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Scheer JK, Ames CP. Artificial Intelligence in Spine Surgery. Neurosurg Clin N Am 2024; 35:253-262. [PMID: 38423741 DOI: 10.1016/j.nec.2023.11.001] [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: 03/02/2024]
Abstract
The amount and quality of data being used in our everyday lives continue to advance in an unprecedented pace. This digital revolution has permeated healthcare, specifically spine surgery, allowing for very advanced and complex computational analytics, such as artificial intelligence (AI) and machine learning (ML). The integration of these methods into clinical practice has just begun, and the following review article will describe AI/ML, demonstrate how it has been applied in adult spinal deformity surgery, and show its potential to improve patient care touching on future directions.
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Affiliation(s)
- Justin K Scheer
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.
| | - Christopher P Ames
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
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2
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Lin Y, Zhang N, Zhang J, Lu J, Liu S, Ma G. The association between hydration state and the metabolism of phospholipids and amino acids among young adults: a metabolomic analysis. Curr Dev Nutr 2024; 8:102087. [PMID: 38425438 PMCID: PMC10904166 DOI: 10.1016/j.cdnut.2024.102087] [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: 11/28/2023] [Revised: 01/15/2024] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
Background Water is vital for humans' survival and general health, which is involved in various metabolic activities. Objectives The aim of this study was to investigate the variation in urine metabolome and associated metabolic pathways among people with different hydration states. Methods A metabolomic analysis was conducted using 24-h urine samples collected during a cross-sectional study on fluid intake behavior from December 9 to 11, 2021, in Hebei, China. Subjects were divided into the optimal hydration (OH, ≤500 mOsm/kg, n = 21), middle hydration (500-800 mOsm/kg, n = 33), and hypohydration groups (HH, >800 mOsm/kg, n = 13) based on the 3-d average 24-h urine osmolality. Collected 24-h urine samples from 67 subjects (43 males and 34 females) were analyzed for urine metabolome using liquid chromatography-MS. Results The untargeted metabolomic analysis yielded 1055 metabolites by peak intensities. Integrating the results of the orthogonal projections to latent structures discriminant analysis and fold change test, 115 differential metabolites between the OH and HH groups, including phospholipids (PLs) and lysophospholipids, were identified. Among the 115 metabolites identified as differential metabolites, 85 were recorded by the Human Metabolome Database and uploaded to the Kyoto Encyclopedia of Genes and Genomes databases for pathway analysis. Twenty-one metabolic pathways were recognized. Phenylalanine metabolism (0.50, P = 0.007), phenylalanine, tyrosine, and tryptophan biosynthesis (0.50, P = 0.051), glycerophospholipid metabolism (0.31, P < 0.001), sphingolipid metabolism (0.27, P = 0.029), and cysteine and methionine metabolism (0.10, P = 0.066) had the leading pathway impacts. Conclusions We found variations in the urinary PLs and amino acids among subjects with different hydration states. Pathways associated with these differential metabolites could further impact various physiologic and pathologic functions. A more comprehensive and in-depth investigation of the physiologic and pathologic impact of the hydration state and the underlying mechanisms to elucidate and advocate optimal fluid intake habits is needed.This trial was registered at Chinese Clinical Trial Registry as ChiCTR2100045268.
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Affiliation(s)
- Yongwei Lin
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Na Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
- Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing, China
| | - Jianfen Zhang
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Junbo Lu
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
| | - Shufang Liu
- School of Public Health, Hebei University Health Science Center, Baoding, China
| | - Guansheng Ma
- Department of Nutrition and Food Hygiene, School of Public Health, Peking University, Beijing, China
- Laboratory of Toxicological Research and Risk Assessment for Food Safety, Beijing, China
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3
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Olkowicz M, Ramadan K, Rosales-Solano H, Yu M, Wang A, Cypel M, Pawliszyn J. Mapping the metabolic responses to oxaliplatin-based chemotherapy with in vivo spatiotemporal metabolomics. J Pharm Anal 2024; 14:196-210. [PMID: 38464782 PMCID: PMC10921245 DOI: 10.1016/j.jpha.2023.08.001] [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: 04/15/2023] [Revised: 07/14/2023] [Accepted: 08/07/2023] [Indexed: 03/12/2024] Open
Abstract
Adjuvant chemotherapy improves the survival outlook for patients undergoing operations for lung metastases caused by colorectal cancer (CRC). However, a multidisciplinary approach that evaluates several factors related to patient and tumor characteristics is necessary for managing chemotherapy treatment in metastatic CRC patients with lung disease, as such factors dictate the timing and drug regimen, which may affect treatment response and prognosis. In this study, we explore the potential of spatial metabolomics for evaluating metabolic phenotypes and therapy outcomes during the local delivery of the anticancer drug, oxaliplatin, to the lung. 12 male Yorkshire pigs underwent a 3 h left lung in vivo lung perfusion (IVLP) with various doses of oxaliplatin (7.5, 10, 20, 40, and 80 mg/L), which were administered to the perfusion circuit reservoir as a bolus. Biocompatible solid-phase microextraction (SPME) microprobes were combined with global metabolite profiling to obtain spatiotemporal information about the activity of the drug, determine toxic doses that exceed therapeutic efficacy, and conduct a mechanistic exploration of associated lung injury. Mild and subclinical lung injury was observed at 40 mg/L of oxaliplatin, and significant compromise of the hemodynamic lung function was found at 80 mg/L. This result was associated with massive alterations in metabolic patterns of lung tissue and perfusate, resulting in a total of 139 discriminant compounds. Uncontrolled inflammatory response, abnormalities in energy metabolism, and mitochondrial dysfunction next to accelerated kynurenine and aldosterone production were recognized as distinct features of dysregulated metabolipidome. Spatial pharmacometabolomics may be a promising tool for identifying pathological responses to chemotherapy.
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Affiliation(s)
- Mariola Olkowicz
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
- Jagiellonian Centre for Experimental Therapeutics (JCET), Jagiellonian University, Krakow, Poland
| | - Khaled Ramadan
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | | | - Miao Yu
- The Jackson Laboratory, JAX Genomic Medicine, Farmington, CT, USA
| | - Aizhou Wang
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
| | - Marcelo Cypel
- Latner Thoracic Surgery Research Laboratories, Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Division of Thoracic Surgery, Department of Surgery, University Health Network, University of Toronto, Toronto Lung Transplant Program, Toronto, ON, Canada
| | - Janusz Pawliszyn
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada
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4
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Yang Q, Chen S, Jiang W, Mi L, Liu J, Hu Y, Ji X, Wang J, Zhu F. MultiClassMetabo: A Superior Classification Model Constructed Using Metabolic Markers in Multiclass Metabolomics. Anal Chem 2024; 96:1410-1418. [PMID: 38221713 DOI: 10.1021/acs.analchem.3c03212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Multiclass metabolomics has become a popular technique for revealing the mechanisms underlying certain physiological processes, different tumor types, or different therapeutic responses. In multiclass metabolomics, it is highly important to uncover the underlying biological information on biosamples by identifying the metabolic markers with the most associations and classifying the different sample classes. The classification problem of multiclass metabolomics is more difficult than that of the binary problem. To date, various methods exist for constructing classification models and identifying metabolic markers consisting of well-established techniques and newly emerging machine learning algorithms. However, how to construct a superior classification model using these methods remains unclear for a given multiclass metabolomic data set. Herein, MultiClassMetabo has been developed for constructing a superior classification model using metabolic markers identified in multiclass metabolomics. MultiClassMetabo can enable online services, including (a) identifying metabolic markers by marker identification methods, (b) constructing classification models by classification methods, and (c) performing a comprehensive assessment from multiple perspectives to construct a superior classification model for multiclass metabolomics. In summary, MultiClassMetabo is distinguished for its capability to construct a superior classification model using the most appropriate method through a comprehensive assessment, which makes it an important complement to other available tools in multiclass metabolomics. MultiClassMetabo can be accessed at http://idrblab.cn/multiclassmetabo/.
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Affiliation(s)
- Qingxia Yang
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Shuman Chen
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Wenyu Jiang
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Lan Mi
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jiarui Liu
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Yu Hu
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Xinglai Ji
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Jun Wang
- Department of Bioinformatics, School of Geographic and Biologic Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| | - Feng Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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5
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Harrer DC, Lüke F, Pukrop T, Ghibelli L, Gerner C, Reichle A, Heudobler D. Peroxisome proliferator-activated receptorα/γ agonist pioglitazone for rescuing relapsed or refractory neoplasias by unlocking phenotypic plasticity. Front Oncol 2024; 13:1289222. [PMID: 38273846 PMCID: PMC10808445 DOI: 10.3389/fonc.2023.1289222] [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: 09/05/2023] [Accepted: 12/15/2023] [Indexed: 01/27/2024] Open
Abstract
A series of seven clinical trials on relapsed or refractory (r/r) metastatic neoplasias followed the question: Are networks of ligand-receptor cross-talks that support tumor-specific cancer hallmarks, druggable with tumor tissue editing approaches therapeutically exploiting tumor plasticity? Differential recombinations of pioglitazone, a dual peroxisome-proliferator activated receptorα/γ (PPARα/γ) agonist, with transcriptional modulators, i.e., all-trans retinoic acid, interferon-α, or dexamethasone plus metronomic low-dose chemotherapy (MCT) or epigenetic modeling with azacitidine plus/minus cyclooxygenase-2 inhibition initiated tumor-specific reprogramming of cancer hallmarks, as exemplified by inflammation control in r/r melanoma, renal clear cell carcinoma (RCCC), Hodgkin's lymphoma (HL) and multisystem Langerhans cell histiocytosis (mLCH) or differentiation induction in non-promyelocytic acute myeloid leukemia (non-PML AML). Pioglitazone, integrated in differentially designed editing schedules, facilitated induction of tumor cell death as indicated by complete remission (CR) in r/r non-PML AML, continuous CR in r/r RCCC, mLCH, and in HL by addition of everolimus, or long-term disease control in melanoma by efficaciously controlling metastasis, post-therapy cancer repopulation and acquired cell-resistance and genetic/molecular-genetic tumor cell heterogeneity (M-CRAC). PPARα/γ agonists provided tumor-type agnostic biomodulatory efficacy across different histologic neoplasias. Tissue editing techniques disclose that wide-ranging functions of PPARα/γ agonists may be on-topic focused for differentially unlocking tumor phenotypes. Low-dose MCT facilitates targeted reprogramming of cancer hallmarks with transcriptional modulators, induction of tumor cell death, M-CRAC control and editing of non-oncogene addiction. Thus, pioglitazone, integrated in tumor tissue editing protocols, is an important biomodulatory drug for addressing urgent therapeutic problems, such as M-CRAC in relapsed or refractory tumor disease.
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Affiliation(s)
- Dennis Christoph Harrer
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Florian Lüke
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
- Division of Personalized Tumor Therapy, Fraunhofer Institute for Toxicology and Experimental Medicine, Regensburg, Germany
| | - Tobias Pukrop
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
- Bavarian Cancer Research Center (BZKF), University Hospital Regensburg, Regensburg, Germany
| | - Lina Ghibelli
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Christopher Gerner
- Department of Analytical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Albrecht Reichle
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
| | - Daniel Heudobler
- Department of Internal Medicine III, Hematology and Oncology, University Hospital Regensburg, Regensburg, Germany
- Bavarian Cancer Research Center (BZKF), University Hospital Regensburg, Regensburg, Germany
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Shakartalla SB, Ashmawy NS, Semreen MH, Fayed B, Al Shareef ZM, Jayakumar MN, Ibrahim S, Rahmani M, Hamdy R, Soliman SSM. 1H-NMR metabolomics analysis identifies hypoxanthine as a novel metastasis-associated metabolite in breast cancer. Sci Rep 2024; 14:253. [PMID: 38167685 PMCID: PMC10762038 DOI: 10.1038/s41598-023-50866-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 12/27/2023] [Indexed: 01/05/2024] Open
Abstract
Breast cancer is one of the leading causes of death in females, mainly because of metastasis. Oncometabolites, produced via metabolic reprogramming, can influence metastatic signaling cascades. Accordingly, and based on our previous results, we propose that metabolites from highly metastatic breast cancer cells behave differently from less-metastatic cells and may play a significant role in metastasis. For instance, we aim to identify these metabolites and their role in breast cancer metastasis. Less metastatic cells (MCF-7) were treated with metabolites secreted from highly metastatic cells (MDA-MB-231) and the gene expression of three epithelial-to-mesenchymal transition (EMT) markers including E-cadherin, N-cadherin and vimentin were examined. Some metabolites secreted from MDA-MB-231 cells significantly induced EMT activity. Specifically, hypoxanthine demonstrated a significant EMT effect and increased the migration and invasion effects of MCF-7 cells through a hypoxia-associated mechanism. Hypoxanthine exhibited pro-angiogenic effects via increasing the VEGF and PDGF gene expression and affected lipid metabolism by increasing the gene expression of PCSK-9. Notably, knockdown of purine nucleoside phosphorylase, a gene encoding for an important enzyme in the biosynthesis of hypoxanthine, and inhibition of hypoxanthine uptake caused a significant decrease in hypoxanthine-associated EMT effects. Collectively for the first time, hypoxanthine was identified as a novel metastasis-associated metabolite in breast cancer cells and represents a promising target for diagnosis and therapy.
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Affiliation(s)
- Sarra B Shakartalla
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- College of Medicine, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Faculty of Pharmacy, University of Gezira, P.O. Box. 21111, Wadmedani, Sudan
| | - Naglaa S Ashmawy
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Department of Pharmaceutical Sciences, College of Pharmacy, Gulf Medical University, P.O. Box 4184, Ajman, United Arab Emirates
- Department of Pharmacognosy, Faculty of Pharmacy, Ain Shams University, Abbassia, P.O. Box 11566, Cairo, Egypt
| | - Mohammad H Semreen
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Bahgat Fayed
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Chemistry of Natural and Microbial Product Department, National Research Centre, P.O. Box 12622, Cairo, Egypt
| | - Zainab M Al Shareef
- College of Medicine, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Manju N Jayakumar
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
| | - Saleh Ibrahim
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
| | - Mohamed Rahmani
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Center for Biotechnology, Khalifa University, Abu Dhabi, United Arab Emirates
- College of Medicine and Health Sciences, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates
- Faculty of Pharmacy, Zagazig University, P.O. Box 44519, Zagazig, Egypt
| | - Sameh S M Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
- Department of Medicinal Chemistry, College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, United Arab Emirates.
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7
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Ren J, Chen Z, Ma E, Wang W, Zheng S, Wang H. Dual-source powered nanomotors coupled with dual-targeting ligands for efficient capture and detection of CTCs in whole blood and in vivo tumor imaging. Colloids Surf B Biointerfaces 2023; 231:113568. [PMID: 37826963 DOI: 10.1016/j.colsurfb.2023.113568] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/02/2023] [Accepted: 09/26/2023] [Indexed: 10/14/2023]
Abstract
Circulating tumor cells (CTCs) are important biomarkers in cancer diagnosis. However, the specific labeling of CTCs with high capture efficiency in whole blood remains a problem. Herein, a dual-source-driven nanomotor coupled with dual-targeting ligands (CD@NM) was designed for efficient capture, specific imaging and quantitative detection of CTCs. In both water and biological fluid, CD@NMs moved autonomously under the propulsion of a magnetic field and H2O2 solution, which improved the capture efficiency of CTCs to 97.50 ± 2.38%. More importantly, specific labeling of CTCs was achieved by fluorescence quenching and recovery of fluorescent carbon dots modified on the CD@NMs. As a result, the CD@NMs exhibited efficient CTC capture, specific CTC imaging and recognition in whole blood. CD@NMs were also successfully deployed in the specific imaging of tumor tissues in vivo. On this basis, CD@NMs are expected to provide a new platform for tumor diagnosis both in vitro and in vivo.
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Affiliation(s)
- Jiaoyu Ren
- School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou, Jiangsu 221116, PR China
| | - Zekun Chen
- School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou, Jiangsu 221116, PR China
| | - Enhui Ma
- School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou, Jiangsu 221116, PR China
| | - Wenjun Wang
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu 221116, PR China
| | - Shaohui Zheng
- School of Medical Imaging, Xuzhou Medical University, Xuzhou, Jiangsu 221116, PR China.
| | - Hong Wang
- School of Chemical Engineering & Technology, China University of Mining and Technology, Xuzhou, Jiangsu 221116, PR China.
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Baquer G, Sementé L, Ràfols P, Martín-Saiz L, Bookmeyer C, Fernández JA, Correig X, García-Altares M. rMSIfragment: improving MALDI-MSI lipidomics through automated in-source fragment annotation. J Cheminform 2023; 15:80. [PMID: 37715285 PMCID: PMC10504721 DOI: 10.1186/s13321-023-00756-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 08/29/2023] [Indexed: 09/17/2023] Open
Abstract
Matrix-Assisted Laser Desorption Ionization Mass Spectrometry Imaging (MALDI-MSI) spatially resolves the chemical composition of tissues. Lipids are of particular interest, as they influence important biological processes in health and disease. However, the identification of lipids in MALDI-MSI remains a challenge due to the lack of chromatographic separation or untargeted tandem mass spectrometry. Recent studies have proposed the use of MALDI in-source fragmentation to infer structural information and aid identification. Here we present rMSIfragment, an open-source R package that exploits known adducts and fragmentation pathways to confidently annotate lipids in MALDI-MSI. The annotations are ranked using a novel score that demonstrates an area under the curve of 0.7 in ROC analyses using HPLC-MS and Target-Decoy validations. rMSIfragment applies to multiple MALDI-MSI sample types and experimental setups. Finally, we demonstrate that overlooking in-source fragments increases the number of incorrect annotations. Annotation workflows should consider in-source fragmentation tools such as rMSIfragment to increase annotation confidence and reduce the number of false positives.
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Affiliation(s)
- Gerard Baquer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain.
| | - Lluc Sementé
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
| | - Pere Ràfols
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain.
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain.
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain.
| | - Lucía Martín-Saiz
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Christoph Bookmeyer
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Institute of Hygiene, University of Münster, Münster, Germany
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Xavier Correig
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
- Institut D'Investigacio Sanitaria Pere Virgili, Tarragona, Spain
| | - María García-Altares
- Department of Electronic Engineering, University Rovira I Virgili, Tarragona, Spain
- Spanish Biomedical Research Center in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain
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Cao K, Lyu Y, Chen J, He C, Lyu X, Zhang Y, Chen L, Jiang Y, Xiang J, Liu B, Wu C. Prognostic Implication of Plasma Metabolites in Gastric Cancer. Int J Mol Sci 2023; 24:12774. [PMID: 37628957 PMCID: PMC10454100 DOI: 10.3390/ijms241612774] [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: 07/04/2023] [Revised: 08/02/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
Gastric cancer (GC) typically carries a poor prognosis as it is often diagnosed at a late stage. Altered metabolism has been found to impact cancer outcomes and affect patients' quality of life, and the role of metabolites in gastric cancer prognosis has not been sufficiently understood. We aimed to establish a prognostic prediction model for GC patients based on a metabolism-associated signature and identify the unique role of metabolites in the prognosis of GC. Thus, we conducted untargeted metabolomics to detect the plasma metabolites of 218 patients with gastric adenocarcinoma and explored the metabolites related to the survival of patients with gastric cancer. Firstly, we divided patients into two groups based on the cutoff value of the abundance of each of the 60 metabolites and compared the differences using Kaplan-Meier (K-M) survival analysis. As a result, 23 metabolites associated with gastric cancer survival were identified. To establish a risk score model, we performed LASSO regression and Cox regression analysis on the 60 metabolites and identified 8 metabolites as an independent prognostic factor. Furthermore, a nomogram incorporating clinical parameters and the metabolic signature was constructed to help individualize outcome predictions. The results of the ROC curve and nomogram plot showed good predictive performance of metabolic risk features. Finally, we performed pathway analysis on the 24 metabolites identified in the two parts, and the results indicated that purine metabolism and arachidonic acid metabolism play important roles in gastric cancer prognosis. Our study highlights the important role of metabolites in the progression of gastric cancer and newly identified metabolites could be potential biomarkers or therapeutic targets for gastric cancer patients.
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Affiliation(s)
- Kang Cao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yanping Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jingwen Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Chenzhou He
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Xuejie Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yuling Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Liangping Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Yu Jiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Jianjun Xiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Baoying Liu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
| | - Chuancheng Wu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350122, China; (K.C.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350122, China
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10
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Wan Y, Cohen J, Szenk M, Farquhar KS, Coraci D, Krzysztoń R, Azukas J, Van Nest N, Smashnov A, Chern YJ, De Martino D, Nguyen LC, Bien H, Bravo-Cordero JJ, Chan CH, Rosner MR, Balázsi G. Nonmonotone invasion landscape by noise-aware control of metastasis activator levels. Nat Chem Biol 2023; 19:887-899. [PMID: 37231268 PMCID: PMC10299915 DOI: 10.1038/s41589-023-01344-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: 03/12/2022] [Accepted: 04/18/2023] [Indexed: 05/27/2023]
Abstract
A major pharmacological assumption is that lowering disease-promoting protein levels is generally beneficial. For example, inhibiting metastasis activator BACH1 is proposed to decrease cancer metastases. Testing such assumptions requires approaches to measure disease phenotypes while precisely adjusting disease-promoting protein levels. Here we developed a two-step strategy to integrate protein-level tuning, noise-aware synthetic gene circuits into a well-defined human genomic safe harbor locus. Unexpectedly, engineered MDA-MB-231 metastatic human breast cancer cells become more, then less and then more invasive as we tune BACH1 levels up, irrespective of the native BACH1. BACH1 expression shifts in invading cells, and expression of BACH1's transcriptional targets confirm BACH1's nonmonotone phenotypic and regulatory effects. Thus, chemical inhibition of BACH1 could have unwanted effects on invasion. Additionally, BACH1's expression variability aids invasion at high BACH1 expression. Overall, precisely engineered, noise-aware protein-level control is necessary and important to unravel disease effects of genes to improve clinical drug efficacy.
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Affiliation(s)
- Yiming Wan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Joseph Cohen
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Mariola Szenk
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Kevin S Farquhar
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center, UT Health Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Damiano Coraci
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Rafał Krzysztoń
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Joshua Azukas
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
| | - Nicholas Van Nest
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Alex Smashnov
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Yi-Jye Chern
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Daniela De Martino
- Department of Medicine, Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Long Chi Nguyen
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Harold Bien
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Jose Javier Bravo-Cordero
- Department of Medicine, Division of Hematology and Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Chia-Hsin Chan
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY, USA
- Department of Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Marsha Rich Rosner
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Gábor Balázsi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.
- Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY, USA.
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11
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Hebert JD, Neal JW, Winslow MM. Dissecting metastasis using preclinical models and methods. Nat Rev Cancer 2023; 23:391-407. [PMID: 37138029 DOI: 10.1038/s41568-023-00568-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/27/2023] [Indexed: 05/05/2023]
Abstract
Metastasis has long been understood to lead to the overwhelming majority of cancer-related deaths. However, our understanding of the metastatic process, and thus our ability to prevent or eliminate metastases, remains frustratingly limited. This is largely due to the complexity of metastasis, which is a multistep process that likely differs across cancer types and is greatly influenced by many aspects of the in vivo microenvironment. In this Review, we discuss the key variables to consider when designing assays to study metastasis: which source of metastatic cancer cells to use and where to introduce them into mice to address different questions of metastasis biology. We also examine methods that are being used to interrogate specific steps of the metastatic cascade in mouse models, as well as emerging techniques that may shed new light on previously inscrutable aspects of metastasis. Finally, we explore approaches for developing and using anti-metastatic therapies, and how mouse models can be used to test them.
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Affiliation(s)
- Jess D Hebert
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joel W Neal
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
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12
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Cao Z, An L, Han Y, Jiao S, Zhou Z. The Hippo signaling pathway in gastric cancer. Acta Biochim Biophys Sin (Shanghai) 2023. [PMID: 36924251 DOI: 10.3724/abbs.2023038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023] Open
Abstract
Gastric cancer (GC) is an aggressive malignant disease which still lacks effective early diagnosis markers and targeted therapies, representing the fourth-leading cause of cancer-associated death worldwide. The Hippo signaling pathway plays crucial roles in organ size control and tissue homeostasis under physiological conditions, yet its aberrations have been closely associated with several hallmarks of cancer. The last decade witnessed a burst of investigations dissecting how Hippo dysregulation contributes to tumorigenesis, highlighting the therapeutic potential of targeting this pathway for tumor intervention. In this review, we systemically document studies on the Hippo pathway in the contexts of gastric tumor initiation, progression, metastasis, acquired drug resistance, and the emerging development of Hippo-targeting strategies. By summarizing major open questions in this field, we aim to inspire further in-depth understanding of Hippo signaling in GC development, as well as the translational implications of targeting Hippo for GC treatment.
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Affiliation(s)
- Zhifa Cao
- Department of Stomatology, Shanghai Tenth People's Hospital, Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200072, China.,CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Liwei An
- Department of Stomatology, Shanghai Tenth People's Hospital, Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200072, China
| | - Yi Han
- Department of Stomatology, Shanghai Tenth People's Hospital, Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai 200072, China
| | - Shi Jiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Zhaocai Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China.,Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing 211166, China
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13
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Danzi F, Pacchiana R, Mafficini A, Scupoli MT, Scarpa A, Donadelli M, Fiore A. To metabolomics and beyond: a technological portfolio to investigate cancer metabolism. Signal Transduct Target Ther 2023; 8:137. [PMID: 36949046 PMCID: PMC10033890 DOI: 10.1038/s41392-023-01380-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 03/24/2023] Open
Abstract
Tumour cells have exquisite flexibility in reprogramming their metabolism in order to support tumour initiation, progression, metastasis and resistance to therapies. These reprogrammed activities include a complete rewiring of the bioenergetic, biosynthetic and redox status to sustain the increased energetic demand of the cells. Over the last decades, the cancer metabolism field has seen an explosion of new biochemical technologies giving more tools than ever before to navigate this complexity. Within a cell or a tissue, the metabolites constitute the direct signature of the molecular phenotype and thus their profiling has concrete clinical applications in oncology. Metabolomics and fluxomics, are key technological approaches that mainly revolutionized the field enabling researchers to have both a qualitative and mechanistic model of the biochemical activities in cancer. Furthermore, the upgrade from bulk to single-cell analysis technologies provided unprecedented opportunity to investigate cancer biology at cellular resolution allowing an in depth quantitative analysis of complex and heterogenous diseases. More recently, the advent of functional genomic screening allowed the identification of molecular pathways, cellular processes, biomarkers and novel therapeutic targets that in concert with other technologies allow patient stratification and identification of new treatment regimens. This review is intended to be a guide for researchers to cancer metabolism, highlighting current and emerging technologies, emphasizing advantages, disadvantages and applications with the potential of leading the development of innovative anti-cancer therapies.
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Affiliation(s)
- Federica Danzi
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Raffaella Pacchiana
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
| | - Andrea Mafficini
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Maria T Scupoli
- Department of Neurosciences, Biomedicine and Movement Sciences, Biology and Genetics Section, University of Verona, Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- ARC-NET Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Massimo Donadelli
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy.
| | - Alessandra Fiore
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biochemistry, University of Verona, Verona, Italy
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14
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He S, Ding L, Yuan H, Zhao G, Yang X, Wu Y. A review of sensors for classification and subtype discrimination of cancer: Insights into circulating tumor cells and tumor-derived extracellular vesicles. Anal Chim Acta 2023; 1244:340703. [PMID: 36737145 DOI: 10.1016/j.aca.2022.340703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 12/02/2022] [Accepted: 12/03/2022] [Indexed: 12/14/2022]
Abstract
Liquid biopsy can reflect the state of tumors in vivo non-invasively, thus providing a strong basis for the early diagnosis, individualized treatment monitoring and prognosis of tumors. Circulating tumor cells (CTCs) and tumor-derived extracellular vesicles (tdEVs) contain information-rich components, such as nucleic acids and proteins, and they are essential markers for liquid biopsies. Their capture and analysis are of great importance for the study of disease occurrence and development and, consequently, have been the subject of many reviews. However, both CTCs and tdEVs carry the biological characteristics of their original tissue, and few reviews have focused on their function in the staging and classification of cancer. In this review, we focus on state-of-the-art sensors based on the simultaneous detection of multiple biomarkers within CTCs and tdEVs, with clinical applications centered on cancer classification and subtyping. We also provide a thorough discussion of the current challenges and prospects for novel sensors with the ultimate goal of cancer classification and staging. It is hoped that these most advanced technologies will bring new insights into the clinical practice of cancer screening and diagnosis.
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Affiliation(s)
- Sitian He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Huijie Yuan
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Gaofeng Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450001, China.
| | - Xiaonan Yang
- School of Information Engineering, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
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15
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Gonzales LISA, Qiao JW, Buffier AW, Rogers LJ, Suchowerska N, McKenzie DR, Kwan AH. An omics approach to delineating the molecular mechanisms that underlie the biological effects of physical plasma. BIOPHYSICS REVIEWS 2023; 4:011312. [PMID: 38510160 PMCID: PMC10903421 DOI: 10.1063/5.0089831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 02/24/2023] [Indexed: 03/22/2024]
Abstract
The use of physical plasma to treat cancer is an emerging field, and interest in its applications in oncology is increasing rapidly. Physical plasma can be used directly by aiming the plasma jet onto cells or tissue, or indirectly, where a plasma-treated solution is applied. A key scientific question is the mechanism by which physical plasma achieves selective killing of cancer over normal cells. Many studies have focused on specific pathways and mechanisms, such as apoptosis and oxidative stress, and the role of redox biology. However, over the past two decades, there has been a rise in omics, the systematic analysis of entire collections of molecules in a biological entity, enabling the discovery of the so-called "unknown unknowns." For example, transcriptomics, epigenomics, proteomics, and metabolomics have helped to uncover molecular mechanisms behind the action of physical plasma, revealing critical pathways beyond those traditionally associated with cancer treatments. This review showcases a selection of omics and then summarizes the insights gained from these studies toward understanding the biological pathways and molecular mechanisms implicated in physical plasma treatment. Omics studies have revealed how reactive species generated by plasma treatment preferentially affect several critical cellular pathways in cancer cells, resulting in epigenetic, transcriptional, and post-translational changes that promote cell death. Finally, this review considers the outlook for omics in uncovering both synergies and antagonisms with other common cancer therapies, as well as in overcoming challenges in the clinical translation of physical plasma.
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Affiliation(s)
- Lou I. S. A. Gonzales
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Jessica W. Qiao
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | - Aston W. Buffier
- School of Life and Environmental Sciences, The University of Sydney, NSW 2006, Australia
| | | | | | | | - Ann H. Kwan
- Author to whom correspondence should be addressed:
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16
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Cancer Genetics and Clinical Research. J Pers Med 2022; 12:jpm12101649. [PMID: 36294788 PMCID: PMC9605496 DOI: 10.3390/jpm12101649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022] Open
Abstract
Understanding how complex diseases as well as cancers arise is one of the great challenges of modern medicine [...].
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