems. Currently, there are no effective strategies to treat these diseases. SLC4 proteins are also found to contribute to tumorigenesis and development, and some of them are regarded as therapeutic targets in quite a few clinical trials. This indicates that SLC4 proteins have potential clinical prospects. In view of their functional characteristics, there is a critical need to review the specific functions of bicarbonate transporters, their related diseases, and the involved pathological mechanisms. We summarize the diseases caused by the mutations in SLC4 family genes and briefly introduce the clinical manifestations of these diseases as well as the current treatment strategies. Additionally, we illustrate their roles in terms of the physiology and pathogenesis that has been currently researched, which might be the future therapeutic and diagnostic targets of diseases and a new direction for drug research and development.
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Affiliation(s)
| | | | | | - Xiaohong Duan
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, National Clinical Research Center for Oral Disease, Shaanxi Key Laboratory of Stomatology, Department of Oral Biology & Clinic of Oral Rare Diseases and Genetic Diseases, School of Stomatology, The Fourth Military Medical University, Xi’an 710032, China; (J.Z.); (J.D.); (W.R.)
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4
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Baran K, Waśko J, Kryczka J, Boncela J, Jabłoński S, Kolesińska B, Brzeziańska-Lasota E, Kordiak J. The Comparison of Serum Exosome Protein Profile in Diagnosis of NSCLC Patients. Int J Mol Sci 2023; 24:13669. [PMID: 37761972 PMCID: PMC10650331 DOI: 10.3390/ijms241813669] [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: 08/10/2023] [Revised: 08/31/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
A thorough study of the exosomal proteomic cargo may enable the identification of proteins that play an important role in cancer development. The aim of this study was to compare the protein profiles of the serum exosomes derived from non-small lung cancer (NSCLC) patients and healthy volunteers (control) using the high-performance liquid chromatography coupled to mass spectrometry (HPLC-MS) method to identify potentially new diagnostic and/or prognostic protein biomarkers. Proteins exclusively identified in NSCLC and control groups were analyzed using several bioinformatic tools and platforms (FunRich, Vesiclepedia, STRING, and TIMER2.0) to find key protein hubs involved in NSCLC progression and the acquisition of metastatic potential. This analysis revealed 150 NSCLC proteins, which are significantly involved in osmoregulation, cell-cell adhesion, cell motility, and differentiation. Among them, 3 proteins: Interleukin-34 (IL-34), HLA class II histocompatibility antigen, DM alpha chain (HLA-DMA), and HLA class II histocompatibility antigen, DO beta chain (HLA-DOB) were shown to be significantly involved in the cancer-associated fibroblasts (CAFs) and tumor-associated macrophages (TAMs) infiltration processes. Additionally, detected proteins were analyzed according to the presence of lymph node metastasis, showing that differences in frequency of detection of protein FAM166B, killer cell immunoglobulin-like receptor 2DL1, and olfactory receptor 52R1 correlate with the N feature according to the TNM Classification of Malignant Tumors. These results prove their involvement in NSCLC lymph node spread and metastasis. However, this study requires further investigation.
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Affiliation(s)
- Kamila Baran
- Department of Biomedicine and Genetics, Medical University of Lodz, 92-213 Lodz, Poland;
| | - Joanna Waśko
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (J.W.); (B.K.)
| | - Jakub Kryczka
- Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.K.); (J.B.)
| | - Joanna Boncela
- Institute of Medical Biology, Polish Academy of Sciences, 93-232 Lodz, Poland; (J.K.); (J.B.)
| | - Sławomir Jabłoński
- Department of Thoracic, General and Oncological Surgery, Medical University of Lodz, 90-549 Lodz, Poland; (S.J.); (J.K.)
| | - Beata Kolesińska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (J.W.); (B.K.)
| | - Ewa Brzeziańska-Lasota
- Department of Biomedicine and Genetics, Medical University of Lodz, 92-213 Lodz, Poland;
| | - Jacek Kordiak
- Department of Thoracic, General and Oncological Surgery, Medical University of Lodz, 90-549 Lodz, Poland; (S.J.); (J.K.)
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5
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Yang C. Prediction of hearing preservation after acoustic neuroma surgery based on SMOTE-XGBoost. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:10757-10772. [PMID: 37322959 DOI: 10.3934/mbe.2023477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Prior to the surgical removal of an acoustic neuroma, the majority of patients anticipate that their hearing will be preserved to the greatest possible extent following surgery. This paper proposes a postoperative hearing preservation prediction model for the characteristics of class-imbalanced hospital real data based on the extreme gradient boost tree (XGBoost). In order to eliminate sample imbalance, the synthetic minority oversampling technique (SMOTE) is applied to increase the number of underclass samples in the data. Multiple machine learning models are also used for the accurate prediction of surgical hearing preservation in acoustic neuroma patients. In comparison to research results from existing literature, the experimental results found the model proposed in this paper to be superior. In summary, the method this paper proposes can make a significant contribution to the development of personalized preoperative diagnosis and treatment plans for patients, leading to effective judgment for the hearing retention of patients with acoustic neuroma following surgery, a simplified long medical treatment process and saved medical resources.
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Affiliation(s)
- Cenyi Yang
- School of Mathematics and Statistics, Central South University, Changsha 410083, China
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6
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Yu S, Zhang M, Ye Z, Wang Y, Wang X, Chen YG. Development of a 32-gene signature using machine learning for accurate prediction of inflammatory bowel disease. CELL REGENERATION (LONDON, ENGLAND) 2023; 12:8. [PMID: 36600111 PMCID: PMC9813306 DOI: 10.1186/s13619-022-00143-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/09/2022] [Indexed: 01/06/2023]
Abstract
Inflammatory bowel disease (IBD) is a chronic inflammatory condition caused by multiple genetic and environmental factors. Numerous genes are implicated in the etiology of IBD, but the diagnosis of IBD is challenging. Here, XGBoost, a machine learning prediction model, has been used to distinguish IBD from healthy cases following elaborative feature selection. Using combined unsupervised clustering analysis and the XGBoost feature selection method, we successfully identified a 32-gene signature that can predict IBD occurrence in new cohorts with 0.8651 accuracy. The signature shows enrichment in neutrophil extracellular trap formation and cytokine signaling in the immune system. The probability threshold of the XGBoost-based classification model can be adjusted to fit personalized lifestyle and health status. Therefore, this study reveals potential IBD-related biomarkers that facilitate an effective personalized diagnosis of IBD.
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Affiliation(s)
- Shicheng Yu
- grid.9227.e0000000119573309Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou, 510530 China ,Guangzhou Laboratory, Guangzhou, 510700 China
| | - Mengxian Zhang
- grid.12527.330000 0001 0662 3178The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China
| | - Zhaofeng Ye
- grid.12527.330000 0001 0662 3178School of Medicine, Tsinghua University, Beijing, 100084 China
| | - Yalong Wang
- grid.9227.e0000000119573309Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou, 510530 China ,Guangzhou Laboratory, Guangzhou, 510700 China
| | - Xu Wang
- Guangzhou Laboratory, Guangzhou, 510700 China
| | - Ye-Guang Chen
- Guangzhou Laboratory, Guangzhou, 510700 China ,grid.12527.330000 0001 0662 3178The State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084 China ,grid.260463.50000 0001 2182 8825School of Basic Medicine, Nanchang University, Nanchang, 330031 China
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7
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Brosch PK, Korsa T, Taban D, Eiring P, Hildebrand S, Neubauer J, Zimmermann H, Sauer M, Shirakashi R, Djuzenova CS, Sisario D, Sukhorukov VL. Glucose and Inositol Transporters, SLC5A1 and SLC5A3, in Glioblastoma Cell Migration. Cancers (Basel) 2022; 14:5794. [PMID: 36497276 PMCID: PMC9738886 DOI: 10.3390/cancers14235794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 11/04/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022] Open
Abstract
(1) Background: The recurrence of glioblastoma multiforme (GBM) is mainly due to invasion of the surrounding brain tissue, where organic solutes, including glucose and inositol, are abundant. Invasive cell migration has been linked to the aberrant expression of transmembrane solute-linked carriers (SLC). Here, we explore the role of glucose (SLC5A1) and inositol transporters (SLC5A3) in GBM cell migration. (2) Methods: Using immunofluorescence microscopy, we visualized the subcellular localization of SLC5A1 and SLC5A3 in two highly motile human GBM cell lines. We also employed wound-healing assays to examine the effect of SLC inhibition on GBM cell migration and examined the chemotactic potential of inositol. (3) Results: While GBM cell migration was significantly increased by extracellular inositol and glucose, it was strongly impaired by SLC transporter inhibition. In the GBM cell monolayers, both SLCs were exclusively detected in the migrating cells at the monolayer edge. In single GBM cells, both transporters were primarily localized at the leading edge of the lamellipodium. Interestingly, in GBM cells migrating via blebbing, SLC5A1 and SLC5A3 were predominantly detected in nascent and mature blebs, respectively. (4) Conclusion: We provide several lines of evidence for the involvement of SLC5A1 and SLC5A3 in GBM cell migration, thereby complementing the migration-associated transportome. Our findings suggest that SLC inhibition is a promising approach to GBM treatment.
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Affiliation(s)
- Philippa K. Brosch
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Tessa Korsa
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Danush Taban
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Patrick Eiring
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Sascha Hildebrand
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Julia Neubauer
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Heiko Zimmermann
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
- Department of Molecular and Cellular Biotechnology, Saarland University, 66123 Saarbrücken, Germany
- Faculty of Marine Science, Universidad Católica del Norte, Coquimbo 1281, Chile
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Ryo Shirakashi
- Institute of Industrial Science, The University of Tokyo, Tokyo 153-8505, Japan
| | - Cholpon S. Djuzenova
- Department of Radiation Oncology, University Hospital of Würzburg, 97080 Würzburg, Germany
| | - Dmitri Sisario
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Vladimir L. Sukhorukov
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
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8
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Zheng Z, Wang Y, Li M, Li D, Nie A, Chen M, Ruan Q, Guo Y, Guo J. Albumins as Extracellular Protein Nanoparticles Collaborate with Plasma Ions to Control Biological Osmotic Pressure. Int J Nanomedicine 2022; 17:4743-4756. [PMID: 36238535 PMCID: PMC9553280 DOI: 10.2147/ijn.s383530] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/03/2022] [Indexed: 11/07/2022] Open
Abstract
Introduction Plasma albumins as protein nanoparticles (PNs) exert essential functions in the control of biological osmotic pressure (OP), being involved in regulating water metabolism, cell morphology and cell tension. Understanding how plasma albumins and different electrolytes co-determine biological OP effects is crucial for correct interpretation of hemodynamic disorders, and practical treatment of hypo/hyper-proteinemia. Methods Optical measurement based on intermediate filament (IF) tension probe was used for real-time evaluation of transmembrane osmotic effects in live cells. Ion fluorescent probes were employed to evaluate intracellular ion levels, and a current clamp was used to measure membrane potential, thus exploring association of electrochemical and osmotic effects. Results Albumins are involved in regulation of intracellular osmolarity by a quantitative relationship. Extracellular PNs can alter membrane potentials by adsorbing counterions, induce production of intracellular PNs and further control the opening of ion channels and ion flow, contributing to electrochemical and osmotic re-equilibrium. Furthermore, various ions interplay with extracellular PNs, showing different osmotic effects: increased levels of calcium ions result in a hypotonic effect, whereas potassium ions induce hyper-osmolarity. Conclusion Extracellular PNs and Ca2+/K+ display antagonistic or synergetic effects in regulating biological OP. Live cells can spontaneously regulate osmotic effects through changing membrane potential and controlling intracellular ion content. Various plasma components need to be comprehensively analyzed, further developing a diagnostic index that considers the biological OP effects of various blood components and improves the evaluation of symptoms and diseases, such as calcium/potassium-hemodynamic disorders and edema.
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Affiliation(s)
- Zihui Zheng
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Yuanyuan Wang
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Meng Li
- Children’s Hospital of Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Dongfang Li
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Aobo Nie
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Miao Chen
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Qinli Ruan
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China
| | - Yichen Guo
- Biomedical Engineering, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA,Yichen Guo Biomedical Engineering, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA, Email
| | - Jun Guo
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Key Laboratory of Drug Target and Drug for Degenerative Disease, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, People’s Republic of China,Correspondence: Jun Guo, School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, People’s Republic of China, Tel +86 13813909055, Email
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9
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Taïeb HM, Garske DS, Contzen J, Gossen M, Bertinetti L, Robinson T, Cipitria A. Osmotic pressure modulates single cell cycle dynamics inducing reversible growth arrest and reactivation of human metastatic cells. Sci Rep 2021; 11:13455. [PMID: 34188099 PMCID: PMC8242012 DOI: 10.1038/s41598-021-92054-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Biophysical cues such as osmotic pressure modulate proliferation and growth arrest of bacteria, yeast cells and seeds. In tissues, osmotic regulation takes place through blood and lymphatic capillaries and, at a single cell level, water and osmoregulation play a critical role. However, the effect of osmotic pressure on single cell cycle dynamics remains poorly understood. Here, we investigate the effect of osmotic pressure on single cell cycle dynamics, nuclear growth, proliferation, migration and protein expression, by quantitative time-lapse imaging of single cells genetically modified with fluorescent ubiquitination-based cell cycle indicator 2 (FUCCI2). Single cell data reveals that under hyperosmotic stress, distinct cell subpopulations emerge with impaired nuclear growth, delayed or growth arrested cell cycle and reduced migration. This state is reversible for mild hyperosmotic stress, where cells return to regular cell cycle dynamics, proliferation and migration. Thus, osmotic pressure can modulate the reversible growth arrest and reactivation of human metastatic cells.
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Affiliation(s)
- Hubert M. Taïeb
- grid.419564.bDepartment of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Daniela S. Garske
- grid.419564.bDepartment of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Jörg Contzen
- grid.6363.00000 0001 2218 4662Department of Experimental Neurology, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany ,grid.24999.3f0000 0004 0541 3699Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany ,grid.484013.aBIH Center for Regenerative Therapies, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Manfred Gossen
- grid.24999.3f0000 0004 0541 3699Institute of Active Polymers, Helmholtz-Zentrum Hereon, 14513 Teltow, Germany ,grid.484013.aBIH Center for Regenerative Therapies, Berlin Institute of Health at Charité-Universitätsmedizin Berlin, 13353 Berlin, Germany
| | - Luca Bertinetti
- grid.419564.bDepartment of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Tom Robinson
- grid.419564.bDepartment of Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Amaia Cipitria
- grid.419564.bDepartment of Biomaterials, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany
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10
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van der Weyden L, Harle V, Turner G, Offord V, Iyer V, Droop A, Swiatkowska A, Rabbie R, Campbell AD, Sansom OJ, Pardo M, Choudhary JS, Ferreira I, Tullett M, Arends MJ, Speak AO, Adams DJ. CRISPR activation screen in mice identifies novel membrane proteins enhancing pulmonary metastatic colonisation. Commun Biol 2021; 4:395. [PMID: 33758365 PMCID: PMC7987976 DOI: 10.1038/s42003-021-01912-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 02/25/2021] [Indexed: 02/08/2023] Open
Abstract
Melanoma represents ~5% of all cutaneous malignancies, yet accounts for the majority of skin cancer deaths due to its propensity to metastasise. To develop new therapies, novel target molecules must to be identified and the accessibility of cell surface proteins makes them attractive targets. Using CRISPR activation technology, we screened a library of guide RNAs targeting membrane protein-encoding genes to identify cell surface molecules whose upregulation enhances the metastatic pulmonary colonisation capabilities of tumour cells in vivo. We show that upregulated expression of the cell surface protein LRRN4CL led to increased pulmonary metastases in mice. Critically, LRRN4CL expression was elevated in melanoma patient samples, with high expression levels correlating with decreased survival. Collectively, our findings uncover an unappreciated role for LRRN4CL in the outcome of melanoma patients and identifies a potential therapeutic target and biomarker.
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MESH Headings
- Animals
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- CRISPR-Cas Systems
- Cell Line, Tumor
- Cell Movement
- Female
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/secondary
- Male
- Melanoma, Experimental/genetics
- Melanoma, Experimental/metabolism
- Melanoma, Experimental/secondary
- Membrane Proteins/genetics
- Membrane Proteins/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Inbred NOD
- Mice, Knockout
- Neoplasm Invasiveness
- Skin Neoplasms/genetics
- Skin Neoplasms/metabolism
- Skin Neoplasms/pathology
- Up-Regulation
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Affiliation(s)
| | - Victoria Harle
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gemma Turner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Vivek Iyer
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Alastair Droop
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Roy Rabbie
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Owen J Sansom
- Cancer Research UK Beatson Institute, Glasgow, UK
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Ingrid Ferreira
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mark Tullett
- Western Sussex NHS Foundation Trust, Chichester, West Sussex, UK
| | - Mark J Arends
- University of Edinburgh Division of Pathology, Edinburgh Cancer Research UK Cancer Centre, Institute of Genetics & Molecular Medicine, Edinburgh, UK
| | - Anneliese O Speak
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
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11
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Forget NL, Duplisea DE, Sardenne F, McKindsey CW. Using qualitative network models to assess the influence of mussel culture on ecosystem dynamics. Ecol Modell 2020. [DOI: 10.1016/j.ecolmodel.2020.109070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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12
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Jia Y, Liu W, Zhan HE, Yi XP, Liang H, Zheng QL, Jiang XY, Zhou HY, Zhao L, Zhao XL, Zeng H. Roles of hsa-miR-12462 and SLC9A1 in acute myeloid leukemia. J Hematol Oncol 2020; 13:101. [PMID: 32703317 PMCID: PMC7376648 DOI: 10.1186/s13045-020-00935-w] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/13/2020] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) play important roles in cell proliferation, differentiation, and survival and may be useful for acute myeloid leukemia (AML) diagnosis and prognosis. In this study, we defined a novel miRNA, hsa-miR-12462, through small RNA sequencing of the bone marrow (BM) cells from 128 AML patients. Overexpression of hsa-miR-12462 in AML cells (U937 and HL-60) significantly decreased their growth rate when compared with those of the wild-type and MOCK controls. In a xenograft mouse model, tumor weight and size in the mice bearing the U937 cells with hsa-miR-12462 overexpression were significantly reduced when compared with those bearing the mock cells. The AML cells overexpressing hsa-miR-12462 had increased sensitivity to cytarabine chemotherapy. Combining the data from the MiRDB, an online microRNA database (http://mirdb.org), with the RNA-sequencing results, SLC9A1 was predicted to be one of the targets of hsa-miR-12462. hsa-miR-12462 was further confirmed to bind exclusively to the 3′UTR of SLC9A1 in U937 cells, leading to downregulation of SLC9A1. In summary, a higher level of hsa-miR-12462 in AML cells is associated with increased sensitivity to cytarabine chemotherapy via downregulation of SLC9A1.
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Affiliation(s)
- Yan Jia
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Liu
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui-En Zhan
- Department of Hematology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China
| | - Xiao-Ping Yi
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Liang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qi-Li Zheng
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin-Ya Jiang
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hai-Yan Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liang Zhao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xie-Lan Zhao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Zeng
- Department of Hematology, The First Affiliated Hospital of Jinan University, Guangzhou, Guangdong, China.
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13
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Abstract
Making decisions on how best to treat cancer patients requires the integration of different data sets, including genomic profiles, tumour histopathology, radiological images, proteomic analysis and more. This wealth of biological information calls for novel strategies to integrate such information in a meaningful, predictive and experimentally verifiable way. In this Perspective we explain how executable computational models meet this need. Such models provide a means for comprehensive data integration, can be experimentally validated, are readily interpreted both biologically and clinically, and have the potential to predict effective therapies for different cancer types and subtypes. We explain what executable models are and how they can be used to represent the dynamic biological behaviours inherent in cancer, and demonstrate how such models, when coupled with automated reasoning, facilitate our understanding of the mechanisms by which oncogenic signalling pathways regulate tumours. We explore how executable models have impacted the field of cancer research and argue that extending them to represent a tumour in a specific patient (that is, an avatar) will pave the way for improved personalized treatments and precision medicine. Finally, we highlight some of the ongoing challenges in developing executable models and stress that effective cross-disciplinary efforts are key to forward progress in the field.
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Affiliation(s)
- Matthew A Clarke
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jasmin Fisher
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
- UCL Cancer Institute, University College London, London, UK.
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14
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Jacobsen A, Ivanova O, Amini S, Heringa J, Kemmeren P, Feenstra KA. A framework for exhaustive modelling of genetic interaction patterns using Petri nets. Bioinformatics 2020; 36:2142-2149. [PMID: 31845959 DOI: 10.1093/bioinformatics/btz917] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/09/2019] [Accepted: 12/13/2019] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Genetic interaction (GI) patterns are characterized by the phenotypes of interacting single and double mutated gene pairs. Uncovering the regulatory mechanisms of GIs would provide a better understanding of their role in biological processes, diseases and drug response. Computational analyses can provide insights into the underpinning mechanisms of GIs. RESULTS In this study, we present a framework for exhaustive modelling of GI patterns using Petri nets (PN). Four-node models were defined and generated on three levels with restrictions, to enable an exhaustive approach. Simulations suggest ∼5 million models of GIs. Generalizing these we propose putative mechanisms for the GI patterns, inversion and suppression. We demonstrate that exhaustive PN modelling enables reasoning about mechanisms of GIs when only the phenotypes of gene pairs are known. The framework can be applied to other GI or genetic regulatory datasets. AVAILABILITY AND IMPLEMENTATION The framework is available at http://www.ibi.vu.nl/programs/ExhMod. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Annika Jacobsen
- Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
| | - Olga Ivanova
- Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
| | - Saman Amini
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, Netherlands.,Divison of Biomedical Genetics, Center for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, Netherlands
| | - Jaap Heringa
- Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
| | - Patrick Kemmeren
- Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, Netherlands.,Divison of Biomedical Genetics, Center for Molecular Medicine, University Medical Centre Utrecht, 3584 CX Utrecht, Netherlands
| | - K Anton Feenstra
- Department of Computer Science, Centre for Integrative Bioinformatics (IBIVU), Vrije Universiteit Amsterdam, 1081 HV Amsterdam, Netherlands
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15
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Hall BA, Fisher J. Constructing and Analyzing Computational Models of Cell Signaling with BioModelAnalyzer. CURRENT PROTOCOLS IN BIOINFORMATICS 2020; 69:e95. [PMID: 32078258 DOI: 10.1002/cpbi.95] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BioModelAnalyzer (BMA) is an open-source graphical tool for the development of executable models of protein and gene networks within cells. Based upon the Qualitative Networks formalism, the user can rapidly construct large networks, either manually or by connecting motifs selected from a built-in library. After the appropriate functions for each variable are defined, the user has access to three analysis engines to test the model. In addition to standard simulation tools, BMA includes an interface to the stability-testing algorithm and to a graphical Linear Temporal Logic (LTL) editor and analysis tool. Alongside this, we have developed a novel ChatBot to aid users constructing LTL queries and to explain the interface and run through tutorials. Here we present worked examples of model construction and testing via the interface. As an initial example, we discuss fate decisions in Dictyostelium discoidum and cAMP signaling. We go on to describe the workflow leading to the construction of a published model of the germline of C. elegans. Finally, we demonstrate how to construct simple models from the built-in network motif library. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Modeling the signaling network of Dictyostelium discoidum Basic Protocol 2: Modeling the germline progression of Caenorhabditis elegans Basic Protocol 3: Constructing a model of the cell cycle using motifs.
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Affiliation(s)
- Benjamin A Hall
- MRC Cancer Unit, University of Cambridge, Cambridge, United Kingdom
| | - Jasmin Fisher
- UCL Cancer Institute, University College London, London, United Kingdom
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16
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Bogusławska J, Popławski P, Alseekh S, Koblowska M, Iwanicka-Nowicka R, Rybicka B, Kędzierska H, Głuchowska K, Hanusek K, Tański Z, Fernie AR, Piekiełko-Witkowska A. MicroRNA-Mediated Metabolic Reprograming in Renal Cancer. Cancers (Basel) 2019; 11:cancers11121825. [PMID: 31756931 PMCID: PMC6966432 DOI: 10.3390/cancers11121825] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023] Open
Abstract
Metabolic reprogramming is one of the hallmarks of renal cell cancer (RCC). We hypothesized that altered metabolism of RCC cells results from dysregulation of microRNAs targeting metabolically relevant genes. Combined large-scale transcriptomic and metabolic analysis of RCC patients tissue samples revealed a group of microRNAs that contribute to metabolic reprogramming in RCC. miRNAs expressions correlated with their predicted target genes and with gas chromatography-mass spectrometry (GC-MS) metabolome profiles of RCC tumors. Assays performed in RCC-derived cell lines showed that miR-146a-5p and miR-155-5p targeted genes of PPP (the pentose phosphate pathway) (G6PD and TKT), the TCA (tricarboxylic acid cycle) cycle (SUCLG2), and arginine metabolism (GATM), respectively. miR-106b-5p and miR-122-5p regulated the NFAT5 osmoregulatory transcription factor. Altered expressions of G6PD, TKT, SUCLG2, GATM, miR-106b-5p, miR-155-5p, and miR-342-3p correlated with poor survival of RCC patients. miR-106b-5p, miR-146a-5p, and miR-342-3p stimulated proliferation of RCC cells. The analysis involving >6000 patients revealed that miR-34a-5p, miR-106b-5p, miR-146a-5p, and miR-155-5p are PanCancer metabomiRs possibly involved in global regulation of cancer metabolism. In conclusion, we found that microRNAs upregulated in renal cancer contribute to disturbed expression of key genes involved in the regulation of RCC metabolome. miR-146a-5p and miR-155-5p emerge as a key “metabomiRs” that target genes of crucial metabolic pathways (PPP (the pentose phosphate pathway), TCA cycle, and arginine metabolism).
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Affiliation(s)
- Joanna Bogusławska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Piotr Popławski
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Saleh Alseekh
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (S.A.); (A.R.F.)
- Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Marta Koblowska
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland; (M.K.); (R.I.-N.)
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland; (M.K.); (R.I.-N.)
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Beata Rybicka
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Katarzyna Głuchowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Karolina Hanusek
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
| | - Zbigniew Tański
- Masovian Specialist Hospital in Ostroleka, 07-410 Ostroleka, Poland;
| | - Alisdair R. Fernie
- Max-Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; (S.A.); (A.R.F.)
- Center for Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland; (J.B.); (P.P.); (B.R.); (H.K.); (K.G.); (K.H.)
- Correspondence: ; Tel.: +48-22-5693810
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